From 8d929ed89984137fc00009b322074f7a0908d2a5 Mon Sep 17 00:00:00 2001 From: jamesemery Date: Mon, 26 Feb 2018 18:39:18 -0500 Subject: [PATCH] Port of GATK3 Variant Annotator Tool (#3803) * Beta port of GATK3 version of VariantAnnotator with the necessary changes to the annotation engine and client annotations to support annotating variants independent of the haplotype caller. * The annotations closely match the GATK3 output, including replicating existing bugs in some cases * closes #51 * close #2493 --- .../engine/filters/WellformedReadFilter.java | 2 +- .../tools/HaplotypeCallerSpark.java | 2 +- .../tools/walkers/CombineGVCFs.java | 2 +- .../tools/walkers/GenotypeGVCFs.java | 2 +- .../walkers/annotator/AnnotationUtils.java | 7 + .../annotator/BaseQualityRankSumTest.java | 7 + .../annotator/ClippingRankSumTest.java | 8 + .../annotator/DepthPerAlleleBySample.java | 45 ++- .../tools/walkers/annotator/FisherStrand.java | 12 +- .../annotator/LikelihoodRankSumTest.java | 11 +- .../annotator/MappingQualityRankSumTest.java | 6 + .../tools/walkers/annotator/QualByDepth.java | 5 +- .../walkers/annotator/RMSMappingQuality.java | 80 ++--- .../tools/walkers/annotator/RankSumTest.java | 71 ++-- .../walkers/annotator/ReadPosRankSumTest.java | 101 +++++- .../walkers/annotator/StrandBiasTest.java | 44 ++- .../walkers/annotator/StrandOddsRatio.java | 12 +- .../walkers/annotator/VariantAnnotation.java | 2 +- .../walkers/annotator/VariantAnnotator.java | 259 ++++++++++++++ .../annotator/VariantAnnotatorEngine.java | 283 ++++++++++++++- .../allelespecific/AS_RMSMappingQuality.java | 72 ++-- .../allelespecific/AS_RankSumTest.java | 49 ++- .../allelespecific/AS_ReadPosRankSumTest.java | 1 + .../allelespecific/AS_StrandBiasTest.java | 33 +- .../HaplotypeCallerEngine.java | 2 +- .../tools/walkers/mutect/Mutect2Engine.java | 2 +- .../utils/genotyper/ReadLikelihoods.java | 37 +- .../genotyper/UnfilledReadsLikelihoods.java | 140 ++++++++ .../utils/logging/OneShotLogger.java | 4 + .../utils/pileup/PileupElement.java | 41 +++ .../hellbender/utils/pileup/ReadPileup.java | 13 +- .../variant/GATKVariantContextUtils.java | 7 +- ...onfidenceVariantContextMergerUnitTest.java | 2 +- .../DepthPerAlleleBySampleUnitTest.java | 30 +- .../annotator/FisherStrandUnitTest.java | 15 +- .../LikelihoodRankSumTestUnitTest.java | 7 - .../annotator/QualByDepthUnitTest.java | 6 +- .../annotator/RMSMappingQualityUnitTest.java | 12 +- .../annotator/ReadPosRankSumTestUnitTest.java | 154 ++++++++ .../VariantAnnotatorEngineUnitTest.java | 17 +- .../VariantAnnotatorIntegrationTest.java | 335 ++++++++++++++++++ .../AS_BaseQualityRankSumTestUnitTest.java | 8 +- .../AS_MappingQualityRankSumTestUnitTest.java | 3 +- .../AS_ReadPosRankSumTestUnitTest.java | 8 +- .../CEUTrio.multisample.b37.1M-1M50k.bam | 3 + .../CEUTrio.multisample.b37.1M-1M50k.bam.bai | 3 + ...ted.testGenotypeGivenAllelesMode.gatk4.vcf | 2 +- ...otypeGivenAllelesMode_givenAlleles.vcf.idx | Bin 442 -> 476 bytes .../NA12878.AS.chr20snippet.g.vcf.idx | Bin 944 -> 887 bytes .../NA12892.AS.chr20snippet.g.vcf.idx | Bin 944 -> 887 bytes .../annotator/VariantAnnotator/AlleleTrim.vcf | 172 +++++++++ .../HCOutput.NoAnnotations.vcf | 287 +++++++++++++++ .../HCOutput.NoAnnotations.vcf.idx | Bin 0 -> 2892 bytes .../HCOutputNoAnnotations.vcf | 138 ++++++++ .../HCOutputNoAnnotations.vcf.idx | Bin 0 -> 440 bytes .../HCOutputNoFSAnnotation.vcf | 138 ++++++++ .../HCOutputNoFSAnnotation.vcf.idx | Bin 0 -> 441 bytes .../VariantAnnotator/alleleTrim.vcf.gz.tbi | Bin 0 -> 201 bytes .../annotationResourceWithFilter.vcf | 9 + .../annotationResourceWithFilter.vcf.idx | Bin 0 -> 405 bytes .../annotator/VariantAnnotator/empty.vcf | 47 +++ .../VariantAnnotator/exacAlleleTrim.vcf | 226 ++++++++++++ .../VariantAnnotator/exacAlleleTrim.vcf.idx | Bin 0 -> 520 bytes ...e.gatk3.8-4-g7b0250253f.alleleSpecific.vcf | 287 +++++++++++++++ .../expected/integrationTest.vcf | 289 +++++++++++++++ .../VariantAnnotator/expected/noQual.vcf | 47 +++ .../expected/testAlleleTrimming.vcf | 172 +++++++++ .../expected/testDBTagWithHapMap.vcf | 36 ++ .../expected/testDBTagWithTwoComps.vcf | 37 ++ .../expected/testFilterInExpression.vcf | 26 ++ .../expected/testHasAnnotsAsking1.vcf | 88 +++++ .../expected/testHasAnnotsAsking1.vcf.idx | Bin 0 -> 351 bytes .../expected/testHasNoAnnotsAsking1.vcf | 82 +++++ .../expected/testHasNoAnnotsAsking1.vcf.idx | Bin 0 -> 353 bytes .../expected/testHasNoAnnotsNotAsking1.vcf | 67 ++++ .../testHasNoAnnotsNotAsking1.vcf.idx | Bin 0 -> 356 bytes .../expected/testHsAnnotsNotAsking1.vcf | 75 ++++ .../expected/testHsAnnotsNotAsking1.vcf.idx | Bin 0 -> 353 bytes .../expected/testMultipleIdsWithDbsnp.vcf | 114 ++++++ .../VariantAnnotator/expected/testNoReads.vcf | 35 ++ .../expected/testReplaceHeader.vcf | 23 ++ .../expected/testUsingExpression.vcf | 36 ++ .../testUsingExpressionAlleleMisMatch.vcf | 36 ++ .../testUsingExpressionMultiAllele.vcf | 27 ++ .../expected/testUsingExpressionWithID.vcf | 36 ++ .../expected/testWithAllAnnotations.vcf | 310 ++++++++++++++++ .../annotator/VariantAnnotator/fakeHM3.vcf | 9 + .../VariantAnnotator/fakeHM3.vcf.idx | Bin 0 -> 384 bytes .../annotator/VariantAnnotator/noQual.vcf | 47 +++ .../annotator/VariantAnnotator/noQual.vcf.idx | Bin 0 -> 384 bytes .../annotator/VariantAnnotator/noQuol.vcf | 47 +++ .../annotator/VariantAnnotator/noQuol.vcf.idx | Bin 0 -> 384 bytes .../targetAnnotations-multiAllele.vcf | 8 + .../targetAnnotations-multiAllele.vcf.idx | Bin 0 -> 406 bytes .../VariantAnnotator/targetAnnotations.vcf | 7 + .../targetAnnotations.vcf.idx | Bin 0 -> 394 bytes .../VariantAnnotator/vcfdbsnpwithIDs.vcf | 14 + .../VariantAnnotator/vcfdbsnpwithIDs.vcf.idx | Bin 0 -> 422 bytes .../VariantAnnotator/vcfexample2.vcf | 33 ++ .../VariantAnnotator/vcfexample2.vcf.idx | Bin 0 -> 389 bytes .../VariantAnnotator/vcfexample3empty-mod.vcf | 18 + .../vcfexample3empty-mod.vcf.idx | Bin 0 -> 398 bytes .../vcfexample3empty-multiAllele.vcf | 10 + .../vcfexample3empty-multiAllele.vcf.idx | Bin 0 -> 408 bytes .../VariantAnnotator/vcfexample3empty.vcf | 18 + .../VariantAnnotator/vcfexample3empty.vcf.idx | Bin 0 -> 394 bytes .../vcfexample3withIDs.vcf.idx | Bin 0 -> 378 bytes .../VariantAnnotator/vcfexample4.vcf | 6 + .../VariantAnnotator/vcfexample4.vcf.idx | Bin 0 -> 324 bytes .../vcfexamplemultisample.test.vcf.idx | Bin 0 -> 438 bytes .../vcfexamplemultisample.vcf | 74 ++++ .../vcfexamplemultisample.vcf.idx | Bin 0 -> 433 bytes .../vcfexamplemultisampleempty.vcf | 66 ++++ .../vcfexamplemultisampleempty.vcf.idx | Bin 0 -> 438 bytes 114 files changed, 4952 insertions(+), 212 deletions(-) create mode 100644 src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator.java create mode 100644 src/main/java/org/broadinstitute/hellbender/utils/genotyper/UnfilledReadsLikelihoods.java create mode 100644 src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java create mode 100644 src/test/resources/large/CEUTrio.multisample.b37.1M-1M50k.bam create mode 100644 src/test/resources/large/CEUTrio.multisample.b37.1M-1M50k.bam.bai create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/AlleleTrim.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/HCOutput.NoAnnotations.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/HCOutput.NoAnnotations.vcf.idx create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/HCOutputNoAnnotations.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/HCOutputNoAnnotations.vcf.idx create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/HCOutputNoFSAnnotation.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/HCOutputNoFSAnnotation.vcf.idx create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/alleleTrim.vcf.gz.tbi create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/annotationResourceWithFilter.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/annotationResourceWithFilter.vcf.idx create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/empty.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/exacAlleleTrim.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/exacAlleleTrim.vcf.idx create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected.testVCFMode.gatk3.8-4-g7b0250253f.alleleSpecific.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/integrationTest.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/noQual.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testAlleleTrimming.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testDBTagWithHapMap.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testDBTagWithTwoComps.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testFilterInExpression.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testHasAnnotsAsking1.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testHasAnnotsAsking1.vcf.idx create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testHasNoAnnotsAsking1.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testHasNoAnnotsAsking1.vcf.idx create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testHasNoAnnotsNotAsking1.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testHasNoAnnotsNotAsking1.vcf.idx create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testHsAnnotsNotAsking1.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testHsAnnotsNotAsking1.vcf.idx create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testMultipleIdsWithDbsnp.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testNoReads.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testReplaceHeader.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testUsingExpression.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testUsingExpressionAlleleMisMatch.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testUsingExpressionMultiAllele.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testUsingExpressionWithID.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testWithAllAnnotations.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/fakeHM3.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/fakeHM3.vcf.idx create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/noQual.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/noQual.vcf.idx create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/noQuol.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/noQuol.vcf.idx create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/targetAnnotations-multiAllele.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/targetAnnotations-multiAllele.vcf.idx create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/targetAnnotations.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/targetAnnotations.vcf.idx create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/vcfdbsnpwithIDs.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/vcfdbsnpwithIDs.vcf.idx create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/vcfexample2.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/vcfexample2.vcf.idx create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/vcfexample3empty-mod.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/vcfexample3empty-mod.vcf.idx create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/vcfexample3empty-multiAllele.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/vcfexample3empty-multiAllele.vcf.idx create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/vcfexample3empty.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/vcfexample3empty.vcf.idx create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/vcfexample3withIDs.vcf.idx create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/vcfexample4.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/vcfexample4.vcf.idx create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/vcfexamplemultisample.test.vcf.idx create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/vcfexamplemultisample.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/vcfexamplemultisample.vcf.idx create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/vcfexamplemultisampleempty.vcf create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/vcfexamplemultisampleempty.vcf.idx diff --git a/src/main/java/org/broadinstitute/hellbender/engine/filters/WellformedReadFilter.java b/src/main/java/org/broadinstitute/hellbender/engine/filters/WellformedReadFilter.java index 064c1a1e07b..9549a0ec8ad 100644 --- a/src/main/java/org/broadinstitute/hellbender/engine/filters/WellformedReadFilter.java +++ b/src/main/java/org/broadinstitute/hellbender/engine/filters/WellformedReadFilter.java @@ -46,7 +46,7 @@ public final class WellformedReadFilter extends ReadFilter { private ReadFilter wellFormedFilter = null; // Command line parser requires a no-arg constructor - public WellformedReadFilter() { + public WellformedReadFilter() { } @Override diff --git a/src/main/java/org/broadinstitute/hellbender/tools/HaplotypeCallerSpark.java b/src/main/java/org/broadinstitute/hellbender/tools/HaplotypeCallerSpark.java index 17905cbe977..3856c34b719 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/HaplotypeCallerSpark.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/HaplotypeCallerSpark.java @@ -231,7 +231,7 @@ public static JavaRDD callVariantsWithHaplotypeCaller( final Broadcast referenceBroadcast = ctx.broadcast(reference); final Broadcast hcArgsBroadcast = ctx.broadcast(hcArgs); - final VariantAnnotatorEngine variantAnnotatorEngine = VariantAnnotatorEngine.ofSelectedMinusExcluded(hcArgs.defaultGATKVariantAnnotationArgumentCollection, hcArgs.dbsnp.dbsnp, hcArgs.comps); + final VariantAnnotatorEngine variantAnnotatorEngine = VariantAnnotatorEngine.ofSelectedMinusExcluded(hcArgs.defaultGATKVariantAnnotationArgumentCollection, hcArgs.dbsnp.dbsnp, hcArgs.comps, hcArgs.emitReferenceConfidence == ReferenceConfidenceMode.GVCF); final Broadcast annotatorEngineBroadcast = ctx.broadcast(variantAnnotatorEngine); final List shardBoundaries = getShardBoundaries(header, intervals, shardingArgs.readShardSize, shardingArgs.readShardPadding); diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs.java index ba48632666d..1536ef7d113 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs.java @@ -207,7 +207,7 @@ private void resizeReferenceIfNeeded(SimpleInterval intervalToClose) { @Override public void onTraversalStart() { // create the annotation engine - annotationEngine = VariantAnnotatorEngine.ofSelectedMinusExcluded(variantAnnotationArgumentCollection, dbsnp.dbsnp, Collections.emptyList()); + annotationEngine = VariantAnnotatorEngine.ofSelectedMinusExcluded(variantAnnotationArgumentCollection, dbsnp.dbsnp, Collections.emptyList(), false); vcfWriter = getVCFWriter(); diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs.java index 84f382fd32b..615223bd077 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs.java @@ -154,7 +154,7 @@ public void onTraversalStart() { final SampleList samples = new IndexedSampleList(inputVCFHeader.getGenotypeSamples()); //todo should this be getSampleNamesInOrder? - annotationEngine = VariantAnnotatorEngine.ofSelectedMinusExcluded(defaultGATKVariantAnnotationArgumentCollection, dbsnp.dbsnp, Collections.emptyList()); + annotationEngine = VariantAnnotatorEngine.ofSelectedMinusExcluded(defaultGATKVariantAnnotationArgumentCollection, dbsnp.dbsnp, Collections.emptyList(), false); // We only want the engine to generate the AS_QUAL key if we are using AlleleSpecific annotations. genotypingEngine = new MinimalGenotypingEngine(createUAC(), samples, new GeneralPloidyFailOverAFCalculatorProvider(genotypeArgs), annotationEngine.isRequestedReducibleRawKey(GATKVCFConstants.AS_QUAL_KEY)); diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/AnnotationUtils.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/AnnotationUtils.java index b3cf6ac9558..8262c6d40a4 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/AnnotationUtils.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/AnnotationUtils.java @@ -1,6 +1,13 @@ package org.broadinstitute.hellbender.tools.walkers.annotator; +import htsjdk.samtools.Cigar; +import htsjdk.samtools.CigarElement; +import htsjdk.samtools.CigarOperator; +import htsjdk.samtools.SAMRecord; import org.apache.commons.lang.StringUtils; +import org.broadinstitute.hellbender.utils.pairhmm.PairHMM; +import org.broadinstitute.hellbender.utils.read.AlignmentUtils; +import org.broadinstitute.hellbender.utils.read.GATKRead; import java.util.ArrayList; import java.util.List; diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/BaseQualityRankSumTest.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/BaseQualityRankSumTest.java index 2ae6b7a32a2..eeaf6278ade 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/BaseQualityRankSumTest.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/BaseQualityRankSumTest.java @@ -4,6 +4,7 @@ import org.broadinstitute.barclay.help.DocumentedFeature; import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.utils.help.HelpConstants; +import org.broadinstitute.hellbender.utils.pileup.PileupElement; import org.broadinstitute.hellbender.utils.read.GATKRead; import org.broadinstitute.hellbender.utils.read.ReadUtils; import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; @@ -41,4 +42,10 @@ public static OptionalDouble getReadBaseQuality(final GATKRead read, final int r Utils.nonNull(read); return OptionalDouble.of(read.getBaseQuality(ReadUtils.getReadCoordinateForReferenceCoordinateUpToEndOfRead(read, refLoc, ReadUtils.ClippingTail.RIGHT_TAIL))); } + + @Override + // When we have a pileupe element we only need its underlying read in order to com + protected OptionalDouble getElementForPileupElement(final PileupElement p, final int refLoc) { + return OptionalDouble.of(p.getQual()); + } } diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/ClippingRankSumTest.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/ClippingRankSumTest.java index 6488d3602cb..dcc01db5d7b 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/ClippingRankSumTest.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/ClippingRankSumTest.java @@ -4,6 +4,7 @@ import org.broadinstitute.barclay.help.DocumentedFeature; import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.utils.help.HelpConstants; +import org.broadinstitute.hellbender.utils.pileup.PileupElement; import org.broadinstitute.hellbender.utils.read.AlignmentUtils; import org.broadinstitute.hellbender.utils.read.GATKRead; import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; @@ -36,4 +37,11 @@ protected OptionalDouble getElementForRead(final GATKRead read, final int refLoc Utils.nonNull(read); return OptionalDouble.of(AlignmentUtils.getNumHardClippedBases(read)); } + + @Override + protected OptionalDouble getElementForPileupElement(final PileupElement p, final int refLoc) { + Utils.nonNull(p); + // default to returning the same value + return getElementForRead(p.getRead(),refLoc); + } } diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/DepthPerAlleleBySample.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/DepthPerAlleleBySample.java index 68ffdba7313..ad04522ba60 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/DepthPerAlleleBySample.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/DepthPerAlleleBySample.java @@ -12,6 +12,7 @@ import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.utils.genotyper.ReadLikelihoods; import org.broadinstitute.hellbender.utils.help.HelpConstants; +import org.broadinstitute.hellbender.utils.pileup.PileupElement; import java.util.*; import java.util.stream.Collectors; @@ -56,6 +57,46 @@ public void annotate(final ReferenceContext ref, // make sure that there's a meaningful relationship between the alleles in the likelihoods and our VariantContext Utils.validateArg(likelihoods.alleles().containsAll(alleles), () -> "VC alleles " + alleles + " not a subset of ReadLikelihoods alleles " + likelihoods.alleles()); + int[] counts; + if (likelihoods.hasFilledLikelihoods()) { + // Compute based on the alignment map + counts = annotateWithLikelihoods(vc, g, alleles, likelihoods); + } else if (likelihoods.readCount()==0) { + // No reads, thus cant compute the AD so do nothing + return; + } else if (vc.isSNP()) { + // Compute based on pileup bases at the snp site (won't match haplotype caller output) + counts = annotateWithPileup(vc, likelihoods.getStratifiedPileups(vc).get(g.getSampleName())); + } else { + // Otherwise return an empty AD field for an indel. + counts = new int[vc.getNAlleles()]; + } + + gb.AD(counts); + } + + private int[] annotateWithPileup(final VariantContext vc, List pileupElements) { + + final HashMap alleleCounts = new HashMap<>(); + for ( final Allele allele : vc.getAlleles() ) { + alleleCounts.put(allele.getBases()[0], 0); + } + for ( final PileupElement p : pileupElements) { + // only count bases that support alleles in the variant context + alleleCounts.computeIfPresent(p.getBase(), (base, count) -> count+ 1); + } + + // we need to add counts in the correct order + final int[] counts = new int[alleleCounts.size()]; + counts[0] = alleleCounts.get(vc.getReference().getBases()[0]); + for (int i = 0; i < vc.getNAlleles() -1; i++) { + counts[i + 1] = alleleCounts.get(vc.getAlternateAllele(i).getBases()[0]); + } + return counts; + } + + private int[] annotateWithLikelihoods(VariantContext vc, Genotype g, Set alleles, ReadLikelihoods likelihoods) { + final Map alleleCounts = new LinkedHashMap<>(); for ( final Allele allele : vc.getAlleles() ) { alleleCounts.put(allele, 0); @@ -68,11 +109,11 @@ public void annotate(final ReferenceContext ref, final int[] counts = new int[alleleCounts.size()]; counts[0] = alleleCounts.get(vc.getReference()); //first one in AD is always ref - for (int i = 0; i < vc.getAlternateAlleles().size(); i++) { + for (int i = 0; i < vc.getNAlleles() -1; i++) { counts[i + 1] = alleleCounts.get(vc.getAlternateAllele(i)); } - gb.AD(counts); + return counts; } @Override diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/FisherStrand.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/FisherStrand.java index fc2d29c9ba3..ee2262b79f4 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/FisherStrand.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/FisherStrand.java @@ -4,14 +4,13 @@ import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.GenotypesContext; import htsjdk.variant.variantcontext.VariantContext; -import htsjdk.variant.vcf.VCFInfoHeaderLine; import org.broadinstitute.barclay.help.DocumentedFeature; import org.broadinstitute.hellbender.utils.FisherExactTest; import org.broadinstitute.hellbender.utils.QualityUtils; import org.broadinstitute.hellbender.utils.genotyper.ReadLikelihoods; import org.broadinstitute.hellbender.utils.help.HelpConstants; +import org.broadinstitute.hellbender.utils.pileup.PileupElement; import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; -import org.broadinstitute.hellbender.utils.variant.GATKVCFHeaderLines; import java.util.Collections; import java.util.List; @@ -44,6 +43,7 @@ public final class FisherStrand extends StrandBiasTest implements StandardAnnota static final double MIN_PVALUE = 1E-320; private static final int MIN_COUNT = ARRAY_DIM; + private static final int MIN_QUAL_FOR_FILTERED_TEST = 17; // how large do we want the normalized table to be? (ie, sum of all entries must be smaller that this) private static final double TARGET_TABLE_SIZE = 200.0; @@ -59,6 +59,14 @@ protected Map calculateAnnotationFromGTfield(final GenotypesCont return ( tableFromPerSampleAnnotations != null )? annotationForOneTable(pValueForContingencyTable(tableFromPerSampleAnnotations)) : null; } + @Override + protected Map calculateAnnotationFromStratifiedContexts(final Map> stratifiedContexts, + final VariantContext vc){ + final int[][] tableNoFiltering = getPileupContingencyTable(stratifiedContexts, vc.getReference(), vc.getAlternateAlleles(), -1, MIN_COUNT); + final int[][] tableFiltering = getPileupContingencyTable(stratifiedContexts, vc.getReference(), vc.getAlternateAlleles(), MIN_QUAL_FOR_FILTERED_TEST, MIN_COUNT); + return annotationForOneTable(Math.max(pValueForContingencyTable(tableFiltering), pValueForContingencyTable(tableNoFiltering))); + } + @Override protected Map calculateAnnotationFromLikelihoods(final ReadLikelihoods likelihoods, final VariantContext vc){ diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/LikelihoodRankSumTest.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/LikelihoodRankSumTest.java index b10d3847367..b60236d2729 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/LikelihoodRankSumTest.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/LikelihoodRankSumTest.java @@ -6,6 +6,7 @@ import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.utils.genotyper.ReadLikelihoods; import org.broadinstitute.hellbender.utils.help.HelpConstants; +import org.broadinstitute.hellbender.utils.pileup.PileupElement; import org.broadinstitute.hellbender.utils.read.GATKRead; import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; import org.broadinstitute.hellbender.utils.variant.GATKVCFHeaderLines; @@ -44,7 +45,13 @@ protected OptionalDouble getElementForRead(final GATKRead read, final int refLoc @Override protected OptionalDouble getElementForRead(final GATKRead read, final int refLoc) { - Utils.nonNull(read); - throw new IllegalStateException("This method should never have been called as getElementForRead(read,refloc,mostLikelyAllele) was overriden"); + // todo its possible this should throw, as This method should never have been called as getElementForRead(read,refloc,mostLikelyAllele) was overriden + return OptionalDouble.empty(); + } + + @Override + protected OptionalDouble getElementForPileupElement(final PileupElement p, final int refLoc) { + // todo its possible this should throw, as This method should never have been called as getElementForRead(read,refloc,mostLikelyAllele) was overriden + return OptionalDouble.empty(); } } diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/MappingQualityRankSumTest.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/MappingQualityRankSumTest.java index ac2460780ca..734be2943ce 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/MappingQualityRankSumTest.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/MappingQualityRankSumTest.java @@ -4,6 +4,7 @@ import org.broadinstitute.barclay.help.DocumentedFeature; import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.utils.help.HelpConstants; +import org.broadinstitute.hellbender.utils.pileup.PileupElement; import org.broadinstitute.hellbender.utils.read.GATKRead; import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; import org.broadinstitute.hellbender.utils.variant.GATKVCFHeaderLines; @@ -42,4 +43,9 @@ protected OptionalDouble getElementForRead(final GATKRead read, final int refLoc Utils.nonNull(read); return OptionalDouble.of(read.getMappingQuality()); } + + protected OptionalDouble getElementForPileupElement(final PileupElement p, final int refLoc) { + // default to returning the same value + return OptionalDouble.of(p.getMappingQual()); + } } diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/QualByDepth.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/QualByDepth.java index 64f4e2255fd..783c372e4b2 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/QualByDepth.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/QualByDepth.java @@ -85,8 +85,11 @@ public Map annotate(final ReferenceContext ref, ADrestrictedDepth += totalADdepth; } depth += totalADdepth; + continue; } - } else if (likelihoods != null) { + } + // if there is no AD value or it is a dummy value, we want to look to other means to get the depth + if (likelihoods != null) { depth += likelihoods.sampleReadCount(likelihoods.indexOfSample(genotype.getSampleName())); } else if ( genotype.hasDP() ) { depth += genotype.getDP(); diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/RMSMappingQuality.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/RMSMappingQuality.java index a0e5c3fc8ad..5fb3324d685 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/RMSMappingQuality.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/RMSMappingQuality.java @@ -114,22 +114,21 @@ public Map finalizeRawData(final VariantContext vc, final Varian ReducibleAnnotationData myData = new ReducibleAnnotationData(rawMQdata); parseRawDataString(myData); - String annotationString = makeFinalizedAnnotationString(vc, myData.getAttributeMap()); - return Collections.singletonMap(getKeyNames().get(0), (Object)annotationString); + String annotationString = makeFinalizedAnnotationString(getNumOfReads(vc, null), myData.getAttributeMap()); + return Collections.singletonMap(getKeyNames().get(0), annotationString); } - public String makeFinalizedAnnotationString(final VariantContext vc, final Map perAlleleData) { - int numOfReads = getNumOfReads(vc); - return String.format("%.2f", Math.sqrt((double)perAlleleData.get(Allele.NO_CALL)/numOfReads)); + public String makeFinalizedAnnotationString(final int numOfReads, final Map perAlleleData) { + return String.format("%.2f", Math.sqrt(perAlleleData.get(Allele.NO_CALL)/numOfReads)); } - public void combineAttributeMap(ReducibleAnnotationData toAdd, ReducibleAnnotationData combined) { - if (combined.getAttribute(Allele.NO_CALL) != null) - combined.putAttribute(Allele.NO_CALL, (Double) combined.getAttribute(Allele.NO_CALL) + (Double) toAdd.getAttribute(Allele.NO_CALL)); - else + public void combineAttributeMap(ReducibleAnnotationData toAdd, ReducibleAnnotationData combined) { + if (combined.getAttribute(Allele.NO_CALL) != null) { + combined.putAttribute(Allele.NO_CALL, combined.getAttribute(Allele.NO_CALL) + toAdd.getAttribute(Allele.NO_CALL)); + } else { combined.putAttribute(Allele.NO_CALL, toAdd.getAttribute(Allele.NO_CALL)); - + } } @SuppressWarnings({"unchecked", "rawtypes"})//FIXME @@ -150,7 +149,17 @@ public void calculateRawData(final VariantContext vc, public Map annotate(final ReferenceContext ref, final VariantContext vc, final ReadLikelihoods likelihoods) { - return annotateRawData(ref, vc, likelihoods); + Utils.nonNull(vc); + if (likelihoods == null || likelihoods.readCount() < 1 ) { + return new HashMap<>(); + } + + final Map annotations = new HashMap<>(); + final ReducibleAnnotationData myData = new ReducibleAnnotationData<>(null); + calculateRawData(vc, likelihoods, myData); + final String annotationString = makeFinalizedAnnotationString(getNumOfReads(vc, likelihoods), myData.getAttributeMap()); + annotations.put(getKeyNames().get(0), annotationString); + return annotations; } @VisibleForTesting @@ -170,7 +179,7 @@ public VariantContext finalizeRawMQ(final VariantContext vc) { return vc; } else { final double squareSum = parseRawDataString(rawMQdata); - final int numOfReads = getNumOfReads(vc); + final int numOfReads = getNumOfReads(vc, null); final double rms = Math.sqrt(squareSum / (double)numOfReads); final String finalizedRMSMAppingQuality = formattedValue(rms); return new VariantContextBuilder(vc) @@ -198,38 +207,11 @@ private static double parseRawDataString(String rawDataString) { */ final double squareSum = Double.parseDouble(rawDataString.split(",")[0]); return squareSum; - } catch (final NumberFormatException e){ - throw new UserException.BadInput("malformed " + GATKVCFConstants.RAW_RMS_MAPPING_QUALITY_KEY +" annotation: " + rawDataString); + } catch (final NumberFormatException e) { + throw new UserException.BadInput("malformed " + GATKVCFConstants.RAW_RMS_MAPPING_QUALITY_KEY + " annotation: " + rawDataString); } } - /** - * - * @return the number of reads at the given site, calculated as InfoField {@link VCFConstants#DEPTH_KEY} minus the - * format field {@link GATKVCFConstants#MIN_DP_FORMAT_KEY} or DP of each of the HomRef genotypes at that site - * @throws UserException.BadInput if the {@link VCFConstants#DEPTH_KEY} is missing or if the calculated depth is <= 0 - */ - @VisibleForTesting - static int getNumOfReads(final VariantContext vc) { - //don't use the full depth because we don't calculate MQ for reference blocks - int numOfReads = vc.getAttributeAsInt(VCFConstants.DEPTH_KEY, -1); - if(vc.hasGenotypes()) { - for(final Genotype gt : vc.getGenotypes()) { - if(gt.isHomRef()) { - //site-level DP contribution will come from MIN_DP for gVCF-called reference variants or DP for BP resolution - if (gt.hasExtendedAttribute(GATKVCFConstants.MIN_DP_FORMAT_KEY)) { - numOfReads -= Integer.parseInt(gt.getExtendedAttribute(GATKVCFConstants.MIN_DP_FORMAT_KEY).toString()); - } else if (gt.hasDP()) { - numOfReads -= gt.getDP(); - } - } - } - } - if (numOfReads <= 0){ - numOfReads = -1; //return -1 to result in a NaN - } - return numOfReads; - } /** * @@ -243,7 +225,21 @@ static int getNumOfReads(final VariantContext vc, final ReadLikelihoods likelihoods) { int numOfReads = 0; if (vc.hasAttribute(VCFConstants.DEPTH_KEY)) { - return getNumOfReads(vc); + numOfReads = vc.getAttributeAsInt(VCFConstants.DEPTH_KEY, -1); + if(vc.hasGenotypes()) { + for(final Genotype gt : vc.getGenotypes()) { + if(gt.isHomRef()) { + //site-level DP contribution will come from MIN_DP for gVCF-called reference variants or DP for BP resolution + if (gt.hasExtendedAttribute(GATKVCFConstants.MIN_DP_FORMAT_KEY)) { + numOfReads -= Integer.parseInt(gt.getExtendedAttribute(GATKVCFConstants.MIN_DP_FORMAT_KEY).toString()); + } else if (gt.hasDP()) { + numOfReads -= gt.getDP(); + } + } + } + } + + // If there is no depth key, try to compute from the likelihoods } else if (likelihoods != null && likelihoods.numberOfAlleles() != 0) { for (int i = 0; i < likelihoods.numberOfSamples(); i++) { for (GATKRead read : likelihoods.sampleReads(i)) { diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/RankSumTest.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/RankSumTest.java index 33694d52e29..4f803d43cfe 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/RankSumTest.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/RankSumTest.java @@ -4,31 +4,23 @@ import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.GenotypesContext; import htsjdk.variant.variantcontext.VariantContext; -import org.apache.commons.lang.ArrayUtils; import org.broadinstitute.hellbender.engine.ReferenceContext; import org.broadinstitute.hellbender.utils.MannWhitneyU; import org.broadinstitute.hellbender.utils.QualityUtils; import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.utils.genotyper.ReadLikelihoods; +import org.broadinstitute.hellbender.utils.pileup.PileupElement; import org.broadinstitute.hellbender.utils.read.GATKRead; import java.util.*; +import java.util.stream.Collectors; /** * Abstract root for all RankSum based annotations */ -public abstract class RankSumTest extends InfoFieldAnnotation { - protected static double INVALID_ELEMENT_FROM_READ = Double.NEGATIVE_INFINITY; - private boolean useDithering = true; - - public RankSumTest(final boolean useDithering){ - this.useDithering = useDithering; - } - - public RankSumTest(){ - this(false); - } +public abstract class RankSumTest extends InfoFieldAnnotation implements Annotation { + protected final static double INVALID_ELEMENT_FROM_READ = Double.NEGATIVE_INFINITY; @Override public Map annotate(final ReferenceContext ref, @@ -47,17 +39,21 @@ public Map annotate(final ReferenceContext ref, final int refLoc = vc.getStart(); if( likelihoods != null) { - for (final ReadLikelihoods.BestAllele bestAllele : likelihoods.bestAlleles()) { - final GATKRead read = bestAllele.read; - final Allele allele = bestAllele.allele; - if (bestAllele.isInformative() && isUsableRead(read, refLoc)) { - final OptionalDouble value = getElementForRead(read, refLoc, bestAllele); - // Bypass read if the clipping goal is not reached or the refloc is inside a spanning deletion - if (value.isPresent() && value.getAsDouble() != INVALID_ELEMENT_FROM_READ) { - if (allele.isReference()) { - refQuals.add(value.getAsDouble()); - } else if (vc.hasAllele(allele)) { - altQuals.add(value.getAsDouble()); + if (likelihoods.hasFilledLikelihoods()) { + // Default to using the likelihoods to calculate the rank sum + fillQualsFromLikelihood(vc, likelihoods, refQuals, altQuals, refLoc); + + // Use the pileup to stratify otherwise + } else { + for (final PileupElement p : likelihoods.getStratifiedPileups(vc).values().stream().flatMap(Collection::stream).collect(Collectors.toList())) { + if (PileupElement.isUsableBaseForAnnotation(p)) { + final OptionalDouble value = getElementForPileupElement(p, refLoc); + if (value.isPresent() && value.getAsDouble() != INVALID_ELEMENT_FROM_READ) { + if (vc.getReference().equals(Allele.create(p.getBase(), true))) { + refQuals.add(value.getAsDouble()); + } else if (vc.hasAllele(Allele.create(p.getBase()))) { + altQuals.add(value.getAsDouble()); + } } } } @@ -82,6 +78,24 @@ public Map annotate(final ReferenceContext ref, } } + protected void fillQualsFromLikelihood(VariantContext vc, ReadLikelihoods likelihoods, List refQuals, List altQuals, int refLoc) { + for (final ReadLikelihoods.BestAllele bestAllele : likelihoods.bestAlleles()) { + final GATKRead read = bestAllele.read; + final Allele allele = bestAllele.allele; + if (bestAllele.isInformative() && isUsableRead(read, refLoc)) { + final OptionalDouble value = getElementForRead(read, refLoc, bestAllele); + // Bypass read if the clipping goal is not reached or the refloc is inside a spanning deletion + if (value.isPresent() && value.getAsDouble() != INVALID_ELEMENT_FROM_READ) { + if (allele.isReference()) { + refQuals.add(value.getAsDouble()); + } else if (vc.hasAllele(allele)) { + altQuals.add(value.getAsDouble()); + } + } + } + } + } + /** * Get the element for the given read at the given reference position * @@ -114,4 +128,15 @@ protected boolean isUsableRead(final GATKRead read, final int refLoc) { Utils.nonNull(read); return read.getMappingQuality() != 0 && read.getMappingQuality() != QualityUtils.MAPPING_QUALITY_UNAVAILABLE; } + + /** + * Get the element for the given read at the given reference position + * + * This can return an OptionalDouble.empty() if the annotation should not be computed based on the pileups. + * + * @param p the pileup element + * @return a Double representing the element to be used in the rank sum test, or null if it should not be used + */ + protected abstract OptionalDouble getElementForPileupElement(final PileupElement p, final int refLoc); + } diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/ReadPosRankSumTest.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/ReadPosRankSumTest.java index 4d8bf1f30fe..a778f830a1e 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/ReadPosRankSumTest.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/ReadPosRankSumTest.java @@ -1,14 +1,15 @@ package org.broadinstitute.hellbender.tools.walkers.annotator; -import htsjdk.variant.vcf.VCFInfoHeaderLine; +import htsjdk.samtools.CigarElement; +import htsjdk.samtools.CigarOperator; import org.broadinstitute.barclay.help.DocumentedFeature; import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.utils.help.HelpConstants; +import org.broadinstitute.hellbender.utils.pileup.PileupElement; import org.broadinstitute.hellbender.utils.read.AlignmentUtils; import org.broadinstitute.hellbender.utils.read.GATKRead; import org.broadinstitute.hellbender.utils.read.ReadUtils; import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; -import org.broadinstitute.hellbender.utils.variant.GATKVCFHeaderLines; import java.util.Collections; import java.util.List; @@ -33,6 +34,8 @@ @DocumentedFeature(groupName=HelpConstants.DOC_CAT_ANNOTATORS, groupSummary=HelpConstants.DOC_CAT_ANNOTATORS_SUMMARY, summary="Rank sum test for relative positioning of REF versus ALT alleles within reads (ReadPosRankSum)") public final class ReadPosRankSumTest extends RankSumTest implements StandardAnnotation { + public static final int LEGACY_PAIRHMM_BASE_QUALITY_SCORE_THRESHOLD = 20; //TODO the 20 hard value here is in lieu of PairHMM.BASE_QUALITY_SCORE_THRESHOLD in order to directly match GATK3 output + @Override public List getKeyNames() { return Collections.singletonList(GATKVCFConstants.READ_POS_RANK_SUM_KEY); } @@ -69,5 +72,99 @@ public static OptionalDouble getReadPosition(final GATKRead read, final int refL return OptionalDouble.of(readPos); } + @Override + protected OptionalDouble getElementForPileupElement(final PileupElement p, int refLoc) { + final int offset = AlignmentUtils.calcAlignmentByteArrayOffset(p.getRead().getCigar(), p, 0, 0); + return OptionalDouble.of(getFinalVariantReadPosition(p.getRead(), offset)); + } + + // Utility methods necessary for computing the rank sum using read pileups. + // TODO these methods contain bugs ported from GATK3, see issue https://github.com/broadinstitute/gatk/issues/4450 for progress towards fixing them + /** + * Get the position of a variant within a read with respect to the closer end, accounting for hard clipped bases and low quality ends + * Used by ReadPosRankSum annotations + * + * @param read a read containing the variant + * @param initialReadPosition the position based on the modified, post-hard-clipped CIGAR + * @return read position + */ + public static int getFinalVariantReadPosition(final GATKRead read, final int initialReadPosition) { + final int numAlignedBases = getNumAlignedBases(read); + + int readPos = initialReadPosition; + //TODO: this doesn't work for the middle-right position if we index from zero + if (initialReadPosition > numAlignedBases / 2) { + readPos = numAlignedBases - (initialReadPosition + 1); + } + return readPos; + } + + /** + * + * @param read read to count bases upon + * @return the number of hard clipped and low qual bases at the read start (where start is the leftmost end w.r.t. the reference) + */ + public static int getNumClippedBasesAtStart(final GATKRead read) { + // check for hard clips (never consider these bases): + final CigarElement first = read.getCigarElement(0); + + final byte[] unclippedReadBases = read.getBases(); + final byte[] unclippedReadQuals = read.getBaseQualities(); + + // Do a stricter base clipping than provided by CIGAR string, since this one may be too conservative, + // and may leave a string of Q2 bases still hanging off the reads. + //TODO: this code may not even get used because HaplotypeCaller already hard clips low quality tails + + int numStartClippedBasesCounter = (first.getOperator() == CigarOperator.H)? first.getLength(): 0; + + for (int i = numStartClippedBasesCounter; i < unclippedReadBases.length; i++) { + if (unclippedReadQuals[i] < LEGACY_PAIRHMM_BASE_QUALITY_SCORE_THRESHOLD) { + numStartClippedBasesCounter++; + } else { + break; + } + } + + return numStartClippedBasesCounter; + } + + /** + * + * @param read a read containing the variant + * @return number of non-hard clipped, aligned bases (excluding low quality bases at either end) + */ + //TODO: this is bizarre -- this code counts hard clips, but then subtracts them from the read length, which already doesn't count hard clips + public static int getNumAlignedBases(final GATKRead read) { + return read.getLength() - getNumClippedBasesAtStart(read) - getNumClippedBasesAtEnd(read); + } + + /** + * + * @param read a read containing the variant + * @return number of hard clipped and low qual bases at the read end (where end is right end w.r.t. the reference) + */ + public static int getNumClippedBasesAtEnd(final GATKRead read) { + // check for hard clips (never consider these bases): + CigarElement last = read.getCigarElement(read.numCigarElements() - 1); + + final byte[] unclippedReadBases = read.getBases(); + final byte[] unclippedReadQuals = read.getBaseQualities(); + + // Do a stricter base clipping than provided by CIGAR string, since this one may be too conservative, + // and may leave a string of Q2 bases still hanging off the reads. + //TODO: this code may not even get used because HaplotypeCaller already hard clips low quality tails + + int endClippedBasesCounter = last.getOperator() == CigarOperator.H ? last.getLength() : 0; + + for (int i = unclippedReadBases.length - endClippedBasesCounter - 1; i >= 0; i--) { + if (unclippedReadQuals[i] < LEGACY_PAIRHMM_BASE_QUALITY_SCORE_THRESHOLD) { + + endClippedBasesCounter++; + } else { + break; + } + } + return endClippedBasesCounter; + } } diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/StrandBiasTest.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/StrandBiasTest.java index c8c4918dc39..8859f0d0e59 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/StrandBiasTest.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/StrandBiasTest.java @@ -6,8 +6,10 @@ import htsjdk.variant.variantcontext.VariantContext; import org.broadinstitute.hellbender.engine.ReferenceContext; import org.broadinstitute.hellbender.exceptions.GATKException; +import org.broadinstitute.hellbender.utils.QualityUtils; import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.utils.genotyper.ReadLikelihoods; +import org.broadinstitute.hellbender.utils.pileup.PileupElement; import org.broadinstitute.hellbender.utils.read.GATKRead; import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; @@ -41,13 +43,22 @@ public Map annotate(final ReferenceContext ref, } if (likelihoods != null) { - return calculateAnnotationFromLikelihoods(likelihoods, vc); + if (vc.isSNP() && !likelihoods.hasFilledLikelihoods() && (likelihoods.readCount() != 0)) { + return calculateAnnotationFromStratifiedContexts(likelihoods.getStratifiedPileups(vc), vc); + } + + if (likelihoods.hasFilledLikelihoods()) { + return calculateAnnotationFromLikelihoods(likelihoods, vc); + } } return Collections.emptyMap(); } protected abstract Map calculateAnnotationFromGTfield(final GenotypesContext genotypes); + protected abstract Map calculateAnnotationFromStratifiedContexts(final Map> stratifiedContexts, + final VariantContext vc); + protected abstract Map calculateAnnotationFromLikelihoods(final ReadLikelihoods likelihoods, final VariantContext vc); @@ -222,4 +233,35 @@ private static int[][] decodeSBBS( final int[] array ) { table[1][1] = array[3]; return table; } + + /** + Allocate and fill a 2x2 strand contingency table. In the end, it'll look something like this: + * fw rc + * allele1 # # + * allele2 # # + * @return a 2x2 contingency table over SNP sites + */ + protected static int[][] getPileupContingencyTable(final Map> stratifiedContexts, + final Allele ref, + final List allAlts, + final int minQScoreToConsider, + final int minCount ) { + int[][] table = new int[ARRAY_DIM][ARRAY_DIM]; + + for (final Map.Entry> sample : stratifiedContexts.entrySet() ) { + final int[] myTable = new int[ARRAY_SIZE]; + for (final PileupElement p : sample.getValue()) { + if (PileupElement.isUsableBaseForAnnotation(p) && Math.min(p.getQual(), p.getMappingQual()) >= minQScoreToConsider) { + updateTable(myTable, Allele.create(p.getBase(), false), p.getRead(), ref, allAlts); + } + } + + if ( passesMinimumThreshold( myTable, minCount ) ) { + copyToMainTable(myTable, table); + } + } + return table; + } + + } diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/StrandOddsRatio.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/StrandOddsRatio.java index d8d86df13b6..07982d83f05 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/StrandOddsRatio.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/StrandOddsRatio.java @@ -4,12 +4,11 @@ import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.GenotypesContext; import htsjdk.variant.variantcontext.VariantContext; -import htsjdk.variant.vcf.VCFInfoHeaderLine; import org.broadinstitute.barclay.help.DocumentedFeature; import org.broadinstitute.hellbender.utils.genotyper.ReadLikelihoods; import org.broadinstitute.hellbender.utils.help.HelpConstants; +import org.broadinstitute.hellbender.utils.pileup.PileupElement; import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; -import org.broadinstitute.hellbender.utils.variant.GATKVCFHeaderLines; import java.util.Collections; import java.util.List; @@ -67,6 +66,15 @@ protected Map calculateAnnotationFromGTfield(final GenotypesCont return tableFromPerSampleAnnotations != null ? annotationForOneTable(calculateSOR(tableFromPerSampleAnnotations)) : null; } + @Override + protected Map calculateAnnotationFromStratifiedContexts(Map> stratifiedContexts, + final VariantContext vc){ + final int[][] tableNoFiltering = getPileupContingencyTable(stratifiedContexts, vc.getReference(), vc.getAlternateAlleles(), -1, MIN_COUNT); + final double ratio = calculateSOR(tableNoFiltering); + return annotationForOneTable(ratio); + } + + @Override protected Map calculateAnnotationFromLikelihoods(final ReadLikelihoods likelihoods, final VariantContext vc){ final int[][] table = getContingencyTable(likelihoods, vc, MIN_COUNT); diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotation.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotation.java index a3a611cf566..dd8d055c4a3 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotation.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotation.java @@ -5,7 +5,7 @@ /** * Superclass of all variant annotations. */ -public abstract class VariantAnnotation { +public abstract class VariantAnnotation implements Annotation { /** * Return the keys diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator.java new file mode 100644 index 00000000000..55cfc01a0d7 --- /dev/null +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator.java @@ -0,0 +1,259 @@ +package org.broadinstitute.hellbender.tools.walkers.annotator; + +import com.google.common.collect.Lists; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.vcf.*; +import org.broadinstitute.barclay.argparser.*; +import org.broadinstitute.hellbender.cmdline.GATKPlugin.DefaultGATKVariantAnnotationArgumentCollection; +import org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationArgumentCollection; +import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; +import org.broadinstitute.hellbender.cmdline.argumentcollections.DbsnpArgumentCollection; +import org.broadinstitute.hellbender.engine.*; +import org.broadinstitute.hellbender.engine.filters.ReadFilter; +import org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary; +import org.broadinstitute.hellbender.engine.filters.WellformedReadFilter; +import org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils; +import org.broadinstitute.hellbender.utils.BaseUtils; +import org.broadinstitute.hellbender.utils.Utils; +import org.broadinstitute.hellbender.utils.genotyper.*; +import org.broadinstitute.hellbender.utils.genotyper.SampleList; +import org.broadinstitute.hellbender.utils.read.GATKRead; +import picard.cmdline.programgroups.VariantManipulationProgramGroup; + +import java.io.File; +import java.util.*; +import java.util.stream.Collectors; + + +/** + * Annotate variant calls with context information + * + *

+ * This tool is designed to annotate variant calls based on their context (as opposed to functional annotation). + * Various annotation modules are available; see the "Annotation Modules" page linked in the Tool Documentation sidebar for a complete list. + * + *

Input

+ *

+ * A variant set to annotate and optionally one or more BAM files. + *

+ * + *

Output

+ *

+ * An annotated VCF. + *

+ * + *

Usage examples

+ *
+ * + *

Annotate a VCF with dbSNP IDs and depth of coverage for each sample

+ * 
+ *   VariantAnnotator \
+ *   -R reference.fasta \
+ *   -I input.bam \
+ *   -V input.vcf \
+ *   -o output.vcf \
+ *   -A Coverage \
+ *   --dbsnp dbsnp.vcf
+ *
+ * + *

Annotate a VCF with allele frequency by an external resource. Annotation will only occur if there is allele concordance between the resource and the input VCF

+ * 
+ *   VariantAnnotator \
+ *   -R reference.fasta \
+ *   -I input.bam \
+ *   -V input.vcf \
+ *   -o output.vcf \
+ *   -L anotherInput.vcf \
+ *   --resource foo:resource.vcf \
+ *   -E foo.AF \
+ *   --resource-allele-concordance
+ *
+ * + *

Annotate with AF and FILTER fields from an external resource

+ * 
+ *   VariantAnnotator \
+ *   -R reference.fasta \
+ *   -V input.vcf \
+ *   -o output.vcf \
+ *   --resource foo:resource.vcf \
+ *   --expression foo.AF \
+ *   --expression foo.FILTER
+ *
+ * + *

Caveat

+ *

This tool will not output every annotation as many cannot be made without computing the per-read AlleleLikelihoods, + * which is generated in either the HaplotypeCaller or Mutect2.

+ * + *

Special note on RankSumTestAnnotations

+ *

RankSumAnnotations produced by this tool are not the same as those produced by the HaplotypeCaller. Without the + * likelihoods, the tool resorts to a pileup heuristic to categorize reads which means that RankSumAnnotations will only + * be present for SNP variants.

+ */ +@CommandLineProgramProperties(summary="Tool for adding annotations to VCF files", + oneLineSummary = "Tool for adding annotations to VCF files", + programGroup = VariantManipulationProgramGroup.class) +@BetaFeature +public class VariantAnnotator extends VariantWalker { + private VariantContextWriter vcfWriter; + + /** + * The rsIDs from this file are used to populate the ID column of the output. Also, the DB INFO flag will be set when appropriate. Note that dbSNP is not used in any way for the calculations themselves. + */ + @ArgumentCollection + protected DbsnpArgumentCollection dbsnp = new DbsnpArgumentCollection(); + + /** + * If a call overlaps with a record from the provided comp track, the INFO field will be annotated + * as such in the output with the track name (e.g. -comp:FOO will have 'FOO' in the INFO field). Records that are + * filtered in the comp track will be ignored. Note that 'dbSNP' has been special-cased (see the --dbsnp argument). + */ + @Advanced + @Argument(fullName = "comp", doc = "Comparison VCF file(s)", optional = true) + public List> comps = new ArrayList<>(); + + /** + * An external resource VCF file or files from which to annotate. + * + * Use this option to add annotations from a resource file to the output. + * For example, if you want to annotate your callset with the AC field value from a VCF file named + * 'resource_file.vcf', you tag it with '-resource:my_resource resource_file.vcf' and you additionally specify + * '-E my_resource.AC' (-E is short for --expression, also documented on this page). In the resulting output + * VCF, any records for which there is a record at the same position in the resource file will be annotated with + * 'my_resource.AC=N'. Note that if there are multiple records in the resource file that overlap the given + * position, one is chosen randomly. Check for allele concordance if using --resource-allele-concordance, otherwise + * the match is based on position only. + */ + @Argument(fullName="resource", doc="External resource VCF file", optional=true) + public List> resources; + + @Argument(fullName= StandardArgumentDefinitions.OUTPUT_LONG_NAME, + shortName=StandardArgumentDefinitions.OUTPUT_SHORT_NAME, + doc="The file to whcih variants should be written", optional=false) + protected File outputFile; + + /** + * See the --list argument to view available annotations. + */ + @ArgumentCollection + public GATKAnnotationArgumentCollection variantAnnotationArgumentCollection = new DefaultGATKVariantAnnotationArgumentCollection( + Collections.emptyList(), + Collections.emptyList(), + Collections.emptyList()); + + /** + * This option enables you to add annotations from one VCF to another. + * + * For example, if you want to annotate your callset with the AC field value from a VCF file named + * 'resource_file.vcf', you tag it with '-resource:my_resource resource_file.vcf' (see the -resource argument, also + * documented on this page) and you specify '-E my_resource.AC'. In the resulting output VCF, any records for + * which there is a record at the same position in the resource file will be annotated with 'my_resource.AC=N'. + * INFO field data, ID, ALT, and FILTER fields may be used as expression values. + * Note that if there are multiple records in the resource file that overlap the given position, one is chosen + * randomly. + */ + @Argument(fullName="expression", shortName="E", doc="One or more specific expressions to apply to variant calls", optional=true) + protected Set expressionsToUse = new HashSet<>(); + + /** + * If this argument is specified, add annotations (specified by --expression) from an external resource + * (specified by --resource) to the input VCF (specified by --variant) only if the alleles are + * concordant between input and the resource VCFs. Otherwise, always add the annotations. + */ + @Argument(fullName="resource-allele-concordance", shortName="rac", doc="Check for allele concordances when using an external resource VCF file", optional=true) + protected Boolean expressionAlleleConcordance = false; + + /** + * You can use the -XA argument in combination with this one to exclude specific annotations.Note that some + * annotations may not be actually applied if they are not applicable to the data provided or if they are + * unavailable to the tool (e.g. there are several annotations that are currently not hooked up to + * HaplotypeCaller). At present no error or warning message will be provided, the annotation will simply be + * skipped silently. You can check the output VCF header to see which annotations were actually applied (although + * this does not guarantee that the annotation was applied to all records in the VCF, since some annotations have + * additional requirements, e.g. minimum number of samples or heterozygous sites only -- see the documentation + * for individual annotations' requirements). + */ + @Argument(fullName="use-all-annotations", shortName="all", doc="Use all possible annotations (not for the faint of heart)", optional=true) + protected Boolean USE_ALL_ANNOTATIONS = false; + + private VariantAnnotatorEngine annotatorEngine; + private SampleList variantSamples; + + /** + * Prepare the output file and the list of available features. + */ + public void onTraversalStart() { + // get the list of all sample names from the variant VCF, if applicable + final List samples = getHeaderForVariants().getGenotypeSamples(); + variantSamples = new IndexedSampleList(samples); + + if ( USE_ALL_ANNOTATIONS ) { + annotatorEngine = VariantAnnotatorEngine.ofAllMinusExcluded(variantAnnotationArgumentCollection.getUserDisabledAnnotationNames(), dbsnp.dbsnp, comps, false); + } else { + annotatorEngine = VariantAnnotatorEngine.ofSelectedMinusExcluded(variantAnnotationArgumentCollection, dbsnp.dbsnp, comps, false); + } + annotatorEngine.addExpressions(expressionsToUse, resources, expressionAlleleConcordance ); + + // setup the header fields + // note that if any of the definitions conflict with our new ones, then we want to overwrite the old ones + final Set hInfo = new HashSet<>(); + + hInfo.addAll(annotatorEngine.getVCFAnnotationDescriptions(false)); + hInfo.addAll(getHeaderForVariants().getMetaDataInInputOrder()); + + // TODO ask reviewer, VCFUtils.withUpdatedContigs is what GATK3 calls into, it isn't used anywhere in 4 though so should it be used here? + VCFHeader vcfHeader = new VCFHeader(hInfo, samples); + vcfWriter = createVCFWriter(outputFile); + vcfWriter.writeHeader(VCFUtils.withUpdatedContigs(vcfHeader, hasReference()? new File(referenceArguments.getReferenceFileName()): null, referenceArguments.getReferencePath()==null ? getBestAvailableSequenceDictionary(): getReferenceDictionary())); + } + + /** + * For each site of interest, annotate based on the requested annotation types + * + * @param vc + * @param readsContext Reads overlapping the current variant. Will be an empty, but non-null, context object + * if there is no backing source of reads data (in which case all queries on it will return + * an empty array/iterator) + * @param refContext + * @param fc + */ + @Override + public void apply(final VariantContext vc, final ReadsContext readsContext, final ReferenceContext refContext, final FeatureContext fc) { + + // if the reference is present and base is not ambiguous, we can annotate + if (refContext.getBases().length ==0 || BaseUtils.simpleBaseToBaseIndex(refContext.getBase()) != -1 ) { + //TODO remove this filter and update the tests, this implementation filters out reads that start in a spanning deleting according to variant context in order to match gatk3, + //TODO this will cause the reads to be assigned and annotated in a different manner than the haplotype caller. + final List reads = Utils.stream(readsContext).filter(r -> r.getStart() <= vc.getStart()).collect(Collectors.toList()); + + ReadLikelihoods likelihoods = new UnfilledReadsLikelihoods<>( variantSamples, new IndexedAlleleList<>(vc.getAlleles()), + AssemblyBasedCallerUtils.splitReadsBySample(variantSamples, getHeaderForReads(), reads)); + + VariantContext annotatedVC = annotatorEngine.annotateContext(vc, fc, refContext, likelihoods, a -> true); + vcfWriter.add(annotatedVC); + + } else { + vcfWriter.add(vc); + } + } + + public List getDefaultReadFilters() { + return Lists.newArrayList( new WellformedReadFilter(), + ReadFilterLibrary.NOT_DUPLICATE, + ReadFilterLibrary.PRIMARY_LINE, + ReadFilterLibrary.PASSES_VENDOR_QUALITY_CHECK, + ReadFilterLibrary.MAPPED); + } + + /** + * Make sure that the writer is closed upon completing the tool. + */ + @Override + public void closeTool() { + if (vcfWriter !=null) { + vcfWriter.close(); + } + } +} + diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotatorEngine.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotatorEngine.java index e3be62e3af1..16271eab082 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotatorEngine.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotatorEngine.java @@ -3,18 +3,20 @@ import com.google.common.collect.Sets; import htsjdk.variant.variantcontext.*; import htsjdk.variant.vcf.*; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.broadinstitute.barclay.argparser.CommandLineException; import org.broadinstitute.hellbender.cmdline.GATKPlugin.DefaultGATKVariantAnnotationArgumentCollection; import org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationArgumentCollection; -import org.broadinstitute.hellbender.engine.FeatureContext; -import org.broadinstitute.hellbender.engine.FeatureInput; -import org.broadinstitute.hellbender.engine.ReferenceContext; +import org.broadinstitute.hellbender.engine.*; import org.broadinstitute.hellbender.exceptions.GATKException; +import org.broadinstitute.hellbender.exceptions.UserException; import org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.ReducibleAnnotation; import org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.ReducibleAnnotationData; import org.broadinstitute.hellbender.utils.ClassUtils; import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.utils.genotyper.ReadLikelihoods; +import org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils; import org.reflections.ReflectionUtils; import java.util.*; @@ -31,16 +33,23 @@ public final class VariantAnnotatorEngine { private final List infoAnnotations; private final List genotypeAnnotations; private Set reducibleKeys; + private List expressions = new ArrayList<>(); private final VariantOverlapAnnotator variantOverlapAnnotator; + private boolean expressionAlleleConcordance; + private final boolean useRawAnnotations; + + private final static Logger logger = LogManager.getLogger(VariantAnnotatorEngine.class); private VariantAnnotatorEngine(final AnnotationManager annots, final FeatureInput dbSNPInput, - final List> featureInputs){ + final List> featureInputs, + final boolean useRaw){ infoAnnotations = annots.createInfoFieldAnnotations(); genotypeAnnotations = annots.createGenotypeAnnotations(); variantOverlapAnnotator = initializeOverlapAnnotator(dbSNPInput, featureInputs); reducibleKeys = new HashSet<>(); + useRawAnnotations = useRaw; for (InfoFieldAnnotation annot : infoAnnotations) { if (annot instanceof ReducibleAnnotation) { reducibleKeys.add(((ReducibleAnnotation) annot).getRawKeyName()); @@ -77,6 +86,7 @@ public VariantAnnotatorEngine(final List annotationList, } variantOverlapAnnotator = initializeOverlapAnnotator(dbSNPInput, featureInputs); reducibleKeys = new HashSet<>(); + useRawAnnotations = useRaw; for (InfoFieldAnnotation annot : infoAnnotations) { if (annot instanceof ReducibleAnnotation) { reducibleKeys.add(((ReducibleAnnotation) annot).getRawKeyName()); @@ -98,10 +108,11 @@ public VariantAnnotatorEngine(final List annotationList, */ public static VariantAnnotatorEngine ofAllMinusExcluded(final List annotationsToExclude, final FeatureInput dbSNPInput, - final List> comparisonFeatureInputs) { + final List> comparisonFeatureInputs, + final boolean useRawAnnotations) { Utils.nonNull(annotationsToExclude, "annotationsToExclude is null"); Utils.nonNull(comparisonFeatureInputs, "comparisonFeatureInputs is null"); - return new VariantAnnotatorEngine(AnnotationManager.ofAllMinusExcluded(annotationsToExclude), dbSNPInput, comparisonFeatureInputs); + return new VariantAnnotatorEngine(AnnotationManager.ofAllMinusExcluded(annotationsToExclude), dbSNPInput, comparisonFeatureInputs, useRawAnnotations); } /** @@ -125,7 +136,33 @@ public static VariantAnnotatorEngine ofSelectedMinusExcluded(final List Utils.nonNull(annotationsToUse, "annotationsToUse is null"); Utils.nonNull(annotationsToExclude, "annotationsToExclude is null"); Utils.nonNull(comparisonFeatureInputs, "comparisonFeatureInputs is null"); - return new VariantAnnotatorEngine(AnnotationManager.ofSelectedMinusExcluded(annotationGroupsToUse, annotationsToUse, annotationsToExclude), dbSNPInput, comparisonFeatureInputs); + return new VariantAnnotatorEngine(AnnotationManager.ofSelectedMinusExcluded(annotationGroupsToUse, annotationsToUse, annotationsToExclude), dbSNPInput, comparisonFeatureInputs, false); + } + + /** + * Makes the engine for given annotation types and groups (minus the excluded ones). + * @param annotationGroupsToUse list of annotations groups to include + * @param annotationsToUse list of of annotations to include + * @param annotationsToExclude list of annotations to exclude + * @param dbSNPInput input for variants from a known set from DbSNP or null if not provided. + * The annotation engine will mark variants overlapping anything in this set using {@link htsjdk.variant.vcf.VCFConstants#DBSNP_KEY}. + * @param comparisonFeatureInputs list of inputs with known variants. + * The annotation engine will mark variants overlapping anything in those sets using the name given by {@link FeatureInput#getName()}. + * Note: the DBSNP FeatureInput should be passed in separately, and not as part of this List - an GATKException will be thrown otherwise. + * Note: there are no non-DBSNP comparison FeatureInputs an empty List should be passed in here, rather than null. + * @param useRawAnnotations Specify whether the annotation engine will attempt to output raw annotations for reducible annotations + */ + public static VariantAnnotatorEngine ofSelectedMinusExcluded(final List annotationGroupsToUse, + final List annotationsToUse, + final List annotationsToExclude, + final FeatureInput dbSNPInput, + final List> comparisonFeatureInputs, + final boolean useRawAnnotations) { + Utils.nonNull(annotationGroupsToUse, "annotationGroupsToUse is null"); + Utils.nonNull(annotationsToUse, "annotationsToUse is null"); + Utils.nonNull(annotationsToExclude, "annotationsToExclude is null"); + Utils.nonNull(comparisonFeatureInputs, "comparisonFeatureInputs is null"); + return new VariantAnnotatorEngine(AnnotationManager.ofSelectedMinusExcluded(annotationGroupsToUse, annotationsToUse, annotationsToExclude), dbSNPInput, comparisonFeatureInputs, useRawAnnotations); } /** @@ -142,11 +179,12 @@ public static VariantAnnotatorEngine ofSelectedMinusExcluded(final List */ public static VariantAnnotatorEngine ofSelectedMinusExcluded(final GATKAnnotationArgumentCollection argumentCollection, final FeatureInput dbSNPInput, - final List> comparisonFeatureInputs) { + final List> comparisonFeatureInputs, + final boolean useRawAnnotations) { return ofSelectedMinusExcluded(argumentCollection.getUserEnabledAnnotationGroups(), argumentCollection.getUserEnabledAnnotationNames(), argumentCollection.getUserDisabledAnnotationNames(), - dbSNPInput, comparisonFeatureInputs); + dbSNPInput, comparisonFeatureInputs, useRawAnnotations); } private VariantOverlapAnnotator initializeOverlapAnnotator(final FeatureInput dbSNPInput, final List> featureInputs) { final Map, String> overlaps = new LinkedHashMap<>(); @@ -211,11 +249,38 @@ public Set getVCFAnnotationDescriptions(boolean useRaw) { } } + // Add header lines corresponding to the expression target files + for (final VariantAnnotatorEngine.VAExpression expression : getRequestedExpressions()) { + // special case the ID field + if (expression.fieldName.equals("ID")) { + descriptions.add(new VCFInfoHeaderLine(expression.fullName, 1, VCFHeaderLineType.String, "ID field transferred from external VCF resource")); + } else { + final VCFInfoHeaderLine targetHeaderLine = ((VCFHeader) new FeatureDataSource<>(expression.binding, 100, VariantContext.class).getHeader()) + .getInfoHeaderLines().stream() + .filter(l -> l.getID().equals(expression.fieldName)) + .findFirst().orElse(null); + + VCFInfoHeaderLine lineToAdd; + if (targetHeaderLine != null) { + expression.sethInfo(targetHeaderLine); + if (targetHeaderLine.getCountType() == VCFHeaderLineCount.INTEGER) { + lineToAdd = new VCFInfoHeaderLine(expression.fullName, targetHeaderLine.getCount(), targetHeaderLine.getType(), targetHeaderLine.getDescription()); + } else { + lineToAdd = new VCFInfoHeaderLine(expression.fullName, targetHeaderLine.getCountType(), targetHeaderLine.getType(), targetHeaderLine.getDescription()); + } + } else { + lineToAdd = new VCFInfoHeaderLine(expression.fullName, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "Value transferred from another external VCF resource"); + logger.warn(String.format("The requested expression attribute \"%s\" is missing from the header in its resource file %s", expression.fullName, expression.binding.getName())); + } + descriptions.add(lineToAdd); + expression.sethInfo(lineToAdd); + } + } + Utils.validate(!descriptions.contains(null), "getVCFAnnotationDescriptions should not contain null. This error is likely due to an incorrect implementation of getDescriptions() in one or more of the annotation classes"); return descriptions; } - /** * Combine (raw) data for reducible annotations (those that use raw data in gVCFs) * Mutates annotationMap by removing the annotations that were combined @@ -285,6 +350,7 @@ public VariantContext finalizeAnnotations(VariantContext vc, VariantContext orig * @param ref the reference context of the variant to annotate or null if there is none * @param likelihoods likelihoods indexed by sample, allele, and read within sample. May be null * @param addAnnot function that indicates if the given annotation type should be added to the variant + * */ public VariantContext annotateContext(final VariantContext vc, final FeatureContext features, @@ -300,9 +366,16 @@ public VariantContext annotateContext(final VariantContext vc, final VariantContext newGenotypeAnnotatedVC = builder.make(); final Map infoAnnotMap = new LinkedHashMap<>(newGenotypeAnnotatedVC.getAttributes()); + annotateExpressions(vc, features, ref, infoAnnotMap); + for ( final InfoFieldAnnotation annotationType : this.infoAnnotations) { if (addAnnot.test(annotationType)){ - final Map annotationsFromCurrentType = annotationType.annotate(ref, newGenotypeAnnotatedVC, likelihoods); + final Map annotationsFromCurrentType; + if (useRawAnnotations && annotationType instanceof ReducibleAnnotation) { + annotationsFromCurrentType = ((ReducibleAnnotation) annotationType).annotateRawData(ref, newGenotypeAnnotatedVC, likelihoods); + } else { + annotationsFromCurrentType = annotationType.annotate(ref, newGenotypeAnnotatedVC, likelihoods); + } if ( annotationsFromCurrentType != null ) { infoAnnotMap.putAll(annotationsFromCurrentType); } @@ -458,7 +531,195 @@ private List filterAnnotations(final List al return Collections.unmodifiableList(new ArrayList<>(annotations)); } + } + + /** + * A container object for storing the objects necessary for carrying over expression annotations. + * It holds onto the source feature input as well as any relevant header lines in order to alter the vcfHeader. + */ + public static class VAExpression { + + final private String fullName, fieldName; + final private FeatureInput binding; + private VCFInfoHeaderLine hInfo; + + public VAExpression(String fullExpression, List> dataSourceList){ + final int indexOfDot = fullExpression.lastIndexOf("."); + if ( indexOfDot == -1 ) { + throw new UserException.BadInput("The requested expression '"+fullExpression+"' is invalid, it should be in VCFFile.value format"); + } + + fullName = fullExpression; + fieldName = fullExpression.substring(indexOfDot+1); + + final String bindingName = fullExpression.substring(0, indexOfDot); + Optional> binding = dataSourceList.stream().filter(ds -> ds.getName().equals(bindingName)).findFirst(); + if (!binding.isPresent()) { + throw new UserException.BadInput("The requested expression '"+fullExpression+"' is invalid, could not find vcf input file"); + } + this.binding = binding.get(); + } + + public void sethInfo(VCFInfoHeaderLine hInfo) { + this.hInfo = hInfo; + } + } + + protected List getRequestedExpressions() { return expressions; } + + // select specific expressions to use + public void addExpressions(Set expressionsToUse, List> dataSources, boolean expressionAlleleConcordance) {//, Set) { + // set up the expressions + for ( final String expression : expressionsToUse ) { + expressions.add(new VAExpression(expression, dataSources)); + } + this.expressionAlleleConcordance = expressionAlleleConcordance; + } + + /** + * Handles logic for expressions for variant contexts. Used to add annotations from one vcf file into the fields + * of another if the variant contexts match sufficiently between the two files. + * + * @param vc VariantContext to add annotations to + * @param features FeatureContext object containing extra VCF features to add to vc + * @param ref Reference context object corresponding to the region overlapping vc + * @param attributes running list of attributes into which to place new annotations + */ + private void annotateExpressions(final VariantContext vc, + final FeatureContext features, + final ReferenceContext ref, + final Map attributes){ + Utils.nonNull(vc); + + // each requested expression + for ( final VAExpression expression : expressions ) { + List variantContexts = features.getValues(expression.binding, vc.getStart()); + + if (!variantContexts.isEmpty()) { + // get the expression's variant context + VariantContext expressionVC = variantContexts.iterator().next(); + + // special-case the ID field + if (expression.fieldName.equals("ID")) { + if (expressionVC.hasID()) { + attributes.put(expression.fullName, expressionVC.getID()); + } + } else if (expression.fieldName.equals("ALT")) { + attributes.put(expression.fullName, expressionVC.getAlternateAllele(0).getDisplayString()); + } else if (expression.fieldName.equals("FILTER")) { + final String filterString = expressionVC.isFiltered() ? expressionVC.getFilters().stream().collect(Collectors.joining(",")) : "PASS"; + attributes.put(expression.fullName, filterString); + } else if (expressionVC.hasAttribute(expression.fieldName)) { + // find the info field + final VCFInfoHeaderLine hInfo = expression.hInfo; + if (hInfo == null) { + throw new UserException("Cannot annotate expression " + expression.fullName + " at " + ref.getInterval() + " for variant allele(s) " + vc.getAlleles() + ", missing header info"); + } + + // + // Add the info field annotations + // + final boolean useRefAndAltAlleles = VCFHeaderLineCount.R == hInfo.getCountType(); + final boolean useAltAlleles = VCFHeaderLineCount.A == hInfo.getCountType(); + + // Annotation uses ref and/or alt alleles or enforce allele concordance + if ((useAltAlleles || useRefAndAltAlleles) || expressionAlleleConcordance) { + + // remove brackets and spaces from expression value + final String cleanedExpressionValue = expressionVC.getAttribute(expression.fieldName,"").toString().replaceAll("[\\[\\]\\s]", ""); + + // get comma separated expression values + final ArrayList expressionValuesList = new ArrayList<>(Arrays.asList(cleanedExpressionValue.split(","))); + + boolean canAnnotate = false; + // get the minimum biallelics without genotypes + + final List minBiallelicVCs = getMinRepresentationBiallelics(vc); + final List minBiallelicExprVCs = getMinRepresentationBiallelics(expressionVC); + + // check concordance + final List annotationValues = new ArrayList<>(); + for (final VariantContext biallelicVC : minBiallelicVCs) { + // check that ref and alt alleles are the same + List exprAlleles = biallelicVC.getAlleles(); + boolean isAlleleConcordant = false; + int i = 0; + for (final VariantContext biallelicExprVC : minBiallelicExprVCs) { + List alleles = biallelicExprVC.getAlleles(); + // concordant + if (alleles.equals(exprAlleles)) { + // get the value for the reference if needed. + if (i == 0 && useRefAndAltAlleles) { + annotationValues.add(expressionValuesList.get(i++)); + } + // use annotation expression and add to vc + annotationValues.add(expressionValuesList.get(i)); + isAlleleConcordant = true; + canAnnotate = true; + break; + } + i++; + } + + // can not find allele match so set to annotation value to zero + if (!isAlleleConcordant) { + annotationValues.add("0"); + } + } + + // some allele matches so add the annotation values + if (canAnnotate) { + attributes.put(expression.fullName, annotationValues); + } + } else { + // use all of the expression values + attributes.put(expression.fullName, expressionVC.getAttribute(expression.fieldName)); + } + } + } + } + } + + /** + * Break the variant context into bialleles (reference and alternate alleles) and trim to a minimum representation + * + * @param vc variant context to annotate + * @return list of biallelics trimmed to a minimum representation + */ + private List getMinRepresentationBiallelics(final VariantContext vc) { + final List minRepresentationBiallelicVCs = new ArrayList<>(); + if (vc.getNAlleles() > 2) { + // TODO, this doesn't actually need to be done, we can simulate it at less cost + for (int i = 1; i < vc.getNAlleles(); i++) { + // Determining if the biallelic would have been considered a SNP + if (! (vc.getReference().length() == 1 && vc.getAlternateAllele(i-1).length() == 1) ) { + minRepresentationBiallelicVCs.add(GATKVariantContextUtils.trimAlleles( + new VariantContextBuilder(vc) + .alleles(Arrays.asList(vc.getReference(),vc.getAlternateAllele(i-1))) + .attributes(removeIrrelevantAttributes(vc.getAttributes())).make(), true, true)); + } else { + minRepresentationBiallelicVCs.add(new VariantContextBuilder(vc) + .alleles(Arrays.asList(vc.getReference(),vc.getAlternateAllele(i-1))) + .attributes(removeIrrelevantAttributes(vc.getAttributes())).make()); + } + } + } else { + minRepresentationBiallelicVCs.add(vc); + } + + return minRepresentationBiallelicVCs; + } + + private Map removeIrrelevantAttributes(Map attributes) { + // since the VC has been subset, remove the invalid attributes + Map ret = new HashMap<>(attributes); + for ( final String key : attributes.keySet() ) { + if ( !(key.equals(VCFConstants.ALLELE_COUNT_KEY) || key.equals(VCFConstants.ALLELE_FREQUENCY_KEY) || key.equals(VCFConstants.ALLELE_NUMBER_KEY)) ) { + ret.remove(key); + } + } + return ret; } } diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_RMSMappingQuality.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_RMSMappingQuality.java index 9184f057a75..af378b5059d 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_RMSMappingQuality.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_RMSMappingQuality.java @@ -4,18 +4,15 @@ import htsjdk.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.GenotypesContext; import htsjdk.variant.variantcontext.VariantContext; -import htsjdk.variant.vcf.VCFInfoHeaderLine; -import org.apache.log4j.Logger; import org.broadinstitute.barclay.help.DocumentedFeature; -import org.broadinstitute.hellbender.engine.AlignmentContext; import org.broadinstitute.hellbender.engine.ReferenceContext; import org.broadinstitute.hellbender.tools.walkers.annotator.InfoFieldAnnotation; import org.broadinstitute.hellbender.utils.QualityUtils; import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.utils.genotyper.ReadLikelihoods; +import org.broadinstitute.hellbender.utils.logging.OneShotLogger; import org.broadinstitute.hellbender.utils.help.HelpConstants; import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; -import org.broadinstitute.hellbender.utils.variant.GATKVCFHeaderLines; import java.util.*; @@ -49,7 +46,8 @@ public final class AS_RMSMappingQuality extends InfoFieldAnnotation implements A private final String printFormat = "%.2f"; - private static final Logger logger = Logger.getLogger(AS_RMSMappingQuality.class); + private static final OneShotLogger allele_logger = new OneShotLogger(AS_RMSMappingQuality.class); + private static final OneShotLogger genotype_logger = new OneShotLogger(AS_RMSMappingQuality.class); public static final String SPLIT_DELIM = "\\|"; //String.split takes a regex, so we need to escape the pipe public static final String PRINT_DELIM = "|"; @@ -58,26 +56,51 @@ public final class AS_RMSMappingQuality extends InfoFieldAnnotation implements A public Map annotate(final ReferenceContext ref, final VariantContext vc, final ReadLikelihoods likelihoods) { - return annotateRawData(ref, vc, likelihoods); + Utils.nonNull(vc); + if ( likelihoods == null) { + return Collections.emptyMap(); + } + final Map annotations = new HashMap<>(); + final ReducibleAnnotationData myData = new ReducibleAnnotationData<>(null); + getRMSDataFromLikelihoods(likelihoods, myData); + final String annotationString = makeFinalizedAnnotationString(vc, myData.getAttributeMap()); + annotations.put(getKeyNames().get(0), annotationString); + return annotations; } + @Override public Map annotateRawData(final ReferenceContext ref, final VariantContext vc, final ReadLikelihoods likelihoods ) { Utils.nonNull(vc); - if ( likelihoods == null) { + if ( likelihoods == null || !likelihoods.hasFilledLikelihoods()) { return Collections.emptyMap(); } final Map annotations = new LinkedHashMap<>(); - final ReducibleAnnotationData myData = new ReducibleAnnotationData<>(null); - calculateRawData(vc, likelihoods, myData); + final ReducibleAnnotationData myData = new ReducibleAnnotationData<>(null); + getRMSDataFromLikelihoods(likelihoods, myData); final String annotationString = makeRawAnnotationString(vc.getAlleles(), myData.getAttributeMap()); annotations.put(getRawKeyName(), annotationString); return annotations; } + @SuppressWarnings({"unchecked", "rawtypes"})//FIXME + public void calculateRawData(final VariantContext vc, + final ReadLikelihoods likelihoods, + final ReducibleAnnotationData myData){ + //For the raw data here, we're only keeping track of the sum of the squares of our values + //When we go to reduce, we'll use the AD info to get the number of reads + + //must use likelihoods for allele-specific annotations + if (likelihoods == null) { + return; + } + getRMSDataFromLikelihoods(likelihoods, myData); + } + + /** * For AS_RMSMappingQuality annotations, the annotations will simply consist of a list of the total value for * every allele computed by parsing all of the individual AS_RMSMappingQuality Raw Key values as doubles @@ -87,10 +110,10 @@ public Map annotateRawData(final ReferenceContext ref, @SuppressWarnings({"unchecked", "rawtypes"})//FIXME generics here blow up public Map combineRawData(final List vcAlleles, final List> annotationList) { //VC already contains merged alleles from ReferenceConfidenceVariantContextMerger - ReducibleAnnotationData combinedData = new AlleleSpecificAnnotationData(vcAlleles, null); + ReducibleAnnotationData combinedData = new AlleleSpecificAnnotationData(vcAlleles, null); for (final ReducibleAnnotationData currentValue : annotationList) { - ReducibleAnnotationData value = (ReducibleAnnotationData)currentValue; + ReducibleAnnotationData value = (ReducibleAnnotationData)currentValue; parseRawDataString(value); combineAttributeMap(value, combinedData); @@ -101,7 +124,7 @@ public Map combineRawData(final List vcAlleles, final Li return annotations; } - public void combineAttributeMap(final ReducibleAnnotationData toAdd, final ReducibleAnnotationData combined) { + public void combineAttributeMap(final ReducibleAnnotationData toAdd, final ReducibleAnnotationData combined) { //check that alleles match for (final Allele currentAllele : combined.getAlleles()){ //combined is initialized with all alleles, but toAdd might have only a subset @@ -115,7 +138,7 @@ public void combineAttributeMap(final ReducibleAnnotationData toAdd, fin } } - protected void parseRawDataString(final ReducibleAnnotationData myData) { + protected void parseRawDataString(final ReducibleAnnotationData myData) { final String rawDataString = myData.getRawData(); //get per-allele data by splitting on allele delimiter final String[] rawDataPerAllele = rawDataString.split(SPLIT_DELIM); @@ -152,19 +175,6 @@ public Map finalizeRawData(final VariantContext vc, final Varian return annotations; } - @SuppressWarnings({"unchecked", "rawtypes"})//FIXME - public void calculateRawData(final VariantContext vc, - final ReadLikelihoods likelihoods, - final ReducibleAnnotationData myData){ - //For the raw data here, we're only keeping track of the sum of the squares of our values - //When we go to reduce, we'll use the AD info to get the number of reads - - //must use likelihoods for allele-specific annotations - if (likelihoods == null) { - return; - } - getRMSDataFromLikelihoods(likelihoods, myData); - } @Override public List getKeyNames() { return Arrays.asList(GATKVCFConstants.AS_RMS_MAPPING_QUALITY_KEY); } @@ -172,7 +182,7 @@ public void calculateRawData(final VariantContext vc, @Override public String getRawKeyName() { return GATKVCFConstants.AS_RAW_RMS_MAPPING_QUALITY_KEY; } - private void getRMSDataFromLikelihoods(final ReadLikelihoods likelihoods, ReducibleAnnotationData myData) { + private void getRMSDataFromLikelihoods(final ReadLikelihoods likelihoods, ReducibleAnnotationData myData) { for ( final ReadLikelihoods.BestAllele bestAllele : likelihoods.bestAlleles() ) { if (bestAllele.isInformative()) { final int mq = bestAllele.read.getMappingQuality(); @@ -184,7 +194,7 @@ private void getRMSDataFromLikelihoods(final ReadLikelihoods likelihoods } } - private String makeRawAnnotationString(final List vcAlleles, final Map perAlleleValues) { + private String makeRawAnnotationString(final List vcAlleles, final Map perAlleleValues) { String annotationString = ""; for (final Allele current : vcAlleles) { if (!annotationString.isEmpty()) { @@ -199,7 +209,7 @@ private String makeRawAnnotationString(final List vcAlleles, final Map perAlleleValues) { + private String makeFinalizedAnnotationString(final VariantContext vc, final Map perAlleleValues) { final Map variantADs = getADcounts(vc); String annotationString = ""; for (final Allele current : vc.getAlternateAlleles()) { @@ -209,7 +219,7 @@ private String makeFinalizedAnnotationString(final VariantContext vc, final Map< if (perAlleleValues.containsKey(current)) { annotationString += String.format(printFormat, Math.sqrt((double) perAlleleValues.get(current) / variantADs.get(current))); } else { - logger.warn("ERROR: VC allele is not found in annotation alleles -- maybe there was trimming?"); + allele_logger.warn("ERROR: VC allele is not found in annotation alleles -- maybe there was trimming?"); } } return annotationString; @@ -218,7 +228,7 @@ private String makeFinalizedAnnotationString(final VariantContext vc, final Map< private Map getADcounts(final VariantContext vc) { final GenotypesContext genotypes = vc.getGenotypes(); if ( genotypes == null || genotypes.size() == 0 ) { - logger.warn("VC does not have genotypes -- annotations were calculated in wrong order"); + genotype_logger.warn("VC does not have genotypes -- annotations were calculated in wrong order"); return null; } diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_RankSumTest.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_RankSumTest.java index f1c39989edb..fa451a06898 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_RankSumTest.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_RankSumTest.java @@ -1,6 +1,8 @@ package org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific; +import com.google.common.primitives.Doubles; import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.GenotypesContext; import htsjdk.variant.variantcontext.VariantContext; import org.apache.commons.lang.ArrayUtils; import org.apache.log4j.Logger; @@ -9,7 +11,9 @@ import org.broadinstitute.hellbender.utils.CompressedDataList; import org.broadinstitute.hellbender.utils.Histogram; import org.broadinstitute.hellbender.utils.MannWhitneyU; +import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.utils.genotyper.ReadLikelihoods; +import org.broadinstitute.hellbender.utils.pileup.PileupElement; import java.util.*; @@ -27,7 +31,40 @@ public abstract class AS_RankSumTest extends RankSumTest implements ReducibleAnn public Map annotate(final ReferenceContext ref, final VariantContext vc, final ReadLikelihoods likelihoods) { - return annotateRawData(ref, vc, likelihoods); + Utils.nonNull(vc, "vc is null"); + + final GenotypesContext genotypes = vc.getGenotypes(); + if (genotypes == null || genotypes.isEmpty()) { + return Collections.emptyMap(); + } + + final List refQuals = new ArrayList<>(); + final List altQuals = new ArrayList<>(); + + final int refLoc = vc.getStart(); + + if( likelihoods != null) { + // Default to using the likelihoods to calculate the rank sum + if (likelihoods.hasFilledLikelihoods()) { + fillQualsFromLikelihood(vc, likelihoods, refQuals, altQuals, refLoc); + } + } + + if ( refQuals.isEmpty() && altQuals.isEmpty() ) { + return Collections.emptyMap(); + } + + final MannWhitneyU mannWhitneyU = new MannWhitneyU(); + + // we are testing that set1 (the alt bases) have lower quality scores than set2 (the ref bases) + final MannWhitneyU.Result result = mannWhitneyU.test(Doubles.toArray(altQuals), Doubles.toArray(refQuals), MannWhitneyU.TestType.FIRST_DOMINATES); + final double zScore = result.getZ(); + + if (Double.isNaN(zScore)) { + return Collections.emptyMap(); + } else { + return Collections.singletonMap(getKeyNames().get(0), String.format("%.3f", zScore)); + } } /** @@ -45,7 +82,7 @@ public Map annotate(final ReferenceContext ref, public Map annotateRawData(final ReferenceContext ref, final VariantContext vc, final ReadLikelihoods likelihoods ) { - if ( likelihoods == null) { + if ( likelihoods == null || !likelihoods.hasFilledLikelihoods()) { return Collections.emptyMap(); } @@ -112,7 +149,7 @@ protected String makeRawAnnotationString(final List vcAlleles, final Map // Generates as CompressedDataList over integer values over each read @SuppressWarnings({"unchecked", "rawtypes"})//FIXME generics here blow up - public void calculateRawData(VariantContext vc, final ReadLikelihoods likelihoods, ReducibleAnnotationData myData) { + private void calculateRawData(VariantContext vc, final ReadLikelihoods likelihoods, ReducibleAnnotationData myData) { if( vc.getGenotypes().getSampleNames().size() != 1) { throw new IllegalStateException("Calculating raw data for allele-specific rank sums requires variant context input with exactly one sample, as in a gVCF."); } @@ -314,5 +351,9 @@ public String outputSingletonValueAsHistogram(final Double rankSumValue) { return h.toString(); } - + @Override + // Unnecessary for this implementation of Annotate + protected final OptionalDouble getElementForPileupElement(PileupElement p, int refLoc) { + return null; + } } diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_ReadPosRankSumTest.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_ReadPosRankSumTest.java index d01c1b0af45..007a91f2fbd 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_ReadPosRankSumTest.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_ReadPosRankSumTest.java @@ -5,6 +5,7 @@ import org.broadinstitute.hellbender.tools.walkers.annotator.ReadPosRankSumTest; import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.utils.help.HelpConstants; +import org.broadinstitute.hellbender.utils.pileup.PileupElement; import org.broadinstitute.hellbender.utils.read.AlignmentUtils; import org.broadinstitute.hellbender.utils.read.GATKRead; import org.broadinstitute.hellbender.utils.read.ReadUtils; diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_StrandBiasTest.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_StrandBiasTest.java index 552a026b256..878bebf2764 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_StrandBiasTest.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_StrandBiasTest.java @@ -3,14 +3,13 @@ import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.GenotypesContext; import htsjdk.variant.variantcontext.VariantContext; -import htsjdk.variant.vcf.VCFInfoHeaderLine; import org.apache.log4j.Logger; import org.broadinstitute.hellbender.engine.ReferenceContext; import org.broadinstitute.hellbender.tools.walkers.annotator.StrandBiasTest; import org.broadinstitute.hellbender.utils.genotyper.ReadLikelihoods; +import org.broadinstitute.hellbender.utils.pileup.PileupElement; import org.broadinstitute.hellbender.utils.read.GATKRead; import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; -import org.broadinstitute.hellbender.utils.variant.GATKVCFHeaderLines; import java.util.*; @@ -36,13 +35,6 @@ public AS_StrandBiasTest(){ @Override public String getRawKeyName() { return GATKVCFConstants.AS_SB_TABLE_KEY; } - @Override - public Map annotate(final ReferenceContext ref, - final VariantContext vc, - final ReadLikelihoods likelihoods) { - return annotateRawData(ref, vc, likelihoods); - } - /** * Method which determines how the Strand Bias read direction allele data must be combined into a final annotation * Must be overridden by client methods. @@ -68,14 +60,14 @@ public Map annotateRawData(final ReferenceContext ref, final ReadLikelihoods likelihoods ) { //for allele-specific annotations we only call from HC and we only use likelihoods - if ( likelihoods == null) { + if ( likelihoods == null || !likelihoods.hasFilledLikelihoods()) { return Collections.emptyMap(); } // calculate the annotation from the likelihoods // likelihoods can come from HaplotypeCaller call to VariantAnnotatorEngine final Map annotations = new HashMap<>(); final ReducibleAnnotationData> myData = new AlleleSpecificAnnotationData<>(vc.getAlleles(),null); - calculateRawData(vc, likelihoods, myData); + getStrandCountsFromLikelihoodMap(vc, likelihoods, myData, MIN_COUNT); final Map> perAlleleValues = myData.getAttributeMap(); final String annotationString = makeRawAnnotationString(vc.getAlleles(), perAlleleValues); annotations.put(getRawKeyName(), annotationString); @@ -201,18 +193,6 @@ protected void parseRawDataString(ReducibleAnnotationData> myData) myData.setAttributeMap(perAlleleValues); } - - @SuppressWarnings({"unchecked", "rawtypes"})//FIXME - public void calculateRawData(final VariantContext vc, - final ReadLikelihoods likelihoods, - final ReducibleAnnotationData rawAnnotations) { - if(likelihoods == null) { - return; - } - - getStrandCountsFromLikelihoodMap(vc, likelihoods, rawAnnotations, MIN_COUNT); - } - /** Allocate and fill a 2x2 strand contingency table. In the end, it'll look something like this: * fw rc @@ -308,6 +288,13 @@ protected Map calculateAnnotationFromGTfield(final GenotypesCont return Collections.emptyMap(); } + @Override + //Allele-specific annotations cannot be called from walkers other than HaplotypeCaller + protected Map calculateAnnotationFromStratifiedContexts(final Map> stratifiedContexts, + final VariantContext vc){ + return new HashMap<>(); + } + public static String rawValueAsString(int[][] table) { return table[0][0]+","+table[0][1]+ PRINT_DELIM +table[1][0]+","+table[1][1]; } diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java index 70847054687..43d4e80782c 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java @@ -171,7 +171,7 @@ private void initialize(boolean createBamOutIndex, final boolean createBamOutMD5 initializeActiveRegionEvaluationGenotyperEngine(); if (annotationEngine == null) { - annotationEngine = VariantAnnotatorEngine.ofSelectedMinusExcluded(hcArgs.defaultGATKVariantAnnotationArgumentCollection, hcArgs.dbsnp.dbsnp, hcArgs.comps); + annotationEngine = VariantAnnotatorEngine.ofSelectedMinusExcluded(hcArgs.defaultGATKVariantAnnotationArgumentCollection, hcArgs.dbsnp.dbsnp, hcArgs.comps, emitReferenceConfidence()); } diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2Engine.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2Engine.java index f63c2610970..0d4086c7304 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2Engine.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2Engine.java @@ -120,7 +120,7 @@ private void initialize(final boolean createBamOutIndex, final boolean createBam " sample name " + normalSampleName); } - annotationEngine = VariantAnnotatorEngine.ofSelectedMinusExcluded(MTAC.defaultGATKVariantAnnotationArgumentCollection, null, Collections.emptyList()); + annotationEngine = VariantAnnotatorEngine.ofSelectedMinusExcluded(MTAC.defaultGATKVariantAnnotationArgumentCollection, null, Collections.emptyList(), false); assemblyEngine = AssemblyBasedCallerUtils.createReadThreadingAssembler(MTAC); likelihoodCalculationEngine = AssemblyBasedCallerUtils.createLikelihoodCalculationEngine(MTAC.likelihoodArgs); diff --git a/src/main/java/org/broadinstitute/hellbender/utils/genotyper/ReadLikelihoods.java b/src/main/java/org/broadinstitute/hellbender/utils/genotyper/ReadLikelihoods.java index 19b0a099dc7..ea2fb878d91 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/genotyper/ReadLikelihoods.java +++ b/src/main/java/org/broadinstitute/hellbender/utils/genotyper/ReadLikelihoods.java @@ -8,10 +8,13 @@ import it.unimi.dsi.fastutil.objects.Object2IntOpenHashMap; import org.apache.commons.collections.ListUtils; import org.apache.commons.math3.stat.descriptive.rank.Median; +import org.broadinstitute.hellbender.tools.walkers.qc.Pileup; import org.broadinstitute.hellbender.utils.IndexRange; import org.broadinstitute.hellbender.utils.SimpleInterval; import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.utils.downsampling.AlleleBiasedDownsamplingUtils; +import org.broadinstitute.hellbender.utils.pileup.PileupElement; +import org.broadinstitute.hellbender.utils.pileup.ReadPileup; import org.broadinstitute.hellbender.utils.read.GATKRead; import java.util.*; @@ -27,7 +30,7 @@ * * @author Valentin Ruano-Rubio <valentin@broadinstitute.org> */ -public final class ReadLikelihoods implements SampleList, AlleleList { +public class ReadLikelihoods implements SampleList, AlleleList { /** * Index indicaintg that the reference allele is missing. @@ -37,7 +40,7 @@ public final class ReadLikelihoods implements SampleList, Alle /** * Reads by sample index. Each sub array contains reference to the reads of the ith sample. */ - private final GATKRead[][] readsBySampleIndex; + protected final GATKRead[][] readsBySampleIndex; /** * Indexed per sample, allele and finally read (within sample). @@ -45,17 +48,17 @@ public final class ReadLikelihoods implements SampleList, Alle * valuesBySampleIndex[s][a][r] == lnLk(R_r | A_a) where R_r comes from Sample s. *

*/ - private final double[][][] valuesBySampleIndex; + protected final double[][][] valuesBySampleIndex; /** * Sample list */ - private final SampleList samples; + protected final SampleList samples; /** * Allele list */ - private AlleleList alleles; + protected AlleleList alleles; /** * Cached allele list. @@ -90,6 +93,13 @@ public final class ReadLikelihoods implements SampleList, Alle */ private final LikelihoodMatrix[] sampleMatrices; + /** + * Is this container expected to have the per-allele liklihoods calculations filled in. + */ + public boolean hasFilledLikelihoods() { + return true; + } + /** * Constructs a new read-likelihood collection. * @@ -135,7 +145,7 @@ public ReadLikelihoods(final SampleList samples, // Internally used constructor. @SuppressWarnings({"unchecked", "rawtypes"}) - private ReadLikelihoods(final AlleleList alleles, + ReadLikelihoods(final AlleleList alleles, final SampleList samples, final GATKRead[][] readsBySampleIndex, final Object2IntMap[] readIndex, @@ -178,7 +188,8 @@ private void setupSampleData(final int sampleIndex, /** * Create an independent copy of this read-likelihoods collection */ - public ReadLikelihoods copy() { + @VisibleForTesting + ReadLikelihoods copy() { final int sampleCount = samples.numberOfSamples(); final int alleleCount = alleles.numberOfAlleles(); @@ -1296,6 +1307,18 @@ private Object2IntMap readIndexBySampleIndex(final int sampleIndex) { return readIndexBySampleIndex[sampleIndex]; } + + /** + * Collect a map stratified per-sample of the base pileups at the provided Location + * NOTE: Since we shouldn't need to use the pileup if we have more reliable liklihoods, we want to discourage their use + * + * @param loc reference location to construct pileups for + * @return + */ + public Map> getStratifiedPileups(final Locatable loc) { + return null; + } + /** * Implements a likelihood matrix per sample given its index. */ diff --git a/src/main/java/org/broadinstitute/hellbender/utils/genotyper/UnfilledReadsLikelihoods.java b/src/main/java/org/broadinstitute/hellbender/utils/genotyper/UnfilledReadsLikelihoods.java new file mode 100644 index 00000000000..79740a2cd92 --- /dev/null +++ b/src/main/java/org/broadinstitute/hellbender/utils/genotyper/UnfilledReadsLikelihoods.java @@ -0,0 +1,140 @@ +package org.broadinstitute.hellbender.utils.genotyper; + +import com.google.common.annotations.VisibleForTesting; +import htsjdk.samtools.util.Locatable; +import htsjdk.variant.variantcontext.Allele; +import it.unimi.dsi.fastutil.objects.Object2IntMap; +import org.broadinstitute.hellbender.utils.IndexRange; +import org.broadinstitute.hellbender.utils.SimpleInterval; +import org.broadinstitute.hellbender.utils.Utils; +import org.broadinstitute.hellbender.utils.pileup.PileupElement; +import org.broadinstitute.hellbender.utils.pileup.ReadPileup; +import org.broadinstitute.hellbender.utils.read.GATKRead; + +import java.util.Collections; +import java.util.HashMap; +import java.util.List; +import java.util.Map; + +/** + * Dummy Read-Likelihood container that computes partial likelihoods based on the read pileups for snps. + * + * Note: this class uses FastUtil collections for speed. + */ +public class UnfilledReadsLikelihoods extends ReadLikelihoods { + + private Map> stratifiedPileups; + + /** + * Constructs a new read-likelihood collection. + *

+ *

+ * The initial likelihoods for all allele-read combinations are + * 0. + *

+ * + * @param samples all supported samples in the collection. + * @param alleles all supported alleles in the collection. + * @param reads reads stratified per sample. + * @throws IllegalArgumentException if any of {@code allele}, {@code samples} + * or {@code reads} is {@code null}, + * or if they contain null values. + */ + public UnfilledReadsLikelihoods(SampleList samples, AlleleList alleles, Map> reads) { + super(samples, alleles, reads); + } + + // Internally used constructor. + @SuppressWarnings({"unchecked", "rawtypes"}) + private UnfilledReadsLikelihoods(final AlleleList alleles, + final SampleList samples, + final GATKRead[][] readsBySampleIndex, + final Object2IntMap[] readIndex, + final double[][][] values) { + super(alleles, samples, readsBySampleIndex, readIndex, values); + } + + /** + * Is this container expected to have the per-allele likelihoods calculations filled in. + * This will always be false for this class because we can't compute the likelihoods without re-genotyping the reads + */ + @Override + public boolean hasFilledLikelihoods() { + return false; + } + + /** + * Collect a map stratified per-sample of the base pileups at the provided Location + * + * @param loc reference location to construct pileups for + * @return + */ + public Map> getStratifiedPileups(final Locatable loc) { + if (stratifiedPileups != null) { + return stratifiedPileups; + } + Map> pileupMap = new HashMap<>(); + for (int i = 0; i < samples.numberOfSamples(); i++) { + pileupMap.put(samples.getSample(i), ReadPileup.locToReadsPileup(sampleReads(i), loc)); + } + stratifiedPileups = Collections.unmodifiableMap(pileupMap); + return stratifiedPileups; + } + + /** + * Create an independent copy of this read-likelihoods collection + */ + @Override + ReadLikelihoods copy() { + + final int sampleCount = samples.numberOfSamples(); + final int alleleCount = alleles.numberOfAlleles(); + + final double[][][] newLikelihoodValues = new double[sampleCount][alleleCount][]; + + @SuppressWarnings({"unchecked", "rawtypes"}) + final Object2IntMap[] newReadIndexBySampleIndex = new Object2IntMap[sampleCount]; + final GATKRead[][] newReadsBySampleIndex = new GATKRead[sampleCount][]; + + for (int s = 0; s < sampleCount; s++) { + newReadsBySampleIndex[s] = readsBySampleIndex[s].clone(); + for (int a = 0; a < alleleCount; a++) { + newLikelihoodValues[s][a] = valuesBySampleIndex[s][a].clone(); + } + } + + // Finally we create the new read-likelihood + return new UnfilledReadsLikelihoods( + alleles, + samples, + newReadsBySampleIndex, + newReadIndexBySampleIndex, + newLikelihoodValues); + } + + // Methods Which Modify Reads that must be turned off + @Override + public void changeReads(final Map readRealignments) { + throw new UnsupportedOperationException("Cannot alter reads in UnfilledReadsLikelihoods object or cached pileups may be rendered inaccurate, please use a normal ReadsLikelihoods object"); + } + + @Override + public void filterPoorlyModeledReads(final double maximumErrorPerBase) { + throw new UnsupportedOperationException("Cannot alter reads in UnfilledReadsLikelihoods object or cached pileups may be rendered inaccurate, please use a normal ReadsLikelihoods object"); + } + + @Override + public void addReads(final Map> readsBySample, final double initialLikelihood) { + throw new UnsupportedOperationException("Cannot alter reads in UnfilledReadsLikelihoods object or cached pileups may be rendered inaccurate, please use a normal ReadsLikelihoods object"); + } + + @Override + public void contaminationDownsampling(final Map perSampleDownsamplingFraction) { + throw new UnsupportedOperationException("Cannot alter reads in UnfilledReadsLikelihoods object or cached pileups may be rendered inaccurate, please use a normal ReadsLikelihoods object"); + } + + @Override + public void filterToOnlyOverlappingUnclippedReads(final SimpleInterval location) { + throw new UnsupportedOperationException("Cannot alter reads in UnfilledReadsLikelihoods object or cached pileups may be rendered inaccurate, please use a normal ReadsLikelihoods object"); + } +} diff --git a/src/main/java/org/broadinstitute/hellbender/utils/logging/OneShotLogger.java b/src/main/java/org/broadinstitute/hellbender/utils/logging/OneShotLogger.java index ded3eadbeed..69cfe76c2c9 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/logging/OneShotLogger.java +++ b/src/main/java/org/broadinstitute/hellbender/utils/logging/OneShotLogger.java @@ -16,6 +16,10 @@ public OneShotLogger(final Class clazz) { logger = LogManager.getLogger(clazz); } + public OneShotLogger(final Logger logger) { + this.logger = logger; + } + /* * Will write a warning only once for an instance, otherwise it doesn't emit a message */ diff --git a/src/main/java/org/broadinstitute/hellbender/utils/pileup/PileupElement.java b/src/main/java/org/broadinstitute/hellbender/utils/pileup/PileupElement.java index 34a16e2cb2d..b17381f65aa 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/pileup/PileupElement.java +++ b/src/main/java/org/broadinstitute/hellbender/utils/pileup/PileupElement.java @@ -3,6 +3,8 @@ import com.google.common.annotations.VisibleForTesting; import htsjdk.samtools.CigarElement; import htsjdk.samtools.CigarOperator; +import htsjdk.samtools.util.Locatable; +import org.broadinstitute.hellbender.utils.QualityUtils; import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.utils.locusiterator.AlignmentStateMachine; import org.broadinstitute.hellbender.utils.read.GATKRead; @@ -90,6 +92,31 @@ public static PileupElement createPileupForReadAndOffset(final GATKRead read, fi " but we never saw such an offset in the alignment state machine"); } + /** + * Create a pileup element for read at a particular spot on the genome. + * + * offset must correspond to a valid read offset read's alignment and cigar, or an IllegalStateException will be throw + * + * @param read a read + * @param loc A one base location you want to generate your genome + * @return a valid PileupElement with read and at offset + */ + public static PileupElement createPileupForReadAndGenomeLoc(final GATKRead read, final Locatable loc) { + Utils.nonNull(read, "read is null"); + + final AlignmentStateMachine stateMachine = new AlignmentStateMachine(read); + + while ( stateMachine.stepForwardOnGenome() != null ) { + if ( stateMachine.getGenomePosition() == loc.getStart()) { + return stateMachine.makePileupElement(); + } + } + + throw new IllegalStateException("Tried to create a pileup for read " + read + " with genome loc " + loc + + " but we never saw such an offset in the alignment state machine"); + } + + /** * Is this element a deletion w.r.t. the reference genome? * @@ -504,4 +531,18 @@ public boolean atStartOfCurrentCigar() { return offsetInCurrentCigar == 0; } + /** + * Can the base in this pileup element be used in comparative tests? + * + * @param p the pileup element to consider + * + * @return true if this base is part of a meaningful read for comparison, false otherwise + */ + public static boolean isUsableBaseForAnnotation(final PileupElement p) { + return !( p.isDeletion() || + p.getMappingQual() == 0 || + p.getMappingQual() == QualityUtils.MAPPING_QUALITY_UNAVAILABLE || + ((int) p.getQual()) < QualityUtils.MIN_USABLE_Q_SCORE); + } + } diff --git a/src/main/java/org/broadinstitute/hellbender/utils/pileup/ReadPileup.java b/src/main/java/org/broadinstitute/hellbender/utils/pileup/ReadPileup.java index dac1f162a92..99b5f3e5076 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/pileup/ReadPileup.java +++ b/src/main/java/org/broadinstitute/hellbender/utils/pileup/ReadPileup.java @@ -57,7 +57,7 @@ public ReadPileup(final Locatable loc, final Map stratifiedP * Create a new pileup without any aligned reads */ public ReadPileup(final Locatable loc) { - this(loc, Collections.emptyList()); + this(loc, new ArrayList<>()); } /** @@ -108,6 +108,17 @@ private static List readsOffsetsToPileup(final List rea return reads.stream().map(r -> PileupElement.createPileupForReadAndOffset(r, offset)).collect(Collectors.toList()); } + /** + * Helper routine for converting reads and a single offset to a PileupElement list. + */ + public static List locToReadsPileup(final List reads, final Locatable loc) { + Utils.nonNull(reads, "Illegal null read list"); + return reads.stream().filter(r -> !r.isUnmapped()) + .filter(r -> r.getStart()<=loc.getStart() && r.getEnd()>=loc.getEnd() ) + .map(r -> PileupElement.createPileupForReadAndGenomeLoc(r, loc)) + .collect(Collectors.toList()); + } + /** * Make a new pileup consisting of elements of this pileup that satisfy the predicate. * NOTE: the new pileup will not be independent of the old one (no deep copy of the underlying data is performed). diff --git a/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVariantContextUtils.java b/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVariantContextUtils.java index adaa4640c6d..4fa7cdbe301 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVariantContextUtils.java +++ b/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVariantContextUtils.java @@ -17,11 +17,10 @@ import org.apache.commons.lang3.tuple.Pair; import org.apache.logging.log4j.LogManager; import org.apache.logging.log4j.Logger; -import org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAlleleCounts; -import org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAssignmentMethod; -import org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeLikelihoodCalculator; -import org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeLikelihoodCalculators; +import org.broadinstitute.hellbender.tools.walkers.genotyper.*; import org.broadinstitute.hellbender.utils.*; +import org.broadinstitute.hellbender.utils.collections.Permutation; +import org.broadinstitute.hellbender.utils.genotyper.IndexedAlleleList; import org.broadinstitute.hellbender.utils.param.ParamUtils; import java.io.File; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/ReferenceConfidenceVariantContextMergerUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/ReferenceConfidenceVariantContextMergerUnitTest.java index 261d8e804bd..1f39708a08a 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/ReferenceConfidenceVariantContextMergerUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/ReferenceConfidenceVariantContextMergerUnitTest.java @@ -34,7 +34,7 @@ public class ReferenceConfidenceVariantContextMergerUnitTest extends GATKBaseTes private static VariantAnnotatorEngine getAnnotationEngine() { - return VariantAnnotatorEngine.ofAllMinusExcluded(Collections.emptyList(), null, Collections.emptyList()); + return VariantAnnotatorEngine.ofAllMinusExcluded(Collections.emptyList(), null, Collections.emptyList(), false); } @Test(dataProvider = "referenceConfidenceMergeData") diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/DepthPerAlleleBySampleUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/DepthPerAlleleBySampleUnitTest.java index 0c337ad7978..28a2af5f114 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/DepthPerAlleleBySampleUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/DepthPerAlleleBySampleUnitTest.java @@ -1,14 +1,12 @@ package org.broadinstitute.hellbender.tools.walkers.annotator; import com.google.common.collect.ImmutableMap; +import com.google.common.collect.Lists; import htsjdk.samtools.TextCigarCodec; import htsjdk.variant.variantcontext.*; import htsjdk.variant.vcf.VCFConstants; import htsjdk.variant.vcf.VCFStandardHeaderLines; -import org.broadinstitute.hellbender.utils.genotyper.AlleleList; -import org.broadinstitute.hellbender.utils.genotyper.IndexedAlleleList; -import org.broadinstitute.hellbender.utils.genotyper.IndexedSampleList; -import org.broadinstitute.hellbender.utils.genotyper.ReadLikelihoods; +import org.broadinstitute.hellbender.utils.genotyper.*; import org.broadinstitute.hellbender.utils.read.ArtificialReadUtils; import org.broadinstitute.hellbender.utils.read.GATKRead; import org.broadinstitute.hellbender.utils.test.ArtificialAnnotationUtils; @@ -17,10 +15,7 @@ import org.testng.annotations.DataProvider; import org.testng.annotations.Test; -import java.util.Arrays; -import java.util.Collections; -import java.util.List; -import java.util.Map; +import java.util.*; import java.util.stream.Collectors; import java.util.stream.IntStream; @@ -95,5 +90,24 @@ public void testBlowUp(){ new DepthPerAlleleBySample().annotate(null, vc, gAC, gb, likelihoods); } + @Test + public void testEmptyLikelihoodsFallback(){ + final int dpDepth = 30; + final Genotype gAC = new GenotypeBuilder(SAMPLE, ALLELES).DP(dpDepth).make(); + + final double log10PError = -5; + + Map> emptyMap = new HashMap<>(); + emptyMap.put(SAMPLE, Collections.emptyList()); + final ReadLikelihoods likelihoods = new UnfilledReadsLikelihoods(new IndexedSampleList(SAMPLE), new IndexedAlleleList<>(ALLELES), emptyMap); + + final VariantContext vc = new VariantContextBuilder("test", "20", 10, 10, ALLELES).log10PError(log10PError).genotypes(Arrays.asList(gAC)).make(); + + final GenotypeBuilder gb = new GenotypeBuilder(gAC); + new DepthPerAlleleBySample().annotate(null, vc, gAC, gb, likelihoods); + final int[] ad = gb.make().getAD(); + Assert.assertEquals(ad, null); + + } } diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/FisherStrandUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/FisherStrandUnitTest.java index 88255d1134a..1f9c36b6ac6 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/FisherStrandUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/FisherStrandUnitTest.java @@ -198,9 +198,7 @@ public void testUsingLikelihoods() { @Test public void testUsingLikelihoods_Raw() { - final AS_StrandBiasTest ann = new AS_FisherStrand(); - final String key = GATKVCFConstants.AS_SB_TABLE_KEY; - + final AS_FisherStrand ann = new AS_FisherStrand(); final int[][] table = {{4, 0}, // ref: 4 reads fwd, 0 reads back {2, 2}}; // alt: two reads in each direction @@ -214,13 +212,14 @@ public void testUsingLikelihoods_Raw() { final Map annotatedMapRaw = ann.annotateRawData(null, vc, likelihoods); final Map annotatedMapNonRaw = ann.annotate(null, vc, likelihoods); Assert.assertNotNull(annotatedMapRaw, vc.toString()); - final String actualStringRaw = (String) annotatedMapRaw.get(key); + final String actualStringRaw = (String) annotatedMapRaw.get(GATKVCFConstants.AS_SB_TABLE_KEY); Assert.assertNotNull(annotatedMapNonRaw, vc.toString()); - final String actualStringNonRaw = (String) annotatedMapNonRaw.get(key); + final String actualStringNonRaw = (String) annotatedMapNonRaw.get(ann.getKeyNames().get(0)); - final String expectedString = AS_StrandBiasTest.rawValueAsString(table); - Assert.assertEquals(actualStringRaw, expectedString); - Assert.assertEquals(actualStringNonRaw, expectedString); + final String expectedRawString = AS_StrandBiasTest.rawValueAsString(table); + final String expectedFullStringString = "3.680"; + Assert.assertEquals(actualStringRaw, expectedRawString); + Assert.assertEquals(actualStringNonRaw, expectedFullStringString); } @Test diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/LikelihoodRankSumTestUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/LikelihoodRankSumTestUnitTest.java index b5087d1c416..73ccbb18ce1 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/LikelihoodRankSumTestUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/LikelihoodRankSumTestUnitTest.java @@ -82,11 +82,4 @@ public void testReadPos(){ Assert.assertEquals(annotate.get(GATKVCFConstants.LIKELIHOOD_RANK_SUM_KEY), zScoreStr); } - @Test(expectedExceptions = IllegalStateException.class) - public void testBlowupOnCallWithoutAllele(){ - final LikelihoodRankSumTest ann = new LikelihoodRankSumTest(); - final GATKRead read1 = makeRead(); - ann.getElementForRead(read1, read1.getStart()); - } - } diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/QualByDepthUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/QualByDepthUnitTest.java index 3b4fb2af497..3a4458dfefa 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/QualByDepthUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/QualByDepthUnitTest.java @@ -38,6 +38,7 @@ public Object[][] makeUsingADData() { final List ACG = Arrays.asList(A, C, G); final Genotype gAC = new GenotypeBuilder("1", AC).DP(10).AD(new int[]{5,5}).make(); + final Genotype gACNoADNoDP = new GenotypeBuilder("1", AC).AD(new int[]{0,0}).make(); final Genotype gACNoAD = new GenotypeBuilder("1", AC).DP(10).AD(new int[]{0,0}).make(); final Genotype gAA = new GenotypeBuilder("2", AA).DP(10).AD(new int[]{10,0}).make(); final Genotype gACerror = new GenotypeBuilder("3", AC).DP(10).AD(new int[]{9,1}).make(); @@ -47,8 +48,9 @@ public Object[][] makeUsingADData() { final double log10PError = -5; final double qual = -10.0 * log10PError; tests.add(new Object[]{new VariantContextBuilder("test", "20", 10, 10, AC).log10PError(log10PError).genotypes(Arrays.asList(gAC)).make(), qual / 10}); //het - tests.add(new Object[]{new VariantContextBuilder("test", "20", 10, 10, AC).log10PError(log10PError).genotypes(Arrays.asList(gACNoAD)).make(), 0.0}); // No AD - tests.add(new Object[]{new VariantContextBuilder("test", "20", 10, 10, ACG).log10PError(log10PError).genotypes(Arrays.asList(gAC, gACNoAD)).make(), qual / 10}); // No AD + tests.add(new Object[]{new VariantContextBuilder("test", "20", 10, 10, AC).log10PError(log10PError).genotypes(Arrays.asList(gACNoADNoDP)).make(), 0.0}); // No AD + tests.add(new Object[]{new VariantContextBuilder("test", "20", 10, 10, AC).log10PError(log10PError).genotypes(Arrays.asList(gACNoAD)).make(), qual / 10}); // No AD but present DP, expect it to default to the DP + tests.add(new Object[]{new VariantContextBuilder("test", "20", 10, 10, ACG).log10PError(log10PError).genotypes(Arrays.asList(gAC, gACNoADNoDP)).make(), qual / 10}); // No AD tests.add(new Object[]{new VariantContextBuilder("test", "20", 10, 10, AC).log10PError(log10PError).genotypes(Arrays.asList(gACerror)).make(), qual / 10}); //het but use 1+X if AD=1,X tests.add(new Object[]{new VariantContextBuilder("test", "20", 10, 10, AC).log10PError(log10PError).genotypes(Arrays.asList(gAA, gAC)).make(), qual / 10}); //het, skip hom diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/RMSMappingQualityUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/RMSMappingQualityUnitTest.java index 96a1b6f6690..f97113581d2 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/RMSMappingQualityUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/RMSMappingQualityUnitTest.java @@ -96,10 +96,10 @@ public void testLikelihoods(){ final ReferenceContext referenceContext= null; final Map annotate = new RMSMappingQuality().annotate(referenceContext, vc, likelihoods); Assert.assertEquals(annotate.size(), 1, "size"); - Assert.assertEquals(annotate.keySet(), Collections.singleton(GATKVCFConstants.RAW_RMS_MAPPING_QUALITY_KEY), "annots"); + Assert.assertEquals(annotate.keySet(), Collections.singleton(VCFConstants.RMS_MAPPING_QUALITY_KEY), "annots"); final double rms= MathUtils.sumOfSquares(MQsListOK); //only those are MQ0 - Assert.assertNull(annotate.get(VCFConstants.RMS_MAPPING_QUALITY_KEY)); - Assert.assertEquals(annotate.get(GATKVCFConstants.RAW_RMS_MAPPING_QUALITY_KEY), String.format("%.2f", rms)); + Assert.assertNull(annotate.get(GATKVCFConstants.RAW_RMS_MAPPING_QUALITY_KEY)); + Assert.assertEquals(annotate.get(VCFConstants.RMS_MAPPING_QUALITY_KEY), String.format("%.2f", Math.sqrt(rms/(reads.size()-1)))); } @Test @@ -186,7 +186,7 @@ public void testLikelihoodsEmpty_AS() throws Exception { final VariantContext vc= makeVC(); final ReferenceContext referenceContext= null; - final Map annotate = new AS_RMSMappingQuality().annotate(referenceContext, vc, likelihoods); + final Map annotate = new AS_RMSMappingQuality().annotateRawData(referenceContext, vc, likelihoods); final String[] split =((String)annotate.get(GATKVCFConstants.AS_RAW_RMS_MAPPING_QUALITY_KEY)).split(AS_RMSMappingQuality.SPLIT_DELIM); Assert.assertEquals(split.length, 2); Assert.assertEquals(split[0], String.format("%.2f", 0.0)); @@ -277,13 +277,13 @@ public void testGetNumReads(){ .attribute(VCFConstants.DEPTH_KEY, 5 + 10 + 100) .make(); - Assert.assertEquals(RMSMappingQuality.getNumOfReads(vc), 115 - 5 - 10); + Assert.assertEquals(RMSMappingQuality.getNumOfReads(vc, null), 115 - 5 - 10); } @Test public void testGetNumReadsReturnsNegativeOneWhenDataIsBad(){ final VariantContext emptyVariantContext = makeVC(); - Assert.assertEquals(RMSMappingQuality.getNumOfReads(emptyVariantContext), -1); + Assert.assertEquals(RMSMappingQuality.getNumOfReads(emptyVariantContext, null), -1); } diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/ReadPosRankSumTestUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/ReadPosRankSumTestUnitTest.java index 30d168b9851..ca74dde0536 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/ReadPosRankSumTestUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/ReadPosRankSumTestUnitTest.java @@ -1,6 +1,8 @@ package org.broadinstitute.hellbender.tools.walkers.annotator; import htsjdk.samtools.Cigar; +import htsjdk.samtools.CigarElement; +import htsjdk.samtools.CigarOperator; import htsjdk.samtools.TextCigarCodec; import htsjdk.variant.variantcontext.*; import org.broadinstitute.hellbender.engine.ReferenceContext; @@ -13,6 +15,7 @@ import org.broadinstitute.hellbender.GATKBaseTest; import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; import org.testng.Assert; +import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; @@ -115,4 +118,155 @@ public void testIsUsableRead(final String cigarString, final int mappingQuality, read.setPosition(CONTIG, start); Assert.assertEquals(readPosRankSumTest.isUsableRead(read, refLoc), isUsable); } + + //Basic aligned read + private GATKRead allMatch; + + //Read with insertion and deletion + private GATKRead twoIndels; + + //Read with soft clips at start + private GATKRead softClipStart; + + //Read with hard clips at start + private GATKRead hardClipStart; + + //Read with low quality tail + private GATKRead lowQualTail; + + //Read with low quality tail, partially soft clipped + private GATKRead lowQualClippedTail; + + //Read with low quality bases at start + private GATKRead lowQualStart; + + //Read with low quality bases, partially soft clipped at both ends + private GATKRead lowQualBothEnds; + + @BeforeClass + public void init() { + List cigarElements_allMatch = new LinkedList<>(); + cigarElements_allMatch.add(new CigarElement(151, CigarOperator.M)); + allMatch = ArtificialReadUtils.createArtificialRead(new Cigar(cigarElements_allMatch)); + + List cigarElements_2indels = new LinkedList<>(); + cigarElements_2indels.add(new CigarElement(66, CigarOperator.M)); + cigarElements_2indels.add(new CigarElement(10, CigarOperator.I)); + cigarElements_2indels.add(new CigarElement(7, CigarOperator.M)); + cigarElements_2indels.add(new CigarElement(10, CigarOperator.D)); + cigarElements_2indels.add(new CigarElement(68, CigarOperator.M)); + twoIndels = ArtificialReadUtils.createArtificialRead(new Cigar(cigarElements_2indels)); + + List cigarElements_softClipStart = new LinkedList<>(); + cigarElements_softClipStart.add(new CigarElement(17, CigarOperator.S)); + cigarElements_softClipStart.add(new CigarElement(134, CigarOperator.M)); + softClipStart = ArtificialReadUtils.createArtificialRead(new Cigar(cigarElements_softClipStart)); + + List cigarElements_hardClipStart = new LinkedList<>(); + cigarElements_hardClipStart.add(new CigarElement(17, CigarOperator.H)); + cigarElements_hardClipStart.add(new CigarElement(134, CigarOperator.M)); + hardClipStart = ArtificialReadUtils.createArtificialRead(new Cigar(cigarElements_hardClipStart)); + + + final byte [] bases_lowQualTail = {'A', 'C', 'T', 'G', 'A', 'A', 'A', 'A', 'A', 'A'}; + final byte [] quals_lowQualTail = {30, 15, 25, 30, 2, 2, 2, 2, 2, 2}; + lowQualTail = ArtificialReadUtils.createArtificialRead(bases_lowQualTail, quals_lowQualTail, "10M"); + + final byte [] bases_lowQualClippedTail = {'A', 'C', 'T', 'G', 'A', 'A', 'A', 'A', 'A', 'A'}; + final byte [] quals_lowQualClippedTail = {30, 15, 25, 30, 2, 2, 2, 2, 2, 2}; + lowQualClippedTail = ArtificialReadUtils.createArtificialRead(bases_lowQualClippedTail, quals_lowQualClippedTail, "8M2S"); + + final byte [] bases_lowQualStart = {'A', 'A', 'A', 'A', 'A', 'A', 'A', 'C', 'T', 'G'}; + final byte [] quals_lowQualStart = {2, 2, 2, 2, 2, 2, 30, 15, 25, 30}; + lowQualStart = ArtificialReadUtils.createArtificialRead(bases_lowQualStart, quals_lowQualStart, "10M"); + + final byte [] bases_lowQualBothEnds = {'A', 'A', 'A', 'A', 'A', 'A', 'G', 'C', 'T', 'G', 'A', 'A', 'A', 'A', 'A', 'A'}; + final byte [] quals_lowQualBothEnds = { 2, 2, 2, 2, 2, 2, 30, 15, 25, 30, 2, 2, 2, 2, 2, 2}; + lowQualBothEnds = ArtificialReadUtils.createArtificialRead(bases_lowQualBothEnds, quals_lowQualBothEnds, "2S12M2S"); + + } + + @DataProvider(name = "makeGetFinalVariantReadPositionTestReads") + public Object[][] makeFinalPosTestReads() { + final List tests = new ArrayList<>(); + tests.add(new Object[] {allMatch, 10, 10}); + tests.add(new Object[] {allMatch, 140, 10}); + tests.add(new Object[] {twoIndels, 10, 10}); + tests.add(new Object[] {twoIndels, 140, 10}); + tests.add(new Object[] {hardClipStart, 20, 20}); + tests.add(new Object[] {hardClipStart, 110, 6}); //this is what the code produces as-is + tests.add(new Object[] {softClipStart, 10, 10}); + tests.add(new Object[] {softClipStart, 140, 10}); + tests.add(new Object[] {lowQualTail, 3, 0}); + tests.add(new Object[] {lowQualTail, 2, 2}); + tests.add(new Object[] {lowQualClippedTail, 3, 0}); + tests.add(new Object[] {lowQualClippedTail, 2, 2}); + tests.add(new Object[] {lowQualStart, 7, -4}); //this is what the code produces as-is, but should be 1 + tests.add(new Object[] {lowQualStart, 8, -5}); //this is what the code produces as-is, but should be 1 + tests.add(new Object[] {lowQualBothEnds, 7, -4}); //this is what the code produces as-is, but should be 1 + tests.add(new Object[] {lowQualBothEnds, 8, -5}); //this is what the code produces as-is, but should be 1 + return tests.toArray(new Object[][]{}); + } + + @Test(dataProvider = "makeGetFinalVariantReadPositionTestReads") + public void testGetFinalVariantReadPosition(GATKRead read, int variantPosition, int expected) throws Exception { + Assert.assertEquals(ReadPosRankSumTest.getFinalVariantReadPosition(read, variantPosition), expected); + } + + @DataProvider(name = "getNumClippedBasesAtStartTestReads") + public Object[][] numClipStart() { + final List tests = new ArrayList<>(); + tests.add(new Object[] {allMatch, 0}); + tests.add(new Object[] {twoIndels, 0}); + tests.add(new Object[] {softClipStart, 0}); + tests.add(new Object[] {hardClipStart, 17}); + tests.add(new Object[] {lowQualTail, 0}); + tests.add(new Object[] {lowQualClippedTail, 0}); + tests.add(new Object[] {lowQualStart, 6}); + tests.add(new Object[] {lowQualBothEnds, 6}); + return tests.toArray(new Object[][]{}); + } + + @Test(dataProvider = "getNumClippedBasesAtStartTestReads") + public void testGetNumClippedBasesAtStart(GATKRead read, int expected) throws Exception { + Assert.assertEquals(ReadPosRankSumTest.getNumClippedBasesAtStart(read),expected); + } + + @DataProvider(name = "getNumAlignedBasesTestReads") + public Object[][] numAligned() { + final List tests = new ArrayList<>(); + tests.add(new Object[] {allMatch, 151}); + tests.add(new Object[] {twoIndels, 151}); + tests.add(new Object[] {softClipStart, 151}); + tests.add(new Object[] {hardClipStart, 117}); //This is what the code produces, but it's wrong + tests.add(new Object[] {lowQualTail, 4}); + tests.add(new Object[] {lowQualClippedTail, 4}); + tests.add(new Object[] {lowQualStart, 4}); + tests.add(new Object[] {lowQualBothEnds, 4}); + return tests.toArray(new Object[][]{}); + } + + @Test(dataProvider = "getNumAlignedBasesTestReads") + public void testGetNumAlignedBases(GATKRead read, int expected) throws Exception { + Assert.assertEquals(ReadPosRankSumTest.getNumAlignedBases(read),expected); + } + + @DataProvider(name = "getNumClippedBasesAtEndTestReads") + public Object[][] numClipEnd() { + final List tests = new ArrayList<>(); + tests.add(new Object[] {allMatch, 0}); + tests.add(new Object[] {twoIndels, 0}); + tests.add(new Object[] {softClipStart, 0}); + tests.add(new Object[] {hardClipStart, 0}); + tests.add(new Object[] {lowQualTail, 6}); + tests.add(new Object[] {lowQualClippedTail, 6}); + tests.add(new Object[] {lowQualStart, 0}); + tests.add(new Object[] {lowQualBothEnds, 6}); + return tests.toArray(new Object[][]{}); + } + + @Test(dataProvider = "getNumClippedBasesAtEndTestReads") + public void testGetNumClippedBasesAtEnd(GATKRead read, int expected) throws Exception { + Assert.assertEquals(ReadPosRankSumTest.getNumClippedBasesAtEnd(read), expected); + } } diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotatorEngineUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotatorEngineUnitTest.java index 15041a8553d..e1c219f70c6 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotatorEngineUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotatorEngineUnitTest.java @@ -132,7 +132,7 @@ public void testAll(){ final List annotationsToExclude= Collections.emptyList(); final FeatureInput dbSNPBinding = null; final List> features = Collections.emptyList(); - final VariantAnnotatorEngine vae = VariantAnnotatorEngine.ofAllMinusExcluded(annotationsToExclude, dbSNPBinding, features); + final VariantAnnotatorEngine vae = VariantAnnotatorEngine.ofAllMinusExcluded(annotationsToExclude, dbSNPBinding, features, false); Assert.assertFalse(vae.getVCFAnnotationDescriptions(false).contains(null)); Assert.assertFalse(vae.getGenotypeAnnotations().isEmpty()); Assert.assertFalse(vae.getInfoAnnotations().isEmpty()); @@ -155,7 +155,7 @@ public void testAllMinusCoverage(){ final List annotationsToExclude= Arrays.asList(Coverage.class.getSimpleName()); final FeatureInput dbSNPBinding = null; final List> features = Collections.emptyList(); - final VariantAnnotatorEngine vae = VariantAnnotatorEngine.ofAllMinusExcluded(annotationsToExclude, dbSNPBinding, features); + final VariantAnnotatorEngine vae = VariantAnnotatorEngine.ofAllMinusExcluded(annotationsToExclude, dbSNPBinding, features, false); Assert.assertFalse(vae.getVCFAnnotationDescriptions(false).contains(null)); Assert.assertFalse(vae.getGenotypeAnnotations().isEmpty()); Assert.assertFalse(vae.getInfoAnnotations().isEmpty()); @@ -195,7 +195,7 @@ public void testBadExcludeAnnot(){ final List annotationsToExclude= Arrays.asList("fred"); final FeatureInput dbSNPBinding = null; final List> features = Collections.emptyList(); - final VariantAnnotatorEngine vae = VariantAnnotatorEngine.ofAllMinusExcluded(annotationsToExclude, dbSNPBinding, features); + final VariantAnnotatorEngine vae = VariantAnnotatorEngine.ofAllMinusExcluded(annotationsToExclude, dbSNPBinding, features, false); Assert.assertFalse(vae.getVCFAnnotationDescriptions(false).contains(null)); Assert.assertFalse(vae.getGenotypeAnnotations().isEmpty()); Assert.assertFalse(vae.getInfoAnnotations().isEmpty()); @@ -277,7 +277,7 @@ public void testAllAnnotations() throws Exception { final List annotationsToExclude= Arrays.asList( "ReferenceBases"); final FeatureInput dbSNPBinding = null; final List> features = Collections.emptyList(); - final VariantAnnotatorEngine vae = VariantAnnotatorEngine.ofAllMinusExcluded(annotationsToExclude, dbSNPBinding, features); + final VariantAnnotatorEngine vae = VariantAnnotatorEngine.ofAllMinusExcluded(annotationsToExclude, dbSNPBinding, features, false); Assert.assertFalse(vae.getVCFAnnotationDescriptions(false).contains(null)); final int alt = 5; @@ -293,8 +293,8 @@ public void testAllAnnotations() throws Exception { Assert.assertEquals(resultVC.getCommonInfo().getAttribute(VCFConstants.ALLELE_NUMBER_KEY), 2); Assert.assertEquals(resultVC.getCommonInfo().getAttribute(GATKVCFConstants.FISHER_STRAND_KEY), FisherStrand.makeValueObjectForAnnotation(new int[][]{{ref,0},{alt,0}})); Assert.assertEquals(resultVC.getCommonInfo().getAttribute(GATKVCFConstants.NOCALL_CHROM_KEY), 0); - Assert.assertNull(resultVC.getCommonInfo().getAttribute(VCFConstants.RMS_MAPPING_QUALITY_KEY)); - Assert.assertEquals(resultVC.getCommonInfo().getAttribute(GATKVCFConstants.RAW_RMS_MAPPING_QUALITY_KEY), RMSMappingQuality.formattedValue(0.0)); + Assert.assertNull(resultVC.getCommonInfo().getAttribute(GATKVCFConstants.RAW_RMS_MAPPING_QUALITY_KEY)); + Assert.assertEquals(resultVC.getCommonInfo().getAttribute(VCFConstants.RMS_MAPPING_QUALITY_KEY), RMSMappingQuality.formattedValue(0.0)); Assert.assertEquals(resultVC.getCommonInfo().getAttribute(VCFConstants.MAPPING_QUALITY_ZERO_KEY), MappingQualityZero.formattedValue(8)); Assert.assertEquals(resultVC.getCommonInfo().getAttribute(GATKVCFConstants.SAMPLE_LIST_KEY), "sample1"); Assert.assertEquals(resultVC.getCommonInfo().getAttribute(GATKVCFConstants.STRAND_ODDS_RATIO_KEY), StrandOddsRatio.formattedValue(StrandOddsRatio.calculateSOR(new int[][]{{ref,0},{alt,0}}))); @@ -502,7 +502,7 @@ public void testAnnotationsHaveDescriptions() throws Exception { final FeatureInput dbSNPBinding = null; final List> features = Collections.emptyList(); - headerInfo.addAll(VariantAnnotatorEngine.ofAllMinusExcluded(annotationsToExclude, dbSNPBinding, features).getVCFAnnotationDescriptions(false)); + headerInfo.addAll(VariantAnnotatorEngine.ofAllMinusExcluded(annotationsToExclude, dbSNPBinding, features, false).getVCFAnnotationDescriptions(false)); Assert.assertFalse(headerInfo.contains(null)); new VCFHeader(headerInfo, sampleSet);//make sure this does not blow up: https://github.com/broadinstitute/gatk/issues/1713 @@ -514,7 +514,7 @@ public void testNoNullInKeysAndDescriptions() throws Exception { final FeatureInput dbSNPBinding = null; final List> features = Collections.emptyList(); - final VariantAnnotatorEngine variantAnnotatorEngine = VariantAnnotatorEngine.ofAllMinusExcluded(annotationsToExclude, dbSNPBinding, features); + final VariantAnnotatorEngine variantAnnotatorEngine = VariantAnnotatorEngine.ofAllMinusExcluded(annotationsToExclude, dbSNPBinding, features, false); for (GenotypeAnnotation ga : variantAnnotatorEngine.getGenotypeAnnotations()) { Assert.assertFalse(ga.getDescriptions().contains(null), "getDescriptions contains null:" + ga); Assert.assertFalse(ga.getKeyNames().contains(null), "getKeyNames contains null" + ga); @@ -526,5 +526,4 @@ public void testNoNullInKeysAndDescriptions() throws Exception { Assert.assertFalse(variantAnnotatorEngine.getVCFAnnotationDescriptions(false).contains(null)); } - //TODO add test for AnnotateContextForActiveRegion } diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java new file mode 100644 index 00000000000..d4fa631e39e --- /dev/null +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java @@ -0,0 +1,335 @@ +package org.broadinstitute.hellbender.tools.walkers.annotator; + +import htsjdk.samtools.seekablestream.SeekablePathStream; +import htsjdk.tribble.Feature; +import htsjdk.tribble.readers.LineIterator; +import htsjdk.tribble.readers.PositionalBufferedStream; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.vcf.*; +import org.broadinstitute.hellbender.CommandLineProgramTest; +import org.broadinstitute.hellbender.engine.FeatureDataSource; +import org.broadinstitute.hellbender.engine.FeatureDataSourceUnitTest; +import org.broadinstitute.hellbender.utils.Utils; +import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.utils.test.VariantContextTestUtils; +import org.seqdoop.hadoop_bam.util.VCFHeaderReader; +import org.testng.Assert; +import org.testng.annotations.Test; + +import java.io.File; +import java.io.FileInputStream; +import java.io.IOException; +import java.util.*; +import java.util.function.BiConsumer; +import java.util.stream.Collectors; + +public class VariantAnnotatorIntegrationTest extends CommandLineProgramTest { + final static String STANDARD_ANNOTATIONS = " -G StandardAnnotation "; + private static final List ATTRIBUTES_TO_IGNORE = Arrays.asList( + "QD",//TODO QD has a cap value and anything that reaches that is randomized. It's difficult to reproduce the same random numbers across gatk3 -> 4 + "FS");//TODO There's some bug in either gatk3 or gatk4 fisherstrand that's making them not agree still, I'm not sure which is correct + private static final List HEADER_LINES_TO_IGNORE = Arrays.asList( + "reference", + "HaplotypeScore", + "GATKCommandLine.VariantAnnotator", + "RAW_MQ" + ); + + //TODO because of differences between how GATK3 and GATK4 handle capturing reads for spanning deletions (Namely 3 only looks for reads overlapping the first site, 4 gets all reads over the span) + //TODO then we want to ignore affected attributes for concordance tests + private static final List DEPTH_ATTRIBUTES_TO_IGNORE = Arrays.asList( + "QD", + "DP", + "MQ"); + + //================================================================================================================== + // Testing + //================================================================================================================== + private void assertVariantContextsMatch(File input, File expected, List extraArgs, String reference) throws IOException { + assertVariantContextsMatch(input, expected, extraArgs,reference, ATTRIBUTES_TO_IGNORE); + } + + private void assertVariantContextsMatch(File input, File expected, List extraArgs, String reference, List ignoreAtrributes) throws IOException { + final VCFHeader header = getHeaderFromFile(expected); + + runVariantAnnotatorAndAssertSomething(input, expected, extraArgs, (a, e) -> { + VariantContextTestUtils.assertVariantContextsAreEqualAlleleOrderIndependent(a, e, ATTRIBUTES_TO_IGNORE, header); + }, reference); + } + + private void assertHeadersMatch(File input, File expected, List linesToIgnore) throws IOException { + final VCFHeader expectedHeader = getHeaderFromFile(expected); + final VCFHeader inputHeader = getHeaderFromFile(input); + + final Iterator itr = expectedHeader.getMetaDataInSortedOrder().stream().filter(line -> !shouldFilterLine(line, linesToIgnore)).iterator(); + final Iterator itr2 = inputHeader.getMetaDataInSortedOrder().stream().filter(line -> !shouldFilterLine(line, linesToIgnore)).iterator(); + Assert.assertEquals(itr, itr2); + } + + private boolean shouldFilterLine(VCFHeaderLine line, List linesToIgnore) { + return (line != null) + && ((line instanceof VCFIDHeaderLine && linesToIgnore.contains(((VCFIDHeaderLine)line).getID())) + || linesToIgnore.contains(line.getKey())); + } + + private void runVariantAnnotatorAndAssertSomething(File input, File expected, List additionalArguments, BiConsumer assertion, String reference) throws IOException { + final File output = createTempFile("variantAnnotator", ".vcf"); + + final ArgumentsBuilder args = new ArgumentsBuilder(); + if (reference!=null) { + args.addReference(new File(reference)); + } + args.addOutput(output).addArgument("V", input.getAbsolutePath()); + + + // Handling a difference in syntax between GATK3 and GATK4 wrt. annotation groups + additionalArguments = additionalArguments.stream().map(a -> a.contains("Standard") ? a + "Annotation" : a).collect(Collectors.toList()); + additionalArguments.forEach(args::add); + + Utils.resetRandomGenerator(); + runCommandLine(args); + + assertHeadersMatch(output, expected, HEADER_LINES_TO_IGNORE); + final List expectedVC = getVariantContexts(expected); + final List actualVC = getVariantContexts(output); + assertForEachElementInLists(actualVC, expectedVC, assertion); + } + + /** + * Returns a list of VariantContext records from a VCF file + * + * @param vcfFile VCF file + * @return list of VariantContext records + * @throws IOException if the file does not exist or can not be opened + */ + private static List getVariantContexts(final File vcfFile) throws IOException { + final VCFCodec codec = new VCFCodec(); + final FileInputStream s = new FileInputStream(vcfFile); + final LineIterator lineIteratorVCF = codec.makeSourceFromStream(new PositionalBufferedStream(s)); + codec.readHeader(lineIteratorVCF); + + final List VCs = new ArrayList<>(); + while (lineIteratorVCF.hasNext()) { + final String line = lineIteratorVCF.next(); + Assert.assertFalse(line == null); + VCs.add(codec.decode(line)); + } + + return VCs; + } + + private static VCFHeader getHeaderFromFile(final File vcfFile) throws IOException { + try (SeekablePathStream stream = new SeekablePathStream(vcfFile.toPath())) { + return VCFHeaderReader.readHeaderFrom(stream); + } + } + + private static void assertForEachElementInLists(final List actual, final List expected, final BiConsumer assertion) { + Assert.assertEquals(actual.size(), expected.size(), "different number of elements in lists:\n" + + actual.stream().map(Object::toString).collect(Collectors.joining("\n","actual:\n","\n")) + + expected.stream().map(Object::toString).collect(Collectors.joining("\n","expected:\n","\n"))); + for (int i = 0; i < actual.size(); i++) { + + assertion.accept(actual.get(i), expected.get(i)); + } + } + + //================================================================================================================== + // Tests + //================================================================================================================== + + @Test + public void GATK3LargeConcordanceTest() throws IOException { + assertVariantContextsMatch(getTestFile("HCOutput.NoAnnotations.vcf"), new File(getToolTestDataDir() + "expected/integrationTest.vcf"), Arrays.asList("-G", "Standard", "-G", "AS_Standard", "-L", "20:10000000-10100000", "-I", NA12878_20_21_WGS_bam), b37_reference_20_21); + } + + @Test + public void testHasAnnotsNotAsking() throws IOException { + final File expected = new File(getToolTestDataDir() + "expected/testHsAnnotsNotAsking1.vcf"); + final VCFHeader header = getHeaderFromFile(expected); + runVariantAnnotatorAndAssertSomething(getTestFile("vcfexamplemultisample.vcf"), new File(getToolTestDataDir() + "expected/testHsAnnotsNotAsking1.vcf"), Arrays.asList( "-I", largeFileTestDir + "CEUTrio.multisample.b37.1M-1M50k.bam"), + (a, e) -> { + // We need to filter out sites where we saw a DP of 250 because we are comparing the results to GATK3, which downsamples to 250 reads per sample, which GATK4 does not currently support. + if (!e.getGenotypes().stream().anyMatch(g -> g.hasDP() && g.getDP() >= 250)) { + VariantContextTestUtils.assertVariantContextsAreEqualAlleleOrderIndependent(a, e, ATTRIBUTES_TO_IGNORE, header); + } + }, + b37_reference_20_21); + } + + @Test + public void testHasAnnotsAsking() throws IOException { + final File expected = new File(getToolTestDataDir() + "expected/testHasAnnotsAsking1.vcf"); + final VCFHeader header = getHeaderFromFile(expected); + runVariantAnnotatorAndAssertSomething(getTestFile("vcfexamplemultisample.vcf"), new File(getToolTestDataDir() + "expected/testHasAnnotsAsking1.vcf"), Arrays.asList("-G", "Standard", "-I", largeFileTestDir + "CEUTrio.multisample.b37.1M-1M50k.bam"), + (a, e) -> { + // We need to filter out sites where we saw a DP of 250 because we are comparing the results to GATK3, which downsamples to 250 reads per sample, which GATK4 does not currently support. + if (e.getGenotypes().stream().noneMatch(g -> g.hasDP() && g.getDP() >= 250)) { + VariantContextTestUtils.assertVariantContextsAreEqualAlleleOrderIndependent(a, e, ATTRIBUTES_TO_IGNORE, header); + } + }, + b37_reference_20_21); + } + + @Test + public void testNoAnnotsNotAsking() throws IOException { + final File expected = new File(getToolTestDataDir() + "expected/testHsAnnotsNotAsking1.vcf"); + final VCFHeader header = getHeaderFromFile(expected); + runVariantAnnotatorAndAssertSomething(getTestFile("vcfexamplemultisampleempty.vcf"), new File(getToolTestDataDir() + "expected/testHasNoAnnotsNotAsking1.vcf"), Arrays.asList( "-I", largeFileTestDir + "CEUTrio.multisample.b37.1M-1M50k.bam"), + (a, e) -> { + // We need to filter out sites where we saw a DP of 250 because we are comparing the results to GATK3, which downsamples to 250 reads per sample, which GATK4 does not currently support. + if (e.getGenotypes().stream().noneMatch(g -> g.hasDP() && g.getDP() >= 250)) { + VariantContextTestUtils.assertVariantContextsAreEqualAlleleOrderIndependent(a, e, ATTRIBUTES_TO_IGNORE, header); + } + }, + b37_reference_20_21); + } + + @Test + public void testNoAnnotsAsking() throws IOException { + final File expected = new File(getToolTestDataDir() + "expected/testHasNoAnnotsAsking1.vcf"); + final VCFHeader header = getHeaderFromFile(expected); + runVariantAnnotatorAndAssertSomething(getTestFile("vcfexamplemultisampleempty.vcf"), new File(getToolTestDataDir() + "expected/testHasNoAnnotsAsking1.vcf"), Arrays.asList("-G", "Standard", "-I", largeFileTestDir + "CEUTrio.multisample.b37.1M-1M50k.bam"), + (a, e) -> { + // We need to filter out sites where we saw a DP of 250 because we are comparing the results to GATK3, which downsamples to 250 reads per sample, which GATK4 does not currently support. + if (e.getGenotypes().stream().noneMatch(g -> g.hasDP() && g.getDP() >= 250)) { + VariantContextTestUtils.assertVariantContextsAreEqualAlleleOrderIndependent(a, e, ATTRIBUTES_TO_IGNORE, header); + } + }, + b37_reference_20_21); + } + @Test + public void testOverwritingHeader() throws IOException { + assertVariantContextsMatch(getTestFile("vcfexample4.vcf"), getTestFile("expected/testReplaceHeader.vcf"), Arrays.asList("-G", "Standard", "-L", "20:10,001,292"), b37_reference_20_21); + } + @Test + public void testNoReads() throws IOException { + assertVariantContextsMatch(getTestFile("vcfexample3empty.vcf"), getTestFile("expected/testNoReads.vcf"), Arrays.asList("-G", "Standard", "-L", getToolTestDataDir() + "vcfexample3empty.vcf"), b37_reference_20_21); + } + @Test + public void testMultipleIdsWithDbsnp() throws IOException { + assertVariantContextsMatch(getTestFile("vcfdbsnpwithIDs.vcf"), getTestFile("expected/testMultipleIdsWithDbsnp.vcf"), Arrays.asList("-G", "Standard", "-L",getToolTestDataDir() + "vcfdbsnpwithIDs.vcf", "--dbsnp", dbsnp_138_b37_20_21_vcf), null); + } + @Test + public void testDBTagWithHapMap() throws IOException { + assertVariantContextsMatch(getTestFile("vcfexample3empty.vcf"), + getTestFile("expected/testDBTagWithHapMap.vcf"), + Arrays.asList("-G", "Standard", "-L", getToolTestDataDir() + "vcfexample3empty.vcf", "--comp", "H3:" + getToolTestDataDir() + "fakeHM3.vcf"), + b37_reference_20_21, Collections.emptyList()); + } + + // Specific results from this method have not been rigorously vetted, this test asserts that the annotations we expect are present (compared to gatk3 but not gatk3 output because of non-ported annotations ) + @Test + public void testWithAllAnnotations() throws IOException { + assertVariantContextsMatch(getTestFile("HCOutput.NoAnnotations.vcf"), + getTestFile("expected/testWithAllAnnotations.vcf"), + //TODO remove the -AX here when https://github.com/broadinstitute/gatk/issues/3944 is resolved + Arrays.asList("--use-all-annotations", "-AX", "ReferenceBases", "-L", "20:10000000-10100000", "-I", NA12878_20_21_WGS_bam), + b37_reference_20_21); + } + + @Test + public void testDBTagWithTwoComps() throws IOException { + assertVariantContextsMatch(getTestFile("vcfexample3empty.vcf"), + getTestFile("expected/testDBTagWithTwoComps.vcf"), + Arrays.asList("-G", "Standard", "-L", getToolTestDataDir() + "vcfexample3empty.vcf", "--comp", "H3:" + getToolTestDataDir() + "fakeHM3.vcf", "--comp", "foo:" + getToolTestDataDir() + "fakeHM3.vcf"), + b37_reference_20_21, Collections.emptyList()); + } + + @Test + public void testNoQuals() throws IOException { + // NOTE, this test is asserting that the QD calculation is dependant on existing QUAL field, the values themselves are subject to random jitter + assertVariantContextsMatch(getTestFile("noQual.vcf"), + getTestFile("expected/noQual.vcf"), + Arrays.asList( "-L", getToolTestDataDir() + "noQual.vcf", "-I", NA12878_20_21_WGS_bam, "-A", "QualByDepth"), + b37_reference_20_21, Collections.emptyList()); + } + + @Test + public void testUsingExpression() throws IOException { + assertVariantContextsMatch(getTestFile("vcfexample3empty.vcf"), + new File(getToolTestDataDir() + "expected/testUsingExpression.vcf"), + Arrays.asList("--resource-allele-concordance", "--resource", "foo:" + getToolTestDataDir() + "targetAnnotations.vcf", + "-G", "Standard", "-E", "foo.AF", "-L", getToolTestDataDir()+"vcfexample3empty.vcf"), b37_reference_20_21); + } + + @Test + public void testUsingExpressionAlleleMisMatch() throws IOException { + assertVariantContextsMatch(getTestFile("vcfexample3empty-mod.vcf"), + new File(getToolTestDataDir() + "expected/testUsingExpressionAlleleMisMatch.vcf"), + Arrays.asList("--resource-allele-concordance", "--resource", "foo:" + getToolTestDataDir() + "targetAnnotations.vcf", + "-G", "Standard", "-E", "foo.AF", "-L", getToolTestDataDir()+"vcfexample3empty-mod.vcf"), b37_reference_20_21); + } + + @Test + public void testUsingExpressionMultiAllele() throws IOException { + assertVariantContextsMatch(getTestFile("vcfexample3empty-multiAllele.vcf"), + getTestFile("expected/testUsingExpressionMultiAllele.vcf"), + Arrays.asList("-G", "Standard", "-L", getToolTestDataDir() + "vcfexample3empty-multiAllele.vcf", "--resource", "foo:" + getToolTestDataDir() + "targetAnnotations-multiAllele.vcf", "-E", "foo.AF", "-E", "foo.AC"), + b37_reference_20_21, Collections.emptyList()); + } + + @Test + public void testFilterInExpression() throws IOException { + /* The order of filters in the output seems platform-dependent. May need to change htsjdk to make the order consistent across platforms. [Sato] */ + assertVariantContextsMatch(getTestFile("vcfexample3empty-multiAllele.vcf"), + getTestFile("expected/testFilterInExpression.vcf"), + Arrays.asList("-G", "Standard", "-L", getToolTestDataDir() + "vcfexample3empty-multiAllele.vcf", "--resource", "foo:" + getToolTestDataDir() + "annotationResourceWithFilter.vcf", "-E", "foo.FILTER"), + b37_reference_20_21, Collections.emptyList()); + } + + @Test + public void testUsingExpressionWithID() throws IOException { + assertVariantContextsMatch(getTestFile("vcfexample3empty.vcf"), + getTestFile("expected/testUsingExpressionWithID.vcf"), + Arrays.asList("-G", "Standard", "-L", getToolTestDataDir() + "vcfexample3empty.vcf", "--resource", "foo:" + getToolTestDataDir() + "targetAnnotations.vcf", "-E", "foo.ID"), + b37_reference_20_21, Collections.emptyList()); + } + + + @Test + public void testAlleleTrimming() throws IOException { + // This test makes sure that the expression code works in a complex case with many overlapping variant contexts + assertVariantContextsMatch(getTestFile("AlleleTrim.vcf"), + getTestFile("expected/testAlleleTrimming.vcf"), + Arrays.asList( "--resource", "exac:" + getToolTestDataDir() + "exacAlleleTrim.vcf", "-E", "exac.AC_Adj", "-A", "InbreedingCoeff"), + null, Collections.emptyList()); + } + + @Test + public void testStrandBiasBySample() throws IOException { + // Created variants via HalotypeCaller GATK3 with no default annotations + final File outputVCF = getTestFile("HCOutputNoAnnotations.vcf"); + + // Created variant via HalotypeCaller GATK3; include StrandBiasBySample, exclude FisherStrand annotation + // re-Annotate the variant with VariantAnnotator using FisherStrand annotation + final File outputVCFNoFS = getTestFile("HCOutputNoFSAnnotation.vcf"); + + final File outputWithAddedFS = createTempFile("variantannotator", ".vcf"); + + final ArgumentsBuilder args = new ArgumentsBuilder(); + args.addReference(new File(b37_reference_20_21)); + args.addVCF(outputVCFNoFS); + args.addOutput(outputWithAddedFS); + args.add("-L 20:10130000-10134800"); + args.add("-A FisherStrand"); + runCommandLine(args); + + // confirm that the FisherStrand values are identical for the two pipelines + Iterator outFeatureInput = new FeatureDataSource<>(outputVCF).iterator(); + Iterator expectedFeatureInput = new FeatureDataSource<>(outputVCF).iterator(); + + while( outFeatureInput.hasNext() && expectedFeatureInput.hasNext() ) { + final VariantContext vc = (VariantContext) outFeatureInput.next(); + final VariantContext vcAnn = (VariantContext) expectedFeatureInput.next(); + + Assert.assertTrue(vc.hasAttribute("FS")); + Assert.assertTrue(vcAnn.hasAttribute("FS")); + Assert.assertEquals(vc.getAttributeAsDouble("FS", 0.0), vcAnn.getAttributeAsDouble("FS", -1.0)); + } + + Assert.assertFalse(outFeatureInput.hasNext()); + Assert.assertFalse(expectedFeatureInput.hasNext()); + } + +} diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_BaseQualityRankSumTestUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_BaseQualityRankSumTestUnitTest.java index c71964cebaa..1397716c75e 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_BaseQualityRankSumTestUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_BaseQualityRankSumTestUnitTest.java @@ -1,5 +1,6 @@ package org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific; +import com.google.common.primitives.Doubles; import htsjdk.variant.variantcontext.*; import org.broadinstitute.hellbender.engine.ReferenceContext; import org.broadinstitute.hellbender.utils.test.ArtificialAnnotationUtils; @@ -13,6 +14,7 @@ import java.util.*; import java.util.stream.Collectors; +import java.util.stream.Stream; /** * Created by emeryj on 8/11/17. @@ -85,8 +87,12 @@ public void testBaseQualRawAnnotate() { // Note, when we output the raw annotated RankSum score, we output the MannWhitneyU test Z value as a histogram for each alt allele final String expectedAnnotation = AS_RankSumTest.PRINT_DELIM + firstExpected + ",1" + AS_RankSumTest.PRINT_DELIM + secondExpected + ",1"; + + final MannWhitneyU.Result annotateResult = mannWhitneyU.test(Stream.concat(Arrays.stream(alt1BaseQuals).boxed(), Arrays.stream(alt2BaseQuals).boxed()).mapToDouble(i->(double)i).toArray(), Arrays.stream(refBaseQuals).asDoubleStream().toArray(), MannWhitneyU.TestType.FIRST_DOMINATES); + final double annotateZScore = annotateResult.getZ(); + Assert.assertEquals(annotateRaw.get(key1), expectedAnnotation); - Assert.assertEquals(annotateNonRaw.get(key1), expectedAnnotation); + Assert.assertEquals(annotateNonRaw.get(key2), String.format("%.3f",annotateZScore)); Assert.assertEquals(ann.getRawDescriptions().size(), 1); Assert.assertEquals(ann.getRawDescriptions().get(0).getID(), key1); diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_MappingQualityRankSumTestUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_MappingQualityRankSumTestUnitTest.java index cff4fcf738a..aadab9d1cf4 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_MappingQualityRankSumTestUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_MappingQualityRankSumTestUnitTest.java @@ -84,8 +84,9 @@ public void testAS_MQRaw(){ MannWhitneyU.Result expectedAlt = mannWhitneyU.test(new double[]{10.0, 20.0},new double[]{100.0, 110.0}, MannWhitneyU.TestType.FIRST_DOMINATES); String expected = "|"+String.format("%.1f",Math.round(Math.floor((expectedAlt.getZ() )/0.1))*0.1)+",1"; + String expectedAnnotate = String.format("%.3f",expectedAlt.getZ()); - Assert.assertEquals(annotate.get(key1), expected); + Assert.assertEquals(annotate.get(key2), expectedAnnotate); Assert.assertEquals(annotateRaw.get(key1), expected); Assert.assertEquals(ann.getDescriptions().size(), 1); diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_ReadPosRankSumTestUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_ReadPosRankSumTestUnitTest.java index bf3a361473d..94d0cd9e6a4 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_ReadPosRankSumTestUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_ReadPosRankSumTestUnitTest.java @@ -102,9 +102,10 @@ public void testReadPos_Raw(){ MannWhitneyU.Result expectedAlt = mannWhitneyU.test(new double[]{1.0, 2.0},new double[]{3.0, 4.0}, MannWhitneyU.TestType.FIRST_DOMINATES); String firstExpected = "|"+String.format("%.1f",Math.round(Math.floor((expectedAlt.getZ() )/0.1))*0.1)+",1"; + String firstNonRawExpected = String.format("%.3f",expectedAlt.getZ()); Assert.assertEquals(annotateRaw.get(key1), firstExpected); - Assert.assertEquals(annotateNonRaw.get(key1), firstExpected); + Assert.assertEquals(annotateNonRaw.get(key2), firstNonRawExpected); final long positionEnd = 8L; //past middle final VariantContext vcEnd= makeVC(positionEnd); @@ -115,9 +116,10 @@ public void testReadPos_Raw(){ expectedAlt = mannWhitneyU.test(new double[]{(positionEnd-startAlts[1]),(positionEnd-startAlts[0]) },new double[]{(startRefs[0]+readLength-positionEnd-1), (startRefs[1]+readLength-positionEnd-1)}, MannWhitneyU.TestType.FIRST_DOMINATES); String secondExpected = "|"+String.format("%.1f",Math.round(Math.floor((expectedAlt.getZ() )/0.1))*0.1)+",1"; + String secondNonRawExpected = String.format("%.3f",expectedAlt.getZ()); Assert.assertEquals(annotateEndRaw.get(key1), secondExpected ); - Assert.assertEquals(annotateEndNonRaw.get(key1), secondExpected ); + Assert.assertEquals(annotateEndNonRaw.get(key2), secondNonRawExpected ); final long positionPastEnd = 20L; //past middle final VariantContext vcPastEnd= makeVC(positionPastEnd); @@ -126,7 +128,7 @@ public void testReadPos_Raw(){ final Map annotatePastEndRaw = ann.annotateRawData(ref, vcPastEnd, likelihoods); final Map annotatePastEndNonRaw = ann.annotate(ref, vcPastEnd, likelihoods); Assert.assertEquals(annotatePastEndRaw.get(key1), "|"); - Assert.assertEquals(annotatePastEndNonRaw.get(key1), "|"); + Assert.assertEquals(annotatePastEndNonRaw.get(key2), null); } @Override diff --git a/src/test/resources/large/CEUTrio.multisample.b37.1M-1M50k.bam b/src/test/resources/large/CEUTrio.multisample.b37.1M-1M50k.bam new file mode 100644 index 00000000000..9497b926f81 --- /dev/null +++ b/src/test/resources/large/CEUTrio.multisample.b37.1M-1M50k.bam @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:b68d62f2e0a21b6ec40e61b1dfde1539313f4c427314266361d44f771bc6dc14 +size 3993792 diff --git a/src/test/resources/large/CEUTrio.multisample.b37.1M-1M50k.bam.bai b/src/test/resources/large/CEUTrio.multisample.b37.1M-1M50k.bam.bai new file mode 100644 index 00000000000..ef96c53b6f8 --- /dev/null +++ b/src/test/resources/large/CEUTrio.multisample.b37.1M-1M50k.bam.bai @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ceaeb963b02c43580646eae55cd6e720dd26b509f4d4440bda28bfe98956eb94 +size 5088 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGenotypeGivenAllelesMode.gatk4.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGenotypeGivenAllelesMode.gatk4.vcf index 5881c455b3c..ebab2a0d5c0 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGenotypeGivenAllelesMode.gatk4.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGenotypeGivenAllelesMode.gatk4.vcf @@ -31,4 +31,4 @@ 20 10001661 . T C 3606.77 . AC=2;AF=1.00;AN=2;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.33;QD=28.73;SOR=1.193 GT:AD:DP:GQ:PL 1/1:0,81:81:99:3635,249,0 20 10004094 . A T 0 LowQual DP=53;FS=0.000;MLEAC=0;MLEAF=NaN;MQ=52.75;SOR=0.693 GT ./. 20 10004769 . TAAAACTATGC T 980.73 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.603;ClippingRankSum=0.000;DP=79;ExcessHet=3.0103;FS=3.758;MLEAC=1;MLEAF=0.500;MQ=52.37;MQRankSum=-6.625;QD=15.32;ReadPosRankSum=2.215;SOR=1.306 GT:AD:DP:GQ:PL 0/1:37,27:64:99:1018,0,1471 -20 10006819 . AAAAC T 0 LowQual AC=0;AF=0.00;AN=2;DP=75;ExcessHet=3.0103;FS=0.000;MLEAC=0;MLEAF=0.00;MQ=NaN;SOR=0.572 GT:AD:DP:GQ:PL 0/0:75,0:75:99:0,244,2147483647 +20 10006819 . AAAAC T 0 LowQual AC=0;AF=0.00;AN=2;DP=75;ExcessHet=3.0103;FS=0.000;MLEAC=0;MLEAF=0.00;MQ=61.14;SOR=0.572 GT:AD:DP:GQ:PL 0/0:75,0:75:99:0,244,2147483647 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/testGenotypeGivenAllelesMode_givenAlleles.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/testGenotypeGivenAllelesMode_givenAlleles.vcf.idx index 5dd38d64d3eaeb09b59bb69e071614634f7ef1fd..516a369ed172603b023dc25a815eccf61047630a 100644 GIT binary patch delta 49 zcmdnRe200$Zbr6=d%6`}Je@Gi(Mm diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/NA12878.AS.chr20snippet.g.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/NA12878.AS.chr20snippet.g.vcf.idx index 12104ef21deea0a5ffa0ba8771c859d0260a5743..04c16c4aa3e4467cf5447f3d10e90c3bbe3917aa 100644 GIT binary patch delta 46 ucmdnM{+(@t&O~z;9_Rerq|Cfj_b_L-;)#>h1wJrqsU|Wqz`@2hN0dF0KT6ch1wJrqsU|Wqz`@2hN0 13.0"> +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FILTER= 60.0"> +##FILTER= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##OriginalSnpEffCmd="SnpEff eff -v -onlyCoding true -c /mnt/isilon/cag/ngs/hiseq/respublica/pipeline/gatk/snpEff_2_0_5/snpEff.config -i vcf -o vcf GRCh37.64 /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/unifiedgenotyper.snp.filtered.vcf " +##OriginalSnpEffVersion="2.0.5 (build 2011-12-24), by Pablo Cingolani" +##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/0331797407/SID0331797407.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/0428635906/SID0428635906.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/0762331062/SID0762331062.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/0789066272/SID0789066272.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/0849531882/SID0849531882.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/0866893807/SID0866893807.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/0882656781/SID0882656781.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/0890132763/SID0890132763.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/1023974731/SID1023974731.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/1235071895/SID1235071895.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/1303957288/SID1303957288.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/1312115500/SID1312115500.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/1321927176/SID1321927176.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/1346824419/SID1346824419.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/1367085234/SID1367085234.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/1409682918/SID1409682918.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/1650009662/SID1650009662.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/1683598360/SID1683598360.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/1807697538/SID1807697538.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/1948826458/SID1948826458.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/2267793227/SID2267793227.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/2418827587/SID2418827587.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/2431213059/SID2431213059.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/2441141906/SID2441141906.dedup.indelrealigner.recal.bam, 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/mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/3168498448/SID3168498448.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/3177448087/SID3177448087.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/3257203815/SID3257203815.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/3362319470/SID3362319470.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/3443100884/SID3443100884.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/3574989497/SID3574989497.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/3685265559/SID3685265559.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/3926929135/SID3926929135.dedup.indelrealigner.recal.bam, 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/mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/8043825956/SID8043825956.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/8097401602/SID8097401602.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/8110976167/SID8110976167.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/8166168399/SID8166168399.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/8339622917/SID8339622917.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/8477905688/SID8477905688.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/8709441792/SID8709441792.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/8720399204/SID8720399204.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/8934996880/SID8934996880.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/8991335698/SID8991335698.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/9286156078/SID9286156078.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/9310548349/SID9310548349.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/9349366102/SID9349366102.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/9411685596/SID9411685596.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/9509562229/SID9509562229.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/9892329939/SID9892329939.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/9931218560/SID9931218560.dedup.indelrealigner.recal.bam] read_buffer_size=null phone_home=NO_ET gatk_key=/mnt/isilon/cag/ngs/hiseq/respublica/pipeline/TianL_email.chop.edu.key tag=NA read_filter=[] intervals=[/mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/.queue/scatterGather/UnifiedGenotyper.vqsr-2-sg/temp_01_of_50/scatter.intervals] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/mnt/isilon/cag/ngs/hiseq/tianl/cagpipelines/cag.hg19/cag.hg19.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=1 num_cpu_threads_per_data_thread=6 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false version=false genotype_likelihoods_model=SNP pcr_error_rate=1.0E-4 computeSLOD=false annotateNDA=false pair_hmm_implementation=ORIGINAL min_base_quality_score=17 max_deletion_fraction=0.05 min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 indelDebug=false ignoreSNPAlleles=false allReadsSP=false ignoreLaneInfo=false reference_sample_calls=(RodBinding name= source=UNBOUND) reference_sample_name=null sample_ploidy=2 min_quality_score=1 max_quality_score=40 site_quality_prior=20 min_power_threshold_for_calling=0.95 min_reference_depth=100 exclude_filtered_reference_sites=false heterozygosity=0.0010 indel_heterozygosity=1.25E-4 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=6 input_prior=[] contamination_fraction_to_filter=0.05 contamination_fraction_per_sample_file=null p_nonref_model=EXACT_INDEPENDENT exactcallslog=null dbsnp=(RodBinding name= source=UNBOUND) comp=[] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_mismatching_base_and_quals=false filter_bases_not_stored=false" +##VariantAnnotator="analysis_type=VariantAnnotator input_file=[] read_buffer_size=null phone_home=STANDARD gatk_key=null tag=NA read_filter=[] intervals=[/mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/.queue/scatterGather/.qlog/unifiedgenotyper.snp.filtered.snpEff.vcf.varannotator-sg/temp_01_of_50/scatter.intervals] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/mnt/isilon/cag/ngs/hiseq/tianl/cagpipelines/cag.hg19/cag.hg19.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=/mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/unifiedgenotyper.snp.filtered.vcf) snpEffFile=(RodBinding name=snpEffFile source=/mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/unifiedgenotyper.snp.filtered.snpEff.out) dbsnp=(RodBinding name=dbsnp source=/mnt/isilon/cag/ngs/hiseq/tianl/cagpipelines/cag.hg19/dbsnp_138.hg19.vcf) comp=[] resource=[] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub annotation=[SnpEff] excludeAnnotation=[] group=[] expression={} useAllAnnotations=false list=false alwaysAppendDbsnpId=true MendelViolationGenotypeQualityThreshold=0.0 requireStrictAlleleMatch=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false" +##VariantFiltration="analysis_type=VariantFiltration input_file=[] read_buffer_size=null phone_home=NO_ET gatk_key=/mnt/isilon/cag/ngs/hiseq/respublica/pipeline/TianL_email.chop.edu.key tag=NA read_filter=[] intervals=[/mnt/isilon/cag/ngs/hiseq/respublica/pipeline/gatk/bed/SureSelectV4UTR.bed] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/mnt/isilon/cag/ngs/hiseq/tianl/cagpipelines/cag.hg19/cag.hg19.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=/mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/unifiedgenotyper.snp.vcf) mask=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub filterExpression=[QD < 2.0, MQ < 40.0, FS > 60.0, HaplotypeScore > 13.0, MQRankSum < -12.5, ReadPosRankSum < -8.0] filterName=[LowQualityDepth, MappingQuality, StrandBias, HaplotypeScoreHigh, MQRankSumLow, ReadPosRankSumLow] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=0 maskExtension=0 maskName=Mask filterNotInMask=false missingValuesInExpressionsShouldEvaluateAsFailing=false invalidatePreviousFilters=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false" +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##reference=file:///seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta +##source_20140619.1=/mnt/isilon/cag/ngs/hiseq/respublica/pipeline/annotation_pipeline/vcf-annotate -a /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/annovar/UG.snp.all.sum.genome_summary.csv.gz -c CHROM,FROM,TO,INFO/Func,INFO/Gene,INFO/ExonicFunc,INFO/AAChange,INFO/Conserved,INFO/SegDup,INFO/ESP6500_ALL,INFO/1000g2012Apr_ALL,INFO/dbSNP135,INFO/AVSIFT,INFO/LJB_PhyloP,INFO/LJB_PhyloP_Pred,INFO/LJB_SIFT,INFO/LJB_SIFT_Pred,INFO/LJB_PolyPhen2,INFO/LJB_PolyPhen2_Pred,INFO/LJB_LRT,INFO/LJB_LRT_Pred,INFO/LRT_MutationTaster,INFO/LRT_MutationTaster_Pred,INFO/LJB_GERP++ -d /mnt/isilon/cag/ngs/hiseq/respublica/pipeline/annotation_pipeline/annovar_description.txt +##VEP=v77 cache=/humgen/atgu1/fs03/konradk/vep/gold//homo_sapiens/77_GRCh37 db=. +##LoF_info=Info used for LoF annotation +##LoF_flags=Possible warning flags for LoF +##LoF_filter=Reason for LoF not being HC +##LoF=Loss-of-function annotation (HC = High Confidence; LC = Low Confidence) +##INFO= +#CHROM POS ID REF ALT QUAL FILTER INFO +1 26608873 rs1134583 T A,C 8647.13 VQSRTrancheSNP99.90to100.00 AAChange=uc001bly.3:c.A1120T:p.S374C;AC=35,5;AF=0.269,0.038;AN=130;AVSIFT=0;BaseQRankSum=-2.407;DB;DP=2659;Dels=0.00;ExonicFunc=nonsynonymousSNV;FS=27.067;Func=exonic;Gene=UBXN11;HaplotypeScore=11.0781;InbreedingCoeff=-0.3011;LJB_GERP++=0.0;LJB_LRT=0.825324;LJB_LRT_Pred=NA;LJB_PhyloP=0.887806;LJB_PhyloP_Pred=N;LJB_PolyPhen2=0.515975;LJB_PolyPhen2_Pred=NA;LJB_SIFT=1.0;LJB_SIFT_Pred=D;LRT_MutationTaster=7.8E-5;LRT_MutationTaster_Pred=N;MLEAC=35,3;MLEAF=0.269,0.023;MQ=48.46;MQ0=1;MQRankSum=-11.748;NEGATIVE_TRAIN_SITE;QD=5.85;ReadPosRankSum=-6.714;SNPEFF_AMINO_ACID_CHANGE=S251G;SNPEFF_CODON_CHANGE=Agt/Ggt;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_26608773_26609060;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=UBXN11;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000374223;VQSLOD=-4.019e+00;culprit=MQRankSum;dbSNP135=rs1134583;CSQ=A|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2262|||||rs1134583&COSM1602122|1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2262A>T||||||||||0&1|||||||||,C|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2262|||||rs1134583&COSM1602122|2||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2262A>G||||||||||0&1|||||||||,A|ENSG00000158062|ENST00000374217|Transcript|missense_variant|1748|1381|461|S/C|Agt/Tgt|rs1134583&COSM1602122|1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|deleterious(0.01)|unknown(0)|15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1381A>T|ENSP00000363334.2:p.Ser461Cys|||||||||0&1|||||||||,C|ENSG00000158062|ENST00000374217|Transcript|missense_variant|1748|1381|461|S/G|Agt/Ggt|rs1134583&COSM1602122|2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|deleterious(0.03)|unknown(0)|15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1381A>G|ENSP00000363334.2:p.Ser461Gly|||||||||0&1|||||||||,A|ENSG00000158062|ENST00000374222|Transcript|missense_variant|1945|1480|494|S/C|Agt/Tgt|rs1134583&COSM1602122|1||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|deleterious(0.01)|unknown(0)|16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1480A>T|ENSP00000363339.1:p.Ser494Cys|||||||||0&1|||||||||,C|ENSG00000158062|ENST00000374222|Transcript|missense_variant|1945|1480|494|S/G|Agt/Ggt|rs1134583&COSM1602122|2||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|deleterious(0.03)|unknown(0)|16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1480A>G|ENSP00000363339.1:p.Ser494Gly|||||||||0&1|||||||||,A|ENSG00000158062|ENST00000357089|Transcript|missense_variant|1457|1381|461|S/C|Agt/Tgt|rs1134583&COSM1602122|1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|deleterious(0.01)|unknown(0)|14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1381A>T|ENSP00000349601.4:p.Ser461Cys|||||||||0&1|||||||||,C|ENSG00000158062|ENST00000357089|Transcript|missense_variant|1457|1381|461|S/G|Agt/Ggt|rs1134583&COSM1602122|2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|deleterious(0.03)|unknown(0)|14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1381A>G|ENSP00000349601.4:p.Ser461Gly|||||||||0&1|||||||||,A|ENSG00000158062|ENST00000314675|Transcript|missense_variant|1200|1120|374|S/C|Agt/Tgt|rs1134583&COSM1602122|1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|deleterious(0.01)|unknown(0)|11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1120A>T|ENSP00000324721.7:p.Ser374Cys|||||||||0&1|||||||||,C|ENSG00000158062|ENST00000314675|Transcript|missense_variant|1200|1120|374|S/G|Agt/Ggt|rs1134583&COSM1602122|2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|deleterious(0.03)|unknown(0)|11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1120A>G|ENSP00000324721.7:p.Ser374Gly|||||||||0&1|||||||||,A|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2442|||||rs1134583&COSM1602122|1||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2442A>T||||||||||0&1|||||||||,C|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2442|||||rs1134583&COSM1602122|2||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2442A>G||||||||||0&1|||||||||,A|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2227|||||rs1134583&COSM1602122|1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2227A>T||||||||||0&1|||||||||,C|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2227|||||rs1134583&COSM1602122|2||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2227A>G||||||||||0&1|||||||||,A|ENSG00000158062|ENST00000374221|Transcript|missense_variant|1694|1480|494|S/C|Agt/Tgt|rs1134583&COSM1602122|1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|deleterious(0.01)|unknown(0)|16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1480A>T|ENSP00000363338.3:p.Ser494Cys|||||||||0&1|||||||||,C|ENSG00000158062|ENST00000374221|Transcript|missense_variant|1694|1480|494|S/G|Agt/Ggt|rs1134583&COSM1602122|2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|deleterious(0.03)|unknown(0)|16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1480A>G|ENSP00000363338.3:p.Ser494Gly|||||||||0&1|||||||||,A|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2545|||||rs1134583&COSM1602122|1||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2545A>T||||||||||0&1|||||||||,C|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2545|||||rs1134583&COSM1602122|2||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2545A>G||||||||||0&1|||||||||,A|ENSG00000158062|ENST00000374223|Transcript|missense_variant|1212|751|251|S/C|Agt/Tgt|rs1134583&COSM1602122|1||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|deleterious(0.03)|unknown(0)|12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.751A>T|ENSP00000363340.1:p.Ser251Cys|||||||||0&1|||||||||,C|ENSG00000158062|ENST00000374223|Transcript|missense_variant|1212|751|251|S/G|Agt/Ggt|rs1134583&COSM1602122|2||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|tolerated(0.06)|unknown(0)|12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.751A>G|ENSP00000363340.1:p.Ser251Gly|||||||||0&1|||||||||,A||ENSR00000533083|RegulatoryFeature|regulatory_region_variant||||||rs1134583&COSM1602122|1||||||regulatory_region||||||||||||||||||||||0&1|||||||||,C||ENSR00000533083|RegulatoryFeature|regulatory_region_variant||||||rs1134583&COSM1602122|2||||||regulatory_region||||||||||||||||||||||0&1||||||||| diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/HCOutput.NoAnnotations.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/HCOutput.NoAnnotations.vcf new file mode 100644 index 00000000000..dddeb8aca67 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/HCOutput.NoAnnotations.vcf @@ -0,0 +1,287 @@ +##fileformat=VCFv4.2 +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##contig= +##contig= +##reference=file:///Users/louisb/Workspace/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 +20 10000117 . C T 905.77 . . GT:AD:DP:GQ:PL 0/1:36,28:64:99:934,0,1248 +20 10000211 . C T 941.77 . . GT:AD:DP:GQ:PL 0/1:26,27:53:99:970,0,906 +20 10000439 . T G 2804.77 . . GT:AD:DP:GQ:PL 1/1:0,80:80:99:2833,240,0 +20 10000598 . T A 1941.77 . . GT:AD:DP:GQ:PL 1/1:0,49:49:99:1970,147,0 +20 10000694 . G A 1008.77 . . GT:AD:DP:GQ:PL 0/1:45,37:82:99:1037,0,1601 +20 10000758 . T A 3838.77 . . GT:AD:DP:GQ:PL 1/1:0,95:95:99:3867,286,0 +20 10001019 . T G 650.77 . . GT:AD:DP:GQ:PL 0/1:39,26:65:99:679,0,1426 +20 10001298 . T A 2917.77 . . GT:AD:DP:GQ:PL 1/1:0,73:73:99:2946,220,0 +20 10001436 . A AAGGCT 2301.73 . . GT:AD:DP:GQ:PL 1/1:0,50:50:99:2339,156,0 +20 10001474 . C T 2640.77 . . GT:AD:DP:GQ:PL 1/1:0,73:73:99:2669,219,0 +20 10001617 . C A 1731.77 . . GT:AD:DP:GQ:PL 0/1:52,51:103:99:1760,0,1781 +20 10001628 . G A 3898.77 . . GT:AD:DP:GQ:PL 1/1:0,95:95:99:3927,285,0 +20 10001661 . T C 3606.77 . . GT:AD:DP:GQ:PL 1/1:0,81:81:99:3635,249,0 +20 10001670 . T G 3673.77 . . GT:AD:DP:GQ:PL 1/1:0,81:81:99:3702,253,0 +20 10002058 . T G 2963.77 . . GT:AD:DP:GQ:PL 1/1:1,74:75:99:2992,216,0 +20 10002099 . C T 1194.77 . . GT:AD:DP:GQ:PL 0/1:27,38:65:99:1223,0,844 +20 10002138 . C G 2443.77 . . GT:AD:DP:GQ:PL 1/1:0,53:53:99:2472,169,0 +20 10002142 . G C 2407.77 . . GT:AD:DP:GQ:PL 1/1:0,52:52:99:2436,166,0 +20 10002470 . C T 2522.77 . . GT:AD:DP:GQ:PL 1/1:0,61:61:99:2551,189,0 +20 10002625 . G T 2665.77 . . GT:AD:DP:GQ:PL 1/1:0,64:64:99:2694,193,0 +20 10003021 . C T 2383.77 . . GT:AD:DP:GQ:PL 1/1:0,60:60:99:2412,181,0 +20 10003358 . A C 1454.77 . . GT:AD:DP:GQ:PL 0/1:45,44:89:99:1483,0,1477 +20 10003651 . T C 3620.77 . . GT:AD:DP:GQ:PL 1/1:0,93:93:99:3649,279,0 +20 10003692 . A G 2609.77 . . GT:AD:DP:GQ:PL 1/1:0,68:68:99:2638,205,0 +20 10003832 . G A 2705.77 . . GT:AD:DP:GQ:PL 1/1:0,66:66:99:2734,199,0 +20 10004094 . A C 1825.77 . . GT:AD:DP:GQ:PL 1/1:0,53:53:99:1854,157,0 +20 10004147 . A G 1837.77 . . GT:AD:DP:GQ:PL 1/1:0,52:52:99:1866,156,0 +20 10004193 . G T 916.77 . . GT:AD:DP:GQ:PL 0/1:23,28:51:99:945,0,776 +20 10004222 . C CA 12.96 . . GT:AD:DP:GQ:PL 0/1:31,8:39:50:50,0,923 +20 10004223 . A AG 47.73 . . GT:AD:DP:GQ:PL 0/1:36,11:47:85:85,0,982 +20 10004351 . C G 2755.77 . . GT:AD:DP:GQ:PL 1/1:0,70:70:99:2784,211,0 +20 10004389 . T G 2494.77 . . GT:AD:DP:GQ:PL 1/1:0,62:62:99:2523,187,0 +20 10004610 . A C 3625.77 . . GT:AD:DP:GQ:PL 1/1:0,89:89:99:3654,267,0 +20 10004725 . A G 951.77 . . GT:AD:DP:GQ:PL 0/1:35,30:65:99:980,0,1168 +20 10004769 . TAAAACTATGC T 981.73 . . GT:AD:DP:GQ:PL 0/1:37,27:64:99:1019,0,1470 +20 10004874 . A C 3602.77 . . GT:AD:DP:GQ:PL 1/1:0,87:87:99:3631,261,0 +20 10004887 . A G 1323.77 . . GT:AD:DP:GQ:PL 0/1:45,40:85:99:1352,0,1542 +20 10005010 . C T 2934.77 . . GT:AD:DP:GQ:PL 1/1:0,72:72:99:2963,217,0 +20 10005427 . C T 2214.77 . . GT:AD:DP:GQ:PL 1/1:0,55:55:99:2243,165,0 +20 10005499 . A G 3053.77 . . GT:AD:DP:GQ:PL 1/1:0,76:76:99:3082,229,0 +20 10005587 . A G 1229.77 . . GT:AD:DP:GQ:PL 0/1:36,36:72:99:1258,0,1236 +20 10005723 . A G 3062.77 . . GT:AD:DP:GQ:PL 1/1:0,86:86:99:3091,258,0 +20 10006291 . G A 978.77 . . GT:AD:DP:GQ:PL 0/1:53,31:84:99:1007,0,1905 +20 10006404 . A C 2928.77 . . GT:AD:DP:GQ:PL 1/1:0,76:76:99:2957,228,0 +20 10006682 . T A 2874.77 . . GT:AD:DP:GQ:PL 1/1:0,73:73:99:2903,219,0 +20 10006819 . AAAAC A 2531.73 . . GT:AD:DP:GQ:PL 1/1:0,58:58:99:2569,176,0 +20 10007150 . G C 669.77 . . GT:AD:DP:GQ:PL 0/1:38,25:63:99:698,0,1479 +20 10007175 . C T 1350.77 . . GT:AD:DP:GQ:PL 0/1:23,38:61:99:1379,0,780 +20 10007352 . C T 2764.77 . . GT:AD:DP:GQ:PL 1/1:0,69:69:99:2793,208,0 +20 10007531 . A G 2920.77 . . GT:AD:DP:GQ:PL 1/1:0,72:72:99:2949,217,0 +20 10007980 . A C 3524.77 . . GT:AD:DP:GQ:PL 1/1:0,90:90:99:3553,270,0 +20 10008029 . T TA 1986.73 . . GT:AD:DP:GQ:PL 1/1:3,72:75:99:2024,145,0 +20 10008146 . TA T 2141.73 . . GT:AD:DP:GQ:PL 1/1:0,70:70:99:2179,211,0 +20 10008221 . T C 3224.77 . . GT:AD:DP:GQ:PL 1/1:0,80:80:99:3253,240,0 +20 10008458 . T G 2654.77 . . GT:AD:DP:GQ:PL 1/1:0,69:69:99:2683,207,0 +20 10008742 . G T 715.77 . . GT:AD:DP:GQ:PL 0/1:23,26:49:99:744,0,580 +20 10008758 . C CA 684.14 . . GT:AD:DP:GQ:PL 1/1:4,31:35:10:721,10,0 +20 10008921 . C CA 253.73 . . GT:AD:DP:GQ:PL 0/1:18,16:34:99:291,0,366 +20 10008948 . TA T 2057.73 . . GT:AD:DP:GQ:PL 1/1:1,50:51:99:2095,107,0 +20 10008952 . CACACACACACA C,CCACACACACA 1666.73 . . GT:AD:DP:GQ:PL 1/2:1,17,18:36:99:1704,525,844,582,0,531 +20 10009227 . A G 1369.77 . . GT:AD:DP:GQ:PL 0/1:23,39:62:99:1398,0,740 +20 10009246 . A G 3002.77 . . GT:AD:DP:GQ:PL 1/1:0,77:77:99:3031,231,0 +20 10009400 . T A 2998.77 . . GT:AD:DP:GQ:PL 1/1:0,74:74:99:3027,223,0 +20 10009512 . C G 3039.77 . . GT:AD:DP:GQ:PL 1/1:0,77:77:99:3068,231,0 +20 10009719 . A G 1895.77 . . GT:AD:DP:GQ:PL 1/1:0,59:59:99:1924,175,0 +20 10009795 . A G 1880.77 . . GT:AD:DP:GQ:PL 1/1:0,47:47:99:1909,141,0 +20 10009842 . G GAA 532.73 . . GT:AD:DP:GQ:PL 0/1:19,15:34:99:570,0,690 +20 10009844 . G A 661.77 . . GT:AD:DP:GQ:PL 0/1:16,19:35:99:690,0,586 +20 10009871 . A G 658.77 . . GT:AD:DP:GQ:PL 0/1:17,19:36:99:687,0,594 +20 10009875 . A G,AGGGAGG 2369.73 . . GT:AD:DP:GQ:PL 1/2:2,15,13:30:99:2407,645,533,697,0,574 +20 10009879 . A G 2244.77 . . GT:AD:DP:GQ:PL 1/1:2,47:49:99:2273,150,0 +20 10009883 . A G 2151.77 . . GT:AD:DP:GQ:PL 1/1:0,47:47:99:2180,147,0 +20 10010393 . T G 1464.77 . . GT:AD:DP:GQ:PL 0/1:36,43:79:99:1493,0,1230 +20 10010536 . G GA 2462.73 . . GT:AD:DP:GQ:PL 1/1:0,79:79:99:2500,243,0 +20 10010766 . T G 2411.77 . . GT:AD:DP:GQ:PL 1/1:0,66:66:99:2440,199,0 +20 10010832 . T C 2951.77 . . GT:AD:DP:GQ:PL 1/1:0,75:75:99:2980,226,0 +20 10011075 . C T 1325.77 . . GT:AD:DP:GQ:PL 0/1:44,39:83:99:1354,0,1333 +20 10011309 . T C 2692.77 . . GT:AD:DP:GQ:PL 1/1:0,77:77:99:2721,231,0 +20 10011517 . GA G 490.73 . . GT:AD:DP:GQ:PL 0/1:46,30:76:99:528,0,875 +20 10011666 . C T 2961.77 . . GT:AD:DP:GQ:PL 1/1:0,73:73:99:2990,220,0 +20 10011939 . C T 2513.77 . . GT:AD:DP:GQ:PL 1/1:0,62:62:99:2542,187,0 +20 10012021 . CA C 1975.73 . . GT:AD:DP:GQ:PL 1/1:0,66:66:99:2013,198,0 +20 10012362 . G T 835.77 . . GT:AD:DP:GQ:PL 1/1:0,23:23:69:864,69,0 +20 10012384 . T C 229.77 . . GT:AD:DP:GQ:PL 0/1:10,8:18:99:258,0,355 +20 10012387 . T C 533.77 . . GT:AD:DP:GQ:PL 1/1:0,16:16:50:562,50,0 +20 10012479 . A G 592.77 . . GT:AD:DP:GQ:PL 1/1:0,17:17:50:621,50,0 +20 10012498 . C G 466.77 . . GT:AD:DP:GQ:PL 1/1:0,11:11:33:495,33,0 +20 10012518 . T C 406.77 . . GT:AD:DP:GQ:PL 1/1:0,9:9:30:435,30,0 +20 10012521 . C T 46.77 . . GT:AD:DP:GQ:PL 0/1:8,3:11:75:75,0,224 +20 10012570 . G GCA 457.73 . . GT:AD:DP:GQ:PL 1/1:0,9:9:33:495,33,0 +20 10012572 . GT G 457.73 . . GT:AD:DP:GQ:PL 1/1:0,11:11:33:495,33,0 +20 10012631 . C CG 484.73 . . GT:AD:DP:GQ:PL 0/1:8,13:21:99:522,0,297 +20 10012636 . G C 527.77 . . GT:AD:DP:GQ:PL 0/1:8,14:22:99:556,0,294 +20 10012714 . G C 1300.77 . . GT:AD:DP:GQ:PL 1/1:0,35:35:99:1329,105,0 +20 10012751 . T C 937.77 . . GT:AD:DP:GQ:PL 1/1:0,30:30:89:966,89,0 +20 10013119 . C T 1011.77 . . GT:AD:DP:GQ:PL 0/1:29,30:59:99:1040,0,936 +20 10013574 . G A 1050.77 . . GT:AD:DP:GQ:PL 0/1:38,31:69:99:1079,0,1301 +20 10014990 . C CAT 1237.73 . . GT:AD:DP:GQ:PL 0/1:38,38:76:99:1275,0,1248 +20 10015679 . C T 140.77 . . GT:AD:DP:GQ:PL 0/1:5,5:10:99:169,0,166 +20 10015761 . T C 344.77 . . GT:AD:DP:GQ:PL 0/1:9,13:22:99:373,0,284 +20 10018158 . G C 1639.77 . . GT:AD:DP:GQ:PL 0/1:40,48:88:99:1668,0,1165 +20 10018555 . G A 1567.77 . . GT:AD:DP:GQ:PL 0/1:35,45:80:99:1596,0,1211 +20 10019093 . A G 1244.77 . . GT:AD:DP:GQ:PL 0/1:33,36:69:99:1273,0,1104 +20 10020229 . G A 1538.77 . . GT:AD:DP:GQ:PL 0/1:38,44:82:99:1567,0,1130 +20 10023689 . G A 1852.77 . . GT:AD:DP:GQ:PL 0/1:29,51:80:99:1881,0,946 +20 10024107 . C T 1694.77 . . GT:AD:DP:GQ:PL 0/1:38,48:86:99:1723,0,1086 +20 10024300 . C CTT 87.76 . . GT:AD:DP:GQ:PL 0/1:9,8:17:99:103,0,137 +20 10026357 . T C 1166.77 . . GT:AD:DP:GQ:PL 0/1:28,35:63:99:1195,0,932 +20 10026794 . C T 1084.77 . . GT:AD:DP:GQ:PL 0/1:19,33:52:99:1113,0,529 +20 10027234 . A ATTAG 1320.73 . . GT:AD:DP:GQ:PL 0/1:34,35:69:99:1358,0,1964 +20 10027868 . A G 1739.77 . . GT:AD:DP:GQ:PL 0/1:44,45:89:99:1768,0,3201 +20 10027872 . A G 1724.77 . . GT:AD:DP:GQ:PL 0/1:40,45:85:99:1753,0,3136 +20 10028867 . A ATG 1106.73 . . GT:AD:DP:GQ:PL 0/1:32,39:71:99:1144,0,916 +20 10030188 . T A 1372.77 . . GT:AD:DP:GQ:PL 0/1:42,39:81:99:1401,0,1524 +20 10031254 . A AT 1463.73 . . GT:AD:DP:GQ:PL 0/1:38,47:85:99:1501,0,1159 +20 10031342 . G A 1834.77 . . GT:AD:DP:GQ:PL 0/1:41,52:93:99:1863,0,1375 +20 10031798 . G A 4296.77 . . GT:AD:DP:GQ:PL 1/1:0,104:104:99:4325,313,0 +20 10031827 . C T 2004.77 . . GT:AD:DP:GQ:PL 0/1:52,56:108:99:2033,0,1798 +20 10032094 . G A 1220.77 . . GT:AD:DP:GQ:PL 0/1:47,36:83:99:1249,0,1497 +20 10032413 . T G 869.77 . . GT:AD:DP:GQ:PL 0/1:35,31:66:99:898,0,1277 +20 10032882 . A T 1202.77 . . GT:AD:DP:GQ:PL 0/1:39,36:75:99:1231,0,1406 +20 10032972 . C CAT 1122.73 . . GT:AD:DP:GQ:PL 0/1:33,30:63:99:1160,0,1477 +20 10034306 . T C 782.77 . . GT:AD:DP:GQ:PL 0/1:46,29:75:99:811,0,1593 +20 10036930 . CGATAGCCCTAGCCCTAGATA C 1036.73 . . GT:AD:DP:GQ:PL 0/1:39,29:68:99:1074,0,5569 +20 10037037 . C T 1436.77 . . GT:AD:DP:GQ:PL 0/1:39,42:81:99:1465,0,1124 +20 10037110 . T TGATA 2780.73 . . GT:AD:DP:GQ:PL 1/1:0,61:61:99:2818,189,0 +20 10037144 . T TGATAGATA 1823.73 . . GT:AD:DP:GQ:PL 1/1:0,36:36:99:1861,127,0 +20 10037709 . A T 1003.77 . . GT:AD:DP:GQ:PL 0/1:39,32:71:99:1032,0,1354 +20 10039371 . T G 1324.77 . . GT:AD:DP:GQ:PL 0/1:34,40:74:99:1353,0,1194 +20 10040772 . C CT 1995.73 . . GT:AD:DP:GQ:PL 1/1:0,70:70:99:2033,210,0 +20 10040812 . AT A 2607.73 . . GT:AD:DP:GQ:PL 1/1:0,71:71:99:2645,214,0 +20 10040821 . T A 1171.77 . . GT:AD:DP:GQ:PL 0/1:38,40:78:99:1200,0,1099 +20 10041304 . C T 2765.77 . . GT:AD:DP:GQ:PL 1/1:0,68:68:99:2794,204,0 +20 10041701 . A ATATG 1403.73 . . GT:AD:DP:GQ:PL 0/1:9,49:58:58:1441,0,58 +20 10042319 . C T 2658.77 . . GT:AD:DP:GQ:PL 1/1:0,66:66:99:2687,199,0 +20 10042761 . A G 3553.77 . . GT:AD:DP:GQ:PL 1/1:0,91:91:99:3582,272,0 +20 10042829 . A G 3055.77 . . GT:AD:DP:GQ:PL 1/1:0,78:78:99:3084,235,0 +20 10043002 . A T 1287.77 . . GT:AD:DP:GQ:PL 0/1:48,38:86:99:1316,0,1659 +20 10044849 . A G 2091.77 . . GT:AD:DP:GQ:PL 1/1:0,59:59:99:2120,177,0 +20 10045078 . G T 3271.77 . . GT:AD:DP:GQ:PL 1/1:0,81:81:99:3300,244,0 +20 10045642 . G C 3138.77 . . GT:AD:DP:GQ:PL 1/1:0,82:82:99:3167,246,0 +20 10046178 . AAGAAAGAAAG A 2159.73 . . GT:AD:DP:GQ:PL 1/1:0,50:50:99:2197,153,0 +20 10046537 . A G 819.77 . . GT:AD:DP:GQ:PL 0/1:28,29:57:99:848,0,902 +20 10050828 . T C 1227.77 . . GT:AD:DP:GQ:PL 0/1:49,37:86:99:1256,0,1768 +20 10051448 . T C 1134.77 . . GT:AD:DP:GQ:PL 0/1:35,35:70:99:1163,0,1150 +20 10052688 . C A 1062.77 . . GT:AD:DP:GQ:PL 0/1:45,32:77:99:1091,0,1645 +20 10058022 . T C 975.77 . . GT:AD:DP:GQ:PL 0/1:36,32:68:99:1004,0,1261 +20 10062935 . C CA 92.84 . . GT:AD:DP:GQ:PL 0/1:13,10:23:99:130,0,101 +20 10067049 . TAAAAAAAA T,TA 614.73 . . GT:AD:DP:GQ:PL 1/2:2,11,9:22:99:652,164,339,135,0,106 +20 10067090 . C A 2004.77 . . GT:AD:DP:GQ:PL 1/1:0,55:55:99:2033,164,0 +20 10067264 . G A 2922.77 . . GT:AD:DP:GQ:PL 1/1:0,73:73:99:2951,219,0 +20 10067722 . A C 2146.77 . . GT:AD:DP:GQ:PL 1/1:0,54:54:99:2175,163,0 +20 10068158 . GTGTATATATATA G 66.73 . . GT:AD:DP:GQ:PL 0/1:3,4:7:57:104,0,57 +20 10068981 . G A 2503.77 . . GT:AD:DP:GQ:PL 1/1:0,61:61:99:2532,184,0 +20 10070602 . T C 2691.77 . . GT:AD:DP:GQ:PL 1/1:0,72:72:99:2720,216,0 +20 10070936 . T A 3631.77 . . GT:AD:DP:GQ:PL 1/1:0,81:81:99:3660,247,0 +20 10070938 . G GA 3656.73 . . GT:AD:DP:GQ:PL 1/1:0,79:79:99:3694,250,0 +20 10071135 . C T 3257.77 . . GT:AD:DP:GQ:PL 1/1:0,79:79:99:3286,238,0 +20 10071187 . G A 3410.77 . . GT:AD:DP:GQ:PL 1/1:0,82:82:99:3439,246,0 +20 10071890 . T C 1974.77 . . GT:AD:DP:GQ:PL 1/1:0,57:57:99:2003,171,0 +20 10072505 . A G 2099.77 . . GT:AD:DP:GQ:PL 1/1:0,64:64:99:2128,191,0 +20 10074187 . A G 3101.77 . . GT:AD:DP:GQ:PL 1/1:0,79:79:99:3130,238,0 +20 10074240 . T C 3406.77 . . GT:AD:DP:GQ:PL 1/1:0,85:85:99:3435,255,0 +20 10074716 . G A 2400.77 . . GT:AD:DP:GQ:PL 1/1:0,64:64:99:2429,192,0 +20 10074806 . G A 2817.77 . . GT:AD:DP:GQ:PL 1/1:0,71:71:99:2846,213,0 +20 10075043 . T C 2405.77 . . GT:AD:DP:GQ:PL 1/1:0,61:61:99:2434,184,0 +20 10075168 . C T 3612.77 . . GT:AD:DP:GQ:PL 1/1:0,88:88:99:3641,264,0 +20 10075508 . GA G 1928.73 . . GT:AD:DP:GQ:PL 1/1:0,70:70:99:1966,210,0 +20 10076250 . A G 1107.77 . . GT:AD:DP:GQ:PL 0/1:40,39:79:99:1136,0,1339 +20 10076339 . A G 1309.77 . . GT:AD:DP:GQ:PL 0/1:32,40:72:99:1338,0,1035 +20 10076399 . G A 1807.77 . . GT:AD:DP:GQ:PL 0/1:44,50:94:99:1836,0,1544 +20 10076989 . CA C 221.73 . . GT:AD:DP:GQ:PL 0/1:24,18:42:99:218,0,332 +20 10077752 . T C 1345.77 . . GT:AD:DP:GQ:PL 0/1:34,45:79:99:1374,0,1187 +20 10079476 . T G 11.12 . . GT:AD:DP:GQ:PL 0/1:33,11:44:39:39,0,1137 +20 10081750 . C A 1353.77 . . GT:AD:DP:GQ:PL 0/1:44,39:83:99:1382,0,1525 +20 10081800 . C T 1109.77 . . GT:AD:DP:GQ:PL 0/1:35,33:68:99:1138,0,1222 +20 10082892 . C T 1712.77 . . GT:AD:DP:GQ:PL 1/1:0,44:44:99:1741,132,0 +20 10085211 . A T 1210.77 . . GT:AD:DP:GQ:PL 0/1:40,36:76:99:1239,0,1443 +20 10086110 . G A 1274.77 . . GT:AD:DP:GQ:PL 0/1:43,38:81:99:1303,0,1506 +20 10086283 . G T 1025.77 . . GT:AD:DP:GQ:PL 0/1:52,32:84:99:1054,0,1771 +20 10086619 . T A 796.77 . . GT:AD:DP:GQ:PL 0/1:45,25:70:99:825,0,1603 +20 10086853 . G A 1002.77 . . GT:AD:DP:GQ:PL 0/1:41,32:73:99:1031,0,1280 +20 10086954 . G A 1095.77 . . GT:AD:DP:GQ:PL 0/1:34,34:68:99:1124,0,1051 +20 10087230 . A G 1842.77 . . GT:AD:DP:GQ:PL 0/1:42,54:96:99:1871,0,1428 +20 10087394 . T G 1688.77 . . GT:AD:DP:GQ:PL 0/1:35,49:84:99:1717,0,1186 +20 10087754 . T G 1347.77 . . 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AC=3;AF=0.500;AN=6;BaseQRankSum=-1.703;ClippingRankSum=0.000;DP=180;ExcessHet=1.5490;FS=3.443;MLEAC=3;MLEAF=0.500;MQ=51.29;MQRankSum=-6.094;QD=31.65;ReadPosRankSum=-0.207;SOR=0.982 GT:AD:DP:GQ:PL 0/1:28,32:60:99:1181,0,1358 1/1:0,60:60:99:2653,181,0 0/0:58,0:58:99:0,177,3402 +20 10132682 . A ATG 171.02 . AC=1;AF=0.167;AN=6;BaseQRankSum=-2.012;ClippingRankSum=0.000;DP=203;ExcessHet=3.0103;FS=20.999;MLEAC=1;MLEAF=0.167;MQ=51.37;MQRankSum=0.726;QD=6.33;ReadPosRankSum=-0.802;SOR=2.544 GT:AD:DP:GQ:PL 0/0:25,2:27:34:0,34,879 0/1:13,14:27:99:196,0,218 0/0:29,0:29:87:0,87,1016 +20 10132706 . G GAC 216.13 . AC=2;AF=0.333;AN=6;BaseQRankSum=-0.437;ClippingRankSum=0.000;DP=191;ExcessHet=3.9794;FS=13.059;MLEAC=2;MLEAF=0.333;MQ=50.97;MQRankSum=-4.345;QD=3.43;ReadPosRankSum=4.274;SOR=1.697 GT:AD:DP:GQ:PL 0/1:24,8:32:99:227,0,969 0/0:50,0:50:99:0,161,2349 0/1:26,5:31:30:30,0,1013 +20 10132707 . T A 295.16 . AC=2;AF=0.333;AN=6;BaseQRankSum=-0.370;ClippingRankSum=0.000;DP=189;ExcessHet=3.9794;FS=18.398;MLEAC=2;MLEAF=0.333;MQ=51.00;MQRankSum=-4.567;QD=4.69;ReadPosRankSum=4.730;SOR=2.074 GT:AD:DP:GQ:PL 0/1:24,8:32:99:228,0,954 0/0:52,0:52:99:0,160,2347 0/1:26,5:31:99:99,0,1021 +20 10132709 . T A 294.16 . AC=2;AF=0.333;AN=6;BaseQRankSum=0.901;ClippingRankSum=0.000;DP=187;ExcessHet=3.9794;FS=18.464;MLEAC=2;MLEAF=0.333;MQ=50.84;MQRankSum=-4.589;QD=4.60;ReadPosRankSum=4.577;SOR=2.072 GT:AD:DP:GQ:PL 0/1:24,8:32:99:229,0,953 0/0:52,0:52:99:0,169,2482 0/1:27,5:32:97:97,0,1063 +20 10132711 . T A 291.16 . AC=2;AF=0.333;AN=6;BaseQRankSum=0.593;ClippingRankSum=0.000;DP=188;ExcessHet=3.9794;FS=18.487;MLEAC=2;MLEAF=0.333;MQ=50.53;MQRankSum=-4.668;QD=4.48;ReadPosRankSum=4.407;SOR=2.070 GT:AD:DP:GQ:PL 0/1:24,8:32:99:226,0,994 0/0:55,0:55:99:0,169,2481 0/1:28,5:33:97:97,0,1063 +20 10132713 . T A 292.16 . AC=2;AF=0.333;AN=6;BaseQRankSum=2.289;ClippingRankSum=0.000;DP=178;ExcessHet=3.9794;FS=18.487;MLEAC=2;MLEAF=0.333;MQ=49.79;MQRankSum=-4.605;QD=4.49;ReadPosRankSum=4.149;SOR=2.070 GT:AD:DP:GQ:PL 0/1:24,8:32:99:227,0,994 0/0:55,0:55:99:0,168,2480 0/1:28,5:33:97:97,0,1062 +20 10132715 . T A 294.16 . AC=2;AF=0.333;AN=6;BaseQRankSum=0.494;ClippingRankSum=0.000;DP=171;ExcessHet=3.9794;FS=22.720;MLEAC=2;MLEAF=0.333;MQ=49.27;MQRankSum=-4.547;QD=4.74;ReadPosRankSum=3.769;SOR=2.061 GT:AD:DP:GQ:PL 0/1:22,8:30:99:231,0,951 0/0:52,0:52:99:0,168,2480 0/1:27,5:32:95:95,0,1104 +20 10132717 . T A 304.16 . AC=2;AF=0.333;AN=6;BaseQRankSum=1.754;ClippingRankSum=0.000;DP=166;ExcessHet=3.9794;FS=23.264;MLEAC=2;MLEAF=0.333;MQ=48.91;MQRankSum=-4.478;QD=4.99;ReadPosRankSum=3.038;SOR=2.058 GT:AD:DP:GQ:PL 0/1:21,8:29:99:238,0,866 0/0:50,0:50:99:0,162,2390 0/1:27,5:32:98:98,0,1061 +20 10132719 . T A 302.12 . AC=2;AF=0.333;AN=6;BaseQRankSum=2.068;ClippingRankSum=0.000;DP=162;ExcessHet=3.9794;FS=29.529;MLEAC=2;MLEAF=0.333;MQ=49.03;MQRankSum=-4.584;QD=5.04;ReadPosRankSum=1.902;SOR=2.044 GT:AD:DP:GQ:PL 0/1:21,8:29:99:241,0,812 0/0:51,0:51:99:0,162,2332 0/1:26,5:31:99:102,0,998 +20 10132722 . CAG C,GAG 2305.09 . AC=3,2;AF=0.500,0.333;AN=6;BaseQRankSum=0.772;ClippingRankSum=0.000;DP=155;ExcessHet=3.0103;FS=1.556;MLEAC=2,2;MLEAF=0.333,0.333;MQ=48.66;MQRankSum=0.122;QD=27.12;ReadPosRankSum=0.545;SOR=0.393 GT:AD:DP:GQ:PL 1/2:0,15,16:31:99:987,587,603,440,0,679 1/1:0,24,2:26:72:687,72,0,767,97,1568 0/2:8,3,17:28:99:628,583,839,0,177,591 +20 10133139 . T C 1050.13 . AC=1;AF=0.167;AN=6;BaseQRankSum=-6.774;ClippingRankSum=0.000;DP=226;ExcessHet=3.0103;FS=2.267;MLEAC=1;MLEAF=0.167;MQ=59.55;MQRankSum=-2.276;QD=15.00;ReadPosRankSum=2.770;SOR=0.946 GT:AD:DP:GQ:PL 0/0:86,0:86:99:0,259,3582 0/1:32,38:70:99:1081,0,1029 0/0:67,0:67:99:0,201,2680 +20 10134410 . AAAAGAAAG A,AAAAG 1904.12 . AC=2,2;AF=0.333,0.333;AN=6;BaseQRankSum=0.026;ClippingRankSum=0.000;DP=216;ExcessHet=3.9794;FS=3.602;MLEAC=2,2;MLEAF=0.333,0.333;MQ=57.52;MQRankSum=0.837;QD=24.41;ReadPosRankSum=0.000;SOR=1.277 GT:AD:DP:GQ:PL 1/2:0,19,10:29:99:1167,400,585,753,0,717 0/1:15,12,0:27:99:484,0,650,481,643,1113 0/2:14,0,8:22:99:294,373,2121,0,697,594 +20 10134456 . AAGAAAG A 668.09 . AC=1;AF=0.167;AN=6;BaseQRankSum=-1.140;ClippingRankSum=0.000;DP=217;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.167;MQ=57.66;MQRankSum=-2.912;QD=13.36;ReadPosRankSum=0.426;SOR=0.576 GT:AD:DP:GQ:PL 0/0:71,0:71:99:0,213,3044 0/1:30,20:50:99:708,0,1283 0/0:78,0:78:99:0,233,3762 +20 10134479 . A C 2526.16 . AC=2;AF=0.333;AN=6;BaseQRankSum=-0.781;ClippingRankSum=0.000;DP=205;ExcessHet=3.9794;FS=3.921;MLEAC=2;MLEAF=0.333;MQ=57.39;MQRankSum=-1.373;QD=19.74;ReadPosRankSum=-1.052;SOR=1.030 GT:AD:DP:GQ:PL 0/1:36,39:75:99:1439,0,1255 0/1:22,31:53:99:1119,0,860 0/0:73,0:73:99:0,220,3447 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/HCOutputNoAnnotations.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/HCOutputNoAnnotations.vcf.idx new file mode 100644 index 0000000000000000000000000000000000000000..208eb34052a37b2b4652b3905b467be3bf20dbd0 GIT binary patch literal 440 zcmb_YK~BR!3^alh9C!e{fJ2<7jS>)-C|PJFNJU8_PDI;uTS7w??K(xA`3O(o6+DO+ zu!~4lac1PPEz2H_oQ;yZ9RS!hTvW9h%#HL|xBBGZzY%oK~n+i6k_k z5?Z#Z6dI*k;!H_CuNqAiwIsH$NXlB{3$IsJl{bwfPEujcRmB^MHiKb2Zt1zDRQ}E? z*=T27F5vUrxHI^;dHcGzZY}l18%7u33~q=!AZ6JN|CnW=WB-96Tos z!oKf%L2uytejn_4(MjgfWE7<_GkRV)ICb4F2OGV3JWVt30 +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##reference=file:///humgen/gsa-hpprojects/GATK/bundle/current/b37/human_g1k_v37.fasta +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 NA12891 NA12892 +20 10130017 . G A 7871.13 . AC=5;AF=0.833;AN=6;BaseQRankSum=2.700;ClippingRankSum=0.000;DP=247;ExcessHet=3.0103;MLEAC=5;MLEAF=0.833;MQ=58.04;MQRankSum=-1.055;QD=32.13;ReadPosRankSum=-0.506;SOR=0.685 GT:AD:DP:GQ:PL:SB 1/1:0,99:99:99:4007,298,0:0,0,58,41 1/1:0,71:71:99:2852,214,0:0,0,36,35 0/1:42,33:75:99:1043,0,1475:19,23,14,19 +20 10130249 . AACAC A,AAC 2877.09 . AC=3,2;AF=0.500,0.333;AN=6;BaseQRankSum=-1.563;ClippingRankSum=0.000;DP=154;ExcessHet=3.0103;MLEAC=3,2;MLEAF=0.500,0.333;MQ=54.34;MQRankSum=0.476;QD=27.14;ReadPosRankSum=0.073;SOR=1.669 GT:AD:DP:GQ:PL:SB 1/2:2,19,18:39:99:1189,476,600,528,0,487:1,1,9,28 1/1:0,37,1:38:81:1516,90,0,1230,81,1183:0,0,15,23 0/2:17,3,9:29:99:212,154,968,0,441,450:10,7,3,9 +20 10130306 . A ATG 1556.12 . AC=2;AF=0.333;AN=6;BaseQRankSum=0.034;ClippingRankSum=0.000;DP=193;ExcessHet=3.9794;MLEAC=2;MLEAF=0.333;MQ=54.71;MQRankSum=-6.363;QD=13.30;ReadPosRankSum=2.217;SOR=1.143 GT:AD:DP:GQ:PL:SB 0/1:35,36:71:99:1169,0,1122:6,29,8,28 0/0:47,0:47:99:0,142,1810:20,27,0,0 0/1:32,14:46:99:428,0,1067:11,21,4,10 +20 10130345 . G GTA 1436.12 . AC=2;AF=0.333;AN=6;BaseQRankSum=-0.224;ClippingRankSum=0.000;DP=178;ExcessHet=3.9794;MLEAC=2;MLEAF=0.333;MQ=56.18;MQRankSum=-2.726;QD=14.36;ReadPosRankSum=-1.000;SOR=1.513 GT:AD:DP:GQ:PL:SB 0/1:34,25:59:99:814,0,1126:11,23,10,15 0/0:43,0:43:99:0,130,1634:28,15,0,0 0/1:21,20:41:99:663,0,678:13,8,5,15 +20 10130722 . G A 3680.90 . AC=3;AF=0.500;AN=6;BaseQRankSum=1.846;ClippingRankSum=0.000;DP=185;ExcessHet=1.5490;MLEAC=3;MLEAF=0.500;MQ=54.98;MQRankSum=-2.592;QD=28.98;ReadPosRankSum=0.587;SOR=0.569 GT:AD:DP:GQ:PL:SB 0/1:37,37:74:99:1385,0,2356:15,22,22,15 1/1:0,53:53:99:2332,169,0:0,0,26,27 0/0:57,0:57:99:0,171,4215:23,34,0,0 +20 10130767 . ATGTATG A 2739.86 . AC=3;AF=0.500;AN=6;BaseQRankSum=1.251;ClippingRankSum=0.000;DP=133;ExcessHet=1.5490;MLEAC=3;MLEAF=0.500;MQ=51.18;MQRankSum=-4.543;QD=30.78;ReadPosRankSum=-0.487;SOR=1.487 GT:AD:DP:GQ:PL:SB 0/1:25,29:54:99:1200,0,2325:9,16,20,9 1/1:0,35:35:99:1585,108,0:0,0,23,12 0/0:44,0:44:99:0,135,4314:18,26,0,0 +20 10131196 . T C 3678.13 . AC=5;AF=0.833;AN=6;BaseQRankSum=-1.550;ClippingRankSum=0.000;DP=130;ExcessHet=3.0103;MLEAC=5;MLEAF=0.833;MQ=58.37;MQRankSum=-0.569;QD=30.40;ReadPosRankSum=0.542;SOR=0.238 GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1695,132,0:0,0,21,23 1/1:0,36:36:99:1443,108,0:0,0,6,30 0/1:22,19:41:99:571,0,748:4,18,6,13 +20 10131980 . T C 6397.13 . AC=5;AF=0.833;AN=6;BaseQRankSum=2.988;ClippingRankSum=0.000;DP=202;ExcessHet=3.0103;MLEAC=5;MLEAF=0.833;MQ=58.64;MQRankSum=-1.025;QD=31.83;ReadPosRankSum=0.043;SOR=0.170 GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:2771,202,0:0,0,33,34 1/1:0,68:68:99:2679,204,0:0,0,35,33 0/1:40,26:66:99:978,0,1333:29,11,12,14 +20 10131998 . G A 1983.16 . AC=2;AF=0.333;AN=6;BaseQRankSum=1.870;ClippingRankSum=0.000;DP=191;ExcessHet=3.9794;MLEAC=2;MLEAF=0.333;MQ=57.84;MQRankSum=2.536;QD=16.53;ReadPosRankSum=-1.829;SOR=0.784 GT:AD:DP:GQ:PL:SB 0/1:27,33:60:99:1145,0,964:14,13,13,20 0/0:70,0:70:99:0,211,2973:36,34,0,0 0/1:33,27:60:99:870,0,1305:26,7,13,14 +20 10132023 . T C 1815.16 . AC=2;AF=0.333;AN=6;BaseQRankSum=-6.287;ClippingRankSum=0.000;DP=182;ExcessHet=3.9794;MLEAC=2;MLEAF=0.333;MQ=56.92;MQRankSum=2.490;QD=16.50;ReadPosRankSum=2.500;SOR=1.002 GT:AD:DP:GQ:PL:SB 0/1:26,31:57:99:1109,0,820:13,13,10,21 0/0:69,2:71:99:0,178,2593:37,32,0,2 0/1:33,20:53:99:738,0,1126:26,7,11,9 +20 10132091 . A G 1590.16 . AC=2;AF=0.333;AN=6;BaseQRankSum=-0.860;ClippingRankSum=0.000;DP=182;ExcessHet=3.9794;MLEAC=2;MLEAF=0.333;MQ=58.00;MQRankSum=1.765;QD=14.07;ReadPosRankSum=-1.718;SOR=0.952 GT:AD:DP:GQ:PL:SB 0/1:32,27:59:99:905,0,1141:19,13,13,14 0/0:69,0:69:99:0,207,2595:33,36,0,0 0/1:31,23:54:99:717,0,1058:14,17,9,14 +20 10132301 . GACACACACAC G 3227.15 . AC=3;AF=0.500;AN=6;BaseQRankSum=2.075;ClippingRankSum=0.000;DP=196;ExcessHet=1.5490;MLEAC=3;MLEAF=0.500;MQ=52.51;MQRankSum=-5.926;QD=31.64;ReadPosRankSum=-1.509;SOR=0.540 GT:AD:DP:GQ:PL:SB 0/1:24,23:47:99:882,0,1490:14,4,11,12 1/1:0,55:55:99:2368,168,0:0,0,29,23 0/0:56,0:56:99:0,169,3314:20,21,0,0 +20 10132340 . A G 3797.90 . AC=3;AF=0.500;AN=6;BaseQRankSum=-1.703;ClippingRankSum=0.000;DP=180;ExcessHet=1.5490;MLEAC=3;MLEAF=0.500;MQ=51.29;MQRankSum=-6.094;QD=31.65;ReadPosRankSum=-0.207;SOR=0.982 GT:AD:DP:GQ:PL:SB 0/1:28,32:60:99:1181,0,1358:16,12,17,15 1/1:0,60:60:99:2653,181,0:0,0,35,25 0/0:58,0:58:99:0,177,3402:27,31,0,0 +20 10132682 . A ATG 171.02 . AC=1;AF=0.167;AN=6;BaseQRankSum=-2.012;ClippingRankSum=0.000;DP=203;ExcessHet=3.0103;MLEAC=1;MLEAF=0.167;MQ=51.37;MQRankSum=0.726;QD=6.33;ReadPosRankSum=-0.802;SOR=2.544 GT:AD:DP:GQ:PL:SB 0/0:25,2:27:34:0,34,879:10,5,0,2 0/1:13,14:27:99:196,0,218:6,5,3,11 0/0:29,0:29:87:0,87,1016:6,5,0,0 +20 10132706 . G GAC 216.13 . AC=2;AF=0.333;AN=6;BaseQRankSum=-0.437;ClippingRankSum=0.000;DP=191;ExcessHet=3.9794;MLEAC=2;MLEAF=0.333;MQ=50.97;MQRankSum=-4.345;QD=3.43;ReadPosRankSum=4.274;SOR=1.697 GT:AD:DP:GQ:PL:SB 0/1:24,8:32:99:227,0,969:10,14,5,3 0/0:50,0:50:99:0,161,2349:20,30,0,0 0/1:26,5:31:30:30,0,1013:8,17,3,0 +20 10132707 . T A 295.16 . AC=2;AF=0.333;AN=6;BaseQRankSum=-0.370;ClippingRankSum=0.000;DP=189;ExcessHet=3.9794;MLEAC=2;MLEAF=0.333;MQ=51.00;MQRankSum=-4.567;QD=4.69;ReadPosRankSum=4.730;SOR=2.074 GT:AD:DP:GQ:PL:SB 0/1:24,8:32:99:228,0,954:10,14,5,3 0/0:52,0:52:99:0,160,2347:20,32,0,0 0/1:26,5:31:99:99,0,1021:9,17,5,0 +20 10132709 . T A 294.16 . AC=2;AF=0.333;AN=6;BaseQRankSum=0.901;ClippingRankSum=0.000;DP=187;ExcessHet=3.9794;MLEAC=2;MLEAF=0.333;MQ=50.84;MQRankSum=-4.589;QD=4.60;ReadPosRankSum=4.577;SOR=2.072 GT:AD:DP:GQ:PL:SB 0/1:24,8:32:99:229,0,953:10,14,5,3 0/0:52,0:52:99:0,169,2482:20,32,0,0 0/1:27,5:32:97:97,0,1063:9,18,5,0 +20 10132711 . T A 291.16 . AC=2;AF=0.333;AN=6;BaseQRankSum=0.593;ClippingRankSum=0.000;DP=188;ExcessHet=3.9794;MLEAC=2;MLEAF=0.333;MQ=50.53;MQRankSum=-4.668;QD=4.48;ReadPosRankSum=4.407;SOR=2.070 GT:AD:DP:GQ:PL:SB 0/1:24,8:32:99:226,0,994:10,14,5,3 0/0:55,0:55:99:0,169,2481:21,34,0,0 0/1:28,5:33:97:97,0,1063:9,19,5,0 +20 10132713 . T A 292.16 . AC=2;AF=0.333;AN=6;BaseQRankSum=2.289;ClippingRankSum=0.000;DP=178;ExcessHet=3.9794;MLEAC=2;MLEAF=0.333;MQ=49.79;MQRankSum=-4.605;QD=4.49;ReadPosRankSum=4.149;SOR=2.070 GT:AD:DP:GQ:PL:SB 0/1:24,8:32:99:227,0,994:10,14,5,3 0/0:55,0:55:99:0,168,2480:21,34,0,0 0/1:28,5:33:97:97,0,1062:9,19,5,0 +20 10132715 . T A 294.16 . AC=2;AF=0.333;AN=6;BaseQRankSum=0.494;ClippingRankSum=0.000;DP=171;ExcessHet=3.9794;MLEAC=2;MLEAF=0.333;MQ=49.27;MQRankSum=-4.547;QD=4.74;ReadPosRankSum=3.769;SOR=2.061 GT:AD:DP:GQ:PL:SB 0/1:22,8:30:99:231,0,951:8,14,5,3 0/0:52,0:52:99:0,168,2480:19,33,0,0 0/1:27,5:32:95:95,0,1104:8,19,5,0 +20 10132717 . T A 304.16 . AC=2;AF=0.333;AN=6;BaseQRankSum=1.754;ClippingRankSum=0.000;DP=166;ExcessHet=3.9794;MLEAC=2;MLEAF=0.333;MQ=48.91;MQRankSum=-4.478;QD=4.99;ReadPosRankSum=3.038;SOR=2.058 GT:AD:DP:GQ:PL:SB 0/1:21,8:29:99:238,0,866:8,13,5,3 0/0:50,0:50:99:0,162,2390:17,33,0,0 0/1:27,5:32:98:98,0,1061:8,19,5,0 +20 10132719 . T A 302.12 . AC=2;AF=0.333;AN=6;BaseQRankSum=2.068;ClippingRankSum=0.000;DP=162;ExcessHet=3.9794;MLEAC=2;MLEAF=0.333;MQ=49.03;MQRankSum=-4.584;QD=5.04;ReadPosRankSum=1.902;SOR=2.044 GT:AD:DP:GQ:PL:SB 0/1:21,8:29:99:241,0,812:7,12,5,3 0/0:51,0:51:99:0,162,2332:11,31,0,0 0/1:26,5:31:99:102,0,998:5,16,5,0 +20 10132722 . CAG C,GAG 2305.09 . AC=3,2;AF=0.500,0.333;AN=6;BaseQRankSum=0.772;ClippingRankSum=0.000;DP=155;ExcessHet=3.0103;MLEAC=2,2;MLEAF=0.333,0.333;MQ=48.66;MQRankSum=0.122;QD=27.12;ReadPosRankSum=0.545;SOR=0.393 GT:AD:DP:GQ:PL:SB 1/2:0,15,16:31:99:987,587,603,440,0,679:0,0,10,13 1/1:0,24,2:26:72:687,72,0,767,97,1568:0,0,5,16 0/2:8,3,17:28:99:628,583,839,0,177,591:2,6,5,4 +20 10133139 . T C 1050.13 . AC=1;AF=0.167;AN=6;BaseQRankSum=-6.774;ClippingRankSum=0.000;DP=226;ExcessHet=3.0103;MLEAC=1;MLEAF=0.167;MQ=59.55;MQRankSum=-2.276;QD=15.00;ReadPosRankSum=2.770;SOR=0.946 GT:AD:DP:GQ:PL:SB 0/0:86,0:86:99:0,259,3582:45,41,0,0 0/1:32,38:70:99:1081,0,1029:11,21,16,22 0/0:67,0:67:99:0,201,2680:33,34,0,0 +20 10134410 . AAAAGAAAG A,AAAAG 1904.12 . AC=2,2;AF=0.333,0.333;AN=6;BaseQRankSum=0.026;ClippingRankSum=0.000;DP=216;ExcessHet=3.9794;MLEAC=2,2;MLEAF=0.333,0.333;MQ=57.52;MQRankSum=0.837;QD=24.41;ReadPosRankSum=0.000;SOR=1.277 GT:AD:DP:GQ:PL:SB 1/2:0,19,10:29:99:1167,400,585,753,0,717:0,0,21,8 0/1:15,12,0:27:99:484,0,650,481,643,1113:9,6,9,3 0/2:14,0,8:22:99:294,373,2121,0,697,594:10,4,7,1 +20 10134456 . AAGAAAG A 668.09 . AC=1;AF=0.167;AN=6;BaseQRankSum=-1.140;ClippingRankSum=0.000;DP=217;ExcessHet=3.0103;MLEAC=1;MLEAF=0.167;MQ=57.66;MQRankSum=-2.912;QD=13.36;ReadPosRankSum=0.426;SOR=0.576 GT:AD:DP:GQ:PL:SB 0/0:71,0:71:99:0,213,3044:57,14,0,0 0/1:30,20:50:99:708,0,1283:21,9,15,5 0/0:78,0:78:99:0,233,3762:57,21,0,0 +20 10134479 . A C 2526.16 . AC=2;AF=0.333;AN=6;BaseQRankSum=-0.781;ClippingRankSum=0.000;DP=205;ExcessHet=3.9794;MLEAC=2;MLEAF=0.333;MQ=57.39;MQRankSum=-1.373;QD=19.74;ReadPosRankSum=-1.052;SOR=1.030 GT:AD:DP:GQ:PL:SB 0/1:36,39:75:99:1439,0,1255:28,8,32,7 0/1:22,31:53:99:1119,0,860:16,6,22,9 0/0:73,0:73:99:0,220,3447:49,24,0,0 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/HCOutputNoFSAnnotation.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/HCOutputNoFSAnnotation.vcf.idx new file mode 100644 index 0000000000000000000000000000000000000000..4d5c5e2d2fa17e1623b304861ed9c43a617d116e GIT binary patch literal 441 zcmb_Y%TB{U3^alh95``;Z-~>hQ34kfCFw(gRBDq7E=1dOTSCJw+I2wO`4GO5FJKpu zs^ZMZV_TLz8abaNcLxA)Xt=H$euapI=1L=f=IZ?kA9>R(xma<98%A5yszTzLP;o6= zRdJ0{ZE&e1Th&5SO)c^LE0VI&_{N&8Rb@g*Vk8wVn5vneXg3(g)0SRZ%H(kVJFTT~ zUaK|SUmJTCXCGe=)~>~o;V_NzVwRRSX*SBojWYZ%`CWnJ*%)HdCyuRaPpq7^C%_}>Yc>|o)1=T}f({(Zs0 zyCBfK+j`+7k#`fmzq`4*bV2(nDUaX(?^d6?m)&bQJu`2XioNG6bI-P*_mz9%``*pG qvArn1=-blkW=;Jhg8!QP-))JJHL9M=XUxDLkLFlu24=9^K?DE_;92 +##FILTER= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT FOO +20 10001292 rs1 G A 42.22 alt_allele_in_normal;panel_of_normals AF=0.50;AC=1 GT:RD:GQ 1/0:23:19.28 +20 10002963 . C G 42.22 PASS AF=0.30 GT:RD:GQ 0/1:30:33.07 +20 10005008 rs2 A T 123.78 PASS AF=1.00 GT:RD:GQ 1/1:30:8.26 +20 10044557 rs3 C T 42.22 PASS AC=2 GT:RD:GQ 0/1:31:15.01 +20 10048580 . T A 42.22 alt_allele_in_normal;panel_of_normals AF=0.75 GT:RD:GQ 1/0:33:23.49 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/annotationResourceWithFilter.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/annotationResourceWithFilter.vcf.idx new file mode 100644 index 0000000000000000000000000000000000000000..aa61b3886b48ab7477d6677c548fa45ac2abb85f GIT binary patch literal 405 zcmb_XOG*Pl5G{Wj5xhxi6x_HQG93-*2;WXGFIqfftJ!EL`H!%(jCa*;^n;Pr#8@F7J@*UP?8hS` zKFYU~E*+h47&%dS-BhZ(QRP*A-QB9ZgtJlhSHG`|u23yx(MmPl(AVbGG%v^M+Zn|1 eT~pR@0cp{B2Jn6g$1xrD9>x4KGU31C@ZcBZXk~r? literal 0 HcmV?d00001 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/empty.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/empty.vcf new file mode 100644 index 00000000000..c2732f4354e --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/empty.vcf @@ -0,0 +1,47 @@ +##fileformat=VCFv4.2 +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##contig= +##contig= +##reference=file:///Users/louisb/Workspace/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 +20 10000117 . C T 905.77 . . GT:AD:DP:GQ:PL 0/1:36,28:64:99:934,0,1248 +20 10000211 . C T 941.77 . . GT:AD:DP:GQ:PL 0/1:26,27:53:99:970,0,906 +20 10000439 . T G 2804.77 . . GT:AD:DP:GQ:PL 1/1:0,80:80:99:2833,240,0 +20 10000598 . T A 1941.77 . . GT:AD:DP:GQ:PL 1/1:0,49:49:99:1970,147,0 +20 10000694 . G A 1008.77 . . GT:AD:DP:GQ:PL 0/1:45,37:82:99:1037,0,1601 +20 10000758 . T A 3838.77 . . GT:AD:DP:GQ:PL 1/1:0,95:95:99:3867,286,0 +20 10001019 . T G 650.77 . . GT:AD:DP:GQ:PL 0/1:39,26:65:99:679,0,1426 +20 10001298 . T A 2917.77 . . GT:AD:DP:GQ:PL 1/1:0,73:73:99:2946,220,0 +20 10001436 . A AAGGCT 2301.73 . . GT:AD:DP:GQ:PL 1/1:0,50:50:99:2339,156,0 +20 10001474 . C T 2640.77 . . GT:AD:DP:GQ:PL 1/1:0,73:73:99:2669,219,0 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/exacAlleleTrim.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/exacAlleleTrim.vcf new file mode 100644 index 00000000000..0f08f93d03c --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/exacAlleleTrim.vcf @@ -0,0 +1,226 @@ +##fileformat=VCFv4.1 +##ALT= +##FILTER= +##FILTER= +##FILTER= +##FILTER= -2.632 && InbreedingCoeff >-0.8"> +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##GATKCommandLine= +##GATKCommandLine= +##GATKCommandLine= +##GATKCommandLine= -2.632 && InbreedingCoeff >-0.8, InbreedingCoeff <= -0.8] filterName=[NewCut_Filter, InbreedingCoeff_Filter] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=0 maskExtension=0 maskName=Mask filterNotInMask=false missingValuesInExpressionsShouldEvaluateAsFailing=false invalidatePreviousFilters=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false"> +##GVCFBlock=minGQ=0(inclusive),maxGQ=5(exclusive) +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##reference=file:///seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta +##source=SelectVariants +##INFO= +##INFO= +##VEP=v77 cache=/humgen/atgu1/fs03/konradk/vep/tin//homo_sapiens/77_GRCh37 db=. +##LoF_info=Info used for LoF annotation +##LoF_flags=Possible warning flags for LoF +##LoF_filter=Reason for LoF not being HC +##LoF=Loss-of-function annotation (HC = High Confidence; LC = Low Confidence) +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +#CHROM POS ID REF ALT QUAL FILTER INFO +1 26608807 . TGGGTCCAGGACAGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC TGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC,T,TGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC 252674.46 VQSRTrancheINDEL99.00to99.50 AC=404,1,1;AC_AFR=316,0,0;AC_AMR=15,0,0;AC_Adj=335,1,0;AC_EAS=0,1,0;AC_FIN=0,0,0;AC_Het=315,1,0,0,0,0;AC_Hom=10,0,0;AC_NFE=4,0,0;AC_OTH=0,0,0;AC_SAS=0,0,0;AF=3.393e-03,8.399e-06,8.399e-06;AN=119064;AN_AFR=6270;AN_AMR=7122;AN_Adj=82928;AN_EAS=4686;AN_FIN=5414;AN_NFE=51630;AN_OTH=616;AN_SAS=7190;BaseQRankSum=0.667;ClippingRankSum=-1.850e-01;DP=1077765;FS=9.660;GQ_MEAN=48.60;GQ_STDDEV=55.15;Het_AFR=296,0,0,0,0,0;Het_AMR=15,0,0,0,0,0;Het_EAS=0,1,0,0,0,0;Het_FIN=0,0,0,0,0,0;Het_NFE=4,0,0,0,0,0;Het_OTH=0,0,0,0,0,0;Het_SAS=0,0,0,0,0,0;Hom_AFR=10,0,0;Hom_AMR=0,0,0;Hom_EAS=0,0,0;Hom_FIN=0,0,0;Hom_NFE=0,0,0;Hom_OTH=0,0,0;Hom_SAS=0,0,0;InbreedingCoeff=0.0407;MQ=45.18;MQ0=0;MQRankSum=-2.259e+00;NCC=3161;QD=6.38;ReadPosRankSum=0.585;VQSLOD=-6.220e-02;culprit=FS;DP_HIST=5320|12128|7298|2808|19139|6562|2959|1212|710|403|310|231|144|97|80|36|35|11|17|32,10|51|102|91|66|34|20|5|5|4|2|0|0|0|0|0|1|0|0|0,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1|0|0|0,0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;GQ_HIST=670|5046|901|1062|11224|2270|3067|2171|816|1090|1059|402|16574|3819|1601|1978|1348|614|702|3118,1|3|1|3|0|1|1|3|7|8|5|5|5|4|7|8|6|6|3|314,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1;CSQ=-|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2250-2327||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2250_2327delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCC|||||||||||||||||||,GGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2250-2327||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2250_2327delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCCinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCC|||||||||||||||||||,GGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2250-2327||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2250_2327delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCCinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC|||||||||||||||||||,-|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1736-1813|1369-1446|457-482|GPGPSPGPGPGPSPGPGPGPSPCPGP/-|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCC/-||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1369_1446delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCC|ENSP00000363334.2:p.Gly457_Pro482del||||||||||||||||||,GGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1736-1813|1369-1446|457-482|GPGPSPGPGPGPSPGPGPGPSPCPGP/GPGPSPGPGPGPSPGPGP|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCC/GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCC||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1369_1446delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCCinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCC|ENSP00000363334.2:p.Gly475_Pro482del||||||||||||||||||,GGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1736-1813|1369-1446|457-482|GPGPSPGPGPGPSPGPGPGPSPCPGP/GPGPSPGPGPGPSPGPGPGPSP|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCC/GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1369_1446delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCCinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC|ENSP00000363334.2:p.Cys479_Pro482del||||||||||||||||||,-|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1933-2010|1468-1545|490-515|GPGPSPGPGPGPSPGPGPGPSPCPGP/-|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCC/-||2||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1468_1545delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCC|ENSP00000363339.1:p.Gly490_Pro515del||||||||||||||||||,GGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1933-2010|1468-1545|490-515|GPGPSPGPGPGPSPGPGPGPSPCPGP/GPGPSPGPGPGPSPGPGP|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCC/GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCC||3||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1468_1545delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCCinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCC|ENSP00000363339.1:p.Gly508_Pro515del||||||||||||||||||,GGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1933-2010|1468-1545|490-515|GPGPSPGPGPGPSPGPGPGPSPCPGP/GPGPSPGPGPGPSPGPGPGPSP|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCC/GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC||1||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1468_1545delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCCinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC|ENSP00000363339.1:p.Cys512_Pro515del||||||||||||||||||,-|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1445-1522|1369-1446|457-482|GPGPSPGPGPGPSPGPGPGPSPCPGP/-|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCC/-||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1369_1446delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCC|ENSP00000349601.4:p.Gly457_Pro482del||||||||||||||||||,GGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1445-1522|1369-1446|457-482|GPGPSPGPGPGPSPGPGPGPSPCPGP/GPGPSPGPGPGPSPGPGP|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCC/GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCC||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1369_1446delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCCinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCC|ENSP00000349601.4:p.Gly475_Pro482del||||||||||||||||||,GGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1445-1522|1369-1446|457-482|GPGPSPGPGPGPSPGPGPGPSPCPGP/GPGPSPGPGPGPSPGPGPGPSP|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCC/GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1369_1446delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCCinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC|ENSP00000349601.4:p.Cys479_Pro482del||||||||||||||||||,-|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1188-1265|1108-1185|370-395|GPGPSPGPGPGPSPGPGPGPSPCPGP/-|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCC/-||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1108_1185delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCC|ENSP00000324721.7:p.Gly370_Pro395del||||||||||||||||||,GGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1188-1265|1108-1185|370-395|GPGPSPGPGPGPSPGPGPGPSPCPGP/GPGPSPGPGPGPSPGPGP|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCC/GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCC||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1108_1185delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCCinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCC|ENSP00000324721.7:p.Gly388_Pro395del||||||||||||||||||,GGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1188-1265|1108-1185|370-395|GPGPSPGPGPGPSPGPGPGPSPCPGP/GPGPSPGPGPGPSPGPGPGPSP|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCC/GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1108_1185delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCCinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC|ENSP00000324721.7:p.Cys392_Pro395del||||||||||||||||||,-|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2430-2507||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2430_2507delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCC|||||||||||||||||||,GGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2430-2507||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2430_2507delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCCinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCC|||||||||||||||||||,GGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2430-2507||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2430_2507delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCCinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC|||||||||||||||||||,-|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2215-2292||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2215_2292delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCC|||||||||||||||||||,GGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2215-2292||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2215_2292delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCCinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCC|||||||||||||||||||,GGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2215-2292||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2215_2292delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCCinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC|||||||||||||||||||,-|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1682-1759|1468-1545|490-515|GPGPSPGPGPGPSPGPGPGPSPCPGP/-|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCC/-||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1468_1545delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCC|ENSP00000363338.3:p.Gly490_Pro515del||||||||||||||||||,GGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1682-1759|1468-1545|490-515|GPGPSPGPGPGPSPGPGPGPSPCPGP/GPGPSPGPGPGPSPGPGP|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCC/GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCC||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1468_1545delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCCinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCC|ENSP00000363338.3:p.Gly508_Pro515del||||||||||||||||||,GGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1682-1759|1468-1545|490-515|GPGPSPGPGPGPSPGPGPGPSPCPGP/GPGPSPGPGPGPSPGPGPGPSP|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCC/GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1468_1545delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCCinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC|ENSP00000363338.3:p.Cys512_Pro515del||||||||||||||||||,-|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2533-2610||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2533_2610delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCC|||||||||||||||||||,GGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2533-2610||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2533_2610delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCCinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCC|||||||||||||||||||,GGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2533-2610||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2533_2610delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCCinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC|||||||||||||||||||,-|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1200-1277|739-816|247-272|GPGPSPGPGPGPSPGPGPGPSPCPGP/-|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCC/-||2||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.739_816delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCC|ENSP00000363340.1:p.Gly247_Pro272del||||||||||||||||||,GGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1200-1277|739-816|247-272|GPGPSPGPGPGPSPGPGPGPSPCPGP/GPGPSPGPGPGPSPGPGP|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCC/GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCC||3||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.739_816delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCCinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCC|ENSP00000363340.1:p.Gly265_Pro272del||||||||||||||||||,GGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1200-1277|739-816|247-272|GPGPSPGPGPGPSPGPGPGPSPCPGP/GPGPSPGPGPGPSPGPGPGPSP|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCC/GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC||1||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.739_816delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGACCCinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC|ENSP00000363340.1:p.Cys269_Pro272del||||||||||||||||||,-||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||2||||||regulatory_region|||||||||||||||||||||||||||||||,GGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||3||||||regulatory_region|||||||||||||||||||||||||||||||,GGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||1||||||regulatory_region|||||||||||||||||||||||||||||||;AC_POPMAX=316,1,NA;AN_POPMAX=6270,4686,NA;POPMAX=AFR,EAS,NA +1 26608811 . TCCAGGACAGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA T,TCCGGGACCGGGACTGGGGCCGGGACCGGGA,TCCGGGACCGGGA,GCCAGGACAGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA,TCCGGGA 19760465.46 VQSRTrancheINDEL99.50to99.90 AC=35790,141,4,13,1;AC_AFR=2142,93,0,0,1;AC_AMR=2721,22,0,1,0;AC_Adj=34861,123,4,6,1;AC_EAS=1450,0,0,0,0;AC_FIN=2246,0,0,1,0;AC_Het=34861,123,4,6,1,0,0,0,0,0,0,0,0,0,0;AC_Hom=0,0,0,0,0;AC_NFE=22933,8,4,4,0;AC_OTH=266,0,0,0,0;AC_SAS=3103,0,0,0,0;AF=0.302,1.191e-03,3.378e-05,1.098e-04,8.445e-06;AN=118418;AN_AFR=6734;AN_AMR=7972;AN_Adj=93220;AN_EAS=5038;AN_FIN=5858;AN_NFE=56800;AN_OTH=718;AN_SAS=10100;BaseQRankSum=1.03;ClippingRankSum=0.526;DP=4211203;FS=48.878;GQ_MEAN=241.52;GQ_STDDEV=303.28;Het_AFR=2142,93,0,0,1,0,0,0,0,0,0,0,0,0,0;Het_AMR=2721,22,0,1,0,0,0,0,0,0,0,0,0,0,0;Het_EAS=1450,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_FIN=2246,0,0,1,0,0,0,0,0,0,0,0,0,0,0;Het_NFE=22933,8,4,4,0,0,0,0,0,0,0,0,0,0,0;Het_OTH=266,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_SAS=3103,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Hom_AFR=0,0,0,0,0;Hom_AMR=0,0,0,0,0;Hom_EAS=0,0,0,0,0;Hom_FIN=0,0,0,0,0;Hom_NFE=0,0,0,0,0;Hom_OTH=0,0,0,0,0;Hom_SAS=0,0,0,0,0;InbreedingCoeff=-0.4015;MQ=55.52;MQ0=0;MQRankSum=-2.666e+00;NCC=3595;NEGATIVE_TRAIN_SITE;QD=0.14;ReadPosRankSum=0.847;VQSLOD=-8.705e-01;culprit=FS;DP_HIST=3891|6060|2762|1573|5275|1840|977|651|653|785|1048|1257|1416|1692|1881|1922|1959|1986|1974|19607,3|58|264|580|637|501|463|465|512|657|897|1101|1229|1475|1656|1710|1781|1790|1787|18224,8|4|8|7|11|7|9|13|7|8|11|8|7|7|4|3|2|3|1|8,0|0|0|0|0|0|1|0|0|0|0|0|0|1|0|0|0|0|0|2,1|3|1|1|2|2|1|0|1|0|0|0|0|0|0|0|0|0|0|0,0|0|0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;GQ_HIST=1637|4045|1010|1173|5147|1130|1213|913|669|713|789|691|4179|1192|751|800|684|595|588|31290,173|209|227|259|235|262|249|265|290|303|300|335|320|318|346|348|371|365|379|30236,1|2|3|2|0|0|0|0|0|1|1|0|1|1|0|0|0|1|1|122,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|4,2|1|0|0|0|0|1|0|0|0|0|0|1|0|0|1|1|0|0|5,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1;CSQ=T|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2246-2324||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2246_2324delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsA|||||||||||||||||||,GCCAGGACAGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2246-2324||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2246_2324delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGC|||||||||||||||||||,TCCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2246-2324||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2246_2324delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGA|||||||||||||||||||,TCCGGGACCGGGA|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2246-2324||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2246_2324delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGTCCCGGA|||||||||||||||||||,TCCGGGA|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2246-2324||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2246_2324delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGA|||||||||||||||||||,T|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1732-1810|1365-1443|455-481|GPGPGPSPGPGPGPSPGPGPGPSPCPG/G|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGA/ggA||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1365_1443delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsA|ENSP00000363334.2:p.Pro456_Gly481del||||||||||||||||||,GCCAGGACAGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000374217|Transcript|synonymous_variant|1732-1810|1365-1443|455-481|GPGPGPSPGPGPGPSPGPGPGPSPCPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGA/ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGC||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1365_1443delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGC|ENST00000374217.2:c.1365_1443delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGC(p.%3D)||||||||||||||||||,TCCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1732-1810|1365-1443|455-481|GPGPGPSPGPGPGPSPGPGPGPSPCPG/GPGPGPSPGPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGA/ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGA||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1365_1443delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGA|ENSP00000363334.2:p.Pro466_Gly481del||||||||||||||||||,TCCGGGACCGGGA|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1732-1810|1365-1443|455-481|GPGPGPSPGPGPGPSPGPGPGPSPCPG/GPGPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGA/ggTCCCGGTCCCGGA||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1365_1443delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGTCCCGGA|ENSP00000363334.2:p.Pro460_Gly481del||||||||||||||||||,TCCGGGA|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1732-1810|1365-1443|455-481|GPGPGPSPGPGPGPSPGPGPGPSPCPG/GPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGA/ggTCCCGGA||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1365_1443delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGA|ENSP00000363334.2:p.Pro458_Gly481del||||||||||||||||||,T|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1929-2007|1464-1542|488-514|GPGPGPSPGPGPGPSPGPGPGPSPCPG/G|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGA/ggA||1||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1464_1542delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsA|ENSP00000363339.1:p.Pro489_Gly514del||||||||||||||||||,GCCAGGACAGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000374222|Transcript|synonymous_variant|1929-2007|1464-1542|488-514|GPGPGPSPGPGPGPSPGPGPGPSPCPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGA/ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGC||4||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1464_1542delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGC|ENST00000374222.1:c.1464_1542delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGC(p.%3D)||||||||||||||||||,TCCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1929-2007|1464-1542|488-514|GPGPGPSPGPGPGPSPGPGPGPSPCPG/GPGPGPSPGPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGA/ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGA||2||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1464_1542delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGA|ENSP00000363339.1:p.Pro499_Gly514del||||||||||||||||||,TCCGGGACCGGGA|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1929-2007|1464-1542|488-514|GPGPGPSPGPGPGPSPGPGPGPSPCPG/GPGPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGA/ggTCCCGGTCCCGGA||3||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1464_1542delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGTCCCGGA|ENSP00000363339.1:p.Pro493_Gly514del||||||||||||||||||,TCCGGGA|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1929-2007|1464-1542|488-514|GPGPGPSPGPGPGPSPGPGPGPSPCPG/GPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGA/ggTCCCGGA||5||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1464_1542delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGA|ENSP00000363339.1:p.Pro491_Gly514del||||||||||||||||||,T|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1441-1519|1365-1443|455-481|GPGPGPSPGPGPGPSPGPGPGPSPCPG/G|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGA/ggA||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1365_1443delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsA|ENSP00000349601.4:p.Pro456_Gly481del||||||||||||||||||,GCCAGGACAGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000357089|Transcript|synonymous_variant|1441-1519|1365-1443|455-481|GPGPGPSPGPGPGPSPGPGPGPSPCPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGA/ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGC||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1365_1443delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGC|ENST00000357089.4:c.1365_1443delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGC(p.%3D)||||||||||||||||||,TCCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1441-1519|1365-1443|455-481|GPGPGPSPGPGPGPSPGPGPGPSPCPG/GPGPGPSPGPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGA/ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGA||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1365_1443delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGA|ENSP00000349601.4:p.Pro466_Gly481del||||||||||||||||||,TCCGGGACCGGGA|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1441-1519|1365-1443|455-481|GPGPGPSPGPGPGPSPGPGPGPSPCPG/GPGPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGA/ggTCCCGGTCCCGGA||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1365_1443delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGTCCCGGA|ENSP00000349601.4:p.Pro460_Gly481del||||||||||||||||||,TCCGGGA|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1441-1519|1365-1443|455-481|GPGPGPSPGPGPGPSPGPGPGPSPCPG/GPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGA/ggTCCCGGA||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1365_1443delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGA|ENSP00000349601.4:p.Pro458_Gly481del||||||||||||||||||,T|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1184-1262|1104-1182|368-394|GPGPGPSPGPGPGPSPGPGPGPSPCPG/G|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGA/ggA||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1104_1182delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsA|ENSP00000324721.7:p.Pro369_Gly394del||||||||||||||||||,GCCAGGACAGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000314675|Transcript|synonymous_variant|1184-1262|1104-1182|368-394|GPGPGPSPGPGPGPSPGPGPGPSPCPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGA/ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGC||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1104_1182delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGC|ENST00000314675.7:c.1104_1182delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGC(p.%3D)||||||||||||||||||,TCCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1184-1262|1104-1182|368-394|GPGPGPSPGPGPGPSPGPGPGPSPCPG/GPGPGPSPGPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGA/ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGA||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1104_1182delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGA|ENSP00000324721.7:p.Pro379_Gly394del||||||||||||||||||,TCCGGGACCGGGA|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1184-1262|1104-1182|368-394|GPGPGPSPGPGPGPSPGPGPGPSPCPG/GPGPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGA/ggTCCCGGTCCCGGA||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1104_1182delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGTCCCGGA|ENSP00000324721.7:p.Pro373_Gly394del||||||||||||||||||,TCCGGGA|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1184-1262|1104-1182|368-394|GPGPGPSPGPGPGPSPGPGPGPSPCPG/GPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGA/ggTCCCGGA||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1104_1182delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGA|ENSP00000324721.7:p.Pro371_Gly394del||||||||||||||||||,T|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2426-2504||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2426_2504delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsA|||||||||||||||||||,GCCAGGACAGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2426-2504||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2426_2504delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGC|||||||||||||||||||,TCCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2426-2504||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2426_2504delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGA|||||||||||||||||||,TCCGGGACCGGGA|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2426-2504||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2426_2504delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGTCCCGGA|||||||||||||||||||,TCCGGGA|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2426-2504||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2426_2504delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGA|||||||||||||||||||,T|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2211-2289||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2211_2289delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsA|||||||||||||||||||,GCCAGGACAGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2211-2289||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2211_2289delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGC|||||||||||||||||||,TCCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2211-2289||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2211_2289delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGA|||||||||||||||||||,TCCGGGACCGGGA|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2211-2289||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2211_2289delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGTCCCGGA|||||||||||||||||||,TCCGGGA|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2211-2289||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2211_2289delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGA|||||||||||||||||||,T|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1678-1756|1464-1542|488-514|GPGPGPSPGPGPGPSPGPGPGPSPCPG/G|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGA/ggA||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1464_1542delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsA|ENSP00000363338.3:p.Pro489_Gly514del||||||||||||||||||,GCCAGGACAGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000374221|Transcript|synonymous_variant|1678-1756|1464-1542|488-514|GPGPGPSPGPGPGPSPGPGPGPSPCPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGA/ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGC||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1464_1542delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGC|ENST00000374221.3:c.1464_1542delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGC(p.%3D)||||||||||||||||||,TCCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1678-1756|1464-1542|488-514|GPGPGPSPGPGPGPSPGPGPGPSPCPG/GPGPGPSPGPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGA/ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGA||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1464_1542delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGA|ENSP00000363338.3:p.Pro499_Gly514del||||||||||||||||||,TCCGGGACCGGGA|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1678-1756|1464-1542|488-514|GPGPGPSPGPGPGPSPGPGPGPSPCPG/GPGPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGA/ggTCCCGGTCCCGGA||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1464_1542delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGTCCCGGA|ENSP00000363338.3:p.Pro493_Gly514del||||||||||||||||||,TCCGGGA|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1678-1756|1464-1542|488-514|GPGPGPSPGPGPGPSPGPGPGPSPCPG/GPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGA/ggTCCCGGA||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1464_1542delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGA|ENSP00000363338.3:p.Pro491_Gly514del||||||||||||||||||,T|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2529-2607||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2529_2607delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsA|||||||||||||||||||,GCCAGGACAGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2529-2607||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2529_2607delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGC|||||||||||||||||||,TCCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2529-2607||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2529_2607delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGA|||||||||||||||||||,TCCGGGACCGGGA|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2529-2607||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2529_2607delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGTCCCGGA|||||||||||||||||||,TCCGGGA|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2529-2607||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2529_2607delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGA|||||||||||||||||||,T|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1196-1274|735-813|245-271|GPGPGPSPGPGPGPSPGPGPGPSPCPG/G|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGA/ggA||1||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.735_813delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsA|ENSP00000363340.1:p.Pro246_Gly271del||||||||||||||||||,GCCAGGACAGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000374223|Transcript|synonymous_variant|1196-1274|735-813|245-271|GPGPGPSPGPGPGPSPGPGPGPSPCPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGA/ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGC||4||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.735_813delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGC|ENST00000374223.1:c.735_813delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGC(p.%3D)||||||||||||||||||,TCCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1196-1274|735-813|245-271|GPGPGPSPGPGPGPSPGPGPGPSPCPG/GPGPGPSPGPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGA/ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGA||2||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.735_813delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGA|ENSP00000363340.1:p.Pro256_Gly271del||||||||||||||||||,TCCGGGACCGGGA|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1196-1274|735-813|245-271|GPGPGPSPGPGPGPSPGPGPGPSPCPG/GPGPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGA/ggTCCCGGTCCCGGA||3||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.735_813delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGTCCCGGA|ENSP00000363340.1:p.Pro250_Gly271del||||||||||||||||||,TCCGGGA|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1196-1274|735-813|245-271|GPGPGPSPGPGPGPSPGPGPGPSPCPG/GPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGA/ggTCCCGGA||5||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.735_813delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGGAinsTCCCGGA|ENSP00000363340.1:p.Pro248_Gly271del||||||||||||||||||,T||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||1||||||regulatory_region|||||||||||||||||||||||||||||||,GCCAGGACAGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||4||||||regulatory_region|||||||||||||||||||||||||||||||,TCCGGGACCGGGACTGGGGCCGGGACCGGGA||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||2||||||regulatory_region|||||||||||||||||||||||||||||||,TCCGGGACCGGGA||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||3||||||regulatory_region|||||||||||||||||||||||||||||||,TCCGGGA||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||5||||||regulatory_region|||||||||||||||||||||||||||||||;AC_POPMAX=22933,93,4,1,1;AN_POPMAX=56800,6734,56800,5858,6734;POPMAX=NFE,AFR,NFE,FIN,AFR +1 26608814 . AGGACAGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG GGGACAGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG,A,AGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG,AGGACCGGGACTGGGGCCGGGACCGGGACCG,AGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG,AGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG 52526951.62 InbreedingCoeff_Filter AC=62792,54,2,5,2,1;AC_AFR=4039,3,0,0,0,0;AC_AMR=4358,10,0,0,0,0;AC_Adj=48156,46,2,4,2,1;AC_EAS=2559,20,2,4,0,1;AC_FIN=3156,2,0,0,0,0;AC_Het=39953,37,2,4,0,1,9,0,0,2,0,0,0,0,0,0,0,0,0,0,0;AC_Hom=4096,0,0,0,0,0;AC_NFE=29190,1,0,0,1,0;AC_OTH=370,0,0,0,0,0;AC_SAS=4484,10,0,0,1,0;AF=0.538,4.626e-04,1.713e-05,4.284e-05,1.713e-05,8.567e-06;AN=116724;AN_AFR=6892;AN_AMR=8426;AN_Adj=89850;AN_EAS=5390;AN_FIN=5734;AN_NFE=54302;AN_OTH=678;AN_SAS=8428;BaseQRankSum=-4.850e-01;ClippingRankSum=-4.330e-01;DP=1211393;FS=4.698;GQ_MEAN=491.61;GQ_STDDEV=582.85;Het_AFR=2752,2,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_AMR=3779,9,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_EAS=2299,18,2,4,0,1,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_FIN=2565,1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_NFE=24881,1,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0;Het_OTH=302,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_SAS=3375,6,0,0,0,0,4,0,0,1,0,0,0,0,0,0,0,0,0,0,0;Hom_AFR=643,0,0,0,0,0;Hom_AMR=289,0,0,0,0,0;Hom_EAS=129,0,0,0,0,0;Hom_FIN=295,0,0,0,0,0;Hom_NFE=2154,0,0,0,0,0;Hom_OTH=34,0,0,0,0,0;Hom_SAS=552,0,0,0,0,0;InbreedingCoeff=-0.5921;MQ=53.23;MQ0=0;MQRankSum=1.54;NCC=5053;NEGATIVE_TRAIN_SITE;QD=30.86;ReadPosRankSum=-4.190e-01;VQSLOD=3.42;culprit=MQRankSum;DP_HIST=3459|7848|9861|11298|9387|6155|3576|2110|1276|823|623|453|326|268|206|169|96|79|58|275,2680|6559|9151|10915|9003|5936|3494|2072|1245|802|610|447|314|258|197|153|87|63|36|148,0|1|5|4|3|1|0|1|0|2|2|1|3|2|1|4|5|3|2|14,0|0|0|0|0|0|0|0|0|0|0|1|0|1|0|0|0|0|0|0,0|0|0|0|0|0|0|1|0|1|1|0|1|0|1|0|0|0|0|0,0|0|1|0|0|0|0|0|1|0|0|0|0|0|0|0|0|0|0|0,0|0|0|0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;GQ_HIST=2491|1518|1105|1448|1714|964|898|746|585|586|567|439|589|497|387|424|428|340|350|42286,503|1019|952|1306|1171|874|824|683|541|539|530|403|398|439|362|384|413|329|340|42170,0|2|1|4|6|2|0|4|2|3|4|3|2|5|1|2|1|1|1|10,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|2,0|0|1|0|0|1|1|0|0|0|0|0|0|0|0|0|0|0|0|2,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|2,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1;CSQ=A|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2243-2321||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2243_2321delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsT|||||||||||||||||||,AGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2243-2321||||||6||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2243_2321delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCT|||||||||||||||||||,GGGACAGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2243-2321||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2243_2321delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCC|||||||||||||||||||,AGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2243-2321||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2243_2321delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCT|||||||||||||||||||,AGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2243-2321||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2243_2321delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCT|||||||||||||||||||,AGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2243-2321||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2243_2321delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCT|||||||||||||||||||,A|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1729-1807|1362-1440|454-480|PGPGPGPSPGPGPGPSPGPGPGPSPCP/P|ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCT/ccT||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1362_1440delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsT|ENSP00000363334.2:p.Gly455_Pro480del||||||||||||||||||,AGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1729-1807|1362-1440|454-480|PGPGPGPSPGPGPGPSPGPGPGPSPCP/PGPGPGPSPGPGPGPSPGPGP|ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCT/ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCT||6||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1362_1440delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCT|ENSP00000363334.2:p.Gly475_Pro480del||||||||||||||||||,GGGACAGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000374217|Transcript|synonymous_variant|1729-1807|1362-1440|454-480|PGPGPGPSPGPGPGPSPGPGPGPSPCP|ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCT/ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCC||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1362_1440delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCC|ENST00000374217.2:c.1362_1440delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCC(p.%3D)||||||||||||||||||,AGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1729-1807|1362-1440|454-480|PGPGPGPSPGPGPGPSPGPGPGPSPCP/PGPGPGPSPGPGP|ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCT/ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCT||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1362_1440delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCT|ENSP00000363334.2:p.Gly467_Pro480del||||||||||||||||||,AGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1729-1807|1362-1440|454-480|PGPGPGPSPGPGPGPSPGPGPGPSPCP/PGPGPGPSPGP|ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCT/ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCT||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1362_1440delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCT|ENSP00000363334.2:p.Gly465_Pro480del||||||||||||||||||,AGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1729-1807|1362-1440|454-480|PGPGPGPSPGPGPGPSPGPGPGPSPCP/PGPGPGPSPGPGPGPSPGP|ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCT/ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCT||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1362_1440delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCT|ENSP00000363334.2:p.Gly473_Pro480del||||||||||||||||||,A|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1926-2004|1461-1539|487-513|PGPGPGPSPGPGPGPSPGPGPGPSPCP/P|ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCT/ccT||2||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1461_1539delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsT|ENSP00000363339.1:p.Gly488_Pro513del||||||||||||||||||,AGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1926-2004|1461-1539|487-513|PGPGPGPSPGPGPGPSPGPGPGPSPCP/PGPGPGPSPGPGPGPSPGPGP|ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCT/ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCT||6||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1461_1539delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCT|ENSP00000363339.1:p.Gly508_Pro513del||||||||||||||||||,GGGACAGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000374222|Transcript|synonymous_variant|1926-2004|1461-1539|487-513|PGPGPGPSPGPGPGPSPGPGPGPSPCP|ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCT/ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCC||1||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1461_1539delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCC|ENST00000374222.1:c.1461_1539delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCC(p.%3D)||||||||||||||||||,AGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1926-2004|1461-1539|487-513|PGPGPGPSPGPGPGPSPGPGPGPSPCP/PGPGPGPSPGPGP|ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCT/ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCT||5||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1461_1539delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCT|ENSP00000363339.1:p.Gly500_Pro513del||||||||||||||||||,AGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1926-2004|1461-1539|487-513|PGPGPGPSPGPGPGPSPGPGPGPSPCP/PGPGPGPSPGP|ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCT/ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCT||4||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1461_1539delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCT|ENSP00000363339.1:p.Gly498_Pro513del||||||||||||||||||,AGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1926-2004|1461-1539|487-513|PGPGPGPSPGPGPGPSPGPGPGPSPCP/PGPGPGPSPGPGPGPSPGP|ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCT/ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCT||3||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1461_1539delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCT|ENSP00000363339.1:p.Gly506_Pro513del||||||||||||||||||,A|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1438-1516|1362-1440|454-480|PGPGPGPSPGPGPGPSPGPGPGPSPCP/P|ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCT/ccT||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1362_1440delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsT|ENSP00000349601.4:p.Gly455_Pro480del||||||||||||||||||,AGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1438-1516|1362-1440|454-480|PGPGPGPSPGPGPGPSPGPGPGPSPCP/PGPGPGPSPGPGPGPSPGPGP|ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCT/ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCT||6||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1362_1440delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCT|ENSP00000349601.4:p.Gly475_Pro480del||||||||||||||||||,GGGACAGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000357089|Transcript|synonymous_variant|1438-1516|1362-1440|454-480|PGPGPGPSPGPGPGPSPGPGPGPSPCP|ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCT/ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCC||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1362_1440delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCC|ENST00000357089.4:c.1362_1440delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCC(p.%3D)||||||||||||||||||,AGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1438-1516|1362-1440|454-480|PGPGPGPSPGPGPGPSPGPGPGPSPCP/PGPGPGPSPGPGP|ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCT/ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCT||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1362_1440delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCT|ENSP00000349601.4:p.Gly467_Pro480del||||||||||||||||||,AGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1438-1516|1362-1440|454-480|PGPGPGPSPGPGPGPSPGPGPGPSPCP/PGPGPGPSPGP|ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCT/ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCT||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1362_1440delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCT|ENSP00000349601.4:p.Gly465_Pro480del||||||||||||||||||,AGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1438-1516|1362-1440|454-480|PGPGPGPSPGPGPGPSPGPGPGPSPCP/PGPGPGPSPGPGPGPSPGP|ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCT/ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCT||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1362_1440delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCT|ENSP00000349601.4:p.Gly473_Pro480del||||||||||||||||||,A|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1181-1259|1101-1179|367-393|PGPGPGPSPGPGPGPSPGPGPGPSPCP/P|ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCT/ccT||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1101_1179delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsT|ENSP00000324721.7:p.Gly368_Pro393del||||||||||||||||||,AGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1181-1259|1101-1179|367-393|PGPGPGPSPGPGPGPSPGPGPGPSPCP/PGPGPGPSPGPGPGPSPGPGP|ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCT/ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCT||6||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1101_1179delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCT|ENSP00000324721.7:p.Gly388_Pro393del||||||||||||||||||,GGGACAGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000314675|Transcript|synonymous_variant|1181-1259|1101-1179|367-393|PGPGPGPSPGPGPGPSPGPGPGPSPCP|ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCT/ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCC||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1101_1179delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCC|ENST00000314675.7:c.1101_1179delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCC(p.%3D)||||||||||||||||||,AGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1181-1259|1101-1179|367-393|PGPGPGPSPGPGPGPSPGPGPGPSPCP/PGPGPGPSPGPGP|ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCT/ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCT||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1101_1179delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCT|ENSP00000324721.7:p.Gly380_Pro393del||||||||||||||||||,AGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1181-1259|1101-1179|367-393|PGPGPGPSPGPGPGPSPGPGPGPSPCP/PGPGPGPSPGP|ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCT/ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCT||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1101_1179delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCT|ENSP00000324721.7:p.Gly378_Pro393del||||||||||||||||||,AGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1181-1259|1101-1179|367-393|PGPGPGPSPGPGPGPSPGPGPGPSPCP/PGPGPGPSPGPGPGPSPGP|ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCT/ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCT||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1101_1179delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCT|ENSP00000324721.7:p.Gly386_Pro393del||||||||||||||||||,A|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2423-2501||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2423_2501delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsT|||||||||||||||||||,AGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2423-2501||||||6||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2423_2501delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCT|||||||||||||||||||,GGGACAGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2423-2501||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2423_2501delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCC|||||||||||||||||||,AGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2423-2501||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2423_2501delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCT|||||||||||||||||||,AGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2423-2501||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2423_2501delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCT|||||||||||||||||||,AGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2423-2501||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2423_2501delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCT|||||||||||||||||||,A|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2208-2286||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2208_2286delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsT|||||||||||||||||||,AGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2208-2286||||||6||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2208_2286delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCT|||||||||||||||||||,GGGACAGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2208-2286||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2208_2286delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCC|||||||||||||||||||,AGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2208-2286||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2208_2286delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCT|||||||||||||||||||,AGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2208-2286||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2208_2286delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCT|||||||||||||||||||,AGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2208-2286||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2208_2286delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCT|||||||||||||||||||,A|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1675-1753|1461-1539|487-513|PGPGPGPSPGPGPGPSPGPGPGPSPCP/P|ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCT/ccT||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1461_1539delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsT|ENSP00000363338.3:p.Gly488_Pro513del||||||||||||||||||,AGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1675-1753|1461-1539|487-513|PGPGPGPSPGPGPGPSPGPGPGPSPCP/PGPGPGPSPGPGPGPSPGPGP|ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCT/ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCT||6||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1461_1539delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCT|ENSP00000363338.3:p.Gly508_Pro513del||||||||||||||||||,GGGACAGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000374221|Transcript|synonymous_variant|1675-1753|1461-1539|487-513|PGPGPGPSPGPGPGPSPGPGPGPSPCP|ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCT/ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCC||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1461_1539delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCC|ENST00000374221.3:c.1461_1539delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCC(p.%3D)||||||||||||||||||,AGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1675-1753|1461-1539|487-513|PGPGPGPSPGPGPGPSPGPGPGPSPCP/PGPGPGPSPGPGP|ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCT/ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCT||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1461_1539delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCT|ENSP00000363338.3:p.Gly500_Pro513del||||||||||||||||||,AGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1675-1753|1461-1539|487-513|PGPGPGPSPGPGPGPSPGPGPGPSPCP/PGPGPGPSPGP|ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCT/ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCT||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1461_1539delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCT|ENSP00000363338.3:p.Gly498_Pro513del||||||||||||||||||,AGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1675-1753|1461-1539|487-513|PGPGPGPSPGPGPGPSPGPGPGPSPCP/PGPGPGPSPGPGPGPSPGP|ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCT/ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCT||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1461_1539delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCT|ENSP00000363338.3:p.Gly506_Pro513del||||||||||||||||||,A|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2526-2604||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2526_2604delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsT|||||||||||||||||||,AGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2526-2604||||||6||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2526_2604delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCT|||||||||||||||||||,GGGACAGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2526-2604||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2526_2604delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCC|||||||||||||||||||,AGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2526-2604||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2526_2604delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCT|||||||||||||||||||,AGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2526-2604||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2526_2604delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCT|||||||||||||||||||,AGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2526-2604||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2526_2604delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCT|||||||||||||||||||,A|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1193-1271|732-810|244-270|PGPGPGPSPGPGPGPSPGPGPGPSPCP/P|ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCT/ccT||2||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.732_810delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsT|ENSP00000363340.1:p.Gly245_Pro270del||||||||||||||||||,AGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1193-1271|732-810|244-270|PGPGPGPSPGPGPGPSPGPGPGPSPCP/PGPGPGPSPGPGPGPSPGPGP|ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCT/ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCT||6||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.732_810delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCT|ENSP00000363340.1:p.Gly265_Pro270del||||||||||||||||||,GGGACAGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000374223|Transcript|synonymous_variant|1193-1271|732-810|244-270|PGPGPGPSPGPGPGPSPGPGPGPSPCP|ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCT/ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCC||1||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.732_810delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCC|ENST00000374223.1:c.732_810delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCC(p.%3D)||||||||||||||||||,AGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1193-1271|732-810|244-270|PGPGPGPSPGPGPGPSPGPGPGPSPCP/PGPGPGPSPGPGP|ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCT/ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCT||5||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.732_810delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCT|ENSP00000363340.1:p.Gly257_Pro270del||||||||||||||||||,AGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1193-1271|732-810|244-270|PGPGPGPSPGPGPGPSPGPGPGPSPCP/PGPGPGPSPGP|ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCT/ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCT||4||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.732_810delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCT|ENSP00000363340.1:p.Gly255_Pro270del||||||||||||||||||,AGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1193-1271|732-810|244-270|PGPGPGPSPGPGPGPSPGPGPGPSPCP/PGPGPGPSPGPGPGPSPGP|ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCT/ccCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCT||3||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.732_810delCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTinsCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCT|ENSP00000363340.1:p.Gly263_Pro270del||||||||||||||||||,A||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||2||||||regulatory_region|||||||||||||||||||||||||||||||,AGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||6||||||regulatory_region|||||||||||||||||||||||||||||||,GGGACAGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||1||||||regulatory_region|||||||||||||||||||||||||||||||,AGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||5||||||regulatory_region|||||||||||||||||||||||||||||||,AGGACCGGGACTGGGGCCGGGACCGGGACCG||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||4||||||regulatory_region|||||||||||||||||||||||||||||||,AGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCG||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||3||||||regulatory_region|||||||||||||||||||||||||||||||;AC_POPMAX=4039,20,2,4,1,1;AN_POPMAX=6892,5390,5390,5390,8428,5390;POPMAX=AFR,EAS,EAS,EAS,SAS,EAS +1 26608815 . GGACAGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGA G 1913.95 VQSRTrancheINDEL99.00to99.50 AC=3;AC_AFR=0;AC_AMR=0;AC_Adj=3;AC_EAS=2;AC_FIN=0;AC_Het=3;AC_Hom=0;AC_NFE=1;AC_OTH=0;AC_SAS=0;AF=8.538e-05;AN=35138;AN_AFR=2218;AN_AMR=3084;AN_Adj=20902;AN_EAS=2696;AN_FIN=1026;AN_NFE=8062;AN_OTH=142;AN_SAS=3674;BaseQRankSum=-9.380e-01;ClippingRankSum=0.747;DP=290729;FS=0.906;GQ_MEAN=36.72;GQ_STDDEV=29.60;Het_AFR=0;Het_AMR=0;Het_EAS=2;Het_FIN=0;Het_NFE=1;Het_OTH=0;Het_SAS=0;Hom_AFR=0;Hom_AMR=0;Hom_EAS=0;Hom_FIN=0;Hom_NFE=0;Hom_OTH=0;Hom_SAS=0;InbreedingCoeff=-0.0198;MQ=45.47;MQ0=0;MQRankSum=0.207;NCC=65498;QD=0.35;ReadPosRankSum=0.747;VQSLOD=-7.004e-01;culprit=InbreedingCoeff;DP_HIST=2893|3830|2468|2197|2057|1610|1013|585|360|210|133|68|44|37|26|9|9|3|5|12,0|0|0|0|0|0|0|0|0|0|0|0|0|1|0|1|0|0|0|1;GQ_HIST=496|2768|770|1075|2811|766|977|848|381|560|479|248|2255|1081|404|526|324|120|162|518,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|3;CSQ=-|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2252-2319||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2252_2319delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTC|||||||||||||||||||,-|ENSG00000158062|ENST00000374217|Transcript|frameshift_variant&feature_truncation|1738-1805|1371-1438|457-480|GPGPSPGPGPGPSPGPGPGPSPCP/GX|ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCct/ggct||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1371_1438delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTC|ENSP00000363334.2:p.Pro458TrpfsTer?|||||||||||||||POSITION:0.98224043715847&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,-|ENSG00000158062|ENST00000374222|Transcript|frameshift_variant&feature_truncation|1935-2002|1470-1537|490-513|GPGPSPGPGPGPSPGPGPGPSPCP/GX|ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCct/ggct||1||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1470_1537delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTC|ENSP00000363339.1:p.Pro491TrpfsTer?|||||||||||||||POSITION:0.983365323096609&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,-|ENSG00000158062|ENST00000357089|Transcript|frameshift_variant&feature_truncation|1447-1514|1371-1438|457-480|GPGPSPGPGPGPSPGPGPGPSPCP/GX|ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCct/ggct||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1371_1438delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTC|ENSP00000349601.4:p.Pro458TrpfsTer?|||||||||||||||POSITION:0.98224043715847&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,-|ENSG00000158062|ENST00000314675|Transcript|frameshift_variant&feature_truncation|1190-1257|1110-1177|370-393|GPGPSPGPGPGPSPGPGPGPSPCP/GX|ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCct/ggct||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1110_1177delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTC|ENSP00000324721.7:p.Pro371TrpfsTer142|||||||||||||||POSITION:0.978387364921031&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,-|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2432-2499||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2432_2499delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTC|||||||||||||||||||,-|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2217-2284||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2217_2284delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTC|||||||||||||||||||,-|ENSG00000158062|ENST00000374221|Transcript|frameshift_variant&feature_truncation|1684-1751|1470-1537|490-513|GPGPSPGPGPGPSPGPGPGPSPCP/GX|ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCct/ggct||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1470_1537delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTC|ENSP00000363338.3:p.Pro491TrpfsTer?|||||||||||||||POSITION:0.983365323096609&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,-|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2535-2602||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2535_2602delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTC|||||||||||||||||||,-|ENSG00000158062|ENST00000374223|Transcript|frameshift_variant&feature_truncation|1202-1269|741-808|247-270|GPGPSPGPGPGPSPGPGPGPSPCP/GX|ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCct/ggct||1||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.741_808delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTC|ENSP00000363340.1:p.Pro248TrpfsTer?|||||||||||||||POSITION:0.968824940047962&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,-||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||1||||||regulatory_region|||||||||||||||||||||||||||||||;AC_POPMAX=2;AN_POPMAX=2696;POPMAX=EAS +1 26608819 . AGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC AGGGACTGGGGCCGGGACC,AGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC,CGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC,AGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC,A,AGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC 407990.66 VQSRTrancheINDEL99.50to99.90 AC=66,1564,49,32,7,35;AC_AFR=1,24,0,0,0,0;AC_AMR=14,61,0,4,0,0;AC_Adj=55,1276,39,26,6,34;AC_EAS=0,279,37,15,3,34;AC_FIN=0,48,0,0,0,0;AC_Het=54,1216,38,24,6,34,1,0,0,0,0,1,2,0,0,0,0,0,0,0,0;AC_Hom=0,28,0,0,0,0;AC_NFE=3,468,0,0,1,0;AC_OTH=0,3,1,0,0,0;AC_SAS=37,393,1,7,2,0;AF=1.677e-03,0.040,1.245e-03,8.131e-04,1.779e-04,8.894e-04;AN=39354;AN_AFR=2038;AN_AMR=1606;AN_Adj=19634;AN_EAS=1592;AN_FIN=1048;AN_NFE=9186;AN_OTH=174;AN_SAS=3990;BaseQRankSum=0.441;ClippingRankSum=-5.060e-01;DP=359799;FS=0.000;GQ_MEAN=41.13;GQ_STDDEV=71.92;Het_AFR=1,24,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_AMR=14,61,0,4,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_EAS=0,265,36,14,3,34,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0;Het_FIN=0,48,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_NFE=3,458,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_OTH=0,3,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_SAS=36,357,1,6,2,0,1,0,0,0,0,0,1,0,0,0,0,0,0,0,0;Hom_AFR=0,0,0,0,0,0;Hom_AMR=0,0,0,0,0,0;Hom_EAS=0,6,0,0,0,0;Hom_FIN=0,0,0,0,0,0;Hom_NFE=0,5,0,0,0,0;Hom_OTH=0,0,0,0,0,0;Hom_SAS=0,17,0,0,0,0;InbreedingCoeff=0.2033;MQ=54.25;MQ0=0;MQRankSum=1.78;NCC=62391;NEGATIVE_TRAIN_SITE;QD=0.91;ReadPosRankSum=-1.067e+00;VQSLOD=-9.233e-01;culprit=QD;DP_HIST=2567|3461|2935|3029|2633|1955|1269|685|410|252|155|104|67|42|42|15|17|7|11|21,4|5|6|3|2|2|4|5|5|7|5|5|5|3|2|1|1|0|1|0,27|113|253|321|288|175|111|69|46|31|19|19|12|6|5|4|2|2|3|3,0|9|17|12|2|5|1|0|2|0|1|0|0|0|0|0|0|0|0|0,1|4|1|1|6|8|3|2|1|1|0|0|2|1|0|0|0|0|0|0,0|0|1|0|2|0|0|1|0|0|0|0|0|0|0|1|0|2|0|0,0|1|2|2|7|7|5|3|3|1|0|2|0|0|2|0|0|0|0|0;GQ_HIST=4230|2675|753|729|2294|666|734|491|272|373|327|212|2047|946|381|440|281|153|189|1484,1|0|0|2|0|0|0|0|0|2|3|0|0|0|1|0|0|0|0|57,27|40|25|41|44|42|32|24|34|33|39|32|29|28|32|38|36|35|36|862,1|1|0|0|0|0|0|0|2|5|0|2|3|2|0|1|3|0|1|28,0|0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|30,0|0|0|1|0|1|1|0|0|0|0|0|0|0|0|0|0|0|1|3,0|0|0|0|0|0|0|0|0|1|2|0|1|1|0|0|0|0|0|30;CSQ=A|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2250-2316||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2250_2316delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsT|||||||||||||||||||,AGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2250-2316||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2250_2316delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCT|||||||||||||||||||,AGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2250-2316||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2250_2316delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCT|||||||||||||||||||,CGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2250-2316||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2250_2316delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCG|||||||||||||||||||,AGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2250-2316||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2250_2316delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCT|||||||||||||||||||,AGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2250-2316||||||6||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2250_2316delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCT|||||||||||||||||||,A|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1736-1802|1369-1435|457-479|GPGPSPGPGPGPSPGPGPGPSPC/C|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt/Tgt||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1369_1435delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsT|ENSP00000363334.2:p.Gly457_Pro478del||||||||||||||||||,AGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1736-1802|1369-1435|457-479|GPGPSPGPGPGPSPGPGPGPSPC/GPGPSPGPGPGPSPC|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt/GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1369_1435delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCT|ENSP00000363334.2:p.Gly471_Pro478del||||||||||||||||||,AGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1736-1802|1369-1435|457-479|GPGPSPGPGPGPSPGPGPGPSPC/GPGPSPC|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt/GGTCCCGGCCCCAGTCCCTgt||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1369_1435delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCT|ENSP00000363334.2:p.Gly463_Pro478del||||||||||||||||||,CGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000374217|Transcript|missense_variant|1736-1802|1369-1435|457-479|GPGPSPGPGPGPSPGPGPGPSPC/GPGPSPGPGPGPSPGPGPGPSPG|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt/GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1369_1435delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCG|ENSP00000363334.2:p.Cys479Gly||||||||||||||||||,AGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1736-1802|1369-1435|457-479|GPGPSPGPGPGPSPGPGPGPSPC/GPGPSPGPGPGPSPGPC|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt/GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCTgt||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1369_1435delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCT|ENSP00000363334.2:p.Gly473_Pro478del||||||||||||||||||,AGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1736-1802|1369-1435|457-479|GPGPSPGPGPGPSPGPGPGPSPC/GPGPSPGPGPGPSPGPGPC|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt/GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCTgt||6||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1369_1435delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCT|ENSP00000363334.2:p.Gly475_Pro478del||||||||||||||||||,A|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1933-1999|1468-1534|490-512|GPGPSPGPGPGPSPGPGPGPSPC/C|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt/Tgt||5||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1468_1534delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsT|ENSP00000363339.1:p.Gly490_Pro511del||||||||||||||||||,AGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1933-1999|1468-1534|490-512|GPGPSPGPGPGPSPGPGPGPSPC/GPGPSPGPGPGPSPC|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt/GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt||2||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1468_1534delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCT|ENSP00000363339.1:p.Gly504_Pro511del||||||||||||||||||,AGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1933-1999|1468-1534|490-512|GPGPSPGPGPGPSPGPGPGPSPC/GPGPSPC|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt/GGTCCCGGCCCCAGTCCCTgt||1||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1468_1534delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCT|ENSP00000363339.1:p.Gly496_Pro511del||||||||||||||||||,CGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000374222|Transcript|missense_variant|1933-1999|1468-1534|490-512|GPGPSPGPGPGPSPGPGPGPSPC/GPGPSPGPGPGPSPGPGPGPSPG|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt/GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt||3||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1468_1534delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCG|ENSP00000363339.1:p.Cys512Gly||||||||||||||||||,AGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1933-1999|1468-1534|490-512|GPGPSPGPGPGPSPGPGPGPSPC/GPGPSPGPGPGPSPGPC|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt/GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCTgt||4||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1468_1534delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCT|ENSP00000363339.1:p.Gly506_Pro511del||||||||||||||||||,AGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1933-1999|1468-1534|490-512|GPGPSPGPGPGPSPGPGPGPSPC/GPGPSPGPGPGPSPGPGPC|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt/GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCTgt||6||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1468_1534delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCT|ENSP00000363339.1:p.Gly508_Pro511del||||||||||||||||||,A|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1445-1511|1369-1435|457-479|GPGPSPGPGPGPSPGPGPGPSPC/C|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt/Tgt||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1369_1435delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsT|ENSP00000349601.4:p.Gly457_Pro478del||||||||||||||||||,AGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1445-1511|1369-1435|457-479|GPGPSPGPGPGPSPGPGPGPSPC/GPGPSPGPGPGPSPC|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt/GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1369_1435delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCT|ENSP00000349601.4:p.Gly471_Pro478del||||||||||||||||||,AGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1445-1511|1369-1435|457-479|GPGPSPGPGPGPSPGPGPGPSPC/GPGPSPC|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt/GGTCCCGGCCCCAGTCCCTgt||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1369_1435delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCT|ENSP00000349601.4:p.Gly463_Pro478del||||||||||||||||||,CGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000357089|Transcript|missense_variant|1445-1511|1369-1435|457-479|GPGPSPGPGPGPSPGPGPGPSPC/GPGPSPGPGPGPSPGPGPGPSPG|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt/GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1369_1435delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCG|ENSP00000349601.4:p.Cys479Gly||||||||||||||||||,AGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1445-1511|1369-1435|457-479|GPGPSPGPGPGPSPGPGPGPSPC/GPGPSPGPGPGPSPGPC|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt/GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCTgt||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1369_1435delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCT|ENSP00000349601.4:p.Gly473_Pro478del||||||||||||||||||,AGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1445-1511|1369-1435|457-479|GPGPSPGPGPGPSPGPGPGPSPC/GPGPSPGPGPGPSPGPGPC|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt/GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCTgt||6||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1369_1435delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCT|ENSP00000349601.4:p.Gly475_Pro478del||||||||||||||||||,A|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1188-1254|1108-1174|370-392|GPGPSPGPGPGPSPGPGPGPSPC/C|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt/Tgt||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1108_1174delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsT|ENSP00000324721.7:p.Gly370_Pro391del||||||||||||||||||,AGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1188-1254|1108-1174|370-392|GPGPSPGPGPGPSPGPGPGPSPC/GPGPSPGPGPGPSPC|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt/GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1108_1174delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCT|ENSP00000324721.7:p.Gly384_Pro391del||||||||||||||||||,AGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1188-1254|1108-1174|370-392|GPGPSPGPGPGPSPGPGPGPSPC/GPGPSPC|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt/GGTCCCGGCCCCAGTCCCTgt||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1108_1174delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCT|ENSP00000324721.7:p.Gly376_Pro391del||||||||||||||||||,CGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000314675|Transcript|missense_variant|1188-1254|1108-1174|370-392|GPGPSPGPGPGPSPGPGPGPSPC/GPGPSPGPGPGPSPGPGPGPSPG|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt/GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1108_1174delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCG|ENSP00000324721.7:p.Cys392Gly||||||||||||||||||,AGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1188-1254|1108-1174|370-392|GPGPSPGPGPGPSPGPGPGPSPC/GPGPSPGPGPGPSPGPC|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt/GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCTgt||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1108_1174delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCT|ENSP00000324721.7:p.Gly386_Pro391del||||||||||||||||||,AGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1188-1254|1108-1174|370-392|GPGPSPGPGPGPSPGPGPGPSPC/GPGPSPGPGPGPSPGPGPC|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt/GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCTgt||6||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1108_1174delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCT|ENSP00000324721.7:p.Gly388_Pro391del||||||||||||||||||,A|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2430-2496||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2430_2496delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsT|||||||||||||||||||,AGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2430-2496||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2430_2496delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCT|||||||||||||||||||,AGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2430-2496||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2430_2496delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCT|||||||||||||||||||,CGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2430-2496||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2430_2496delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCG|||||||||||||||||||,AGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2430-2496||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2430_2496delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCT|||||||||||||||||||,AGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2430-2496||||||6||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2430_2496delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCT|||||||||||||||||||,A|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2215-2281||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2215_2281delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsT|||||||||||||||||||,AGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2215-2281||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2215_2281delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCT|||||||||||||||||||,AGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2215-2281||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2215_2281delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCT|||||||||||||||||||,CGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2215-2281||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2215_2281delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCG|||||||||||||||||||,AGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2215-2281||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2215_2281delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCT|||||||||||||||||||,AGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2215-2281||||||6||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2215_2281delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCT|||||||||||||||||||,A|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1682-1748|1468-1534|490-512|GPGPSPGPGPGPSPGPGPGPSPC/C|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt/Tgt||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1468_1534delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsT|ENSP00000363338.3:p.Gly490_Pro511del||||||||||||||||||,AGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1682-1748|1468-1534|490-512|GPGPSPGPGPGPSPGPGPGPSPC/GPGPSPGPGPGPSPC|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt/GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1468_1534delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCT|ENSP00000363338.3:p.Gly504_Pro511del||||||||||||||||||,AGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1682-1748|1468-1534|490-512|GPGPSPGPGPGPSPGPGPGPSPC/GPGPSPC|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt/GGTCCCGGCCCCAGTCCCTgt||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1468_1534delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCT|ENSP00000363338.3:p.Gly496_Pro511del||||||||||||||||||,CGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000374221|Transcript|missense_variant|1682-1748|1468-1534|490-512|GPGPSPGPGPGPSPGPGPGPSPC/GPGPSPGPGPGPSPGPGPGPSPG|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt/GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1468_1534delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCG|ENSP00000363338.3:p.Cys512Gly||||||||||||||||||,AGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1682-1748|1468-1534|490-512|GPGPSPGPGPGPSPGPGPGPSPC/GPGPSPGPGPGPSPGPC|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt/GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCTgt||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1468_1534delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCT|ENSP00000363338.3:p.Gly506_Pro511del||||||||||||||||||,AGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1682-1748|1468-1534|490-512|GPGPSPGPGPGPSPGPGPGPSPC/GPGPSPGPGPGPSPGPGPC|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt/GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCTgt||6||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1468_1534delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCT|ENSP00000363338.3:p.Gly508_Pro511del||||||||||||||||||,A|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2533-2599||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2533_2599delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsT|||||||||||||||||||,AGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2533-2599||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2533_2599delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCT|||||||||||||||||||,AGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2533-2599||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2533_2599delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCT|||||||||||||||||||,CGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2533-2599||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2533_2599delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCG|||||||||||||||||||,AGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2533-2599||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2533_2599delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCT|||||||||||||||||||,AGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2533-2599||||||6||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2533_2599delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCT|||||||||||||||||||,A|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1200-1266|739-805|247-269|GPGPSPGPGPGPSPGPGPGPSPC/C|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt/Tgt||5||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.739_805delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsT|ENSP00000363340.1:p.Gly247_Pro268del||||||||||||||||||,AGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1200-1266|739-805|247-269|GPGPSPGPGPGPSPGPGPGPSPC/GPGPSPGPGPGPSPC|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt/GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt||2||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.739_805delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCT|ENSP00000363340.1:p.Gly261_Pro268del||||||||||||||||||,AGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1200-1266|739-805|247-269|GPGPSPGPGPGPSPGPGPGPSPC/GPGPSPC|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt/GGTCCCGGCCCCAGTCCCTgt||1||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.739_805delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCT|ENSP00000363340.1:p.Gly253_Pro268del||||||||||||||||||,CGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000374223|Transcript|missense_variant|1200-1266|739-805|247-269|GPGPSPGPGPGPSPGPGPGPSPC/GPGPSPGPGPGPSPGPGPGPSPG|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt/GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt||3||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.739_805delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCG|ENSP00000363340.1:p.Cys269Gly||||||||||||||||||,AGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1200-1266|739-805|247-269|GPGPSPGPGPGPSPGPGPGPSPC/GPGPSPGPGPGPSPGPC|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt/GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCTgt||4||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.739_805delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCT|ENSP00000363340.1:p.Gly263_Pro268del||||||||||||||||||,AGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1200-1266|739-805|247-269|GPGPSPGPGPGPSPGPGPGPSPC/GPGPSPGPGPGPSPGPGPC|GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt/GGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCTgt||6||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.739_805delGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTinsGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCT|ENSP00000363340.1:p.Gly265_Pro268del||||||||||||||||||,A||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||5||||||regulatory_region|||||||||||||||||||||||||||||||,AGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||2||||||regulatory_region|||||||||||||||||||||||||||||||,AGGGACTGGGGCCGGGACC||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||1||||||regulatory_region|||||||||||||||||||||||||||||||,CGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||3||||||regulatory_region|||||||||||||||||||||||||||||||,AGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||4||||||regulatory_region|||||||||||||||||||||||||||||||,AGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACC||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||6||||||regulatory_region|||||||||||||||||||||||||||||||;AC_POPMAX=37,279,37,15,3,34;AN_POPMAX=3990,1592,1592,1592,1592,1592;POPMAX=SAS,EAS,EAS,EAS,EAS,EAS +1 26608829 . GCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGA GCCGGGACTGGGGCCGGGA,TCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGA,G,GCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGA,GCCGGGACCGGGACTGGGGCCGGGA,ACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGA 807223.87 PASS AC=120,436,446,5,218,4;AC_AFR=85,342,41,0,7,0;AC_AMR=8,18,6,4,186,0;AC_Adj=95,368,247,4,208,3;AC_EAS=0,0,3,0,2,0;AC_FIN=0,0,9,0,2,0;AC_Het=86,342,242,4,208,3,4,1,0,0,0,0,0,0,0,0,0,0,0,0,0;AC_Hom=2,11,2,0,0,0;AC_NFE=1,7,125,0,7,2;AC_OTH=0,0,4,0,3,0;AC_SAS=1,1,59,0,1,1;AF=4.426e-03,0.016,0.016,1.844e-04,8.041e-03,1.475e-04;AN=27110;AN_AFR=2344;AN_AMR=3178;AN_Adj=15938;AN_EAS=2298;AN_FIN=564;AN_NFE=4548;AN_OTH=106;AN_SAS=2900;BaseQRankSum=0.143;ClippingRankSum=0.00;DP=273738;FS=0.000;GQ_MEAN=64.21;GQ_STDDEV=179.73;Het_AFR=76,316,40,0,7,0,4,1,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_AMR=8,18,6,4,186,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_EAS=0,0,3,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_FIN=0,0,9,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_NFE=1,7,123,0,7,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_OTH=0,0,4,0,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_SAS=1,1,57,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Hom_AFR=2,11,0,0,0,0;Hom_AMR=0,0,0,0,0,0;Hom_EAS=0,0,0,0,0,0;Hom_FIN=0,0,0,0,0,0;Hom_NFE=0,0,1,0,0,0;Hom_OTH=0,0,0,0,0,0;Hom_SAS=0,0,1,0,0,0;InbreedingCoeff=0.2480;MQ=50.97;MQ0=0;MQRankSum=-1.380e+00;NCC=72295;QD=1.88;ReadPosRankSum=0.533;VQSLOD=1.35;culprit=QD;DP_HIST=1659|1968|1661|1782|2204|1616|1057|563|371|243|158|96|50|44|25|15|10|4|3|26,7|12|15|9|1|12|18|10|9|2|5|4|2|0|2|2|1|0|0|3,12|50|96|90|68|24|28|16|9|10|6|4|2|2|2|1|0|0|0|2,49|117|110|56|30|13|3|5|0|4|6|5|2|5|1|4|0|2|0|7,0|1|2|2|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0,2|5|2|5|9|16|26|28|32|28|23|15|5|11|4|2|0|1|0|2,0|1|0|0|1|1|0|0|0|1|0|0|0|0|0|0|0|0|0|0;GQ_HIST=1555|2049|469|465|2138|754|880|582|281|316|188|63|1499|578|199|212|128|67|66|1066,1|1|1|2|3|0|1|0|0|1|0|0|0|0|0|1|0|0|1|102,5|3|0|3|1|3|0|2|5|2|5|1|4|3|6|5|4|7|4|359,13|10|6|6|8|10|6|13|4|7|7|8|14|9|7|8|9|12|9|253,1|0|0|0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|3,0|0|2|3|0|0|0|0|0|0|0|0|0|0|0|1|0|0|0|210,0|0|0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|3;CSQ=ACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2252-2306||||||6||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2252_2306delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGT|||||||||||||||||||,GCCGGGACCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2252-2306||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2252_2306delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGC|||||||||||||||||||,GCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_elongation|2252-2306||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2252_2306delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC|||||||||||||||||||,TCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2252-2306||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2252_2306delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGA|||||||||||||||||||,G|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2252-2306||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2252_2306delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsC|||||||||||||||||||,GCCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2252-2306||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2252_2306delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGC|||||||||||||||||||,ACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000374217|Transcript|synonymous_variant|1738-1792|1371-1425|457-475|GPGPSPGPGPGPSPGPGPG|ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGT||6||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1371_1425delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGT|ENST00000374217.2:c.1371_1425delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGT(p.%3D)||||||||||||||||||,GCCGGGACCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1738-1792|1371-1425|457-475|GPGPSPGPGPGPSPGPGPG/GPGPSPGPG|ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGCCCCAGTCCCGGTCCCGGC||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1371_1425delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGC|ENSP00000363334.2:p.Pro466_Gly475del||||||||||||||||||,GCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000374217|Transcript|inframe_insertion|1738-1792|1371-1425|457-475|GPGPSPGPGPGPSPGPGPG/GPGPSPGPGPGPSPGPGPGPGPSPGPGPG|ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1371_1425delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC|ENSP00000363334.2:p.Gly475_Pro476insProGlyProSerProGlyProGlyProGly||||||||||||||||||,TCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000374217|Transcript|synonymous_variant|1738-1792|1371-1425|457-475|GPGPSPGPGPGPSPGPGPG|ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGA||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1371_1425delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGA|ENST00000374217.2:c.1371_1425delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGA(p.%3D)||||||||||||||||||,G|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1738-1792|1371-1425|457-475|GPGPSPGPGPGPSPGPGPG/G|ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggC||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1371_1425delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsC|ENSP00000363334.2:p.Pro458_Gly475del||||||||||||||||||,GCCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1738-1792|1371-1425|457-475|GPGPSPGPGPGPSPGPGPG/GPGPSPG|ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGCCCCAGTCCCGGC||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1371_1425delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGC|ENSP00000363334.2:p.Pro464_Gly475del||||||||||||||||||,ACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000374222|Transcript|synonymous_variant|1935-1989|1470-1524|490-508|GPGPSPGPGPGPSPGPGPG|ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGT||6||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1470_1524delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGT|ENST00000374222.1:c.1470_1524delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGT(p.%3D)||||||||||||||||||,GCCGGGACCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1935-1989|1470-1524|490-508|GPGPSPGPGPGPSPGPGPG/GPGPSPGPG|ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGCCCCAGTCCCGGTCCCGGC||5||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1470_1524delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGC|ENSP00000363339.1:p.Pro499_Gly508del||||||||||||||||||,GCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000374222|Transcript|inframe_insertion|1935-1989|1470-1524|490-508|GPGPSPGPGPGPSPGPGPG/GPGPSPGPGPGPSPGPGPGPGPSPGPGPG|ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC||4||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1470_1524delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC|ENSP00000363339.1:p.Gly508_Pro509insProGlyProSerProGlyProGlyProGly||||||||||||||||||,TCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000374222|Transcript|synonymous_variant|1935-1989|1470-1524|490-508|GPGPSPGPGPGPSPGPGPG|ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGA||2||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1470_1524delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGA|ENST00000374222.1:c.1470_1524delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGA(p.%3D)||||||||||||||||||,G|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1935-1989|1470-1524|490-508|GPGPSPGPGPGPSPGPGPG/G|ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggC||3||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1470_1524delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsC|ENSP00000363339.1:p.Pro491_Gly508del||||||||||||||||||,GCCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1935-1989|1470-1524|490-508|GPGPSPGPGPGPSPGPGPG/GPGPSPG|ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGCCCCAGTCCCGGC||1||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1470_1524delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGC|ENSP00000363339.1:p.Pro497_Gly508del||||||||||||||||||,ACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000357089|Transcript|synonymous_variant|1447-1501|1371-1425|457-475|GPGPSPGPGPGPSPGPGPG|ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGT||6||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1371_1425delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGT|ENST00000357089.4:c.1371_1425delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGT(p.%3D)||||||||||||||||||,GCCGGGACCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1447-1501|1371-1425|457-475|GPGPSPGPGPGPSPGPGPG/GPGPSPGPG|ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGCCCCAGTCCCGGTCCCGGC||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1371_1425delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGC|ENSP00000349601.4:p.Pro466_Gly475del||||||||||||||||||,GCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000357089|Transcript|inframe_insertion|1447-1501|1371-1425|457-475|GPGPSPGPGPGPSPGPGPG/GPGPSPGPGPGPSPGPGPGPGPSPGPGPG|ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1371_1425delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC|ENSP00000349601.4:p.Gly475_Pro476insProGlyProSerProGlyProGlyProGly||||||||||||||||||,TCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000357089|Transcript|synonymous_variant|1447-1501|1371-1425|457-475|GPGPSPGPGPGPSPGPGPG|ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGA||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1371_1425delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGA|ENST00000357089.4:c.1371_1425delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGA(p.%3D)||||||||||||||||||,G|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1447-1501|1371-1425|457-475|GPGPSPGPGPGPSPGPGPG/G|ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggC||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1371_1425delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsC|ENSP00000349601.4:p.Pro458_Gly475del||||||||||||||||||,GCCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1447-1501|1371-1425|457-475|GPGPSPGPGPGPSPGPGPG/GPGPSPG|ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGCCCCAGTCCCGGC||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1371_1425delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGC|ENSP00000349601.4:p.Pro464_Gly475del||||||||||||||||||,ACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000314675|Transcript|synonymous_variant|1190-1244|1110-1164|370-388|GPGPSPGPGPGPSPGPGPG|ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGT||6||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1110_1164delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGT|ENST00000314675.7:c.1110_1164delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGT(p.%3D)||||||||||||||||||,GCCGGGACCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1190-1244|1110-1164|370-388|GPGPSPGPGPGPSPGPGPG/GPGPSPGPG|ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGCCCCAGTCCCGGTCCCGGC||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1110_1164delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGC|ENSP00000324721.7:p.Pro379_Gly388del||||||||||||||||||,GCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000314675|Transcript|inframe_insertion|1190-1244|1110-1164|370-388|GPGPSPGPGPGPSPGPGPG/GPGPSPGPGPGPSPGPGPGPGPSPGPGPG|ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1110_1164delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC|ENSP00000324721.7:p.Gly388_Pro389insProGlyProSerProGlyProGlyProGly||||||||||||||||||,TCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000314675|Transcript|synonymous_variant|1190-1244|1110-1164|370-388|GPGPSPGPGPGPSPGPGPG|ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGA||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1110_1164delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGA|ENST00000314675.7:c.1110_1164delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGA(p.%3D)||||||||||||||||||,G|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1190-1244|1110-1164|370-388|GPGPSPGPGPGPSPGPGPG/G|ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggC||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1110_1164delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsC|ENSP00000324721.7:p.Pro371_Gly388del||||||||||||||||||,GCCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1190-1244|1110-1164|370-388|GPGPSPGPGPGPSPGPGPG/GPGPSPG|ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGCCCCAGTCCCGGC||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1110_1164delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGC|ENSP00000324721.7:p.Pro377_Gly388del||||||||||||||||||,ACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2432-2486||||||6||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2432_2486delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGT|||||||||||||||||||,GCCGGGACCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2432-2486||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2432_2486delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGC|||||||||||||||||||,GCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_elongation|2432-2486||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2432_2486delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC|||||||||||||||||||,TCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2432-2486||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2432_2486delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGA|||||||||||||||||||,G|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2432-2486||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2432_2486delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsC|||||||||||||||||||,GCCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2432-2486||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2432_2486delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGC|||||||||||||||||||,ACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2217-2271||||||6||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2217_2271delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGT|||||||||||||||||||,GCCGGGACCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2217-2271||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2217_2271delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGC|||||||||||||||||||,GCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_elongation|2217-2271||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2217_2271delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC|||||||||||||||||||,TCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2217-2271||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2217_2271delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGA|||||||||||||||||||,G|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2217-2271||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2217_2271delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsC|||||||||||||||||||,GCCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2217-2271||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2217_2271delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGC|||||||||||||||||||,ACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000374221|Transcript|synonymous_variant|1684-1738|1470-1524|490-508|GPGPSPGPGPGPSPGPGPG|ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGT||6||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1470_1524delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGT|ENST00000374221.3:c.1470_1524delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGT(p.%3D)||||||||||||||||||,GCCGGGACCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1684-1738|1470-1524|490-508|GPGPSPGPGPGPSPGPGPG/GPGPSPGPG|ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGCCCCAGTCCCGGTCCCGGC||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1470_1524delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGC|ENSP00000363338.3:p.Pro499_Gly508del||||||||||||||||||,GCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000374221|Transcript|inframe_insertion|1684-1738|1470-1524|490-508|GPGPSPGPGPGPSPGPGPG/GPGPSPGPGPGPSPGPGPGPGPSPGPGPG|ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1470_1524delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC|ENSP00000363338.3:p.Gly508_Pro509insProGlyProSerProGlyProGlyProGly||||||||||||||||||,TCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000374221|Transcript|synonymous_variant|1684-1738|1470-1524|490-508|GPGPSPGPGPGPSPGPGPG|ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGA||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1470_1524delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGA|ENST00000374221.3:c.1470_1524delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGA(p.%3D)||||||||||||||||||,G|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1684-1738|1470-1524|490-508|GPGPSPGPGPGPSPGPGPG/G|ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggC||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1470_1524delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsC|ENSP00000363338.3:p.Pro491_Gly508del||||||||||||||||||,GCCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1684-1738|1470-1524|490-508|GPGPSPGPGPGPSPGPGPG/GPGPSPG|ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGCCCCAGTCCCGGC||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1470_1524delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGC|ENSP00000363338.3:p.Pro497_Gly508del||||||||||||||||||,ACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2535-2589||||||6||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2535_2589delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGT|||||||||||||||||||,GCCGGGACCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2535-2589||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2535_2589delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGC|||||||||||||||||||,GCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_elongation|2535-2589||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2535_2589delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC|||||||||||||||||||,TCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2535-2589||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2535_2589delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGA|||||||||||||||||||,G|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2535-2589||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2535_2589delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsC|||||||||||||||||||,GCCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2535-2589||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2535_2589delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGC|||||||||||||||||||,ACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000374223|Transcript|synonymous_variant|1202-1256|741-795|247-265|GPGPSPGPGPGPSPGPGPG|ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGT||6||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.741_795delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGT|ENST00000374223.1:c.741_795delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGT(p.%3D)||||||||||||||||||,GCCGGGACCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1202-1256|741-795|247-265|GPGPSPGPGPGPSPGPGPG/GPGPSPGPG|ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGCCCCAGTCCCGGTCCCGGC||5||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.741_795delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGC|ENSP00000363340.1:p.Pro256_Gly265del||||||||||||||||||,GCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000374223|Transcript|inframe_insertion|1202-1256|741-795|247-265|GPGPSPGPGPGPSPGPGPG/GPGPSPGPGPGPSPGPGPGPGPSPGPGPG|ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC||4||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.741_795delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC|ENSP00000363340.1:p.Gly265_Pro266insProGlyProSerProGlyProGlyProGly||||||||||||||||||,TCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000374223|Transcript|synonymous_variant|1202-1256|741-795|247-265|GPGPSPGPGPGPSPGPGPG|ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGA||2||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.741_795delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGA|ENST00000374223.1:c.741_795delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGA(p.%3D)||||||||||||||||||,G|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1202-1256|741-795|247-265|GPGPSPGPGPGPSPGPGPG/G|ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggC||3||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.741_795delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsC|ENSP00000363340.1:p.Pro248_Gly265del||||||||||||||||||,GCCGGGACTGGGGCCGGGA|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1202-1256|741-795|247-265|GPGPSPGPGPGPSPGPGPG/GPGPSPG|ggTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGCCCCAGTCCCGGC||1||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.741_795delTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGCCCCAGTCCCGGC|ENSP00000363340.1:p.Pro254_Gly265del||||||||||||||||||,ACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGA||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||6||||||regulatory_region|||||||||||||||||||||||||||||||,GCCGGGACCGGGACTGGGGCCGGGA||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||5||||||regulatory_region|||||||||||||||||||||||||||||||,GCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGA||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||4||||||regulatory_region|||||||||||||||||||||||||||||||,TCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGA||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||2||||||regulatory_region|||||||||||||||||||||||||||||||,G||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||3||||||regulatory_region|||||||||||||||||||||||||||||||,GCCGGGACTGGGGCCGGGA||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||1||||||regulatory_region|||||||||||||||||||||||||||||||;AC_POPMAX=85,342,125,4,186,2;AN_POPMAX=2344,2344,4548,3178,3178,4548;POPMAX=AFR,AFR,NFE,AMR,AMR,NFE +1 26608835 . ACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG AGCCGGGACCGGGACCGGGACTGGGG,AG,A,ACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG,ACCGGGACCGGGACCGGGACTGGGG,CCCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG 38602123.63 VQSRTrancheINDEL97.00to99.00 AC=37610,13,29,5,29,1;AC_AFR=2240,2,1,0,3,0;AC_AMR=3141,0,9,0,2,0;AC_Adj=33957,13,27,4,24,1;AC_EAS=1923,0,7,4,1,0;AC_FIN=2236,0,0,0,0,0;AC_Het=33308,11,25,3,24,1,2,2,1,0,0,0,0,0,0,0,0,0,0,0,0;AC_Hom=322,0,0,0,0,0;AC_NFE=21528,9,8,0,9,1;AC_OTH=246,0,0,0,0,0;AC_SAS=2643,2,2,0,9,0;AF=0.370,1.279e-04,2.852e-04,4.918e-05,2.852e-04,9.836e-06;AN=101666;AN_AFR=6150;AN_AMR=9434;AN_Adj=84284;AN_EAS=6472;AN_FIN=5064;AN_NFE=48432;AN_OTH=600;AN_SAS=8132;BaseQRankSum=-2.980e-01;ClippingRankSum=-6.500e-01;DP=1614162;FS=7.389;GQ_MEAN=500.40;GQ_STDDEV=643.62;Het_AFR=2191,1,1,0,3,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_AMR=3129,0,9,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_EAS=1914,0,7,3,1,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0;Het_FIN=2150,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_NFE=21052,9,6,0,9,1,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_OTH=244,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_SAS=2628,1,2,0,9,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Hom_AFR=24,0,0,0,0,0;Hom_AMR=6,0,0,0,0,0;Hom_EAS=4,0,0,0,0,0;Hom_FIN=43,0,0,0,0,0;Hom_NFE=237,0,0,0,0,0;Hom_OTH=1,0,0,0,0,0;Hom_SAS=7,0,0,0,0,0;InbreedingCoeff=-0.4744;MQ=54.51;MQ0=0;MQRankSum=2.25;NCC=15893;NEGATIVE_TRAIN_SITE;QD=3.52;ReadPosRankSum=0.867;VQSLOD=0.317;culprit=FS;DP_HIST=2013|3722|3246|4020|6452|6956|6384|4997|3665|2626|1822|1224|825|611|426|345|290|223|193|793,500|1946|1913|2484|3896|4950|4936|4180|3136|2300|1624|1094|758|573|408|336|278|217|190|779,0|0|2|1|0|0|2|0|1|1|1|1|0|1|3|0|0|0|0|0,0|1|0|0|1|0|1|5|4|1|3|2|2|1|0|0|2|1|0|5,0|0|0|1|0|0|3|0|0|1|0|0|0|0|0|0|0|0|0|0,0|3|0|2|2|3|8|2|4|3|0|0|0|0|0|0|2|0|0|0,0|0|0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;GQ_HIST=2121|2077|721|749|2429|963|1049|736|558|588|461|389|2108|823|461|489|388|294|330|33099,108|164|198|269|314|272|289|204|220|207|200|199|196|188|177|203|191|179|201|32519,0|0|0|0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|12,1|0|0|0|0|0|0|0|0|0|1|0|0|0|0|1|0|0|1|25,0|0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1|0|3,0|1|1|0|0|1|0|1|0|0|1|0|0|0|0|1|0|0|0|23,0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0|0|0|0|0;CSQ=ACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_elongation|2258-2300||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2258_2300delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT|||||||||||||||||||,A|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2258-2300||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2258_2300delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsT|||||||||||||||||||,AG|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2258-2300||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2258_2300delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCT|||||||||||||||||||,AGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2258-2300||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2258_2300delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGCT|||||||||||||||||||,CCCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2258-2300||||||6||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2258_2300delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGG|||||||||||||||||||,ACCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2258-2300||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2258_2300delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGT|||||||||||||||||||,ACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000374217|Transcript|inframe_insertion|1744-1786|1377-1419|459-473|GPSPGPGPGPSPGPG/GPSPGPGPGPSPGPGPSPGPGPGPSPGPG|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT/ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1377_1419delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT|ENSP00000363334.2:p.Gly473_Pro474insProSerProGlyProGlyProGlyProSerProGlyProGly||||||||||||||||||,A|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1744-1786|1377-1419|459-473|GPSPGPGPGPSPGPG/G|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT/ggT||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1377_1419delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsT|ENSP00000363334.2:p.Pro460_Gly473del||||||||||||||||||,AG|ENSG00000158062|ENST00000374217|Transcript|frameshift_variant&feature_truncation|1744-1786|1377-1419|459-473|GPSPGPGPGPSPGPG/GX|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT/ggCT||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1377_1419delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCT|ENSP00000363334.2:p.Pro460SerfsTer?|||||||||||||||POSITION:0.969262295081967&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,AGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000374217|Transcript|frameshift_variant&feature_truncation|1744-1786|1377-1419|459-473|GPSPGPGPGPSPGPG/GPSPGPGPGX|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT/ggCCCCAGTCCCGGTCCCGGTCCCGGCT||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1377_1419delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGCT|ENSP00000363334.2:p.Pro468SerfsTer?|||||||||||||||POSITION:0.969262295081967&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,CCCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000374217|Transcript|synonymous_variant|1744-1786|1377-1419|459-473|GPSPGPGPGPSPGPG|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT/ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGG||6||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1377_1419delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGG|ENST00000374217.2:c.1377_1419delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGG(p.%3D)||||||||||||||||||,ACCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1744-1786|1377-1419|459-473|GPSPGPGPGPSPGPG/GPSPGPGPG|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT/ggCCCCAGTCCCGGTCCCGGTCCCGGT||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1377_1419delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGT|ENSP00000363334.2:p.Pro468_Gly473del||||||||||||||||||,ACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000374222|Transcript|inframe_insertion|1941-1983|1476-1518|492-506|GPSPGPGPGPSPGPG/GPSPGPGPGPSPGPGPSPGPGPGPSPGPG|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT/ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT||4||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1476_1518delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT|ENSP00000363339.1:p.Gly506_Pro507insProSerProGlyProGlyProGlyProSerProGlyProGly||||||||||||||||||,A|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1941-1983|1476-1518|492-506|GPSPGPGPGPSPGPG/G|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT/ggT||3||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1476_1518delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsT|ENSP00000363339.1:p.Pro493_Gly506del||||||||||||||||||,AG|ENSG00000158062|ENST00000374222|Transcript|frameshift_variant&feature_truncation|1941-1983|1476-1518|492-506|GPSPGPGPGPSPGPG/GX|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT/ggCT||2||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1476_1518delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCT|ENSP00000363339.1:p.Pro493SerfsTer?|||||||||||||||POSITION:0.971209213051823&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,AGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000374222|Transcript|frameshift_variant&feature_truncation|1941-1983|1476-1518|492-506|GPSPGPGPGPSPGPG/GPSPGPGPGX|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT/ggCCCCAGTCCCGGTCCCGGTCCCGGCT||1||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1476_1518delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGCT|ENSP00000363339.1:p.Pro501SerfsTer?|||||||||||||||POSITION:0.971209213051823&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,CCCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000374222|Transcript|synonymous_variant|1941-1983|1476-1518|492-506|GPSPGPGPGPSPGPG|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT/ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGG||6||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1476_1518delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGG|ENST00000374222.1:c.1476_1518delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGG(p.%3D)||||||||||||||||||,ACCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1941-1983|1476-1518|492-506|GPSPGPGPGPSPGPG/GPSPGPGPG|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT/ggCCCCAGTCCCGGTCCCGGTCCCGGT||5||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1476_1518delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGT|ENSP00000363339.1:p.Pro501_Gly506del||||||||||||||||||,ACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000357089|Transcript|inframe_insertion|1453-1495|1377-1419|459-473|GPSPGPGPGPSPGPG/GPSPGPGPGPSPGPGPSPGPGPGPSPGPG|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT/ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1377_1419delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT|ENSP00000349601.4:p.Gly473_Pro474insProSerProGlyProGlyProGlyProSerProGlyProGly||||||||||||||||||,A|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1453-1495|1377-1419|459-473|GPSPGPGPGPSPGPG/G|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT/ggT||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1377_1419delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsT|ENSP00000349601.4:p.Pro460_Gly473del||||||||||||||||||,AG|ENSG00000158062|ENST00000357089|Transcript|frameshift_variant&feature_truncation|1453-1495|1377-1419|459-473|GPSPGPGPGPSPGPG/GX|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT/ggCT||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1377_1419delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCT|ENSP00000349601.4:p.Pro460SerfsTer?|||||||||||||||POSITION:0.969262295081967&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,AGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000357089|Transcript|frameshift_variant&feature_truncation|1453-1495|1377-1419|459-473|GPSPGPGPGPSPGPG/GPSPGPGPGX|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT/ggCCCCAGTCCCGGTCCCGGTCCCGGCT||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1377_1419delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGCT|ENSP00000349601.4:p.Pro468SerfsTer?|||||||||||||||POSITION:0.969262295081967&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,CCCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000357089|Transcript|synonymous_variant|1453-1495|1377-1419|459-473|GPSPGPGPGPSPGPG|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT/ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGG||6||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1377_1419delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGG|ENST00000357089.4:c.1377_1419delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGG(p.%3D)||||||||||||||||||,ACCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1453-1495|1377-1419|459-473|GPSPGPGPGPSPGPG/GPSPGPGPG|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT/ggCCCCAGTCCCGGTCCCGGTCCCGGT||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1377_1419delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGT|ENSP00000349601.4:p.Pro468_Gly473del||||||||||||||||||,ACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000314675|Transcript|inframe_insertion|1196-1238|1116-1158|372-386|GPSPGPGPGPSPGPG/GPSPGPGPGPSPGPGPSPGPGPGPSPGPG|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT/ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1116_1158delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT|ENSP00000324721.7:p.Gly386_Pro387insProSerProGlyProGlyProGlyProSerProGlyProGly||||||||||||||||||,A|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1196-1238|1116-1158|372-386|GPSPGPGPGPSPGPG/G|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT/ggT||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1116_1158delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsT|ENSP00000324721.7:p.Pro373_Gly386del||||||||||||||||||,AG|ENSG00000158062|ENST00000314675|Transcript|frameshift_variant&feature_truncation|1196-1238|1116-1158|372-386|GPSPGPGPGPSPGPG/GX|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT/ggCT||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1116_1158delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCT|ENSP00000324721.7:p.Pro373SerfsTer149|||||||||||||||POSITION:0.962593516209476&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,AGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000314675|Transcript|frameshift_variant&feature_truncation|1196-1238|1116-1158|372-386|GPSPGPGPGPSPGPG/GPSPGPGPGX|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT/ggCCCCAGTCCCGGTCCCGGTCCCGGCT||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1116_1158delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGCT|ENSP00000324721.7:p.Pro381SerfsTer149|||||||||||||||POSITION:0.962593516209476&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,CCCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000314675|Transcript|synonymous_variant|1196-1238|1116-1158|372-386|GPSPGPGPGPSPGPG|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT/ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGG||6||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1116_1158delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGG|ENST00000314675.7:c.1116_1158delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGG(p.%3D)||||||||||||||||||,ACCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1196-1238|1116-1158|372-386|GPSPGPGPGPSPGPG/GPSPGPGPG|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT/ggCCCCAGTCCCGGTCCCGGTCCCGGT||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1116_1158delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGT|ENSP00000324721.7:p.Pro381_Gly386del||||||||||||||||||,ACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_elongation|2438-2480||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2438_2480delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT|||||||||||||||||||,A|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2438-2480||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2438_2480delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsT|||||||||||||||||||,AG|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2438-2480||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2438_2480delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCT|||||||||||||||||||,AGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2438-2480||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2438_2480delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGCT|||||||||||||||||||,CCCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2438-2480||||||6||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2438_2480delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGG|||||||||||||||||||,ACCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2438-2480||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2438_2480delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGT|||||||||||||||||||,ACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_elongation|2223-2265||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2223_2265delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT|||||||||||||||||||,A|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2223-2265||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2223_2265delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsT|||||||||||||||||||,AG|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2223-2265||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2223_2265delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCT|||||||||||||||||||,AGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2223-2265||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2223_2265delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGCT|||||||||||||||||||,CCCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2223-2265||||||6||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2223_2265delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGG|||||||||||||||||||,ACCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2223-2265||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2223_2265delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGT|||||||||||||||||||,ACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000374221|Transcript|inframe_insertion|1690-1732|1476-1518|492-506|GPSPGPGPGPSPGPG/GPSPGPGPGPSPGPGPSPGPGPGPSPGPG|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT/ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1476_1518delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT|ENSP00000363338.3:p.Gly506_Pro507insProSerProGlyProGlyProGlyProSerProGlyProGly||||||||||||||||||,A|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1690-1732|1476-1518|492-506|GPSPGPGPGPSPGPG/G|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT/ggT||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1476_1518delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsT|ENSP00000363338.3:p.Pro493_Gly506del||||||||||||||||||,AG|ENSG00000158062|ENST00000374221|Transcript|frameshift_variant&feature_truncation|1690-1732|1476-1518|492-506|GPSPGPGPGPSPGPG/GX|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT/ggCT||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1476_1518delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCT|ENSP00000363338.3:p.Pro493SerfsTer?|||||||||||||||POSITION:0.971209213051823&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,AGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000374221|Transcript|frameshift_variant&feature_truncation|1690-1732|1476-1518|492-506|GPSPGPGPGPSPGPG/GPSPGPGPGX|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT/ggCCCCAGTCCCGGTCCCGGTCCCGGCT||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1476_1518delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGCT|ENSP00000363338.3:p.Pro501SerfsTer?|||||||||||||||POSITION:0.971209213051823&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,CCCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000374221|Transcript|synonymous_variant|1690-1732|1476-1518|492-506|GPSPGPGPGPSPGPG|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT/ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGG||6||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1476_1518delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGG|ENST00000374221.3:c.1476_1518delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGG(p.%3D)||||||||||||||||||,ACCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1690-1732|1476-1518|492-506|GPSPGPGPGPSPGPG/GPSPGPGPG|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT/ggCCCCAGTCCCGGTCCCGGTCCCGGT||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1476_1518delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGT|ENSP00000363338.3:p.Pro501_Gly506del||||||||||||||||||,ACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_elongation|2541-2583||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2541_2583delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT|||||||||||||||||||,A|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2541-2583||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2541_2583delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsT|||||||||||||||||||,AG|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2541-2583||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2541_2583delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCT|||||||||||||||||||,AGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2541-2583||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2541_2583delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGCT|||||||||||||||||||,CCCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2541-2583||||||6||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2541_2583delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGG|||||||||||||||||||,ACCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2541-2583||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2541_2583delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGT|||||||||||||||||||,ACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000374223|Transcript|inframe_insertion|1208-1250|747-789|249-263|GPSPGPGPGPSPGPG/GPSPGPGPGPSPGPGPSPGPGPGPSPGPG|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT/ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT||4||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.747_789delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT|ENSP00000363340.1:p.Gly263_Pro264insProSerProGlyProGlyProGlyProSerProGlyProGly||||||||||||||||||,A|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1208-1250|747-789|249-263|GPSPGPGPGPSPGPG/G|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT/ggT||3||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.747_789delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsT|ENSP00000363340.1:p.Pro250_Gly263del||||||||||||||||||,AG|ENSG00000158062|ENST00000374223|Transcript|frameshift_variant&feature_truncation|1208-1250|747-789|249-263|GPSPGPGPGPSPGPG/GX|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT/ggCT||2||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.747_789delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCT|ENSP00000363340.1:p.Pro250SerfsTer?|||||||||||||||POSITION:0.946043165467626&PHYLOCSF_TOO_SHORT|||HC,AGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000374223|Transcript|frameshift_variant&feature_truncation|1208-1250|747-789|249-263|GPSPGPGPGPSPGPG/GPSPGPGPGX|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT/ggCCCCAGTCCCGGTCCCGGTCCCGGCT||1||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.747_789delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGCT|ENSP00000363340.1:p.Pro258SerfsTer?|||||||||||||||POSITION:0.946043165467626&PHYLOCSF_TOO_SHORT|||HC,CCCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000374223|Transcript|synonymous_variant|1208-1250|747-789|249-263|GPSPGPGPGPSPGPG|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT/ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGG||6||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.747_789delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGG|ENST00000374223.1:c.747_789delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGG(p.%3D)||||||||||||||||||,ACCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1208-1250|747-789|249-263|GPSPGPGPGPSPGPG/GPSPGPGPG|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGT/ggCCCCAGTCCCGGTCCCGGTCCCGGT||5||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.747_789delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTinsCCCCAGTCCCGGTCCCGGTCCCGGT|ENSP00000363340.1:p.Pro258_Gly263del||||||||||||||||||,ACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||4||||||regulatory_region|||||||||||||||||||||||||||||||,A||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||3||||||regulatory_region|||||||||||||||||||||||||||||||,AG||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||2||||||regulatory_region|||||||||||||||||||||||||||||||,AGCCGGGACCGGGACCGGGACTGGGG||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||1||||||regulatory_region|||||||||||||||||||||||||||||||,CCCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||6||||||regulatory_region|||||||||||||||||||||||||||||||,ACCGGGACCGGGACCGGGACTGGGG||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||5||||||regulatory_region|||||||||||||||||||||||||||||||;AC_POPMAX=21528,2,7,4,9,1;AN_POPMAX=48432,6150,6472,6472,8132,48432;POPMAX=NFE,AFR,EAS,EAS,SAS,NFE +1 26608837 . CGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACT AGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACT,C,CGGGGCCGGGACCGGGACCGGGACT 4344.18 VQSRTrancheINDEL99.50to99.90 AC=2,1,1;AC_AFR=0,0,0;AC_AMR=1,1,0;AC_Adj=2,1,1;AC_EAS=0,0,0;AC_FIN=0,0,0;AC_Het=2,1,1,0,0,0;AC_Hom=0,0,0;AC_NFE=1,0,0;AC_OTH=0,0,0;AC_SAS=0,0,1;AF=8.376e-05,4.188e-05,4.188e-05;AN=23878;AN_AFR=1464;AN_AMR=3216;AN_Adj=15466;AN_EAS=2640;AN_FIN=474;AN_NFE=4622;AN_OTH=94;AN_SAS=2956;BaseQRankSum=-1.107e+00;ClippingRankSum=-1.690e-01;DP=261910;FS=36.976;GQ_MEAN=33.84;GQ_STDDEV=33.08;Het_AFR=0,0,0,0,0,0;Het_AMR=1,1,0,0,0,0;Het_EAS=0,0,0,0,0,0;Het_FIN=0,0,0,0,0,0;Het_NFE=1,0,0,0,0,0;Het_OTH=0,0,0,0,0,0;Het_SAS=0,0,1,0,0,0;Hom_AFR=0,0,0;Hom_AMR=0,0,0;Hom_EAS=0,0,0;Hom_FIN=0,0,0;Hom_NFE=0,0,0;Hom_OTH=0,0,0;Hom_SAS=0,0,0;InbreedingCoeff=0.1055;MQ=55.09;MQ0=0;MQRankSum=-4.500e-01;NCC=74761;NEGATIVE_TRAIN_SITE;QD=6.26;ReadPosRankSum=0.736;VQSLOD=-1.088e+00;culprit=FS;DP_HIST=1479|1613|1059|1210|2317|1596|1148|582|378|216|133|85|48|28|11|9|8|3|3|12,0|0|0|1|0|0|0|0|0|0|0|1|0|0|0|0|0|0|0|0,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1|0|0|0,0|0|0|0|0|0|0|0|1|0|0|0|0|0|0|0|0|0|0|0;GQ_HIST=938|1816|337|326|2194|654|772|502|254|293|216|51|2125|612|209|226|130|59|55|170,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|2,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1;CSQ=CGGGGCCGGGACCGGGACCGGGACT|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2262-2298||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2262_2298delAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGinsAGTCCCGGTCCCGGTCCCGGCCCCG|||||||||||||||||||,C|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2262-2298||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2262_2298delAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGinsG|||||||||||||||||||,AGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACT|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2262-2298||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2262_2298delAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGinsAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCT|||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACT|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1748-1784|1381-1417|461-473|SPGPGPGPSPGPG/SPGPGPGPG|AGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGgt/AGTCCCGGTCCCGGTCCCGGCCCCGgt||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1381_1417delAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGinsAGTCCCGGTCCCGGTCCCGGCCCCG|ENSP00000363334.2:p.Ser469_Pro472del||||||||||||||||||,C|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1748-1784|1381-1417|461-473|SPGPGPGPSPGPG/G|AGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGgt/Ggt||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1381_1417delAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGinsG|ENSP00000363334.2:p.Ser461_Pro472del||||||||||||||||||,AGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACT|ENSG00000158062|ENST00000374217|Transcript|missense_variant|1748-1784|1381-1417|461-473|SPGPGPGPSPGPG/SPGPGPGPSPGPC|AGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGgt/AGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCTgt||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1381_1417delAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGinsAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCT|ENSP00000363334.2:p.Gly473Cys||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACT|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1945-1981|1480-1516|494-506|SPGPGPGPSPGPG/SPGPGPGPG|AGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGgt/AGTCCCGGTCCCGGTCCCGGCCCCGgt||3||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1480_1516delAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGinsAGTCCCGGTCCCGGTCCCGGCCCCG|ENSP00000363339.1:p.Ser502_Pro505del||||||||||||||||||,C|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1945-1981|1480-1516|494-506|SPGPGPGPSPGPG/G|AGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGgt/Ggt||2||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1480_1516delAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGinsG|ENSP00000363339.1:p.Ser494_Pro505del||||||||||||||||||,AGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACT|ENSG00000158062|ENST00000374222|Transcript|missense_variant|1945-1981|1480-1516|494-506|SPGPGPGPSPGPG/SPGPGPGPSPGPC|AGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGgt/AGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCTgt||1||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1480_1516delAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGinsAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCT|ENSP00000363339.1:p.Gly506Cys||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACT|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1457-1493|1381-1417|461-473|SPGPGPGPSPGPG/SPGPGPGPG|AGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGgt/AGTCCCGGTCCCGGTCCCGGCCCCGgt||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1381_1417delAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGinsAGTCCCGGTCCCGGTCCCGGCCCCG|ENSP00000349601.4:p.Ser469_Pro472del||||||||||||||||||,C|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1457-1493|1381-1417|461-473|SPGPGPGPSPGPG/G|AGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGgt/Ggt||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1381_1417delAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGinsG|ENSP00000349601.4:p.Ser461_Pro472del||||||||||||||||||,AGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACT|ENSG00000158062|ENST00000357089|Transcript|missense_variant|1457-1493|1381-1417|461-473|SPGPGPGPSPGPG/SPGPGPGPSPGPC|AGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGgt/AGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCTgt||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1381_1417delAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGinsAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCT|ENSP00000349601.4:p.Gly473Cys||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACT|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1200-1236|1120-1156|374-386|SPGPGPGPSPGPG/SPGPGPGPG|AGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGgt/AGTCCCGGTCCCGGTCCCGGCCCCGgt||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1120_1156delAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGinsAGTCCCGGTCCCGGTCCCGGCCCCG|ENSP00000324721.7:p.Ser382_Pro385del||||||||||||||||||,C|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1200-1236|1120-1156|374-386|SPGPGPGPSPGPG/G|AGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGgt/Ggt||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1120_1156delAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGinsG|ENSP00000324721.7:p.Ser374_Pro385del||||||||||||||||||,AGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACT|ENSG00000158062|ENST00000314675|Transcript|missense_variant|1200-1236|1120-1156|374-386|SPGPGPGPSPGPG/SPGPGPGPSPGPC|AGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGgt/AGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCTgt||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1120_1156delAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGinsAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCT|ENSP00000324721.7:p.Gly386Cys||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACT|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2442-2478||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2442_2478delAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGinsAGTCCCGGTCCCGGTCCCGGCCCCG|||||||||||||||||||,C|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2442-2478||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2442_2478delAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGinsG|||||||||||||||||||,AGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACT|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2442-2478||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2442_2478delAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGinsAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCT|||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACT|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2227-2263||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2227_2263delAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGinsAGTCCCGGTCCCGGTCCCGGCCCCG|||||||||||||||||||,C|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2227-2263||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2227_2263delAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGinsG|||||||||||||||||||,AGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACT|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2227-2263||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2227_2263delAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGinsAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCT|||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACT|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1694-1730|1480-1516|494-506|SPGPGPGPSPGPG/SPGPGPGPG|AGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGgt/AGTCCCGGTCCCGGTCCCGGCCCCGgt||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1480_1516delAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGinsAGTCCCGGTCCCGGTCCCGGCCCCG|ENSP00000363338.3:p.Ser502_Pro505del||||||||||||||||||,C|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1694-1730|1480-1516|494-506|SPGPGPGPSPGPG/G|AGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGgt/Ggt||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1480_1516delAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGinsG|ENSP00000363338.3:p.Ser494_Pro505del||||||||||||||||||,AGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACT|ENSG00000158062|ENST00000374221|Transcript|missense_variant|1694-1730|1480-1516|494-506|SPGPGPGPSPGPG/SPGPGPGPSPGPC|AGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGgt/AGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCTgt||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1480_1516delAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGinsAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCT|ENSP00000363338.3:p.Gly506Cys||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACT|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2545-2581||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2545_2581delAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGinsAGTCCCGGTCCCGGTCCCGGCCCCG|||||||||||||||||||,C|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2545-2581||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2545_2581delAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGinsG|||||||||||||||||||,AGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACT|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2545-2581||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2545_2581delAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGinsAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCT|||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACT|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1212-1248|751-787|251-263|SPGPGPGPSPGPG/SPGPGPGPG|AGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGgt/AGTCCCGGTCCCGGTCCCGGCCCCGgt||3||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.751_787delAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGinsAGTCCCGGTCCCGGTCCCGGCCCCG|ENSP00000363340.1:p.Ser259_Pro262del||||||||||||||||||,C|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1212-1248|751-787|251-263|SPGPGPGPSPGPG/G|AGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGgt/Ggt||2||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.751_787delAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGinsG|ENSP00000363340.1:p.Ser251_Pro262del||||||||||||||||||,AGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACT|ENSG00000158062|ENST00000374223|Transcript|missense_variant|1212-1248|751-787|251-263|SPGPGPGPSPGPG/SPGPGPGPSPGPC|AGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGgt/AGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCTgt||1||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.751_787delAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGinsAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCT|ENSP00000363340.1:p.Gly263Cys||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACT||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||3||||||regulatory_region|||||||||||||||||||||||||||||||,C||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||2||||||regulatory_region|||||||||||||||||||||||||||||||,AGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACT||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||1||||||regulatory_region|||||||||||||||||||||||||||||||;AC_POPMAX=1,1,1;AN_POPMAX=3216,3216,2956;POPMAX=AMR,AMR,SAS +1 26608841 . ACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG AGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG,A,ACCGGGACCGGGACCGGGACTGGGG,ACCGGGACTGGGGCCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG,AACCGGGACTGGGG,ACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG 274356.68 VQSRTrancheINDEL99.00to99.50 AC=397,8,4,1,1,1;AC_AFR=261,1,0,0,0,0;AC_AMR=18,0,0,1,0,0;AC_Adj=295,7,4,1,1,1;AC_EAS=3,5,0,0,0,0;AC_FIN=2,0,0,0,0,0;AC_Het=275,7,4,1,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;AC_Hom=10,0,0,0,0,0;AC_NFE=10,1,3,0,0,0;AC_OTH=0,0,0,0,0,0;AC_SAS=1,0,1,0,1,1;AF=0.016,3.222e-04,1.611e-04,4.028e-05,4.028e-05,4.028e-05;AN=24828;AN_AFR=2016;AN_AMR=3376;AN_Adj=16712;AN_EAS=2764;AN_FIN=452;AN_NFE=4918;AN_OTH=104;AN_SAS=3082;BaseQRankSum=1.64;ClippingRankSum=0.036;DP=275184;FS=7.378;GQ_MEAN=47.01;GQ_STDDEV=118.53;Het_AFR=241,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_AMR=18,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_EAS=3,5,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_FIN=2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_NFE=10,1,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_OTH=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_SAS=1,0,1,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Hom_AFR=10,0,0,0,0,0;Hom_AMR=0,0,0,0,0,0;Hom_EAS=0,0,0,0,0,0;Hom_FIN=0,0,0,0,0,0;Hom_NFE=0,0,0,0,0,0;Hom_OTH=0,0,0,0,0,0;Hom_SAS=0,0,0,0,0,0;InbreedingCoeff=0.1410;MQ=44.98;MQ0=0;MQRankSum=-1.738e+00;NCC=74020;NEGATIVE_TRAIN_SITE;QD=25.69;ReadPosRankSum=0.00;VQSLOD=-8.139e-01;culprit=FS;DP_HIST=1487|1649|1102|1183|2405|1663|1237|662|430|230|140|81|59|38|12|8|8|3|5|10,21|65|108|86|42|27|13|5|13|1|2|0|0|0|0|0|0|0|0|0,0|1|1|0|0|0|0|0|0|0|2|1|1|0|0|0|0|2|0|0,0|0|0|0|1|1|2|0|0|0|0|0|0|0|0|0|0|0|0|0,0|0|0|0|0|0|1|0|0|0|0|0|0|0|0|0|0|0|0|0,0|0|0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0|0,0|0|0|0|0|0|0|1|0|0|0|0|0|0|0|0|0|0|0|0;GQ_HIST=744|1872|301|276|2246|605|734|460|215|250|157|85|2489|689|251|258|163|73|68|478,2|3|10|6|1|2|3|9|4|5|6|3|5|4|5|5|10|6|6|289,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|8,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|4,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1;CSQ=-|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2258-2293||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2258_2293delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGG|||||||||||||||||||,CCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2258-2293||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2258_2293delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGinsCCCCAGTCCCGGTCCCGGTCCCGG|||||||||||||||||||,ACCGGGACTGGGG|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2258-2293||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2258_2293delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGinsCCCCAGTCCCGGT|||||||||||||||||||,CCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_elongation|2258-2293||||||6||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2258_2293dupCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGG|||||||||||||||||||,CCGGGACTGGGGCCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_elongation|2258-2293||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2258_2293delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGCCCCAGTCCCGG|||||||||||||||||||,GGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2258-2293||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2258_2293delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC|||||||||||||||||||,-|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1744-1779|1377-1412|459-471|GPSPGPGPGPSPG/G|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGt/ggt||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1377_1412delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGG|ENSP00000363334.2:p.Pro460_Gly471del||||||||||||||||||,CCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1744-1779|1377-1412|459-471|GPSPGPGPGPSPG/GPSPGPGPG|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGt/ggCCCCAGTCCCGGTCCCGGTCCCGGt||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1377_1412delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGinsCCCCAGTCCCGGTCCCGGTCCCGG|ENSP00000363334.2:p.Pro468_Gly471del||||||||||||||||||,ACCGGGACTGGGG|ENSG00000158062|ENST00000374217|Transcript|frameshift_variant&feature_truncation|1744-1779|1377-1412|459-471|GPSPGPGPGPSPG/GPSPGX|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGt/ggCCCCAGTCCCGGTt||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1377_1412delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGinsCCCCAGTCCCGGT|ENSP00000363334.2:p.Pro464SerfsTer?|||||||||||||||POSITION:0.96448087431694&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,CCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000374217|Transcript|inframe_insertion|1744-1779|1377-1412|459-471|GPSPGPGPGPSPG/GPSPGPGPGPSPGPSPGPGPGPSPG|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGt/ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGt||6||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1377_1412dupCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGG|ENSP00000363334.2:p.Gly471_Pro472insProSerProGlyProGlyProGlyProSerProGly||||||||||||||||||,CCGGGACTGGGGCCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000374217|Transcript|inframe_insertion|1744-1779|1377-1412|459-471|GPSPGPGPGPSPG/GPSPGPGPGPSPGPSPG|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGt/ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGCCCCAGTCCCGGt||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1377_1412delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGCCCCAGTCCCGG|ENSP00000363334.2:p.Gly471_Pro472insProSerProGly||||||||||||||||||,GGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000374217|Transcript|frameshift_variant&missense_variant&feature_truncation|1744-1779|1377-1412|459-471|GPSPGPGPGPSPG/GPSPGPGPGPSPX|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGt/ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCt||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1377_1412delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC|ENSP00000363334.2:p.Gly471SerfsTer?|||||||||||||||POSITION:0.96448087431694&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,-|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1941-1976|1476-1511|492-504|GPSPGPGPGPSPG/G|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGt/ggt||2||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1476_1511delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGG|ENSP00000363339.1:p.Pro493_Gly504del||||||||||||||||||,CCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1941-1976|1476-1511|492-504|GPSPGPGPGPSPG/GPSPGPGPG|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGt/ggCCCCAGTCCCGGTCCCGGTCCCGGt||3||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1476_1511delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGinsCCCCAGTCCCGGTCCCGGTCCCGG|ENSP00000363339.1:p.Pro501_Gly504del||||||||||||||||||,ACCGGGACTGGGG|ENSG00000158062|ENST00000374222|Transcript|frameshift_variant&feature_truncation|1941-1976|1476-1511|492-504|GPSPGPGPGPSPG/GPSPGX|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGt/ggCCCCAGTCCCGGTt||5||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1476_1511delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGinsCCCCAGTCCCGGT|ENSP00000363339.1:p.Pro497SerfsTer?|||||||||||||||POSITION:0.966730646193218&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,CCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000374222|Transcript|inframe_insertion|1941-1976|1476-1511|492-504|GPSPGPGPGPSPG/GPSPGPGPGPSPGPSPGPGPGPSPG|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGt/ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGt||6||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1476_1511dupCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGG|ENSP00000363339.1:p.Gly504_Pro505insProSerProGlyProGlyProGlyProSerProGly||||||||||||||||||,CCGGGACTGGGGCCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000374222|Transcript|inframe_insertion|1941-1976|1476-1511|492-504|GPSPGPGPGPSPG/GPSPGPGPGPSPGPSPG|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGt/ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGCCCCAGTCCCGGt||4||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1476_1511delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGCCCCAGTCCCGG|ENSP00000363339.1:p.Gly504_Pro505insProSerProGly||||||||||||||||||,GGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000374222|Transcript|frameshift_variant&missense_variant&feature_truncation|1941-1976|1476-1511|492-504|GPSPGPGPGPSPG/GPSPGPGPGPSPX|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGt/ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCt||1||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1476_1511delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC|ENSP00000363339.1:p.Gly504SerfsTer?|||||||||||||||POSITION:0.966730646193218&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,-|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1453-1488|1377-1412|459-471|GPSPGPGPGPSPG/G|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGt/ggt||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1377_1412delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGG|ENSP00000349601.4:p.Pro460_Gly471del||||||||||||||||||,CCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1453-1488|1377-1412|459-471|GPSPGPGPGPSPG/GPSPGPGPG|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGt/ggCCCCAGTCCCGGTCCCGGTCCCGGt||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1377_1412delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGinsCCCCAGTCCCGGTCCCGGTCCCGG|ENSP00000349601.4:p.Pro468_Gly471del||||||||||||||||||,ACCGGGACTGGGG|ENSG00000158062|ENST00000357089|Transcript|frameshift_variant&feature_truncation|1453-1488|1377-1412|459-471|GPSPGPGPGPSPG/GPSPGX|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGt/ggCCCCAGTCCCGGTt||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1377_1412delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGinsCCCCAGTCCCGGT|ENSP00000349601.4:p.Pro464SerfsTer?|||||||||||||||POSITION:0.96448087431694&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,CCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000357089|Transcript|inframe_insertion|1453-1488|1377-1412|459-471|GPSPGPGPGPSPG/GPSPGPGPGPSPGPSPGPGPGPSPG|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGt/ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGt||6||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1377_1412dupCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGG|ENSP00000349601.4:p.Gly471_Pro472insProSerProGlyProGlyProGlyProSerProGly||||||||||||||||||,CCGGGACTGGGGCCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000357089|Transcript|inframe_insertion|1453-1488|1377-1412|459-471|GPSPGPGPGPSPG/GPSPGPGPGPSPGPSPG|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGt/ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGCCCCAGTCCCGGt||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1377_1412delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGCCCCAGTCCCGG|ENSP00000349601.4:p.Gly471_Pro472insProSerProGly||||||||||||||||||,GGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000357089|Transcript|frameshift_variant&missense_variant&feature_truncation|1453-1488|1377-1412|459-471|GPSPGPGPGPSPG/GPSPGPGPGPSPX|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGt/ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCt||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1377_1412delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC|ENSP00000349601.4:p.Gly471SerfsTer?|||||||||||||||POSITION:0.96448087431694&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,-|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1196-1231|1116-1151|372-384|GPSPGPGPGPSPG/G|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGt/ggt||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1116_1151delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGG|ENSP00000324721.7:p.Pro373_Gly384del||||||||||||||||||,CCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1196-1231|1116-1151|372-384|GPSPGPGPGPSPG/GPSPGPGPG|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGt/ggCCCCAGTCCCGGTCCCGGTCCCGGt||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1116_1151delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGinsCCCCAGTCCCGGTCCCGGTCCCGG|ENSP00000324721.7:p.Pro381_Gly384del||||||||||||||||||,ACCGGGACTGGGG|ENSG00000158062|ENST00000314675|Transcript|frameshift_variant&feature_truncation|1196-1231|1116-1151|372-384|GPSPGPGPGPSPG/GPSPGX|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGt/ggCCCCAGTCCCGGTt||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1116_1151delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGinsCCCCAGTCCCGGT|ENSP00000324721.7:p.Pro377SerfsTer151|||||||||||||||POSITION:0.956774729842061&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,CCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000314675|Transcript|inframe_insertion|1196-1231|1116-1151|372-384|GPSPGPGPGPSPG/GPSPGPGPGPSPGPSPGPGPGPSPG|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGt/ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGt||6||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1116_1151dupCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGG|ENSP00000324721.7:p.Gly384_Pro385insProSerProGlyProGlyProGlyProSerProGly||||||||||||||||||,CCGGGACTGGGGCCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000314675|Transcript|inframe_insertion|1196-1231|1116-1151|372-384|GPSPGPGPGPSPG/GPSPGPGPGPSPGPSPG|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGt/ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGCCCCAGTCCCGGt||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1116_1151delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGCCCCAGTCCCGG|ENSP00000324721.7:p.Gly384_Pro385insProSerProGly||||||||||||||||||,GGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000314675|Transcript|frameshift_variant&missense_variant&feature_truncation|1196-1231|1116-1151|372-384|GPSPGPGPGPSPG/GPSPGPGPGPSPX|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGt/ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCt||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1116_1151delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC|ENSP00000324721.7:p.Gly384SerfsTer151|||||||||||||||POSITION:0.956774729842061&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,-|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2438-2473||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2438_2473delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGG|||||||||||||||||||,CCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2438-2473||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2438_2473delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGinsCCCCAGTCCCGGTCCCGGTCCCGG|||||||||||||||||||,ACCGGGACTGGGG|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2438-2473||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2438_2473delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGinsCCCCAGTCCCGGT|||||||||||||||||||,CCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_elongation|2438-2473||||||6||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2438_2473dupCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGG|||||||||||||||||||,CCGGGACTGGGGCCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_elongation|2438-2473||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2438_2473delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGCCCCAGTCCCGG|||||||||||||||||||,GGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2438-2473||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2438_2473delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC|||||||||||||||||||,-|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2223-2258||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2223_2258delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGG|||||||||||||||||||,CCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2223-2258||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2223_2258delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGinsCCCCAGTCCCGGTCCCGGTCCCGG|||||||||||||||||||,ACCGGGACTGGGG|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2223-2258||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2223_2258delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGinsCCCCAGTCCCGGT|||||||||||||||||||,CCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_elongation|2223-2258||||||6||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2223_2258dupCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGG|||||||||||||||||||,CCGGGACTGGGGCCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_elongation|2223-2258||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2223_2258delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGCCCCAGTCCCGG|||||||||||||||||||,GGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2223-2258||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2223_2258delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC|||||||||||||||||||,-|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1690-1725|1476-1511|492-504|GPSPGPGPGPSPG/G|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGt/ggt||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1476_1511delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGG|ENSP00000363338.3:p.Pro493_Gly504del||||||||||||||||||,CCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1690-1725|1476-1511|492-504|GPSPGPGPGPSPG/GPSPGPGPG|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGt/ggCCCCAGTCCCGGTCCCGGTCCCGGt||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1476_1511delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGinsCCCCAGTCCCGGTCCCGGTCCCGG|ENSP00000363338.3:p.Pro501_Gly504del||||||||||||||||||,ACCGGGACTGGGG|ENSG00000158062|ENST00000374221|Transcript|frameshift_variant&feature_truncation|1690-1725|1476-1511|492-504|GPSPGPGPGPSPG/GPSPGX|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGt/ggCCCCAGTCCCGGTt||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1476_1511delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGinsCCCCAGTCCCGGT|ENSP00000363338.3:p.Pro497SerfsTer?|||||||||||||||POSITION:0.966730646193218&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,CCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000374221|Transcript|inframe_insertion|1690-1725|1476-1511|492-504|GPSPGPGPGPSPG/GPSPGPGPGPSPGPSPGPGPGPSPG|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGt/ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGt||6||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1476_1511dupCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGG|ENSP00000363338.3:p.Gly504_Pro505insProSerProGlyProGlyProGlyProSerProGly||||||||||||||||||,CCGGGACTGGGGCCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000374221|Transcript|inframe_insertion|1690-1725|1476-1511|492-504|GPSPGPGPGPSPG/GPSPGPGPGPSPGPSPG|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGt/ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGCCCCAGTCCCGGt||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1476_1511delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGCCCCAGTCCCGG|ENSP00000363338.3:p.Gly504_Pro505insProSerProGly||||||||||||||||||,GGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000374221|Transcript|frameshift_variant&missense_variant&feature_truncation|1690-1725|1476-1511|492-504|GPSPGPGPGPSPG/GPSPGPGPGPSPX|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGt/ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCt||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1476_1511delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC|ENSP00000363338.3:p.Gly504SerfsTer?|||||||||||||||POSITION:0.966730646193218&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,-|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2541-2576||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2541_2576delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGG|||||||||||||||||||,CCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2541-2576||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2541_2576delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGinsCCCCAGTCCCGGTCCCGGTCCCGG|||||||||||||||||||,ACCGGGACTGGGG|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2541-2576||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2541_2576delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGinsCCCCAGTCCCGGT|||||||||||||||||||,CCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_elongation|2541-2576||||||6||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2541_2576dupCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGG|||||||||||||||||||,CCGGGACTGGGGCCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_elongation|2541-2576||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2541_2576delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGCCCCAGTCCCGG|||||||||||||||||||,GGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2541-2576||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2541_2576delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC|||||||||||||||||||,-|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1208-1243|747-782|249-261|GPSPGPGPGPSPG/G|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGt/ggt||2||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.747_782delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGG|ENSP00000363340.1:p.Pro250_Gly261del||||||||||||||||||,CCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1208-1243|747-782|249-261|GPSPGPGPGPSPG/GPSPGPGPG|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGt/ggCCCCAGTCCCGGTCCCGGTCCCGGt||3||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.747_782delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGinsCCCCAGTCCCGGTCCCGGTCCCGG|ENSP00000363340.1:p.Pro258_Gly261del||||||||||||||||||,ACCGGGACTGGGG|ENSG00000158062|ENST00000374223|Transcript|frameshift_variant&feature_truncation|1208-1243|747-782|249-261|GPSPGPGPGPSPG/GPSPGX|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGt/ggCCCCAGTCCCGGTt||5||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.747_782delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGinsCCCCAGTCCCGGT|ENSP00000363340.1:p.Pro254SerfsTer?|||||||||||||||POSITION:0.937649880095923&PHYLOCSF_TOO_SHORT|||HC,CCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000374223|Transcript|inframe_insertion|1208-1243|747-782|249-261|GPSPGPGPGPSPG/GPSPGPGPGPSPGPSPGPGPGPSPG|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGt/ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGt||6||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.747_782dupCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGG|ENSP00000363340.1:p.Gly261_Pro262insProSerProGlyProGlyProGlyProSerProGly||||||||||||||||||,CCGGGACTGGGGCCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000374223|Transcript|inframe_insertion|1208-1243|747-782|249-261|GPSPGPGPGPSPG/GPSPGPGPGPSPGPSPG|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGt/ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGCCCCAGTCCCGGt||4||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.747_782delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGCCCCAGTCCCGG|ENSP00000363340.1:p.Gly261_Pro262insProSerProGly||||||||||||||||||,GGGACTGGGGCCGGGACCGGGACCGGGACTGGGG|ENSG00000158062|ENST00000374223|Transcript|frameshift_variant&missense_variant&feature_truncation|1208-1243|747-782|249-261|GPSPGPGPGPSPG/GPSPGPGPGPSPX|ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGt/ggCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCt||1||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.747_782delCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGinsCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC|ENSP00000363340.1:p.Gly261SerfsTer?|||||||||||||||POSITION:0.937649880095923&PHYLOCSF_TOO_SHORT|||HC,-||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||2||||||regulatory_region|||||||||||||||||||||||||||||||,CCGGGACCGGGACCGGGACTGGGG||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||3||||||regulatory_region|||||||||||||||||||||||||||||||,ACCGGGACTGGGG||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||5||||||regulatory_region|||||||||||||||||||||||||||||||,CCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||6||||||regulatory_region|||||||||||||||||||||||||||||||,CCGGGACTGGGGCCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGG||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||4||||||regulatory_region|||||||||||||||||||||||||||||||,GGGACTGGGGCCGGGACCGGGACCGGGACTGGGG||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||1||||||regulatory_region|||||||||||||||||||||||||||||||;AC_POPMAX=261,5,3,1,1,1;AN_POPMAX=2016,2764,4918,3376,3082,3082;POPMAX=AFR,EAS,NFE,AMR,SAS,SAS +1 26608843 . CGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACA AGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACA,CACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACA,CGGGGCCGGGACCGGGACCGGGACA,CGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACA,C 133888.87 PASS AC=73,12,2,3,1;AC_AFR=43,10,0,1,0;AC_AMR=3,1,0,0,0;AC_Adj=63,11,2,2,1;AC_EAS=3,0,0,0,0;AC_FIN=0,0,0,0,0;AC_Het=63,11,2,2,1,0,0,0,0,0,0,0,0,0,0;AC_Hom=0,0,0,0,0;AC_NFE=13,0,1,1,1;AC_OTH=1,0,0,0,0;AC_SAS=0,0,1,0,0;AF=3.174e-03,5.218e-04,8.696e-05,1.304e-04,4.348e-05;AN=22998;AN_AFR=790;AN_AMR=2592;AN_Adj=9956;AN_EAS=2582;AN_FIN=172;AN_NFE=1454;AN_OTH=58;AN_SAS=2308;BaseQRankSum=-3.870e-01;ClippingRankSum=-7.900e-02;DP=291581;FS=3.379;GQ_MEAN=32.58;GQ_STDDEV=102.85;Het_AFR=43,10,0,1,0,0,0,0,0,0,0,0,0,0,0;Het_AMR=3,1,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_EAS=3,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_FIN=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_NFE=13,0,1,1,1,0,0,0,0,0,0,0,0,0,0;Het_OTH=1,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_SAS=0,0,1,0,0,0,0,0,0,0,0,0,0,0,0;Hom_AFR=0,0,0,0,0;Hom_AMR=0,0,0,0,0;Hom_EAS=0,0,0,0,0;Hom_FIN=0,0,0,0,0;Hom_NFE=0,0,0,0,0;Hom_OTH=0,0,0,0,0;Hom_SAS=0,0,0,0,0;InbreedingCoeff=0.3085;MQ=57.23;MQ0=0;MQRankSum=0.00;NCC=75439;QD=29.02;ReadPosRankSum=0.329;VQSLOD=2.29;culprit=QD;DP_HIST=1301|1544|953|983|2155|1599|1199|662|408|262|141|110|61|50|23|11|12|6|7|12,1|7|10|6|10|12|14|5|5|2|0|0|0|0|0|0|0|0|0|0,1|0|3|0|2|1|3|0|1|0|0|0|0|1|0|0|0|0|0|0,0|0|0|1|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0|0,0|1|0|1|0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1|0;GQ_HIST=4100|1351|215|176|1272|327|280|221|140|128|106|105|1675|474|187|164|105|53|56|364,0|0|0|2|0|0|1|1|4|0|2|0|0|0|1|0|0|0|0|61,0|0|0|0|0|0|0|0|0|0|0|2|0|0|0|0|0|0|1|9,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|2,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|3,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1;CSQ=CACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2238-2292||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2238_2292delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTG|||||||||||||||||||,AGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2238-2292||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2238_2292delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCT|||||||||||||||||||,C|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2238-2292||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2238_2292delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsG|||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2238-2292||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2238_2292delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCG|||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2238-2292||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2238_2292delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCG|||||||||||||||||||,CACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1724-1778|1357-1411|453-471|CPGPGPGPSPGPGPGPSPG/CPGPGPGPSPGPGPGPSG|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTGgt||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1357_1411delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTG|ENSP00000363334.2:p.Pro470del||||||||||||||||||,AGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000374217|Transcript|missense_variant|1724-1778|1357-1411|453-471|CPGPGPGPSPGPGPGPSPG/CPGPGPGPSPGPGPGPSPC|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1357_1411delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCT|ENSP00000363334.2:p.Gly471Cys||||||||||||||||||,C|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1724-1778|1357-1411|453-471|CPGPGPGPSPGPGPGPSPG/G|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/Ggt||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1357_1411delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsG|ENSP00000363334.2:p.Cys453_Pro470del||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1724-1778|1357-1411|453-471|CPGPGPGPSPGPGPGPSPG/CPGPGPGPSPGPGPGPG|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCGgt||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1357_1411delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCG|ENSP00000363334.2:p.Ser469_Pro470del||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1724-1778|1357-1411|453-471|CPGPGPGPSPGPGPGPSPG/CPGPGPGPG|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/TGTCCCGGTCCCGGTCCCGGCCCCGgt||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1357_1411delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCG|ENSP00000363334.2:p.Ser461_Pro470del||||||||||||||||||,CACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1921-1975|1456-1510|486-504|CPGPGPGPSPGPGPGPSPG/CPGPGPGPSPGPGPGPSG|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTGgt||2||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1456_1510delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTG|ENSP00000363339.1:p.Pro503del||||||||||||||||||,AGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000374222|Transcript|missense_variant|1921-1975|1456-1510|486-504|CPGPGPGPSPGPGPGPSPG/CPGPGPGPSPGPGPGPSPC|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt||1||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1456_1510delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCT|ENSP00000363339.1:p.Gly504Cys||||||||||||||||||,C|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1921-1975|1456-1510|486-504|CPGPGPGPSPGPGPGPSPG/G|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/Ggt||5||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1456_1510delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsG|ENSP00000363339.1:p.Cys486_Pro503del||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1921-1975|1456-1510|486-504|CPGPGPGPSPGPGPGPSPG/CPGPGPGPSPGPGPGPG|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCGgt||4||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1456_1510delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCG|ENSP00000363339.1:p.Ser502_Pro503del||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1921-1975|1456-1510|486-504|CPGPGPGPSPGPGPGPSPG/CPGPGPGPG|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/TGTCCCGGTCCCGGTCCCGGCCCCGgt||3||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1456_1510delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCG|ENSP00000363339.1:p.Ser494_Pro503del||||||||||||||||||,CACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1433-1487|1357-1411|453-471|CPGPGPGPSPGPGPGPSPG/CPGPGPGPSPGPGPGPSG|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTGgt||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1357_1411delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTG|ENSP00000349601.4:p.Pro470del||||||||||||||||||,AGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000357089|Transcript|missense_variant|1433-1487|1357-1411|453-471|CPGPGPGPSPGPGPGPSPG/CPGPGPGPSPGPGPGPSPC|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1357_1411delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCT|ENSP00000349601.4:p.Gly471Cys||||||||||||||||||,C|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1433-1487|1357-1411|453-471|CPGPGPGPSPGPGPGPSPG/G|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/Ggt||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1357_1411delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsG|ENSP00000349601.4:p.Cys453_Pro470del||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1433-1487|1357-1411|453-471|CPGPGPGPSPGPGPGPSPG/CPGPGPGPSPGPGPGPG|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCGgt||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1357_1411delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCG|ENSP00000349601.4:p.Ser469_Pro470del||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1433-1487|1357-1411|453-471|CPGPGPGPSPGPGPGPSPG/CPGPGPGPG|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/TGTCCCGGTCCCGGTCCCGGCCCCGgt||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1357_1411delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCG|ENSP00000349601.4:p.Ser461_Pro470del||||||||||||||||||,CACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1176-1230|1096-1150|366-384|CPGPGPGPSPGPGPGPSPG/CPGPGPGPSPGPGPGPSG|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTGgt||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1096_1150delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTG|ENSP00000324721.7:p.Pro383del||||||||||||||||||,AGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000314675|Transcript|missense_variant|1176-1230|1096-1150|366-384|CPGPGPGPSPGPGPGPSPG/CPGPGPGPSPGPGPGPSPC|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1096_1150delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCT|ENSP00000324721.7:p.Gly384Cys||||||||||||||||||,C|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1176-1230|1096-1150|366-384|CPGPGPGPSPGPGPGPSPG/G|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/Ggt||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1096_1150delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsG|ENSP00000324721.7:p.Cys366_Pro383del||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1176-1230|1096-1150|366-384|CPGPGPGPSPGPGPGPSPG/CPGPGPGPSPGPGPGPG|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCGgt||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1096_1150delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCG|ENSP00000324721.7:p.Ser382_Pro383del||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1176-1230|1096-1150|366-384|CPGPGPGPSPGPGPGPSPG/CPGPGPGPG|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/TGTCCCGGTCCCGGTCCCGGCCCCGgt||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1096_1150delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCG|ENSP00000324721.7:p.Ser374_Pro383del||||||||||||||||||,CACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2418-2472||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2418_2472delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTG|||||||||||||||||||,AGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2418-2472||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2418_2472delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCT|||||||||||||||||||,C|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2418-2472||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2418_2472delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsG|||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2418-2472||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2418_2472delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCG|||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2418-2472||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2418_2472delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCG|||||||||||||||||||,CACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2203-2257||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2203_2257delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTG|||||||||||||||||||,AGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2203-2257||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2203_2257delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCT|||||||||||||||||||,C|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2203-2257||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2203_2257delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsG|||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2203-2257||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2203_2257delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCG|||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2203-2257||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2203_2257delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCG|||||||||||||||||||,CACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1670-1724|1456-1510|486-504|CPGPGPGPSPGPGPGPSPG/CPGPGPGPSPGPGPGPSG|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTGgt||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1456_1510delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTG|ENSP00000363338.3:p.Pro503del||||||||||||||||||,AGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000374221|Transcript|missense_variant|1670-1724|1456-1510|486-504|CPGPGPGPSPGPGPGPSPG/CPGPGPGPSPGPGPGPSPC|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1456_1510delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCT|ENSP00000363338.3:p.Gly504Cys||||||||||||||||||,C|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1670-1724|1456-1510|486-504|CPGPGPGPSPGPGPGPSPG/G|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/Ggt||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1456_1510delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsG|ENSP00000363338.3:p.Cys486_Pro503del||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1670-1724|1456-1510|486-504|CPGPGPGPSPGPGPGPSPG/CPGPGPGPSPGPGPGPG|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCGgt||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1456_1510delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCG|ENSP00000363338.3:p.Ser502_Pro503del||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1670-1724|1456-1510|486-504|CPGPGPGPSPGPGPGPSPG/CPGPGPGPG|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/TGTCCCGGTCCCGGTCCCGGCCCCGgt||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1456_1510delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCG|ENSP00000363338.3:p.Ser494_Pro503del||||||||||||||||||,CACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2521-2575||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2521_2575delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTG|||||||||||||||||||,AGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2521-2575||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2521_2575delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCT|||||||||||||||||||,C|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2521-2575||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2521_2575delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsG|||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2521-2575||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2521_2575delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCG|||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2521-2575||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2521_2575delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCG|||||||||||||||||||,CACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1188-1242|727-781|243-261|CPGPGPGPSPGPGPGPSPG/CPGPGPGPSPGPGPGPSG|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTGgt||2||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.727_781delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTG|ENSP00000363340.1:p.Pro260del||||||||||||||||||,AGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000374223|Transcript|missense_variant|1188-1242|727-781|243-261|CPGPGPGPSPGPGPGPSPG/CPGPGPGPSPGPGPGPSPC|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt||1||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.727_781delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCT|ENSP00000363340.1:p.Gly261Cys||||||||||||||||||,C|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1188-1242|727-781|243-261|CPGPGPGPSPGPGPGPSPG/G|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/Ggt||5||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.727_781delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsG|ENSP00000363340.1:p.Cys243_Pro260del||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1188-1242|727-781|243-261|CPGPGPGPSPGPGPGPSPG/CPGPGPGPSPGPGPGPG|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCGgt||4||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.727_781delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCG|ENSP00000363340.1:p.Ser259_Pro260del||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1188-1242|727-781|243-261|CPGPGPGPSPGPGPGPSPG/CPGPGPGPG|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/TGTCCCGGTCCCGGTCCCGGCCCCGgt||3||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.727_781delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCG|ENSP00000363340.1:p.Ser251_Pro260del||||||||||||||||||,CACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACA||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||2||||||regulatory_region|||||||||||||||||||||||||||||||,AGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACA||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||1||||||regulatory_region|||||||||||||||||||||||||||||||,C||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||5||||||regulatory_region|||||||||||||||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACA||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||4||||||regulatory_region|||||||||||||||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACA||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||3||||||regulatory_region|||||||||||||||||||||||||||||||;AC_POPMAX=43,10,1,1,1;AN_POPMAX=790,790,1454,790,1454;POPMAX=AFR,AFR,NFE,AFR,NFE +1 26608844 . GGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC TGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC,G,AGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC,GCCGGGACCGGGAC 21967.79 VQSRTrancheINDEL99.00to99.50 AC=2,19,2,1;AC_AFR=0,2,1,0;AC_AMR=0,1,0,0;AC_Adj=2,19,2,1;AC_EAS=2,3,0,0;AC_FIN=0,2,0,0;AC_Het=2,19,2,1,0,0,0,0,0,0;AC_Hom=0,0,0,0;AC_NFE=0,7,1,1;AC_OTH=0,0,0,0;AC_SAS=0,4,0,0;AF=8.277e-05,7.863e-04,8.277e-05,4.138e-05;AN=24164;AN_AFR=1302;AN_AMR=3414;AN_Adj=15750;AN_EAS=2932;AN_FIN=226;AN_NFE=4550;AN_OTH=112;AN_SAS=3214;BaseQRankSum=0.886;ClippingRankSum=0.652;DP=311779;FS=10.291;GQ_MEAN=38.00;GQ_STDDEV=43.85;Het_AFR=0,2,1,0,0,0,0,0,0,0;Het_AMR=0,1,0,0,0,0,0,0,0,0;Het_EAS=2,3,0,0,0,0,0,0,0,0;Het_FIN=0,2,0,0,0,0,0,0,0,0;Het_NFE=0,7,1,1,0,0,0,0,0,0;Het_OTH=0,0,0,0,0,0,0,0,0,0;Het_SAS=0,4,0,0,0,0,0,0,0,0;Hom_AFR=0,0,0,0;Hom_AMR=0,0,0,0;Hom_EAS=0,0,0,0;Hom_FIN=0,0,0,0;Hom_NFE=0,0,0,0;Hom_OTH=0,0,0,0;Hom_SAS=0,0,0,0;InbreedingCoeff=0.1129;MQ=54.83;MQ0=0;MQRankSum=-1.270e+00;NCC=74531;QD=0.64;ReadPosRankSum=0.308;VQSLOD=-5.683e-01;culprit=FS;DP_HIST=1341|1528|885|935|2244|1729|1360|752|464|309|183|120|70|53|30|19|13|13|7|27,0|0|1|0|0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0,0|0|2|2|0|2|1|0|0|0|0|0|0|0|1|2|1|2|1|5,0|0|0|1|0|0|0|1|0|0|0|0|0|0|0|0|0|0|0|0,0|0|0|0|0|0|0|0|1|0|0|0|0|0|0|0|0|0|0|0;GQ_HIST=1358|1611|250|327|1650|473|584|445|242|349|263|151|2178|829|330|345|208|95|108|286,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|2,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|19,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|2,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1;CSQ=TGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2239-2291||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2239_2291delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCA|||||||||||||||||||,GCCGGGACCGGGAC|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2239-2291||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2239_2291delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGC|||||||||||||||||||,AGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2239-2291||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2239_2291delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCT|||||||||||||||||||,G|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2239-2291||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2239_2291delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsC|||||||||||||||||||,TGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000374217|Transcript|synonymous_variant|1725-1777|1358-1410|453-470|CPGPGPGPSPGPGPGPSP|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC/tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCA||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1358_1410delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCA|ENST00000374217.2:c.1358_1410delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCA(p.%3D)||||||||||||||||||,GCCGGGACCGGGAC|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1725-1777|1358-1410|453-470|CPGPGPGPSPGPGPGPSP/CPGPG|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC/tGTCCCGGTCCCGGC||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1358_1410delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGC|ENSP00000363334.2:p.Pro458_Pro470del||||||||||||||||||,AGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000374217|Transcript|synonymous_variant|1725-1777|1358-1410|453-470|CPGPGPGPSPGPGPGPSP|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC/tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCT||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1358_1410delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCT|ENST00000374217.2:c.1358_1410delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCT(p.%3D)||||||||||||||||||,G|ENSG00000158062|ENST00000374217|Transcript|frameshift_variant&feature_truncation|1725-1777|1358-1410|453-470|CPGPGPGPSPGPGPGPSP/X|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC/tC||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1358_1410delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsC|ENSP00000363334.2:p.Cys453SerfsTer?|||||||||||||||POSITION:0.963114754098361&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,TGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000374222|Transcript|synonymous_variant|1922-1974|1457-1509|486-503|CPGPGPGPSPGPGPGPSP|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC/tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCA||1||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1457_1509delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCA|ENST00000374222.1:c.1457_1509delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCA(p.%3D)||||||||||||||||||,GCCGGGACCGGGAC|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1922-1974|1457-1509|486-503|CPGPGPGPSPGPGPGPSP/CPGPG|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC/tGTCCCGGTCCCGGC||4||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1457_1509delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGC|ENSP00000363339.1:p.Pro491_Pro503del||||||||||||||||||,AGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000374222|Transcript|synonymous_variant|1922-1974|1457-1509|486-503|CPGPGPGPSPGPGPGPSP|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC/tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCT||3||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1457_1509delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCT|ENST00000374222.1:c.1457_1509delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCT(p.%3D)||||||||||||||||||,G|ENSG00000158062|ENST00000374222|Transcript|frameshift_variant&feature_truncation|1922-1974|1457-1509|486-503|CPGPGPGPSPGPGPGPSP/X|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC/tC||2||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1457_1509delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsC|ENSP00000363339.1:p.Cys486SerfsTer?|||||||||||||||POSITION:0.965451055662188&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,TGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000357089|Transcript|synonymous_variant|1434-1486|1358-1410|453-470|CPGPGPGPSPGPGPGPSP|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC/tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCA||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1358_1410delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCA|ENST00000357089.4:c.1358_1410delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCA(p.%3D)||||||||||||||||||,GCCGGGACCGGGAC|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1434-1486|1358-1410|453-470|CPGPGPGPSPGPGPGPSP/CPGPG|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC/tGTCCCGGTCCCGGC||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1358_1410delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGC|ENSP00000349601.4:p.Pro458_Pro470del||||||||||||||||||,AGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000357089|Transcript|synonymous_variant|1434-1486|1358-1410|453-470|CPGPGPGPSPGPGPGPSP|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC/tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCT||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1358_1410delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCT|ENST00000357089.4:c.1358_1410delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCT(p.%3D)||||||||||||||||||,G|ENSG00000158062|ENST00000357089|Transcript|frameshift_variant&feature_truncation|1434-1486|1358-1410|453-470|CPGPGPGPSPGPGPGPSP/X|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC/tC||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1358_1410delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsC|ENSP00000349601.4:p.Cys453SerfsTer?|||||||||||||||POSITION:0.963114754098361&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,TGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000314675|Transcript|synonymous_variant|1177-1229|1097-1149|366-383|CPGPGPGPSPGPGPGPSP|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC/tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCA||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1097_1149delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCA|ENST00000314675.7:c.1097_1149delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCA(p.%3D)||||||||||||||||||,GCCGGGACCGGGAC|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1177-1229|1097-1149|366-383|CPGPGPGPSPGPGPGPSP/CPGPG|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC/tGTCCCGGTCCCGGC||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1097_1149delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGC|ENSP00000324721.7:p.Pro371_Pro383del||||||||||||||||||,AGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000314675|Transcript|synonymous_variant|1177-1229|1097-1149|366-383|CPGPGPGPSPGPGPGPSP|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC/tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCT||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1097_1149delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCT|ENST00000314675.7:c.1097_1149delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCT(p.%3D)||||||||||||||||||,G|ENSG00000158062|ENST00000314675|Transcript|frameshift_variant&feature_truncation|1177-1229|1097-1149|366-383|CPGPGPGPSPGPGPGPSP/X|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC/tC||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1097_1149delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsC|ENSP00000324721.7:p.Cys366SerfsTer60|||||||||||||||POSITION:0.955112219451372&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,TGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2419-2471||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2419_2471delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCA|||||||||||||||||||,GCCGGGACCGGGAC|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2419-2471||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2419_2471delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGC|||||||||||||||||||,AGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2419-2471||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2419_2471delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCT|||||||||||||||||||,G|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2419-2471||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2419_2471delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsC|||||||||||||||||||,TGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2204-2256||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2204_2256delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCA|||||||||||||||||||,GCCGGGACCGGGAC|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2204-2256||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2204_2256delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGC|||||||||||||||||||,AGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2204-2256||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2204_2256delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCT|||||||||||||||||||,G|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2204-2256||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2204_2256delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsC|||||||||||||||||||,TGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000374221|Transcript|synonymous_variant|1671-1723|1457-1509|486-503|CPGPGPGPSPGPGPGPSP|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC/tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCA||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1457_1509delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCA|ENST00000374221.3:c.1457_1509delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCA(p.%3D)||||||||||||||||||,GCCGGGACCGGGAC|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1671-1723|1457-1509|486-503|CPGPGPGPSPGPGPGPSP/CPGPG|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC/tGTCCCGGTCCCGGC||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1457_1509delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGC|ENSP00000363338.3:p.Pro491_Pro503del||||||||||||||||||,AGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000374221|Transcript|synonymous_variant|1671-1723|1457-1509|486-503|CPGPGPGPSPGPGPGPSP|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC/tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCT||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1457_1509delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCT|ENST00000374221.3:c.1457_1509delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCT(p.%3D)||||||||||||||||||,G|ENSG00000158062|ENST00000374221|Transcript|frameshift_variant&feature_truncation|1671-1723|1457-1509|486-503|CPGPGPGPSPGPGPGPSP/X|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC/tC||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1457_1509delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsC|ENSP00000363338.3:p.Cys486SerfsTer?|||||||||||||||POSITION:0.965451055662188&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,TGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2522-2574||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2522_2574delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCA|||||||||||||||||||,GCCGGGACCGGGAC|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2522-2574||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2522_2574delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGC|||||||||||||||||||,AGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2522-2574||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2522_2574delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCT|||||||||||||||||||,G|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2522-2574||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2522_2574delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsC|||||||||||||||||||,TGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000374223|Transcript|synonymous_variant|1189-1241|728-780|243-260|CPGPGPGPSPGPGPGPSP|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC/tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCA||1||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.728_780delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCA|ENST00000374223.1:c.728_780delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCA(p.%3D)||||||||||||||||||,GCCGGGACCGGGAC|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1189-1241|728-780|243-260|CPGPGPGPSPGPGPGPSP/CPGPG|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC/tGTCCCGGTCCCGGC||4||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.728_780delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGC|ENSP00000363340.1:p.Pro248_Pro260del||||||||||||||||||,AGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000374223|Transcript|synonymous_variant|1189-1241|728-780|243-260|CPGPGPGPSPGPGPGPSP|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC/tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCT||3||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.728_780delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCT|ENST00000374223.1:c.728_780delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCT(p.%3D)||||||||||||||||||,G|ENSG00000158062|ENST00000374223|Transcript|frameshift_variant&feature_truncation|1189-1241|728-780|243-260|CPGPGPGPSPGPGPGPSP/X|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC/tC||2||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.728_780delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsC|ENSP00000363340.1:p.Cys243SerfsTer?|||||||||||||||POSITION:0.935251798561151&PHYLOCSF_TOO_SHORT|||HC,TGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||1||||||regulatory_region|||||||||||||||||||||||||||||||,GCCGGGACCGGGAC||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||4||||||regulatory_region|||||||||||||||||||||||||||||||,AGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||3||||||regulatory_region|||||||||||||||||||||||||||||||,G||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||2||||||regulatory_region|||||||||||||||||||||||||||||||;AC_POPMAX=2,2,1,1;AN_POPMAX=2932,226,1302,4550;POPMAX=EAS,FIN,AFR,NFE +1 26608849 . TGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC CGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC,AGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC,TGGGGCCGGGACCGGGACCGGGACCGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC,TGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC,TGGGACC,T 258591.24 PASS AC=10,171,18,57,1,1;AC_AFR=0,10,0,1,0,0;AC_AMR=0,1,1,0,0,0;AC_Adj=9,77,16,55,1,1;AC_EAS=9,2,0,0,1,0;AC_FIN=0,8,0,6,0,0;AC_Het=9,75,16,55,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;AC_Hom=0,1,0,0,0,0;AC_NFE=0,51,12,48,0,1;AC_OTH=0,0,0,0,0,0;AC_SAS=0,5,3,0,0,0;AF=5.302e-04,9.067e-03,9.544e-04,3.022e-03,5.302e-05,5.302e-05;AN=18860;AN_AFR=970;AN_AMR=2698;AN_Adj=11750;AN_EAS=3148;AN_FIN=218;AN_NFE=1740;AN_OTH=56;AN_SAS=2920;BaseQRankSum=0.101;ClippingRankSum=0.134;DP=186117;FS=1.921;GQ_MEAN=52.76;GQ_STDDEV=175.67;Het_AFR=0,10,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_AMR=0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_EAS=9,2,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_FIN=0,8,0,6,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_NFE=0,49,12,48,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_OTH=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_SAS=0,5,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Hom_AFR=0,0,0,0,0,0;Hom_AMR=0,0,0,0,0,0;Hom_EAS=0,0,0,0,0,0;Hom_FIN=0,0,0,0,0,0;Hom_NFE=0,1,0,0,0,0;Hom_OTH=0,0,0,0,0,0;Hom_SAS=0,0,0,0,0,0;InbreedingCoeff=0.2466;MQ=53.03;MQ0=0;MQRankSum=-9.500e-02;NCC=78416;QD=21.04;ReadPosRankSum=-3.800e-02;VQSLOD=2.10;culprit=InbreedingCoeff;DP_HIST=1241|1573|900|691|1817|1272|977|399|236|126|77|45|23|17|13|6|5|3|0|7,0|1|2|1|1|1|1|2|0|0|1|0|0|0|0|0|0|0|0|0,20|40|44|20|14|3|2|0|1|1|0|0|0|0|0|0|0|0|0|0,0|2|0|1|3|2|1|0|3|2|1|2|0|1|0|0|0|0|0|0,1|1|2|0|5|6|3|8|6|8|5|5|3|1|0|1|1|0|0|1,0|0|0|0|0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0,0|0|0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0|0;GQ_HIST=813|1515|302|263|1335|367|404|273|132|146|107|62|1792|633|276|285|174|86|73|392,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1|0|0|9,5|5|5|9|3|4|5|5|6|5|4|2|1|2|2|1|3|2|4|74,0|0|0|0|1|0|1|0|0|0|0|0|0|0|0|0|0|0|0|16,0|0|0|0|0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|56,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1;CSQ=AGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2244-2286||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2244_2286delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCT|||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2244-2286||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2244_2286delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCG|||||||||||||||||||,T|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2244-2286||||||6||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2244_2286delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsA|||||||||||||||||||,TGGGGCCGGGACCGGGACCGGGACCGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_elongation|2244-2286||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2244_2286delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCGGTCCCGGTCCCGGTCCCGGCCCCA|||||||||||||||||||,TGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2244-2286||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2244_2286delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCA|||||||||||||||||||,TGGGACC|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2244-2286||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2244_2286delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCA|||||||||||||||||||,AGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000374217|Transcript|missense_variant|1730-1772|1363-1405|455-469|GPGPGPSPGPGPGPS/GPGPGPSPGPGPGPC|GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAgt/GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCTgt||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1363_1405delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCT|ENSP00000363334.2:p.Ser469Cys||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000374217|Transcript|missense_variant|1730-1772|1363-1405|455-469|GPGPGPSPGPGPGPS/GPGPGPSPGPGPGPG|GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAgt/GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCGgt||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1363_1405delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCG|ENSP00000363334.2:p.Ser469Gly||||||||||||||||||,T|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1730-1772|1363-1405|455-469|GPGPGPSPGPGPGPS/S|GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAgt/Agt||6||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1363_1405delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsA|ENSP00000363334.2:p.Gly455_Pro468del||||||||||||||||||,TGGGGCCGGGACCGGGACCGGGACCGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000374217|Transcript|inframe_insertion|1730-1772|1363-1405|455-469|GPGPGPSPGPGPGPS/GPGPGPSPGPGPGPGPGPGPGPS|GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAgt/GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCGGTCCCGGTCCCGGTCCCGGCCCCAgt||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1363_1405delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCGGTCCCGGTCCCGGTCCCGGCCCCA|ENSP00000363334.2:p.Pro468_Ser469insGlyProGlyProGlyProGlyPro||||||||||||||||||,TGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1730-1772|1363-1405|455-469|GPGPGPSPGPGPGPS/GPGPGPSPGPGPS|GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAgt/GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCAgt||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1363_1405delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCA|ENSP00000363334.2:p.Gly467_Pro468del||||||||||||||||||,TGGGACC|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1730-1772|1363-1405|455-469|GPGPGPSPGPGPGPS/GPS|GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAgt/GGTCCCAgt||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1363_1405delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCA|ENSP00000363334.2:p.Gly457_Pro468del||||||||||||||||||,AGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000374222|Transcript|missense_variant|1927-1969|1462-1504|488-502|GPGPGPSPGPGPGPS/GPGPGPSPGPGPGPC|GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAgt/GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCTgt||2||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1462_1504delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCT|ENSP00000363339.1:p.Ser502Cys||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000374222|Transcript|missense_variant|1927-1969|1462-1504|488-502|GPGPGPSPGPGPGPS/GPGPGPSPGPGPGPG|GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAgt/GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCGgt||1||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1462_1504delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCG|ENSP00000363339.1:p.Ser502Gly||||||||||||||||||,T|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1927-1969|1462-1504|488-502|GPGPGPSPGPGPGPS/S|GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAgt/Agt||6||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1462_1504delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsA|ENSP00000363339.1:p.Gly488_Pro501del||||||||||||||||||,TGGGGCCGGGACCGGGACCGGGACCGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000374222|Transcript|inframe_insertion|1927-1969|1462-1504|488-502|GPGPGPSPGPGPGPS/GPGPGPSPGPGPGPGPGPGPGPS|GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAgt/GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCGGTCCCGGTCCCGGTCCCGGCCCCAgt||3||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1462_1504delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCGGTCCCGGTCCCGGTCCCGGCCCCA|ENSP00000363339.1:p.Pro501_Ser502insGlyProGlyProGlyProGlyPro||||||||||||||||||,TGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1927-1969|1462-1504|488-502|GPGPGPSPGPGPGPS/GPGPGPSPGPGPS|GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAgt/GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCAgt||4||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1462_1504delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCA|ENSP00000363339.1:p.Gly500_Pro501del||||||||||||||||||,TGGGACC|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1927-1969|1462-1504|488-502|GPGPGPSPGPGPGPS/GPS|GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAgt/GGTCCCAgt||5||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1462_1504delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCA|ENSP00000363339.1:p.Gly490_Pro501del||||||||||||||||||,AGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000357089|Transcript|missense_variant|1439-1481|1363-1405|455-469|GPGPGPSPGPGPGPS/GPGPGPSPGPGPGPC|GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAgt/GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCTgt||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1363_1405delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCT|ENSP00000349601.4:p.Ser469Cys||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000357089|Transcript|missense_variant|1439-1481|1363-1405|455-469|GPGPGPSPGPGPGPS/GPGPGPSPGPGPGPG|GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAgt/GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCGgt||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1363_1405delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCG|ENSP00000349601.4:p.Ser469Gly||||||||||||||||||,T|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1439-1481|1363-1405|455-469|GPGPGPSPGPGPGPS/S|GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAgt/Agt||6||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1363_1405delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsA|ENSP00000349601.4:p.Gly455_Pro468del||||||||||||||||||,TGGGGCCGGGACCGGGACCGGGACCGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000357089|Transcript|inframe_insertion|1439-1481|1363-1405|455-469|GPGPGPSPGPGPGPS/GPGPGPSPGPGPGPGPGPGPGPS|GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAgt/GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCGGTCCCGGTCCCGGTCCCGGCCCCAgt||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1363_1405delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCGGTCCCGGTCCCGGTCCCGGCCCCA|ENSP00000349601.4:p.Pro468_Ser469insGlyProGlyProGlyProGlyPro||||||||||||||||||,TGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1439-1481|1363-1405|455-469|GPGPGPSPGPGPGPS/GPGPGPSPGPGPS|GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAgt/GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCAgt||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1363_1405delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCA|ENSP00000349601.4:p.Gly467_Pro468del||||||||||||||||||,TGGGACC|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1439-1481|1363-1405|455-469|GPGPGPSPGPGPGPS/GPS|GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAgt/GGTCCCAgt||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1363_1405delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCA|ENSP00000349601.4:p.Gly457_Pro468del||||||||||||||||||,AGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000314675|Transcript|missense_variant|1182-1224|1102-1144|368-382|GPGPGPSPGPGPGPS/GPGPGPSPGPGPGPC|GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAgt/GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCTgt||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1102_1144delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCT|ENSP00000324721.7:p.Ser382Cys||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000314675|Transcript|missense_variant|1182-1224|1102-1144|368-382|GPGPGPSPGPGPGPS/GPGPGPSPGPGPGPG|GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAgt/GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCGgt||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1102_1144delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCG|ENSP00000324721.7:p.Ser382Gly||||||||||||||||||,T|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1182-1224|1102-1144|368-382|GPGPGPSPGPGPGPS/S|GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAgt/Agt||6||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1102_1144delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsA|ENSP00000324721.7:p.Gly368_Pro381del||||||||||||||||||,TGGGGCCGGGACCGGGACCGGGACCGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000314675|Transcript|inframe_insertion|1182-1224|1102-1144|368-382|GPGPGPSPGPGPGPS/GPGPGPSPGPGPGPGPGPGPGPS|GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAgt/GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCGGTCCCGGTCCCGGTCCCGGCCCCAgt||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1102_1144delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCGGTCCCGGTCCCGGTCCCGGCCCCA|ENSP00000324721.7:p.Pro381_Ser382insGlyProGlyProGlyProGlyPro||||||||||||||||||,TGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1182-1224|1102-1144|368-382|GPGPGPSPGPGPGPS/GPGPGPSPGPGPS|GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAgt/GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCAgt||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1102_1144delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCA|ENSP00000324721.7:p.Gly380_Pro381del||||||||||||||||||,TGGGACC|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1182-1224|1102-1144|368-382|GPGPGPSPGPGPGPS/GPS|GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAgt/GGTCCCAgt||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1102_1144delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCA|ENSP00000324721.7:p.Gly370_Pro381del||||||||||||||||||,AGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2424-2466||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2424_2466delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCT|||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2424-2466||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2424_2466delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCG|||||||||||||||||||,T|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2424-2466||||||6||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2424_2466delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsA|||||||||||||||||||,TGGGGCCGGGACCGGGACCGGGACCGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_elongation|2424-2466||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2424_2466delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCGGTCCCGGTCCCGGTCCCGGCCCCA|||||||||||||||||||,TGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2424-2466||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2424_2466delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCA|||||||||||||||||||,TGGGACC|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2424-2466||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2424_2466delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCA|||||||||||||||||||,AGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2209-2251||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2209_2251delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCT|||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2209-2251||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2209_2251delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCG|||||||||||||||||||,T|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2209-2251||||||6||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2209_2251delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsA|||||||||||||||||||,TGGGGCCGGGACCGGGACCGGGACCGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_elongation|2209-2251||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2209_2251delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCGGTCCCGGTCCCGGTCCCGGCCCCA|||||||||||||||||||,TGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2209-2251||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2209_2251delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCA|||||||||||||||||||,TGGGACC|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2209-2251||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2209_2251delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCA|||||||||||||||||||,AGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000374221|Transcript|missense_variant|1676-1718|1462-1504|488-502|GPGPGPSPGPGPGPS/GPGPGPSPGPGPGPC|GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAgt/GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCTgt||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1462_1504delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCT|ENSP00000363338.3:p.Ser502Cys||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000374221|Transcript|missense_variant|1676-1718|1462-1504|488-502|GPGPGPSPGPGPGPS/GPGPGPSPGPGPGPG|GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAgt/GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCGgt||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1462_1504delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCG|ENSP00000363338.3:p.Ser502Gly||||||||||||||||||,T|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1676-1718|1462-1504|488-502|GPGPGPSPGPGPGPS/S|GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAgt/Agt||6||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1462_1504delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsA|ENSP00000363338.3:p.Gly488_Pro501del||||||||||||||||||,TGGGGCCGGGACCGGGACCGGGACCGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000374221|Transcript|inframe_insertion|1676-1718|1462-1504|488-502|GPGPGPSPGPGPGPS/GPGPGPSPGPGPGPGPGPGPGPS|GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAgt/GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCGGTCCCGGTCCCGGTCCCGGCCCCAgt||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1462_1504delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCGGTCCCGGTCCCGGTCCCGGCCCCA|ENSP00000363338.3:p.Pro501_Ser502insGlyProGlyProGlyProGlyPro||||||||||||||||||,TGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1676-1718|1462-1504|488-502|GPGPGPSPGPGPGPS/GPGPGPSPGPGPS|GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAgt/GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCAgt||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1462_1504delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCA|ENSP00000363338.3:p.Gly500_Pro501del||||||||||||||||||,TGGGACC|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1676-1718|1462-1504|488-502|GPGPGPSPGPGPGPS/GPS|GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAgt/GGTCCCAgt||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1462_1504delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCA|ENSP00000363338.3:p.Gly490_Pro501del||||||||||||||||||,AGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2527-2569||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2527_2569delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCT|||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2527-2569||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2527_2569delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCG|||||||||||||||||||,T|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2527-2569||||||6||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2527_2569delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsA|||||||||||||||||||,TGGGGCCGGGACCGGGACCGGGACCGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_elongation|2527-2569||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2527_2569delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCGGTCCCGGTCCCGGTCCCGGCCCCA|||||||||||||||||||,TGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2527-2569||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2527_2569delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCA|||||||||||||||||||,TGGGACC|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2527-2569||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2527_2569delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCA|||||||||||||||||||,AGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000374223|Transcript|missense_variant|1194-1236|733-775|245-259|GPGPGPSPGPGPGPS/GPGPGPSPGPGPGPC|GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAgt/GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCTgt||2||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.733_775delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCT|ENSP00000363340.1:p.Ser259Cys||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000374223|Transcript|missense_variant|1194-1236|733-775|245-259|GPGPGPSPGPGPGPS/GPGPGPSPGPGPGPG|GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAgt/GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCGgt||1||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.733_775delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCG|ENSP00000363340.1:p.Ser259Gly||||||||||||||||||,T|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1194-1236|733-775|245-259|GPGPGPSPGPGPGPS/S|GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAgt/Agt||6||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.733_775delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsA|ENSP00000363340.1:p.Gly245_Pro258del||||||||||||||||||,TGGGGCCGGGACCGGGACCGGGACCGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000374223|Transcript|inframe_insertion|1194-1236|733-775|245-259|GPGPGPSPGPGPGPS/GPGPGPSPGPGPGPGPGPGPGPS|GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAgt/GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCGGTCCCGGTCCCGGTCCCGGCCCCAgt||3||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.733_775delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCGGTCCCGGTCCCGGTCCCGGCCCCA|ENSP00000363340.1:p.Pro258_Ser259insGlyProGlyProGlyProGlyPro||||||||||||||||||,TGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1194-1236|733-775|245-259|GPGPGPSPGPGPGPS/GPGPGPSPGPGPS|GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAgt/GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCAgt||4||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.733_775delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCA|ENSP00000363340.1:p.Gly257_Pro258del||||||||||||||||||,TGGGACC|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1194-1236|733-775|245-259|GPGPGPSPGPGPGPS/GPS|GGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAgt/GGTCCCAgt||5||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.733_775delGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAinsGGTCCCA|ENSP00000363340.1:p.Gly247_Pro258del||||||||||||||||||,AGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||2||||||regulatory_region|||||||||||||||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||1||||||regulatory_region|||||||||||||||||||||||||||||||,T||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||6||||||regulatory_region|||||||||||||||||||||||||||||||,TGGGGCCGGGACCGGGACCGGGACCGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||3||||||regulatory_region|||||||||||||||||||||||||||||||,TGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||4||||||regulatory_region|||||||||||||||||||||||||||||||,TGGGACC||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||5||||||regulatory_region|||||||||||||||||||||||||||||||;AC_POPMAX=9,8,12,48,1,1;AN_POPMAX=3148,218,1740,1740,3148,1740;POPMAX=EAS,FIN,NFE,NFE,EAS,NFE +1 26608850 . GGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC G,GGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC,AGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC 48867.68 VQSRTrancheINDEL97.00to99.00 AC=26,2,1;AC_AFR=23,0,0;AC_AMR=1,0,0;AC_Adj=25,1,0;AC_EAS=0,0,0;AC_FIN=0,0,0;AC_Het=25,1,0,0,0,0;AC_Hom=0,0,0;AC_NFE=1,1,0;AC_OTH=0,0,0;AC_SAS=0,0,0;AF=1.422e-03,1.094e-04,5.469e-05;AN=18286;AN_AFR=952;AN_AMR=2704;AN_Adj=11392;AN_EAS=3124;AN_FIN=188;AN_NFE=1488;AN_OTH=56;AN_SAS=2880;BaseQRankSum=-6.550e-01;ClippingRankSum=-2.200e-01;DP=184071;FS=3.407;GQ_MEAN=39.22;GQ_STDDEV=74.80;Het_AFR=23,0,0,0,0,0;Het_AMR=1,0,0,0,0,0;Het_EAS=0,0,0,0,0,0;Het_FIN=0,0,0,0,0,0;Het_NFE=1,1,0,0,0,0;Het_OTH=0,0,0,0,0,0;Het_SAS=0,0,0,0,0,0;Hom_AFR=0,0,0;Hom_AMR=0,0,0;Hom_EAS=0,0,0;Hom_FIN=0,0,0;Hom_NFE=0,0,0;Hom_OTH=0,0,0;Hom_SAS=0,0,0;InbreedingCoeff=0.0792;MQ=53.28;MQ0=0;MQRankSum=-2.550e-01;NCC=78860;QD=1.08;ReadPosRankSum=-4.700e-01;VQSLOD=0.575;culprit=QD;DP_HIST=1185|1483|840|671|1763|1277|987|399|218|121|69|42|20|17|12|7|5|8|1|18,0|1|0|0|1|1|1|1|0|1|2|1|0|0|1|0|2|3|1|10,0|1|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0,0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;GQ_HIST=558|1672|355|320|1278|343|426|303|138|144|110|68|1732|612|268|278|164|73|67|234,0|0|0|1|0|0|0|0|0|0|0|1|0|0|0|0|0|0|0|24,0|0|0|0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|1,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1;CSQ=GGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2239-2285||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2239_2285delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCC|||||||||||||||||||,AGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2239-2285||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2239_2285delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCT|||||||||||||||||||,G|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2239-2285||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2239_2285delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCinsC|||||||||||||||||||,GGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000374217|Transcript|frameshift_variant&feature_truncation|1725-1771|1358-1404|453-468|CPGPGPGPSPGPGPGP/CPGPGPGPSPGPGPX|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCC/tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCC||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1358_1404delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCC|ENSP00000363334.2:p.Gly467GlnfsTer?|||||||||||||||POSITION:0.959016393442623&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,AGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000374217|Transcript|synonymous_variant|1725-1771|1358-1404|453-468|CPGPGPGPSPGPGPGP|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCC/tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCT||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1358_1404delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCT|ENST00000374217.2:c.1358_1404delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCT(p.%3D)||||||||||||||||||,G|ENSG00000158062|ENST00000374217|Transcript|frameshift_variant&feature_truncation|1725-1771|1358-1404|453-468|CPGPGPGPSPGPGPGP/X|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCC/tC||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1358_1404delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCinsC|ENSP00000363334.2:p.Cys453SerfsTer?|||||||||||||||POSITION:0.959016393442623&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,GGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000374222|Transcript|frameshift_variant&feature_truncation|1922-1968|1457-1503|486-501|CPGPGPGPSPGPGPGP/CPGPGPGPSPGPGPX|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCC/tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCC||2||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1457_1503delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCC|ENSP00000363339.1:p.Gly500GlnfsTer?|||||||||||||||POSITION:0.961612284069098&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,AGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000374222|Transcript|synonymous_variant|1922-1968|1457-1503|486-501|CPGPGPGPSPGPGPGP|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCC/tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCT||3||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1457_1503delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCT|ENST00000374222.1:c.1457_1503delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCT(p.%3D)||||||||||||||||||,G|ENSG00000158062|ENST00000374222|Transcript|frameshift_variant&feature_truncation|1922-1968|1457-1503|486-501|CPGPGPGPSPGPGPGP/X|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCC/tC||1||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1457_1503delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCinsC|ENSP00000363339.1:p.Cys486SerfsTer?|||||||||||||||POSITION:0.961612284069098&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,GGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000357089|Transcript|frameshift_variant&feature_truncation|1434-1480|1358-1404|453-468|CPGPGPGPSPGPGPGP/CPGPGPGPSPGPGPX|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCC/tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCC||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1358_1404delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCC|ENSP00000349601.4:p.Gly467GlnfsTer?|||||||||||||||POSITION:0.959016393442623&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,AGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000357089|Transcript|synonymous_variant|1434-1480|1358-1404|453-468|CPGPGPGPSPGPGPGP|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCC/tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCT||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1358_1404delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCT|ENST00000357089.4:c.1358_1404delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCT(p.%3D)||||||||||||||||||,G|ENSG00000158062|ENST00000357089|Transcript|frameshift_variant&feature_truncation|1434-1480|1358-1404|453-468|CPGPGPGPSPGPGPGP/X|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCC/tC||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1358_1404delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCinsC|ENSP00000349601.4:p.Cys453SerfsTer?|||||||||||||||POSITION:0.959016393442623&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,GGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000314675|Transcript|frameshift_variant&feature_truncation|1177-1223|1097-1143|366-381|CPGPGPGPSPGPGPGP/CPGPGPGPSPGPGPX|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCC/tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCC||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1097_1143delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCC|ENSP00000324721.7:p.Gly380GlnfsTer154|||||||||||||||POSITION:0.950124688279302&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,AGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000314675|Transcript|synonymous_variant|1177-1223|1097-1143|366-381|CPGPGPGPSPGPGPGP|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCC/tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCT||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1097_1143delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCT|ENST00000314675.7:c.1097_1143delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCT(p.%3D)||||||||||||||||||,G|ENSG00000158062|ENST00000314675|Transcript|frameshift_variant&feature_truncation|1177-1223|1097-1143|366-381|CPGPGPGPSPGPGPGP/X|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCC/tC||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1097_1143delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCinsC|ENSP00000324721.7:p.Cys366SerfsTer62|||||||||||||||POSITION:0.950124688279302&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,GGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2419-2465||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2419_2465delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCC|||||||||||||||||||,AGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2419-2465||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2419_2465delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCT|||||||||||||||||||,G|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2419-2465||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2419_2465delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCinsC|||||||||||||||||||,GGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2204-2250||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2204_2250delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCC|||||||||||||||||||,AGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2204-2250||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2204_2250delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCT|||||||||||||||||||,G|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2204-2250||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2204_2250delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCinsC|||||||||||||||||||,GGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000374221|Transcript|frameshift_variant&feature_truncation|1671-1717|1457-1503|486-501|CPGPGPGPSPGPGPGP/CPGPGPGPSPGPGPX|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCC/tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCC||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1457_1503delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCC|ENSP00000363338.3:p.Gly500GlnfsTer?|||||||||||||||POSITION:0.961612284069098&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,AGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000374221|Transcript|synonymous_variant|1671-1717|1457-1503|486-501|CPGPGPGPSPGPGPGP|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCC/tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCT||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1457_1503delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCT|ENST00000374221.3:c.1457_1503delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCT(p.%3D)||||||||||||||||||,G|ENSG00000158062|ENST00000374221|Transcript|frameshift_variant&feature_truncation|1671-1717|1457-1503|486-501|CPGPGPGPSPGPGPGP/X|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCC/tC||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1457_1503delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCinsC|ENSP00000363338.3:p.Cys486SerfsTer?|||||||||||||||POSITION:0.961612284069098&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,GGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2522-2568||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2522_2568delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCC|||||||||||||||||||,AGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2522-2568||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2522_2568delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCT|||||||||||||||||||,G|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2522-2568||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2522_2568delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCinsC|||||||||||||||||||,GGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000374223|Transcript|frameshift_variant&feature_truncation|1189-1235|728-774|243-258|CPGPGPGPSPGPGPGP/CPGPGPGPSPGPGPX|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCC/tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCC||2||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.728_774delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCC|ENSP00000363340.1:p.Gly257GlnfsTer?|||||||||||||||POSITION:0.928057553956835&PHYLOCSF_TOO_SHORT|||HC,AGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000374223|Transcript|synonymous_variant|1189-1235|728-774|243-258|CPGPGPGPSPGPGPGP|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCC/tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCT||3||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.728_774delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCT|ENST00000374223.1:c.728_774delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCT(p.%3D)||||||||||||||||||,G|ENSG00000158062|ENST00000374223|Transcript|frameshift_variant&feature_truncation|1189-1235|728-774|243-258|CPGPGPGPSPGPGPGP/X|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCC/tC||1||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.728_774delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCinsC|ENSP00000363340.1:p.Cys243SerfsTer?|||||||||||||||POSITION:0.928057553956835&PHYLOCSF_TOO_SHORT|||HC,GGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||2||||||regulatory_region|||||||||||||||||||||||||||||||,AGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGAC||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||3||||||regulatory_region|||||||||||||||||||||||||||||||,G||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||1||||||regulatory_region|||||||||||||||||||||||||||||||;AC_POPMAX=23,1,NA;AN_POPMAX=952,1488,NA;POPMAX=AFR,NFE,NA +1 26608853 . GCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA GCCGGGA,ACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA,GCCGGGACTGGGGCCGGGACCGGGA,G,GCCGGGACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA,GACGGGACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA 465752.87 VQSRTrancheINDEL95.00to96.00 AC=90,114,308,25,19,1;AC_AFR=41,10,235,0,12,1;AC_AMR=3,1,15,1,1,0;AC_Adj=85,63,260,24,16,1;AC_EAS=6,0,3,0,1,0;AC_FIN=0,7,0,0,0,0;AC_Het=84,55,238,24,16,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0;AC_Hom=0,4,10,0,0,0;AC_NFE=21,40,7,23,0,0;AC_OTH=1,1,0,0,0,0;AC_SAS=13,4,0,0,2,0;AF=3.541e-03,4.486e-03,0.012,9.837e-04,7.476e-04,3.935e-05;AN=25414;AN_AFR=1524;AN_AMR=2904;AN_Adj=14354;AN_EAS=3334;AN_FIN=426;AN_NFE=2948;AN_OTH=70;AN_SAS=3148;BaseQRankSum=-5.730e-01;ClippingRankSum=-3.500e-01;DP=260714;FS=0.000;GQ_MEAN=51.63;GQ_STDDEV=155.18;Het_AFR=40,8,213,0,12,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0;Het_AMR=3,1,15,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_EAS=6,0,3,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_FIN=0,7,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_NFE=21,34,7,23,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_OTH=1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_SAS=13,4,0,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Hom_AFR=0,1,10,0,0,0;Hom_AMR=0,0,0,0,0,0;Hom_EAS=0,0,0,0,0,0;Hom_FIN=0,0,0,0,0,0;Hom_NFE=0,3,0,0,0,0;Hom_OTH=0,0,0,0,0,0;Hom_SAS=0,0,0,0,0,0;InbreedingCoeff=0.2083;MQ=49.30;MQ0=0;MQRankSum=-1.663e+00;NCC=72918;QD=4.38;ReadPosRankSum=0.00;VQSLOD=1.12;culprit=FS;DP_HIST=1559|2346|1444|1054|1903|1567|1263|564|354|202|124|96|52|54|36|17|21|17|5|29,0|4|5|5|2|1|6|1|6|5|5|8|7|5|8|4|5|5|3|4,9|27|32|18|8|3|3|0|2|0|0|0|0|0|0|0|0|0|0|0,10|26|45|41|43|26|26|29|15|11|6|4|2|4|3|2|0|1|1|0,0|1|1|0|1|0|1|0|1|2|0|1|3|0|0|1|2|0|0|11,0|1|1|4|2|4|4|1|0|1|0|0|0|0|0|0|0|0|0|0,0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0|0|0|0;GQ_HIST=1472|2015|586|675|1450|469|562|422|221|287|179|69|1778|730|321|353|219|103|100|696,0|0|0|0|0|0|0|1|1|0|0|1|0|0|0|0|0|1|0|85,3|1|1|5|1|4|3|4|4|5|2|1|1|3|2|0|2|1|1|58,2|2|4|3|4|7|3|5|6|7|2|4|5|1|5|4|5|3|7|216,1|0|0|0|0|0|0|1|0|0|0|0|0|0|0|0|0|0|0|23,1|0|0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|16,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1;CSQ=ACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2246-2282||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2246_2282delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGT|||||||||||||||||||,GACGGGACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_elongation|2246-2282||||||6||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2246_2282delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGTC|||||||||||||||||||,G|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2246-2282||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2246_2282delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsC|||||||||||||||||||,GCCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2246-2282||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2246_2282delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGC|||||||||||||||||||,GCCGGGACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_elongation|2246-2282||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2246_2282delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGGC|||||||||||||||||||,GCCGGGA|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2246-2282||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2246_2282delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGC|||||||||||||||||||,ACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000374217|Transcript|synonymous_variant|1732-1768|1365-1401|455-467|GPGPGPSPGPGPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGT||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1365_1401delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGT|ENST00000374217.2:c.1365_1401delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGT(p.%3D)||||||||||||||||||,GACGGGACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000374217|Transcript|inframe_insertion|1732-1768|1365-1401|455-467|GPGPGPSPGPGPG/GPGPGPSPGPGPGPV|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGTC||6||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1365_1401delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGTC|ENSP00000363334.2:p.Gly467_Pro468insProVal||||||||||||||||||,G|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1732-1768|1365-1401|455-467|GPGPGPSPGPGPG/G|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggC||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1365_1401delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsC|ENSP00000363334.2:p.Pro456_Gly467del||||||||||||||||||,GCCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1732-1768|1365-1401|455-467|GPGPGPSPGPGPG/GPGPGPSPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGTCCCGGCCCCAGTCCCGGC||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1365_1401delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGC|ENSP00000363334.2:p.Pro464_Gly467del||||||||||||||||||,GCCGGGACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000374217|Transcript|inframe_insertion|1732-1768|1365-1401|455-467|GPGPGPSPGPGPG/GPGPGPSPGPGPGPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGGC||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1365_1401delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGGC|ENSP00000363334.2:p.Gly467_Pro468insProGly||||||||||||||||||,GCCGGGA|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1732-1768|1365-1401|455-467|GPGPGPSPGPGPG/GPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGC||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1365_1401delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGC|ENSP00000363334.2:p.Pro458_Gly467del||||||||||||||||||,ACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000374222|Transcript|synonymous_variant|1929-1965|1464-1500|488-500|GPGPGPSPGPGPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGT||2||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1464_1500delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGT|ENST00000374222.1:c.1464_1500delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGT(p.%3D)||||||||||||||||||,GACGGGACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000374222|Transcript|inframe_insertion|1929-1965|1464-1500|488-500|GPGPGPSPGPGPG/GPGPGPSPGPGPGPV|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGTC||6||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1464_1500delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGTC|ENSP00000363339.1:p.Gly500_Pro501insProVal||||||||||||||||||,G|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1929-1965|1464-1500|488-500|GPGPGPSPGPGPG/G|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggC||4||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1464_1500delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsC|ENSP00000363339.1:p.Pro489_Gly500del||||||||||||||||||,GCCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1929-1965|1464-1500|488-500|GPGPGPSPGPGPG/GPGPGPSPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGTCCCGGCCCCAGTCCCGGC||3||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1464_1500delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGC|ENSP00000363339.1:p.Pro497_Gly500del||||||||||||||||||,GCCGGGACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000374222|Transcript|inframe_insertion|1929-1965|1464-1500|488-500|GPGPGPSPGPGPG/GPGPGPSPGPGPGPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGGC||5||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1464_1500delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGGC|ENSP00000363339.1:p.Gly500_Pro501insProGly||||||||||||||||||,GCCGGGA|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1929-1965|1464-1500|488-500|GPGPGPSPGPGPG/GPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGC||1||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1464_1500delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGC|ENSP00000363339.1:p.Pro491_Gly500del||||||||||||||||||,ACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000357089|Transcript|synonymous_variant|1441-1477|1365-1401|455-467|GPGPGPSPGPGPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGT||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1365_1401delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGT|ENST00000357089.4:c.1365_1401delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGT(p.%3D)||||||||||||||||||,GACGGGACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000357089|Transcript|inframe_insertion|1441-1477|1365-1401|455-467|GPGPGPSPGPGPG/GPGPGPSPGPGPGPV|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGTC||6||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1365_1401delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGTC|ENSP00000349601.4:p.Gly467_Pro468insProVal||||||||||||||||||,G|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1441-1477|1365-1401|455-467|GPGPGPSPGPGPG/G|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggC||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1365_1401delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsC|ENSP00000349601.4:p.Pro456_Gly467del||||||||||||||||||,GCCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1441-1477|1365-1401|455-467|GPGPGPSPGPGPG/GPGPGPSPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGTCCCGGCCCCAGTCCCGGC||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1365_1401delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGC|ENSP00000349601.4:p.Pro464_Gly467del||||||||||||||||||,GCCGGGACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000357089|Transcript|inframe_insertion|1441-1477|1365-1401|455-467|GPGPGPSPGPGPG/GPGPGPSPGPGPGPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGGC||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1365_1401delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGGC|ENSP00000349601.4:p.Gly467_Pro468insProGly||||||||||||||||||,GCCGGGA|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1441-1477|1365-1401|455-467|GPGPGPSPGPGPG/GPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGC||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1365_1401delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGC|ENSP00000349601.4:p.Pro458_Gly467del||||||||||||||||||,ACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000314675|Transcript|synonymous_variant|1184-1220|1104-1140|368-380|GPGPGPSPGPGPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGT||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1104_1140delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGT|ENST00000314675.7:c.1104_1140delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGT(p.%3D)||||||||||||||||||,GACGGGACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000314675|Transcript|inframe_insertion|1184-1220|1104-1140|368-380|GPGPGPSPGPGPG/GPGPGPSPGPGPGPV|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGTC||6||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1104_1140delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGTC|ENSP00000324721.7:p.Gly380_Pro381insProVal||||||||||||||||||,G|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1184-1220|1104-1140|368-380|GPGPGPSPGPGPG/G|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggC||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1104_1140delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsC|ENSP00000324721.7:p.Pro369_Gly380del||||||||||||||||||,GCCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1184-1220|1104-1140|368-380|GPGPGPSPGPGPG/GPGPGPSPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGTCCCGGCCCCAGTCCCGGC||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1104_1140delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGC|ENSP00000324721.7:p.Pro377_Gly380del||||||||||||||||||,GCCGGGACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000314675|Transcript|inframe_insertion|1184-1220|1104-1140|368-380|GPGPGPSPGPGPG/GPGPGPSPGPGPGPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGGC||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1104_1140delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGGC|ENSP00000324721.7:p.Gly380_Pro381insProGly||||||||||||||||||,GCCGGGA|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1184-1220|1104-1140|368-380|GPGPGPSPGPGPG/GPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGC||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1104_1140delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGC|ENSP00000324721.7:p.Pro371_Gly380del||||||||||||||||||,ACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2426-2462||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2426_2462delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGT|||||||||||||||||||,GACGGGACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_elongation|2426-2462||||||6||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2426_2462delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGTC|||||||||||||||||||,G|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2426-2462||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2426_2462delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsC|||||||||||||||||||,GCCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2426-2462||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2426_2462delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGC|||||||||||||||||||,GCCGGGACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_elongation|2426-2462||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2426_2462delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGGC|||||||||||||||||||,GCCGGGA|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2426-2462||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2426_2462delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGC|||||||||||||||||||,ACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2211-2247||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2211_2247delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGT|||||||||||||||||||,GACGGGACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_elongation|2211-2247||||||6||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2211_2247delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGTC|||||||||||||||||||,G|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2211-2247||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2211_2247delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsC|||||||||||||||||||,GCCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2211-2247||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2211_2247delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGC|||||||||||||||||||,GCCGGGACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_elongation|2211-2247||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2211_2247delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGGC|||||||||||||||||||,GCCGGGA|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2211-2247||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2211_2247delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGC|||||||||||||||||||,ACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000374221|Transcript|synonymous_variant|1678-1714|1464-1500|488-500|GPGPGPSPGPGPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGT||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1464_1500delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGT|ENST00000374221.3:c.1464_1500delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGT(p.%3D)||||||||||||||||||,GACGGGACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000374221|Transcript|inframe_insertion|1678-1714|1464-1500|488-500|GPGPGPSPGPGPG/GPGPGPSPGPGPGPV|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGTC||6||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1464_1500delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGTC|ENSP00000363338.3:p.Gly500_Pro501insProVal||||||||||||||||||,G|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1678-1714|1464-1500|488-500|GPGPGPSPGPGPG/G|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggC||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1464_1500delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsC|ENSP00000363338.3:p.Pro489_Gly500del||||||||||||||||||,GCCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1678-1714|1464-1500|488-500|GPGPGPSPGPGPG/GPGPGPSPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGTCCCGGCCCCAGTCCCGGC||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1464_1500delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGC|ENSP00000363338.3:p.Pro497_Gly500del||||||||||||||||||,GCCGGGACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000374221|Transcript|inframe_insertion|1678-1714|1464-1500|488-500|GPGPGPSPGPGPG/GPGPGPSPGPGPGPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGGC||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1464_1500delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGGC|ENSP00000363338.3:p.Gly500_Pro501insProGly||||||||||||||||||,GCCGGGA|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1678-1714|1464-1500|488-500|GPGPGPSPGPGPG/GPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGC||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1464_1500delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGC|ENSP00000363338.3:p.Pro491_Gly500del||||||||||||||||||,ACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2529-2565||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2529_2565delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGT|||||||||||||||||||,GACGGGACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_elongation|2529-2565||||||6||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2529_2565delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGTC|||||||||||||||||||,G|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2529-2565||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2529_2565delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsC|||||||||||||||||||,GCCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2529-2565||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2529_2565delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGC|||||||||||||||||||,GCCGGGACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_elongation|2529-2565||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2529_2565delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGGC|||||||||||||||||||,GCCGGGA|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2529-2565||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2529_2565delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGC|||||||||||||||||||,ACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000374223|Transcript|synonymous_variant|1196-1232|735-771|245-257|GPGPGPSPGPGPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGT||2||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.735_771delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGT|ENST00000374223.1:c.735_771delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGT(p.%3D)||||||||||||||||||,GACGGGACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000374223|Transcript|inframe_insertion|1196-1232|735-771|245-257|GPGPGPSPGPGPG/GPGPGPSPGPGPGPV|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGTC||6||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.735_771delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGTC|ENSP00000363340.1:p.Gly257_Pro258insProVal||||||||||||||||||,G|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1196-1232|735-771|245-257|GPGPGPSPGPGPG/G|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggC||4||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.735_771delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsC|ENSP00000363340.1:p.Pro246_Gly257del||||||||||||||||||,GCCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1196-1232|735-771|245-257|GPGPGPSPGPGPG/GPGPGPSPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGTCCCGGCCCCAGTCCCGGC||3||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.735_771delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGC|ENSP00000363340.1:p.Pro254_Gly257del||||||||||||||||||,GCCGGGACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA|ENSG00000158062|ENST00000374223|Transcript|inframe_insertion|1196-1232|735-771|245-257|GPGPGPSPGPGPG/GPGPGPSPGPGPGPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGGC||5||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.735_771delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGTCCCGGC|ENSP00000363340.1:p.Gly257_Pro258insProGly||||||||||||||||||,GCCGGGA|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1196-1232|735-771|245-257|GPGPGPSPGPGPG/GPG|ggTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGC/ggTCCCGGC||1||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.735_771delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCinsTCCCGGC|ENSP00000363340.1:p.Pro248_Gly257del||||||||||||||||||,ACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||2||||||regulatory_region|||||||||||||||||||||||||||||||,GACGGGACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||6||||||regulatory_region|||||||||||||||||||||||||||||||,G||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||4||||||regulatory_region|||||||||||||||||||||||||||||||,GCCGGGACTGGGGCCGGGACCGGGA||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||3||||||regulatory_region|||||||||||||||||||||||||||||||,GCCGGGACCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||5||||||regulatory_region|||||||||||||||||||||||||||||||,GCCGGGA||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||1||||||regulatory_region|||||||||||||||||||||||||||||||;AC_POPMAX=41,7,235,23,12,1;AN_POPMAX=1524,426,1524,2948,1524,1524;POPMAX=AFR,FIN,AFR,NFE,AFR,AFR +1 26608855 . CGGGACCGGGACCGGGACT TGGGACCGGGACCGGGACT,C,CACCGGGACCGGGACT 54328.98 VQSRTrancheINDEL99.00to99.50 AC=94,7,1;AC_AFR=10,0,0;AC_AMR=1,1,0;AC_Adj=61,5,0;AC_EAS=0,0,0;AC_FIN=7,0,0;AC_Het=53,5,0,0,0,0;AC_Hom=4,0,0;AC_NFE=37,1,0;AC_OTH=1,0,0;AC_SAS=5,3,0;AF=4.053e-03,3.019e-04,4.312e-05;AN=23190;AN_AFR=782;AN_AMR=2820;AN_Adj=12780;AN_EAS=3310;AN_FIN=370;AN_NFE=2524;AN_OTH=60;AN_SAS=2914;BaseQRankSum=-5.920e-01;ClippingRankSum=0.467;DP=244490;FS=16.783;GQ_MEAN=33.33;GQ_STDDEV=46.94;Het_AFR=8,0,0,0,0,0;Het_AMR=1,1,0,0,0,0;Het_EAS=0,0,0,0,0,0;Het_FIN=7,0,0,0,0,0;Het_NFE=33,1,0,0,0,0;Het_OTH=1,0,0,0,0,0;Het_SAS=3,3,0,0,0,0;Hom_AFR=1,0,0;Hom_AMR=0,0,0;Hom_EAS=0,0,0;Hom_FIN=0,0,0;Hom_NFE=2,0,0;Hom_OTH=0,0,0;Hom_SAS=1,0,0;InbreedingCoeff=0.2034;MQ=49.96;MQ0=0;MQRankSum=-1.444e+00;NCC=74518;NEGATIVE_TRAIN_SITE;QD=24.62;ReadPosRankSum=-7.310e-01;VQSLOD=-7.243e-01;culprit=FS;DP_HIST=1433|2225|1345|880|1609|1404|1224|577|320|199|117|88|46|41|29|15|13|10|2|18,5|15|31|18|5|3|3|1|2|0|0|0|0|0|0|0|0|0|0|0,0|2|1|0|1|0|0|0|1|0|0|0|1|1|0|0|0|0|0|0,0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;GQ_HIST=1893|1599|502|665|1159|399|468|383|220|347|278|127|1602|662|290|308|199|86|81|327,1|2|1|4|1|3|3|3|4|3|2|1|1|1|2|0|2|1|0|48,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|7,0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0|0|0|0|0;CSQ=CACCGGGACCGGGACT|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2262-2280||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2262_2280delAGTCCCGGTCCCGGTCCCGinsAGTCCCGGTCCCGGTG|||||||||||||||||||,C|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2262-2280||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2262_2280delAGTCCCGGTCCCGGTCCCGinsG|||||||||||||||||||,TGGGACCGGGACCGGGACT|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2262-2280||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2262_2280delAGTCCCGGTCCCGGTCCCGinsAGTCCCGGTCCCGGTCCCA|||||||||||||||||||,CACCGGGACCGGGACT|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1748-1766|1381-1399|461-467|SPGPGPG/SPGPGG|AGTCCCGGTCCCGGTCCCGgc/AGTCCCGGTCCCGGTGgc||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1381_1399delAGTCCCGGTCCCGGTCCCGinsAGTCCCGGTCCCGGTG|ENSP00000363334.2:p.Pro466del||||||||||||||||||,C|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1748-1766|1381-1399|461-467|SPGPGPG/G|AGTCCCGGTCCCGGTCCCGgc/Ggc||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1381_1399delAGTCCCGGTCCCGGTCCCGinsG|ENSP00000363334.2:p.Ser461_Pro466del||||||||||||||||||,TGGGACCGGGACCGGGACT|ENSG00000158062|ENST00000374217|Transcript|missense_variant|1748-1766|1381-1399|461-467|SPGPGPG/SPGPGPS|AGTCCCGGTCCCGGTCCCGgc/AGTCCCGGTCCCGGTCCCAgc||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1381_1399delAGTCCCGGTCCCGGTCCCGinsAGTCCCGGTCCCGGTCCCA|ENSP00000363334.2:p.Gly467Ser||||||||||||||||||,CACCGGGACCGGGACT|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1945-1963|1480-1498|494-500|SPGPGPG/SPGPGG|AGTCCCGGTCCCGGTCCCGgc/AGTCCCGGTCCCGGTGgc||3||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1480_1498delAGTCCCGGTCCCGGTCCCGinsAGTCCCGGTCCCGGTG|ENSP00000363339.1:p.Pro499del||||||||||||||||||,C|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1945-1963|1480-1498|494-500|SPGPGPG/G|AGTCCCGGTCCCGGTCCCGgc/Ggc||2||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1480_1498delAGTCCCGGTCCCGGTCCCGinsG|ENSP00000363339.1:p.Ser494_Pro499del||||||||||||||||||,TGGGACCGGGACCGGGACT|ENSG00000158062|ENST00000374222|Transcript|missense_variant|1945-1963|1480-1498|494-500|SPGPGPG/SPGPGPS|AGTCCCGGTCCCGGTCCCGgc/AGTCCCGGTCCCGGTCCCAgc||1||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1480_1498delAGTCCCGGTCCCGGTCCCGinsAGTCCCGGTCCCGGTCCCA|ENSP00000363339.1:p.Gly500Ser||||||||||||||||||,CACCGGGACCGGGACT|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1457-1475|1381-1399|461-467|SPGPGPG/SPGPGG|AGTCCCGGTCCCGGTCCCGgc/AGTCCCGGTCCCGGTGgc||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1381_1399delAGTCCCGGTCCCGGTCCCGinsAGTCCCGGTCCCGGTG|ENSP00000349601.4:p.Pro466del||||||||||||||||||,C|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1457-1475|1381-1399|461-467|SPGPGPG/G|AGTCCCGGTCCCGGTCCCGgc/Ggc||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1381_1399delAGTCCCGGTCCCGGTCCCGinsG|ENSP00000349601.4:p.Ser461_Pro466del||||||||||||||||||,TGGGACCGGGACCGGGACT|ENSG00000158062|ENST00000357089|Transcript|missense_variant|1457-1475|1381-1399|461-467|SPGPGPG/SPGPGPS|AGTCCCGGTCCCGGTCCCGgc/AGTCCCGGTCCCGGTCCCAgc||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1381_1399delAGTCCCGGTCCCGGTCCCGinsAGTCCCGGTCCCGGTCCCA|ENSP00000349601.4:p.Gly467Ser||||||||||||||||||,CACCGGGACCGGGACT|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1200-1218|1120-1138|374-380|SPGPGPG/SPGPGG|AGTCCCGGTCCCGGTCCCGgc/AGTCCCGGTCCCGGTGgc||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1120_1138delAGTCCCGGTCCCGGTCCCGinsAGTCCCGGTCCCGGTG|ENSP00000324721.7:p.Pro379del||||||||||||||||||,C|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1200-1218|1120-1138|374-380|SPGPGPG/G|AGTCCCGGTCCCGGTCCCGgc/Ggc||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1120_1138delAGTCCCGGTCCCGGTCCCGinsG|ENSP00000324721.7:p.Ser374_Pro379del||||||||||||||||||,TGGGACCGGGACCGGGACT|ENSG00000158062|ENST00000314675|Transcript|missense_variant|1200-1218|1120-1138|374-380|SPGPGPG/SPGPGPS|AGTCCCGGTCCCGGTCCCGgc/AGTCCCGGTCCCGGTCCCAgc||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1120_1138delAGTCCCGGTCCCGGTCCCGinsAGTCCCGGTCCCGGTCCCA|ENSP00000324721.7:p.Gly380Ser||||||||||||||||||,CACCGGGACCGGGACT|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2442-2460||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2442_2460delAGTCCCGGTCCCGGTCCCGinsAGTCCCGGTCCCGGTG|||||||||||||||||||,C|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2442-2460||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2442_2460delAGTCCCGGTCCCGGTCCCGinsG|||||||||||||||||||,TGGGACCGGGACCGGGACT|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2442-2460||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2442_2460delAGTCCCGGTCCCGGTCCCGinsAGTCCCGGTCCCGGTCCCA|||||||||||||||||||,CACCGGGACCGGGACT|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2227-2245||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2227_2245delAGTCCCGGTCCCGGTCCCGinsAGTCCCGGTCCCGGTG|||||||||||||||||||,C|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2227-2245||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2227_2245delAGTCCCGGTCCCGGTCCCGinsG|||||||||||||||||||,TGGGACCGGGACCGGGACT|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2227-2245||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2227_2245delAGTCCCGGTCCCGGTCCCGinsAGTCCCGGTCCCGGTCCCA|||||||||||||||||||,CACCGGGACCGGGACT|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1694-1712|1480-1498|494-500|SPGPGPG/SPGPGG|AGTCCCGGTCCCGGTCCCGgc/AGTCCCGGTCCCGGTGgc||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1480_1498delAGTCCCGGTCCCGGTCCCGinsAGTCCCGGTCCCGGTG|ENSP00000363338.3:p.Pro499del||||||||||||||||||,C|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1694-1712|1480-1498|494-500|SPGPGPG/G|AGTCCCGGTCCCGGTCCCGgc/Ggc||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1480_1498delAGTCCCGGTCCCGGTCCCGinsG|ENSP00000363338.3:p.Ser494_Pro499del||||||||||||||||||,TGGGACCGGGACCGGGACT|ENSG00000158062|ENST00000374221|Transcript|missense_variant|1694-1712|1480-1498|494-500|SPGPGPG/SPGPGPS|AGTCCCGGTCCCGGTCCCGgc/AGTCCCGGTCCCGGTCCCAgc||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1480_1498delAGTCCCGGTCCCGGTCCCGinsAGTCCCGGTCCCGGTCCCA|ENSP00000363338.3:p.Gly500Ser||||||||||||||||||,CACCGGGACCGGGACT|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2545-2563||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2545_2563delAGTCCCGGTCCCGGTCCCGinsAGTCCCGGTCCCGGTG|||||||||||||||||||,C|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2545-2563||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2545_2563delAGTCCCGGTCCCGGTCCCGinsG|||||||||||||||||||,TGGGACCGGGACCGGGACT|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2545-2563||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2545_2563delAGTCCCGGTCCCGGTCCCGinsAGTCCCGGTCCCGGTCCCA|||||||||||||||||||,CACCGGGACCGGGACT|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1212-1230|751-769|251-257|SPGPGPG/SPGPGG|AGTCCCGGTCCCGGTCCCGgc/AGTCCCGGTCCCGGTGgc||3||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.751_769delAGTCCCGGTCCCGGTCCCGinsAGTCCCGGTCCCGGTG|ENSP00000363340.1:p.Pro256del||||||||||||||||||,C|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1212-1230|751-769|251-257|SPGPGPG/G|AGTCCCGGTCCCGGTCCCGgc/Ggc||2||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.751_769delAGTCCCGGTCCCGGTCCCGinsG|ENSP00000363340.1:p.Ser251_Pro256del||||||||||||||||||,TGGGACCGGGACCGGGACT|ENSG00000158062|ENST00000374223|Transcript|missense_variant|1212-1230|751-769|251-257|SPGPGPG/SPGPGPS|AGTCCCGGTCCCGGTCCCGgc/AGTCCCGGTCCCGGTCCCAgc||1||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.751_769delAGTCCCGGTCCCGGTCCCGinsAGTCCCGGTCCCGGTCCCA|ENSP00000363340.1:p.Gly257Ser||||||||||||||||||,CACCGGGACCGGGACT||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||3||||||regulatory_region|||||||||||||||||||||||||||||||,C||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||2||||||regulatory_region|||||||||||||||||||||||||||||||,TGGGACCGGGACCGGGACT||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||1||||||regulatory_region|||||||||||||||||||||||||||||||;AC_POPMAX=7,3,NA;AN_POPMAX=370,2914,NA;POPMAX=FIN,SAS,NA +1 26608856 . GGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACAGGGACCA G 6225.79 VQSRTrancheINDEL95.00to96.00 AC=2;AC_AFR=0;AC_AMR=0;AC_Adj=2;AC_EAS=2;AC_FIN=0;AC_Het=2;AC_Hom=0;AC_NFE=0;AC_OTH=0;AC_SAS=0;AF=8.560e-05;AN=23364;AN_AFR=860;AN_AMR=2926;AN_Adj=13592;AN_EAS=3442;AN_FIN=426;AN_NFE=2830;AN_OTH=64;AN_SAS=3044;BaseQRankSum=1.22;ClippingRankSum=-7.260e-01;DP=247199;FS=1.583;GQ_MEAN=33.10;GQ_STDDEV=32.27;Het_AFR=0;Het_AMR=0;Het_EAS=2;Het_FIN=0;Het_NFE=0;Het_OTH=0;Het_SAS=0;Hom_AFR=0;Hom_AMR=0;Hom_EAS=0;Hom_FIN=0;Hom_NFE=0;Hom_OTH=0;Hom_SAS=0;InbreedingCoeff=0.0874;MQ=54.16;MQ0=0;MQRankSum=-9.400e-02;NCC=74348;QD=4.14;ReadPosRankSum=0.553;VQSLOD=1.13;culprit=InbreedingCoeff;DP_HIST=1514|2200|1328|859|1580|1364|1306|595|329|217|117|97|45|45|28|16|15|8|4|15,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1|0|1|0|0;GQ_HIST=1069|2057|555|604|1434|458|513|412|207|293|165|69|1832|729|316|320|211|87|85|266,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|2;CSQ=-|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2231-2278||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2231_2278delTGGTCCCTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCC|||||||||||||||||||,-|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1717-1764|1350-1397|450-466|PGPCPGPGPGPSPGPGP/P|ccTGGTCCCTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCc/ccc||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1350_1397delTGGTCCCTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCC|ENSP00000363334.2:p.Gly451_Pro466del||||||||||||||||||,-|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1914-1961|1449-1496|483-499|PGPCPGPGPGPSPGPGP/P|ccTGGTCCCTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCc/ccc||1||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1449_1496delTGGTCCCTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCC|ENSP00000363339.1:p.Gly484_Pro499del||||||||||||||||||,-|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1426-1473|1350-1397|450-466|PGPCPGPGPGPSPGPGP/P|ccTGGTCCCTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCc/ccc||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1350_1397delTGGTCCCTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCC|ENSP00000349601.4:p.Gly451_Pro466del||||||||||||||||||,-|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1169-1216|1089-1136|363-379|PGPCPGPGPGPSPGPGP/P|ccTGGTCCCTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCc/ccc||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1089_1136delTGGTCCCTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCC|ENSP00000324721.7:p.Gly364_Pro379del||||||||||||||||||,-|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2411-2458||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2411_2458delTGGTCCCTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCC|||||||||||||||||||,-|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2196-2243||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2196_2243delTGGTCCCTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCC|||||||||||||||||||,-|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1663-1710|1449-1496|483-499|PGPCPGPGPGPSPGPGP/P|ccTGGTCCCTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCc/ccc||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1449_1496delTGGTCCCTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCC|ENSP00000363338.3:p.Gly484_Pro499del||||||||||||||||||,-|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2514-2561||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2514_2561delTGGTCCCTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCC|||||||||||||||||||,-|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1181-1228|720-767|240-256|PGPCPGPGPGPSPGPGP/P|ccTGGTCCCTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCc/ccc||1||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.720_767delTGGTCCCTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCC|ENSP00000363340.1:p.Gly241_Pro256del||||||||||||||||||,-||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||1||||||regulatory_region|||||||||||||||||||||||||||||||;AC_POPMAX=2;AN_POPMAX=3442;POPMAX=EAS +1 26608859 . ACCGGGACCGGGACTGGGGCC AGGGACTGGGGCC,AGGGACCGGGACTGGGGCC,A,ACC,ACCGGGACCGGGACTGGGGCCGGGACCGGGACTGGGGCC 7077919.26 VQSRTrancheINDEL99.50to99.90 AC=14459,4,8,17,2;AC_AFR=1107,0,2,0,0;AC_AMR=623,0,2,0,0;AC_Adj=13017,4,8,16,2;AC_EAS=113,0,0,1,1;AC_FIN=1073,0,0,0,0;AC_Het=11572,3,6,10,2,1,2,4,0,0,0,0,0,0,0;AC_Hom=719,0,0,1,0;AC_NFE=8930,4,4,11,0;AC_OTH=104,0,0,0,0;AC_SAS=1067,0,0,4,1;AF=0.279,7.715e-05,1.543e-04,3.279e-04,3.857e-05;AN=51850;AN_AFR=2942;AN_AMR=4114;AN_Adj=38396;AN_EAS=3666;AN_FIN=2426;AN_NFE=19972;AN_OTH=260;AN_SAS=5016;BaseQRankSum=1.15;ClippingRankSum=-6.550e-01;DP=724683;FS=0.000;GQ_MEAN=154.71;GQ_STDDEV=229.35;Het_AFR=963,0,2,0,0,0,0,0,0,0,0,0,0,0,0;Het_AMR=598,0,1,0,0,0,1,0,0,0,0,0,0,0,0;Het_EAS=111,0,0,1,1,0,0,0,0,0,0,0,0,0,0;Het_FIN=939,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_NFE=7916,3,3,7,0,1,1,4,0,0,0,0,0,0,0;Het_OTH=100,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_SAS=945,0,0,2,1,0,0,0,0,0,0,0,0,0,0;Hom_AFR=72,0,0,0,0;Hom_AMR=12,0,0,0,0;Hom_EAS=1,0,0,0,0;Hom_FIN=67,0,0,0,0;Hom_NFE=504,0,0,0,0;Hom_OTH=2,0,0,0,0;Hom_SAS=61,0,0,1,0;InbreedingCoeff=-0.1440;MQ=45.01;MQ0=0;MQRankSum=-3.477e+00;NCC=52987;NEGATIVE_TRAIN_SITE;QD=3.95;ReadPosRankSum=1.20;VQSLOD=-1.003e+00;culprit=FS;DP_HIST=1717|2983|2316|2137|3139|3150|3031|2034|1505|1127|792|608|391|273|192|148|101|77|57|147,173|764|931|1237|1521|1673|1601|1333|1106|870|643|496|327|216|159|128|82|67|53|127,0|0|0|1|1|1|0|0|0|0|0|1|0|0|0|0|0|0|0|0,0|0|1|0|0|1|0|0|0|2|1|2|1|0|0|0|0|0|0|0,0|0|1|1|1|0|0|2|1|0|1|3|0|1|0|0|2|0|1|2,0|0|0|0|0|1|0|0|0|0|0|1|0|0|0|0|0|0|0|0;GQ_HIST=1928|2154|640|592|1618|577|603|487|392|394|311|266|2192|921|486|478|398|258|263|10967,70|111|119|133|141|139|143|138|181|184|159|168|155|174|171|145|179|163|178|10656,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|4,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|8,0|0|1|0|0|0|0|0|0|1|0|0|0|0|0|0|0|0|0|14,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|2;CSQ=-|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2256-2275||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2256_2275delGGCCCCAGTCCCGGTCCCGG|||||||||||||||||||,CC|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2256-2275||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2256_2275delGGCCCCAGTCCCGGTCCCGGinsGG|||||||||||||||||||,GGGACTGGGGCC|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2256-2275||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2256_2275delGGCCCCAGTCCCGGTCCCGGinsGGCCCCAGTCCC|||||||||||||||||||,CCGGGACCGGGACTGGGGCCGGGACCGGGACTGGGGCC|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_elongation|2256-2275||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2256_2275delGGCCCCAGTCCCGGTCCCGGinsGGCCCCAGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGG|||||||||||||||||||,GGGACCGGGACTGGGGCC|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2256-2275||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2256_2275delGGCCCCAGTCCCGGTCCCGGinsGGCCCCAGTCCCGGTCCC|||||||||||||||||||,-|ENSG00000158062|ENST00000374217|Transcript|frameshift_variant&feature_truncation|1742-1761|1375-1394|459-465|GPSPGPG/X|GGCCCCAGTCCCGGTCCCGGt/t||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1375_1394delGGCCCCAGTCCCGGTCCCGG|ENSP00000363334.2:p.Gly459SerfsTer?|||||||||||||||POSITION:0.952185792349727&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,CC|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1742-1761|1375-1394|459-465|GPSPGPG/G|GGCCCCAGTCCCGGTCCCGGt/GGt||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1375_1394delGGCCCCAGTCCCGGTCCCGGinsGG|ENSP00000363334.2:p.Pro460_Gly465del||||||||||||||||||,GGGACTGGGGCC|ENSG00000158062|ENST00000374217|Transcript|frameshift_variant&feature_truncation|1742-1761|1375-1394|459-465|GPSPGPG/GPSPX|GGCCCCAGTCCCGGTCCCGGt/GGCCCCAGTCCCt||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1375_1394delGGCCCCAGTCCCGGTCCCGGinsGGCCCCAGTCCC|ENSP00000363334.2:p.Gly463SerfsTer?|||||||||||||||POSITION:0.952185792349727&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,CCGGGACCGGGACTGGGGCCGGGACCGGGACTGGGGCC|ENSG00000158062|ENST00000374217|Transcript|inframe_insertion|1742-1761|1375-1394|459-465|GPSPGPG/GPSPGPGPSPGPG|GGCCCCAGTCCCGGTCCCGGt/GGCCCCAGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGt||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1375_1394delGGCCCCAGTCCCGGTCCCGGinsGGCCCCAGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGG|ENSP00000363334.2:p.Pro460_Gly465dup||||||||||||||||||,GGGACCGGGACTGGGGCC|ENSG00000158062|ENST00000374217|Transcript|frameshift_variant&missense_variant&feature_truncation|1742-1761|1375-1394|459-465|GPSPGPG/GPSPGPX|GGCCCCAGTCCCGGTCCCGGt/GGCCCCAGTCCCGGTCCCt||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1375_1394delGGCCCCAGTCCCGGTCCCGGinsGGCCCCAGTCCCGGTCCC|ENSP00000363334.2:p.Gly465SerfsTer?|||||||||||||||POSITION:0.952185792349727&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,-|ENSG00000158062|ENST00000374222|Transcript|frameshift_variant&feature_truncation|1939-1958|1474-1493|492-498|GPSPGPG/X|GGCCCCAGTCCCGGTCCCGGt/t||3||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1474_1493delGGCCCCAGTCCCGGTCCCGG|ENSP00000363339.1:p.Gly492SerfsTer?|||||||||||||||POSITION:0.955214331413948&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,CC|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1939-1958|1474-1493|492-498|GPSPGPG/G|GGCCCCAGTCCCGGTCCCGGt/GGt||4||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1474_1493delGGCCCCAGTCCCGGTCCCGGinsGG|ENSP00000363339.1:p.Pro493_Gly498del||||||||||||||||||,GGGACTGGGGCC|ENSG00000158062|ENST00000374222|Transcript|frameshift_variant&feature_truncation|1939-1958|1474-1493|492-498|GPSPGPG/GPSPX|GGCCCCAGTCCCGGTCCCGGt/GGCCCCAGTCCCt||1||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1474_1493delGGCCCCAGTCCCGGTCCCGGinsGGCCCCAGTCCC|ENSP00000363339.1:p.Gly496SerfsTer?|||||||||||||||POSITION:0.955214331413948&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,CCGGGACCGGGACTGGGGCCGGGACCGGGACTGGGGCC|ENSG00000158062|ENST00000374222|Transcript|inframe_insertion|1939-1958|1474-1493|492-498|GPSPGPG/GPSPGPGPSPGPG|GGCCCCAGTCCCGGTCCCGGt/GGCCCCAGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGt||5||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1474_1493delGGCCCCAGTCCCGGTCCCGGinsGGCCCCAGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGG|ENSP00000363339.1:p.Pro493_Gly498dup||||||||||||||||||,GGGACCGGGACTGGGGCC|ENSG00000158062|ENST00000374222|Transcript|frameshift_variant&missense_variant&feature_truncation|1939-1958|1474-1493|492-498|GPSPGPG/GPSPGPX|GGCCCCAGTCCCGGTCCCGGt/GGCCCCAGTCCCGGTCCCt||2||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1474_1493delGGCCCCAGTCCCGGTCCCGGinsGGCCCCAGTCCCGGTCCC|ENSP00000363339.1:p.Gly498SerfsTer?|||||||||||||||POSITION:0.955214331413948&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,-|ENSG00000158062|ENST00000357089|Transcript|frameshift_variant&feature_truncation|1451-1470|1375-1394|459-465|GPSPGPG/X|GGCCCCAGTCCCGGTCCCGGt/t||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1375_1394delGGCCCCAGTCCCGGTCCCGG|ENSP00000349601.4:p.Gly459SerfsTer?|||||||||||||||POSITION:0.952185792349727&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,CC|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1451-1470|1375-1394|459-465|GPSPGPG/G|GGCCCCAGTCCCGGTCCCGGt/GGt||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1375_1394delGGCCCCAGTCCCGGTCCCGGinsGG|ENSP00000349601.4:p.Pro460_Gly465del||||||||||||||||||,GGGACTGGGGCC|ENSG00000158062|ENST00000357089|Transcript|frameshift_variant&feature_truncation|1451-1470|1375-1394|459-465|GPSPGPG/GPSPX|GGCCCCAGTCCCGGTCCCGGt/GGCCCCAGTCCCt||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1375_1394delGGCCCCAGTCCCGGTCCCGGinsGGCCCCAGTCCC|ENSP00000349601.4:p.Gly463SerfsTer?|||||||||||||||POSITION:0.952185792349727&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,CCGGGACCGGGACTGGGGCCGGGACCGGGACTGGGGCC|ENSG00000158062|ENST00000357089|Transcript|inframe_insertion|1451-1470|1375-1394|459-465|GPSPGPG/GPSPGPGPSPGPG|GGCCCCAGTCCCGGTCCCGGt/GGCCCCAGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGt||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1375_1394delGGCCCCAGTCCCGGTCCCGGinsGGCCCCAGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGG|ENSP00000349601.4:p.Pro460_Gly465dup||||||||||||||||||,GGGACCGGGACTGGGGCC|ENSG00000158062|ENST00000357089|Transcript|frameshift_variant&missense_variant&feature_truncation|1451-1470|1375-1394|459-465|GPSPGPG/GPSPGPX|GGCCCCAGTCCCGGTCCCGGt/GGCCCCAGTCCCGGTCCCt||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1375_1394delGGCCCCAGTCCCGGTCCCGGinsGGCCCCAGTCCCGGTCCC|ENSP00000349601.4:p.Gly465SerfsTer?|||||||||||||||POSITION:0.952185792349727&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,-|ENSG00000158062|ENST00000314675|Transcript|frameshift_variant&feature_truncation|1194-1213|1114-1133|372-378|GPSPGPG/X|GGCCCCAGTCCCGGTCCCGGt/t||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1114_1133delGGCCCCAGTCCCGGTCCCGG|ENSP00000324721.7:p.Gly372SerfsTer157|||||||||||||||POSITION:0.941812136325852&PHYLOCSF_TOO_SHORT|||HC,CC|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1194-1213|1114-1133|372-378|GPSPGPG/G|GGCCCCAGTCCCGGTCCCGGt/GGt||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1114_1133delGGCCCCAGTCCCGGTCCCGGinsGG|ENSP00000324721.7:p.Pro373_Gly378del||||||||||||||||||,GGGACTGGGGCC|ENSG00000158062|ENST00000314675|Transcript|frameshift_variant&feature_truncation|1194-1213|1114-1133|372-378|GPSPGPG/GPSPX|GGCCCCAGTCCCGGTCCCGGt/GGCCCCAGTCCCt||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1114_1133delGGCCCCAGTCCCGGTCCCGGinsGGCCCCAGTCCC|ENSP00000324721.7:p.Gly376SerfsTer157|||||||||||||||POSITION:0.941812136325852&PHYLOCSF_TOO_SHORT|||HC,CCGGGACCGGGACTGGGGCCGGGACCGGGACTGGGGCC|ENSG00000158062|ENST00000314675|Transcript|inframe_insertion|1194-1213|1114-1133|372-378|GPSPGPG/GPSPGPGPSPGPG|GGCCCCAGTCCCGGTCCCGGt/GGCCCCAGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGt||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1114_1133delGGCCCCAGTCCCGGTCCCGGinsGGCCCCAGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGG|ENSP00000324721.7:p.Pro373_Gly378dup||||||||||||||||||,GGGACCGGGACTGGGGCC|ENSG00000158062|ENST00000314675|Transcript|frameshift_variant&missense_variant&feature_truncation|1194-1213|1114-1133|372-378|GPSPGPG/GPSPGPX|GGCCCCAGTCCCGGTCCCGGt/GGCCCCAGTCCCGGTCCCt||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1114_1133delGGCCCCAGTCCCGGTCCCGGinsGGCCCCAGTCCCGGTCCC|ENSP00000324721.7:p.Gly378SerfsTer157|||||||||||||||POSITION:0.941812136325852&PHYLOCSF_TOO_SHORT|||HC,-|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2436-2455||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2436_2455delGGCCCCAGTCCCGGTCCCGG|||||||||||||||||||,CC|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2436-2455||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2436_2455delGGCCCCAGTCCCGGTCCCGGinsGG|||||||||||||||||||,GGGACTGGGGCC|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2436-2455||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2436_2455delGGCCCCAGTCCCGGTCCCGGinsGGCCCCAGTCCC|||||||||||||||||||,CCGGGACCGGGACTGGGGCCGGGACCGGGACTGGGGCC|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_elongation|2436-2455||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2436_2455delGGCCCCAGTCCCGGTCCCGGinsGGCCCCAGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGG|||||||||||||||||||,GGGACCGGGACTGGGGCC|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2436-2455||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2436_2455delGGCCCCAGTCCCGGTCCCGGinsGGCCCCAGTCCCGGTCCC|||||||||||||||||||,-|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2221-2240||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2221_2240delGGCCCCAGTCCCGGTCCCGG|||||||||||||||||||,CC|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2221-2240||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2221_2240delGGCCCCAGTCCCGGTCCCGGinsGG|||||||||||||||||||,GGGACTGGGGCC|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2221-2240||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2221_2240delGGCCCCAGTCCCGGTCCCGGinsGGCCCCAGTCCC|||||||||||||||||||,CCGGGACCGGGACTGGGGCCGGGACCGGGACTGGGGCC|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_elongation|2221-2240||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2221_2240delGGCCCCAGTCCCGGTCCCGGinsGGCCCCAGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGG|||||||||||||||||||,GGGACCGGGACTGGGGCC|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2221-2240||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2221_2240delGGCCCCAGTCCCGGTCCCGGinsGGCCCCAGTCCCGGTCCC|||||||||||||||||||,-|ENSG00000158062|ENST00000374221|Transcript|frameshift_variant&feature_truncation|1688-1707|1474-1493|492-498|GPSPGPG/X|GGCCCCAGTCCCGGTCCCGGt/t||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1474_1493delGGCCCCAGTCCCGGTCCCGG|ENSP00000363338.3:p.Gly492SerfsTer?|||||||||||||||POSITION:0.955214331413948&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,CC|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1688-1707|1474-1493|492-498|GPSPGPG/G|GGCCCCAGTCCCGGTCCCGGt/GGt||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1474_1493delGGCCCCAGTCCCGGTCCCGGinsGG|ENSP00000363338.3:p.Pro493_Gly498del||||||||||||||||||,GGGACTGGGGCC|ENSG00000158062|ENST00000374221|Transcript|frameshift_variant&feature_truncation|1688-1707|1474-1493|492-498|GPSPGPG/GPSPX|GGCCCCAGTCCCGGTCCCGGt/GGCCCCAGTCCCt||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1474_1493delGGCCCCAGTCCCGGTCCCGGinsGGCCCCAGTCCC|ENSP00000363338.3:p.Gly496SerfsTer?|||||||||||||||POSITION:0.955214331413948&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,CCGGGACCGGGACTGGGGCCGGGACCGGGACTGGGGCC|ENSG00000158062|ENST00000374221|Transcript|inframe_insertion|1688-1707|1474-1493|492-498|GPSPGPG/GPSPGPGPSPGPG|GGCCCCAGTCCCGGTCCCGGt/GGCCCCAGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGt||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1474_1493delGGCCCCAGTCCCGGTCCCGGinsGGCCCCAGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGG|ENSP00000363338.3:p.Pro493_Gly498dup||||||||||||||||||,GGGACCGGGACTGGGGCC|ENSG00000158062|ENST00000374221|Transcript|frameshift_variant&missense_variant&feature_truncation|1688-1707|1474-1493|492-498|GPSPGPG/GPSPGPX|GGCCCCAGTCCCGGTCCCGGt/GGCCCCAGTCCCGGTCCCt||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1474_1493delGGCCCCAGTCCCGGTCCCGGinsGGCCCCAGTCCCGGTCCC|ENSP00000363338.3:p.Gly498SerfsTer?|||||||||||||||POSITION:0.955214331413948&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,-|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2539-2558||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2539_2558delGGCCCCAGTCCCGGTCCCGG|||||||||||||||||||,CC|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2539-2558||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2539_2558delGGCCCCAGTCCCGGTCCCGGinsGG|||||||||||||||||||,GGGACTGGGGCC|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2539-2558||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2539_2558delGGCCCCAGTCCCGGTCCCGGinsGGCCCCAGTCCC|||||||||||||||||||,CCGGGACCGGGACTGGGGCCGGGACCGGGACTGGGGCC|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_elongation|2539-2558||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2539_2558delGGCCCCAGTCCCGGTCCCGGinsGGCCCCAGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGG|||||||||||||||||||,GGGACCGGGACTGGGGCC|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2539-2558||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2539_2558delGGCCCCAGTCCCGGTCCCGGinsGGCCCCAGTCCCGGTCCC|||||||||||||||||||,-|ENSG00000158062|ENST00000374223|Transcript|frameshift_variant&feature_truncation|1206-1225|745-764|249-255|GPSPGPG/X|GGCCCCAGTCCCGGTCCCGGt/t||3||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.745_764delGGCCCCAGTCCCGGTCCCGG|ENSP00000363340.1:p.Gly249SerfsTer?|||||||||||||||POSITION:0.916067146282974&PHYLOCSF_TOO_SHORT|||HC,CC|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1206-1225|745-764|249-255|GPSPGPG/G|GGCCCCAGTCCCGGTCCCGGt/GGt||4||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.745_764delGGCCCCAGTCCCGGTCCCGGinsGG|ENSP00000363340.1:p.Pro250_Gly255del||||||||||||||||||,GGGACTGGGGCC|ENSG00000158062|ENST00000374223|Transcript|frameshift_variant&feature_truncation|1206-1225|745-764|249-255|GPSPGPG/GPSPX|GGCCCCAGTCCCGGTCCCGGt/GGCCCCAGTCCCt||1||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.745_764delGGCCCCAGTCCCGGTCCCGGinsGGCCCCAGTCCC|ENSP00000363340.1:p.Gly253SerfsTer?|||||||||||||||POSITION:0.916067146282974&PHYLOCSF_TOO_SHORT|||HC,CCGGGACCGGGACTGGGGCCGGGACCGGGACTGGGGCC|ENSG00000158062|ENST00000374223|Transcript|inframe_insertion|1206-1225|745-764|249-255|GPSPGPG/GPSPGPGPSPGPG|GGCCCCAGTCCCGGTCCCGGt/GGCCCCAGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGt||5||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.745_764delGGCCCCAGTCCCGGTCCCGGinsGGCCCCAGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGG|ENSP00000363340.1:p.Pro250_Gly255dup||||||||||||||||||,GGGACCGGGACTGGGGCC|ENSG00000158062|ENST00000374223|Transcript|frameshift_variant&missense_variant&feature_truncation|1206-1225|745-764|249-255|GPSPGPG/GPSPGPX|GGCCCCAGTCCCGGTCCCGGt/GGCCCCAGTCCCGGTCCCt||2||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.745_764delGGCCCCAGTCCCGGTCCCGGinsGGCCCCAGTCCCGGTCCC|ENSP00000363340.1:p.Gly255SerfsTer?|||||||||||||||POSITION:0.916067146282974&PHYLOCSF_TOO_SHORT|||HC,-||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||3||||||regulatory_region|||||||||||||||||||||||||||||||,CC||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||4||||||regulatory_region|||||||||||||||||||||||||||||||,GGGACTGGGGCC||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||1||||||regulatory_region|||||||||||||||||||||||||||||||,CCGGGACCGGGACTGGGGCCGGGACCGGGACTGGGGCC||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||5||||||regulatory_region|||||||||||||||||||||||||||||||,GGGACCGGGACTGGGGCC||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||2||||||regulatory_region|||||||||||||||||||||||||||||||;AC_POPMAX=8930,4,2,4,1;AN_POPMAX=19972,19972,2942,5016,3666;POPMAX=NFE,NFE,AFR,SAS,EAS +1 26608865 . ACCGGGACTGGGG AGGGACTGGGG,AGACTGGGG,AACTGGGG,A,GCCGGGACTGGGG 15289728.26 VQSRTrancheINDEL97.00to99.00 AC=14731,4,1,2,1;AC_AFR=1426,0,0,0,0;AC_AMR=1704,2,0,0,0;AC_Adj=12968,2,1,2,1;AC_EAS=1048,0,0,0,1;AC_FIN=597,0,0,1,0;AC_Het=11499,1,1,2,1,1,0,0,0,0,0,0,0,0,0;AC_Hom=734,0,0,0,0;AC_NFE=6105,0,1,0,0;AC_OTH=99,0,0,0,0;AC_SAS=1989,0,0,1,0;AF=0.333,9.037e-05,2.259e-05,4.518e-05,2.259e-05;AN=44264;AN_AFR=3138;AN_AMR=5178;AN_Adj=33660;AN_EAS=4576;AN_FIN=1418;AN_NFE=13556;AN_OTH=210;AN_SAS=5584;BaseQRankSum=-5.640e-01;ClippingRankSum=-3.260e-01;DP=602596;FS=0.000;GQ_MEAN=381.27;GQ_STDDEV=425.42;Het_AFR=1196,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_AMR=1523,1,0,0,0,1,0,0,0,0,0,0,0,0,0;Het_EAS=934,0,0,0,1,0,0,0,0,0,0,0,0,0,0;Het_FIN=561,0,0,1,0,0,0,0,0,0,0,0,0,0,0;Het_NFE=5551,0,1,0,0,0,0,0,0,0,0,0,0,0,0;Het_OTH=85,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_SAS=1649,0,0,1,0,0,0,0,0,0,0,0,0,0,0;Hom_AFR=115,0,0,0,0;Hom_AMR=90,0,0,0,0;Hom_EAS=57,0,0,0,0;Hom_FIN=18,0,0,0,0;Hom_NFE=277,0,0,0,0;Hom_OTH=7,0,0,0,0;Hom_SAS=170,0,0,0,0;InbreedingCoeff=-0.2328;MQ=52.06;MQ0=0;MQRankSum=-2.192e+00;NCC=58586;QD=24.17;ReadPosRankSum=0.437;VQSLOD=0.204;culprit=FS;DP_HIST=1744|2791|1793|1546|2469|2631|2647|1940|1429|952|646|452|308|205|143|107|95|45|38|150,366|954|918|1161|1493|1822|1765|1508|1124|753|512|362|243|149|110|85|77|33|32|129,0|2|0|1|0|0|0|0|1|0|0|0|0|0|0|0|0|0|0|0,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1,0|0|0|0|0|0|0|0|0|1|0|1|0|0|0|0|0|0|0|0,0|0|0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0|0;GQ_HIST=965|1618|329|214|1298|269|215|165|116|110|89|91|1621|682|321|311|235|119|107|13257,13|23|17|12|19|22|27|50|43|42|46|39|40|29|38|42|46|40|32|12977,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1|0|3,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|2,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1;CSQ=A|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2258-2270||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2258_2270delCCCCAGTCCCGGTinsT|||||||||||||||||||,AACTGGGG|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2258-2270||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2258_2270delCCCCAGTCCCGGTinsCCCCAGTT|||||||||||||||||||,AGACTGGGG|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2258-2270||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2258_2270delCCCCAGTCCCGGTinsCCCCAGTCT|||||||||||||||||||,GCCGGGACTGGGG|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2258-2270||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2258_2270delCCCCAGTCCCGGTinsCCCCAGTCCCGGC|||||||||||||||||||,AGGGACTGGGG|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2258-2270||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2258_2270delCCCCAGTCCCGGTinsCCCCAGTCCCT|||||||||||||||||||,A|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1744-1756|1377-1389|459-463|GPSPG/G|ggCCCCAGTCCCGGT/ggT||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1377_1389delCCCCAGTCCCGGTinsT|ENSP00000363334.2:p.Pro460_Gly463del||||||||||||||||||,AACTGGGG|ENSG00000158062|ENST00000374217|Transcript|frameshift_variant&feature_truncation|1744-1756|1377-1389|459-463|GPSPG/GPSX|ggCCCCAGTCCCGGT/ggCCCCAGTT||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1377_1389delCCCCAGTCCCGGTinsCCCCAGTT|ENSP00000363334.2:p.Pro462SerfsTer?|||||||||||||||POSITION:0.948770491803279&PHYLOCSF_TOO_SHORT|||HC,AGACTGGGG|ENSG00000158062|ENST00000374217|Transcript|frameshift_variant&feature_truncation|1744-1756|1377-1389|459-463|GPSPG/GPSX|ggCCCCAGTCCCGGT/ggCCCCAGTCT||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1377_1389delCCCCAGTCCCGGTinsCCCCAGTCT|ENSP00000363334.2:p.Pro462LeufsTer?|||||||||||||||POSITION:0.948770491803279&PHYLOCSF_TOO_SHORT|||HC,GCCGGGACTGGGG|ENSG00000158062|ENST00000374217|Transcript|synonymous_variant|1744-1756|1377-1389|459-463|GPSPG|ggCCCCAGTCCCGGT/ggCCCCAGTCCCGGC||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1377_1389delCCCCAGTCCCGGTinsCCCCAGTCCCGGC|ENST00000374217.2:c.1377_1389delCCCCAGTCCCGGTinsCCCCAGTCCCGGC(p.%3D)||||||||||||||||||,AGGGACTGGGG|ENSG00000158062|ENST00000374217|Transcript|frameshift_variant&missense_variant&feature_truncation|1744-1756|1377-1389|459-463|GPSPG/GPSPX|ggCCCCAGTCCCGGT/ggCCCCAGTCCCT||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1377_1389delCCCCAGTCCCGGTinsCCCCAGTCCCT|ENSP00000363334.2:p.Gly463SerfsTer?|||||||||||||||POSITION:0.948770491803279&PHYLOCSF_TOO_SHORT|||HC,A|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1941-1953|1476-1488|492-496|GPSPG/G|ggCCCCAGTCCCGGT/ggT||4||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1476_1488delCCCCAGTCCCGGTinsT|ENSP00000363339.1:p.Pro493_Gly496del||||||||||||||||||,AACTGGGG|ENSG00000158062|ENST00000374222|Transcript|frameshift_variant&feature_truncation|1941-1953|1476-1488|492-496|GPSPG/GPSX|ggCCCCAGTCCCGGT/ggCCCCAGTT||3||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1476_1488delCCCCAGTCCCGGTinsCCCCAGTT|ENSP00000363339.1:p.Pro495SerfsTer?|||||||||||||||POSITION:0.952015355086372&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,AGACTGGGG|ENSG00000158062|ENST00000374222|Transcript|frameshift_variant&feature_truncation|1941-1953|1476-1488|492-496|GPSPG/GPSX|ggCCCCAGTCCCGGT/ggCCCCAGTCT||2||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1476_1488delCCCCAGTCCCGGTinsCCCCAGTCT|ENSP00000363339.1:p.Pro495LeufsTer?|||||||||||||||POSITION:0.952015355086372&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,GCCGGGACTGGGG|ENSG00000158062|ENST00000374222|Transcript|synonymous_variant|1941-1953|1476-1488|492-496|GPSPG|ggCCCCAGTCCCGGT/ggCCCCAGTCCCGGC||5||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1476_1488delCCCCAGTCCCGGTinsCCCCAGTCCCGGC|ENST00000374222.1:c.1476_1488delCCCCAGTCCCGGTinsCCCCAGTCCCGGC(p.%3D)||||||||||||||||||,AGGGACTGGGG|ENSG00000158062|ENST00000374222|Transcript|frameshift_variant&missense_variant&feature_truncation|1941-1953|1476-1488|492-496|GPSPG/GPSPX|ggCCCCAGTCCCGGT/ggCCCCAGTCCCT||1||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1476_1488delCCCCAGTCCCGGTinsCCCCAGTCCCT|ENSP00000363339.1:p.Gly496SerfsTer?|||||||||||||||POSITION:0.952015355086372&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,A|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1453-1465|1377-1389|459-463|GPSPG/G|ggCCCCAGTCCCGGT/ggT||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1377_1389delCCCCAGTCCCGGTinsT|ENSP00000349601.4:p.Pro460_Gly463del||||||||||||||||||,AACTGGGG|ENSG00000158062|ENST00000357089|Transcript|frameshift_variant&feature_truncation|1453-1465|1377-1389|459-463|GPSPG/GPSX|ggCCCCAGTCCCGGT/ggCCCCAGTT||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1377_1389delCCCCAGTCCCGGTinsCCCCAGTT|ENSP00000349601.4:p.Pro462SerfsTer?|||||||||||||||POSITION:0.948770491803279&PHYLOCSF_TOO_SHORT|||HC,AGACTGGGG|ENSG00000158062|ENST00000357089|Transcript|frameshift_variant&feature_truncation|1453-1465|1377-1389|459-463|GPSPG/GPSX|ggCCCCAGTCCCGGT/ggCCCCAGTCT||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1377_1389delCCCCAGTCCCGGTinsCCCCAGTCT|ENSP00000349601.4:p.Pro462LeufsTer?|||||||||||||||POSITION:0.948770491803279&PHYLOCSF_TOO_SHORT|||HC,GCCGGGACTGGGG|ENSG00000158062|ENST00000357089|Transcript|synonymous_variant|1453-1465|1377-1389|459-463|GPSPG|ggCCCCAGTCCCGGT/ggCCCCAGTCCCGGC||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1377_1389delCCCCAGTCCCGGTinsCCCCAGTCCCGGC|ENST00000357089.4:c.1377_1389delCCCCAGTCCCGGTinsCCCCAGTCCCGGC(p.%3D)||||||||||||||||||,AGGGACTGGGG|ENSG00000158062|ENST00000357089|Transcript|frameshift_variant&missense_variant&feature_truncation|1453-1465|1377-1389|459-463|GPSPG/GPSPX|ggCCCCAGTCCCGGT/ggCCCCAGTCCCT||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1377_1389delCCCCAGTCCCGGTinsCCCCAGTCCCT|ENSP00000349601.4:p.Gly463SerfsTer?|||||||||||||||POSITION:0.948770491803279&PHYLOCSF_TOO_SHORT|||HC,A|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1196-1208|1116-1128|372-376|GPSPG/G|ggCCCCAGTCCCGGT/ggT||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1116_1128delCCCCAGTCCCGGTinsT|ENSP00000324721.7:p.Pro373_Gly376del||||||||||||||||||,AACTGGGG|ENSG00000158062|ENST00000314675|Transcript|frameshift_variant&feature_truncation|1196-1208|1116-1128|372-376|GPSPG/GPSX|ggCCCCAGTCCCGGT/ggCCCCAGTT||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1116_1128delCCCCAGTCCCGGTinsCCCCAGTT|ENSP00000324721.7:p.Pro375SerfsTer159|||||||||||||||POSITION:0.937655860349127&PHYLOCSF_TOO_SHORT|||HC,AGACTGGGG|ENSG00000158062|ENST00000314675|Transcript|frameshift_variant&feature_truncation|1196-1208|1116-1128|372-376|GPSPG/GPSX|ggCCCCAGTCCCGGT/ggCCCCAGTCT||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1116_1128delCCCCAGTCCCGGTinsCCCCAGTCT|ENSP00000324721.7:p.Pro375LeufsTer67|||||||||||||||POSITION:0.937655860349127&PHYLOCSF_TOO_SHORT|||HC,GCCGGGACTGGGG|ENSG00000158062|ENST00000314675|Transcript|synonymous_variant|1196-1208|1116-1128|372-376|GPSPG|ggCCCCAGTCCCGGT/ggCCCCAGTCCCGGC||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1116_1128delCCCCAGTCCCGGTinsCCCCAGTCCCGGC|ENST00000314675.7:c.1116_1128delCCCCAGTCCCGGTinsCCCCAGTCCCGGC(p.%3D)||||||||||||||||||,AGGGACTGGGG|ENSG00000158062|ENST00000314675|Transcript|frameshift_variant&missense_variant&feature_truncation|1196-1208|1116-1128|372-376|GPSPG/GPSPX|ggCCCCAGTCCCGGT/ggCCCCAGTCCCT||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1116_1128delCCCCAGTCCCGGTinsCCCCAGTCCCT|ENSP00000324721.7:p.Gly376SerfsTer159|||||||||||||||POSITION:0.937655860349127&PHYLOCSF_TOO_SHORT|||HC,A|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2438-2450||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2438_2450delCCCCAGTCCCGGTinsT|||||||||||||||||||,AACTGGGG|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2438-2450||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2438_2450delCCCCAGTCCCGGTinsCCCCAGTT|||||||||||||||||||,AGACTGGGG|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2438-2450||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2438_2450delCCCCAGTCCCGGTinsCCCCAGTCT|||||||||||||||||||,GCCGGGACTGGGG|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2438-2450||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2438_2450delCCCCAGTCCCGGTinsCCCCAGTCCCGGC|||||||||||||||||||,AGGGACTGGGG|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2438-2450||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2438_2450delCCCCAGTCCCGGTinsCCCCAGTCCCT|||||||||||||||||||,A|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2223-2235||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2223_2235delCCCCAGTCCCGGTinsT|||||||||||||||||||,AACTGGGG|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2223-2235||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2223_2235delCCCCAGTCCCGGTinsCCCCAGTT|||||||||||||||||||,AGACTGGGG|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2223-2235||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2223_2235delCCCCAGTCCCGGTinsCCCCAGTCT|||||||||||||||||||,GCCGGGACTGGGG|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2223-2235||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2223_2235delCCCCAGTCCCGGTinsCCCCAGTCCCGGC|||||||||||||||||||,AGGGACTGGGG|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2223-2235||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2223_2235delCCCCAGTCCCGGTinsCCCCAGTCCCT|||||||||||||||||||,A|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1690-1702|1476-1488|492-496|GPSPG/G|ggCCCCAGTCCCGGT/ggT||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1476_1488delCCCCAGTCCCGGTinsT|ENSP00000363338.3:p.Pro493_Gly496del||||||||||||||||||,AACTGGGG|ENSG00000158062|ENST00000374221|Transcript|frameshift_variant&feature_truncation|1690-1702|1476-1488|492-496|GPSPG/GPSX|ggCCCCAGTCCCGGT/ggCCCCAGTT||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1476_1488delCCCCAGTCCCGGTinsCCCCAGTT|ENSP00000363338.3:p.Pro495SerfsTer?|||||||||||||||POSITION:0.952015355086372&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,AGACTGGGG|ENSG00000158062|ENST00000374221|Transcript|frameshift_variant&feature_truncation|1690-1702|1476-1488|492-496|GPSPG/GPSX|ggCCCCAGTCCCGGT/ggCCCCAGTCT||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1476_1488delCCCCAGTCCCGGTinsCCCCAGTCT|ENSP00000363338.3:p.Pro495LeufsTer?|||||||||||||||POSITION:0.952015355086372&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,GCCGGGACTGGGG|ENSG00000158062|ENST00000374221|Transcript|synonymous_variant|1690-1702|1476-1488|492-496|GPSPG|ggCCCCAGTCCCGGT/ggCCCCAGTCCCGGC||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1476_1488delCCCCAGTCCCGGTinsCCCCAGTCCCGGC|ENST00000374221.3:c.1476_1488delCCCCAGTCCCGGTinsCCCCAGTCCCGGC(p.%3D)||||||||||||||||||,AGGGACTGGGG|ENSG00000158062|ENST00000374221|Transcript|frameshift_variant&missense_variant&feature_truncation|1690-1702|1476-1488|492-496|GPSPG/GPSPX|ggCCCCAGTCCCGGT/ggCCCCAGTCCCT||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1476_1488delCCCCAGTCCCGGTinsCCCCAGTCCCT|ENSP00000363338.3:p.Gly496SerfsTer?|||||||||||||||POSITION:0.952015355086372&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,A|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2541-2553||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2541_2553delCCCCAGTCCCGGTinsT|||||||||||||||||||,AACTGGGG|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2541-2553||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2541_2553delCCCCAGTCCCGGTinsCCCCAGTT|||||||||||||||||||,AGACTGGGG|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2541-2553||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2541_2553delCCCCAGTCCCGGTinsCCCCAGTCT|||||||||||||||||||,GCCGGGACTGGGG|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2541-2553||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2541_2553delCCCCAGTCCCGGTinsCCCCAGTCCCGGC|||||||||||||||||||,AGGGACTGGGG|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2541-2553||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2541_2553delCCCCAGTCCCGGTinsCCCCAGTCCCT|||||||||||||||||||,A|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1208-1220|747-759|249-253|GPSPG/G|ggCCCCAGTCCCGGT/ggT||4||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.747_759delCCCCAGTCCCGGTinsT|ENSP00000363340.1:p.Pro250_Gly253del||||||||||||||||||,AACTGGGG|ENSG00000158062|ENST00000374223|Transcript|frameshift_variant&feature_truncation|1208-1220|747-759|249-253|GPSPG/GPSX|ggCCCCAGTCCCGGT/ggCCCCAGTT||3||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.747_759delCCCCAGTCCCGGTinsCCCCAGTT|ENSP00000363340.1:p.Pro252SerfsTer?|||||||||||||||POSITION:0.910071942446043&PHYLOCSF_TOO_SHORT|||HC,AGACTGGGG|ENSG00000158062|ENST00000374223|Transcript|frameshift_variant&feature_truncation|1208-1220|747-759|249-253|GPSPG/GPSX|ggCCCCAGTCCCGGT/ggCCCCAGTCT||2||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.747_759delCCCCAGTCCCGGTinsCCCCAGTCT|ENSP00000363340.1:p.Pro252LeufsTer?|||||||||||||||POSITION:0.910071942446043&PHYLOCSF_TOO_SHORT|||HC,GCCGGGACTGGGG|ENSG00000158062|ENST00000374223|Transcript|synonymous_variant|1208-1220|747-759|249-253|GPSPG|ggCCCCAGTCCCGGT/ggCCCCAGTCCCGGC||5||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.747_759delCCCCAGTCCCGGTinsCCCCAGTCCCGGC|ENST00000374223.1:c.747_759delCCCCAGTCCCGGTinsCCCCAGTCCCGGC(p.%3D)||||||||||||||||||,AGGGACTGGGG|ENSG00000158062|ENST00000374223|Transcript|frameshift_variant&missense_variant&feature_truncation|1208-1220|747-759|249-253|GPSPG/GPSPX|ggCCCCAGTCCCGGT/ggCCCCAGTCCCT||1||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.747_759delCCCCAGTCCCGGTinsCCCCAGTCCCT|ENSP00000363340.1:p.Gly253SerfsTer?|||||||||||||||POSITION:0.910071942446043&PHYLOCSF_TOO_SHORT|||HC,A||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||4||||||regulatory_region|||||||||||||||||||||||||||||||,AACTGGGG||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||3||||||regulatory_region|||||||||||||||||||||||||||||||,AGACTGGGG||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||2||||||regulatory_region|||||||||||||||||||||||||||||||,GCCGGGACTGGGG||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||5||||||regulatory_region|||||||||||||||||||||||||||||||,AGGGACTGGGG||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||1||||||regulatory_region|||||||||||||||||||||||||||||||;AC_POPMAX=1426,2,1,1,1;AN_POPMAX=3138,5178,13556,1418,4576;POPMAX=AFR,AMR,NFE,FIN,EAS +1 26608867 . CGGGACTGGGGCCGGGACCGGGACCGGGACA AGGGACTGGGGCCGGGACCGGGACCGGGACA,C,CGGGGCCGGGACCGGGACCGGGACA,TGGGACTGGGGCCGGGACCGGGACCGGGACA 151660.94 VQSRTrancheINDEL99.00to99.50 AC=178,15,2,5;AC_AFR=91,0,0,0;AC_AMR=26,0,1,0;AC_Adj=139,15,2,5;AC_EAS=0,0,0,0;AC_FIN=1,0,0,0;AC_Het=139,15,2,5,0,0,0,0,0,0;AC_Hom=0,0,0,0;AC_NFE=17,7,1,2;AC_OTH=0,0,0,0;AC_SAS=4,8,0,3;AF=8.495e-03,7.159e-04,9.545e-05,2.386e-04;AN=20954;AN_AFR=1122;AN_AMR=2062;AN_Adj=11978;AN_EAS=2598;AN_FIN=524;AN_NFE=3104;AN_OTH=74;AN_SAS=2494;BaseQRankSum=0.429;ClippingRankSum=-5.450e-01;DP=224191;FS=11.491;GQ_MEAN=49.43;GQ_STDDEV=97.53;Het_AFR=91,0,0,0,0,0,0,0,0,0;Het_AMR=26,0,1,0,0,0,0,0,0,0;Het_EAS=0,0,0,0,0,0,0,0,0,0;Het_FIN=1,0,0,0,0,0,0,0,0,0;Het_NFE=17,7,1,2,0,0,0,0,0,0;Het_OTH=0,0,0,0,0,0,0,0,0,0;Het_SAS=4,8,0,3,0,0,0,0,0,0;Hom_AFR=0,0,0,0;Hom_AMR=0,0,0,0;Hom_EAS=0,0,0,0;Hom_FIN=0,0,0,0;Hom_NFE=0,0,0,0;Hom_OTH=0,0,0,0;Hom_SAS=0,0,0,0;InbreedingCoeff=0.1437;MQ=42.94;MQ0=0;MQRankSum=-4.010e-01;NCC=75531;QD=15.08;ReadPosRankSum=0.204;VQSLOD=-4.103e-01;culprit=FS;DP_HIST=1270|2132|1343|702|1311|998|976|493|346|263|183|115|91|78|44|36|29|17|14|31,11|15|14|12|10|16|15|19|9|14|8|5|6|5|3|0|1|0|2|1,0|0|0|0|0|1|0|0|1|0|1|1|2|1|1|0|1|0|0|6,0|0|0|0|0|0|0|1|0|0|0|0|0|0|0|1|0|0|0|0,0|0|1|0|0|1|0|0|0|0|1|1|0|1|0|0|0|0|0|0;GQ_HIST=1643|1188|244|207|1183|260|233|232|148|155|172|143|1683|766|332|341|253|158|147|989,4|4|3|2|3|1|0|0|0|1|2|2|1|2|2|1|0|1|1|140,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|15,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|2,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|5;CSQ=C|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2238-2268||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2238_2268delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsG|||||||||||||||||||,TGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2238-2268||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2238_2268delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCA|||||||||||||||||||,AGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2238-2268||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2238_2268delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCT|||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2238-2268||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2238_2268delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCG|||||||||||||||||||,C|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1724-1754|1357-1387|453-463|CPGPGPGPSPG/G|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/Ggt||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1357_1387delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsG|ENSP00000363334.2:p.Cys453_Pro462del||||||||||||||||||,TGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000374217|Transcript|missense_variant|1724-1754|1357-1387|453-463|CPGPGPGPSPG/CPGPGPGPSPS|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCAgt||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1357_1387delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCA|ENSP00000363334.2:p.Gly463Ser||||||||||||||||||,AGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000374217|Transcript|missense_variant|1724-1754|1357-1387|453-463|CPGPGPGPSPG/CPGPGPGPSPC|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1357_1387delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCT|ENSP00000363334.2:p.Gly463Cys||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1724-1754|1357-1387|453-463|CPGPGPGPSPG/CPGPGPGPG|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/TGTCCCGGTCCCGGTCCCGGCCCCGgt||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1357_1387delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCG|ENSP00000363334.2:p.Ser461_Pro462del||||||||||||||||||,C|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1921-1951|1456-1486|486-496|CPGPGPGPSPG/G|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/Ggt||2||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1456_1486delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsG|ENSP00000363339.1:p.Cys486_Pro495del||||||||||||||||||,TGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000374222|Transcript|missense_variant|1921-1951|1456-1486|486-496|CPGPGPGPSPG/CPGPGPGPSPS|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCAgt||4||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1456_1486delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCA|ENSP00000363339.1:p.Gly496Ser||||||||||||||||||,AGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000374222|Transcript|missense_variant|1921-1951|1456-1486|486-496|CPGPGPGPSPG/CPGPGPGPSPC|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt||1||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1456_1486delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCT|ENSP00000363339.1:p.Gly496Cys||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1921-1951|1456-1486|486-496|CPGPGPGPSPG/CPGPGPGPG|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/TGTCCCGGTCCCGGTCCCGGCCCCGgt||3||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1456_1486delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCG|ENSP00000363339.1:p.Ser494_Pro495del||||||||||||||||||,C|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1433-1463|1357-1387|453-463|CPGPGPGPSPG/G|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/Ggt||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1357_1387delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsG|ENSP00000349601.4:p.Cys453_Pro462del||||||||||||||||||,TGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000357089|Transcript|missense_variant|1433-1463|1357-1387|453-463|CPGPGPGPSPG/CPGPGPGPSPS|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCAgt||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1357_1387delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCA|ENSP00000349601.4:p.Gly463Ser||||||||||||||||||,AGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000357089|Transcript|missense_variant|1433-1463|1357-1387|453-463|CPGPGPGPSPG/CPGPGPGPSPC|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1357_1387delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCT|ENSP00000349601.4:p.Gly463Cys||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1433-1463|1357-1387|453-463|CPGPGPGPSPG/CPGPGPGPG|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/TGTCCCGGTCCCGGTCCCGGCCCCGgt||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1357_1387delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCG|ENSP00000349601.4:p.Ser461_Pro462del||||||||||||||||||,C|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1176-1206|1096-1126|366-376|CPGPGPGPSPG/G|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/Ggt||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1096_1126delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsG|ENSP00000324721.7:p.Cys366_Pro375del||||||||||||||||||,TGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000314675|Transcript|missense_variant|1176-1206|1096-1126|366-376|CPGPGPGPSPG/CPGPGPGPSPS|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCAgt||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1096_1126delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCA|ENSP00000324721.7:p.Gly376Ser||||||||||||||||||,AGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000314675|Transcript|missense_variant|1176-1206|1096-1126|366-376|CPGPGPGPSPG/CPGPGPGPSPC|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1096_1126delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCT|ENSP00000324721.7:p.Gly376Cys||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1176-1206|1096-1126|366-376|CPGPGPGPSPG/CPGPGPGPG|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/TGTCCCGGTCCCGGTCCCGGCCCCGgt||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1096_1126delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCG|ENSP00000324721.7:p.Ser374_Pro375del||||||||||||||||||,C|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2418-2448||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2418_2448delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsG|||||||||||||||||||,TGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2418-2448||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2418_2448delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCA|||||||||||||||||||,AGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2418-2448||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2418_2448delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCT|||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2418-2448||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2418_2448delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCG|||||||||||||||||||,C|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2203-2233||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2203_2233delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsG|||||||||||||||||||,TGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2203-2233||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2203_2233delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCA|||||||||||||||||||,AGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2203-2233||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2203_2233delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCT|||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2203-2233||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2203_2233delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCG|||||||||||||||||||,C|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1670-1700|1456-1486|486-496|CPGPGPGPSPG/G|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/Ggt||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1456_1486delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsG|ENSP00000363338.3:p.Cys486_Pro495del||||||||||||||||||,TGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000374221|Transcript|missense_variant|1670-1700|1456-1486|486-496|CPGPGPGPSPG/CPGPGPGPSPS|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCAgt||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1456_1486delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCA|ENSP00000363338.3:p.Gly496Ser||||||||||||||||||,AGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000374221|Transcript|missense_variant|1670-1700|1456-1486|486-496|CPGPGPGPSPG/CPGPGPGPSPC|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1456_1486delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCT|ENSP00000363338.3:p.Gly496Cys||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1670-1700|1456-1486|486-496|CPGPGPGPSPG/CPGPGPGPG|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/TGTCCCGGTCCCGGTCCCGGCCCCGgt||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1456_1486delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCG|ENSP00000363338.3:p.Ser494_Pro495del||||||||||||||||||,C|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2521-2551||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2521_2551delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsG|||||||||||||||||||,TGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2521-2551||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2521_2551delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCA|||||||||||||||||||,AGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2521-2551||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2521_2551delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCT|||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2521-2551||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2521_2551delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCG|||||||||||||||||||,C|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1188-1218|727-757|243-253|CPGPGPGPSPG/G|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/Ggt||2||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.727_757delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsG|ENSP00000363340.1:p.Cys243_Pro252del||||||||||||||||||,TGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000374223|Transcript|missense_variant|1188-1218|727-757|243-253|CPGPGPGPSPG/CPGPGPGPSPS|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCAgt||4||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.727_757delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCA|ENSP00000363340.1:p.Gly253Ser||||||||||||||||||,AGGGACTGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000374223|Transcript|missense_variant|1188-1218|727-757|243-253|CPGPGPGPSPG/CPGPGPGPSPC|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTgt||1||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.727_757delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCT|ENSP00000363340.1:p.Gly253Cys||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACA|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1188-1218|727-757|243-253|CPGPGPGPSPG/CPGPGPGPG|TGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGgt/TGTCCCGGTCCCGGTCCCGGCCCCGgt||3||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.727_757delTGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGinsTGTCCCGGTCCCGGTCCCGGCCCCG|ENSP00000363340.1:p.Ser251_Pro252del||||||||||||||||||,C||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||2||||||regulatory_region|||||||||||||||||||||||||||||||,TGGGACTGGGGCCGGGACCGGGACCGGGACA||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||4||||||regulatory_region|||||||||||||||||||||||||||||||,AGGGACTGGGGCCGGGACCGGGACCGGGACA||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||1||||||regulatory_region|||||||||||||||||||||||||||||||,CGGGGCCGGGACCGGGACCGGGACA||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||3||||||regulatory_region|||||||||||||||||||||||||||||||;AC_POPMAX=91,8,1,3;AN_POPMAX=1122,2494,2062,2494;POPMAX=AFR,SAS,AMR,SAS +1 26608868 . GGGACTGGGGCCGGGACCGGGACCGGGAC G,AGGACTGGGGCCGGGACCGGGACCGGGAC 15267856.60 VQSRTrancheINDEL97.00to99.00 AC=14718,1;AC_AFR=1591,0;AC_AMR=1778,0;AC_Adj=14442,1;AC_EAS=1071,0;AC_FIN=620,0;AC_Het=12318,1,0;AC_Hom=1062,0;AC_NFE=6498,1;AC_OTH=121,0;AC_SAS=2763,0;AF=0.276,1.874e-05;AN=53358;AN_AFR=4230;AN_AMR=5808;AN_Adj=42998;AN_EAS=4844;AN_FIN=2016;AN_NFE=18050;AN_OTH=312;AN_SAS=7738;BaseQRankSum=1.03;ClippingRankSum=0.393;DP=1398222;FS=0.694;GQ_MEAN=326.01;GQ_STDDEV=406.34;Het_AFR=1273,0,0;Het_AMR=1554,0,0;Het_EAS=951,0,0;Het_FIN=576,0,0;Het_NFE=5802,1,0;Het_OTH=99,0,0;Het_SAS=2063,0,0;Hom_AFR=159,0;Hom_AMR=112,0;Hom_EAS=60,0;Hom_FIN=22,0;Hom_NFE=348,0;Hom_OTH=11,0;Hom_SAS=350,0;InbreedingCoeff=-0.1741;MQ=54.50;MQ0=0;MQRankSum=-1.231e+00;NCC=51781;QD=1.11;ReadPosRankSum=0.090;VQSLOD=0.609;culprit=QD;DP_HIST=1246|2228|1627|1078|1668|1337|1392|1005|1032|1061|1145|1184|1256|1220|1091|1053|984|839|704|3529,7|142|356|460|419|307|305|330|408|501|662|755|901|890|847|852|830|725|608|3279,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1|0|0|0;GQ_HIST=1623|1518|432|475|1625|455|439|333|206|219|205|142|1920|915|448|520|374|217|266|14347,15|25|15|12|25|20|27|46|45|42|49|36|41|32|36|39|37|38|33|12971,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1;CSQ=AGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2239-2267||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2239_2267delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCT|||||||||||||||||||,G|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2239-2267||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2239_2267delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsC|||||||||||||||||||,AGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000374217|Transcript|synonymous_variant|1725-1753|1358-1386|453-462|CPGPGPGPSP|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCC/tGTCCCGGTCCCGGTCCCGGCCCCAGTCCT||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1358_1386delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCT|ENST00000374217.2:c.1358_1386delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCT(p.%3D)||||||||||||||||||,G|ENSG00000158062|ENST00000374217|Transcript|frameshift_variant&feature_truncation|1725-1753|1358-1386|453-462|CPGPGPGPSP/X|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCC/tC||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1358_1386delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsC|ENSP00000363334.2:p.Cys453SerfsTer?|||||||||||||||POSITION:0.94672131147541&PHYLOCSF_TOO_SHORT|||HC,AGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000374222|Transcript|synonymous_variant|1922-1950|1457-1485|486-495|CPGPGPGPSP|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCC/tGTCCCGGTCCCGGTCCCGGCCCCAGTCCT||2||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1457_1485delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCT|ENST00000374222.1:c.1457_1485delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCT(p.%3D)||||||||||||||||||,G|ENSG00000158062|ENST00000374222|Transcript|frameshift_variant&feature_truncation|1922-1950|1457-1485|486-495|CPGPGPGPSP/X|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCC/tC||1||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1457_1485delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsC|ENSP00000363339.1:p.Cys486SerfsTer?|||||||||||||||POSITION:0.950095969289827&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,AGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000357089|Transcript|synonymous_variant|1434-1462|1358-1386|453-462|CPGPGPGPSP|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCC/tGTCCCGGTCCCGGTCCCGGCCCCAGTCCT||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1358_1386delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCT|ENST00000357089.4:c.1358_1386delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCT(p.%3D)||||||||||||||||||,G|ENSG00000158062|ENST00000357089|Transcript|frameshift_variant&feature_truncation|1434-1462|1358-1386|453-462|CPGPGPGPSP/X|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCC/tC||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1358_1386delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsC|ENSP00000349601.4:p.Cys453SerfsTer?|||||||||||||||POSITION:0.94672131147541&PHYLOCSF_TOO_SHORT|||HC,AGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000314675|Transcript|synonymous_variant|1177-1205|1097-1125|366-375|CPGPGPGPSP|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCC/tGTCCCGGTCCCGGTCCCGGCCCCAGTCCT||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1097_1125delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCT|ENST00000314675.7:c.1097_1125delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCT(p.%3D)||||||||||||||||||,G|ENSG00000158062|ENST00000314675|Transcript|frameshift_variant&feature_truncation|1177-1205|1097-1125|366-375|CPGPGPGPSP/X|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCC/tC||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1097_1125delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsC|ENSP00000324721.7:p.Cys366SerfsTer68|||||||||||||||POSITION:0.935162094763092&PHYLOCSF_TOO_SHORT|||HC,AGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2419-2447||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2419_2447delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCT|||||||||||||||||||,G|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2419-2447||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2419_2447delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsC|||||||||||||||||||,AGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2204-2232||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2204_2232delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCT|||||||||||||||||||,G|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2204-2232||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2204_2232delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsC|||||||||||||||||||,AGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000374221|Transcript|synonymous_variant|1671-1699|1457-1485|486-495|CPGPGPGPSP|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCC/tGTCCCGGTCCCGGTCCCGGCCCCAGTCCT||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1457_1485delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCT|ENST00000374221.3:c.1457_1485delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCT(p.%3D)||||||||||||||||||,G|ENSG00000158062|ENST00000374221|Transcript|frameshift_variant&feature_truncation|1671-1699|1457-1485|486-495|CPGPGPGPSP/X|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCC/tC||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1457_1485delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsC|ENSP00000363338.3:p.Cys486SerfsTer?|||||||||||||||POSITION:0.950095969289827&PHYLOCSF_TOO_SHORT||END_TRUNC|LC,AGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2522-2550||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2522_2550delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCT|||||||||||||||||||,G|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2522-2550||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2522_2550delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsC|||||||||||||||||||,AGGACTGGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000374223|Transcript|synonymous_variant|1189-1217|728-756|243-252|CPGPGPGPSP|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCC/tGTCCCGGTCCCGGTCCCGGCCCCAGTCCT||2||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.728_756delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCT|ENST00000374223.1:c.728_756delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsGTCCCGGTCCCGGTCCCGGCCCCAGTCCT(p.%3D)||||||||||||||||||,G|ENSG00000158062|ENST00000374223|Transcript|frameshift_variant&feature_truncation|1189-1217|728-756|243-252|CPGPGPGPSP/X|tGTCCCGGTCCCGGTCCCGGCCCCAGTCCC/tC||1||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.728_756delGTCCCGGTCCCGGTCCCGGCCCCAGTCCCinsC|ENSP00000363340.1:p.Cys243SerfsTer?|||||||||||||||POSITION:0.906474820143885&PHYLOCSF_TOO_SHORT|||HC,AGGACTGGGGCCGGGACCGGGACCGGGAC||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||2||||||regulatory_region|||||||||||||||||||||||||||||||,G||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||1||||||regulatory_region|||||||||||||||||||||||||||||||;AC_POPMAX=1591,1;AN_POPMAX=4230,18050;POPMAX=AFR,NFE +1 26608870 . GACTGGGGCCGGGACCGGGACCGGGAC G 1155.22 VQSRTrancheINDEL99.50to99.90 AC=2;AC_AFR=0;AC_AMR=2;AC_Adj=2;AC_EAS=0;AC_FIN=0;AC_Het=2;AC_Hom=0;AC_NFE=0;AC_OTH=0;AC_SAS=0;AF=7.635e-05;AN=26194;AN_AFR=1688;AN_AMR=2582;AN_Adj=17336;AN_EAS=2864;AN_FIN=864;AN_NFE=6012;AN_OTH=104;AN_SAS=3222;BaseQRankSum=0.740;ClippingRankSum=-3.740e-01;DP=400510;FS=44.004;GQ_MEAN=43.96;GQ_STDDEV=35.58;Het_AFR=0;Het_AMR=2;Het_EAS=0;Het_FIN=0;Het_NFE=0;Het_OTH=0;Het_SAS=0;Hom_AFR=0;Hom_AMR=0;Hom_EAS=0;Hom_FIN=0;Hom_NFE=0;Hom_OTH=0;Hom_SAS=0;InbreedingCoeff=-0.0178;MQ=54.94;MQ0=0;MQRankSum=-1.378e+00;NCC=71765;NEGATIVE_TRAIN_SITE;QD=1.13;ReadPosRankSum=0.358;VQSLOD=-3.726e+00;culprit=QD;DP_HIST=1189|2165|1271|604|1273|1017|1087|659|592|570|488|434|349|331|249|200|160|107|101|251,0|0|1|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;GQ_HIST=866|1584|425|456|1805|472|481|357|191|215|159|70|2002|935|421|467|338|196|234|1423,0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0|0|0|1;CSQ=-|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2239-2264||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2239_2264delGTCCCGGTCCCGGTCCCGGCCCCAGT|||||||||||||||||||,-|ENSG00000158062|ENST00000374217|Transcript|frameshift_variant&feature_truncation|1725-1750|1358-1383|453-461|CPGPGPGPS/X|tGTCCCGGTCCCGGTCCCGGCCCCAGT/t||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1358_1383delGTCCCGGTCCCGGTCCCGGCCCCAGT|ENSP00000363334.2:p.Cys453SerfsTer?|||||||||||||||POSITION:0.944672131147541&PHYLOCSF_TOO_SHORT|||HC,-|ENSG00000158062|ENST00000374222|Transcript|frameshift_variant&feature_truncation|1922-1947|1457-1482|486-494|CPGPGPGPS/X|tGTCCCGGTCCCGGTCCCGGCCCCAGT/t||1||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1457_1482delGTCCCGGTCCCGGTCCCGGCCCCAGT|ENSP00000363339.1:p.Cys486SerfsTer?|||||||||||||||POSITION:0.948176583493282&PHYLOCSF_TOO_SHORT|||HC,-|ENSG00000158062|ENST00000357089|Transcript|frameshift_variant&feature_truncation|1434-1459|1358-1383|453-461|CPGPGPGPS/X|tGTCCCGGTCCCGGTCCCGGCCCCAGT/t||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1358_1383delGTCCCGGTCCCGGTCCCGGCCCCAGT|ENSP00000349601.4:p.Cys453SerfsTer?|||||||||||||||POSITION:0.944672131147541&PHYLOCSF_TOO_SHORT|||HC,-|ENSG00000158062|ENST00000314675|Transcript|frameshift_variant&feature_truncation|1177-1202|1097-1122|366-374|CPGPGPGPS/X|tGTCCCGGTCCCGGTCCCGGCCCCAGT/t||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1097_1122delGTCCCGGTCCCGGTCCCGGCCCCAGT|ENSP00000324721.7:p.Cys366SerfsTer161|||||||||||||||POSITION:0.932668329177057&PHYLOCSF_TOO_SHORT|||HC,-|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2419-2444||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2419_2444delGTCCCGGTCCCGGTCCCGGCCCCAGT|||||||||||||||||||,-|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2204-2229||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2204_2229delGTCCCGGTCCCGGTCCCGGCCCCAGT|||||||||||||||||||,-|ENSG00000158062|ENST00000374221|Transcript|frameshift_variant&feature_truncation|1671-1696|1457-1482|486-494|CPGPGPGPS/X|tGTCCCGGTCCCGGTCCCGGCCCCAGT/t||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1457_1482delGTCCCGGTCCCGGTCCCGGCCCCAGT|ENSP00000363338.3:p.Cys486SerfsTer?|||||||||||||||POSITION:0.948176583493282&PHYLOCSF_TOO_SHORT|||HC,-|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2522-2547||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2522_2547delGTCCCGGTCCCGGTCCCGGCCCCAGT|||||||||||||||||||,-|ENSG00000158062|ENST00000374223|Transcript|frameshift_variant&feature_truncation|1189-1214|728-753|243-251|CPGPGPGPS/X|tGTCCCGGTCCCGGTCCCGGCCCCAGT/t||1||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.728_753delGTCCCGGTCCCGGTCCCGGCCCCAGT|ENSP00000363340.1:p.Cys243SerfsTer?|||||||||||||||POSITION:0.902877697841727&PHYLOCSF_TOO_SHORT|||HC,-||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||1||||||regulatory_region|||||||||||||||||||||||||||||||;AC_POPMAX=2;AN_POPMAX=2582;POPMAX=AMR +1 26608871 . ACTGGGGCCGGGACCGGGACCGGGAC AGGGGCCGGGACCGGGACCGGGAC,AGGGACCGGGAC,AGGGAC,A,ACCGGGACCGGGACCGGGAC 443413.18 VQSRTrancheINDEL95.00to96.00 AC=201,56,7,1,2;AC_AFR=146,1,0,0,0;AC_AMR=13,0,1,0,1;AC_Adj=182,56,7,1,2;AC_EAS=0,0,0,0,0;AC_FIN=0,5,0,0,0;AC_Het=172,56,7,1,2,0,0,0,0,0,0,0,0,0,0;AC_Hom=5,0,0,0,0;AC_NFE=22,50,0,1,0;AC_OTH=1,0,0,0,0;AC_SAS=0,0,6,0,1;AF=7.582e-03,2.112e-03,2.641e-04,3.772e-05,7.544e-05;AN=26510;AN_AFR=1804;AN_AMR=2574;AN_Adj=17280;AN_EAS=2860;AN_FIN=848;AN_NFE=5984;AN_OTH=102;AN_SAS=3108;BaseQRankSum=0.167;ClippingRankSum=-7.900e-01;DP=412731;FS=0.000;GQ_MEAN=62.37;GQ_STDDEV=178.76;Het_AFR=136,1,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_AMR=13,0,1,0,1,0,0,0,0,0,0,0,0,0,0;Het_EAS=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_FIN=0,5,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_NFE=22,50,0,1,0,0,0,0,0,0,0,0,0,0,0;Het_OTH=1,0,0,0,0,0,0,0,0,0,0,0,0,0,0;Het_SAS=0,0,6,0,1,0,0,0,0,0,0,0,0,0,0;Hom_AFR=5,0,0,0,0;Hom_AMR=0,0,0,0,0;Hom_EAS=0,0,0,0,0;Hom_FIN=0,0,0,0,0;Hom_NFE=0,0,0,0,0;Hom_OTH=0,0,0,0,0;Hom_SAS=0,0,0,0,0;InbreedingCoeff=0.1552;MQ=56.36;MQ0=0;MQRankSum=1.39;NCC=71502;QD=12.31;ReadPosRankSum=0.601;VQSLOD=1.18;culprit=FS;DP_HIST=1140|2201|1268|618|1291|1021|1081|678|590|570|505|465|357|336|258|207|171|111|105|282,4|10|9|13|14|20|15|15|14|6|18|18|10|6|4|5|1|0|4|6,0|0|0|2|1|0|0|1|0|1|4|3|3|1|6|3|4|3|2|22,0|0|0|0|0|0|0|0|0|1|0|0|1|1|2|0|1|0|1|0,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1,0|0|0|0|0|0|0|2|0|0|0|0|0|0|0|0|0|0|0|0;GQ_HIST=1104|1509|414|444|1805|447|465|334|188|200|170|75|1985|896|399|450|325|187|225|1633,0|1|2|2|0|3|1|0|2|0|1|1|1|0|0|1|0|1|0|176,0|0|0|0|0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|55,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|7,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|2;CSQ=-|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2239-2263||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2239_2263delGTCCCGGTCCCGGTCCCGGCCCCAG|||||||||||||||||||,GGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2239-2263||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2239_2263delGTCCCGGTCCCGGTCCCGGCCCCAGinsGTCCCGGTCCCGGTCCCGGCCCC|||||||||||||||||||,GGGAC|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2239-2263||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2239_2263delGTCCCGGTCCCGGTCCCGGCCCCAGinsGTCCC|||||||||||||||||||,GGGACCGGGAC|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2239-2263||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2239_2263delGTCCCGGTCCCGGTCCCGGCCCCAGinsGTCCCGGTCCC|||||||||||||||||||,CCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2239-2263||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2239_2263delGTCCCGGTCCCGGTCCCGGCCCCAGinsGTCCCGGTCCCGGTCCCGG|||||||||||||||||||,-|ENSG00000158062|ENST00000374217|Transcript|frameshift_variant&feature_truncation|1725-1749|1358-1382|453-461|CPGPGPGPS/X|tGTCCCGGTCCCGGTCCCGGCCCCAGt/tt||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1358_1382delGTCCCGGTCCCGGTCCCGGCCCCAG|ENSP00000363334.2:p.Cys453PhefsTer?|||||||||||||||POSITION:0.943989071038251&PHYLOCSF_TOO_SHORT|||HC,GGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000374217|Transcript|frameshift_variant&missense_variant&feature_truncation|1725-1749|1358-1382|453-461|CPGPGPGPS/CPGPGPGPX|tGTCCCGGTCCCGGTCCCGGCCCCAGt/tGTCCCGGTCCCGGTCCCGGCCCCt||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1358_1382delGTCCCGGTCCCGGTCCCGGCCCCAGinsGTCCCGGTCCCGGTCCCGGCCCC|ENSP00000363334.2:p.Pro462ArgfsTer?|||||||||||||||POSITION:0.943989071038251&PHYLOCSF_TOO_SHORT|||HC,GGGAC|ENSG00000158062|ENST00000374217|Transcript|frameshift_variant&feature_truncation|1725-1749|1358-1382|453-461|CPGPGPGPS/CPX|tGTCCCGGTCCCGGTCCCGGCCCCAGt/tGTCCCt||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1358_1382delGTCCCGGTCCCGGTCCCGGCCCCAGinsGTCCC|ENSP00000363334.2:p.Gly455SerfsTer?|||||||||||||||POSITION:0.943989071038251&PHYLOCSF_TOO_SHORT|||HC,GGGACCGGGAC|ENSG00000158062|ENST00000374217|Transcript|frameshift_variant&feature_truncation|1725-1749|1358-1382|453-461|CPGPGPGPS/CPGPX|tGTCCCGGTCCCGGTCCCGGCCCCAGt/tGTCCCGGTCCCt||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1358_1382delGTCCCGGTCCCGGTCCCGGCCCCAGinsGTCCCGGTCCC|ENSP00000363334.2:p.Gly457SerfsTer?|||||||||||||||POSITION:0.943989071038251&PHYLOCSF_TOO_SHORT|||HC,CCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1725-1749|1358-1382|453-461|CPGPGPGPS/CPGPGPG|tGTCCCGGTCCCGGTCCCGGCCCCAGt/tGTCCCGGTCCCGGTCCCGGt||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1358_1382delGTCCCGGTCCCGGTCCCGGCCCCAGinsGTCCCGGTCCCGGTCCCGG|ENSP00000363334.2:p.Ser461_Pro462del||||||||||||||||||,-|ENSG00000158062|ENST00000374222|Transcript|frameshift_variant&feature_truncation|1922-1946|1457-1481|486-494|CPGPGPGPS/X|tGTCCCGGTCCCGGTCCCGGCCCCAGt/tt||4||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1457_1481delGTCCCGGTCCCGGTCCCGGCCCCAG|ENSP00000363339.1:p.Cys486PhefsTer?|||||||||||||||POSITION:0.947536788227767&PHYLOCSF_TOO_SHORT|||HC,GGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000374222|Transcript|frameshift_variant&missense_variant&feature_truncation|1922-1946|1457-1481|486-494|CPGPGPGPS/CPGPGPGPX|tGTCCCGGTCCCGGTCCCGGCCCCAGt/tGTCCCGGTCCCGGTCCCGGCCCCt||1||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1457_1481delGTCCCGGTCCCGGTCCCGGCCCCAGinsGTCCCGGTCCCGGTCCCGGCCCC|ENSP00000363339.1:p.Pro495ArgfsTer?|||||||||||||||POSITION:0.947536788227767&PHYLOCSF_TOO_SHORT|||HC,GGGAC|ENSG00000158062|ENST00000374222|Transcript|frameshift_variant&feature_truncation|1922-1946|1457-1481|486-494|CPGPGPGPS/CPX|tGTCCCGGTCCCGGTCCCGGCCCCAGt/tGTCCCt||3||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1457_1481delGTCCCGGTCCCGGTCCCGGCCCCAGinsGTCCC|ENSP00000363339.1:p.Gly488SerfsTer?|||||||||||||||POSITION:0.947536788227767&PHYLOCSF_TOO_SHORT|||HC,GGGACCGGGAC|ENSG00000158062|ENST00000374222|Transcript|frameshift_variant&feature_truncation|1922-1946|1457-1481|486-494|CPGPGPGPS/CPGPX|tGTCCCGGTCCCGGTCCCGGCCCCAGt/tGTCCCGGTCCCt||2||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1457_1481delGTCCCGGTCCCGGTCCCGGCCCCAGinsGTCCCGGTCCC|ENSP00000363339.1:p.Gly490SerfsTer?|||||||||||||||POSITION:0.947536788227767&PHYLOCSF_TOO_SHORT|||HC,CCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1922-1946|1457-1481|486-494|CPGPGPGPS/CPGPGPG|tGTCCCGGTCCCGGTCCCGGCCCCAGt/tGTCCCGGTCCCGGTCCCGGt||5||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1457_1481delGTCCCGGTCCCGGTCCCGGCCCCAGinsGTCCCGGTCCCGGTCCCGG|ENSP00000363339.1:p.Ser494_Pro495del||||||||||||||||||,-|ENSG00000158062|ENST00000357089|Transcript|frameshift_variant&feature_truncation|1434-1458|1358-1382|453-461|CPGPGPGPS/X|tGTCCCGGTCCCGGTCCCGGCCCCAGt/tt||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1358_1382delGTCCCGGTCCCGGTCCCGGCCCCAG|ENSP00000349601.4:p.Cys453PhefsTer?|||||||||||||||POSITION:0.943989071038251&PHYLOCSF_TOO_SHORT|||HC,GGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000357089|Transcript|frameshift_variant&missense_variant&feature_truncation|1434-1458|1358-1382|453-461|CPGPGPGPS/CPGPGPGPX|tGTCCCGGTCCCGGTCCCGGCCCCAGt/tGTCCCGGTCCCGGTCCCGGCCCCt||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1358_1382delGTCCCGGTCCCGGTCCCGGCCCCAGinsGTCCCGGTCCCGGTCCCGGCCCC|ENSP00000349601.4:p.Pro462ArgfsTer?|||||||||||||||POSITION:0.943989071038251&PHYLOCSF_TOO_SHORT|||HC,GGGAC|ENSG00000158062|ENST00000357089|Transcript|frameshift_variant&feature_truncation|1434-1458|1358-1382|453-461|CPGPGPGPS/CPX|tGTCCCGGTCCCGGTCCCGGCCCCAGt/tGTCCCt||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1358_1382delGTCCCGGTCCCGGTCCCGGCCCCAGinsGTCCC|ENSP00000349601.4:p.Gly455SerfsTer?|||||||||||||||POSITION:0.943989071038251&PHYLOCSF_TOO_SHORT|||HC,GGGACCGGGAC|ENSG00000158062|ENST00000357089|Transcript|frameshift_variant&feature_truncation|1434-1458|1358-1382|453-461|CPGPGPGPS/CPGPX|tGTCCCGGTCCCGGTCCCGGCCCCAGt/tGTCCCGGTCCCt||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1358_1382delGTCCCGGTCCCGGTCCCGGCCCCAGinsGTCCCGGTCCC|ENSP00000349601.4:p.Gly457SerfsTer?|||||||||||||||POSITION:0.943989071038251&PHYLOCSF_TOO_SHORT|||HC,CCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1434-1458|1358-1382|453-461|CPGPGPGPS/CPGPGPG|tGTCCCGGTCCCGGTCCCGGCCCCAGt/tGTCCCGGTCCCGGTCCCGGt||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1358_1382delGTCCCGGTCCCGGTCCCGGCCCCAGinsGTCCCGGTCCCGGTCCCGG|ENSP00000349601.4:p.Ser461_Pro462del||||||||||||||||||,-|ENSG00000158062|ENST00000314675|Transcript|frameshift_variant&feature_truncation|1177-1201|1097-1121|366-374|CPGPGPGPS/X|tGTCCCGGTCCCGGTCCCGGCCCCAGt/tt||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1097_1121delGTCCCGGTCCCGGTCCCGGCCCCAG|ENSP00000324721.7:p.Cys366PhefsTer69|||||||||||||||POSITION:0.931837073981712&PHYLOCSF_TOO_SHORT|||HC,GGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000314675|Transcript|frameshift_variant&missense_variant&feature_truncation|1177-1201|1097-1121|366-374|CPGPGPGPS/CPGPGPGPX|tGTCCCGGTCCCGGTCCCGGCCCCAGt/tGTCCCGGTCCCGGTCCCGGCCCCt||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1097_1121delGTCCCGGTCCCGGTCCCGGCCCCAGinsGTCCCGGTCCCGGTCCCGGCCCC|ENSP00000324721.7:p.Pro375ArgfsTer160|||||||||||||||POSITION:0.931837073981712&PHYLOCSF_TOO_SHORT|||HC,GGGAC|ENSG00000158062|ENST00000314675|Transcript|frameshift_variant&feature_truncation|1177-1201|1097-1121|366-374|CPGPGPGPS/CPX|tGTCCCGGTCCCGGTCCCGGCCCCAGt/tGTCCCt||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1097_1121delGTCCCGGTCCCGGTCCCGGCCCCAGinsGTCCC|ENSP00000324721.7:p.Gly368SerfsTer161|||||||||||||||POSITION:0.931837073981712&PHYLOCSF_TOO_SHORT|||HC,GGGACCGGGAC|ENSG00000158062|ENST00000314675|Transcript|frameshift_variant&feature_truncation|1177-1201|1097-1121|366-374|CPGPGPGPS/CPGPX|tGTCCCGGTCCCGGTCCCGGCCCCAGt/tGTCCCGGTCCCt||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1097_1121delGTCCCGGTCCCGGTCCCGGCCCCAGinsGTCCCGGTCCC|ENSP00000324721.7:p.Gly370SerfsTer161|||||||||||||||POSITION:0.931837073981712&PHYLOCSF_TOO_SHORT|||HC,CCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1177-1201|1097-1121|366-374|CPGPGPGPS/CPGPGPG|tGTCCCGGTCCCGGTCCCGGCCCCAGt/tGTCCCGGTCCCGGTCCCGGt||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1097_1121delGTCCCGGTCCCGGTCCCGGCCCCAGinsGTCCCGGTCCCGGTCCCGG|ENSP00000324721.7:p.Ser374_Pro375del||||||||||||||||||,-|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2419-2443||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2419_2443delGTCCCGGTCCCGGTCCCGGCCCCAG|||||||||||||||||||,GGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2419-2443||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2419_2443delGTCCCGGTCCCGGTCCCGGCCCCAGinsGTCCCGGTCCCGGTCCCGGCCCC|||||||||||||||||||,GGGAC|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2419-2443||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2419_2443delGTCCCGGTCCCGGTCCCGGCCCCAGinsGTCCC|||||||||||||||||||,GGGACCGGGAC|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2419-2443||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2419_2443delGTCCCGGTCCCGGTCCCGGCCCCAGinsGTCCCGGTCCC|||||||||||||||||||,CCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2419-2443||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2419_2443delGTCCCGGTCCCGGTCCCGGCCCCAGinsGTCCCGGTCCCGGTCCCGG|||||||||||||||||||,-|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2204-2228||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2204_2228delGTCCCGGTCCCGGTCCCGGCCCCAG|||||||||||||||||||,GGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2204-2228||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2204_2228delGTCCCGGTCCCGGTCCCGGCCCCAGinsGTCCCGGTCCCGGTCCCGGCCCC|||||||||||||||||||,GGGAC|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2204-2228||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2204_2228delGTCCCGGTCCCGGTCCCGGCCCCAGinsGTCCC|||||||||||||||||||,GGGACCGGGAC|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2204-2228||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2204_2228delGTCCCGGTCCCGGTCCCGGCCCCAGinsGTCCCGGTCCC|||||||||||||||||||,CCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2204-2228||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2204_2228delGTCCCGGTCCCGGTCCCGGCCCCAGinsGTCCCGGTCCCGGTCCCGG|||||||||||||||||||,-|ENSG00000158062|ENST00000374221|Transcript|frameshift_variant&feature_truncation|1671-1695|1457-1481|486-494|CPGPGPGPS/X|tGTCCCGGTCCCGGTCCCGGCCCCAGt/tt||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1457_1481delGTCCCGGTCCCGGTCCCGGCCCCAG|ENSP00000363338.3:p.Cys486PhefsTer?|||||||||||||||POSITION:0.947536788227767&PHYLOCSF_TOO_SHORT|||HC,GGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000374221|Transcript|frameshift_variant&missense_variant&feature_truncation|1671-1695|1457-1481|486-494|CPGPGPGPS/CPGPGPGPX|tGTCCCGGTCCCGGTCCCGGCCCCAGt/tGTCCCGGTCCCGGTCCCGGCCCCt||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1457_1481delGTCCCGGTCCCGGTCCCGGCCCCAGinsGTCCCGGTCCCGGTCCCGGCCCC|ENSP00000363338.3:p.Pro495ArgfsTer?|||||||||||||||POSITION:0.947536788227767&PHYLOCSF_TOO_SHORT|||HC,GGGAC|ENSG00000158062|ENST00000374221|Transcript|frameshift_variant&feature_truncation|1671-1695|1457-1481|486-494|CPGPGPGPS/CPX|tGTCCCGGTCCCGGTCCCGGCCCCAGt/tGTCCCt||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1457_1481delGTCCCGGTCCCGGTCCCGGCCCCAGinsGTCCC|ENSP00000363338.3:p.Gly488SerfsTer?|||||||||||||||POSITION:0.947536788227767&PHYLOCSF_TOO_SHORT|||HC,GGGACCGGGAC|ENSG00000158062|ENST00000374221|Transcript|frameshift_variant&feature_truncation|1671-1695|1457-1481|486-494|CPGPGPGPS/CPGPX|tGTCCCGGTCCCGGTCCCGGCCCCAGt/tGTCCCGGTCCCt||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1457_1481delGTCCCGGTCCCGGTCCCGGCCCCAGinsGTCCCGGTCCC|ENSP00000363338.3:p.Gly490SerfsTer?|||||||||||||||POSITION:0.947536788227767&PHYLOCSF_TOO_SHORT|||HC,CCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1671-1695|1457-1481|486-494|CPGPGPGPS/CPGPGPG|tGTCCCGGTCCCGGTCCCGGCCCCAGt/tGTCCCGGTCCCGGTCCCGGt||5||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1457_1481delGTCCCGGTCCCGGTCCCGGCCCCAGinsGTCCCGGTCCCGGTCCCGG|ENSP00000363338.3:p.Ser494_Pro495del||||||||||||||||||,-|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2522-2546||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2522_2546delGTCCCGGTCCCGGTCCCGGCCCCAG|||||||||||||||||||,GGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2522-2546||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2522_2546delGTCCCGGTCCCGGTCCCGGCCCCAGinsGTCCCGGTCCCGGTCCCGGCCCC|||||||||||||||||||,GGGAC|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2522-2546||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2522_2546delGTCCCGGTCCCGGTCCCGGCCCCAGinsGTCCC|||||||||||||||||||,GGGACCGGGAC|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2522-2546||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2522_2546delGTCCCGGTCCCGGTCCCGGCCCCAGinsGTCCCGGTCCC|||||||||||||||||||,CCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2522-2546||||||5||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2522_2546delGTCCCGGTCCCGGTCCCGGCCCCAGinsGTCCCGGTCCCGGTCCCGG|||||||||||||||||||,-|ENSG00000158062|ENST00000374223|Transcript|frameshift_variant&feature_truncation|1189-1213|728-752|243-251|CPGPGPGPS/X|tGTCCCGGTCCCGGTCCCGGCCCCAGt/tt||4||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.728_752delGTCCCGGTCCCGGTCCCGGCCCCAG|ENSP00000363340.1:p.Cys243PhefsTer?|||||||||||||||POSITION:0.90167865707434&PHYLOCSF_TOO_SHORT|||HC,GGGGCCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000374223|Transcript|frameshift_variant&missense_variant&feature_truncation|1189-1213|728-752|243-251|CPGPGPGPS/CPGPGPGPX|tGTCCCGGTCCCGGTCCCGGCCCCAGt/tGTCCCGGTCCCGGTCCCGGCCCCt||1||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.728_752delGTCCCGGTCCCGGTCCCGGCCCCAGinsGTCCCGGTCCCGGTCCCGGCCCC|ENSP00000363340.1:p.Pro252ArgfsTer?|||||||||||||||POSITION:0.90167865707434&PHYLOCSF_TOO_SHORT|||HC,GGGAC|ENSG00000158062|ENST00000374223|Transcript|frameshift_variant&feature_truncation|1189-1213|728-752|243-251|CPGPGPGPS/CPX|tGTCCCGGTCCCGGTCCCGGCCCCAGt/tGTCCCt||3||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.728_752delGTCCCGGTCCCGGTCCCGGCCCCAGinsGTCCC|ENSP00000363340.1:p.Gly245SerfsTer?|||||||||||||||POSITION:0.90167865707434&PHYLOCSF_TOO_SHORT|||HC,GGGACCGGGAC|ENSG00000158062|ENST00000374223|Transcript|frameshift_variant&feature_truncation|1189-1213|728-752|243-251|CPGPGPGPS/CPGPX|tGTCCCGGTCCCGGTCCCGGCCCCAGt/tGTCCCGGTCCCt||2||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.728_752delGTCCCGGTCCCGGTCCCGGCCCCAGinsGTCCCGGTCCC|ENSP00000363340.1:p.Gly247SerfsTer?|||||||||||||||POSITION:0.90167865707434&PHYLOCSF_TOO_SHORT|||HC,CCGGGACCGGGACCGGGAC|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1189-1213|728-752|243-251|CPGPGPGPS/CPGPGPG|tGTCCCGGTCCCGGTCCCGGCCCCAGt/tGTCCCGGTCCCGGTCCCGGt||5||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.728_752delGTCCCGGTCCCGGTCCCGGCCCCAGinsGTCCCGGTCCCGGTCCCGG|ENSP00000363340.1:p.Ser251_Pro252del||||||||||||||||||,-||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||4||||||regulatory_region|||||||||||||||||||||||||||||||,GGGGCCGGGACCGGGACCGGGAC||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||1||||||regulatory_region|||||||||||||||||||||||||||||||,GGGAC||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||3||||||regulatory_region|||||||||||||||||||||||||||||||,GGGACCGGGAC||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||2||||||regulatory_region|||||||||||||||||||||||||||||||,CCGGGACCGGGACCGGGAC||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||5||||||regulatory_region|||||||||||||||||||||||||||||||;AC_POPMAX=146,50,6,1,1;AN_POPMAX=1804,5984,3108,5984,2574;POPMAX=AFR,NFE,SAS,NFE,AMR +1 26608872 . CTGGGG C 2979.99 VQSRTrancheINDEL99.50to99.90 AC=3;AC_AFR=0;AC_AMR=2;AC_Adj=3;AC_EAS=0;AC_FIN=0;AC_Het=1;AC_Hom=1;AC_NFE=1;AC_OTH=0;AC_SAS=0;AF=1.130e-04;AN=26548;AN_AFR=1560;AN_AMR=2612;AN_Adj=17384;AN_EAS=2874;AN_FIN=866;AN_NFE=6210;AN_OTH=98;AN_SAS=3164;BaseQRankSum=1.61;ClippingRankSum=-9.240e-01;DP=426380;FS=47.240;GQ_MEAN=48.27;GQ_STDDEV=54.05;Het_AFR=0;Het_AMR=0;Het_EAS=0;Het_FIN=0;Het_NFE=1;Het_OTH=0;Het_SAS=0;Hom_AFR=0;Hom_AMR=1;Hom_EAS=0;Hom_FIN=0;Hom_NFE=0;Hom_OTH=0;Hom_SAS=0;InbreedingCoeff=0.0408;MQ=51.01;MQ0=0;MQRankSum=4.14;NCC=71486;NEGATIVE_TRAIN_SITE;QD=14.60;ReadPosRankSum=-1.180e-01;VQSLOD=-1.955e+00;culprit=FS;DP_HIST=1150|2190|1241|616|1305|1013|1065|650|582|559|486|459|352|332|262|204|183|118|111|396,0|0|0|0|0|1|0|0|0|0|0|0|0|0|1|0|0|0|0|0;GQ_HIST=1041|1513|413|482|1780|439|461|352|191|190|164|85|1988|913|405|460|333|192|230|1642,0|0|0|0|0|0|1|0|0|0|0|0|0|0|0|0|0|0|0|1;CSQ=-|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2258-2262||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2258_2262delCCCCA|||||||||||||||||||,-|ENSG00000158062|ENST00000374217|Transcript|frameshift_variant&feature_truncation|1744-1748|1377-1381|459-461|GPS/GX|ggCCCCAgt/gggt||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1377_1381delCCCCA|ENSP00000363334.2:p.Pro460SerfsTer?|||||||||||||||POSITION:0.943306010928962&PHYLOCSF_TOO_SHORT|||HC,-|ENSG00000158062|ENST00000374222|Transcript|frameshift_variant&feature_truncation|1941-1945|1476-1480|492-494|GPS/GX|ggCCCCAgt/gggt||1||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1476_1480delCCCCA|ENSP00000363339.1:p.Pro493SerfsTer?|||||||||||||||POSITION:0.946896992962252&PHYLOCSF_TOO_SHORT|||HC,-|ENSG00000158062|ENST00000357089|Transcript|frameshift_variant&feature_truncation|1453-1457|1377-1381|459-461|GPS/GX|ggCCCCAgt/gggt||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1377_1381delCCCCA|ENSP00000349601.4:p.Pro460SerfsTer?|||||||||||||||POSITION:0.943306010928962&PHYLOCSF_TOO_SHORT|||HC,-|ENSG00000158062|ENST00000314675|Transcript|frameshift_variant&feature_truncation|1196-1200|1116-1120|372-374|GPS/GX|ggCCCCAgt/gggt||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1116_1120delCCCCA|ENSP00000324721.7:p.Pro373SerfsTer161|||||||||||||||POSITION:0.931005818786367&PHYLOCSF_TOO_SHORT|||HC,-|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2438-2442||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2438_2442delCCCCA|||||||||||||||||||,-|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2223-2227||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2223_2227delCCCCA|||||||||||||||||||,-|ENSG00000158062|ENST00000374221|Transcript|frameshift_variant&feature_truncation|1690-1694|1476-1480|492-494|GPS/GX|ggCCCCAgt/gggt||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1476_1480delCCCCA|ENSP00000363338.3:p.Pro493SerfsTer?|||||||||||||||POSITION:0.946896992962252&PHYLOCSF_TOO_SHORT|||HC,-|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2541-2545||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2541_2545delCCCCA|||||||||||||||||||,-|ENSG00000158062|ENST00000374223|Transcript|frameshift_variant&feature_truncation|1208-1212|747-751|249-251|GPS/GX|ggCCCCAgt/gggt||1||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.747_751delCCCCA|ENSP00000363340.1:p.Pro250SerfsTer?|||||||||||||||POSITION:0.900479616306954&PHYLOCSF_TOO_SHORT|||HC,-||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||1||||||regulatory_region|||||||||||||||||||||||||||||||;AC_POPMAX=2;AN_POPMAX=2612;POPMAX=AMR +1 26608873 . TGGGGCCGGGACCGGGACC AGGGGCCGGGACCGGGACC,CGGGGCCGGGACCGGGACC,T,TGGGGCCGGGACCGGGACCGGGACAGGGGCCGGGACCGGGACC 123560.41 VQSRTrancheINDEL97.00to99.00 AC=7,70,5,2;AC_AFR=0,3,0,0;AC_AMR=0,0,1,2;AC_Adj=4,66,5,2;AC_EAS=0,3,0,0;AC_FIN=0,10,0,0;AC_Het=4,66,5,2,0,0,0,0,0,0;AC_Hom=0,0,0,0;AC_NFE=4,47,4,0;AC_OTH=0,0,0,0;AC_SAS=0,3,0,0;AF=2.797e-04,2.797e-03,1.998e-04,7.990e-05;AN=25030;AN_AFR=756;AN_AMR=1818;AN_Adj=9358;AN_EAS=2570;AN_FIN=292;AN_NFE=1912;AN_OTH=52;AN_SAS=1958;BaseQRankSum=0.123;ClippingRankSum=-3.010e-01;DP=426456;FS=7.753;GQ_MEAN=32.47;GQ_STDDEV=98.57;Het_AFR=0,3,0,0,0,0,0,0,0,0;Het_AMR=0,0,1,2,0,0,0,0,0,0;Het_EAS=0,3,0,0,0,0,0,0,0,0;Het_FIN=0,10,0,0,0,0,0,0,0,0;Het_NFE=4,47,4,0,0,0,0,0,0,0;Het_OTH=0,0,0,0,0,0,0,0,0,0;Het_SAS=0,3,0,0,0,0,0,0,0,0;Hom_AFR=0,0,0,0;Hom_AMR=0,0,0,0;Hom_EAS=0,0,0,0;Hom_FIN=0,0,0,0;Hom_NFE=0,0,0,0;Hom_OTH=0,0,0,0;Hom_SAS=0,0,0,0;InbreedingCoeff=0.3239;MQ=47.12;MQ0=0;MQRankSum=0.845;NCC=72664;QD=18.40;ReadPosRankSum=0.496;VQSLOD=0.539;culprit=FS;DP_HIST=1051|2200|1311|652|1198|901|937|538|470|512|456|378|376|324|270|197|173|155|105|311,1|1|0|0|1|0|1|2|0|0|0|0|0|0|0|0|0|0|0|0,1|2|0|2|6|7|4|4|4|7|6|4|4|5|2|1|3|1|3|4,0|0|0|0|0|0|0|0|0|1|0|1|0|1|1|0|1|0|0|0,0|0|0|0|0|0|0|0|1|1|0|0|0|0|0|0|0|0|0|0;GQ_HIST=5204|1007|223|189|1171|248|208|155|109|100|117|84|1556|620|295|281|206|101|99|542,0|0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|5,1|0|0|0|1|1|0|0|0|1|2|1|0|0|0|0|0|0|0|63,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|5,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|2;CSQ=TGGGGCCGGGACCGGGACCGGGACAGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_elongation|2244-2262||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2244_2262delGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCTGTCCCGGTCCCGGTCCCGGCCCCA|||||||||||||||||||,T|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2244-2262||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2244_2262delGGTCCCGGTCCCGGCCCCAinsA|||||||||||||||||||,AGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2244-2262||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2244_2262delGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCT|||||||||||||||||||,CGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2244-2262||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2244_2262delGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCG|||||||||||||||||||,TGGGGCCGGGACCGGGACCGGGACAGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000374217|Transcript|inframe_insertion|1730-1748|1363-1381|455-461|GPGPGPS/GPGPGPCPGPGPGPS|GGTCCCGGTCCCGGCCCCAgt/GGTCCCGGTCCCGGCCCCTGTCCCGGTCCCGGTCCCGGCCCCAgt||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1363_1381delGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCTGTCCCGGTCCCGGTCCCGGCCCCA|ENSP00000363334.2:p.Cys453_Pro460dup||||||||||||||||||,T|ENSG00000158062|ENST00000374217|Transcript|inframe_deletion|1730-1748|1363-1381|455-461|GPGPGPS/S|GGTCCCGGTCCCGGCCCCAgt/Agt||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1363_1381delGGTCCCGGTCCCGGCCCCAinsA|ENSP00000363334.2:p.Gly455_Pro460del||||||||||||||||||,AGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000374217|Transcript|missense_variant|1730-1748|1363-1381|455-461|GPGPGPS/GPGPGPC|GGTCCCGGTCCCGGCCCCAgt/GGTCCCGGTCCCGGCCCCTgt||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1363_1381delGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCT|ENSP00000363334.2:p.Ser461Cys||||||||||||||||||,CGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000374217|Transcript|missense_variant|1730-1748|1363-1381|455-461|GPGPGPS/GPGPGPG|GGTCCCGGTCCCGGCCCCAgt/GGTCCCGGTCCCGGCCCCGgt||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1363_1381delGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCG|ENSP00000363334.2:p.Ser461Gly||||||||||||||||||,TGGGGCCGGGACCGGGACCGGGACAGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000374222|Transcript|inframe_insertion|1927-1945|1462-1480|488-494|GPGPGPS/GPGPGPCPGPGPGPS|GGTCCCGGTCCCGGCCCCAgt/GGTCCCGGTCCCGGCCCCTGTCCCGGTCCCGGTCCCGGCCCCAgt||4||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1462_1480delGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCTGTCCCGGTCCCGGTCCCGGCCCCA|ENSP00000363339.1:p.Cys486_Pro493dup||||||||||||||||||,T|ENSG00000158062|ENST00000374222|Transcript|inframe_deletion|1927-1945|1462-1480|488-494|GPGPGPS/S|GGTCCCGGTCCCGGCCCCAgt/Agt||3||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1462_1480delGGTCCCGGTCCCGGCCCCAinsA|ENSP00000363339.1:p.Gly488_Pro493del||||||||||||||||||,AGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000374222|Transcript|missense_variant|1927-1945|1462-1480|488-494|GPGPGPS/GPGPGPC|GGTCCCGGTCCCGGCCCCAgt/GGTCCCGGTCCCGGCCCCTgt||1||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1462_1480delGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCT|ENSP00000363339.1:p.Ser494Cys||||||||||||||||||,CGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000374222|Transcript|missense_variant|1927-1945|1462-1480|488-494|GPGPGPS/GPGPGPG|GGTCCCGGTCCCGGCCCCAgt/GGTCCCGGTCCCGGCCCCGgt||2||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1462_1480delGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCG|ENSP00000363339.1:p.Ser494Gly||||||||||||||||||,TGGGGCCGGGACCGGGACCGGGACAGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000357089|Transcript|inframe_insertion|1439-1457|1363-1381|455-461|GPGPGPS/GPGPGPCPGPGPGPS|GGTCCCGGTCCCGGCCCCAgt/GGTCCCGGTCCCGGCCCCTGTCCCGGTCCCGGTCCCGGCCCCAgt||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1363_1381delGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCTGTCCCGGTCCCGGTCCCGGCCCCA|ENSP00000349601.4:p.Cys453_Pro460dup||||||||||||||||||,T|ENSG00000158062|ENST00000357089|Transcript|inframe_deletion|1439-1457|1363-1381|455-461|GPGPGPS/S|GGTCCCGGTCCCGGCCCCAgt/Agt||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1363_1381delGGTCCCGGTCCCGGCCCCAinsA|ENSP00000349601.4:p.Gly455_Pro460del||||||||||||||||||,AGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000357089|Transcript|missense_variant|1439-1457|1363-1381|455-461|GPGPGPS/GPGPGPC|GGTCCCGGTCCCGGCCCCAgt/GGTCCCGGTCCCGGCCCCTgt||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1363_1381delGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCT|ENSP00000349601.4:p.Ser461Cys||||||||||||||||||,CGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000357089|Transcript|missense_variant|1439-1457|1363-1381|455-461|GPGPGPS/GPGPGPG|GGTCCCGGTCCCGGCCCCAgt/GGTCCCGGTCCCGGCCCCGgt||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|||14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1363_1381delGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCG|ENSP00000349601.4:p.Ser461Gly||||||||||||||||||,TGGGGCCGGGACCGGGACCGGGACAGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000314675|Transcript|inframe_insertion|1182-1200|1102-1120|368-374|GPGPGPS/GPGPGPCPGPGPGPS|GGTCCCGGTCCCGGCCCCAgt/GGTCCCGGTCCCGGCCCCTGTCCCGGTCCCGGTCCCGGCCCCAgt||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1102_1120delGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCTGTCCCGGTCCCGGTCCCGGCCCCA|ENSP00000324721.7:p.Cys366_Pro373dup||||||||||||||||||,T|ENSG00000158062|ENST00000314675|Transcript|inframe_deletion|1182-1200|1102-1120|368-374|GPGPGPS/S|GGTCCCGGTCCCGGCCCCAgt/Agt||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1102_1120delGGTCCCGGTCCCGGCCCCAinsA|ENSP00000324721.7:p.Gly368_Pro373del||||||||||||||||||,AGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000314675|Transcript|missense_variant|1182-1200|1102-1120|368-374|GPGPGPS/GPGPGPC|GGTCCCGGTCCCGGCCCCAgt/GGTCCCGGTCCCGGCCCCTgt||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1102_1120delGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCT|ENSP00000324721.7:p.Ser374Cys||||||||||||||||||,CGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000314675|Transcript|missense_variant|1182-1200|1102-1120|368-374|GPGPGPS/GPGPGPG|GGTCCCGGTCCCGGCCCCAgt/GGTCCCGGTCCCGGCCCCGgt||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|||11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1102_1120delGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCG|ENSP00000324721.7:p.Ser374Gly||||||||||||||||||,TGGGGCCGGGACCGGGACCGGGACAGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_elongation|2424-2442||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2424_2442delGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCTGTCCCGGTCCCGGTCCCGGCCCCA|||||||||||||||||||,T|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2424-2442||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2424_2442delGGTCCCGGTCCCGGCCCCAinsA|||||||||||||||||||,AGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2424-2442||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2424_2442delGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCT|||||||||||||||||||,CGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2424-2442||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2424_2442delGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCG|||||||||||||||||||,TGGGGCCGGGACCGGGACCGGGACAGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_elongation|2209-2227||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2209_2227delGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCTGTCCCGGTCCCGGTCCCGGCCCCA|||||||||||||||||||,T|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2209-2227||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2209_2227delGGTCCCGGTCCCGGCCCCAinsA|||||||||||||||||||,AGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2209-2227||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2209_2227delGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCT|||||||||||||||||||,CGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2209-2227||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2209_2227delGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCG|||||||||||||||||||,TGGGGCCGGGACCGGGACCGGGACAGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000374221|Transcript|inframe_insertion|1676-1694|1462-1480|488-494|GPGPGPS/GPGPGPCPGPGPGPS|GGTCCCGGTCCCGGCCCCAgt/GGTCCCGGTCCCGGCCCCTGTCCCGGTCCCGGTCCCGGCCCCAgt||4||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1462_1480delGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCTGTCCCGGTCCCGGTCCCGGCCCCA|ENSP00000363338.3:p.Cys486_Pro493dup||||||||||||||||||,T|ENSG00000158062|ENST00000374221|Transcript|inframe_deletion|1676-1694|1462-1480|488-494|GPGPGPS/S|GGTCCCGGTCCCGGCCCCAgt/Agt||3||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1462_1480delGGTCCCGGTCCCGGCCCCAinsA|ENSP00000363338.3:p.Gly488_Pro493del||||||||||||||||||,AGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000374221|Transcript|missense_variant|1676-1694|1462-1480|488-494|GPGPGPS/GPGPGPC|GGTCCCGGTCCCGGCCCCAgt/GGTCCCGGTCCCGGCCCCTgt||1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1462_1480delGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCT|ENSP00000363338.3:p.Ser494Cys||||||||||||||||||,CGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000374221|Transcript|missense_variant|1676-1694|1462-1480|488-494|GPGPGPS/GPGPGPG|GGTCCCGGTCCCGGCCCCAgt/GGTCCCGGTCCCGGCCCCGgt||2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|||16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1462_1480delGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCG|ENSP00000363338.3:p.Ser494Gly||||||||||||||||||,TGGGGCCGGGACCGGGACCGGGACAGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_elongation|2527-2545||||||4||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2527_2545delGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCTGTCCCGGTCCCGGTCCCGGCCCCA|||||||||||||||||||,T|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2527-2545||||||3||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2527_2545delGGTCCCGGTCCCGGCCCCAinsA|||||||||||||||||||,AGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2527-2545||||||1||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2527_2545delGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCT|||||||||||||||||||,CGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2527-2545||||||2||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2527_2545delGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCG|||||||||||||||||||,TGGGGCCGGGACCGGGACCGGGACAGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000374223|Transcript|inframe_insertion|1194-1212|733-751|245-251|GPGPGPS/GPGPGPCPGPGPGPS|GGTCCCGGTCCCGGCCCCAgt/GGTCCCGGTCCCGGCCCCTGTCCCGGTCCCGGTCCCGGCCCCAgt||4||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.733_751delGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCTGTCCCGGTCCCGGTCCCGGCCCCA|ENSP00000363340.1:p.Cys243_Pro250dup||||||||||||||||||,T|ENSG00000158062|ENST00000374223|Transcript|inframe_deletion|1194-1212|733-751|245-251|GPGPGPS/S|GGTCCCGGTCCCGGCCCCAgt/Agt||3||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.733_751delGGTCCCGGTCCCGGCCCCAinsA|ENSP00000363340.1:p.Gly245_Pro250del||||||||||||||||||,AGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000374223|Transcript|missense_variant|1194-1212|733-751|245-251|GPGPGPS/GPGPGPC|GGTCCCGGTCCCGGCCCCAgt/GGTCCCGGTCCCGGCCCCTgt||1||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.733_751delGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCT|ENSP00000363340.1:p.Ser251Cys||||||||||||||||||,CGGGGCCGGGACCGGGACC|ENSG00000158062|ENST00000374223|Transcript|missense_variant|1194-1212|733-751|245-251|GPGPGPS/GPGPGPG|GGTCCCGGTCCCGGCCCCAgt/GGTCCCGGTCCCGGCCCCGgt||2||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|||12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.733_751delGGTCCCGGTCCCGGCCCCAinsGGTCCCGGTCCCGGCCCCG|ENSP00000363340.1:p.Ser251Gly||||||||||||||||||,TGGGGCCGGGACCGGGACCGGGACAGGGGCCGGGACCGGGACC||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||4||||||regulatory_region|||||||||||||||||||||||||||||||,T||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||3||||||regulatory_region|||||||||||||||||||||||||||||||,AGGGGCCGGGACCGGGACC||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||1||||||regulatory_region|||||||||||||||||||||||||||||||,CGGGGCCGGGACCGGGACC||ENSR00000533083|RegulatoryFeature|regulatory_region_variant|||||||2||||||regulatory_region|||||||||||||||||||||||||||||||;AC_POPMAX=4,10,4,2;AN_POPMAX=1912,292,1912,1818;POPMAX=NFE,FIN,NFE,AMR diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/exacAlleleTrim.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/exacAlleleTrim.vcf.idx new file mode 100644 index 0000000000000000000000000000000000000000..26f148c6c3bf7d8872db11e9453a452c4f430f13 GIT binary patch literal 520 zcmdr|+e!m55FOD69|ZMH`~lxORRpnbp_^(!w@|Z-Z%ewJ*4Q+GN$TZq{Hy+sNnu6& z1P2Z?oHLihsB!VU2LSsC3u9@3h*cmCNNeKHS9~FBXXNI@xYTilfm@6eA~FTP;g$k= zUgC_so*NgUiJM5jr=s^Z;Jdb~yj45rqmG`j)@-zk;)kFQ-3n{Tl47&&y|oM2jt-MA zfRl@((QLRC}QJjn7+-8YX?lyGy~>;Dy=RM8Z&hJKQAQ_~IBVmcP(Q0|nD h98RiI!PPb7QW +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##contig= +##contig= +##reference=file:///Users/louisb/Workspace/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 +20 10000117 . C T 905.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=2.136;AS_FS=11.007;AS_MQ=60.00;AS_MQRankSum=0.913;AS_ReadPosRankSum=-0.179;AS_SOR=1.538;BaseQRankSum=2.136;ClippingRankSum=0.000;DP=64;ExcessHet=3.0103;FS=11.007;MLEAC=1;MLEAF=0.500;MQ=59.71;MQRankSum=0.913;QD=14.15;ReadPosRankSum=-0.179;SOR=1.538 GT:AD:DP:GQ:PL 0/1:36,28:64:99:934,0,1248 +20 10000211 . C T 941.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=1.867;AS_FS=5.587;AS_MQ=60.00;AS_MQRankSum=1.057;AS_ReadPosRankSum=1.068;AS_SOR=0.944;BaseQRankSum=1.867;ClippingRankSum=0.000;DP=54;ExcessHet=3.0103;FS=5.587;MLEAC=1;MLEAF=0.500;MQ=59.65;MQRankSum=1.057;QD=17.77;ReadPosRankSum=1.068;SOR=0.944 GT:AD:DP:GQ:PL 0/1:26,27:53:99:970,0,906 +20 10000439 . T G 2804.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=59.06;AS_SOR=1.236;DP=80;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.06;QD=34.24;SOR=1.236 GT:AD:DP:GQ:PL 1/1:0,80:80:99:2833,240,0 +20 10000598 . T A 1941.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=55.26;AS_SOR=1.225;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=55.26;QD=30.63;SOR=1.225 GT:AD:DP:GQ:PL 1/1:0,49:49:99:1970,147,0 +20 10000694 . G A 1008.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=3.599;AS_FS=1.822;AS_MQ=39.92;AS_MQRankSum=-5.114;AS_ReadPosRankSum=0.182;AS_SOR=0.566;BaseQRankSum=3.599;ClippingRankSum=0.000;DP=82;ExcessHet=3.0103;FS=1.822;MLEAC=1;MLEAF=0.500;MQ=48.66;MQRankSum=-5.114;QD=12.30;ReadPosRankSum=0.182;SOR=0.566 GT:AD:DP:GQ:PL 0/1:45,37:82:99:1037,0,1601 +20 10000758 . T A 3838.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=53.37;AS_SOR=0.802;DP=95;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.37;QD=29.09;SOR=0.802 GT:AD:DP:GQ:PL 1/1:0,95:95:99:3867,286,0 +20 10001019 . T G 650.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-2.541;AS_FS=3.406;AS_MQ=29.00;AS_MQRankSum=-7.498;AS_ReadPosRankSum=-1.497;AS_SOR=0.665;BaseQRankSum=-2.541;ClippingRankSum=0.000;DP=65;ExcessHet=3.0103;FS=3.406;MLEAC=1;MLEAF=0.500;MQ=49.49;MQRankSum=-7.498;QD=10.01;ReadPosRankSum=-1.497;SOR=0.665 GT:AD:DP:GQ:PL 0/1:39,26:65:99:679,0,1426 +20 10001298 . T A 2917.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=54.54;AS_SOR=0.963;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=54.34;QD=32.93;SOR=0.963 GT:AD:DP:GQ:PL 1/1:0,73:73:99:2946,220,0 +20 10001436 . A AAGGCT 2301.73 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=39.24;AS_SOR=3.442;DP=56;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=40.88;QD=30.83;SOR=3.442 GT:AD:DP:GQ:PL 1/1:0,50:50:99:2339,156,0 +20 10001474 . C T 2640.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=43.89;AS_SOR=1.516;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=43.72;QD=29.67;SOR=1.516 GT:AD:DP:GQ:PL 1/1:0,73:73:99:2669,219,0 +20 10001617 . C A 1731.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=1.261;AS_FS=13.163;AS_MQ=59.63;AS_MQRankSum=1.373;AS_ReadPosRankSum=-0.578;AS_SOR=1.346;BaseQRankSum=1.261;ClippingRankSum=0.000;DP=103;ExcessHet=3.0103;FS=13.163;MLEAC=1;MLEAF=0.500;MQ=59.00;MQRankSum=1.373;QD=16.81;ReadPosRankSum=-0.578;SOR=1.346 GT:AD:DP:GQ:PL 0/1:52,51:103:99:1760,0,1781 +20 10001628 . G A 3898.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=59.17;AS_SOR=1.053;DP=95;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.17;QD=34.04;SOR=1.053 GT:AD:DP:GQ:PL 1/1:0,95:95:99:3927,285,0 +20 10001661 . T C 3606.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=58.33;AS_SOR=1.193;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.33;QD=32.42;SOR=1.193 GT:AD:DP:GQ:PL 1/1:0,81:81:99:3635,249,0 +20 10001670 . T G 3673.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=57.45;AS_SOR=0.995;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.45;QD=37.76;SOR=0.995 GT:AD:DP:GQ:PL 1/1:0,81:81:99:3702,253,0 +20 10002058 . T G 2963.77 . AC=2;AF=1.00;AN=2;AS_BaseQRankSum=1.931;AS_FS=0.000;AS_MQ=58.05;AS_MQRankSum=3.068;AS_ReadPosRankSum=-0.524;AS_SOR=0.776;BaseQRankSum=1.931;ClippingRankSum=0.000;DP=75;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.76;MQRankSum=3.068;QD=27.64;ReadPosRankSum=-0.524;SOR=0.776 GT:AD:DP:GQ:PL 1/1:1,74:75:99:2992,216,0 +20 10002099 . C T 1194.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-0.282;AS_FS=3.528;AS_MQ=55.49;AS_MQRankSum=-0.850;AS_ReadPosRankSum=-0.360;AS_SOR=0.375;BaseQRankSum=-0.282;ClippingRankSum=0.000;DP=66;ExcessHet=3.0103;FS=3.528;MLEAC=1;MLEAF=0.500;MQ=56.34;MQRankSum=-0.850;QD=18.38;ReadPosRankSum=-0.360;SOR=0.375 GT:AD:DP:GQ:PL 0/1:27,38:65:99:1223,0,844 +20 10002138 . C G 2443.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=56.38;AS_SOR=0.730;DP=53;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.38;QD=29.43;SOR=0.730 GT:AD:DP:GQ:PL 1/1:0,53:53:99:2472,169,0 +20 10002142 . G C 2407.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=56.31;AS_SOR=0.853;DP=52;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.31;QD=30.09;SOR=0.853 GT:AD:DP:GQ:PL 1/1:0,52:52:99:2436,166,0 +20 10002470 . C T 2522.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=48.62;AS_SOR=0.941;DP=61;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=48.62;QD=31.26;SOR=0.941 GT:AD:DP:GQ:PL 1/1:0,61:61:99:2551,189,0 +20 10002625 . G T 2665.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=59.05;AS_SOR=1.127;DP=64;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.05;QD=29.00;SOR=1.127 GT:AD:DP:GQ:PL 1/1:0,64:64:99:2694,193,0 +20 10003021 . C T 2383.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=58.99;AS_SOR=1.071;DP=60;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.99;QD=26.28;SOR=1.071 GT:AD:DP:GQ:PL 1/1:0,60:60:99:2412,181,0 +20 10003358 . A C 1454.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=0.004;AS_FS=0.844;AS_MQ=60.00;AS_MQRankSum=1.011;AS_ReadPosRankSum=-0.444;AS_SOR=0.572;BaseQRankSum=0.004;ClippingRankSum=0.000;DP=90;ExcessHet=3.0103;FS=0.844;MLEAC=1;MLEAF=0.500;MQ=59.79;MQRankSum=1.011;QD=16.35;ReadPosRankSum=-0.444;SOR=0.572 GT:AD:DP:GQ:PL 0/1:45,44:89:99:1483,0,1477 +20 10003651 . T C 3620.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=59.19;AS_SOR=1.511;DP=93;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.19;QD=30.19;SOR=1.511 GT:AD:DP:GQ:PL 1/1:0,93:93:99:3649,279,0 +20 10003692 . A G 2609.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=59.45;AS_SOR=1.352;DP=68;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.45;QD=29.45;SOR=1.352 GT:AD:DP:GQ:PL 1/1:0,68:68:99:2638,205,0 +20 10003832 . G A 2705.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=57.13;AS_SOR=1.473;DP=66;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.13;QD=34.04;SOR=1.473 GT:AD:DP:GQ:PL 1/1:0,66:66:99:2734,199,0 +20 10004094 . A C 1825.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=52.75;AS_SOR=1.524;DP=53;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.75;QD=34.45;SOR=1.524 GT:AD:DP:GQ:PL 1/1:0,53:53:99:1854,157,0 +20 10004147 . A G 1837.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=54.99;AS_SOR=1.136;DP=52;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=54.99;QD=29.82;SOR=1.136 GT:AD:DP:GQ:PL 1/1:0,52:52:99:1866,156,0 +20 10004193 . G T 916.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-0.392;AS_FS=2.369;AS_MQ=62.43;AS_MQRankSum=3.385;AS_ReadPosRankSum=0.995;AS_SOR=0.941;BaseQRankSum=-0.392;ClippingRankSum=0.000;DP=52;ExcessHet=3.0103;FS=2.369;MLEAC=1;MLEAF=0.500;MQ=59.30;MQRankSum=3.385;QD=17.98;ReadPosRankSum=0.995;SOR=0.941 GT:AD:DP:GQ:PL 0/1:23,28:51:99:945,0,776 +20 10004222 . C CA 12.96 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=0.335;AS_FS=1.494;AS_MQ=54.53;AS_MQRankSum=-2.042;AS_ReadPosRankSum=-0.052;AS_SOR=0.434;BaseQRankSum=0.335;ClippingRankSum=0.000;DP=55;ExcessHet=3.0103;FS=1.494;MLEAC=1;MLEAF=0.500;MQ=60.05;MQRankSum=-2.042;QD=0.33;ReadPosRankSum=-0.052;SOR=0.434 GT:AD:DP:GQ:PL 0/1:31,8:39:50:50,0,923 +20 10004223 . A AG 47.73 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-0.632;AS_FS=0.000;AS_MQ=59.88;AS_MQRankSum=1.886;AS_ReadPosRankSum=2.234;AS_SOR=0.638;BaseQRankSum=-0.632;ClippingRankSum=0.000;DP=63;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.33;MQRankSum=1.886;QD=1.02;ReadPosRankSum=2.234;SOR=0.638 GT:AD:DP:GQ:PL 0/1:36,11:47:85:85,0,982 +20 10004351 . C G 2755.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=59.04;AS_SOR=0.874;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.04;QD=33.74;SOR=0.874 GT:AD:DP:GQ:PL 1/1:0,70:70:99:2784,211,0 +20 10004389 . T G 2494.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=56.74;AS_SOR=1.143;DP=62;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.74;QD=33.93;SOR=1.143 GT:AD:DP:GQ:PL 1/1:0,62:62:99:2523,187,0 +20 10004610 . A C 3625.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=58.69;AS_SOR=0.761;DP=89;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.69;QD=33.49;SOR=0.761 GT:AD:DP:GQ:PL 1/1:0,89:89:99:3654,267,0 +20 10004725 . A G 951.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-2.154;AS_FS=15.830;AS_MQ=59.38;AS_MQRankSum=3.008;AS_ReadPosRankSum=1.791;AS_SOR=0.605;BaseQRankSum=-2.154;ClippingRankSum=0.000;DP=65;ExcessHet=3.0103;FS=15.830;MLEAC=1;MLEAF=0.500;MQ=55.27;MQRankSum=3.008;QD=14.64;ReadPosRankSum=1.791;SOR=0.605 GT:AD:DP:GQ:PL 0/1:35,30:65:99:980,0,1168 +20 10004769 . TAAAACTATGC T 981.73 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=1.603;AS_FS=3.758;AS_MQ=34.53;AS_MQRankSum=-6.625;AS_ReadPosRankSum=2.215;AS_SOR=1.306;BaseQRankSum=1.603;ClippingRankSum=0.000;DP=79;ExcessHet=3.0103;FS=3.758;MLEAC=1;MLEAF=0.500;MQ=52.37;MQRankSum=-6.625;QD=15.34;ReadPosRankSum=2.215;SOR=1.306 GT:AD:DP:GQ:PL 0/1:37,27:64:99:1019,0,1470 +20 10004874 . A C 3602.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=59.33;AS_SOR=1.286;DP=87;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.33;QD=33.07;SOR=1.286 GT:AD:DP:GQ:PL 1/1:0,87:87:99:3631,261,0 +20 10004887 . A G 1323.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=0.356;AS_FS=1.793;AS_MQ=59.42;AS_MQRankSum=-0.067;AS_ReadPosRankSum=-0.160;AS_SOR=0.984;BaseQRankSum=0.356;ClippingRankSum=0.000;DP=87;ExcessHet=3.0103;FS=1.793;MLEAC=1;MLEAF=0.500;MQ=59.20;MQRankSum=-0.067;QD=15.57;ReadPosRankSum=-0.160;SOR=0.984 GT:AD:DP:GQ:PL 0/1:45,40:85:99:1352,0,1542 +20 10005010 . C T 2934.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=59.68;AS_SOR=1.226;DP=72;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.68;QD=32.11;SOR=1.226 GT:AD:DP:GQ:PL 1/1:0,72:72:99:2963,217,0 +20 10005427 . C T 2214.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=59.58;AS_SOR=0.729;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.58;QD=26.86;SOR=0.729 GT:AD:DP:GQ:PL 1/1:0,55:55:99:2243,165,0 +20 10005499 . A G 3053.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=60.00;AS_SOR=1.121;DP=76;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.35;SOR=1.121 GT:AD:DP:GQ:PL 1/1:0,76:76:99:3082,229,0 +20 10005587 . A G 1229.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-0.834;AS_FS=1.955;AS_MQ=59.48;AS_MQRankSum=-0.972;AS_ReadPosRankSum=0.649;AS_SOR=0.848;BaseQRankSum=-0.834;ClippingRankSum=0.000;DP=73;ExcessHet=3.0103;FS=1.955;MLEAC=1;MLEAF=0.500;MQ=59.43;MQRankSum=-0.972;QD=17.08;ReadPosRankSum=0.649;SOR=0.848 GT:AD:DP:GQ:PL 0/1:36,36:72:99:1258,0,1236 +20 10005723 . A G 3062.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=59.78;AS_SOR=0.947;DP=86;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.78;QD=30.97;SOR=0.947 GT:AD:DP:GQ:PL 1/1:0,86:86:99:3091,258,0 +20 10006291 . G A 978.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=0.311;AS_FS=0.853;AS_MQ=58.64;AS_MQRankSum=-1.081;AS_ReadPosRankSum=-1.614;AS_SOR=0.659;BaseQRankSum=0.311;ClippingRankSum=0.000;DP=84;ExcessHet=3.0103;FS=0.853;MLEAC=1;MLEAF=0.500;MQ=59.28;MQRankSum=-1.081;QD=11.65;ReadPosRankSum=-1.614;SOR=0.659 GT:AD:DP:GQ:PL 0/1:53,31:84:99:1007,0,1905 +20 10006404 . A C 2928.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=59.39;AS_SOR=1.432;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.16;QD=29.43;SOR=1.432 GT:AD:DP:GQ:PL 1/1:0,76:76:99:2957,228,0 +20 10006682 . T A 2874.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=59.43;AS_SOR=1.179;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.43;QD=28.18;SOR=1.179 GT:AD:DP:GQ:PL 1/1:0,73:73:99:2903,219,0 +20 10006819 . AAAAC A 2531.73 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=61.48;AS_SOR=0.762;DP=76;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=61.13;QD=28.32;SOR=0.762 GT:AD:DP:GQ:PL 1/1:0,58:58:99:2569,176,0 +20 10007150 . G C 669.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-4.476;AS_FS=5.048;AS_MQ=60.00;AS_MQRankSum=0.000;AS_ReadPosRankSum=-1.745;AS_SOR=0.746;BaseQRankSum=-4.476;ClippingRankSum=0.000;DP=63;ExcessHet=3.0103;FS=5.048;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=10.63;ReadPosRankSum=-1.745;SOR=0.746 GT:AD:DP:GQ:PL 0/1:38,25:63:99:698,0,1479 +20 10007175 . C T 1350.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=2.249;AS_FS=2.211;AS_MQ=60.00;AS_MQRankSum=1.319;AS_ReadPosRankSum=-0.730;AS_SOR=0.434;BaseQRankSum=2.249;ClippingRankSum=0.000;DP=61;ExcessHet=3.0103;FS=2.211;MLEAC=1;MLEAF=0.500;MQ=59.62;MQRankSum=1.319;QD=22.14;ReadPosRankSum=-0.730;SOR=0.434 GT:AD:DP:GQ:PL 0/1:23,38:61:99:1379,0,780 +20 10007352 . C T 2764.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=59.67;AS_SOR=1.054;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.67;QD=29.65;SOR=1.054 GT:AD:DP:GQ:PL 1/1:0,69:69:99:2793,208,0 +20 10007531 . A G 2920.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=59.74;AS_SOR=1.577;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.74;QD=35.03;SOR=1.577 GT:AD:DP:GQ:PL 1/1:0,72:72:99:2949,217,0 +20 10007980 . A C 3524.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=60.72;AS_SOR=0.990;DP=90;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.72;QD=25.82;SOR=0.990 GT:AD:DP:GQ:PL 1/1:0,90:90:99:3553,270,0 +20 10008029 . T TA 1986.73 . AC=2;AF=1.00;AN=2;AS_BaseQRankSum=0.409;AS_FS=0.000;AS_MQ=61.07;AS_MQRankSum=0.576;AS_ReadPosRankSum=-1.055;AS_SOR=0.788;BaseQRankSum=0.409;ClippingRankSum=0.000;DP=88;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.98;MQRankSum=0.576;QD=26.49;ReadPosRankSum=-1.055;SOR=0.788 GT:AD:DP:GQ:PL 1/1:3,72:75:99:2024,145,0 +20 10008146 . TA T 2141.73 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=60.62;AS_SOR=0.874;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.59;QD=30.60;SOR=0.874 GT:AD:DP:GQ:PL 1/1:0,70:70:99:2179,211,0 +20 10008221 . T C 3224.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=60.17;AS_SOR=0.850;DP=80;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.17;QD=32.17;SOR=0.850 GT:AD:DP:GQ:PL 1/1:0,80:80:99:3253,240,0 +20 10008458 . T G 2654.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=52.73;AS_SOR=0.980;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.54;QD=32.77;SOR=0.980 GT:AD:DP:GQ:PL 1/1:0,69:69:99:2683,207,0 +20 10008742 . G T 715.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=3.893;AS_FS=0.000;AS_MQ=34.13;AS_MQRankSum=-1.502;AS_ReadPosRankSum=0.772;AS_SOR=0.741;BaseQRankSum=3.893;ClippingRankSum=0.000;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=37.22;MQRankSum=-1.502;QD=14.61;ReadPosRankSum=0.772;SOR=0.741 GT:AD:DP:GQ:PL 0/1:23,26:49:99:744,0,580 +20 10008758 . C CA 684.14 . AC=2;AF=1.00;AN=2;AS_BaseQRankSum=0.130;AS_FS=2.160;AS_MQ=34.84;AS_MQRankSum=-1.168;AS_ReadPosRankSum=-0.234;AS_SOR=0.249;BaseQRankSum=0.130;ClippingRankSum=0.000;DP=44;ExcessHet=3.0103;FS=2.160;MLEAC=2;MLEAF=1.00;MQ=35.24;MQRankSum=-1.168;QD=19.55;ReadPosRankSum=-0.234;SOR=0.249 GT:AD:DP:GQ:PL 1/1:4,31:35:10:721,10,0 +20 10008921 . C CA 253.73 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=0.610;AS_FS=0.000;AS_MQ=52.32;AS_MQRankSum=-1.906;AS_ReadPosRankSum=-0.397;AS_SOR=0.512;BaseQRankSum=0.610;ClippingRankSum=0.000;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.34;MQRankSum=-1.906;QD=7.46;ReadPosRankSum=-0.397;SOR=0.512 GT:AD:DP:GQ:PL 0/1:18,16:34:99:291,0,366 +20 10008948 . TA T 2057.73 . AC=2;AF=1.00;AN=2;AS_BaseQRankSum=0.994;AS_FS=0.000;AS_MQ=51.85;AS_MQRankSum=2.047;AS_ReadPosRankSum=0.748;AS_SOR=0.818;BaseQRankSum=0.994;ClippingRankSum=0.000;DP=53;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.30;MQRankSum=2.047;QD=30.77;ReadPosRankSum=0.748;SOR=0.818 GT:AD:DP:GQ:PL 1/1:1,50:51:99:2095,107,0 +20 10008952 . CACACACACACA C,CCACACACACA 1666.73 . AC=1,1;AF=0.500,0.500;AN=2;AS_BaseQRankSum=0.963;AS_FS=0.000;AS_MQ=26.32,46.90;AS_MQRankSum=1.976;AS_ReadPosRankSum=0.903;AS_SOR=1.112;BaseQRankSum=0.963;ClippingRankSum=0.000;DP=60;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=50.81;MQRankSum=1.976;QD=28.07;ReadPosRankSum=0.903;SOR=1.112 GT:AD:DP:GQ:PL 1/2:1,17,18:36:99:1704,525,844,582,0,531 +20 10009227 . A G 1369.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-2.220;AS_FS=9.110;AS_MQ=58.29;AS_MQRankSum=1.428;AS_ReadPosRankSum=-1.093;AS_SOR=0.281;BaseQRankSum=-2.220;ClippingRankSum=0.000;DP=62;ExcessHet=3.0103;FS=9.110;MLEAC=1;MLEAF=0.500;MQ=57.16;MQRankSum=1.428;QD=22.09;ReadPosRankSum=-1.093;SOR=0.281 GT:AD:DP:GQ:PL 0/1:23,39:62:99:1398,0,740 +20 10009246 . A G 3002.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=56.09;AS_SOR=0.887;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.09;QD=27.93;SOR=0.887 GT:AD:DP:GQ:PL 1/1:0,77:77:99:3031,231,0 +20 10009400 . T A 2998.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=60.00;AS_SOR=0.804;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=25.91;SOR=0.804 GT:AD:DP:GQ:PL 1/1:0,74:74:99:3027,223,0 +20 10009512 . C G 3039.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=58.47;AS_SOR=1.223;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.47;QD=26.83;SOR=1.223 GT:AD:DP:GQ:PL 1/1:0,77:77:99:3068,231,0 +20 10009719 . A G 1895.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=59.29;AS_SOR=0.950;DP=59;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.29;QD=32.13;SOR=0.950 GT:AD:DP:GQ:PL 1/1:0,59:59:99:1924,175,0 +20 10009795 . A G 1880.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=59.60;AS_SOR=1.514;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.60;QD=30.42;SOR=1.514 GT:AD:DP:GQ:PL 1/1:0,47:47:99:1909,141,0 +20 10009842 . G GAA 532.73 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=0.872;AS_FS=0.000;AS_MQ=49.70;AS_MQRankSum=-0.603;AS_ReadPosRankSum=0.052;AS_SOR=0.738;BaseQRankSum=0.872;ClippingRankSum=0.000;DP=51;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.25;MQRankSum=-0.603;QD=15.67;ReadPosRankSum=0.052;SOR=0.738 GT:AD:DP:GQ:PL 0/1:19,15:34:99:570,0,690 +20 10009844 . G A 661.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=1.048;AS_FS=0.000;AS_MQ=52.24;AS_MQRankSum=0.975;AS_ReadPosRankSum=0.259;AS_SOR=0.793;BaseQRankSum=1.048;ClippingRankSum=0.000;DP=51;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.72;MQRankSum=0.975;QD=18.91;ReadPosRankSum=0.259;SOR=0.793 GT:AD:DP:GQ:PL 0/1:16,19:35:99:690,0,586 +20 10009871 . A G 658.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-0.803;AS_FS=2.798;AS_MQ=52.24;AS_MQRankSum=1.495;AS_ReadPosRankSum=1.572;AS_SOR=0.553;BaseQRankSum=-0.803;ClippingRankSum=0.000;DP=61;ExcessHet=3.0103;FS=2.798;MLEAC=1;MLEAF=0.500;MQ=50.95;MQRankSum=1.495;QD=18.30;ReadPosRankSum=1.572;SOR=0.553 GT:AD:DP:GQ:PL 0/1:17,19:36:99:687,0,594 +20 10009875 . A G,AGGGAGG 2369.73 . AC=1,1;AF=0.500,0.500;AN=2;AS_BaseQRankSum=0.378;AS_FS=6.794;AS_MQ=51.77,45.51;AS_MQRankSum=1.361;AS_ReadPosRankSum=-0.083;AS_SOR=0.599;BaseQRankSum=0.378;ClippingRankSum=0.000;DP=58;ExcessHet=3.0103;FS=6.794;MLEAC=1,1;MLEAF=0.500,0.500;MQ=50.44;MQRankSum=1.361;QD=24.50;ReadPosRankSum=-0.083;SOR=0.599 GT:AD:DP:GQ:PL 1/2:2,15,13:30:99:2407,645,533,697,0,574 +20 10009879 . A G 2244.77 . AC=2;AF=1.00;AN=2;AS_BaseQRankSum=1.534;AS_FS=9.369;AS_MQ=50.31;AS_MQRankSum=1.570;AS_ReadPosRankSum=1.391;AS_SOR=1.474;BaseQRankSum=1.534;ClippingRankSum=0.000;DP=50;ExcessHet=3.0103;FS=9.369;MLEAC=2;MLEAF=1.00;MQ=49.85;MQRankSum=1.570;QD=29.65;ReadPosRankSum=1.391;SOR=1.474 GT:AD:DP:GQ:PL 1/1:2,47:49:99:2273,150,0 +20 10009883 . A G 2151.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=52.12;AS_SOR=1.659;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.56;QD=34.02;SOR=1.659 GT:AD:DP:GQ:PL 1/1:0,47:47:99:2180,147,0 +20 10010393 . T G 1464.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-3.351;AS_FS=11.600;AS_MQ=58.92;AS_MQRankSum=-1.284;AS_ReadPosRankSum=-1.630;AS_SOR=0.606;BaseQRankSum=-3.351;ClippingRankSum=0.000;DP=79;ExcessHet=3.0103;FS=11.600;MLEAC=1;MLEAF=0.500;MQ=59.42;MQRankSum=-1.284;QD=18.54;ReadPosRankSum=-1.630;SOR=0.606 GT:AD:DP:GQ:PL 0/1:36,43:79:99:1493,0,1230 +20 10010536 . G GA 2462.73 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=61.76;AS_SOR=0.881;DP=85;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=61.63;QD=31.17;SOR=0.881 GT:AD:DP:GQ:PL 1/1:0,79:79:99:2500,243,0 +20 10010766 . T G 2411.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=60.00;AS_SOR=0.818;DP=67;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=28.35;SOR=0.818 GT:AD:DP:GQ:PL 1/1:0,66:66:99:2440,199,0 +20 10010832 . T C 2951.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=59.50;AS_SOR=1.091;DP=75;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.50;QD=28.36;SOR=1.091 GT:AD:DP:GQ:PL 1/1:0,75:75:99:2980,226,0 +20 10011075 . C T 1325.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=5.364;AS_FS=1.800;AS_MQ=60.00;AS_MQRankSum=0.000;AS_ReadPosRankSum=-1.057;AS_SOR=0.968;BaseQRankSum=5.364;ClippingRankSum=0.000;DP=85;ExcessHet=3.0103;FS=1.800;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=15.97;ReadPosRankSum=-1.057;SOR=0.968 GT:AD:DP:GQ:PL 0/1:44,39:83:99:1354,0,1333 +20 10011309 . T C 2692.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=60.00;AS_SOR=1.223;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=34.97;SOR=1.223 GT:AD:DP:GQ:PL 1/1:0,77:77:99:2721,231,0 +20 10011517 . GA G 490.73 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=0.924;AS_FS=2.130;AS_MQ=59.08;AS_MQRankSum=2.041;AS_ReadPosRankSum=1.637;AS_SOR=0.412;BaseQRankSum=0.924;ClippingRankSum=0.000;DP=91;ExcessHet=3.0103;FS=2.130;MLEAC=1;MLEAF=0.500;MQ=59.90;MQRankSum=2.041;QD=6.46;ReadPosRankSum=1.637;SOR=0.412 GT:AD:DP:GQ:PL 0/1:46,30:76:99:528,0,875 +20 10011666 . C T 2961.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=59.05;AS_SOR=1.103;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.05;QD=33.10;SOR=1.103 GT:AD:DP:GQ:PL 1/1:0,73:73:99:2990,220,0 +20 10011939 . C T 2513.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=56.32;AS_SOR=1.329;DP=62;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.32;QD=30.82;SOR=1.329 GT:AD:DP:GQ:PL 1/1:0,62:62:99:2542,187,0 +20 10012021 . CA C 1975.73 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=57.20;AS_SOR=1.196;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.08;QD=29.94;SOR=1.196 GT:AD:DP:GQ:PL 1/1:0,66:66:99:2013,198,0 +20 10012362 . G T 835.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=53.78;AS_SOR=4.003;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.78;QD=30.58;SOR=4.003 GT:AD:DP:GQ:PL 1/1:0,23:23:69:864,69,0 +20 10012384 . T C 229.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-1.773;AS_FS=7.375;AS_MQ=50.87;AS_MQRankSum=-0.811;AS_ReadPosRankSum=0.190;AS_SOR=0.044;BaseQRankSum=-1.773;ClippingRankSum=0.000;DP=19;ExcessHet=3.0103;FS=7.375;MLEAC=1;MLEAF=0.500;MQ=53.75;MQRankSum=-0.811;QD=12.76;ReadPosRankSum=0.190;SOR=0.044 GT:AD:DP:GQ:PL 0/1:10,8:18:99:258,0,355 +20 10012387 . T C 533.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=52.49;AS_SOR=3.258;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.96;QD=33.36;SOR=3.258 GT:AD:DP:GQ:PL 1/1:0,16:16:50:562,50,0 +20 10012479 . A G 592.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=52.01;AS_SOR=0.804;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.01;QD=34.87;SOR=0.804 GT:AD:DP:GQ:PL 1/1:0,17:17:50:621,50,0 +20 10012498 . C G 466.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=45.03;AS_SOR=1.270;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=45.03;QD=28.92;SOR=1.270 GT:AD:DP:GQ:PL 1/1:0,11:11:33:495,33,0 +20 10012518 . T C 406.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=40.96;AS_SOR=0.892;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=40.96;QD=34.62;SOR=0.892 GT:AD:DP:GQ:PL 1/1:0,9:9:30:435,30,0 +20 10012521 . C T 46.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=2.362;AS_FS=0.000;AS_MQ=41.96;AS_MQRankSum=-0.038;AS_ReadPosRankSum=1.973;AS_SOR=1.179;BaseQRankSum=2.362;ClippingRankSum=0.000;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=41.77;MQRankSum=-0.038;QD=4.25;ReadPosRankSum=1.973;SOR=1.179 GT:AD:DP:GQ:PL 0/1:8,3:11:75:75,0,224 +20 10012570 . G GCA 457.73 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=37.62;AS_SOR=3.056;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=36.55;QD=33.23;SOR=3.056 GT:AD:DP:GQ:PL 1/1:0,9:9:33:495,33,0 +20 10012572 . GT G 457.73 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=39.52;AS_SOR=3.442;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=38.52;QD=26.88;SOR=3.442 GT:AD:DP:GQ:PL 1/1:0,11:11:33:495,33,0 +20 10012631 . C CG 484.73 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-1.030;AS_FS=8.822;AS_MQ=44.53;AS_MQRankSum=-1.670;AS_ReadPosRankSum=-0.835;AS_SOR=0.048;BaseQRankSum=-1.030;ClippingRankSum=0.000;DP=22;ExcessHet=3.0103;FS=8.822;MLEAC=1;MLEAF=0.500;MQ=47.53;MQRankSum=-1.670;QD=23.08;ReadPosRankSum=-0.835;SOR=0.048 GT:AD:DP:GQ:PL 0/1:8,13:21:99:522,0,297 +20 10012636 . G C 527.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=2.711;AS_FS=5.959;AS_MQ=45.81;AS_MQRankSum=-1.513;AS_ReadPosRankSum=-0.718;AS_SOR=0.058;BaseQRankSum=2.711;ClippingRankSum=0.000;DP=22;ExcessHet=3.0103;FS=5.959;MLEAC=1;MLEAF=0.500;MQ=48.93;MQRankSum=-1.513;QD=23.99;ReadPosRankSum=-0.718;SOR=0.058 GT:AD:DP:GQ:PL 0/1:8,14:22:99:556,0,294 +20 10012714 . G C 1300.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=53.04;AS_SOR=2.964;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.04;QD=29.64;SOR=2.964 GT:AD:DP:GQ:PL 1/1:0,35:35:99:1329,105,0 +20 10012751 . T C 937.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=51.17;AS_SOR=0.976;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.56;QD=31.26;SOR=0.976 GT:AD:DP:GQ:PL 1/1:0,30:30:89:966,89,0 +20 10013119 . C T 1011.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=2.724;AS_FS=2.248;AS_MQ=49.96;AS_MQRankSum=-1.089;AS_ReadPosRankSum=0.336;AS_SOR=0.405;BaseQRankSum=2.724;ClippingRankSum=0.000;DP=59;ExcessHet=3.0103;FS=2.248;MLEAC=1;MLEAF=0.500;MQ=51.48;MQRankSum=-1.089;QD=17.15;ReadPosRankSum=0.336;SOR=0.405 GT:AD:DP:GQ:PL 0/1:29,30:59:99:1040,0,936 +20 10013574 . G A 1050.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=3.469;AS_FS=7.109;AS_MQ=57.95;AS_MQRankSum=-0.271;AS_ReadPosRankSum=0.789;AS_SOR=1.675;BaseQRankSum=3.469;ClippingRankSum=0.000;DP=70;ExcessHet=3.0103;FS=7.109;MLEAC=1;MLEAF=0.500;MQ=58.09;MQRankSum=-0.271;QD=15.23;ReadPosRankSum=0.789;SOR=1.675 GT:AD:DP:GQ:PL 0/1:38,31:69:99:1079,0,1301 +20 10014990 . C CAT 1237.73 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=1.930;AS_FS=2.090;AS_MQ=62.24;AS_MQRankSum=3.107;AS_ReadPosRankSum=-0.343;AS_SOR=0.403;BaseQRankSum=1.930;ClippingRankSum=0.000;DP=87;ExcessHet=3.0103;FS=2.090;MLEAC=1;MLEAF=0.500;MQ=60.78;MQRankSum=3.107;QD=16.29;ReadPosRankSum=-0.343;SOR=0.403 GT:AD:DP:GQ:PL 0/1:38,38:76:99:1275,0,1248 +20 10015679 . C T 140.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=0.200;AS_FS=0.000;AS_MQ=60.00;AS_MQRankSum=0.000;AS_ReadPosRankSum=0.355;AS_SOR=0.693;BaseQRankSum=0.200;ClippingRankSum=0.000;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=14.08;ReadPosRankSum=0.355;SOR=0.693 GT:AD:DP:GQ:PL 0/1:5,5:10:99:169,0,166 +20 10015761 . T C 344.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-1.982;AS_FS=0.000;AS_MQ=60.00;AS_MQRankSum=1.294;AS_ReadPosRankSum=-0.425;AS_SOR=0.352;BaseQRankSum=-1.982;ClippingRankSum=0.000;DP=22;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.95;MQRankSum=1.294;QD=15.67;ReadPosRankSum=-0.425;SOR=0.352 GT:AD:DP:GQ:PL 0/1:9,13:22:99:373,0,284 +20 10018158 . G C 1639.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=5.213;AS_FS=0.808;AS_MQ=60.00;AS_MQRankSum=1.118;AS_ReadPosRankSum=0.516;AS_SOR=0.834;BaseQRankSum=5.213;ClippingRankSum=0.000;DP=89;ExcessHet=3.0103;FS=0.808;MLEAC=1;MLEAF=0.500;MQ=59.79;MQRankSum=1.118;QD=18.63;ReadPosRankSum=0.516;SOR=0.834 GT:AD:DP:GQ:PL 0/1:40,48:88:99:1668,0,1165 +20 10018555 . G A 1567.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-0.627;AS_FS=4.241;AS_MQ=60.00;AS_MQRankSum=0.000;AS_ReadPosRankSum=0.463;AS_SOR=0.627;BaseQRankSum=-0.627;ClippingRankSum=0.000;DP=80;ExcessHet=3.0103;FS=4.241;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=19.60;ReadPosRankSum=0.463;SOR=0.627 GT:AD:DP:GQ:PL 0/1:35,45:80:99:1596,0,1211 +20 10019093 . A G 1244.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=0.452;AS_FS=1.990;AS_MQ=60.00;AS_MQRankSum=1.073;AS_ReadPosRankSum=-0.230;AS_SOR=0.665;BaseQRankSum=0.452;ClippingRankSum=0.000;DP=69;ExcessHet=3.0103;FS=1.990;MLEAC=1;MLEAF=0.500;MQ=59.67;MQRankSum=1.073;QD=18.04;ReadPosRankSum=-0.230;SOR=0.665 GT:AD:DP:GQ:PL 0/1:33,36:69:99:1273,0,1104 +20 10020229 . G A 1538.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=5.792;AS_FS=0.833;AS_MQ=59.48;AS_MQRankSum=0.104;AS_ReadPosRankSum=-0.368;AS_SOR=0.573;BaseQRankSum=5.792;ClippingRankSum=0.000;DP=82;ExcessHet=3.0103;FS=0.833;MLEAC=1;MLEAF=0.500;MQ=59.49;MQRankSum=0.104;QD=18.77;ReadPosRankSum=-0.368;SOR=0.573 GT:AD:DP:GQ:PL 0/1:38,44:82:99:1567,0,1130 +20 10023689 . G A 1852.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=2.144;AS_FS=0.877;AS_MQ=60.00;AS_MQRankSum=1.352;AS_ReadPosRankSum=0.764;AS_SOR=0.549;BaseQRankSum=2.144;ClippingRankSum=0.000;DP=80;ExcessHet=3.0103;FS=0.877;MLEAC=1;MLEAF=0.500;MQ=59.77;MQRankSum=1.352;QD=23.16;ReadPosRankSum=0.764;SOR=0.549 GT:AD:DP:GQ:PL 0/1:29,51:80:99:1881,0,946 +20 10024107 . C T 1694.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=5.770;AS_FS=0.817;AS_MQ=58.94;AS_MQRankSum=-1.546;AS_ReadPosRankSum=0.329;AS_SOR=0.823;BaseQRankSum=5.770;ClippingRankSum=0.000;DP=86;ExcessHet=3.0103;FS=0.817;MLEAC=1;MLEAF=0.500;MQ=59.41;MQRankSum=-1.546;QD=19.71;ReadPosRankSum=0.329;SOR=0.823 GT:AD:DP:GQ:PL 0/1:38,48:86:99:1723,0,1086 +20 10024300 . C CTT 87.76 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=2.362;AS_FS=3.090;AS_MQ=50.65;AS_MQRankSum=-0.084;AS_ReadPosRankSum=0.454;AS_SOR=1.773;BaseQRankSum=2.362;ClippingRankSum=0.000;DP=50;ExcessHet=3.0103;FS=3.090;MLEAC=1;MLEAF=0.500;MQ=51.90;MQRankSum=-0.084;QD=5.16;ReadPosRankSum=0.454;SOR=1.773 GT:AD:DP:GQ:PL 0/1:9,8:17:99:103,0,137 +20 10026357 . T C 1166.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-1.700;AS_FS=8.911;AS_MQ=58.38;AS_MQRankSum=-0.148;AS_ReadPosRankSum=-0.549;AS_SOR=0.722;BaseQRankSum=-1.700;ClippingRankSum=0.000;DP=64;ExcessHet=3.0103;FS=8.911;MLEAC=1;MLEAF=0.500;MQ=58.46;MQRankSum=-0.148;QD=18.52;ReadPosRankSum=-0.549;SOR=0.722 GT:AD:DP:GQ:PL 0/1:28,35:63:99:1195,0,932 +20 10026794 . C T 1084.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=2.828;AS_FS=2.399;AS_MQ=59.30;AS_MQRankSum=-0.719;AS_ReadPosRankSum=-0.070;AS_SOR=0.428;BaseQRankSum=2.828;ClippingRankSum=0.000;DP=54;ExcessHet=3.0103;FS=2.399;MLEAC=1;MLEAF=0.500;MQ=59.57;MQRankSum=-0.719;QD=20.86;ReadPosRankSum=-0.070;SOR=0.428 GT:AD:DP:GQ:PL 0/1:19,33:52:99:1113,0,529 +20 10027234 . A ATTAG 1320.73 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-0.406;AS_FS=3.248;AS_MQ=55.09;AS_MQRankSum=-0.845;AS_ReadPosRankSum=-0.931;AS_SOR=0.926;BaseQRankSum=-0.406;ClippingRankSum=0.000;DP=72;ExcessHet=3.0103;FS=3.248;MLEAC=1;MLEAF=0.500;MQ=57.33;MQRankSum=-0.845;QD=19.14;ReadPosRankSum=-0.931;SOR=0.926 GT:AD:DP:GQ:PL 0/1:34,35:69:99:1358,0,1964 +20 10027868 . A G 1739.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-5.793;AS_FS=6.868;AS_MQ=59.49;AS_MQRankSum=0.032;AS_ReadPosRankSum=1.229;AS_SOR=0.881;BaseQRankSum=-5.793;ClippingRankSum=0.000;DP=89;ExcessHet=3.0103;FS=6.868;MLEAC=1;MLEAF=0.500;MQ=59.48;MQRankSum=0.032;QD=19.55;ReadPosRankSum=1.229;SOR=0.881 GT:AD:DP:GQ:PL 0/1:44,45:89:99:1768,0,3201 +20 10027872 . A G 1724.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-5.491;AS_FS=8.870;AS_MQ=59.49;AS_MQRankSum=0.101;AS_ReadPosRankSum=0.173;AS_SOR=0.826;BaseQRankSum=-5.491;ClippingRankSum=0.000;DP=85;ExcessHet=3.0103;FS=8.870;MLEAC=1;MLEAF=0.500;MQ=59.46;MQRankSum=0.101;QD=20.29;ReadPosRankSum=0.173;SOR=0.826 GT:AD:DP:GQ:PL 0/1:40,45:85:99:1753,0,3136 +20 10028867 . A ATG 1106.73 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-0.874;AS_FS=4.652;AS_MQ=62.18;AS_MQRankSum=2.711;AS_ReadPosRankSum=0.075;AS_SOR=0.336;BaseQRankSum=-0.874;ClippingRankSum=0.000;DP=92;ExcessHet=3.0103;FS=4.652;MLEAC=1;MLEAF=0.500;MQ=60.69;MQRankSum=2.711;QD=15.59;ReadPosRankSum=0.075;SOR=0.336 GT:AD:DP:GQ:PL 0/1:32,39:71:99:1144,0,916 +20 10030188 . T A 1372.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=0.711;AS_FS=9.186;AS_MQ=59.41;AS_MQRankSum=-1.013;AS_ReadPosRankSum=-1.072;AS_SOR=1.105;BaseQRankSum=0.711;ClippingRankSum=0.000;DP=81;ExcessHet=3.0103;FS=9.186;MLEAC=1;MLEAF=0.500;MQ=59.72;MQRankSum=-1.013;QD=16.95;ReadPosRankSum=-1.072;SOR=1.105 GT:AD:DP:GQ:PL 0/1:42,39:81:99:1401,0,1524 +20 10031254 . A AT 1463.73 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-0.091;AS_FS=9.250;AS_MQ=59.83;AS_MQRankSum=0.017;AS_ReadPosRankSum=0.478;AS_SOR=0.211;BaseQRankSum=-0.091;ClippingRankSum=0.000;DP=88;ExcessHet=3.0103;FS=9.250;MLEAC=1;MLEAF=0.500;MQ=59.65;MQRankSum=0.017;QD=17.22;ReadPosRankSum=0.478;SOR=0.211 GT:AD:DP:GQ:PL 0/1:38,47:85:99:1501,0,1159 +20 10031342 . G A 1834.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=1.833;AS_FS=1.714;AS_MQ=59.56;AS_MQRankSum=-0.866;AS_ReadPosRankSum=-0.263;AS_SOR=0.955;BaseQRankSum=1.833;ClippingRankSum=0.000;DP=93;ExcessHet=3.0103;FS=1.714;MLEAC=1;MLEAF=0.500;MQ=59.75;MQRankSum=-0.866;QD=19.73;ReadPosRankSum=-0.263;SOR=0.955 GT:AD:DP:GQ:PL 0/1:41,52:93:99:1863,0,1375 +20 10031798 . G A 4296.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=59.60;AS_SOR=0.900;DP=104;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.60;QD=31.35;SOR=0.900 GT:AD:DP:GQ:PL 1/1:0,104:104:99:4325,313,0 +20 10031827 . C T 2004.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=3.552;AS_FS=4.729;AS_MQ=59.67;AS_MQRankSum=-0.945;AS_ReadPosRankSum=-0.390;AS_SOR=0.382;BaseQRankSum=3.552;ClippingRankSum=0.000;DP=108;ExcessHet=3.0103;FS=4.729;MLEAC=1;MLEAF=0.500;MQ=59.83;MQRankSum=-0.945;QD=18.56;ReadPosRankSum=-0.390;SOR=0.382 GT:AD:DP:GQ:PL 0/1:52,56:108:99:2033,0,1798 +20 10032094 . G A 1220.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=5.488;AS_FS=6.039;AS_MQ=60.00;AS_MQRankSum=0.000;AS_ReadPosRankSum=-0.464;AS_SOR=0.260;BaseQRankSum=5.488;ClippingRankSum=0.000;DP=84;ExcessHet=3.0103;FS=6.039;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=14.71;ReadPosRankSum=-0.464;SOR=0.260 GT:AD:DP:GQ:PL 0/1:47,36:83:99:1249,0,1497 +20 10032413 . T G 869.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-6.142;AS_FS=10.444;AS_MQ=59.40;AS_MQRankSum=-0.065;AS_ReadPosRankSum=-0.751;AS_SOR=1.293;BaseQRankSum=-6.142;ClippingRankSum=0.000;DP=66;ExcessHet=3.0103;FS=10.444;MLEAC=1;MLEAF=0.500;MQ=59.43;MQRankSum=-0.065;QD=13.18;ReadPosRankSum=-0.751;SOR=1.293 GT:AD:DP:GQ:PL 0/1:35,31:66:99:898,0,1277 +20 10032882 . A T 1202.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-3.697;AS_FS=4.673;AS_MQ=59.36;AS_MQRankSum=-1.014;AS_ReadPosRankSum=0.579;AS_SOR=0.338;BaseQRankSum=-3.697;ClippingRankSum=0.000;DP=75;ExcessHet=3.0103;FS=4.673;MLEAC=1;MLEAF=0.500;MQ=59.69;MQRankSum=-1.014;QD=16.04;ReadPosRankSum=0.579;SOR=0.338 GT:AD:DP:GQ:PL 0/1:39,36:75:99:1231,0,1406 +20 10032972 . C CAT 1122.73 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-0.354;AS_FS=5.062;AS_MQ=59.23;AS_MQRankSum=-1.017;AS_ReadPosRankSum=-1.239;AS_SOR=1.300;BaseQRankSum=-0.354;ClippingRankSum=0.000;DP=65;ExcessHet=3.0103;FS=5.062;MLEAC=1;MLEAF=0.500;MQ=59.65;MQRankSum=-1.017;QD=17.82;ReadPosRankSum=-1.239;SOR=1.300 GT:AD:DP:GQ:PL 0/1:33,30:63:99:1160,0,1477 +20 10034306 . T C 782.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-3.661;AS_FS=0.890;AS_MQ=60.00;AS_MQRankSum=1.150;AS_ReadPosRankSum=0.280;AS_SOR=0.685;BaseQRankSum=-3.661;ClippingRankSum=0.000;DP=77;ExcessHet=3.0103;FS=0.890;MLEAC=1;MLEAF=0.500;MQ=59.46;MQRankSum=1.150;QD=10.44;ReadPosRankSum=0.280;SOR=0.685 GT:AD:DP:GQ:PL 0/1:46,29:75:99:811,0,1593 +20 10036930 . CGATAGCCCTAGCCCTAGATA C 1036.73 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=0.200;AS_FS=11.152;AS_MQ=44.81;AS_MQRankSum=-4.048;AS_ReadPosRankSum=0.200;AS_SOR=0.269;BaseQRankSum=0.200;ClippingRankSum=0.000;DP=93;ExcessHet=3.0103;FS=11.152;MLEAC=1;MLEAF=0.500;MQ=54.36;MQRankSum=-4.048;QD=15.25;ReadPosRankSum=0.200;SOR=0.269 GT:AD:DP:GQ:PL 0/1:39,29:68:99:1074,0,5569 +20 10037037 . C T 1436.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=3.504;AS_FS=1.943;AS_MQ=59.71;AS_MQRankSum=-1.193;AS_ReadPosRankSum=-1.694;AS_SOR=0.495;BaseQRankSum=3.504;ClippingRankSum=0.000;DP=81;ExcessHet=3.0103;FS=1.943;MLEAC=1;MLEAF=0.500;MQ=60.17;MQRankSum=-1.193;QD=17.74;ReadPosRankSum=-1.694;SOR=0.495 GT:AD:DP:GQ:PL 0/1:39,42:81:99:1465,0,1124 +20 10037110 . T TGATA 2780.73 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=56.31;AS_SOR=1.022;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.98;QD=28.92;SOR=1.022 GT:AD:DP:GQ:PL 1/1:0,61:61:99:2818,189,0 +20 10037144 . T TGATAGATA 1823.73 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=39.95;AS_SOR=1.061;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.73;QD=29.91;SOR=1.061 GT:AD:DP:GQ:PL 1/1:0,36:36:99:1861,127,0 +20 10037709 . A T 1003.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-2.367;AS_FS=0.000;AS_MQ=60.00;AS_MQRankSum=0.934;AS_ReadPosRankSum=0.392;AS_SOR=0.608;BaseQRankSum=-2.367;ClippingRankSum=0.000;DP=72;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.68;MQRankSum=0.934;QD=14.14;ReadPosRankSum=0.392;SOR=0.608 GT:AD:DP:GQ:PL 0/1:39,32:71:99:1032,0,1354 +20 10039371 . T G 1324.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-3.260;AS_FS=6.144;AS_MQ=60.00;AS_MQRankSum=0.000;AS_ReadPosRankSum=0.510;AS_SOR=1.031;BaseQRankSum=-3.260;ClippingRankSum=0.000;DP=74;ExcessHet=3.0103;FS=6.144;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=17.90;ReadPosRankSum=0.510;SOR=1.031 GT:AD:DP:GQ:PL 0/1:34,40:74:99:1353,0,1194 +20 10040772 . C CT 1995.73 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=50.52;AS_SOR=0.811;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.69;QD=28.51;SOR=0.811 GT:AD:DP:GQ:PL 1/1:0,70:70:99:2033,210,0 +20 10040812 . AT A 2607.73 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=49.58;AS_SOR=0.721;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=50.73;QD=26.34;SOR=0.721 GT:AD:DP:GQ:PL 1/1:0,71:71:99:2645,214,0 +20 10040821 . T A 1171.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-0.021;AS_FS=0.000;AS_MQ=50.42;AS_MQRankSum=-0.097;AS_ReadPosRankSum=-1.410;AS_SOR=0.688;BaseQRankSum=-0.021;ClippingRankSum=0.000;DP=78;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.60;MQRankSum=-0.097;QD=15.02;ReadPosRankSum=-1.410;SOR=0.688 GT:AD:DP:GQ:PL 0/1:38,40:78:99:1200,0,1099 +20 10041304 . C T 2765.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=59.39;AS_SOR=0.693;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.40;QD=31.37;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,68:68:99:2794,204,0 +20 10041701 . A ATATG 1403.73 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=0.848;AS_FS=3.477;AS_MQ=55.15;AS_MQRankSum=0.340;AS_ReadPosRankSum=0.328;AS_SOR=0.260;BaseQRankSum=0.848;ClippingRankSum=0.000;DP=78;ExcessHet=3.0103;FS=3.477;MLEAC=1;MLEAF=0.500;MQ=58.90;MQRankSum=0.340;QD=24.20;ReadPosRankSum=0.328;SOR=0.260 GT:AD:DP:GQ:PL 0/1:9,49:58:58:1441,0,58 +20 10042319 . C T 2658.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=59.01;AS_SOR=1.033;DP=66;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.01;QD=33.28;SOR=1.033 GT:AD:DP:GQ:PL 1/1:0,66:66:99:2687,199,0 +20 10042761 . A G 3553.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=60.00;AS_SOR=1.389;DP=91;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.73;SOR=1.389 GT:AD:DP:GQ:PL 1/1:0,91:91:99:3582,272,0 +20 10042829 . A G 3055.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=59.76;AS_SOR=0.855;DP=78;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.76;QD=24.88;SOR=0.855 GT:AD:DP:GQ:PL 1/1:0,78:78:99:3084,235,0 +20 10043002 . A T 1287.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=3.986;AS_FS=2.877;AS_MQ=60.00;AS_MQRankSum=0.000;AS_ReadPosRankSum=0.178;AS_SOR=0.434;BaseQRankSum=3.986;ClippingRankSum=0.000;DP=87;ExcessHet=3.0103;FS=2.877;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=14.97;ReadPosRankSum=0.178;SOR=0.434 GT:AD:DP:GQ:PL 0/1:48,38:86:99:1316,0,1659 +20 10044849 . A G 2091.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=59.61;AS_SOR=1.316;DP=60;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.62;QD=30.99;SOR=1.316 GT:AD:DP:GQ:PL 1/1:0,59:59:99:2120,177,0 +20 10045078 . G T 3271.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=58.73;AS_SOR=0.876;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.73;QD=28.90;SOR=0.876 GT:AD:DP:GQ:PL 1/1:0,81:81:99:3300,244,0 +20 10045642 . G C 3138.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=59.49;AS_SOR=0.846;DP=82;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.49;QD=31.47;SOR=0.846 GT:AD:DP:GQ:PL 1/1:0,82:82:99:3167,246,0 +20 10046178 . AAGAAAGAAAG A 2159.73 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=44.93;AS_SOR=0.859;DP=62;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=48.22;QD=30.91;SOR=0.859 GT:AD:DP:GQ:PL 1/1:0,50:50:99:2197,153,0 +20 10046537 . A G 819.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-3.909;AS_FS=3.724;AS_MQ=55.04;AS_MQRankSum=0.395;AS_ReadPosRankSum=0.412;AS_SOR=1.262;BaseQRankSum=-3.909;ClippingRankSum=0.000;DP=57;ExcessHet=3.0103;FS=3.724;MLEAC=1;MLEAF=0.500;MQ=54.50;MQRankSum=0.395;QD=14.38;ReadPosRankSum=0.412;SOR=1.262 GT:AD:DP:GQ:PL 0/1:28,29:57:99:848,0,902 +20 10050828 . T C 1227.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-2.704;AS_FS=2.887;AS_MQ=60.00;AS_MQRankSum=0.892;AS_ReadPosRankSum=0.073;AS_SOR=0.521;BaseQRankSum=-2.704;ClippingRankSum=0.000;DP=87;ExcessHet=3.0103;FS=2.887;MLEAC=1;MLEAF=0.500;MQ=59.74;MQRankSum=0.892;QD=14.28;ReadPosRankSum=0.073;SOR=0.521 GT:AD:DP:GQ:PL 0/1:49,37:86:99:1256,0,1768 +20 10051448 . T C 1134.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-0.501;AS_FS=3.687;AS_MQ=58.80;AS_MQRankSum=-1.404;AS_ReadPosRankSum=-0.549;AS_SOR=0.302;BaseQRankSum=-0.501;ClippingRankSum=0.000;DP=71;ExcessHet=3.0103;FS=3.687;MLEAC=1;MLEAF=0.500;MQ=59.08;MQRankSum=-1.404;QD=16.21;ReadPosRankSum=-0.549;SOR=0.302 GT:AD:DP:GQ:PL 0/1:35,35:70:99:1163,0,1150 +20 10052688 . C A 1062.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=0.180;AS_FS=3.135;AS_MQ=60.00;AS_MQRankSum=0.870;AS_ReadPosRankSum=1.559;AS_SOR=0.379;BaseQRankSum=0.180;ClippingRankSum=0.000;DP=77;ExcessHet=3.0103;FS=3.135;MLEAC=1;MLEAF=0.500;MQ=59.76;MQRankSum=0.870;QD=13.80;ReadPosRankSum=1.559;SOR=0.379 GT:AD:DP:GQ:PL 0/1:45,32:77:99:1091,0,1645 +20 10058022 . T C 975.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-2.346;AS_FS=0.920;AS_MQ=59.28;AS_MQRankSum=0.466;AS_ReadPosRankSum=-0.453;AS_SOR=0.849;BaseQRankSum=-2.346;ClippingRankSum=0.000;DP=68;ExcessHet=3.0103;FS=0.920;MLEAC=1;MLEAF=0.500;MQ=59.11;MQRankSum=0.466;QD=14.35;ReadPosRankSum=-0.453;SOR=0.849 GT:AD:DP:GQ:PL 0/1:36,32:68:99:1004,0,1261 +20 10062935 . C CA 92.84 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=1.304;AS_FS=0.000;AS_MQ=49.91;AS_MQRankSum=-1.502;AS_ReadPosRankSum=-0.492;AS_SOR=0.743;BaseQRankSum=1.304;ClippingRankSum=0.000;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.23;MQRankSum=-1.502;QD=4.04;ReadPosRankSum=-0.492;SOR=0.743 GT:AD:DP:GQ:PL 0/1:13,10:23:99:130,0,101 +20 10067049 . TAAAAAAAA T,TA 614.73 . AC=1,1;AF=0.500,0.500;AN=2;AS_BaseQRankSum=0.217;AS_FS=0.000;AS_MQ=35.88,38.13;AS_MQRankSum=-0.429;AS_ReadPosRankSum=-0.511;AS_SOR=0.941;BaseQRankSum=0.217;ClippingRankSum=0.000;DP=69;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=54.41;MQRankSum=-0.429;QD=27.94;ReadPosRankSum=-0.511;SOR=0.941 GT:AD:DP:GQ:PL 1/2:2,11,9:22:99:652,164,339,135,0,106 +20 10067090 . C A 2004.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=54.93;AS_SOR=0.729;DP=56;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=54.57;QD=28.90;SOR=0.729 GT:AD:DP:GQ:PL 1/1:0,55:55:99:2033,164,0 +20 10067264 . G A 2922.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=59.37;AS_SOR=0.776;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.37;QD=32.97;SOR=0.776 GT:AD:DP:GQ:PL 1/1:0,73:73:99:2951,219,0 +20 10067722 . A C 2146.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=60.00;AS_SOR=0.846;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=28.56;SOR=0.846 GT:AD:DP:GQ:PL 1/1:0,54:54:99:2175,163,0 +20 10068158 . GTGTATATATATA G 66.73 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-0.652;AS_FS=3.680;AS_MQ=47.12;AS_MQRankSum=0.328;AS_ReadPosRankSum=-0.253;AS_SOR=0.061;BaseQRankSum=-0.652;ClippingRankSum=0.000;DP=29;ExcessHet=3.0103;FS=3.680;MLEAC=1;MLEAF=0.500;MQ=56.74;MQRankSum=0.328;QD=9.53;ReadPosRankSum=-0.253;SOR=0.061 GT:AD:DP:GQ:PL 0/1:3,4:7:57:104,0,57 +20 10068981 . G A 2503.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=60.00;AS_SOR=0.941;DP=62;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.84;SOR=0.941 GT:AD:DP:GQ:PL 1/1:0,61:61:99:2532,184,0 +20 10070602 . T C 2691.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=58.71;AS_SOR=0.749;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.74;QD=31.04;SOR=0.749 GT:AD:DP:GQ:PL 1/1:0,72:72:99:2720,216,0 +20 10070936 . T A 3631.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=58.76;AS_SOR=0.876;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.76;QD=29.30;SOR=0.876 GT:AD:DP:GQ:PL 1/1:0,81:81:99:3660,247,0 +20 10070938 . G GA 3656.73 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=59.10;AS_SOR=0.881;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.10;QD=24.97;SOR=0.881 GT:AD:DP:GQ:PL 1/1:0,79:79:99:3694,250,0 +20 10071135 . C T 3257.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=59.12;AS_SOR=1.003;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.12;QD=25.71;SOR=1.003 GT:AD:DP:GQ:PL 1/1:0,79:79:99:3286,238,0 +20 10071187 . G A 3410.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=59.72;AS_SOR=1.367;DP=82;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.72;QD=32.40;SOR=1.367 GT:AD:DP:GQ:PL 1/1:0,82:82:99:3439,246,0 +20 10071890 . T C 1974.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=59.67;AS_SOR=0.728;DP=57;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.67;QD=34.65;SOR=0.728 GT:AD:DP:GQ:PL 1/1:0,57:57:99:2003,171,0 +20 10072505 . A G 2099.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=60.00;AS_SOR=0.822;DP=64;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.81;SOR=0.822 GT:AD:DP:GQ:PL 1/1:0,64:64:99:2128,191,0 +20 10074187 . A G 3101.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=59.12;AS_SOR=0.881;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.12;QD=32.52;SOR=0.881 GT:AD:DP:GQ:PL 1/1:0,79:79:99:3130,238,0 +20 10074240 . T C 3406.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=59.78;AS_SOR=0.922;DP=86;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.78;QD=27.36;SOR=0.922 GT:AD:DP:GQ:PL 1/1:0,85:85:99:3435,255,0 +20 10074716 . G A 2400.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=59.64;AS_SOR=1.214;DP=66;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.30;QD=29.05;SOR=1.214 GT:AD:DP:GQ:PL 1/1:0,64:64:99:2429,192,0 +20 10074806 . G A 2817.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=59.35;AS_SOR=0.840;DP=71;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.35;QD=31.56;SOR=0.840 GT:AD:DP:GQ:PL 1/1:0,71:71:99:2846,213,0 +20 10075043 . T C 2405.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=59.62;AS_SOR=1.107;DP=62;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.63;QD=29.40;SOR=1.107 GT:AD:DP:GQ:PL 1/1:0,61:61:99:2434,184,0 +20 10075168 . C T 3612.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=59.35;AS_SOR=0.997;DP=89;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.36;QD=24.02;SOR=0.997 GT:AD:DP:GQ:PL 1/1:0,88:88:99:3641,264,0 +20 10075508 . GA G 1928.73 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=61.29;AS_SOR=1.085;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=61.17;QD=27.55;SOR=1.085 GT:AD:DP:GQ:PL 1/1:0,70:70:99:1966,210,0 +20 10076250 . A G 1107.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-3.386;AS_FS=7.546;AS_MQ=58.76;AS_MQRankSum=-1.423;AS_ReadPosRankSum=-0.605;AS_SOR=0.344;BaseQRankSum=-3.386;ClippingRankSum=0.000;DP=80;ExcessHet=3.0103;FS=7.546;MLEAC=1;MLEAF=0.500;MQ=59.40;MQRankSum=-1.423;QD=14.02;ReadPosRankSum=-0.605;SOR=0.344 GT:AD:DP:GQ:PL 0/1:40,39:79:99:1136,0,1339 +20 10076339 . A G 1309.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-0.069;AS_FS=1.992;AS_MQ=59.42;AS_MQRankSum=-0.866;AS_ReadPosRankSum=0.508;AS_SOR=0.446;BaseQRankSum=-0.069;ClippingRankSum=0.000;DP=72;ExcessHet=3.0103;FS=1.992;MLEAC=1;MLEAF=0.500;MQ=59.68;MQRankSum=-0.866;QD=18.19;ReadPosRankSum=0.508;SOR=0.446 GT:AD:DP:GQ:PL 0/1:32,40:72:99:1338,0,1035 +20 10076399 . G A 1807.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=4.154;AS_FS=1.680;AS_MQ=60.00;AS_MQRankSum=0.000;AS_ReadPosRankSum=-0.863;AS_SOR=0.952;BaseQRankSum=4.154;ClippingRankSum=0.000;DP=94;ExcessHet=3.0103;FS=1.680;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=19.23;ReadPosRankSum=-0.863;SOR=0.952 GT:AD:DP:GQ:PL 0/1:44,50:94:99:1836,0,1544 +20 10076989 . CA C 221.73 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-0.984;AS_FS=0.000;AS_MQ=50.99;AS_MQRankSum=0.000;AS_ReadPosRankSum=0.476;AS_SOR=0.666;BaseQRankSum=-0.984;ClippingRankSum=0.000;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.87;MQRankSum=0.000;QD=5.28;ReadPosRankSum=0.476;SOR=0.666 GT:AD:DP:GQ:PL 0/1:24,18:42:99:218,0,332 +20 10077752 . T C 1345.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-6.503;AS_FS=4.458;AS_MQ=60.00;AS_MQRankSum=0.000;AS_ReadPosRankSum=-0.142;AS_SOR=1.251;BaseQRankSum=-6.503;ClippingRankSum=0.000;DP=79;ExcessHet=3.0103;FS=4.458;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=17.04;ReadPosRankSum=-0.142;SOR=1.251 GT:AD:DP:GQ:PL 0/1:34,45:79:99:1374,0,1187 +20 10079476 . T G 11.12 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-4.458;AS_FS=57.922;AS_MQ=57.87;AS_MQRankSum=-0.826;AS_ReadPosRankSum=-4.313;AS_SOR=4.970;BaseQRankSum=-4.458;ClippingRankSum=0.000;DP=44;ExcessHet=3.0103;FS=57.922;MLEAC=1;MLEAF=0.500;MQ=59.05;MQRankSum=-0.826;QD=0.25;ReadPosRankSum=-4.313;SOR=4.970 GT:AD:DP:GQ:PL 0/1:33,11:44:39:39,0,1137 +20 10081750 . C A 1353.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=2.670;AS_FS=0.824;AS_MQ=60.00;AS_MQRankSum=0.000;AS_ReadPosRankSum=-0.626;AS_SOR=0.664;BaseQRankSum=2.670;ClippingRankSum=0.000;DP=83;ExcessHet=3.0103;FS=0.824;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=16.31;ReadPosRankSum=-0.626;SOR=0.664 GT:AD:DP:GQ:PL 0/1:44,39:83:99:1382,0,1525 +20 10081800 . C T 1109.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=0.241;AS_FS=11.086;AS_MQ=60.00;AS_MQRankSum=0.000;AS_ReadPosRankSum=-1.082;AS_SOR=0.143;BaseQRankSum=0.241;ClippingRankSum=0.000;DP=68;ExcessHet=3.0103;FS=11.086;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=16.32;ReadPosRankSum=-1.082;SOR=0.143 GT:AD:DP:GQ:PL 0/1:35,33:68:99:1138,0,1222 +20 10082892 . C T 1712.77 . AC=2;AF=1.00;AN=2;AS_FS=0.000;AS_MQ=59.48;AS_SOR=0.883;DP=44;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.48;QD=28.81;SOR=0.883 GT:AD:DP:GQ:PL 1/1:0,44:44:99:1741,132,0 +20 10085211 . A T 1210.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-1.501;AS_FS=0.870;AS_MQ=59.36;AS_MQRankSum=-1.028;AS_ReadPosRankSum=-0.280;AS_SOR=0.723;BaseQRankSum=-1.501;ClippingRankSum=0.000;DP=77;ExcessHet=3.0103;FS=0.870;MLEAC=1;MLEAF=0.500;MQ=59.46;MQRankSum=-1.028;QD=15.93;ReadPosRankSum=-0.280;SOR=0.723 GT:AD:DP:GQ:PL 0/1:40,36:76:99:1239,0,1443 +20 10086110 . G A 1274.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-0.343;AS_FS=1.810;AS_MQ=58.78;AS_MQRankSum=-0.680;AS_ReadPosRankSum=0.875;AS_SOR=0.495;BaseQRankSum=-0.343;ClippingRankSum=0.000;DP=81;ExcessHet=3.0103;FS=1.810;MLEAC=1;MLEAF=0.500;MQ=59.14;MQRankSum=-0.680;QD=15.74;ReadPosRankSum=0.875;SOR=0.495 GT:AD:DP:GQ:PL 0/1:43,38:81:99:1303,0,1506 +20 10086283 . G T 1025.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=2.304;AS_FS=0.855;AS_MQ=60.00;AS_MQRankSum=0.000;AS_ReadPosRankSum=1.608;AS_SOR=0.529;BaseQRankSum=2.304;ClippingRankSum=0.000;DP=85;ExcessHet=3.0103;FS=0.855;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=12.21;ReadPosRankSum=1.608;SOR=0.529 GT:AD:DP:GQ:PL 0/1:52,32:84:99:1054,0,1771 +20 10086619 . T A 796.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=0.256;AS_FS=0.958;AS_MQ=59.07;AS_MQRankSum=-1.312;AS_ReadPosRankSum=-0.051;AS_SOR=0.846;BaseQRankSum=0.256;ClippingRankSum=0.000;DP=71;ExcessHet=3.0103;FS=0.958;MLEAC=1;MLEAF=0.500;MQ=59.41;MQRankSum=-1.312;QD=11.38;ReadPosRankSum=-0.051;SOR=0.846 GT:AD:DP:GQ:PL 0/1:45,25:70:99:825,0,1603 +20 10086853 . G A 1002.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=3.915;AS_FS=0.000;AS_MQ=59.28;AS_MQRankSum=-0.177;AS_ReadPosRankSum=-0.270;AS_SOR=0.767;BaseQRankSum=3.915;ClippingRankSum=0.000;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.43;MQRankSum=-0.177;QD=13.74;ReadPosRankSum=-0.270;SOR=0.767 GT:AD:DP:GQ:PL 0/1:41,32:73:99:1031,0,1280 +20 10086954 . G A 1095.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=2.606;AS_FS=4.812;AS_MQ=60.00;AS_MQRankSum=0.000;AS_ReadPosRankSum=-0.812;AS_SOR=1.185;BaseQRankSum=2.606;ClippingRankSum=0.000;DP=68;ExcessHet=3.0103;FS=4.812;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=16.11;ReadPosRankSum=-0.812;SOR=1.185 GT:AD:DP:GQ:PL 0/1:34,34:68:99:1124,0,1051 +20 10087230 . A G 1842.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-2.407;AS_FS=3.860;AS_MQ=59.65;AS_MQRankSum=1.707;AS_ReadPosRankSum=0.893;AS_SOR=0.960;BaseQRankSum=-2.407;ClippingRankSum=0.000;DP=96;ExcessHet=3.0103;FS=3.860;MLEAC=1;MLEAF=0.500;MQ=58.88;MQRankSum=1.707;QD=19.20;ReadPosRankSum=0.893;SOR=0.960 GT:AD:DP:GQ:PL 0/1:42,54:96:99:1871,0,1428 +20 10087394 . T G 1688.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-2.340;AS_FS=4.225;AS_MQ=60.00;AS_MQRankSum=1.207;AS_ReadPosRankSum=1.181;AS_SOR=0.436;BaseQRankSum=-2.340;ClippingRankSum=0.000;DP=84;ExcessHet=3.0103;FS=4.225;MLEAC=1;MLEAF=0.500;MQ=59.73;MQRankSum=1.207;QD=20.10;ReadPosRankSum=1.181;SOR=0.436 GT:AD:DP:GQ:PL 0/1:35,49:84:99:1717,0,1186 +20 10087754 . T G 1347.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=0.355;AS_FS=0.869;AS_MQ=61.31;AS_MQRankSum=2.193;AS_ReadPosRankSum=-0.831;AS_SOR=0.562;BaseQRankSum=0.355;ClippingRankSum=0.000;DP=79;ExcessHet=3.0103;FS=0.869;MLEAC=1;MLEAF=0.500;MQ=60.39;MQRankSum=2.193;QD=17.28;ReadPosRankSum=-0.831;SOR=0.562 GT:AD:DP:GQ:PL 0/1:37,41:78:99:1376,0,1239 +20 10087804 . C T 1619.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=1.940;AS_FS=3.847;AS_MQ=61.77;AS_MQRankSum=2.618;AS_ReadPosRankSum=1.024;AS_SOR=0.369;BaseQRankSum=1.940;ClippingRankSum=0.000;DP=100;ExcessHet=3.0103;FS=3.847;MLEAC=1;MLEAF=0.500;MQ=60.77;MQRankSum=2.618;QD=16.20;ReadPosRankSum=1.024;SOR=0.369 GT:AD:DP:GQ:PL 0/1:50,50:100:99:1648,0,1511 +20 10087820 . C CAG 428.73 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-1.974;AS_FS=0.000;AS_MQ=59.57;AS_MQRankSum=0.422;AS_ReadPosRankSum=-0.009;AS_SOR=0.850;BaseQRankSum=-1.974;ClippingRankSum=0.000;DP=99;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.53;MQRankSum=0.422;QD=7.80;ReadPosRankSum=-0.009;SOR=0.850 GT:AD:DP:GQ:PL 0/1:37,18:55:99:466,0,1169 +20 10088063 . C T 1417.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=3.405;AS_FS=2.739;AS_MQ=59.58;AS_MQRankSum=0.515;AS_ReadPosRankSum=0.354;AS_SOR=1.053;BaseQRankSum=3.405;ClippingRankSum=0.000;DP=93;ExcessHet=3.0103;FS=2.739;MLEAC=1;MLEAF=0.500;MQ=59.35;MQRankSum=0.515;QD=15.24;ReadPosRankSum=0.354;SOR=1.053 GT:AD:DP:GQ:PL 0/1:49,44:93:99:1446,0,1403 +20 10088699 . C T 776.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=3.803;AS_FS=16.952;AS_MQ=52.45;AS_MQRankSum=-3.140;AS_ReadPosRankSum=-0.577;AS_SOR=1.914;BaseQRankSum=3.803;ClippingRankSum=0.000;DP=63;ExcessHet=3.0103;FS=16.952;MLEAC=1;MLEAF=0.500;MQ=56.31;MQRankSum=-3.140;QD=12.53;ReadPosRankSum=-0.577;SOR=1.914 GT:AD:DP:GQ:PL 0/1:36,26:62:99:805,0,1088 +20 10088730 . G A 972.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=0.224;AS_FS=15.383;AS_MQ=43.72;AS_MQRankSum=-4.839;AS_ReadPosRankSum=0.433;AS_SOR=1.592;BaseQRankSum=0.224;ClippingRankSum=0.000;DP=53;ExcessHet=3.0103;FS=15.383;MLEAC=1;MLEAF=0.500;MQ=53.06;MQRankSum=-4.839;QD=18.71;ReadPosRankSum=0.433;SOR=1.592 GT:AD:DP:GQ:PL 0/1:29,23:52:99:1001,0,1152 +20 10088736 . A C 1081.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=0.282;AS_FS=9.673;AS_MQ=42.55;AS_MQRankSum=-5.169;AS_ReadPosRankSum=-0.042;AS_SOR=0.851;BaseQRankSum=0.282;ClippingRankSum=0.000;DP=56;ExcessHet=3.0103;FS=9.673;MLEAC=1;MLEAF=0.500;MQ=51.85;MQRankSum=-5.169;QD=19.67;ReadPosRankSum=-0.042;SOR=0.851 GT:AD:DP:GQ:PL 0/1:28,27:55:99:1110,0,1194 +20 10088747 . A G 1111.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-3.877;AS_FS=7.653;AS_MQ=43.71;AS_MQRankSum=-4.907;AS_ReadPosRankSum=-0.339;AS_SOR=1.092;BaseQRankSum=-3.877;ClippingRankSum=0.000;DP=56;ExcessHet=3.0103;FS=7.653;MLEAC=1;MLEAF=0.500;MQ=51.25;MQRankSum=-4.907;QD=20.59;ReadPosRankSum=-0.339;SOR=1.092 GT:AD:DP:GQ:PL 0/1:25,29:54:99:1140,0,995 +20 10088799 . G A 1018.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=5.503;AS_FS=10.098;AS_MQ=49.23;AS_MQRankSum=-2.498;AS_ReadPosRankSum=1.347;AS_SOR=1.003;BaseQRankSum=5.503;ClippingRankSum=0.000;DP=54;ExcessHet=3.0103;FS=10.098;MLEAC=1;MLEAF=0.500;MQ=52.86;MQRankSum=-2.498;QD=19.22;ReadPosRankSum=1.347;SOR=1.003 GT:AD:DP:GQ:PL 0/1:22,31:53:99:1047,0,617 +20 10088895 . C T 532.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=2.462;AS_FS=0.000;AS_MQ=57.92;AS_MQRankSum=0.577;AS_ReadPosRankSum=0.907;AS_SOR=0.653;BaseQRankSum=2.462;ClippingRankSum=0.000;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.86;MQRankSum=0.577;QD=12.99;ReadPosRankSum=0.907;SOR=0.653 GT:AD:DP:GQ:PL 0/1:23,18:41:99:561,0,673 +20 10088968 . C CAAA 1175.73 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=0.497;AS_FS=1.078;AS_MQ=42.97;AS_MQRankSum=-4.750;AS_ReadPosRankSum=1.015;AS_SOR=1.012;BaseQRankSum=0.497;ClippingRankSum=0.000;DP=62;ExcessHet=3.0103;FS=1.078;MLEAC=1;MLEAF=0.500;MQ=53.55;MQRankSum=-4.750;QD=22.18;ReadPosRankSum=1.015;SOR=1.012 GT:AD:DP:GQ:PL 0/1:30,23:53:99:1213,0,1367 +20 10088980 . T C 1247.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-1.585;AS_FS=0.000;AS_MQ=40.73;AS_MQRankSum=-5.232;AS_ReadPosRankSum=0.999;AS_SOR=0.709;BaseQRankSum=-1.585;ClippingRankSum=0.000;DP=68;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.93;MQRankSum=-5.232;QD=18.35;ReadPosRankSum=0.999;SOR=0.709 GT:AD:DP:GQ:PL 0/1:37,31:68:99:1276,0,1627 +20 10088985 . T C 1178.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-0.192;AS_FS=0.890;AS_MQ=40.62;AS_MQRankSum=-5.248;AS_ReadPosRankSum=1.381;AS_SOR=0.742;BaseQRankSum=-0.192;ClippingRankSum=0.000;DP=74;ExcessHet=3.0103;FS=0.890;MLEAC=1;MLEAF=0.500;MQ=50.91;MQRankSum=-5.248;QD=15.93;ReadPosRankSum=1.381;SOR=0.742 GT:AD:DP:GQ:PL 0/1:42,32:74:99:1207,0,1729 +20 10089441 . A G 1179.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-4.885;AS_FS=6.071;AS_MQ=59.41;AS_MQRankSum=-0.948;AS_ReadPosRankSum=0.161;AS_SOR=1.363;BaseQRankSum=-4.885;ClippingRankSum=0.000;DP=76;ExcessHet=3.0103;FS=6.071;MLEAC=1;MLEAF=0.500;MQ=59.70;MQRankSum=-0.948;QD=15.52;ReadPosRankSum=0.161;SOR=1.363 GT:AD:DP:GQ:PL 0/1:37,39:76:99:1208,0,1313 +20 10089525 . C T 1548.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=5.859;AS_FS=4.260;AS_MQ=60.00;AS_MQRankSum=1.531;AS_ReadPosRankSum=0.428;AS_SOR=0.617;BaseQRankSum=5.859;ClippingRankSum=0.000;DP=82;ExcessHet=3.0103;FS=4.260;MLEAC=1;MLEAF=0.500;MQ=59.49;MQRankSum=1.531;QD=19.12;ReadPosRankSum=0.428;SOR=0.617 GT:AD:DP:GQ:PL 0/1:38,43:81:99:1577,0,1088 +20 10090289 . CA C 384.73 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=0.316;AS_FS=1.377;AS_MQ=56.24;AS_MQRankSum=1.531;AS_ReadPosRankSum=-0.018;AS_SOR=1.127;BaseQRankSum=0.316;ClippingRankSum=0.000;DP=80;ExcessHet=3.0103;FS=1.377;MLEAC=1;MLEAF=0.500;MQ=59.97;MQRankSum=1.531;QD=10.12;ReadPosRankSum=-0.018;SOR=1.127 GT:AD:DP:GQ:PL 0/1:14,24:38:99:422,0,230 +20 10090764 . A G 840.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-2.659;AS_FS=4.975;AS_MQ=60.00;AS_MQRankSum=0.000;AS_ReadPosRankSum=0.695;AS_SOR=0.310;BaseQRankSum=-2.659;ClippingRankSum=0.000;DP=63;ExcessHet=3.0103;FS=4.975;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=13.35;ReadPosRankSum=0.695;SOR=0.310 GT:AD:DP:GQ:PL 0/1:34,29:63:99:869,0,1207 +20 10090970 . T C 1257.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-0.484;AS_FS=0.927;AS_MQ=60.00;AS_MQRankSum=1.509;AS_ReadPosRankSum=0.429;AS_SOR=0.518;BaseQRankSum=-0.484;ClippingRankSum=0.000;DP=70;ExcessHet=3.0103;FS=0.927;MLEAC=1;MLEAF=0.500;MQ=59.47;MQRankSum=1.509;QD=18.23;ReadPosRankSum=0.429;SOR=0.518 GT:AD:DP:GQ:PL 0/1:33,36:69:99:1286,0,1092 +20 10091214 . C T 1249.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=0.361;AS_FS=0.000;AS_MQ=59.50;AS_MQRankSum=-0.916;AS_ReadPosRankSum=0.392;AS_SOR=0.625;BaseQRankSum=0.361;ClippingRankSum=0.000;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.73;MQRankSum=-0.916;QD=17.85;ReadPosRankSum=0.392;SOR=0.625 GT:AD:DP:GQ:PL 0/1:33,37:70:99:1278,0,1110 +20 10092415 . A G 1635.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-6.731;AS_FS=0.741;AS_MQ=60.00;AS_MQRankSum=0.000;AS_ReadPosRankSum=-0.070;AS_SOR=0.665;BaseQRankSum=-6.731;ClippingRankSum=0.000;DP=102;ExcessHet=3.0103;FS=0.741;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=16.20;ReadPosRankSum=-0.070;SOR=0.665 GT:AD:DP:GQ:PL 0/1:52,49:101:99:1664,0,1902 +20 10092927 . G T 106.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-2.507;AS_FS=60.191;AS_MQ=56.35;AS_MQRankSum=-3.009;AS_ReadPosRankSum=-4.416;AS_SOR=5.279;BaseQRankSum=-2.507;ClippingRankSum=0.000;DP=73;ExcessHet=3.0103;FS=60.191;MLEAC=1;MLEAF=0.500;MQ=59.37;MQRankSum=-3.009;QD=1.48;ReadPosRankSum=-4.416;SOR=5.279 GT:AD:DP:GQ:PL 0/1:59,13:72:99:135,0,1864 +20 10093568 . GT G 326.73 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=1.131;AS_FS=0.000;AS_MQ=54.72;AS_MQRankSum=1.078;AS_ReadPosRankSum=0.638;AS_SOR=0.693;BaseQRankSum=1.131;ClippingRankSum=0.000;DP=59;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.74;MQRankSum=1.078;QD=7.60;ReadPosRankSum=0.638;SOR=0.693 GT:AD:DP:GQ:PL 0/1:22,21:43:99:364,0,386 +20 10093923 . T A 1075.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-0.667;AS_FS=0.924;AS_MQ=59.24;AS_MQRankSum=0.358;AS_ReadPosRankSum=-2.256;AS_SOR=0.772;BaseQRankSum=-0.667;ClippingRankSum=0.000;DP=67;ExcessHet=3.0103;FS=0.924;MLEAC=1;MLEAF=0.500;MQ=59.19;MQRankSum=0.358;QD=16.06;ReadPosRankSum=-2.256;SOR=0.772 GT:AD:DP:GQ:PL 0/1:35,32:67:99:1104,0,1257 +20 10094251 . T A 1270.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=0.251;AS_FS=11.483;AS_MQ=60.00;AS_MQRankSum=0.000;AS_ReadPosRankSum=1.734;AS_SOR=1.211;BaseQRankSum=0.251;ClippingRankSum=0.000;DP=63;ExcessHet=3.0103;FS=11.483;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=20.50;ReadPosRankSum=1.734;SOR=1.211 GT:AD:DP:GQ:PL 0/1:26,36:62:99:1299,0,781 +20 10094582 . A G 923.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-1.388;AS_FS=0.000;AS_MQ=60.00;AS_MQRankSum=1.270;AS_ReadPosRankSum=-0.527;AS_SOR=0.772;BaseQRankSum=-1.388;ClippingRankSum=0.000;DP=72;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.42;MQRankSum=1.270;QD=13.39;ReadPosRankSum=-0.527;SOR=0.772 GT:AD:DP:GQ:PL 0/1:39,30:69:99:952,0,1350 +20 10094774 . C T 1036.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-0.784;AS_FS=0.000;AS_MQ=60.00;AS_MQRankSum=0.962;AS_ReadPosRankSum=0.494;AS_SOR=0.690;BaseQRankSum=-0.784;ClippingRankSum=0.000;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.70;MQRankSum=0.962;QD=13.82;ReadPosRankSum=0.494;SOR=0.690 GT:AD:DP:GQ:PL 0/1:40,35:75:99:1065,0,1282 +20 10095432 . GTGATGATGA G 839.73 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=1.265;AS_FS=1.102;AS_MQ=39.33;AS_MQRankSum=-4.431;AS_ReadPosRankSum=0.660;AS_SOR=0.460;BaseQRankSum=1.265;ClippingRankSum=0.000;DP=77;ExcessHet=3.0103;FS=1.102;MLEAC=1;MLEAF=0.500;MQ=54.39;MQRankSum=-4.431;QD=16.79;ReadPosRankSum=0.660;SOR=0.460 GT:AD:DP:GQ:PL 0/1:27,23:50:99:877,0,2108 +20 10095741 . A G 1075.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-0.534;AS_FS=4.721;AS_MQ=55.06;AS_MQRankSum=-2.313;AS_ReadPosRankSum=-0.326;AS_SOR=0.515;BaseQRankSum=-0.534;ClippingRankSum=0.000;DP=72;ExcessHet=3.0103;FS=4.721;MLEAC=1;MLEAF=0.500;MQ=57.39;MQRankSum=-2.313;QD=15.37;ReadPosRankSum=-0.326;SOR=0.515 GT:AD:DP:GQ:PL 0/1:36,34:70:99:1104,0,1233 +20 10096293 . C T 1355.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=4.664;AS_FS=0.000;AS_MQ=59.39;AS_MQRankSum=1.397;AS_ReadPosRankSum=0.012;AS_SOR=0.638;BaseQRankSum=4.664;ClippingRankSum=0.000;DP=76;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.59;MQRankSum=1.397;QD=18.08;ReadPosRankSum=0.012;SOR=0.638 GT:AD:DP:GQ:PL 0/1:37,38:75:99:1384,0,1258 +20 10096596 . C T 1562.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=2.728;AS_FS=0.000;AS_MQ=59.01;AS_MQRankSum=0.612;AS_ReadPosRankSum=0.166;AS_SOR=0.640;BaseQRankSum=2.728;ClippingRankSum=0.000;DP=87;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.77;MQRankSum=0.612;QD=17.96;ReadPosRankSum=0.166;SOR=0.640 GT:AD:DP:GQ:PL 0/1:40,47:87:99:1591,0,1273 +20 10096768 . A C 1682.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-2.764;AS_FS=3.983;AS_MQ=58.58;AS_MQRankSum=-1.609;AS_ReadPosRankSum=0.541;AS_SOR=0.445;BaseQRankSum=-2.764;ClippingRankSum=0.000;DP=91;ExcessHet=3.0103;FS=3.983;MLEAC=1;MLEAF=0.500;MQ=59.24;MQRankSum=-1.609;QD=18.49;ReadPosRankSum=0.541;SOR=0.445 GT:AD:DP:GQ:PL 0/1:42,49:91:99:1711,0,1452 +20 10096899 . G T 1614.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=2.755;AS_FS=9.606;AS_MQ=59.06;AS_MQRankSum=-1.387;AS_ReadPosRankSum=0.378;AS_SOR=1.707;BaseQRankSum=2.755;ClippingRankSum=0.000;DP=79;ExcessHet=3.0103;FS=9.606;MLEAC=1;MLEAF=0.500;MQ=59.53;MQRankSum=-1.387;QD=20.44;ReadPosRankSum=0.378;SOR=1.707 GT:AD:DP:GQ:PL 0/1:39,40:79:99:1643,0,1520 +20 10096905 . TA T 1600.73 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-0.755;AS_FS=11.159;AS_MQ=58.58;AS_MQRankSum=-1.677;AS_ReadPosRankSum=0.397;AS_SOR=1.775;BaseQRankSum=-0.755;ClippingRankSum=0.000;DP=83;ExcessHet=3.0103;FS=11.159;MLEAC=1;MLEAF=0.500;MQ=59.27;MQRankSum=-1.677;QD=19.29;ReadPosRankSum=0.397;SOR=1.775 GT:AD:DP:GQ:PL 0/1:40,43:83:99:1638,0,1623 +20 10096933 . G C 1511.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-1.914;AS_FS=23.320;AS_MQ=58.51;AS_MQRankSum=-1.802;AS_ReadPosRankSum=0.238;AS_SOR=1.534;BaseQRankSum=-1.914;ClippingRankSum=0.000;DP=85;ExcessHet=3.0103;FS=23.320;MLEAC=1;MLEAF=0.500;MQ=59.29;MQRankSum=-1.802;QD=17.79;ReadPosRankSum=0.238;SOR=1.534 GT:AD:DP:GQ:PL 0/1:44,41:85:99:1540,0,1770 +20 10096958 . G A 1766.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=2.839;AS_FS=16.778;AS_MQ=58.71;AS_MQRankSum=-1.701;AS_ReadPosRankSum=-1.559;AS_SOR=1.387;BaseQRankSum=2.839;ClippingRankSum=0.000;DP=92;ExcessHet=3.0103;FS=16.778;MLEAC=1;MLEAF=0.500;MQ=59.34;MQRankSum=-1.701;QD=19.20;ReadPosRankSum=-1.860;SOR=1.387 GT:AD:DP:GQ:PL 0/1:45,47:92:99:1795,0,1629 +20 10097075 . T G 1445.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-2.533;AS_FS=6.613;AS_MQ=57.00;AS_MQRankSum=-1.389;AS_ReadPosRankSum=-0.285;AS_SOR=0.628;BaseQRankSum=-2.533;ClippingRankSum=0.000;DP=92;ExcessHet=3.0103;FS=6.613;MLEAC=1;MLEAF=0.500;MQ=58.57;MQRankSum=-1.389;QD=15.71;ReadPosRankSum=-0.285;SOR=0.628 GT:AD:DP:GQ:PL 0/1:44,48:92:99:1474,0,1482 +20 10097101 . C CTTT 1091.73 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-0.894;AS_FS=7.156;AS_MQ=49.02;AS_MQRankSum=-1.750;AS_ReadPosRankSum=1.627;AS_SOR=0.501;BaseQRankSum=-0.894;ClippingRankSum=0.000;DP=76;ExcessHet=3.0103;FS=7.156;MLEAC=1;MLEAF=0.500;MQ=57.62;MQRankSum=-1.750;QD=16.54;ReadPosRankSum=1.627;SOR=0.501 GT:AD:DP:GQ:PL 0/1:34,32:66:99:1129,0,1306 +20 10097436 . CTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT C 1054.73 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=1.820;AS_FS=1.851;AS_MQ=42.30;AS_MQRankSum=-6.464;AS_ReadPosRankSum=-3.231;AS_SOR=0.948;BaseQRankSum=1.820;ClippingRankSum=0.000;DP=89;ExcessHet=3.0103;FS=1.851;MLEAC=1;MLEAF=0.500;MQ=54.27;MQRankSum=-6.464;QD=11.85;ReadPosRankSum=-3.231;SOR=0.948 GT:AD:DP:GQ:PL 0/1:57,32:89:99:1092,0,2241 +20 10097437 . TTTTC T 796.73 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=0.791;AS_FS=4.241;AS_MQ=60.60;AS_MQRankSum=4.881;AS_ReadPosRankSum=2.929;AS_SOR=1.382;BaseQRankSum=0.791;ClippingRankSum=0.000;DP=76;ExcessHet=3.0103;FS=4.241;MLEAC=1;MLEAF=0.500;MQ=53.48;MQRankSum=4.881;QD=14.49;ReadPosRankSum=2.929;SOR=1.382 GT:AD:DP:GQ:PL 0/1:32,23:55:99:834,0,1193 +20 10097626 . C A 626.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=1.085;AS_FS=2.701;AS_MQ=56.91;AS_MQRankSum=-1.331;AS_ReadPosRankSum=1.154;AS_SOR=0.324;BaseQRankSum=1.085;ClippingRankSum=0.000;DP=48;ExcessHet=3.0103;FS=2.701;MLEAC=1;MLEAF=0.500;MQ=58.24;MQRankSum=-1.331;QD=13.06;ReadPosRankSum=1.154;SOR=0.324 GT:AD:DP:GQ:PL 0/1:28,20:48:99:655,0,957 +20 10097789 . T C 688.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-1.157;AS_FS=5.374;AS_MQ=54.77;AS_MQRankSum=-2.805;AS_ReadPosRankSum=-0.092;AS_SOR=0.756;BaseQRankSum=-1.157;ClippingRankSum=0.000;DP=61;ExcessHet=3.0103;FS=5.374;MLEAC=1;MLEAF=0.500;MQ=57.89;MQRankSum=-2.805;QD=12.08;ReadPosRankSum=-0.092;SOR=0.756 GT:AD:DP:GQ:PL 0/1:34,23:57:99:717,0,1190 +20 10097928 . G A 570.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-1.203;AS_FS=1.315;AS_MQ=56.25;AS_MQRankSum=-1.654;AS_ReadPosRankSum=0.057;AS_SOR=0.951;BaseQRankSum=-1.203;ClippingRankSum=0.000;DP=40;ExcessHet=3.0103;FS=1.315;MLEAC=1;MLEAF=0.500;MQ=58.25;MQRankSum=-1.654;QD=15.85;ReadPosRankSum=0.057;SOR=0.951 GT:AD:DP:GQ:PL 0/1:17,19:36:99:599,0,586 +20 10098110 . G C 586.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=2.510;AS_FS=6.658;AS_MQ=57.23;AS_MQRankSum=-1.477;AS_ReadPosRankSum=-0.714;AS_SOR=0.069;BaseQRankSum=2.510;ClippingRankSum=0.000;DP=36;ExcessHet=3.0103;FS=6.658;MLEAC=1;MLEAF=0.500;MQ=58.71;MQRankSum=-1.477;QD=16.30;ReadPosRankSum=-0.714;SOR=0.069 GT:AD:DP:GQ:PL 0/1:19,17:36:99:615,0,727 +20 10098135 . C A 471.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-1.155;AS_FS=4.337;AS_MQ=60.68;AS_MQRankSum=1.546;AS_ReadPosRankSum=-0.769;AS_SOR=0.075;BaseQRankSum=-1.155;ClippingRankSum=0.000;DP=38;ExcessHet=3.0103;FS=4.337;MLEAC=1;MLEAF=0.500;MQ=59.64;MQRankSum=1.546;QD=12.41;ReadPosRankSum=-0.769;SOR=0.075 GT:AD:DP:GQ:PL 0/1:24,14:38:99:500,0,964 +20 10098219 . TATATATA T 295.73 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=3.147;AS_FS=0.000;AS_MQ=52.98;AS_MQRankSum=-0.205;AS_ReadPosRankSum=0.498;AS_SOR=0.465;BaseQRankSum=3.147;ClippingRankSum=0.000;DP=21;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.94;MQRankSum=-0.205;QD=14.08;ReadPosRankSum=0.498;SOR=0.465 GT:AD:DP:GQ:PL 0/1:12,9:21:99:333,0,461 +20 10098237 . A T 244.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=0.006;AS_FS=0.000;AS_MQ=47.00;AS_MQRankSum=-1.742;AS_ReadPosRankSum=1.434;AS_SOR=0.836;BaseQRankSum=0.006;ClippingRankSum=0.000;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.40;MQRankSum=-1.742;QD=18.83;ReadPosRankSum=0.277;SOR=0.836 GT:AD:DP:GQ:PL 0/1:6,7:13:99:273,0,273 +20 10098265 . T C 133.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=1.834;AS_FS=0.000;AS_MQ=29.00;AS_MQRankSum=-1.834;AS_ReadPosRankSum=0.524;AS_SOR=1.329;BaseQRankSum=1.834;ClippingRankSum=0.000;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=41.96;MQRankSum=-1.834;QD=22.29;ReadPosRankSum=0.000;SOR=1.329 GT:AD:DP:GQ:PL 0/1:2,4:6:59:162,0,59 +20 10098885 . C CA 433.73 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=0.165;AS_FS=0.000;AS_MQ=36.04;AS_MQRankSum=-4.449;AS_ReadPosRankSum=-0.159;AS_SOR=0.518;BaseQRankSum=0.165;ClippingRankSum=0.000;DP=31;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.89;MQRankSum=-4.449;QD=13.99;ReadPosRankSum=-0.159;SOR=0.518 GT:AD:DP:GQ:PL 0/1:17,14:31:99:471,0,572 +20 10098945 . T C 407.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=1.475;AS_FS=3.882;AS_MQ=44.29;AS_MQRankSum=-2.504;AS_ReadPosRankSum=0.837;AS_SOR=2.368;BaseQRankSum=1.475;ClippingRankSum=0.000;DP=22;ExcessHet=3.0103;FS=3.882;MLEAC=1;MLEAF=0.500;MQ=51.15;MQRankSum=-2.504;QD=18.53;ReadPosRankSum=0.837;SOR=2.368 GT:AD:DP:GQ:PL 0/1:9,13:22:99:436,0,248 +20 10098987 . C T 379.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=3.127;AS_FS=7.005;AS_MQ=44.15;AS_MQRankSum=-2.734;AS_ReadPosRankSum=0.348;AS_SOR=2.925;BaseQRankSum=3.127;ClippingRankSum=0.000;DP=24;ExcessHet=3.0103;FS=7.005;MLEAC=1;MLEAF=0.500;MQ=51.88;MQRankSum=-2.734;QD=15.82;ReadPosRankSum=0.348;SOR=2.925 GT:AD:DP:GQ:PL 0/1:11,13:24:99:408,0,350 +20 10099029 . T C 334.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-1.809;AS_FS=2.032;AS_MQ=41.29;AS_MQRankSum=-3.641;AS_ReadPosRankSum=-0.793;AS_SOR=1.329;BaseQRankSum=-1.809;ClippingRankSum=0.000;DP=28;ExcessHet=3.0103;FS=2.032;MLEAC=1;MLEAF=0.500;MQ=53.32;MQRankSum=-3.641;QD=11.96;ReadPosRankSum=-0.793;SOR=1.329 GT:AD:DP:GQ:PL 0/1:18,10:28:99:363,0,768 +20 10099034 . C A 334.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=2.757;AS_FS=4.265;AS_MQ=41.29;AS_MQRankSum=-3.641;AS_ReadPosRankSum=-1.540;AS_SOR=1.721;BaseQRankSum=2.757;ClippingRankSum=0.000;DP=28;ExcessHet=3.0103;FS=4.265;MLEAC=1;MLEAF=0.500;MQ=53.32;MQRankSum=-3.641;QD=11.96;ReadPosRankSum=-1.540;SOR=1.721 GT:AD:DP:GQ:PL 0/1:18,10:28:99:363,0,768 +20 10099044 . A C 334.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-1.148;AS_FS=0.000;AS_MQ=29.97;AS_MQRankSum=-4.418;AS_ReadPosRankSum=-2.625;AS_SOR=0.515;BaseQRankSum=-1.148;ClippingRankSum=0.000;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.94;MQRankSum=-4.418;QD=13.95;ReadPosRankSum=-2.625;SOR=0.515 GT:AD:DP:GQ:PL 0/1:15,9:24:99:363,0,768 +20 10099046 . T C 304.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-2.165;AS_FS=0.000;AS_MQ=29.97;AS_MQRankSum=-4.418;AS_ReadPosRankSum=-2.686;AS_SOR=0.515;BaseQRankSum=-2.165;ClippingRankSum=0.000;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.94;MQRankSum=-4.418;QD=12.70;ReadPosRankSum=-2.686;SOR=0.515 GT:AD:DP:GQ:PL 0/1:15,9:24:99:333,0,603 +20 10099055 . T C 256.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-1.554;AS_FS=0.000;AS_MQ=29.12;AS_MQRankSum=-4.316;AS_ReadPosRankSum=-2.131;AS_SOR=0.665;BaseQRankSum=-1.554;ClippingRankSum=0.000;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.46;MQRankSum=-4.316;QD=11.16;ReadPosRankSum=-2.131;SOR=0.665 GT:AD:DP:GQ:PL 0/1:15,8:23:99:285,0,673 +20 10099079 . C T 116.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=1.434;AS_FS=1.862;AS_MQ=37.61;AS_MQRankSum=-2.821;AS_ReadPosRankSum=1.966;AS_SOR=1.289;BaseQRankSum=1.434;ClippingRankSum=0.000;DP=29;ExcessHet=3.0103;FS=1.862;MLEAC=1;MLEAF=0.500;MQ=52.09;MQRankSum=-2.821;QD=4.03;ReadPosRankSum=1.966;SOR=1.289 GT:AD:DP:GQ:PL 0/1:23,6:29:99:145,0,886 +20 10099111 . T TTTTGTTTG 656.73 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-1.207;AS_FS=0.000;AS_MQ=34.74;AS_MQRankSum=-4.071;AS_ReadPosRankSum=-0.120;AS_SOR=0.511;BaseQRankSum=-1.207;ClippingRankSum=0.000;DP=42;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.12;MQRankSum=-4.071;QD=18.76;ReadPosRankSum=-0.120;SOR=0.511 GT:AD:DP:GQ:PL 0/1:22,13:35:99:694,0,802 +20 10099140 . G T 1005.77 . AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-0.114;AS_FS=2.241;AS_MQ=51.39;AS_MQRankSum=-2.469;AS_ReadPosRankSum=0.169;AS_SOR=1.114;BaseQRankSum=-0.114;ClippingRankSum=0.000;DP=62;ExcessHet=3.0103;FS=2.241;MLEAC=1;MLEAF=0.500;MQ=55.72;MQRankSum=-2.469;QD=16.22;ReadPosRankSum=0.169;SOR=1.114 GT:AD:DP:GQ:PL 0/1:30,32:62:99:1034,0,931 +20 10099190 . G T 1034.77 . 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AC=2;AF=1.00;AN=2;AS_MQ;DP=57;ExcessHet=3.0103;FS=0.000;MQ=59.60;QD=26.86;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,57:55:99:2243,165,0 +20 10005499 . A G 3053.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=76;ExcessHet=3.0103;FS=0.000;MQ=60.00;QD=30.35;SOR=1.121 GT:AD:DP:GQ:PL 1/1:0,76:76:99:3082,229,0 +20 10005587 . A G 1229.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-0.834;DP=74;ExcessHet=3.0103;FS=1.955;MQ=59.12;MQRankSum=-0.972;QD=16.85;ReadPosRankSum=0.259;SOR=0.848 GT:AD:DP:GQ:PL 0/1:36,37:72:99:1258,0,1236 +20 10005723 . A G 3062.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=87;ExcessHet=3.0103;FS=0.000;MQ=59.52;QD=30.97;SOR=0.972 GT:AD:DP:GQ:PL 1/1:0,87:86:99:3091,258,0 +20 10006291 . G A 978.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=0.311;DP=85;ExcessHet=3.0103;FS=0.853;MQ=59.29;MQRankSum=-1.081;QD=11.51;ReadPosRankSum=-1.363;SOR=0.659 GT:AD:DP:GQ:PL 0/1:54,31:84:99:1007,0,1905 +20 10006404 . A C 2928.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=79;ExcessHet=3.0103;FS=0.000;MQ=59.18;QD=29.43;SOR=1.358 GT:AD:DP:GQ:PL 1/1:0,79:76:99:2957,228,0 +20 10006682 . T A 2874.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=76;ExcessHet=3.0103;FS=0.000;MQ=59.14;QD=28.18;SOR=1.209 GT:AD:DP:GQ:PL 1/1:0,75:73:99:2903,219,0 +20 10006819 . AAAAC A 2531.73 . AC=2;AF=1.00;AN=2;AS_MQ;DP=78;ExcessHet=3.0103;MQ=60.57;QD=32.46 GT:AD:DP:GQ:PL 1/1:0,0:58:99:2569,176,0 +20 10007150 . G C 669.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-4.476;DP=64;ExcessHet=3.0103;FS=5.048;MQ=60.00;MQRankSum=0.000;QD=10.47;ReadPosRankSum=-1.047;SOR=0.746 GT:AD:DP:GQ:PL 0/1:38,26:63:99:698,0,1479 +20 10007175 . C T 1350.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=2.249;DP=63;ExcessHet=3.0103;FS=2.211;MQ=59.63;MQRankSum=1.319;QD=21.44;ReadPosRankSum=-0.313;SOR=0.434 GT:AD:DP:GQ:PL 0/1:24,39:61:99:1379,0,780 +20 10007352 . C T 2764.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=71;ExcessHet=3.0103;FS=0.000;MQ=59.35;QD=28.32;SOR=1.054 GT:AD:DP:GQ:PL 1/1:0,71:69:99:2793,208,0 +20 10007531 . A G 2920.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=73;ExcessHet=3.0103;FS=0.000;MQ=59.36;QD=29.65;SOR=1.577 GT:AD:DP:GQ:PL 1/1:0,73:72:99:2949,217,0 +20 10007980 . A C 3524.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=93;ExcessHet=3.0103;FS=0.000;MQ=60.11;QD=35.03;SOR=1.038 GT:AD:DP:GQ:PL 1/1:0,93:90:99:3553,270,0 +20 10008029 . T TA 1986.73 . AC=2;AF=1.00;AN=2;AS_MQ;DP=89;ExcessHet=3.0103;MQ=60.92;QD=22.32 GT:AD:DP:GQ:PL 1/1:0,0:75:99:2024,145,0 +20 10008146 . TA T 2141.73 . AC=2;AF=1.00;AN=2;AS_MQ;DP=74;ExcessHet=3.0103;MQ=60.27;QD=28.94 GT:AD:DP:GQ:PL 1/1:0,0:70:99:2179,211,0 +20 10008221 . T C 3224.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=80;ExcessHet=3.0103;FS=0.000;MQ=60.17;QD=25.82;SOR=0.850 GT:AD:DP:GQ:PL 1/1:0,80:80:99:3253,240,0 +20 10008458 . T G 2654.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=73;ExcessHet=3.0103;FS=0.000;MQ=52.14;QD=32.17;SOR=1.002 GT:AD:DP:GQ:PL 1/1:0,73:69:99:2683,207,0 +20 10008742 . G T 715.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=3.649;DP=55;ExcessHet=3.0103;FS=0.000;MQ=36.14;MQRankSum=-1.453;QD=13.01;ReadPosRankSum=0.554;SOR=0.709 GT:AD:DP:GQ:PL 0/1:25,30:49:99:744,0,580 +20 10008758 . C CA 684.14 . AC=2;AF=1.00;AN=2;AS_MQ;DP=54;ExcessHet=3.0103;MQ=34.98;QD=12.67 GT:AD:DP:GQ:PL 1/1:0,0:35:10:721,10,0 +20 10008921 . C CA 253.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=52;ExcessHet=3.0103;MQ=56.17;QD=4.88 GT:AD:DP:GQ:PL 0/1:0,0:34:99:291,0,366 +20 10008948 . TA T 2057.73 . AC=2;AF=1.00;AN=2;AS_MQ;DP=53;ExcessHet=3.0103;MQ=51.20;QD=32.77 GT:AD:DP:GQ:PL 1/1:0,0:51:99:2095,107,0 +20 10008952 . CACACACACACA C,CCACACACACA 1666.73 . AC=1,1;AF=0.500,0.500;AN=2;AS_MQ;DP=52;ExcessHet=3.0103;MQ=50.48;QD=32.05 GT:AD:DP:GQ:PL 1/2:0,0,0:36:99:1704,525,844,582,0,531 +20 10009227 . A G 1369.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-2.220;DP=63;ExcessHet=3.0103;FS=9.110;MQ=56.90;MQRankSum=1.428;QD=21.74;ReadPosRankSum=-1.210;SOR=0.281 GT:AD:DP:GQ:PL 0/1:24,39:62:99:1398,0,740 +20 10009246 . A G 3002.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=77;ExcessHet=3.0103;FS=0.000;MQ=56.09;QD=30.77;SOR=0.887 GT:AD:DP:GQ:PL 1/1:0,77:77:99:3031,231,0 +20 10009400 . T A 2998.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=74;ExcessHet=3.0103;FS=0.000;MQ=60.00;QD=28.07;SOR=0.804 GT:AD:DP:GQ:PL 1/1:0,74:74:99:3027,223,0 +20 10009512 . C G 3039.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=77;ExcessHet=3.0103;FS=0.000;MQ=58.47;QD=27.93;SOR=1.223 GT:AD:DP:GQ:PL 1/1:0,77:77:99:3068,231,0 +20 10009719 . A G 1895.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=64;ExcessHet=3.0103;FS=0.000;MQ=59.35;QD=29.62;SOR=0.986 GT:AD:DP:GQ:PL 1/1:0,64:59:99:1924,175,0 +20 10009795 . A G 1880.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=47;ExcessHet=3.0103;FS=0.000;MQ=59.60;QD=25.91;SOR=1.514 GT:AD:DP:GQ:PL 1/1:0,47:47:99:1909,141,0 +20 10009842 . G GAA 532.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=57;ExcessHet=3.0103;MQ=52.14;QD=9.35 GT:AD:DP:GQ:PL 0/1:0,0:34:99:570,0,690 +20 10009844 . G A 661.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=2.612;DP=57;ExcessHet=3.0103;FS=0.000;MQ=52.14;MQRankSum=4.782;QD=11.61;ReadPosRankSum=2.939;SOR=0.544 GT:AD:DP:GQ:PL 0/1:10,47:35:99:690,0,586 +20 10009871 . A G 658.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-1.969;DP=61;ExcessHet=3.0103;FS=4.140;MQ=50.95;MQRankSum=2.062;QD=10.80;ReadPosRankSum=0.479;SOR=1.445 GT:AD:DP:GQ:PL 0/1:20,41:36:99:687,0,594 +20 10009875 . A G,AGGGAGG 2369.73 . AC=1,1;AF=0.500,0.500;AN=2;AS_MQ;BaseQRankSum=0.473;DP=59;ExcessHet=3.0103;MQ=50.61;MQRankSum=1.097;QD=26.83;ReadPosRankSum=0.565 GT:AD:DP:GQ:PL 1/2:0,0,0:30:99:2407,645,533,697,0,574 +20 10009879 . A G 2244.77 . AC=2;AF=1.00;AN=2;AS_MQ;BaseQRankSum=0.680;DP=52;ExcessHet=3.0103;FS=0.000;MQ=51.08;MQRankSum=1.014;QD=30.42;ReadPosRankSum=2.106;SOR=0.841 GT:AD:DP:GQ:PL 1/1:5,47:49:99:2273,150,0 +20 10009883 . A G 2151.77 . AC=2;AF=1.00;AN=2;AS_MQ;BaseQRankSum=-0.492;DP=52;ExcessHet=3.0103;FS=2.730;MQ=51.84;MQRankSum=1.835;QD=24.50;ReadPosRankSum=1.408;SOR=1.755 GT:AD:DP:GQ:PL 1/1:2,50:47:99:2180,147,0 +20 10010393 . T G 1464.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-3.075;DP=80;ExcessHet=3.0103;FS=11.600;MQ=59.42;MQRankSum=-1.302;QD=18.31;ReadPosRankSum=-1.781;SOR=0.595 GT:AD:DP:GQ:PL 0/1:37,43:79:99:1493,0,1230 +20 10010536 . G GA 2462.73 . AC=2;AF=1.00;AN=2;AS_MQ;DP=85;ExcessHet=3.0103;MQ=61.63;QD=28.97 GT:AD:DP:GQ:PL 1/1:0,0:79:99:2500,243,0 +20 10010766 . T G 2411.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=68;ExcessHet=3.0103;FS=0.000;MQ=59.66;QD=29.65;SOR=0.818 GT:AD:DP:GQ:PL 1/1:0,67:66:99:2440,199,0 +20 10010832 . T C 2951.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=75;ExcessHet=3.0103;FS=0.000;MQ=59.50;QD=34.02;SOR=1.091 GT:AD:DP:GQ:PL 1/1:0,75:75:99:2980,226,0 +20 10011075 . C T 1325.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=5.459;DP=86;ExcessHet=3.0103;FS=0.000;MQ=59.73;MQRankSum=0.956;QD=15.42;ReadPosRankSum=-0.845;SOR=0.902 GT:AD:DP:GQ:PL 0/1:46,40:83:99:1354,0,1333 +20 10011309 . T C 2692.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=78;ExcessHet=3.0103;FS=0.000;MQ=60.00;QD=34.52;SOR=1.223 GT:AD:DP:GQ:PL 1/1:0,78:77:99:2721,231,0 +20 10011517 . GA G 490.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=91;ExcessHet=3.0103;MQ=59.90;QD=5.39 GT:AD:DP:GQ:PL 0/1:0,0:76:99:528,0,875 +20 10011666 . C T 2961.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=73;ExcessHet=3.0103;FS=0.000;MQ=59.05;QD=28.35;SOR=1.103 GT:AD:DP:GQ:PL 1/1:0,73:73:99:2990,220,0 +20 10011939 . C T 2513.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=67;ExcessHet=3.0103;FS=0.000;MQ=54.89;QD=28.36;SOR=1.249 GT:AD:DP:GQ:PL 1/1:0,67:62:99:2542,187,0 +20 10012021 . CA C 1975.73 . AC=2;AF=1.00;AN=2;AS_MQ;DP=71;ExcessHet=3.0103;MQ=56.69;QD=27.83 GT:AD:DP:GQ:PL 1/1:0,0:66:99:2013,198,0 +20 10012362 . G T 835.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=26;ExcessHet=3.0103;FS=0.000;MQ=50.82;QD=32.14;SOR=3.611 GT:AD:DP:GQ:PL 1/1:0,26:23:69:864,69,0 +20 10012384 . T C 229.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-1.508;DP=21;ExcessHet=3.0103;FS=10.620;MQ=50.02;MQRankSum=-0.708;QD=10.94;ReadPosRankSum=0.799;SOR=0.021 GT:AD:DP:GQ:PL 0/1:12,9:18:99:258,0,355 +20 10012387 . T C 533.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=19;ExcessHet=3.0103;FS=0.000;MQ=48.85;QD=28.09;SOR=2.712 GT:AD:DP:GQ:PL 1/1:0,19:16:50:562,50,0 +20 10012479 . A G 592.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=22;ExcessHet=3.0103;FS=0.000;MQ=47.06;QD=26.94;SOR=0.784 GT:AD:DP:GQ:PL 1/1:0,22:17:50:621,50,0 +20 10012498 . C G 466.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=15;ExcessHet=3.0103;FS=0.000;MQ=39.11;QD=31.12;SOR=1.473 GT:AD:DP:GQ:PL 1/1:0,15:11:33:495,33,0 +20 10012518 . T C 406.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=16;ExcessHet=3.0103;FS=0.000;MQ=33.28;QD=25.42;SOR=1.244 GT:AD:DP:GQ:PL 1/1:0,16:9:30:435,30,0 +20 10012521 . C T 46.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=0.751;DP=18;ExcessHet=3.0103;FS=0.000;MQ=34.81;MQRankSum=-0.392;QD=2.60;ReadPosRankSum=1.267;SOR=0.446 GT:AD:DP:GQ:PL 0/1:12,6:11:75:75,0,224 +20 10012570 . G GCA 457.73 . AC=2;AF=1.00;AN=2;AS_MQ;DP=13;ExcessHet=3.0103;MQ=32.18;QD=33.10 GT:AD:DP:GQ:PL 1/1:0,0:9:33:495,33,0 +20 10012572 . GT G 457.73 . AC=2;AF=1.00;AN=2;AS_MQ;DP=12;ExcessHet=3.0103;MQ=35.80;QD=30.82 GT:AD:DP:GQ:PL 1/1:0,0:11:33:495,33,0 +20 10012631 . C CG 484.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=28;ExcessHet=3.0103;MQ=42.71;QD=17.31 GT:AD:DP:GQ:PL 0/1:0,0:21:99:522,0,297 +20 10012636 . G C 527.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=2.490;DP=29;ExcessHet=3.0103;FS=5.798;MQ=42.87;MQRankSum=-1.693;QD=18.20;ReadPosRankSum=-1.053;SOR=0.075 GT:AD:DP:GQ:PL 0/1:11,18:22:99:556,0,294 +20 10012714 . G C 1300.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=37;ExcessHet=3.0103;FS=0.000;MQ=51.65;QD=30.58;SOR=2.712 GT:AD:DP:GQ:PL 1/1:0,37:35:99:1329,105,0 +20 10012751 . T C 937.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=33;ExcessHet=3.0103;FS=0.000;MQ=50.30;QD=28.42;SOR=0.756 GT:AD:DP:GQ:PL 1/1:0,33:30:89:966,89,0 +20 10013119 . C T 1011.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=2.704;DP=62;ExcessHet=3.0103;FS=2.182;MQ=50.57;MQRankSum=-0.979;QD=16.32;ReadPosRankSum=0.455;SOR=0.418 GT:AD:DP:GQ:PL 0/1:31,31:59:99:1040,0,936 +20 10013574 . G A 1050.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=3.309;DP=72;ExcessHet=3.0103;FS=4.921;MQ=57.45;MQRankSum=-0.578;QD=14.59;ReadPosRankSum=1.159;SOR=1.329 GT:AD:DP:GQ:PL 0/1:39,33:69:99:1079,0,1301 +20 10014990 . C CAT 1237.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=88;ExcessHet=3.0103;MQ=60.44;QD=14.07 GT:AD:DP:GQ:PL 0/1:0,0:76:99:1275,0,1248 +20 10015679 . C T 140.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-0.258;DP=13;ExcessHet=3.0103;FS=0.000;MQ=60.00;MQRankSum=0.000;QD=10.83;ReadPosRankSum=0.784;SOR=0.859 GT:AD:DP:GQ:PL 0/1:7,6:10:99:169,0,166 +20 10015761 . T C 344.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-1.982;DP=22;ExcessHet=3.0103;FS=0.000;MQ=58.95;MQRankSum=1.294;QD=15.67;ReadPosRankSum=1.537;SOR=0.352 GT:AD:DP:GQ:PL 0/1:9,13:22:99:373,0,284 +20 10018158 . G C 1639.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=5.213;DP=90;ExcessHet=3.0103;FS=0.000;MQ=59.79;MQRankSum=1.118;QD=18.42;ReadPosRankSum=0.784;SOR=0.834 GT:AD:DP:GQ:PL 0/1:41,48:88:99:1668,0,1165 +20 10018555 . G A 1567.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-0.755;DP=82;ExcessHet=3.0103;FS=4.291;MQ=60.00;MQRankSum=0.000;QD=19.12;ReadPosRankSum=0.590;SOR=0.599 GT:AD:DP:GQ:PL 0/1:36,46:80:99:1596,0,1211 +20 10019093 . A G 1244.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=0.659;DP=70;ExcessHet=3.0103;FS=0.909;MQ=59.34;MQRankSum=1.486;QD=17.78;ReadPosRankSum=-0.259;SOR=0.711 GT:AD:DP:GQ:PL 0/1:34,36:69:99:1273,0,1104 +20 10020229 . G A 1538.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=6.050;DP=86;ExcessHet=3.0103;FS=0.000;MQ=58.97;MQRankSum=1.140;QD=17.89;ReadPosRankSum=-0.405;SOR=0.536 GT:AD:DP:GQ:PL 0/1:40,46:82:99:1567,0,1130 +20 10023689 . G A 1852.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=2.195;DP=84;ExcessHet=3.0103;FS=0.000;MQ=58.89;MQRankSum=1.843;QD=22.06;ReadPosRankSum=0.976;SOR=0.671 GT:AD:DP:GQ:PL 0/1:32,52:80:99:1881,0,946 +20 10024107 . C T 1694.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=5.641;DP=87;ExcessHet=3.0103;FS=0.000;MQ=59.42;MQRankSum=-1.546;QD=19.48;ReadPosRankSum=0.135;SOR=0.823 GT:AD:DP:GQ:PL 0/1:38,49:86:99:1723,0,1086 +20 10024300 . C CTT 87.76 . AC=1;AF=0.500;AN=2;AS_MQ;DP=71;ExcessHet=3.0103;MQ=46.76;QD=1.24 GT:AD:DP:GQ:PL 0/1:0,0:17:99:103,0,137 +20 10026357 . T C 1166.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-1.700;DP=63;ExcessHet=3.0103;FS=8.911;MQ=58.43;MQRankSum=-0.148;QD=18.52;ReadPosRankSum=-0.076;SOR=0.722 GT:AD:DP:GQ:PL 0/1:28,35:63:99:1195,0,932 +20 10026794 . C T 1084.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=2.828;DP=53;ExcessHet=3.0103;FS=2.399;MQ=59.56;MQRankSum=-0.719;QD=20.86;ReadPosRankSum=-0.533;SOR=0.428 GT:AD:DP:GQ:PL 0/1:19,33:52:99:1113,0,529 +20 10027234 . A ATTAG 1320.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=73;ExcessHet=3.0103;MQ=57.21;QD=18.09 GT:AD:DP:GQ:PL 0/1:0,0:69:99:1358,0,1964 +20 10027868 . A G 1739.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-5.563;DP=89;ExcessHet=3.0103;FS=6.868;MQ=59.48;MQRankSum=0.032;QD=19.55;ReadPosRankSum=1.704;SOR=0.881 GT:AD:DP:GQ:PL 0/1:44,45:89:99:1768,0,3201 +20 10027872 . A G 1724.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-5.491;DP=85;ExcessHet=3.0103;FS=8.870;MQ=59.46;MQRankSum=0.101;QD=20.29;ReadPosRankSum=0.837;SOR=0.826 GT:AD:DP:GQ:PL 0/1:40,45:85:99:1753,0,3136 +20 10028867 . A ATG 1106.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=96;ExcessHet=3.0103;MQ=59.58;QD=11.53 GT:AD:DP:GQ:PL 0/1:0,0:71:99:1144,0,916 +20 10030188 . T A 1372.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=0.711;DP=82;ExcessHet=3.0103;FS=9.186;MQ=59.44;MQRankSum=-1.013;QD=16.74;ReadPosRankSum=-0.884;SOR=1.105 GT:AD:DP:GQ:PL 0/1:42,40:81:99:1401,0,1524 +20 10031254 . A AT 1463.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=90;ExcessHet=3.0103;MQ=59.09;QD=16.26 GT:AD:DP:GQ:PL 0/1:0,0:85:99:1501,0,1159 +20 10031342 . G A 1834.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=1.833;DP=93;ExcessHet=3.0103;FS=1.714;MQ=59.75;MQRankSum=-0.866;QD=19.73;ReadPosRankSum=-0.240;SOR=0.955 GT:AD:DP:GQ:PL 0/1:41,52:93:99:1863,0,1375 +20 10031798 . G A 4296.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=105;ExcessHet=3.0103;FS=0.000;MQ=59.60;QD=28.92;SOR=0.876 GT:AD:DP:GQ:PL 1/1:0,105:104:99:4325,313,0 +20 10031827 . C T 2004.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=3.552;DP=108;ExcessHet=3.0103;FS=4.729;MQ=59.83;MQRankSum=-0.945;QD=18.56;ReadPosRankSum=-1.430;SOR=0.382 GT:AD:DP:GQ:PL 0/1:52,56:108:99:2033,0,1798 +20 10032094 . G A 1220.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=5.488;DP=83;ExcessHet=3.0103;FS=6.039;MQ=60.00;MQRankSum=0.000;QD=14.71;ReadPosRankSum=-0.579;SOR=0.260 GT:AD:DP:GQ:PL 0/1:47,36:83:99:1249,0,1497 +20 10032413 . T G 869.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-6.142;DP=66;ExcessHet=3.0103;FS=10.444;MQ=59.43;MQRankSum=-0.065;QD=13.18;ReadPosRankSum=-0.945;SOR=1.293 GT:AD:DP:GQ:PL 0/1:35,31:66:99:898,0,1277 +20 10032882 . A T 1202.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-3.697;DP=76;ExcessHet=3.0103;FS=4.673;MQ=59.39;MQRankSum=-1.014;QD=16.04;ReadPosRankSum=0.594;SOR=0.338 GT:AD:DP:GQ:PL 0/1:39,36:75:99:1231,0,1406 +20 10032972 . C CAT 1122.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=66;ExcessHet=3.0103;MQ=59.39;QD=17.01 GT:AD:DP:GQ:PL 0/1:0,0:63:99:1160,0,1477 +20 10034306 . T C 782.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-3.975;DP=80;ExcessHet=3.0103;FS=0.000;MQ=58.84;MQRankSum=-0.432;QD=9.91;ReadPosRankSum=0.437;SOR=0.681 GT:AD:DP:GQ:PL 0/1:48,31:75:99:811,0,1593 +20 10036930 . CGATAGCCCTAGCCCTAGATA C 1036.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=79;ExcessHet=3.0103;MQ=53.30;QD=13.12 GT:AD:DP:GQ:PL 0/1:0,0:68:99:1074,0,5569 +20 10037037 . C T 1436.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=3.504;DP=82;ExcessHet=3.0103;FS=1.943;MQ=60.17;MQRankSum=-1.193;QD=17.52;ReadPosRankSum=-1.504;SOR=0.495 GT:AD:DP:GQ:PL 0/1:40,42:81:99:1465,0,1124 +20 10037110 . T TGATA 2780.73 . AC=2;AF=1.00;AN=2;AS_MQ;DP=87;ExcessHet=3.0103;MQ=53.47;QD=31.96 GT:AD:DP:GQ:PL 1/1:0,0:61:99:2818,189,0 +20 10037144 . T TGATAGATA 1823.73 . AC=2;AF=1.00;AN=2;AS_MQ;DP=75;ExcessHet=3.0103;MQ=50.22;QD=24.32 GT:AD:DP:GQ:PL 1/1:0,0:36:99:1861,127,0 +20 10037709 . A T 1003.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-2.367;DP=71;ExcessHet=3.0103;FS=0.000;MQ=59.68;MQRankSum=0.934;QD=14.14;ReadPosRankSum=0.330;SOR=0.608 GT:AD:DP:GQ:PL 0/1:39,32:71:99:1032,0,1354 +20 10039371 . T G 1324.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-3.137;DP=76;ExcessHet=3.0103;FS=6.144;MQ=59.39;MQRankSum=-0.884;QD=17.43;ReadPosRankSum=0.676;SOR=1.092 GT:AD:DP:GQ:PL 0/1:34,42:74:99:1353,0,1194 +20 10040772 . C CT 1995.73 . AC=2;AF=1.00;AN=2;AS_MQ;DP=80;ExcessHet=3.0103;MQ=51.46;QD=24.95 GT:AD:DP:GQ:PL 1/1:0,0:70:99:2033,210,0 +20 10040812 . AT A 2607.73 . AC=2;AF=1.00;AN=2;AS_MQ;DP=83;ExcessHet=3.0103;MQ=49.83;QD=31.42 GT:AD:DP:GQ:PL 1/1:0,0:71:99:2645,214,0 +20 10040821 . T A 1171.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-0.131;DP=80;ExcessHet=3.0103;FS=0.856;MQ=50.17;MQRankSum=0.220;QD=15.02;ReadPosRankSum=-1.489;SOR=0.843 GT:AD:DP:GQ:PL 0/1:38,40:78:99:1200,0,1099 +20 10041304 . C T 2765.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=71;ExcessHet=3.0103;FS=0.000;MQ=59.41;QD=34.62;SOR=0.779 GT:AD:DP:GQ:PL 1/1:0,71:68:99:2794,204,0 +20 10041701 . A ATATG 1403.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=80;ExcessHet=3.0103;MQ=58.50;QD=17.55 GT:AD:DP:GQ:PL 0/1:0,0:58:58:1441,0,58 +20 10042319 . C T 2658.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=67;ExcessHet=3.0103;FS=0.000;MQ=58.61;QD=33.23;SOR=1.066 GT:AD:DP:GQ:PL 1/1:0,67:66:99:2687,199,0 +20 10042761 . A G 3553.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=93;ExcessHet=3.0103;FS=0.000;MQ=59.70;QD=26.88;SOR=1.414 GT:AD:DP:GQ:PL 1/1:0,93:91:99:3582,272,0 +20 10042829 . A G 3055.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=80;ExcessHet=3.0103;FS=0.000;MQ=59.42;QD=29.64;SOR=0.881 GT:AD:DP:GQ:PL 1/1:0,80:78:99:3084,235,0 +20 10043002 . A T 1287.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=3.986;DP=86;ExcessHet=3.0103;FS=2.877;MQ=60.00;MQRankSum=0.000;QD=14.97;ReadPosRankSum=-0.209;SOR=0.434 GT:AD:DP:GQ:PL 0/1:48,38:86:99:1316,0,1659 +20 10044849 . A G 2091.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=60;ExcessHet=3.0103;FS=0.000;MQ=59.62;QD=34.86;SOR=1.316 GT:AD:DP:GQ:PL 1/1:0,60:59:99:2120,177,0 +20 10045078 . G T 3271.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=82;ExcessHet=3.0103;FS=0.000;MQ=58.46;QD=31.35;SOR=0.846 GT:AD:DP:GQ:PL 1/1:0,82:81:99:3300,244,0 +20 10045642 . G C 3138.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=82;ExcessHet=3.0103;FS=0.000;MQ=59.49;QD=28.92;SOR=0.846 GT:AD:DP:GQ:PL 1/1:0,82:82:99:3167,246,0 +20 10046178 . AAGAAAGAAAG A 2159.73 . AC=2;AF=1.00;AN=2;AS_MQ;DP=64;ExcessHet=3.0103;MQ=47.11;QD=33.75 GT:AD:DP:GQ:PL 1/1:0,0:50:99:2197,153,0 +20 10046537 . A G 819.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-4.028;DP=59;ExcessHet=3.0103;FS=3.724;MQ=54.18;MQRankSum=0.542;QD=13.89;ReadPosRankSum=0.592;SOR=1.332 GT:AD:DP:GQ:PL 0/1:29,30:57:99:848,0,902 +20 10050828 . T C 1227.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-2.855;DP=88;ExcessHet=3.0103;FS=1.739;MQ=59.48;MQRankSum=1.256;QD=13.95;ReadPosRankSum=0.004;SOR=0.488 GT:AD:DP:GQ:PL 0/1:50,38:86:99:1256,0,1768 +20 10051448 . T C 1134.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-0.289;DP=71;ExcessHet=3.0103;FS=3.871;MQ=59.41;MQRankSum=-1.424;QD=15.98;ReadPosRankSum=-0.719;SOR=0.284 GT:AD:DP:GQ:PL 0/1:36,35:70:99:1163,0,1150 +20 10052688 . C A 1062.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=0.180;DP=77;ExcessHet=3.0103;FS=3.135;MQ=59.76;MQRankSum=0.870;QD=13.80;ReadPosRankSum=1.412;SOR=0.379 GT:AD:DP:GQ:PL 0/1:45,32:77:99:1091,0,1645 +20 10058022 . T C 975.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-2.105;DP=73;ExcessHet=3.0103;FS=0.000;MQ=57.81;MQRankSum=0.931;QD=13.37;ReadPosRankSum=0.039;SOR=0.579 GT:AD:DP:GQ:PL 0/1:39,34:68:99:1004,0,1261 +20 10062935 . C CA 92.84 . AC=1;AF=0.500;AN=2;AS_MQ;DP=67;ExcessHet=3.0103;MQ=52.53;QD=1.39 GT:AD:DP:GQ:PL 0/1:0,0:23:99:130,0,101 +20 10067049 . TAAAAAAAA T,TA 614.73 . AC=1,1;AF=0.500,0.500;AN=2;AS_MQ;DP=54;ExcessHet=3.0103;MQ=52.36;QD=11.38 GT:AD:DP:GQ:PL 1/2:0,0,0:22:99:652,164,339,135,0,106 +20 10067090 . C A 2004.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=58;ExcessHet=3.0103;FS=0.000;MQ=53.81;QD=34.57;SOR=0.767 GT:AD:DP:GQ:PL 1/1:1,57:55:99:2033,164,0 +20 10067264 . G A 2922.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=76;ExcessHet=3.0103;FS=0.000;MQ=59.39;QD=29.91;SOR=0.801 GT:AD:DP:GQ:PL 1/1:0,76:73:99:2951,219,0 +20 10067722 . A C 2146.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=54;ExcessHet=3.0103;FS=0.000;MQ=60.00;QD=26.34;SOR=0.846 GT:AD:DP:GQ:PL 1/1:0,54:54:99:2175,163,0 +20 10068158 . GTGTATATATATA G 66.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=27;ExcessHet=3.0103;MQ=57.39;QD=2.47 GT:AD:DP:GQ:PL 0/1:0,0:7:57:104,0,57 +20 10068981 . G A 2503.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=64;ExcessHet=3.0103;FS=0.000;MQ=59.20;QD=31.37;SOR=0.899 GT:AD:DP:GQ:PL 1/1:0,64:61:99:2532,184,0 +20 10070602 . T C 2691.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=73;ExcessHet=3.0103;FS=0.000;MQ=58.73;QD=33.28;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,73:72:99:2720,216,0 +20 10070936 . T A 3631.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=85;ExcessHet=3.0103;FS=0.000;MQ=57.98;QD=30.73;SOR=0.897 GT:AD:DP:GQ:PL 1/1:0,85:81:99:3660,247,0 +20 10070938 . G GA 3656.73 . AC=2;AF=1.00;AN=2;AS_MQ;DP=84;ExcessHet=3.0103;MQ=58.09;QD=24.88 GT:AD:DP:GQ:PL 1/1:0,0:79:99:3694,250,0 +20 10071135 . C T 3257.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=80;ExcessHet=3.0103;FS=0.000;MQ=59.13;QD=30.99;SOR=1.031 GT:AD:DP:GQ:PL 1/1:0,80:79:99:3286,238,0 +20 10071187 . G A 3410.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=84;ExcessHet=3.0103;FS=0.000;MQ=59.73;QD=28.90;SOR=1.395 GT:AD:DP:GQ:PL 1/1:0,84:82:99:3439,246,0 +20 10071890 . T C 1974.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=57;ExcessHet=3.0103;FS=0.000;MQ=59.67;QD=34.65;SOR=0.728 GT:AD:DP:GQ:PL 1/1:0,57:57:99:2003,171,0 +20 10072505 . A G 2099.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=66;ExcessHet=3.0103;FS=0.000;MQ=59.58;QD=31.81;SOR=0.859 GT:AD:DP:GQ:PL 1/1:1,65:64:99:2128,191,0 +20 10074187 . A G 3101.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=79;ExcessHet=3.0103;FS=0.000;MQ=59.12;QD=31.47;SOR=0.881 GT:AD:DP:GQ:PL 1/1:0,79:79:99:3130,238,0 +20 10074240 . T C 3406.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=87;ExcessHet=3.0103;FS=0.000;MQ=59.79;QD=30.91;SOR=0.922 GT:AD:DP:GQ:PL 1/1:0,86:85:99:3435,255,0 +20 10074716 . G A 2400.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=68;ExcessHet=3.0103;FS=0.000;MQ=59.66;QD=28.90;SOR=1.341 GT:AD:DP:GQ:PL 1/1:0,68:64:99:2429,192,0 +20 10074806 . G A 2817.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=74;ExcessHet=3.0103;FS=0.000;MQ=59.37;QD=32.97;SOR=0.898 GT:AD:DP:GQ:PL 1/1:0,73:71:99:2846,213,0 +20 10075043 . T C 2405.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=63;ExcessHet=3.0103;FS=0.000;MQ=59.27;QD=28.56;SOR=1.143 GT:AD:DP:GQ:PL 1/1:0,63:61:99:2434,184,0 +20 10075168 . C T 3612.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=89;ExcessHet=3.0103;FS=0.000;MQ=59.10;QD=29.84;SOR=0.997 GT:AD:DP:GQ:PL 1/1:0,89:88:99:3641,264,0 +20 10075508 . GA G 1928.73 . AC=2;AF=1.00;AN=2;AS_MQ;DP=81;ExcessHet=3.0103;MQ=60.40;QD=23.81 GT:AD:DP:GQ:PL 1/1:0,0:70:99:1966,210,0 +20 10076250 . A G 1107.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-3.491;DP=80;ExcessHet=3.0103;FS=5.825;MQ=59.40;MQRankSum=-1.441;QD=13.85;ReadPosRankSum=-0.183;SOR=0.374 GT:AD:DP:GQ:PL 0/1:41,39:79:99:1136,0,1339 +20 10076339 . A G 1309.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=0.067;DP=73;ExcessHet=3.0103;FS=1.913;MQ=59.37;MQRankSum=0.157;QD=17.94;ReadPosRankSum=0.821;SOR=0.502 GT:AD:DP:GQ:PL 0/1:33,40:72:99:1338,0,1035 +20 10076399 . G A 1807.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=4.274;DP=95;ExcessHet=3.0103;FS=2.671;MQ=60.00;MQRankSum=0.000;QD=19.03;ReadPosRankSum=-0.951;SOR=0.920 GT:AD:DP:GQ:PL 0/1:45,50:94:99:1836,0,1544 +20 10076989 . CA C 221.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=72;ExcessHet=3.0103;MQ=57.32;QD=3.08 GT:AD:DP:GQ:PL 0/1:0,0:42:99:218,0,332 +20 10077752 . T C 1345.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-6.503;DP=79;ExcessHet=3.0103;FS=4.458;MQ=60.00;MQRankSum=0.000;QD=17.04;ReadPosRankSum=-0.367;SOR=1.251 GT:AD:DP:GQ:PL 0/1:34,45:79:99:1374,0,1187 +20 10079476 . T G 11.12 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-4.512;DP=52;ExcessHet=3.0103;FS=29.747;MQ=58.21;MQRankSum=-1.771;QD=0.21;ReadPosRankSum=-4.216;SOR=4.970 GT:AD:DP:GQ:PL 0/1:34,18:44:39:39,0,1137 +20 10081750 . C A 1353.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=2.670;DP=83;ExcessHet=3.0103;FS=0.824;MQ=60.00;MQRankSum=0.000;QD=16.31;ReadPosRankSum=-0.420;SOR=0.664 GT:AD:DP:GQ:PL 0/1:44,39:83:99:1382,0,1525 +20 10081800 . C T 1109.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=0.241;DP=70;ExcessHet=3.0103;FS=11.086;MQ=60.00;MQRankSum=0.000;QD=15.85;ReadPosRankSum=-2.449;SOR=0.143 GT:AD:DP:GQ:PL 0/1:36,34:68:99:1138,0,1222 +20 10082892 . C T 1712.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=44;ExcessHet=3.0103;FS=0.000;MQ=59.48;QD=31.04;SOR=0.883 GT:AD:DP:GQ:PL 1/1:0,44:44:99:1741,132,0 +20 10085211 . A T 1210.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-1.293;DP=77;ExcessHet=3.0103;FS=0.859;MQ=59.46;MQRankSum=-0.093;QD=15.72;ReadPosRankSum=-1.226;SOR=0.763 GT:AD:DP:GQ:PL 0/1:41,36:76:99:1239,0,1443 +20 10086110 . G A 1274.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-0.545;DP=84;ExcessHet=3.0103;FS=1.816;MQ=58.89;MQRankSum=-0.657;QD=15.18;ReadPosRankSum=0.172;SOR=0.555 GT:AD:DP:GQ:PL 0/1:44,40:81:99:1303,0,1506 +20 10086283 . G T 1025.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=2.379;DP=85;ExcessHet=3.0103;FS=1.827;MQ=60.00;MQRankSum=0.000;QD=12.07;ReadPosRankSum=2.071;SOR=0.481 GT:AD:DP:GQ:PL 0/1:52,33:84:99:1054,0,1771 +20 10086619 . T A 796.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=0.487;DP=74;ExcessHet=3.0103;FS=0.958;MQ=59.31;MQRankSum=-0.387;QD=10.77;ReadPosRankSum=0.340;SOR=0.933 GT:AD:DP:GQ:PL 0/1:47,27:70:99:825,0,1603 +20 10086853 . G A 1002.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=3.915;DP=77;ExcessHet=3.0103;FS=0.000;MQ=58.79;MQRankSum=-0.177;QD=13.02;ReadPosRankSum=-0.245;SOR=0.767 GT:AD:DP:GQ:PL 0/1:43,34:73:99:1031,0,1280 +20 10086954 . G A 1095.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=2.606;DP=69;ExcessHet=3.0103;FS=4.812;MQ=60.00;MQRankSum=0.000;QD=15.88;ReadPosRankSum=-0.657;SOR=1.185 GT:AD:DP:GQ:PL 0/1:34,35:68:99:1124,0,1051 +20 10087230 . A G 1842.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-2.407;DP=96;ExcessHet=3.0103;FS=3.860;MQ=58.88;MQRankSum=1.707;QD=19.20;ReadPosRankSum=0.484;SOR=0.960 GT:AD:DP:GQ:PL 0/1:42,54:96:99:1871,0,1428 +20 10087394 . T G 1688.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-2.437;DP=85;ExcessHet=3.0103;FS=5.504;MQ=59.73;MQRankSum=1.190;QD=19.87;ReadPosRankSum=0.983;SOR=0.410 GT:AD:DP:GQ:PL 0/1:36,49:84:99:1717,0,1186 +20 10087754 . T G 1347.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=0.054;DP=82;ExcessHet=3.0103;FS=0.000;MQ=60.38;MQRankSum=2.140;QD=16.64;ReadPosRankSum=-0.768;SOR=0.631 GT:AD:DP:GQ:PL 0/1:37,44:78:99:1376,0,1239 +20 10087804 . C T 1619.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=1.940;DP=102;ExcessHet=3.0103;FS=3.847;MQ=60.36;MQRankSum=2.618;QD=15.88;ReadPosRankSum=0.893;SOR=0.369 GT:AD:DP:GQ:PL 0/1:51,51:100:99:1648,0,1511 +20 10087820 . C CAG 428.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=96;ExcessHet=3.0103;MQ=60.31;QD=4.47 GT:AD:DP:GQ:PL 0/1:0,0:55:99:466,0,1169 +20 10088063 . C T 1417.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=3.214;DP=95;ExcessHet=3.0103;FS=3.915;MQ=59.17;MQRankSum=0.503;QD=14.92;ReadPosRankSum=0.662;SOR=1.080 GT:AD:DP:GQ:PL 0/1:51,44:93:99:1446,0,1403 +20 10088699 . C T 776.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=4.018;DP=69;ExcessHet=3.0103;FS=16.274;MQ=54.23;MQRankSum=-2.897;QD=11.26;ReadPosRankSum=-0.883;SOR=2.108 GT:AD:DP:GQ:PL 0/1:41,28:62:99:805,0,1088 +20 10088730 . G A 972.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-0.123;DP=59;ExcessHet=3.0103;FS=18.070;MQ=51.33;MQRankSum=-5.029;QD=17.07;ReadPosRankSum=0.399;SOR=1.798 GT:AD:DP:GQ:PL 0/1:30,27:52:99:1001,0,1152 +20 10088736 . A C 1081.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=0.079;DP=60;ExcessHet=3.0103;FS=9.416;MQ=50.85;MQRankSum=-5.075;QD=18.34;ReadPosRankSum=0.249;SOR=1.067 GT:AD:DP:GQ:PL 0/1:30,29:55:99:1110,0,1194 +20 10088747 . A G 1111.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-3.578;DP=56;ExcessHet=3.0103;FS=7.421;MQ=51.12;MQRankSum=-4.708;QD=19.85;ReadPosRankSum=-0.058;SOR=1.206 GT:AD:DP:GQ:PL 0/1:26,30:54:99:1140,0,995 +20 10088799 . G A 1018.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=5.675;DP=56;ExcessHet=3.0103;FS=10.098;MQ=52.08;MQRankSum=-1.830;QD=18.19;ReadPosRankSum=1.503;SOR=0.973 GT:AD:DP:GQ:PL 0/1:24,32:53:99:1047,0,617 +20 10088895 . C T 532.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=2.462;DP=43;ExcessHet=3.0103;FS=0.000;MQ=56.09;MQRankSum=0.577;QD=12.39;ReadPosRankSum=0.933;SOR=0.653 GT:AD:DP:GQ:PL 0/1:25,18:41:99:561,0,673 +20 10088968 . C CAAA 1175.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=71;ExcessHet=3.0103;MQ=52.38;QD=16.56 GT:AD:DP:GQ:PL 0/1:0,0:53:99:1213,0,1367 +20 10088980 . T C 1247.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-1.957;DP=82;ExcessHet=3.0103;FS=0.000;MQ=49.88;MQRankSum=-5.210;QD=17.09;ReadPosRankSum=1.103;SOR=0.699 GT:AD:DP:GQ:PL 0/1:39,34:68:99:1276,0,1627 +20 10088985 . T C 1178.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-0.612;DP=85;ExcessHet=3.0103;FS=0.831;MQ=49.54;MQRankSum=-5.309;QD=14.03;ReadPosRankSum=1.491;SOR=0.804 GT:AD:DP:GQ:PL 0/1:46,38:74:99:1207,0,1729 +20 10089441 . A G 1179.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-4.874;DP=79;ExcessHet=3.0103;FS=4.464;MQ=59.12;MQRankSum=-0.948;QD=15.13;ReadPosRankSum=-0.286;SOR=1.207 GT:AD:DP:GQ:PL 0/1:38,40:76:99:1208,0,1313 +20 10089525 . C T 1548.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=5.738;DP=85;ExcessHet=3.0103;FS=5.639;MQ=58.96;MQRankSum=0.160;QD=18.22;ReadPosRankSum=0.960;SOR=0.732 GT:AD:DP:GQ:PL 0/1:39,46:81:99:1577,0,1088 +20 10090289 . CA C 384.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=78;ExcessHet=3.0103;MQ=59.88;QD=4.93 GT:AD:DP:GQ:PL 0/1:0,0:38:99:422,0,230 +20 10090764 . A G 840.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-2.561;DP=65;ExcessHet=3.0103;FS=3.477;MQ=60.00;MQRankSum=0.000;QD=12.93;ReadPosRankSum=0.803;SOR=0.315 GT:AD:DP:GQ:PL 0/1:35,30:63:99:869,0,1207 +20 10090970 . T C 1257.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-0.297;DP=71;ExcessHet=3.0103;FS=0.898;MQ=59.47;MQRankSum=1.486;QD=17.72;ReadPosRankSum=-0.123;SOR=0.576 GT:AD:DP:GQ:PL 0/1:34,37:69:99:1286,0,1092 +20 10091214 . C T 1249.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=0.184;DP=76;ExcessHet=3.0103;FS=0.915;MQ=59.75;MQRankSum=-0.934;QD=16.44;ReadPosRankSum=-0.149;SOR=0.507 GT:AD:DP:GQ:PL 0/1:36,40:70:99:1278,0,1110 +20 10092415 . A G 1635.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-6.731;DP=102;ExcessHet=3.0103;FS=0.741;MQ=59.77;MQRankSum=0.000;QD=16.04;ReadPosRankSum=0.510;SOR=0.665 GT:AD:DP:GQ:PL 0/1:52,50:101:99:1664,0,1902 +20 10092927 . G T 106.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-2.507;DP=78;ExcessHet=3.0103;FS=49.604;MQ=59.11;MQRankSum=-3.009;QD=1.39;ReadPosRankSum=-3.684;SOR=5.279 GT:AD:DP:GQ:PL 0/1:61,16:72:99:135,0,1864 +20 10093568 . GT G 326.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=62;ExcessHet=3.0103;MQ=58.30;QD=5.27 GT:AD:DP:GQ:PL 0/1:0,0:43:99:364,0,386 +20 10093923 . T A 1075.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-0.667;DP=67;ExcessHet=3.0103;FS=0.924;MQ=59.19;MQRankSum=0.358;QD=16.06;ReadPosRankSum=-1.689;SOR=0.772 GT:AD:DP:GQ:PL 0/1:35,32:67:99:1104,0,1257 +20 10094251 . T A 1270.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=0.502;DP=64;ExcessHet=3.0103;FS=9.104;MQ=60.00;MQRankSum=0.000;QD=19.86;ReadPosRankSum=2.029;SOR=1.235 GT:AD:DP:GQ:PL 0/1:27,37:62:99:1299,0,781 +20 10094582 . A G 923.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-1.388;DP=70;ExcessHet=3.0103;FS=0.000;MQ=59.07;MQRankSum=1.270;QD=13.39;ReadPosRankSum=-0.151;SOR=0.772 GT:AD:DP:GQ:PL 0/1:39,30:69:99:952,0,1350 +20 10094774 . C T 1036.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-1.036;DP=78;ExcessHet=3.0103;FS=0.000;MQ=59.41;MQRankSum=-0.018;QD=13.29;ReadPosRankSum=0.620;SOR=0.525 GT:AD:DP:GQ:PL 0/1:40,38:75:99:1065,0,1282 +20 10095432 . GTGATGATGA G 839.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=76;ExcessHet=3.0103;MQ=53.88;QD=11.05 GT:AD:DP:GQ:PL 0/1:0,0:50:99:877,0,2108 +20 10095741 . A G 1075.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-0.346;DP=73;ExcessHet=3.0103;FS=4.611;MQ=57.10;MQRankSum=-2.354;QD=14.94;ReadPosRankSum=-0.081;SOR=0.550 GT:AD:DP:GQ:PL 0/1:37,35:70:99:1104,0,1233 +20 10096293 . C T 1355.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=4.580;DP=78;ExcessHet=3.0103;FS=0.000;MQ=58.62;MQRankSum=1.396;QD=17.38;ReadPosRankSum=-0.821;SOR=0.641 GT:AD:DP:GQ:PL 0/1:39,39:75:99:1384,0,1258 +20 10096596 . C T 1562.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=3.048;DP=87;ExcessHet=3.0103;FS=0.000;MQ=58.77;MQRankSum=0.612;QD=17.96;ReadPosRankSum=0.017;SOR=0.640 GT:AD:DP:GQ:PL 0/1:40,47:87:99:1591,0,1273 +20 10096768 . A C 1682.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-2.764;DP=91;ExcessHet=3.0103;FS=3.983;MQ=59.24;MQRankSum=-1.609;QD=18.49;ReadPosRankSum=0.526;SOR=0.445 GT:AD:DP:GQ:PL 0/1:42,49:91:99:1711,0,1452 +20 10096899 . G T 1614.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=2.809;DP=81;ExcessHet=3.0103;FS=7.745;MQ=59.25;MQRankSum=-0.541;QD=19.94;ReadPosRankSum=0.558;SOR=1.632 GT:AD:DP:GQ:PL 0/1:40,41:79:99:1643,0,1520 +20 10096905 . TA T 1600.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=84;ExcessHet=3.0103;MQ=59.00;QD=19.06 GT:AD:DP:GQ:PL 0/1:0,0:83:99:1638,0,1623 +20 10096933 . G C 1511.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-1.914;DP=88;ExcessHet=3.0103;FS=23.320;MQ=58.83;MQRankSum=-1.802;QD=17.38;ReadPosRankSum=0.264;SOR=1.534 GT:AD:DP:GQ:PL 0/1:46,41:85:99:1540,0,1770 +20 10096958 . G A 1766.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=2.968;DP=94;ExcessHet=3.0103;FS=16.484;MQ=58.91;MQRankSum=-0.962;QD=18.80;ReadPosRankSum=-1.953;SOR=1.400 GT:AD:DP:GQ:PL 0/1:47,47:92:99:1795,0,1629 +20 10097075 . T G 1445.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-2.641;DP=94;ExcessHet=3.0103;FS=5.232;MQ=58.35;MQRankSum=-1.604;QD=15.38;ReadPosRankSum=-0.200;SOR=0.566 GT:AD:DP:GQ:PL 0/1:45,49:92:99:1474,0,1482 +20 10097101 . C CTTT 1091.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=80;ExcessHet=3.0103;MQ=57.36;QD=13.65 GT:AD:DP:GQ:PL 0/1:0,0:66:99:1129,0,1306 +20 10097436 . CTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT C 1054.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=65;ExcessHet=3.0103;MQ=55.82;QD=16.23 GT:AD:DP:GQ:PL 0/1:0,0:89:99:1092,0,2241 +20 10097437 . TTTTC T 796.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=66;ExcessHet=3.0103;MQ=55.92;QD=12.07 GT:AD:DP:GQ:PL 0/1:0,0:55:99:834,0,1193 +20 10097626 . C A 626.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=1.128;DP=49;ExcessHet=3.0103;FS=2.701;MQ=58.28;MQRankSum=-1.371;QD=12.79;ReadPosRankSum=1.079;SOR=0.299 GT:AD:DP:GQ:PL 0/1:29,20:48:99:655,0,957 +20 10097789 . T C 688.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-1.396;DP=59;ExcessHet=3.0103;FS=5.374;MQ=58.02;MQRankSum=-2.744;QD=11.67;ReadPosRankSum=0.134;SOR=0.863 GT:AD:DP:GQ:PL 0/1:35,24:57:99:717,0,1190 +20 10097928 . G A 570.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-1.621;DP=39;ExcessHet=3.0103;FS=1.281;MQ=56.79;MQRankSum=-1.850;QD=14.64;ReadPosRankSum=-0.309;SOR=0.916 GT:AD:DP:GQ:PL 0/1:18,21:36:99:599,0,586 +20 10098110 . G C 586.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=2.510;DP=37;ExcessHet=3.0103;FS=6.658;MQ=58.11;MQRankSum=-1.477;QD=15.86;ReadPosRankSum=-0.714;SOR=0.069 GT:AD:DP:GQ:PL 0/1:20,17:36:99:615,0,727 +20 10098135 . C A 471.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-1.155;DP=39;ExcessHet=3.0103;FS=4.337;MQ=59.06;MQRankSum=1.546;QD=12.10;ReadPosRankSum=-0.591;SOR=0.075 GT:AD:DP:GQ:PL 0/1:25,14:38:99:500,0,964 +20 10098219 . TATATATA T 295.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=21;ExcessHet=3.0103;MQ=55.94;QD=14.08 GT:AD:DP:GQ:PL 0/1:0,0:21:99:333,0,461 +20 10098237 . A T 244.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=0.527;DP=12;ExcessHet=3.0103;FS=0.000;MQ=52.81;MQRankSum=-2.347;QD=20.40;ReadPosRankSum=1.188;SOR=0.446 GT:AD:DP:GQ:PL 0/1:7,5:13:99:273,0,273 +20 10098265 . T C 133.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=1.645;DP=6;ExcessHet=3.0103;FS=0.000;MQ=41.96;MQRankSum=-1.645;QD=22.30;ReadPosRankSum=0.524;SOR=1.022 GT:AD:DP:GQ:PL 0/1:2,4:6:59:162,0,59 +20 10098885 . C CA 433.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=32;ExcessHet=3.0103;MQ=49.27;QD=13.55 GT:AD:DP:GQ:PL 0/1:0,0:31:99:471,0,572 +20 10098945 . T C 407.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=1.225;DP=23;ExcessHet=3.0103;FS=0.000;MQ=50.09;MQRankSum=-2.636;QD=17.73;ReadPosRankSum=1.042;SOR=2.494 GT:AD:DP:GQ:PL 0/1:9,14:22:99:436,0,248 +20 10098987 . C T 379.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=2.922;DP=25;ExcessHet=3.0103;FS=7.005;MQ=50.88;MQRankSum=-2.877;QD=15.19;ReadPosRankSum=0.329;SOR=3.056 GT:AD:DP:GQ:PL 0/1:11,14:24:99:408,0,350 +20 10099029 . T C 334.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-1.864;DP=28;ExcessHet=3.0103;FS=5.724;MQ=53.32;MQRankSum=-3.439;QD=11.96;ReadPosRankSum=-0.361;SOR=2.494 GT:AD:DP:GQ:PL 0/1:18,10:28:99:363,0,768 +20 10099034 . C A 334.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=2.757;DP=28;ExcessHet=3.0103;FS=4.265;MQ=53.32;MQRankSum=-3.641;QD=11.96;ReadPosRankSum=-1.515;SOR=1.721 GT:AD:DP:GQ:PL 0/1:18,10:28:99:363,0,768 +20 10099044 . A C 334.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-0.861;DP=23;ExcessHet=3.0103;FS=0.000;MQ=51.54;MQRankSum=-4.268;QD=14.56;ReadPosRankSum=-2.046;SOR=0.321 GT:AD:DP:GQ:PL 0/1:16,7:24:99:363,0,768 +20 10099046 . T C 304.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-1.984;DP=22;ExcessHet=3.0103;FS=0.000;MQ=51.12;MQRankSum=-4.268;QD=13.85;ReadPosRankSum=-2.117;SOR=0.321 GT:AD:DP:GQ:PL 0/1:15,7:24:99:333,0,603 +20 10099055 . T C 256.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-1.788;DP=27;ExcessHet=3.0103;FS=0.000;MQ=49.71;MQRankSum=-4.432;QD=9.51;ReadPosRankSum=-2.657;SOR=1.075 GT:AD:DP:GQ:PL 0/1:16,11:23:99:285,0,673 +20 10099079 . C T 116.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=1.336;DP=34;ExcessHet=3.0103;FS=0.000;MQ=50.38;MQRankSum=-4.225;QD=3.43;ReadPosRankSum=1.168;SOR=0.941 GT:AD:DP:GQ:PL 0/1:20,14:29:99:145,0,886 +20 10099111 . T TTTTGTTTG 656.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=48;ExcessHet=3.0103;MQ=49.62;QD=13.68 GT:AD:DP:GQ:PL 0/1:0,0:35:99:694,0,802 +20 10099140 . G T 1005.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=0.536;DP=62;ExcessHet=3.0103;FS=2.232;MQ=55.53;MQRankSum=-1.610;QD=16.22;ReadPosRankSum=0.896;SOR=1.049 GT:AD:DP:GQ:PL 0/1:32,30:62:99:1034,0,931 +20 10099190 . G T 1034.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-0.035;DP=64;ExcessHet=3.0103;FS=0.000;MQ=57.89;MQRankSum=-1.485;QD=16.17;ReadPosRankSum=-0.491;SOR=0.727 GT:AD:DP:GQ:PL 0/1:33,31:65:99:1063,0,1154 +20 10099220 . A G 577.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-1.426;DP=46;ExcessHet=3.0103;FS=0.000;MQ=57.00;MQRankSum=-2.352;QD=12.56;ReadPosRankSum=0.119;SOR=0.610 GT:AD:DP:GQ:PL 0/1:26,20:45:99:606,0,873 +20 10099250 . G A 699.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=2.980;DP=38;ExcessHet=3.0103;FS=5.198;MQ=56.00;MQRankSum=-2.203;QD=18.42;ReadPosRankSum=0.096;SOR=0.188 GT:AD:DP:GQ:PL 0/1:16,22:37:99:728,0,424 +20 10099535 . G A 1335.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=5.034;DP=66;ExcessHet=3.0103;FS=1.007;MQ=59.01;MQRankSum=-1.418;QD=20.55;ReadPosRankSum=-0.771;SOR=0.408 GT:AD:DP:GQ:PL 0/1:26,39:65:99:1364,0,686 +20 10099565 . C T 1346.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=4.595;DP=69;ExcessHet=3.0103;FS=8.736;MQ=59.39;MQRankSum=-1.266;QD=19.52;ReadPosRankSum=1.454;SOR=0.191 GT:AD:DP:GQ:PL 0/1:31,38:69:99:1375,0,994 +20 10099755 . C T 1098.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=1.866;DP=68;ExcessHet=3.0103;FS=2.046;MQ=58.35;MQRankSum=-0.046;QD=16.16;ReadPosRankSum=-0.245;SOR=0.452 GT:AD:DP:GQ:PL 0/1:34,34:65:99:1127,0,1148 +20 10099832 . A G 1073.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-4.563;DP=72;ExcessHet=3.0103;FS=4.632;MQ=58.96;MQRankSum=0.869;QD=14.91;ReadPosRankSum=-0.882;SOR=0.871 GT:AD:DP:GQ:PL 0/1:39,33:72:99:1102,0,1430 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/noQual.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/noQual.vcf new file mode 100644 index 00000000000..2a9ccb92267 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/noQual.vcf @@ -0,0 +1,47 @@ +##fileformat=VCFv4.2 +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##contig= +##contig= +##reference=file:///Users/emeryj/hellbender/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 +20 10000117 . C T 905.77 . QD=14.15 GT:AD:DP:GQ:PL 0/1:36,28:64:99:934,0,1248 +20 10000211 . C T 941.77 . QD=17.77 GT:AD:DP:GQ:PL 0/1:26,27:53:99:970,0,906 +20 10000439 . T G . . . GT:AD:DP:GQ:PL 1/1:0,80:80:99:2833,240,0 +20 10000598 . T A 1941.77 . QD=25.36 GT:AD:DP:GQ:PL 1/1:0,49:49:99:1970,147,0 +20 10000694 . G A . . . GT:AD:DP:GQ:PL 0/1:45,37:82:99:1037,0,1601 +20 10000758 . T A 3838.77 . QD=28.73 GT:AD:DP:GQ:PL 1/1:0,95:95:99:3867,286,0 +20 10001019 . T G . . . GT:AD:DP:GQ:PL 0/1:39,26:65:99:679,0,1426 +20 10001298 . T A 2917.77 . QD=30.97 GT:AD:DP:GQ:PL 1/1:0,73:73:99:2946,220,0 +20 10001436 . A AAGGCT 2301.73 . QD=27.24 GT:AD:DP:GQ:PL 1/1:0,50:50:99:2339,156,0 +20 10001474 . C T . . . GT:AD:DP:GQ:PL 1/1:0,73:73:99:2669,219,0 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testAlleleTrimming.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testAlleleTrimming.vcf new file mode 100644 index 00000000000..3db675e01a2 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testAlleleTrimming.vcf @@ -0,0 +1,172 @@ +##fileformat=VCFv4.2 +##ApplyRecalibration="analysis_type=ApplyRecalibration input_file=[] read_buffer_size=null phone_home=NO_ET gatk_key=/mnt/isilon/cag/ngs/hiseq/respublica/pipeline/TianL_email.chop.edu.key tag=NA read_filter=[] intervals=[/mnt/isilon/cag/ngs/hiseq/respublica/pipeline/gatk/bed/SureSelectV4UTR.bed] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/mnt/isilon/cag/ngs/hiseq/tianl/cagpipelines/cag.hg19/cag.hg19.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=DEBUG log_to_file=null help=false version=false input=[(RodBinding name=input source=/mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/unifiedgenotyper.snp.filtered.snpEff.annovar.vcf)] recal_file=(RodBinding name=recal_file source=/mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/unifiedgenotyper.snp.filtered.snpEff.annovar.recal) tranches_file=/mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/unifiedgenotyper.snp.filtered.snpEff.annovar.tranches out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub ts_filter_level=99.0 ignore_filter=null mode=SNP filter_mismatching_base_and_quals=false filter_bases_not_stored=false" +##FILTER= 13.0"> +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FILTER= 60.0"> +##FILTER= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##LoF=Loss-of-function annotation (HC = High Confidence; LC = Low Confidence) +##LoF_filter=Reason for LoF not being HC +##LoF_flags=Possible warning flags for LoF +##LoF_info=Info used for LoF annotation +##OriginalSnpEffCmd="SnpEff eff -v -onlyCoding true -c /mnt/isilon/cag/ngs/hiseq/respublica/pipeline/gatk/snpEff_2_0_5/snpEff.config -i vcf -o vcf GRCh37.64 /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/unifiedgenotyper.snp.filtered.vcf " +##OriginalSnpEffVersion="2.0.5 (build 2011-12-24), by Pablo Cingolani" +##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/0331797407/SID0331797407.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/0428635906/SID0428635906.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/0762331062/SID0762331062.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/0789066272/SID0789066272.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/0849531882/SID0849531882.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/0866893807/SID0866893807.dedup.indelrealigner.recal.bam, 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/mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/3054380478/SID3054380478.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/3152131298/SID3152131298.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/3168498448/SID3168498448.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/3177448087/SID3177448087.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/3257203815/SID3257203815.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/3362319470/SID3362319470.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/3443100884/SID3443100884.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/3574989497/SID3574989497.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/3685265559/SID3685265559.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/3926929135/SID3926929135.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/5420847580/SID5420847580.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/5446433286/SID5446433286.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/5765404562/SID5765404562.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/6487318768/SID6487318768.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/7070215689/SID7070215689.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/7218257663/SID7218257663.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/7349184565/SID7349184565.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/7617513440/SID7617513440.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/8043825956/SID8043825956.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/8097401602/SID8097401602.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/8110976167/SID8110976167.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/8166168399/SID8166168399.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/8339622917/SID8339622917.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/8477905688/SID8477905688.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/8709441792/SID8709441792.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/8720399204/SID8720399204.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/8934996880/SID8934996880.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/8991335698/SID8991335698.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/9286156078/SID9286156078.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/9310548349/SID9310548349.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/9349366102/SID9349366102.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/9411685596/SID9411685596.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/9509562229/SID9509562229.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/9892329939/SID9892329939.dedup.indelrealigner.recal.bam, /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/BAM/9931218560/SID9931218560.dedup.indelrealigner.recal.bam] read_buffer_size=null phone_home=NO_ET gatk_key=/mnt/isilon/cag/ngs/hiseq/respublica/pipeline/TianL_email.chop.edu.key tag=NA read_filter=[] intervals=[/mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/.queue/scatterGather/UnifiedGenotyper.vqsr-2-sg/temp_01_of_50/scatter.intervals] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/mnt/isilon/cag/ngs/hiseq/tianl/cagpipelines/cag.hg19/cag.hg19.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=1 num_cpu_threads_per_data_thread=6 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false version=false genotype_likelihoods_model=SNP pcr_error_rate=1.0E-4 computeSLOD=false annotateNDA=false pair_hmm_implementation=ORIGINAL min_base_quality_score=17 max_deletion_fraction=0.05 min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 indelDebug=false ignoreSNPAlleles=false allReadsSP=false ignoreLaneInfo=false reference_sample_calls=(RodBinding name= source=UNBOUND) reference_sample_name=null sample_ploidy=2 min_quality_score=1 max_quality_score=40 site_quality_prior=20 min_power_threshold_for_calling=0.95 min_reference_depth=100 exclude_filtered_reference_sites=false heterozygosity=0.0010 indel_heterozygosity=1.25E-4 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=6 input_prior=[] contamination_fraction_to_filter=0.05 contamination_fraction_per_sample_file=null p_nonref_model=EXACT_INDEPENDENT exactcallslog=null dbsnp=(RodBinding name= source=UNBOUND) comp=[] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_mismatching_base_and_quals=false filter_bases_not_stored=false" +##VEP=v77 cache=/humgen/atgu1/fs03/konradk/vep/gold//homo_sapiens/77_GRCh37 db=. +##VariantAnnotator="analysis_type=VariantAnnotator input_file=[] read_buffer_size=null phone_home=STANDARD gatk_key=null tag=NA read_filter=[] intervals=[/mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/.queue/scatterGather/.qlog/unifiedgenotyper.snp.filtered.snpEff.vcf.varannotator-sg/temp_01_of_50/scatter.intervals] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/mnt/isilon/cag/ngs/hiseq/tianl/cagpipelines/cag.hg19/cag.hg19.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=/mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/unifiedgenotyper.snp.filtered.vcf) snpEffFile=(RodBinding name=snpEffFile source=/mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/unifiedgenotyper.snp.filtered.snpEff.out) dbsnp=(RodBinding name=dbsnp source=/mnt/isilon/cag/ngs/hiseq/tianl/cagpipelines/cag.hg19/dbsnp_138.hg19.vcf) comp=[] resource=[] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub annotation=[SnpEff] excludeAnnotation=[] group=[] expression={} useAllAnnotations=false list=false alwaysAppendDbsnpId=true MendelViolationGenotypeQualityThreshold=0.0 requireStrictAlleleMatch=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false" +##VariantFiltration="analysis_type=VariantFiltration input_file=[] read_buffer_size=null phone_home=NO_ET gatk_key=/mnt/isilon/cag/ngs/hiseq/respublica/pipeline/TianL_email.chop.edu.key tag=NA read_filter=[] intervals=[/mnt/isilon/cag/ngs/hiseq/respublica/pipeline/gatk/bed/SureSelectV4UTR.bed] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/mnt/isilon/cag/ngs/hiseq/tianl/cagpipelines/cag.hg19/cag.hg19.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=/mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/unifiedgenotyper.snp.vcf) mask=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub filterExpression=[QD < 2.0, MQ < 40.0, FS > 60.0, HaplotypeScore > 13.0, MQRankSum < -12.5, ReadPosRankSum < -8.0] filterName=[LowQualityDepth, MappingQuality, StrandBias, HaplotypeScoreHigh, MQRankSumLow, ReadPosRankSumLow] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=0 maskExtension=0 maskName=Mask filterNotInMask=false missingValuesInExpressionsShouldEvaluateAsFailing=false invalidatePreviousFilters=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false" +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##source_20140619.1=/mnt/isilon/cag/ngs/hiseq/respublica/pipeline/annotation_pipeline/vcf-annotate -a /mnt/isilon/cag/ngs/hiseq/tianl/NGSC/TGKX-CP/Fastq/annovar/UG.snp.all.sum.genome_summary.csv.gz -c CHROM,FROM,TO,INFO/Func,INFO/Gene,INFO/ExonicFunc,INFO/AAChange,INFO/Conserved,INFO/SegDup,INFO/ESP6500_ALL,INFO/1000g2012Apr_ALL,INFO/dbSNP135,INFO/AVSIFT,INFO/LJB_PhyloP,INFO/LJB_PhyloP_Pred,INFO/LJB_SIFT,INFO/LJB_SIFT_Pred,INFO/LJB_PolyPhen2,INFO/LJB_PolyPhen2_Pred,INFO/LJB_LRT,INFO/LJB_LRT_Pred,INFO/LRT_MutationTaster,INFO/LRT_MutationTaster_Pred,INFO/LJB_GERP++ -d /mnt/isilon/cag/ngs/hiseq/respublica/pipeline/annotation_pipeline/annovar_description.txt +#CHROM POS ID REF ALT QUAL FILTER INFO +1 26608873 rs1134583 T A,C 8647.13 VQSRTrancheSNP99.90to100.00 AAChange=uc001bly.3:c.A1120T:p.S374C;AC=35,5;AF=0.269,0.038;AN=130;AVSIFT=0;BaseQRankSum=-2.407;CSQ=A|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2262|||||rs1134583&COSM1602122|1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2262A>T||||||||||0&1|||||||||,C|ENSG00000158062|ENST00000496466|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2262|||||rs1134583&COSM1602122|2||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000496466.1:n.2262A>G||||||||||0&1|||||||||,A|ENSG00000158062|ENST00000374217|Transcript|missense_variant|1748|1381|461|S/C|Agt/Tgt|rs1134583&COSM1602122|1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|deleterious(0.01)|unknown(0)|15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1381A>T|ENSP00000363334.2:p.Ser461Cys|||||||||0&1|||||||||,C|ENSG00000158062|ENST00000374217|Transcript|missense_variant|1748|1381|461|S/G|Agt/Ggt|rs1134583&COSM1602122|2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000363334|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|deleterious(0.03)|unknown(0)|15/15||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374217.2:c.1381A>G|ENSP00000363334.2:p.Ser461Gly|||||||||0&1|||||||||,A|ENSG00000158062|ENST00000374222|Transcript|missense_variant|1945|1480|494|S/C|Agt/Tgt|rs1134583&COSM1602122|1||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|deleterious(0.01)|unknown(0)|16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1480A>T|ENSP00000363339.1:p.Ser494Cys|||||||||0&1|||||||||,C|ENSG00000158062|ENST00000374222|Transcript|missense_variant|1945|1480|494|S/G|Agt/Ggt|rs1134583&COSM1602122|2||-1|UBXN11|HGNC|30600|protein_coding|YES|CCDS41288.1|ENSP00000363339|UBX11_HUMAN||UPI00004700E1|deleterious(0.03)|unknown(0)|16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374222.1:c.1480A>G|ENSP00000363339.1:p.Ser494Gly|||||||||0&1|||||||||,A|ENSG00000158062|ENST00000357089|Transcript|missense_variant|1457|1381|461|S/C|Agt/Tgt|rs1134583&COSM1602122|1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|deleterious(0.01)|unknown(0)|14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1381A>T|ENSP00000349601.4:p.Ser461Cys|||||||||0&1|||||||||,C|ENSG00000158062|ENST00000357089|Transcript|missense_variant|1457|1381|461|S/G|Agt/Ggt|rs1134583&COSM1602122|2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41286.1|ENSP00000349601|UBX11_HUMAN|Q5T130_HUMAN|UPI00004700E0|deleterious(0.03)|unknown(0)|14/14||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000357089.4:c.1381A>G|ENSP00000349601.4:p.Ser461Gly|||||||||0&1|||||||||,A|ENSG00000158062|ENST00000314675|Transcript|missense_variant|1200|1120|374|S/C|Agt/Tgt|rs1134583&COSM1602122|1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|deleterious(0.01)|unknown(0)|11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1120A>T|ENSP00000324721.7:p.Ser374Cys|||||||||0&1|||||||||,C|ENSG00000158062|ENST00000314675|Transcript|missense_variant|1200|1120|374|S/G|Agt/Ggt|rs1134583&COSM1602122|2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41287.1|ENSP00000324721|UBX11_HUMAN||UPI000013F8CA|deleterious(0.03)|unknown(0)|11/11||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000314675.7:c.1120A>G|ENSP00000324721.7:p.Ser374Gly|||||||||0&1|||||||||,A|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2442|||||rs1134583&COSM1602122|1||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2442A>T||||||||||0&1|||||||||,C|ENSG00000158062|ENST00000475591|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2442|||||rs1134583&COSM1602122|2||-1|UBXN11|HGNC|30600|retained_intron|||||||||13/13|||ENST00000475591.1:n.2442A>G||||||||||0&1|||||||||,A|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2227|||||rs1134583&COSM1602122|1||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2227A>T||||||||||0&1|||||||||,C|ENSG00000158062|ENST00000494942|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2227|||||rs1134583&COSM1602122|2||-1|UBXN11|HGNC|30600|retained_intron|||||||||10/10|||ENST00000494942.1:n.2227A>G||||||||||0&1|||||||||,A|ENSG00000158062|ENST00000374221|Transcript|missense_variant|1694|1480|494|S/C|Agt/Tgt|rs1134583&COSM1602122|1||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|deleterious(0.01)|unknown(0)|16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1480A>T|ENSP00000363338.3:p.Ser494Cys|||||||||0&1|||||||||,C|ENSG00000158062|ENST00000374221|Transcript|missense_variant|1694|1480|494|S/G|Agt/Ggt|rs1134583&COSM1602122|2||-1|UBXN11|HGNC|30600|protein_coding||CCDS41288.1|ENSP00000363338|UBX11_HUMAN||UPI00004700E1|deleterious(0.03)|unknown(0)|16/16||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374221.3:c.1480A>G|ENSP00000363338.3:p.Ser494Gly|||||||||0&1|||||||||,A|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2545|||||rs1134583&COSM1602122|1||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2545A>T||||||||||0&1|||||||||,C|ENSG00000158062|ENST00000472155|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2545|||||rs1134583&COSM1602122|2||-1|UBXN11|HGNC|30600|retained_intron|||||||||14/14|||ENST00000472155.1:n.2545A>G||||||||||0&1|||||||||,A|ENSG00000158062|ENST00000374223|Transcript|missense_variant|1212|751|251|S/C|Agt/Tgt|rs1134583&COSM1602122|1||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|deleterious(0.03)|unknown(0)|12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.751A>T|ENSP00000363340.1:p.Ser251Cys|||||||||0&1|||||||||,C|ENSG00000158062|ENST00000374223|Transcript|missense_variant|1212|751|251|S/G|Agt/Ggt|rs1134583&COSM1602122|2||-1|UBXN11|HGNC|30600|protein_coding|||ENSP00000363340|||UPI00004700DA|tolerated(0.06)|unknown(0)|12/12||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50099|ENST00000374223.1:c.751A>G|ENSP00000363340.1:p.Ser251Gly|||||||||0&1|||||||||,A||ENSR00000533083|RegulatoryFeature|regulatory_region_variant||||||rs1134583&COSM1602122|1||||||regulatory_region||||||||||||||||||||||0&1|||||||||,C||ENSR00000533083|RegulatoryFeature|regulatory_region_variant||||||rs1134583&COSM1602122|2||||||regulatory_region||||||||||||||||||||||0&1|||||||||;DB;DP=2659;Dels=0.00;ExonicFunc=nonsynonymousSNV;FS=27.067;Func=exonic;Gene=UBXN11;HaplotypeScore=11.0781;InbreedingCoeff=-0.3011;LJB_GERP++=0.0;LJB_LRT=0.825324;LJB_LRT_Pred=NA;LJB_PhyloP=0.887806;LJB_PhyloP_Pred=N;LJB_PolyPhen2=0.515975;LJB_PolyPhen2_Pred=NA;LJB_SIFT=1.0;LJB_SIFT_Pred=D;LRT_MutationTaster=7.8E-5;LRT_MutationTaster_Pred=N;MLEAC=35,3;MLEAF=0.269,0.023;MQ=48.46;MQ0=1;MQRankSum=-11.748;NEGATIVE_TRAIN_SITE;QD=5.85;ReadPosRankSum=-6.714;SNPEFF_AMINO_ACID_CHANGE=S251G;SNPEFF_CODON_CHANGE=Agt/Ggt;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_26608773_26609060;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=UBXN11;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000374223;VQSLOD=-4.019e+00;culprit=MQRankSum;dbSNP135=rs1134583;exac.AC_Adj=4,66 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testDBTagWithHapMap.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testDBTagWithHapMap.vcf new file mode 100644 index 00000000000..fcd035d5530 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testDBTagWithHapMap.vcf @@ -0,0 +1,36 @@ +##fileformat=VCFv4.2 +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##contig= +##contig= +##reference=file:///Users/emeryj/hellbender/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta +##source=UnifiedGenotyper +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 +20 10001292 . G A 42.22 . AC=1;AF=0.500;AN=2;H3 GT:GQ:RD 1/0:19:23 +20 10002963 . C G 42.22 . AC=1;AF=0.500;AN=2 GT:GQ:RD 0/1:33:30 +20 10005008 . A T 123.78 . AC=2;AF=1.00;AN=2 GT:GQ:RD 1/1:8:30 +20 10006296 . C T 42.23 . AC=1;AF=0.500;AN=2;H3 GT:GQ:RD 0/1:3:7 +20 10023478 . G C 84.23 . AC=2;AF=1.00;AN=2 GT:GQ:RD 1/1:4:27 +20 10029362 . T C 42.22 . AC=1;AF=0.500;AN=2 GT:GQ:RD 1/0:37:44 +20 10042312 . G C 31.81 . AC=1;AF=0.500;AN=2 GT:GQ:RD 1/0:6:24 +20 10044557 . C T 42.22 . AC=1;AF=0.500;AN=2 GT:GQ:RD 0/1:15:31 +20 10045603 . A G 40.26 . AC=1;AF=0.500;AN=2 GT:GQ:RD 0/1:8:15 +20 10048142 . A G 126.81 . AC=2;AF=1.00;AN=2;H3 GT:GQ:RD 1/1:9:36 +20 10048580 . T A 42.22 . AC=1;AF=0.500;AN=2 GT:GQ:RD 1/0:23:33 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testDBTagWithTwoComps.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testDBTagWithTwoComps.vcf new file mode 100644 index 00000000000..131c08be0fa --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testDBTagWithTwoComps.vcf @@ -0,0 +1,37 @@ +##fileformat=VCFv4.2 +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##contig= +##contig= +##reference=file:///Users/emeryj/hellbender/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta +##source=UnifiedGenotyper +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 +20 10001292 . G A 42.22 . AC=1;AF=0.500;AN=2;H3;foo GT:GQ:RD 1/0:19:23 +20 10002963 . C G 42.22 . AC=1;AF=0.500;AN=2 GT:GQ:RD 0/1:33:30 +20 10005008 . A T 123.78 . AC=2;AF=1.00;AN=2 GT:GQ:RD 1/1:8:30 +20 10006296 . C T 42.23 . AC=1;AF=0.500;AN=2;H3;foo GT:GQ:RD 0/1:3:7 +20 10023478 . G C 84.23 . AC=2;AF=1.00;AN=2 GT:GQ:RD 1/1:4:27 +20 10029362 . T C 42.22 . AC=1;AF=0.500;AN=2 GT:GQ:RD 1/0:37:44 +20 10042312 . G C 31.81 . AC=1;AF=0.500;AN=2 GT:GQ:RD 1/0:6:24 +20 10044557 . C T 42.22 . AC=1;AF=0.500;AN=2 GT:GQ:RD 0/1:15:31 +20 10045603 . A G 40.26 . AC=1;AF=0.500;AN=2 GT:GQ:RD 0/1:8:15 +20 10048142 . A G 126.81 . AC=2;AF=1.00;AN=2;H3;foo GT:GQ:RD 1/1:9:36 +20 10048580 . T A 42.22 . AC=1;AF=0.500;AN=2 GT:GQ:RD 1/0:23:33 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testFilterInExpression.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testFilterInExpression.vcf new file mode 100644 index 00000000000..0a2232a7fed --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testFilterInExpression.vcf @@ -0,0 +1,26 @@ +##fileformat=VCFv4.2 +##FORMAT= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##contig= +##contig= +##reference=file:///Users/emeryj/hellbender/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta +##source=UnifiedGenotyper +#CHROM POS ID REF ALT QUAL FILTER INFO +20 10001292 . G A 42.22 . AC=2;AF=0.2;foo.FILTER=panel_of_normals,alt_allele_in_normal +20 10002963 . C G 42.22 . AC=5;AF=0.5;foo.FILTER=PASS +20 10005008 . A T,CC,G 123.78 . AC=2,1,5;AF=0.2,0.1,0.5;foo.FILTER=PASS +20 10005200 . GTGTGAACCCGC G,GAACCCGC 100 . AC=1,5;AF=0.1,0.5 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testHasAnnotsAsking1.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testHasAnnotsAsking1.vcf new file mode 100644 index 00000000000..8093472c98e --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testHasAnnotsAsking1.vcf @@ -0,0 +1,88 @@ +##fileformat=VCFv4.2 +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##contig= +##contig= +##reference=file:///Users/emeryj/hellbender/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 NA12891 NA12892 +20 10000598 . T A 18.59 . ABHom=1.00;AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;OND=0.00;QD=9.30;SOR=0.693 GT:AD:DP:GQ:PL ./. 1/1:0,2:2:3:45,3,0 ./. +20 10001617 . C A 12.77 . ABHom=1.00;AC=2;AF=1.00;AN=2;DP=1;Dels=0.00;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;OND=0.00;QD=12.77;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:39,3,0 ./. ./. +20 10001628 . G A 18.59 . ABHom=1.00;AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;OND=0.00;QD=9.30;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:3:45,3,0 ./. ./. +20 10001661 . T C 17.49 . ABHom=1.00;AC=2;AF=0.500;AN=4;BaseQRankSum=0.000;DP=3;Dels=0.00;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.000;OND=0.00;QD=8.75;ReadPosRankSum=0.000;SOR=0.223 GT:AD:DP:GQ:PL 1/1:0,2:2:3:45,3,0 ./. 0/0:1,0:1:3:0,3,39 +20 10001670 . T G 14.57 . ABHom=1.00;AC=2;AF=0.500;AN=4;BaseQRankSum=0.967;DP=3;Dels=0.00;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.000;OND=0.00;QD=14.57;ReadPosRankSum=0.967;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:42,3,0 ./. 0/0:2,0:2:3:0,3,45 +20 10002138 . C G 16.63 . ABHom=1.00;AC=2;AF=1.00;AN=2;DP=1;Dels=0.00;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;OND=0.00;QD=16.63;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:43,3,0 ./. ./. +20 10002142 . G C 16.63 . ABHom=1.00;AC=2;AF=1.00;AN=2;DP=1;Dels=0.00;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;OND=0.00;QD=16.63;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:43,3,0 ./. ./. +20 10003021 . C T 12.77 . ABHom=1.00;AC=2;AF=1.00;AN=2;DP=1;Dels=0.00;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;OND=0.00;QD=12.77;SOR=1.609 GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3:39,3,0 ./. +20 10003358 . A C 15.65 . ABHom=1.00;AC=2;AF=1.00;AN=2;DP=1;Dels=0.00;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;OND=0.00;QD=15.65;SOR=1.609 GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3:42,3,0 ./. +20 10003651 . T C 53.42 . ABHom=1.00;AC=4;AF=1.00;AN=4;DP=3;Dels=0.00;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=51.77;MQ0=0;OND=0.00;QD=26.71;SOR=1.179 GT:AD:DP:GQ:PL 1/1:0,1:1:3:33,3,0 1/1:0,2:2:3:45,3,0 ./. +20 10003692 . A G 12.77 . ABHom=1.00;AC=2;AF=1.00;AN=2;DP=1;Dels=0.00;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;OND=0.00;QD=12.77;SOR=1.609 GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3:39,3,0 ./. +20 10003832 . G A 53.42 . ABHom=1.00;AC=4;AF=1.00;AN=4;DP=2;Dels=0.00;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=60.00;MQ0=0;OND=0.00;QD=26.71;SOR=2.303 GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3:39,3,0 1/1:0,1:1:3:39,3,0 +20 10004094 . A C 14.68 . ABHom=1.00;AC=2;AF=1.00;AN=2;DP=1;Dels=0.00;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.00;MQ0=0;OND=0.00;QD=14.68;SOR=1.609 GT:AD:DP:GQ:PL ./. ./. 1/1:0,1:1:3:41,3,0 +20 10004351 . C G 56.42 . ABHom=1.00;AC=4;AF=1.00;AN=4;DP=2;Dels=0.00;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=60.00;MQ0=0;OND=0.00;QD=28.21;SOR=2.303 GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3:39,3,0 1/1:0,1:1:3:42,3,0 +20 10004389 . T G 15.65 . ABHom=1.00;AC=2;AF=1.00;AN=2;DP=1;Dels=0.00;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;OND=0.00;QD=15.65;SOR=1.609 GT:AD:DP:GQ:PL ./. ./. 1/1:0,1:1:3:42,3,0 +20 10004610 . A C 14.68 . ABHom=1.00;AC=2;AF=1.00;AN=2;DP=1;Dels=0.00;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;OND=0.00;QD=14.68;SOR=1.609 GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3:41,3,0 ./. +20 10004725 . A G 14.68 . ABHom=1.00;AC=2;AF=1.00;AN=2;DP=1;Dels=0.00;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;OND=0.00;QD=14.68;SOR=1.609 GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3:41,3,0 ./. +20 10004874 . A C 59.42 . ABHom=1.00;AC=4;AF=1.00;AN=4;DP=2;Dels=0.00;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=60.00;MQ0=0;OND=0.00;QD=29.71;SOR=2.303 GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3:42,3,0 1/1:0,1:1:3:42,3,0 +20 10004887 . A G 14.57 . ABHom=1.00;AC=2;AF=0.500;AN=4;BaseQRankSum=0.674;DP=2;Dels=0.00;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.000;OND=0.00;QD=14.57;ReadPosRankSum=-0.674;SOR=0.693 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3:0,3,38 1/1:0,1:1:3:42,3,0 +20 10005010 . C T 18.59 . ABHom=1.00;AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;OND=0.00;QD=9.30;SOR=0.693 GT:AD:DP:GQ:PL ./. 1/1:0,2:2:3:45,3,0 ./. +20 10005427 . C T 17.49 . ABHom=1.00;AC=2;AF=0.500;AN=4;BaseQRankSum=-0.967;DP=3;Dels=0.00;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.000;OND=0.00;QD=8.75;ReadPosRankSum=0.967;SOR=0.223 GT:AD:DP:GQ:PL ./. 1/1:0,2:2:3:45,3,0 0/0:1,0:1:3:0,3,41 +20 10005723 . A G 10.90 . ABHom=1.00;AC=2;AF=1.00;AN=2;DP=1;Dels=0.00;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;OND=0.00;QD=10.90;SOR=1.609 GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3:37,3,0 ./. +20 10006682 . T A 12.77 . ABHom=1.00;AC=2;AF=1.00;AN=2;DP=1;Dels=0.00;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;OND=0.00;QD=12.77;SOR=1.609 GT:AD:DP:GQ:PL ./. ./. 1/1:0,1:1:3:39,3,0 +20 10007352 . C T 204.23 . ABHom=1.00;AC=6;AF=1.00;AN=6;DP=8;Dels=0.00;ExcessHet=3.0103;FS=0.000;MLEAC=6;MLEAF=1.00;MQ=60.00;MQ0=0;OND=0.00;QD=29.18;SOR=1.863 GT:AD:DP:GQ:PL 1/1:0,1:1:3:39,3,0 1/1:0,3:3:6:79,6,0 1/1:0,4:4:9:111,9,0 +20 10008221 . T C 61.42 . ABHom=1.00;AC=4;AF=1.00;AN=4;DP=3;Dels=0.00;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=60.00;MQ0=0;OND=0.00;QD=30.71;SOR=1.179 GT:AD:DP:GQ:PL 1/1:0,1:1:3:41,3,0 ./. 1/1:0,2:2:3:45,3,0 +20 10009227 . A G 18.59 . ABHom=1.00;AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;OND=0.00;QD=9.30;SOR=0.693 GT:AD:DP:GQ:PL ./. ./. 1/1:0,2:2:3:45,3,0 +20 10009246 . A G 18.59 . ABHom=1.00;AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;OND=0.00;QD=9.30;SOR=0.693 GT:AD:DP:GQ:PL ./. ./. 1/1:0,2:2:3:45,3,0 +20 10009446 . G T 12.77 . ABHom=1.00;AC=2;AF=1.00;AN=2;DP=1;Dels=0.00;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;OND=0.00;QD=12.77;SOR=1.609 GT:AD:DP:GQ:PL ./. ./. 1/1:0,1:1:3:39,3,0 +20 10009512 . C G 15.65 . ABHom=1.00;AC=2;AF=1.00;AN=2;DP=1;Dels=0.00;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;OND=0.00;QD=15.65;SOR=1.609 GT:AD:DP:GQ:PL ./. ./. 1/1:0,1:1:3:42,3,0 +20 10009795 . A G 13.72 . ABHom=1.00;AC=2;AF=1.00;AN=2;DP=1;Dels=0.00;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;OND=0.00;QD=13.72;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:40,3,0 ./. ./. +20 10011075 . C T 17.49 . ABHom=1.00;AC=2;AF=0.500;AN=4;BaseQRankSum=0.967;DP=3;Dels=0.00;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.000;OND=0.00;QD=8.75;ReadPosRankSum=-0.967;SOR=0.223 GT:AD:DP:GQ:PL ./. 1/1:0,2:2:3:45,3,0 0/0:1,0:1:3:0,3,37 +20 10012362 . G T 12.77 . ABHom=1.00;AC=2;AF=1.00;AN=2;DP=1;Dels=0.00;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=37.00;MQ0=0;OND=0.00;QD=12.77;SOR=1.609 GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3:39,3,0 ./. +20 10019093 . A G 9258.92 . ABHet=0.558;AC=3;AF=0.500;AN=6;BaseQRankSum=10.512;DP=750;Dels=0.00;ExcessHet=6.9897;FS=0.000;MLEAC=3;MLEAF=0.500;MQ=59.13;MQ0=0;MQRankSum=-0.972;OND=0.00;QD=12.44;ReadPosRankSum=-0.521;SOR=0.653 GT:AD:DP:GQ:PL 0/1:138,110:250:99:3166,0,3854 0/1:131,117:250:99:3346,0,3750 0/1:146,102:250:99:2777,0,4107 +20 10024107 . C T 26.29 . ABHet=0.778;ABHom=1.00;AC=2;AF=0.333;AN=6;BaseQRankSum=2.121;DP=15;Dels=0.00;ExcessHet=3.9794;FS=0.000;MLEAC=2;MLEAF=0.333;MQ=60.00;MQ0=0;MQRankSum=0.000;OND=0.00;QD=2.92;ReadPosRankSum=-0.768;SOR=0.446 GT:AD:DP:GQ:PL 0/1:3,1:4:27:27,0,101 0/0:6,0:6:18:0,18,215 0/1:4,1:5:31:31,0,81 +20 10026108 . A G 23.15 . ABHet=0.778;ABHom=1.00;AC=1;AF=0.167;AN=6;BaseQRankSum=0.684;DP=38;Dels=0.00;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.167;MQ=59.27;MQ0=0;MQRankSum=0.000;OND=0.00;QD=2.57;ReadPosRankSum=-1.346;SOR=0.007 GT:AD:DP:GQ:PL 0/0:14,0:15:39:0,39,513 0/1:7,2:9:54:54,0,255 0/0:14,0:14:42:0,42,541 +20 10026357 . T C 3067.16 . ABHet=0.467;ABHom=1.00;AC=2;AF=0.333;AN=6;BaseQRankSum=7.144;DP=288;Dels=0.00;ExcessHet=3.9794;FS=2.821;MLEAC=2;MLEAF=0.333;MQ=59.58;MQ0=0;MQRankSum=-1.089;OND=0.00;QD=15.57;ReadPosRankSum=-1.425;SOR=0.890 GT:AD:DP:GQ:PL 0/1:41,46:87:99:1310,0,1044 0/0:90,0:90:99:0,220,2870 0/1:51,59:111:99:1789,0,1374 +20 10026794 . C T 11.83 . ABHom=1.00;AC=2;AF=1.00;AN=2;DP=1;Dels=0.00;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;OND=0.00;QD=11.83;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:38,3,0 ./. ./. +20 10030188 . T A 3747.16 . ABHet=0.448;ABHom=1.00;AC=2;AF=0.333;AN=6;BaseQRankSum=3.540;DP=386;Dels=0.00;ExcessHet=3.9794;FS=0.394;MLEAC=2;MLEAF=0.333;MQ=59.27;MQ0=0;MQRankSum=1.297;OND=0.00;QD=15.11;ReadPosRankSum=-1.340;SOR=0.728 GT:AD:DP:GQ:PL 0/1:47,47:94:99:1333,0,1308 0/0:136,0:137:99:0,328,4257 0/1:64,90:154:99:2446,0,1566 +20 10030931 . C A 56.23 . ABHet=0.700;ABHom=0.960;AC=1;AF=0.167;AN=6;BaseQRankSum=1.176;DP=35;Dels=0.00;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.167;MQ=59.34;MQ0=0;MQRankSum=-2.600;OND=0.029;QD=5.62;ReadPosRankSum=0.111;SOR=0.027 GT:AD:DP:GQ:PL 0/0:9,0:9:24:0,24,299 0/1:7,3:10:87:87,0,229 0/0:15,1:16:16:0,16,440 +20 10031342 . G A 18.59 . ABHom=1.00;AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;OND=0.00;QD=9.30;SOR=0.693 GT:AD:DP:GQ:PL ./. 1/1:0,2:2:3:45,3,0 ./. +20 10031798 . G A 100.34 . ABHom=1.00;AC=6;AF=1.00;AN=6;DP=4;Dels=0.00;ExcessHet=3.0103;FS=0.000;MLEAC=6;MLEAF=1.00;MQ=60.00;MQ0=0;OND=0.00;QD=33.66;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,1:1:3:40,3,0 1/1:0,2:2:3:45,3,0 1/1:0,1:1:3:39,3,0 +20 10031827 . C T 17.49 . ABHom=1.00;AC=2;AF=0.500;AN=4;BaseQRankSum=-0.967;DP=3;Dels=0.00;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.000;OND=0.00;QD=8.75;ReadPosRankSum=0.000;SOR=0.223 GT:AD:DP:GQ:PL 1/1:0,2:2:3:45,3,0 0/0:1,0:1:3:0,3,42 ./. +20 10032413 . T G 3643.16 . ABHet=0.512;ABHom=1.00;AC=2;AF=0.333;AN=6;BaseQRankSum=-0.287;DP=355;Dels=0.00;ExcessHet=3.9794;FS=0.435;MLEAC=2;MLEAF=0.333;MQ=59.61;MQ0=0;MQRankSum=-0.412;OND=0.00;QD=14.12;ReadPosRankSum=0.065;SOR=0.727 GT:AD:DP:GQ:PL 0/1:56,68:124:99:2087,0,1530 0/0:97,0:97:99:0,250,3265 0/1:76,58:134:99:1588,0,2067 +20 10034546 . T C 11.83 . ABHom=1.00;AC=2;AF=1.00;AN=2;DP=1;Dels=0.00;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;OND=0.00;QD=11.83;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:38,3,0 ./. ./. +20 10036107 . T G 12.39 . ABHet=0.477;ABHom=0.630;AC=1;AF=0.167;AN=6;BaseQRankSum=-4.520;DP=117;Dels=0.00;ExcessHet=3.0103;FS=5.027;MLEAC=1;MLEAF=0.167;MQ=58.08;MQ0=0;MQRankSum=0.486;OND=0.231;QD=0.28;ReadPosRankSum=-2.268;SOR=2.833 GT:AD:DP:GQ:PL 0/0:29,20:49:28:0,28,561 0/0:17,7:24:39:0,39,462 0/1:21,23:44:43:43,0,518 +20 10037877 . G C 16.67 . ABHom=1.00;AC=2;AF=0.333;AN=6;BaseQRankSum=0.000;DP=7;Dels=0.00;ExcessHet=0.4576;FS=0.000;MLEAC=2;MLEAF=0.333;MQ=56.62;MQ0=0;MQRankSum=0.000;OND=0.00;QD=8.34;ReadPosRankSum=0.842;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:3:45,3,0 0/0:3,0:3:3:0,3,45 0/0:2,0:2:3:0,3,45 +20 10043441 . T A 11.12 . ABHet=0.500;AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;DP=4;Dels=0.00;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.000;OND=0.00;QD=2.78;ReadPosRankSum=-1.383;SOR=0.693 GT:AD:DP:GQ:PL ./. 0/1:2,2:4:38:39,0,38 ./. +20 10044282 . T C 150.42 . ABHet=0.111;ABHom=1.00;AC=1;AF=0.167;AN=6;BaseQRankSum=-1.564;DP=14;Dels=0.00;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.167;MQ=58.33;MQ0=0;MQRankSum=0.000;OND=0.00;QD=16.71;ReadPosRankSum=0.150;SOR=1.688 GT:AD:DP:GQ:PL 0/0:2,0:2:6:0,6,74 0/1:1,8:9:18:180,0,18 0/0:3,0:3:9:0,9,108 +20 10044849 . A G 57.17 . ABHom=1.00;AC=2;AF=0.500;AN=4;BaseQRankSum=-0.253;DP=5;Dels=0.00;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.000;OND=0.00;QD=19.06;ReadPosRankSum=-1.645;SOR=1.179 GT:AD:DP:GQ:PL ./. 0/0:2,0:2:3:0,3,45 1/1:0,3:3:6:86,6,0 +20 10045078 . G T 12.77 . ABHom=1.00;AC=2;AF=1.00;AN=2;DP=1;Dels=0.00;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;OND=0.00;QD=12.77;SOR=1.609 GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3:39,3,0 ./. +20 10046489 . C T 11.83 . ABHom=1.00;AC=2;AF=1.00;AN=2;DP=1;Dels=0.00;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;OND=0.00;QD=11.83;SOR=1.609 GT:AD:DP:GQ:PL ./. ./. 1/1:0,1:1:3:38,3,0 +20 10047597 . C A 12.77 . ABHom=1.00;AC=2;AF=1.00;AN=2;DP=1;Dels=0.00;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;OND=0.00;QD=12.77;SOR=1.609 GT:AD:DP:GQ:PL ./. ./. 1/1:0,1:1:3:39,3,0 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testHasAnnotsAsking1.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testHasAnnotsAsking1.vcf.idx new file mode 100644 index 0000000000000000000000000000000000000000..00f3c4505e471eefee8bb5732cf9499c703f2e68 GIT binary patch literal 351 zcmb_YONzok5G@g0xS6$=u#;#cx@(eF17ig3h`Yv5`HdM#H=@_@1d2EDWK&VHacx0W zJzo7DCBtA^0)R64YMWq(F&1mgG{XaCmmS++lFTt(V#d}pvuAid;=zW8 zjOKd3P1kn)v{=C-q+Mj*^m$eJ?%XQmLFmhlV?nE7Ij&3KP1w-%Y^UwDUFZrf237eDw10yjsW literal 0 HcmV?d00001 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testHasNoAnnotsAsking1.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testHasNoAnnotsAsking1.vcf new file mode 100644 index 00000000000..2e2574a7993 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testHasNoAnnotsAsking1.vcf @@ -0,0 +1,82 @@ +##fileformat=VCFv4.2 +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##GATKCommandLine.UnifiedGenotyper= +##GATKCommandLine.VariantAnnotator= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##contig= +##contig= +##reference=file:///Users/emeryj/hellbender/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 NA12891 NA12892 +20 10000598 . T A 18.59 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=9.30;SOR=0.693 GT:AD:DP:GQ:PL ./. 1/1:0,2:2:3:45,3,0 ./. +20 10001617 . C A 12.77 . AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=12.77;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:39,3,0 ./. ./. +20 10001628 . G A 18.59 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=9.30;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:3:45,3,0 ./. ./. +20 10001661 . T C 17.49 . AC=2;AF=0.500;AN=4;BaseQRankSum=0.000;DP=3;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=8.75;ReadPosRankSum=0.000;SOR=0.223 GT:AD:DP:GQ:PL 1/1:0,2:2:3:45,3,0 ./. 0/0:1,0:1:3:0,3,39 +20 10001670 . T G 14.57 . AC=2;AF=0.500;AN=4;BaseQRankSum=0.967;DP=3;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=14.57;ReadPosRankSum=0.967;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:42,3,0 ./. 0/0:2,0:2:3:0,3,45 +20 10002138 . C G 16.63 . AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=16.63;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:43,3,0 ./. ./. +20 10002142 . G C 16.63 . AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=16.63;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:43,3,0 ./. ./. +20 10003021 . C T 12.77 . AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=12.77;SOR=1.609 GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3:39,3,0 ./. +20 10003358 . A C 15.65 . AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=15.65;SOR=1.609 GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3:42,3,0 ./. +20 10003651 . T C 53.42 . AC=4;AF=1.00;AN=4;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=51.77;QD=26.71;SOR=1.179 GT:AD:DP:GQ:PL 1/1:0,1:1:3:33,3,0 1/1:0,2:2:3:45,3,0 ./. +20 10003692 . A G 12.77 . AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=12.77;SOR=1.609 GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3:39,3,0 ./. +20 10003832 . G A 53.42 . AC=4;AF=1.00;AN=4;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=60.00;QD=26.71;SOR=2.303 GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3:39,3,0 1/1:0,1:1:3:39,3,0 +20 10004094 . A C 14.68 . AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.00;QD=14.68;SOR=1.609 GT:AD:DP:GQ:PL ./. ./. 1/1:0,1:1:3:41,3,0 +20 10004351 . C G 56.42 . AC=4;AF=1.00;AN=4;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=60.00;QD=28.21;SOR=2.303 GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3:39,3,0 1/1:0,1:1:3:42,3,0 +20 10004389 . T G 15.65 . AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=15.65;SOR=1.609 GT:AD:DP:GQ:PL ./. ./. 1/1:0,1:1:3:42,3,0 +20 10004610 . A C 14.68 . AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=14.68;SOR=1.609 GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3:41,3,0 ./. +20 10004725 . A G 14.68 . AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=14.68;SOR=1.609 GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3:41,3,0 ./. +20 10004874 . A C 59.42 . AC=4;AF=1.00;AN=4;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=60.00;QD=29.71;SOR=2.303 GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3:42,3,0 1/1:0,1:1:3:42,3,0 +20 10004887 . A G 14.57 . AC=2;AF=0.500;AN=4;BaseQRankSum=0.674;DP=2;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=14.57;ReadPosRankSum=-0.674;SOR=0.693 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3:0,3,38 1/1:0,1:1:3:42,3,0 +20 10005010 . C T 18.59 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=9.30;SOR=0.693 GT:AD:DP:GQ:PL ./. 1/1:0,2:2:3:45,3,0 ./. +20 10005427 . C T 17.49 . AC=2;AF=0.500;AN=4;BaseQRankSum=-0.967;DP=3;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=8.75;ReadPosRankSum=0.967;SOR=0.223 GT:AD:DP:GQ:PL ./. 1/1:0,2:2:3:45,3,0 0/0:1,0:1:3:0,3,41 +20 10005723 . A G 10.90 . AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=10.90;SOR=1.609 GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3:37,3,0 ./. +20 10006682 . T A 12.77 . AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=12.77;SOR=1.609 GT:AD:DP:GQ:PL ./. ./. 1/1:0,1:1:3:39,3,0 +20 10007352 . C T 204.23 . AC=6;AF=1.00;AN=6;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=6;MLEAF=1.00;MQ=60.00;QD=29.18;SOR=1.863 GT:AD:DP:GQ:PL 1/1:0,1:1:3:39,3,0 1/1:0,3:3:6:79,6,0 1/1:0,4:4:9:111,9,0 +20 10008221 . T C 61.42 . AC=4;AF=1.00;AN=4;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=60.00;QD=30.71;SOR=1.179 GT:AD:DP:GQ:PL 1/1:0,1:1:3:41,3,0 ./. 1/1:0,2:2:3:45,3,0 +20 10009227 . A G 18.59 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=9.30;SOR=0.693 GT:AD:DP:GQ:PL ./. ./. 1/1:0,2:2:3:45,3,0 +20 10009246 . A G 18.59 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=9.30;SOR=0.693 GT:AD:DP:GQ:PL ./. ./. 1/1:0,2:2:3:45,3,0 +20 10009446 . G T 12.77 . AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=12.77;SOR=1.609 GT:AD:DP:GQ:PL ./. ./. 1/1:0,1:1:3:39,3,0 +20 10009512 . C G 15.65 . AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=15.65;SOR=1.609 GT:AD:DP:GQ:PL ./. ./. 1/1:0,1:1:3:42,3,0 +20 10009795 . A G 13.72 . AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=13.72;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:40,3,0 ./. ./. +20 10011075 . C T 17.49 . AC=2;AF=0.500;AN=4;BaseQRankSum=0.967;DP=3;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=8.75;ReadPosRankSum=-0.967;SOR=0.223 GT:AD:DP:GQ:PL ./. 1/1:0,2:2:3:45,3,0 0/0:1,0:1:3:0,3,37 +20 10012362 . G T 12.77 . AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=37.00;QD=12.77;SOR=1.609 GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3:39,3,0 ./. +20 10019093 . A G 9258.92 . AC=3;AF=0.500;AN=6;BaseQRankSum=10.512;DP=750;ExcessHet=6.9897;FS=0.000;MLEAC=3;MLEAF=0.500;MQ=59.13;MQRankSum=-0.972;QD=12.44;ReadPosRankSum=-0.521;SOR=0.653 GT:AD:DP:GQ:PL 0/1:138,110:250:99:3166,0,3854 0/1:131,117:250:99:3346,0,3750 0/1:146,102:250:99:2777,0,4107 +20 10024107 . C T 26.29 . AC=2;AF=0.333;AN=6;BaseQRankSum=2.121;DP=15;ExcessHet=3.9794;FS=0.000;MLEAC=2;MLEAF=0.333;MQ=60.00;MQRankSum=0.000;QD=2.92;ReadPosRankSum=-0.768;SOR=0.446 GT:AD:DP:GQ:PL 0/1:3,1:4:27:27,0,101 0/0:6,0:6:18:0,18,215 0/1:4,1:5:31:31,0,81 +20 10026108 . A G 23.15 . AC=1;AF=0.167;AN=6;BaseQRankSum=0.684;DP=38;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.167;MQ=59.27;MQRankSum=0.000;QD=2.57;ReadPosRankSum=-1.346;SOR=0.007 GT:AD:DP:GQ:PL 0/0:14,0:15:39:0,39,513 0/1:7,2:9:54:54,0,255 0/0:14,0:14:42:0,42,541 +20 10026357 . T C 3067.16 . AC=2;AF=0.333;AN=6;BaseQRankSum=7.144;DP=288;ExcessHet=3.9794;FS=2.821;MLEAC=2;MLEAF=0.333;MQ=59.58;MQRankSum=-1.089;QD=15.57;ReadPosRankSum=-1.425;SOR=0.890 GT:AD:DP:GQ:PL 0/1:41,46:87:99:1310,0,1044 0/0:90,0:90:99:0,220,2870 0/1:51,59:111:99:1789,0,1374 +20 10026794 . C T 11.83 . AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=11.83;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:38,3,0 ./. ./. +20 10030188 . T A 3747.16 . AC=2;AF=0.333;AN=6;BaseQRankSum=3.540;DP=386;ExcessHet=3.9794;FS=0.394;MLEAC=2;MLEAF=0.333;MQ=59.27;MQRankSum=1.297;QD=15.11;ReadPosRankSum=-1.340;SOR=0.728 GT:AD:DP:GQ:PL 0/1:47,47:94:99:1333,0,1308 0/0:136,0:137:99:0,328,4257 0/1:64,90:154:99:2446,0,1566 +20 10030931 . C A 56.23 . AC=1;AF=0.167;AN=6;BaseQRankSum=1.176;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.167;MQ=59.34;MQRankSum=-2.600;QD=5.62;ReadPosRankSum=0.111;SOR=0.027 GT:AD:DP:GQ:PL 0/0:9,0:9:24:0,24,299 0/1:7,3:10:87:87,0,229 0/0:15,1:16:16:0,16,440 +20 10031342 . G A 18.59 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=9.30;SOR=0.693 GT:AD:DP:GQ:PL ./. 1/1:0,2:2:3:45,3,0 ./. +20 10031798 . G A 100.34 . AC=6;AF=1.00;AN=6;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=6;MLEAF=1.00;MQ=60.00;QD=33.66;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,1:1:3:40,3,0 1/1:0,2:2:3:45,3,0 1/1:0,1:1:3:39,3,0 +20 10031827 . C T 17.49 . AC=2;AF=0.500;AN=4;BaseQRankSum=-0.967;DP=3;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=8.75;ReadPosRankSum=0.000;SOR=0.223 GT:AD:DP:GQ:PL 1/1:0,2:2:3:45,3,0 0/0:1,0:1:3:0,3,42 ./. +20 10032413 . T G 3643.16 . AC=2;AF=0.333;AN=6;BaseQRankSum=-0.287;DP=355;ExcessHet=3.9794;FS=0.435;MLEAC=2;MLEAF=0.333;MQ=59.61;MQRankSum=-0.412;QD=14.12;ReadPosRankSum=0.065;SOR=0.727 GT:AD:DP:GQ:PL 0/1:56,68:124:99:2087,0,1530 0/0:97,0:97:99:0,250,3265 0/1:76,58:134:99:1588,0,2067 +20 10034546 . T C 11.83 . AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=11.83;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:38,3,0 ./. ./. +20 10036107 . T G 12.39 . AC=1;AF=0.167;AN=6;BaseQRankSum=-4.520;DP=117;ExcessHet=3.0103;FS=5.027;MLEAC=1;MLEAF=0.167;MQ=58.08;MQRankSum=0.486;QD=0.28;ReadPosRankSum=-2.268;SOR=2.833 GT:AD:DP:GQ:PL 0/0:29,20:49:28:0,28,561 0/0:17,7:24:39:0,39,462 0/1:21,23:44:43:43,0,518 +20 10037877 . G C 16.67 . AC=2;AF=0.333;AN=6;BaseQRankSum=0.000;DP=7;ExcessHet=0.4576;FS=0.000;MLEAC=2;MLEAF=0.333;MQ=56.62;MQRankSum=0.000;QD=8.34;ReadPosRankSum=0.842;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:3:45,3,0 0/0:3,0:3:3:0,3,45 0/0:2,0:2:3:0,3,45 +20 10043441 . T A 11.12 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=2.78;ReadPosRankSum=-1.383;SOR=0.693 GT:AD:DP:GQ:PL ./. 0/1:2,2:4:38:39,0,38 ./. +20 10044282 . T C 150.42 . AC=1;AF=0.167;AN=6;BaseQRankSum=-1.564;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.167;MQ=58.33;MQRankSum=0.000;QD=16.71;ReadPosRankSum=0.150;SOR=1.688 GT:AD:DP:GQ:PL 0/0:2,0:2:6:0,6,74 0/1:1,8:9:18:180,0,18 0/0:3,0:3:9:0,9,108 +20 10044849 . A G 57.17 . AC=2;AF=0.500;AN=4;BaseQRankSum=-0.253;DP=5;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=19.06;ReadPosRankSum=-1.645;SOR=1.179 GT:AD:DP:GQ:PL ./. 0/0:2,0:2:3:0,3,45 1/1:0,3:3:6:86,6,0 +20 10045078 . G T 12.77 . AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=12.77;SOR=1.609 GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3:39,3,0 ./. +20 10046489 . C T 11.83 . AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=11.83;SOR=1.609 GT:AD:DP:GQ:PL ./. ./. 1/1:0,1:1:3:38,3,0 +20 10047597 . C A 12.77 . AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=12.77;SOR=1.609 GT:AD:DP:GQ:PL ./. ./. 1/1:0,1:1:3:39,3,0 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testHasNoAnnotsAsking1.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testHasNoAnnotsAsking1.vcf.idx new file mode 100644 index 0000000000000000000000000000000000000000..abd0e528e898b82c6d7bb95b921262b527c9ed98 GIT binary patch literal 353 zcmWIXbctYOU|?Vd;)6vh_6)Xc2boLMR3t=!dVgR`XXe+}4eg-Ze6XrA% OAlpv`NKlc6g#iE +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##GATKCommandLine.UnifiedGenotyper= +##GATKCommandLine.VariantAnnotator= +##INFO= +##INFO= +##INFO= +##contig= +##contig= +##reference=file:///Users/emeryj/hellbender/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 NA12891 NA12892 +20 10000598 . T A 18.59 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL ./. 1/1:2:3:45,3,0 ./. +20 10001617 . C A 12.77 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL 1/1:1:3:39,3,0 ./. ./. +20 10001628 . G A 18.59 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL 1/1:2:3:45,3,0 ./. ./. +20 10001661 . T C 17.49 . MLEAC=2;MLEAF=0.500 GT:DP:GQ:PL 1/1:2:3:45,3,0 ./. 0/0:1:3:0,3,39 +20 10001670 . T G 14.57 . MLEAC=2;MLEAF=0.500 GT:DP:GQ:PL 1/1:1:3:42,3,0 ./. 0/0:2:3:0,3,45 +20 10002138 . C G 16.63 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL 1/1:1:3:43,3,0 ./. ./. +20 10002142 . G C 16.63 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL 1/1:1:3:43,3,0 ./. ./. +20 10003021 . C T 12.77 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL ./. 1/1:1:3:39,3,0 ./. +20 10003358 . A C 15.65 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL ./. 1/1:1:3:42,3,0 ./. +20 10003651 . T C 53.42 . MLEAC=4;MLEAF=1.00 GT:DP:GQ:PL 1/1:1:3:33,3,0 1/1:2:3:45,3,0 ./. +20 10003692 . A G 12.77 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL ./. 1/1:1:3:39,3,0 ./. +20 10003832 . G A 53.42 . MLEAC=4;MLEAF=1.00 GT:DP:GQ:PL ./. 1/1:1:3:39,3,0 1/1:1:3:39,3,0 +20 10004094 . A C 14.68 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL ./. ./. 1/1:1:3:41,3,0 +20 10004351 . C G 56.42 . MLEAC=4;MLEAF=1.00 GT:DP:GQ:PL ./. 1/1:1:3:39,3,0 1/1:1:3:42,3,0 +20 10004389 . T G 15.65 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL ./. ./. 1/1:1:3:42,3,0 +20 10004610 . A C 14.68 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL ./. 1/1:1:3:41,3,0 ./. +20 10004725 . A G 14.68 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL ./. 1/1:1:3:41,3,0 ./. +20 10004874 . A C 59.42 . MLEAC=4;MLEAF=1.00 GT:DP:GQ:PL ./. 1/1:1:3:42,3,0 1/1:1:3:42,3,0 +20 10004887 . A G 14.57 . MLEAC=2;MLEAF=0.500 GT:DP:GQ:PL ./. 0/0:1:3:0,3,38 1/1:1:3:42,3,0 +20 10005010 . C T 18.59 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL ./. 1/1:2:3:45,3,0 ./. +20 10005427 . C T 17.49 . MLEAC=2;MLEAF=0.500 GT:DP:GQ:PL ./. 1/1:2:3:45,3,0 0/0:1:3:0,3,41 +20 10005723 . A G 10.90 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL ./. 1/1:1:3:37,3,0 ./. +20 10006682 . T A 12.77 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL ./. ./. 1/1:1:3:39,3,0 +20 10007352 . C T 204.23 . MLEAC=6;MLEAF=1.00 GT:DP:GQ:PL 1/1:1:3:39,3,0 1/1:3:6:79,6,0 1/1:4:9:111,9,0 +20 10008221 . T C 61.42 . MLEAC=4;MLEAF=1.00 GT:DP:GQ:PL 1/1:1:3:41,3,0 ./. 1/1:2:3:45,3,0 +20 10009227 . A G 18.59 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL ./. ./. 1/1:2:3:45,3,0 +20 10009246 . A G 18.59 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL ./. ./. 1/1:2:3:45,3,0 +20 10009446 . G T 12.77 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL ./. ./. 1/1:1:3:39,3,0 +20 10009512 . C G 15.65 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL ./. ./. 1/1:1:3:42,3,0 +20 10009795 . A G 13.72 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL 1/1:1:3:40,3,0 ./. ./. +20 10011075 . C T 17.49 . MLEAC=2;MLEAF=0.500 GT:DP:GQ:PL ./. 1/1:2:3:45,3,0 0/0:1:3:0,3,37 +20 10012362 . G T 12.77 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL ./. 1/1:1:3:39,3,0 ./. +20 10019093 . A G 9258.92 . MLEAC=3;MLEAF=0.500 GT:DP:GQ:PL 0/1:250:99:3166,0,3854 0/1:250:99:3346,0,3750 0/1:250:99:2777,0,4107 +20 10024107 . C T 26.29 . MLEAC=2;MLEAF=0.333 GT:DP:GQ:PL 0/1:4:27:27,0,101 0/0:6:18:0,18,215 0/1:5:31:31,0,81 +20 10026108 . A G 23.15 . MLEAC=1;MLEAF=0.167 GT:DP:GQ:PL 0/0:15:39:0,39,513 0/1:9:54:54,0,255 0/0:14:42:0,42,541 +20 10026357 . T C 3067.16 . MLEAC=2;MLEAF=0.333 GT:DP:GQ:PL 0/1:87:99:1310,0,1044 0/0:90:99:0,220,2870 0/1:111:99:1789,0,1374 +20 10026794 . C T 11.83 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL 1/1:1:3:38,3,0 ./. ./. +20 10030188 . T A 3747.16 . MLEAC=2;MLEAF=0.333 GT:DP:GQ:PL 0/1:94:99:1333,0,1308 0/0:137:99:0,328,4257 0/1:154:99:2446,0,1566 +20 10030931 . C A 56.23 . MLEAC=1;MLEAF=0.167 GT:DP:GQ:PL 0/0:9:24:0,24,299 0/1:10:87:87,0,229 0/0:16:16:0,16,440 +20 10031342 . G A 18.59 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL ./. 1/1:2:3:45,3,0 ./. +20 10031798 . G A 100.34 . MLEAC=6;MLEAF=1.00 GT:DP:GQ:PL 1/1:1:3:40,3,0 1/1:2:3:45,3,0 1/1:1:3:39,3,0 +20 10031827 . C T 17.49 . MLEAC=2;MLEAF=0.500 GT:DP:GQ:PL 1/1:2:3:45,3,0 0/0:1:3:0,3,42 ./. +20 10032413 . T G 3643.16 . MLEAC=2;MLEAF=0.333 GT:DP:GQ:PL 0/1:124:99:2087,0,1530 0/0:97:99:0,250,3265 0/1:134:99:1588,0,2067 +20 10034546 . T C 11.83 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL 1/1:1:3:38,3,0 ./. ./. +20 10036107 . T G 12.39 . MLEAC=1;MLEAF=0.167 GT:DP:GQ:PL 0/0:49:28:0,28,561 0/0:24:39:0,39,462 0/1:44:43:43,0,518 +20 10037877 . G C 16.67 . MLEAC=2;MLEAF=0.333 GT:DP:GQ:PL 1/1:2:3:45,3,0 0/0:3:3:0,3,45 0/0:2:3:0,3,45 +20 10043441 . T A 11.12 . MLEAC=1;MLEAF=0.500 GT:DP:GQ:PL ./. 0/1:4:38:39,0,38 ./. +20 10044282 . T C 150.42 . MLEAC=1;MLEAF=0.167 GT:DP:GQ:PL 0/0:2:6:0,6,74 0/1:9:18:180,0,18 0/0:3:9:0,9,108 +20 10044849 . A G 57.17 . MLEAC=2;MLEAF=0.500 GT:DP:GQ:PL ./. 0/0:2:3:0,3,45 1/1:3:6:86,6,0 +20 10045078 . G T 12.77 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL ./. 1/1:1:3:39,3,0 ./. +20 10046489 . C T 11.83 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL ./. ./. 1/1:1:3:38,3,0 +20 10047597 . C A 12.77 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL ./. ./. 1/1:1:3:39,3,0 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testHasNoAnnotsNotAsking1.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testHasNoAnnotsNotAsking1.vcf.idx new file mode 100644 index 0000000000000000000000000000000000000000..980c9daa86648e05c699a830b548cdb06ca55f70 GIT binary patch literal 356 zcmWIXbctYOU|?Vd;N`chG!}NtY26;OAIlF>oV1my6p?)C@rbY}Pw*YNrSisM~1!TgU QW&&i#$N~u}(y%Z90N+_h+W-In literal 0 HcmV?d00001 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testHsAnnotsNotAsking1.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testHsAnnotsNotAsking1.vcf new file mode 100644 index 00000000000..91829f671be --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/expected/testHsAnnotsNotAsking1.vcf @@ -0,0 +1,75 @@ +##fileformat=VCFv4.2 +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##GATKCommandLine.VariantAnnotator= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##contig= +##contig= +##reference=file:///Users/emeryj/hellbender/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 NA12891 NA12892 +20 10000598 . T A 18.59 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. 1/1:2:3:45,3,0 ./. +20 10001617 . C A 12.77 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL 1/1:1:3:39,3,0 ./. ./. +20 10001628 . G A 18.59 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL 1/1:2:3:45,3,0 ./. ./. +20 10001661 . T C 17.49 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=0.500;MQ0=0;OND=0.00 GT:DP:GQ:PL 1/1:2:3:45,3,0 ./. 0/0:1:3:0,3,39 +20 10001670 . T G 14.57 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=0.500;MQ0=0;OND=0.00 GT:DP:GQ:PL 1/1:1:3:42,3,0 ./. 0/0:2:3:0,3,45 +20 10002138 . C G 16.63 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL 1/1:1:3:43,3,0 ./. ./. +20 10002142 . G C 16.63 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL 1/1:1:3:43,3,0 ./. ./. +20 10003021 . C T 12.77 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. 1/1:1:3:39,3,0 ./. +20 10003358 . A C 15.65 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. 1/1:1:3:42,3,0 ./. +20 10003651 . T C 53.42 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=4;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL 1/1:1:3:33,3,0 1/1:2:3:45,3,0 ./. +20 10003692 . A G 12.77 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. 1/1:1:3:39,3,0 ./. +20 10003832 . G A 53.42 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=4;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. 1/1:1:3:39,3,0 1/1:1:3:39,3,0 +20 10004094 . A C 14.68 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. ./. 1/1:1:3:41,3,0 +20 10004351 . C G 56.42 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=4;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. 1/1:1:3:39,3,0 1/1:1:3:42,3,0 +20 10004389 . T G 15.65 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. ./. 1/1:1:3:42,3,0 +20 10004610 . A C 14.68 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. 1/1:1:3:41,3,0 ./. +20 10004725 . A G 14.68 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. 1/1:1:3:41,3,0 ./. +20 10004874 . A C 59.42 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=4;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. 1/1:1:3:42,3,0 1/1:1:3:42,3,0 +20 10004887 . A G 14.57 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=0.500;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. 0/0:1:3:0,3,38 1/1:1:3:42,3,0 +20 10005010 . C T 18.59 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. 1/1:2:3:45,3,0 ./. +20 10005427 . C T 17.49 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=0.500;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. 1/1:2:3:45,3,0 0/0:1:3:0,3,41 +20 10005723 . A G 10.90 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. 1/1:1:3:37,3,0 ./. +20 10006682 . T A 12.77 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. ./. 1/1:1:3:39,3,0 +20 10007352 . C T 204.23 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=6;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL 1/1:1:3:39,3,0 1/1:3:6:79,6,0 1/1:4:9:111,9,0 +20 10008221 . T C 61.42 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=4;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL 1/1:1:3:41,3,0 ./. 1/1:2:3:45,3,0 +20 10009227 . A G 18.59 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. ./. 1/1:2:3:45,3,0 +20 10009246 . A G 18.59 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. ./. 1/1:2:3:45,3,0 +20 10009446 . G T 12.77 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. ./. 1/1:1:3:39,3,0 +20 10009512 . C G 15.65 . 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C T 905.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=2.136;ClippingRankSum=0.000;DP=64;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.71;MQ0=0;MQRankSum=0.913;NCC=0;QD=14.15;ReadPosRankSum=-0.481;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:36,28:0:0,0:0,0:99:0:0,0:0:0:934,0,1248:0,0,0,0:0 +20 10000211 . C T 941.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=2.000;ClippingRankSum=0.000;DP=56;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.67;MQ0=0;MQRankSum=1.037;NCC=0;QD=16.82;ReadPosRankSum=0.996;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:28,28:0:0,0:0,0:99:0:0,0:0:0:970,0,906:0,0,0,0:0 +20 10000439 . T G 2804.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=80;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.06;MQ0=0;NCC=0;QD=25.36;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,80:0:0,0:0,0:99:0:0,0:0:0:2833,240,0:0,0,0,0:0 +20 10000598 . T A 1941.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=50;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=55.36;MQ0=0;NCC=0;QD=28.73;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,50:0:0,0:0,0:99:0:0,0:0:0:1970,147,0:0,0,0,0:0 +20 10000694 . G A 1008.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=3.709;ClippingRankSum=0.000;DP=86;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=47.86;MQ0=1;MQRankSum=-5.073;NCC=0;QD=11.73;ReadPosRankSum=0.779;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:48,38:0:0,0:0,0:99:0:0,0:0:0:1037,0,1601:0,0,0,0:0 +20 10000758 . T A 3838.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=95;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=53.37;MQ0=0;NCC=0;QD=30.97;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,95:0:0,0:0,0:99:0:0,0:0:0:3867,286,0:0,0,0,0:0 +20 10001019 . T G 650.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-2.344;ClippingRankSum=0.000;DP=73;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=47.38;MQ0=5;MQRankSum=-7.093;NCC=0;QD=8.91;ReadPosRankSum=-0.762;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:41,32:0:0,0:0,0:99:0:0,0:0:0:679,0,1426:0,0,0,0:0 +20 10001298 . T A 2917.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=74;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=54.34;MQ0=0;NCC=0;QD=27.24;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,73:0:0,0:0,0:99:0:0,0:0:0:2946,220,0:0,0,0,0:0 +20 10001436 . A AAGGCT 2301.73 . AC=2;AF=1.00;AN=2;AS_MQ;DP=49;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=42.31;MQ0=0;NCC=0;QD=28.20;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,0:0:0,0:0,0:99:0:0,0:0:0:2339,156,0:0,0,0,0:0 +20 10001474 . C T 2640.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=74;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=43.69;MQ0=0;NCC=0;QD=25.00;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,74:0:0,0:0,0:99:0:0,0:0:0:2669,219,0:0,0,0,0:0 +20 10001617 . C A 1731.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=1.143;ClippingRankSum=0.000;DP=104;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.01;MQ0=0;MQRankSum=1.394;NCC=0;QD=16.65;ReadPosRankSum=-0.725;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:52,52:0:0,0:0,0:99:0:0,0:0:0:1760,0,1781:0,0,0,0:0 +20 10001628 . G A 3898.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=96;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.17;MQ0=0;NCC=0;QD=29.56;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,95:0:0,0:0,0:99:0:0,0:0:0:3927,285,0:0,0,0,0:0 +20 10001661 . T C 3606.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=82;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=58.35;MQ0=0;NCC=0;QD=30.62;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,82:0:0,0:0,0:99:0:0,0:0:0:3635,249,0:0,0,0,0:0 +20 10001670 . T G 3673.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=82;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=57.48;MQ0=0;NCC=0;QD=28.17;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,82:0:0,0:0,0:99:0:0,0:0:0:3702,253,0:0,0,0,0:0 +20 10002058 . T G 2963.77 . AC=2;AF=1.00;AN=2;AS_MQ;BaseQRankSum=1.913;ClippingRankSum=0.000;DP=77;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=57.45;MQ0=0;MQRankSum=2.847;NCC=0;QD=26.80;ReadPosRankSum=0.518;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:1,76:0:0,0:0,0:99:0:0,0:0:0:2992,216,0:0,0,0,0:0 +20 10002099 . C T 1194.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-0.390;ClippingRankSum=0.000;DP=69;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=55.29;MQ0=0;MQRankSum=-1.284;NCC=0;QD=17.32;ReadPosRankSum=-0.352;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:29,40:0:0,0:0,0:99:0:0,0:0:0:1223,0,844:0,0,0,0:0 +20 10002138 . C G 2443.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=56;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=54.99;MQ0=0;NCC=0;QD=26.00;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,56:0:0,0:0,0:99:0:0,0:0:0:2472,169,0:0,0,0,0:0 +20 10002142 . G C 2407.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=55;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=54.90;MQ0=0;NCC=0;QD=30.02;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,55:0:0,0:0,0:99:0:0,0:0:0:2436,166,0:0,0,0,0:0 +20 10002470 . C T 2522.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=70;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=46.87;MQ0=1;NCC=0;QD=31.98;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:1,69:0:0,0:0,0:99:0:0,0:0:0:2551,189,0:0,0,0,0:0 +20 10002625 . G T 2665.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=64;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.05;MQ0=0;NCC=0;QD=27.51;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,64:0:0,0:0,0:99:0:0,0:0:0:2694,193,0:0,0,0,0:0 +20 10003021 . C T 2383.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=62;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.02;MQ0=0;NCC=0;QD=29.11;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,62:0:0,0:0,0:99:0:0,0:0:0:2412,181,0:0,0,0,0:0 +20 10003358 . A C 1454.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=0.452;ClippingRankSum=0.000;DP=90;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.54;MQ0=0;MQRankSum=1.011;NCC=0;QD=16.16;ReadPosRankSum=-0.809;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:45,45:0:0,0:0,0:99:0:0,0:0:0:1483,0,1477:0,0,0,0:0 +20 10003651 . T C 3620.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=93;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.19;MQ0=0;NCC=0;QD=28.08;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,93:0:0,0:0,0:99:0:0,0:0:0:3649,279,0:0,0,0,0:0 +20 10003692 . A G 2609.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=70;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.13;MQ0=0;NCC=0;QD=23.23;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,70:0:0,0:0,0:99:0:0,0:0:0:2638,205,0:0,0,0,0:0 +20 10003832 . G A 2705.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=66;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=57.13;MQ0=0;NCC=0;QD=29.03;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,66:0:0,0:0,0:99:0:0,0:0:0:2734,199,0:0,0,0,0:0 +20 10004094 . A C 1825.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=52;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=52.95;MQ0=1;NCC=0;QD=30.67;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:1,51:0:0,0:0,0:99:0:0,0:0:0:1854,157,0:0,0,0,0:0 +20 10004147 . A G 1837.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=54;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=55.19;MQ0=0;NCC=0;QD=34.03;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,54:0:0,0:0,0:99:0:0,0:0:0:1866,156,0:0,0,0,0:0 +20 10004193 . G T 916.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-0.276;ClippingRankSum=0.000;DP=55;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=58.92;MQ0=0;MQRankSum=3.395;NCC=0;QD=16.67;ReadPosRankSum=1.189;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:25,30:0:0,0:0,0:99:0:0,0:0:0:945,0,776:0,0,0,0:0 +20 10004222 . C CA 12.96 . AC=1;AF=0.500;AN=2;AS_MQ;DP=68;ExcessHet=3.0103;FS=0.000;GQ_MEAN=50.00;MQ=58.08;MQ0=0;NCC=0;QD=0.19;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:0,0:0:0,0:0,0:50:0:0,0:0:0:50,0,923:0,0,0,0:0 +20 10004223 . A AG 47.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=72;ExcessHet=3.0103;FS=0.000;GQ_MEAN=85.00;MQ=56.79;MQ0=0;NCC=0;QD=0.66;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:0,0:0:0,0:0,0:85:0:0,0:0:0:85,0,982:0,0,0,0:0 +20 10004351 . C G 2755.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=70;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.04;MQ0=0;NCC=0;QD=26.61;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,70:0:0,0:0,0:99:0:0,0:0:0:2784,211,0:0,0,0,0:0 +20 10004389 . T G 2494.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=62;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=56.74;MQ0=0;NCC=0;QD=29.20;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,62:0:0,0:0,0:99:0:0,0:0:0:2523,187,0:0,0,0,0:0 +20 10004610 . A C 3625.77 . AC=2;AF=1.00;AN=2;AS_MQ;BaseQRankSum=1.841;ClippingRankSum=0.000;DP=92;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=58.27;MQ0=0;MQRankSum=3.565;NCC=0;QD=28.55;ReadPosRankSum=0.000;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:1,91:0:0,0:0,0:99:0:0,0:0:0:3654,267,0:0,0,0,0:0 +20 10004725 . A G 951.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-2.142;ClippingRankSum=0.000;DP=66;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=55.34;MQ0=0;MQRankSum=3.059;NCC=0;QD=14.42;ReadPosRankSum=1.896;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:35,31:0:0,0:0,0:99:0:0,0:0:0:980,0,1168:0,0,0,0:0 +20 10004769 . TAAAACTATGC T 981.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=71;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=51.81;MQ0=0;NCC=0;QD=13.83;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:0,0:0:0,0:0,0:99:0:0,0:0:0:1019,0,1470:0,0,0,0:0 +20 10004874 . A C 3602.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=87;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.33;MQ0=0;NCC=0;QD=34.42;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,87:0:0,0:0,0:99:0:0,0:0:0:3631,261,0:0,0,0,0:0 +20 10004887 . A G 1323.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=0.356;ClippingRankSum=0.000;DP=86;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.46;MQ0=0;MQRankSum=-0.067;NCC=0;QD=15.39;ReadPosRankSum=-1.198;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:46,40:0:0,0:0,0:99:0:0,0:0:0:1352,0,1542:0,0,0,0:0 +20 10005010 . C T 2934.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=75;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.38;MQ0=0;NCC=0;QD=28.53;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,75:0:0,0:0,0:99:0:0,0:0:0:2963,217,0:0,0,0,0:0 +20 10005427 . C T 2214.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=57;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.60;MQ0=0;NCC=0;QD=27.23;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,57:0:0,0:0,0:99:0:0,0:0:0:2243,165,0:0,0,0,0:0 +20 10005499 . A G 3053.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=76;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=60.00;MQ0=0;NCC=0;QD=29.52;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,76:0:0,0:0,0:99:0:0,0:0:0:3082,229,0:0,0,0,0:0 +20 10005587 . A G 1229.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-0.834;ClippingRankSum=0.000;DP=74;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.12;MQ0=0;MQRankSum=-0.972;NCC=0;QD=16.85;ReadPosRankSum=0.259;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:36,37:0:0,0:0,0:99:0:0,0:0:0:1258,0,1236:0,0,0,0:0 +20 10005723 . A G 3062.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=87;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.52;MQ0=0;NCC=0;QD=33.47;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,87:0:0,0:0,0:99:0:0,0:0:0:3091,258,0:0,0,0,0:0 +20 10006291 . G A 978.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=0.311;ClippingRankSum=0.000;DP=85;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.29;MQ0=0;MQRankSum=-1.081;NCC=0;QD=11.51;ReadPosRankSum=-1.363;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:54,31:0:0,0:0,0:99:0:0,0:0:0:1007,0,1905:0,0,0,0:0 +20 10006404 . A C 2928.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=79;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.18;MQ0=0;NCC=0;QD=32.91;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,79:0:0,0:0,0:99:0:0,0:0:0:2957,228,0:0,0,0,0:0 +20 10006682 . T A 2874.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=76;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.14;MQ0=0;NCC=0;QD=31.31;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,75:0:0,0:0,0:99:0:0,0:0:0:2903,219,0:0,0,0,0:0 +20 10006819 . AAAAC A 2531.73 . AC=2;AF=1.00;AN=2;AS_MQ;DP=78;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=60.57;MQ0=0;NCC=0;QD=32.46;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,0:0:0,0:0,0:99:0:0,0:0:0:2569,176,0:0,0,0,0:0 +20 10007150 . G C 669.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-4.476;ClippingRankSum=0.000;DP=64;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=60.00;MQ0=0;MQRankSum=0.000;NCC=0;QD=10.47;ReadPosRankSum=-1.047;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:38,26:0:0,0:0,0:99:0:0,0:0:0:698,0,1479:0,0,0,0:0 +20 10007175 . C T 1350.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=2.249;ClippingRankSum=0.000;DP=63;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.63;MQ0=0;MQRankSum=1.319;NCC=0;QD=21.44;ReadPosRankSum=-0.313;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:24,39:0:0,0:0,0:99:0:0,0:0:0:1379,0,780:0,0,0,0:0 +20 10007352 . C T 2764.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=71;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.35;MQ0=0;NCC=0;QD=31.45;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,71:0:0,0:0,0:99:0:0,0:0:0:2793,208,0:0,0,0,0:0 +20 10007531 . A G 2920.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=73;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.36;MQ0=0;NCC=0;QD=33.27;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,73:0:0,0:0,0:99:0:0,0:0:0:2949,217,0:0,0,0,0:0 +20 10007980 . A C 3524.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=93;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=60.11;MQ0=0;NCC=0;QD=31.26;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,93:0:0,0:0,0:99:0:0,0:0:0:3553,270,0:0,0,0,0:0 +20 10008029 . T TA 1986.73 . AC=2;AF=1.00;AN=2;AS_MQ;DP=89;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=60.92;MQ0=0;NCC=0;QD=22.32;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,0:0:0,0:0,0:99:0:0,0:0:0:2024,145,0:0,0,0,0:0 +20 10008146 . TA T 2141.73 . AC=2;AF=1.00;AN=2;AS_MQ;DP=74;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=60.27;MQ0=0;NCC=0;QD=28.94;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,0:0:0,0:0,0:99:0:0,0:0:0:2179,211,0:0,0,0,0:0 +20 10008221 . T C 3224.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=80;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=60.17;MQ0=0;NCC=0;QD=27.76;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,80:0:0,0:0,0:99:0:0,0:0:0:3253,240,0:0,0,0,0:0 +20 10008458 . T G 2654.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=73;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=52.14;MQ0=0;NCC=0;QD=29.09;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,73:0:0,0:0,0:99:0:0,0:0:0:2683,207,0:0,0,0,0:0 +20 10008742 . G T 715.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=3.649;ClippingRankSum=0.000;DP=55;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=36.14;MQ0=0;MQRankSum=-1.453;NCC=0;QD=13.01;ReadPosRankSum=0.554;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:25,30:0:0,0:0,0:99:0:0,0:0:0:744,0,580:0,0,0,0:0 +20 10008758 . C CA 684.14 . AC=2;AF=1.00;AN=2;AS_MQ;DP=54;ExcessHet=3.0103;FS=0.000;GQ_MEAN=10.00;MQ=34.98;MQ0=0;NCC=0;QD=12.67;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,0:0:0,0:0,0:10:0:0,0:0:0:721,10,0:0,0,0,0:0 +20 10008921 . C CA 253.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=52;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=56.17;MQ0=0;NCC=0;QD=4.88;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:0,0:0:0,0:0,0:99:0:0,0:0:0:291,0,366:0,0,0,0:0 +20 10008948 . TA T 2057.73 . AC=2;AF=1.00;AN=2;AS_MQ;DP=53;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=51.20;MQ0=0;NCC=0;QD=26.08;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,0:0:0,0:0,0:99:0:0,0:0:0:2095,107,0:0,0,0,0:0 +20 10008952 . CACACACACACA C,CCACACACACA 1666.73 . AC=1,1;AF=0.500,0.500;AN=2;AS_MQ;DP=52;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=50.48;MQ0=0;NCC=0;QD=32.05;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/2:0,0,0:0:0,0,0:0,0,0:99:0,0:0,0,0:0,0:0,0:1704,525,844,582,0,531:0,0,0,0:0 +20 10009227 . A G 1369.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-2.220;ClippingRankSum=0.000;DP=63;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=56.90;MQ0=0;MQRankSum=1.428;NCC=0;QD=21.74;ReadPosRankSum=-1.210;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:24,39:0:0,0:0,0:99:0:0,0:0:0:1398,0,740:0,0,0,0:0 +20 10009246 . A G 3002.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=77;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=56.09;MQ0=0;NCC=0;QD=33.85;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,77:0:0,0:0,0:99:0:0,0:0:0:3031,231,0:0,0,0,0:0 +20 10009400 . T A 2998.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=74;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=60.00;MQ0=0;NCC=0;QD=27.08;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,74:0:0,0:0,0:99:0:0,0:0:0:3027,223,0:0,0,0,0:0 +20 10009512 . C G 3039.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=77;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=58.47;MQ0=0;NCC=0;QD=25.42;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,77:0:0,0:0,0:99:0:0,0:0:0:3068,231,0:0,0,0,0:0 +20 10009719 . A G 1895.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=64;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.35;MQ0=0;NCC=0;QD=29.62;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,64:0:0,0:0,0:99:0:0,0:0:0:1924,175,0:0,0,0,0:0 +20 10009795 . A G 1880.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=47;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.60;MQ0=0;NCC=0;QD=27.65;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,47:0:0,0:0,0:99:0:0,0:0:0:1909,141,0:0,0,0,0:0 +20 10009842 . G GAA 532.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=57;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=52.14;MQ0=0;NCC=0;QD=9.35;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:0,0:0:0,0:0,0:99:0:0,0:0:0:570,0,690:0,0,0,0:0 +20 10009844 . G A 661.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=2.612;ClippingRankSum=0.000;DP=57;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=52.14;MQ0=0;MQRankSum=4.782;NCC=0;QD=11.61;ReadPosRankSum=2.939;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:10,47:0:0,0:0,0:99:0:0,0:0:0:690,0,586:0,0,0,0:0 +20 10009871 . A G 658.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-1.969;ClippingRankSum=0.000;DP=61;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=50.95;MQ0=0;MQRankSum=2.062;NCC=0;QD=10.80;ReadPosRankSum=0.479;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:20,41:0:0,0:0,0:99:0:0,0:0:0:687,0,594:0,0,0,0:0 +20 10009875 . A G,AGGGAGG 2369.73 . AC=1,1;AF=0.500,0.500;AN=2;AS_MQ;BaseQRankSum=0.473;ClippingRankSum=0.000;DP=59;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=50.61;MQ0=0;MQRankSum=1.097;NCC=0;QD=29.48;ReadPosRankSum=0.565;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/2:0,0,0:0:0,0,0:0,0,0:99:0,0:0,0,0:0,0:0,0:2407,645,533,697,0,574:0,0,0,0:0 +20 10009879 . A G 2244.77 . AC=2;AF=1.00;AN=2;AS_MQ;BaseQRankSum=0.680;ClippingRankSum=0.000;DP=52;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=51.08;MQ0=0;MQRankSum=1.014;NCC=0;QD=30.56;ReadPosRankSum=2.106;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:5,47:0:0,0:0,0:99:0:0,0:0:0:2273,150,0:0,0,0,0:0 +20 10009883 . A G 2151.77 . AC=2;AF=1.00;AN=2;AS_MQ;BaseQRankSum=-0.492;ClippingRankSum=0.000;DP=52;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=51.84;MQ0=0;MQRankSum=1.835;NCC=0;QD=33.63;ReadPosRankSum=1.408;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:2,50:0:0,0:0,0:99:0:0,0:0:0:2180,147,0:0,0,0,0:0 +20 10010393 . T G 1464.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-3.075;ClippingRankSum=0.000;DP=80;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.42;MQ0=0;MQRankSum=-1.302;NCC=0;QD=18.31;ReadPosRankSum=-1.781;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:37,43:0:0,0:0,0:99:0:0,0:0:0:1493,0,1230:0,0,0,0:0 +20 10010536 . G GA 2462.73 . AC=2;AF=1.00;AN=2;AS_MQ;DP=85;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=61.63;MQ0=0;NCC=0;QD=28.97;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,0:0:0,0:0,0:99:0:0,0:0:0:2500,243,0:0,0,0,0:0 +20 10010766 . T G 2411.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=68;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.66;MQ0=0;NCC=0;QD=30.55;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,67:0:0,0:0,0:99:0:0,0:0:0:2440,199,0:0,0,0,0:0 +20 10010832 . T C 2951.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=75;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.50;MQ0=0;NCC=0;QD=32.62;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,75:0:0,0:0,0:99:0:0,0:0:0:2980,226,0:0,0,0,0:0 +20 10011075 . C T 1325.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=5.459;ClippingRankSum=0.000;DP=86;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.73;MQ0=0;MQRankSum=0.956;NCC=0;QD=15.42;ReadPosRankSum=-0.845;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:46,40:0:0,0:0,0:99:0:0,0:0:0:1354,0,1333:0,0,0,0:0 +20 10011309 . T C 2692.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=78;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=60.00;MQ0=0;NCC=0;QD=34.52;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,78:0:0,0:0,0:99:0:0,0:0:0:2721,231,0:0,0,0,0:0 +20 10011517 . GA G 490.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=91;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.90;MQ0=0;NCC=0;QD=5.39;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:0,0:0:0,0:0,0:99:0:0,0:0:0:528,0,875:0,0,0,0:0 +20 10011666 . C T 2961.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=73;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.05;MQ0=0;NCC=0;QD=29.33;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,73:0:0,0:0,0:99:0:0,0:0:0:2990,220,0:0,0,0,0:0 +20 10011939 . C T 2513.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=67;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=54.89;MQ0=0;NCC=0;QD=35.36;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,67:0:0,0:0,0:99:0:0,0:0:0:2542,187,0:0,0,0,0:0 +20 10012021 . CA C 1975.73 . AC=2;AF=1.00;AN=2;AS_MQ;DP=71;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=56.69;MQ0=0;NCC=0;QD=27.83;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,0:0:0,0:0,0:99:0:0,0:0:0:2013,198,0:0,0,0,0:0 +20 10012362 . G T 835.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=26;ExcessHet=3.0103;FS=0.000;GQ_MEAN=69.00;MQ=50.82;MQ0=0;NCC=0;QD=32.14;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,26:0:0,0:0,0:69:0:0,0:0:0:864,69,0:0,0,0,0:0 +20 10012384 . T C 229.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-1.508;ClippingRankSum=0.000;DP=21;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=50.02;MQ0=0;MQRankSum=-0.708;NCC=0;QD=10.94;ReadPosRankSum=0.799;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:12,9:0:0,0:0,0:99:0:0,0:0:0:258,0,355:0,0,0,0:0 +20 10012387 . T C 533.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=19;ExcessHet=3.0103;FS=0.000;GQ_MEAN=50.00;MQ=48.85;MQ0=0;NCC=0;QD=28.09;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,19:0:0,0:0,0:50:0:0,0:0:0:562,50,0:0,0,0,0:0 +20 10012479 . A G 592.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=22;ExcessHet=3.0103;FS=0.000;GQ_MEAN=50.00;MQ=47.06;MQ0=0;NCC=0;QD=26.94;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,22:0:0,0:0,0:50:0:0,0:0:0:621,50,0:0,0,0,0:0 +20 10012498 . C G 466.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=15;ExcessHet=3.0103;FS=0.000;GQ_MEAN=33.00;MQ=39.11;MQ0=0;NCC=0;QD=31.12;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,15:0:0,0:0,0:33:0:0,0:0:0:495,33,0:0,0,0,0:0 +20 10012518 . T C 406.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=16;ExcessHet=3.0103;FS=0.000;GQ_MEAN=30.00;MQ=33.28;MQ0=0;NCC=0;QD=25.42;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,16:0:0,0:0,0:30:0:0,0:0:0:435,30,0:0,0,0,0:0 +20 10012521 . C T 46.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=0.751;ClippingRankSum=0.000;DP=18;ExcessHet=3.0103;FS=0.000;GQ_MEAN=75.00;MQ=34.81;MQ0=0;MQRankSum=-0.392;NCC=0;QD=2.60;ReadPosRankSum=1.267;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:12,6:0:0,0:0,0:75:0:0,0:0:0:75,0,224:0,0,0,0:0 +20 10012570 . G GCA 457.73 . AC=2;AF=1.00;AN=2;AS_MQ;DP=13;ExcessHet=3.0103;FS=0.000;GQ_MEAN=33.00;MQ=32.18;MQ0=0;NCC=0;QD=34.30;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,0:0:0,0:0,0:33:0:0,0:0:0:495,33,0:0,0,0,0:0 +20 10012572 . GT G 457.73 . AC=2;AF=1.00;AN=2;AS_MQ;DP=12;ExcessHet=3.0103;FS=0.000;GQ_MEAN=33.00;MQ=35.80;MQ0=0;NCC=0;QD=27.00;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,0:0:0,0:0,0:33:0:0,0:0:0:495,33,0:0,0,0,0:0 +20 10012631 . C CG 484.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=28;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=42.71;MQ0=0;NCC=0;QD=17.31;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:0,0:0:0,0:0,0:99:0:0,0:0:0:522,0,297:0,0,0,0:0 +20 10012636 . G C 527.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=2.490;ClippingRankSum=0.000;DP=29;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=42.87;MQ0=1;MQRankSum=-1.693;NCC=0;QD=18.20;ReadPosRankSum=-1.053;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:11,18:0:0,0:0,0:99:0:0,0:0:0:556,0,294:0,0,0,0:0 +20 10012714 . G C 1300.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=37;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=51.65;MQ0=1;NCC=0;QD=30.82;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,37:0:0,0:0,0:99:0:0,0:0:0:1329,105,0:0,0,0,0:0 +20 10012751 . T C 937.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=33;ExcessHet=3.0103;FS=0.000;GQ_MEAN=89.00;MQ=50.30;MQ0=0;NCC=0;QD=28.42;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,33:0:0,0:0,0:89:0:0,0:0:0:966,89,0:0,0,0,0:0 +20 10013119 . C T 1011.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=2.704;ClippingRankSum=0.000;DP=62;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=50.57;MQ0=0;MQRankSum=-0.979;NCC=0;QD=16.32;ReadPosRankSum=0.455;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:31,31:0:0,0:0,0:99:0:0,0:0:0:1040,0,936:0,0,0,0:0 +20 10013574 . G A 1050.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=3.309;ClippingRankSum=0.000;DP=72;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=57.45;MQ0=0;MQRankSum=-0.578;NCC=0;QD=14.59;ReadPosRankSum=1.159;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:39,33:0:0,0:0,0:99:0:0,0:0:0:1079,0,1301:0,0,0,0:0 +20 10014990 . C CAT 1237.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=88;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=60.44;MQ0=0;NCC=0;QD=14.07;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:0,0:0:0,0:0,0:99:0:0,0:0:0:1275,0,1248:0,0,0,0:0 +20 10015679 . C T 140.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-0.258;ClippingRankSum=0.000;DP=13;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=60.00;MQ0=0;MQRankSum=0.000;NCC=0;QD=10.83;ReadPosRankSum=0.784;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:7,6:0:0,0:0,0:99:0:0,0:0:0:169,0,166:0,0,0,0:0 +20 10015761 . T C 344.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-1.982;ClippingRankSum=0.000;DP=22;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=58.95;MQ0=0;MQRankSum=1.294;NCC=0;QD=15.67;ReadPosRankSum=1.537;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:9,13:0:0,0:0,0:99:0:0,0:0:0:373,0,284:0,0,0,0:0 +20 10018158 . G C 1639.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=5.213;ClippingRankSum=0.000;DP=90;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.79;MQ0=0;MQRankSum=1.118;NCC=0;QD=18.42;ReadPosRankSum=0.784;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:41,48:0:0,0:0,0:99:0:0,0:0:0:1668,0,1165:0,0,0,0:0 +20 10018555 . G A 1567.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-0.755;ClippingRankSum=0.000;DP=82;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=60.00;MQ0=0;MQRankSum=0.000;NCC=0;QD=19.12;ReadPosRankSum=0.590;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:36,46:0:0,0:0,0:99:0:0,0:0:0:1596,0,1211:0,0,0,0:0 +20 10019093 . A G 1244.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=0.659;ClippingRankSum=0.000;DP=70;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.34;MQ0=0;MQRankSum=1.486;NCC=0;QD=17.78;ReadPosRankSum=-0.259;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:34,36:0:0,0:0,0:99:0:0,0:0:0:1273,0,1104:0,0,0,0:0 +20 10020229 . G A 1538.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=6.050;ClippingRankSum=0.000;DP=86;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=58.97;MQ0=0;MQRankSum=1.140;NCC=0;QD=17.89;ReadPosRankSum=-0.405;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:40,46:0:0,0:0,0:99:0:0,0:0:0:1567,0,1130:0,0,0,0:0 +20 10023689 . G A 1852.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=2.195;ClippingRankSum=0.000;DP=84;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=58.89;MQ0=0;MQRankSum=1.843;NCC=0;QD=22.06;ReadPosRankSum=0.976;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:32,52:0:0,0:0,0:99:0:0,0:0:0:1881,0,946:0,0,0,0:0 +20 10024107 . C T 1694.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=5.641;ClippingRankSum=0.000;DP=87;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.42;MQ0=0;MQRankSum=-1.546;NCC=0;QD=19.48;ReadPosRankSum=0.135;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:38,49:0:0,0:0,0:99:0:0,0:0:0:1723,0,1086:0,0,0,0:0 +20 10024300 . C CTT 87.76 . AC=1;AF=0.500;AN=2;AS_MQ;DP=71;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=46.76;MQ0=1;NCC=0;QD=1.24;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:0,0:0:0,0:0,0:99:0:0,0:0:0:103,0,137:0,0,0,0:0 +20 10026357 . T C 1166.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-1.700;ClippingRankSum=0.000;DP=63;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=58.43;MQ0=0;MQRankSum=-0.148;NCC=0;QD=18.52;ReadPosRankSum=-0.076;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:28,35:0:0,0:0,0:99:0:0,0:0:0:1195,0,932:0,0,0,0:0 +20 10026794 . C T 1084.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=2.828;ClippingRankSum=0.000;DP=53;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.56;MQ0=0;MQRankSum=-0.719;NCC=0;QD=20.86;ReadPosRankSum=-0.533;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:19,33:0:0,0:0,0:99:0:0,0:0:0:1113,0,529:0,0,0,0:0 +20 10027234 . A ATTAG 1320.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=73;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=57.21;MQ0=0;NCC=0;QD=18.09;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:0,0:0:0,0:0,0:99:0:0,0:0:0:1358,0,1964:0,0,0,0:0 +20 10027868 . A G 1739.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-5.563;ClippingRankSum=0.000;DP=89;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.48;MQ0=0;MQRankSum=0.032;NCC=0;QD=19.55;ReadPosRankSum=1.704;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:44,45:0:0,0:0,0:99:0:0,0:0:0:1768,0,3201:0,0,0,0:0 +20 10027872 . A G 1724.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-5.491;ClippingRankSum=0.000;DP=85;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.46;MQ0=0;MQRankSum=0.101;NCC=0;QD=20.29;ReadPosRankSum=0.837;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:40,45:0:0,0:0,0:99:0:0,0:0:0:1753,0,3136:0,0,0,0:0 +20 10028867 . A ATG 1106.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=96;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.58;MQ0=1;NCC=0;QD=11.53;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:0,0:0:0,0:0,0:99:0:0,0:0:0:1144,0,916:0,0,0,0:0 +20 10030188 . T A 1372.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=0.711;ClippingRankSum=0.000;DP=82;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.44;MQ0=0;MQRankSum=-1.013;NCC=0;QD=16.74;ReadPosRankSum=-0.884;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:42,40:0:0,0:0,0:99:0:0,0:0:0:1401,0,1524:0,0,0,0:0 +20 10031254 . A AT 1463.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=90;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.09;MQ0=0;NCC=0;QD=16.26;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:0,0:0:0,0:0,0:99:0:0,0:0:0:1501,0,1159:0,0,0,0:0 +20 10031342 . G A 1834.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=1.833;ClippingRankSum=0.000;DP=93;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.75;MQ0=0;MQRankSum=-0.866;NCC=0;QD=19.73;ReadPosRankSum=-0.240;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:41,52:0:0,0:0,0:99:0:0,0:0:0:1863,0,1375:0,0,0,0:0 +20 10031798 . G A 4296.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=105;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.60;MQ0=0;NCC=0;QD=29.27;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,105:0:0,0:0,0:99:0:0,0:0:0:4325,313,0:0,0,0,0:0 +20 10031827 . C T 2004.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=3.552;ClippingRankSum=0.000;DP=108;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.83;MQ0=0;MQRankSum=-0.945;NCC=0;QD=18.56;ReadPosRankSum=-1.430;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:52,56:0:0,0:0,0:99:0:0,0:0:0:2033,0,1798:0,0,0,0:0 +20 10032094 . G A 1220.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=5.488;ClippingRankSum=0.000;DP=83;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=60.00;MQ0=0;MQRankSum=0.000;NCC=0;QD=14.71;ReadPosRankSum=-0.579;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:47,36:0:0,0:0,0:99:0:0,0:0:0:1249,0,1497:0,0,0,0:0 +20 10032413 . T G 869.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-6.142;ClippingRankSum=0.000;DP=66;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.43;MQ0=0;MQRankSum=-0.065;NCC=0;QD=13.18;ReadPosRankSum=-0.945;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:35,31:0:0,0:0,0:99:0:0,0:0:0:898,0,1277:0,0,0,0:0 +20 10032882 . A T 1202.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-3.697;ClippingRankSum=0.000;DP=76;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.39;MQ0=0;MQRankSum=-1.014;NCC=0;QD=16.04;ReadPosRankSum=0.594;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:39,36:0:0,0:0,0:99:0:0,0:0:0:1231,0,1406:0,0,0,0:0 +20 10032972 . C CAT 1122.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=66;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.39;MQ0=0;NCC=0;QD=17.01;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:0,0:0:0,0:0,0:99:0:0,0:0:0:1160,0,1477:0,0,0,0:0 +20 10034306 . T C 782.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-3.975;ClippingRankSum=0.000;DP=80;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=58.84;MQ0=0;MQRankSum=-0.432;NCC=0;QD=9.91;ReadPosRankSum=0.437;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:48,31:0:0,0:0,0:99:0:0,0:0:0:811,0,1593:0,0,0,0:0 +20 10036930 . CGATAGCCCTAGCCCTAGATA C 1036.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=79;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=53.30;MQ0=0;NCC=0;QD=13.12;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:0,0:0:0,0:0,0:99:0:0,0:0:0:1074,0,5569:0,0,0,0:0 +20 10037037 . C T 1436.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=3.504;ClippingRankSum=0.000;DP=82;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=60.17;MQ0=0;MQRankSum=-1.193;NCC=0;QD=17.52;ReadPosRankSum=-1.504;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:40,42:0:0,0:0,0:99:0:0,0:0:0:1465,0,1124:0,0,0,0:0 +20 10037110 . T TGATA 2780.73 . AC=2;AF=1.00;AN=2;AS_MQ;DP=87;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=53.47;MQ0=0;NCC=0;QD=31.96;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,0:0:0,0:0,0:99:0:0,0:0:0:2818,189,0:0,0,0,0:0 +20 10037144 . T TGATAGATA 1823.73 . AC=2;AF=1.00;AN=2;AS_MQ;DP=75;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=50.22;MQ0=0;NCC=0;QD=24.32;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,0:0:0,0:0,0:99:0:0,0:0:0:1861,127,0:0,0,0,0:0 +20 10037709 . A T 1003.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-2.367;ClippingRankSum=0.000;DP=71;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.68;MQ0=0;MQRankSum=0.934;NCC=0;QD=14.14;ReadPosRankSum=0.330;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:39,32:0:0,0:0,0:99:0:0,0:0:0:1032,0,1354:0,0,0,0:0 +20 10039371 . T G 1324.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-3.137;ClippingRankSum=0.000;DP=76;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.39;MQ0=0;MQRankSum=-0.884;NCC=0;QD=17.43;ReadPosRankSum=0.676;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:34,42:0:0,0:0,0:99:0:0,0:0:0:1353,0,1194:0,0,0,0:0 +20 10040772 . C CT 1995.73 . AC=2;AF=1.00;AN=2;AS_MQ;DP=80;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=51.46;MQ0=0;NCC=0;QD=24.95;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,0:0:0,0:0,0:99:0:0,0:0:0:2033,210,0:0,0,0,0:0 +20 10040812 . AT A 2607.73 . AC=2;AF=1.00;AN=2;AS_MQ;DP=83;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=49.83;MQ0=0;NCC=0;QD=31.42;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,0:0:0,0:0,0:99:0:0,0:0:0:2645,214,0:0,0,0,0:0 +20 10040821 . T A 1171.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-0.131;ClippingRankSum=0.000;DP=80;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=50.17;MQ0=0;MQRankSum=0.220;NCC=0;QD=15.02;ReadPosRankSum=-1.489;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:38,40:0:0,0:0,0:99:0:0,0:0:0:1200,0,1099:0,0,0,0:0 +20 10041304 . C T 2765.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=71;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.41;MQ0=0;NCC=0;QD=35.92;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,71:0:0,0:0,0:99:0:0,0:0:0:2794,204,0:0,0,0,0:0 +20 10041701 . A ATATG 1403.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=80;ExcessHet=3.0103;FS=0.000;GQ_MEAN=58.00;MQ=58.50;MQ0=0;NCC=0;QD=17.55;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:0,0:0:0,0:0,0:58:0:0,0:0:0:1441,0,58:0,0,0,0:0 +20 10042319 . C T 2658.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=67;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=58.61;MQ0=0;NCC=0;QD=29.63;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,67:0:0,0:0,0:99:0:0,0:0:0:2687,199,0:0,0,0,0:0 +20 10042761 . A G 3553.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=93;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.70;MQ0=0;NCC=0;QD=28.76;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,93:0:0,0:0,0:99:0:0,0:0:0:3582,272,0:0,0,0,0:0 +20 10042829 . A G 3055.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=80;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.42;MQ0=0;NCC=0;QD=29.94;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,80:0:0,0:0,0:99:0:0,0:0:0:3084,235,0:0,0,0,0:0 +20 10043002 . A T 1287.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=3.986;ClippingRankSum=0.000;DP=86;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=60.00;MQ0=0;MQRankSum=0.000;NCC=0;QD=14.97;ReadPosRankSum=-0.209;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:48,38:0:0,0:0,0:99:0:0,0:0:0:1316,0,1659:0,0,0,0:0 +20 10044849 . A G 2091.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=60;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.62;MQ0=0;NCC=0;QD=34.86;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,60:0:0,0:0,0:99:0:0,0:0:0:2120,177,0:0,0,0,0:0 +20 10045078 . G T 3271.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=82;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=58.46;MQ0=0;NCC=0;QD=31.54;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,82:0:0,0:0,0:99:0:0,0:0:0:3300,244,0:0,0,0,0:0 +20 10045642 . G C 3138.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=82;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.49;MQ0=0;NCC=0;QD=28.86;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,82:0:0,0:0,0:99:0:0,0:0:0:3167,246,0:0,0,0,0:0 +20 10046178 . AAGAAAGAAAG A 2159.73 . AC=2;AF=1.00;AN=2;AS_MQ;DP=64;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=47.11;MQ0=1;NCC=0;QD=33.75;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,0:0:0,0:0,0:99:0:0,0:0:0:2197,153,0:0,0,0,0:0 +20 10046537 . A G 819.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-4.028;ClippingRankSum=0.000;DP=59;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=54.18;MQ0=0;MQRankSum=0.542;NCC=0;QD=13.89;ReadPosRankSum=0.592;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:29,30:0:0,0:0,0:99:0:0,0:0:0:848,0,902:0,0,0,0:0 +20 10050828 . T C 1227.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-2.855;ClippingRankSum=0.000;DP=88;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.48;MQ0=0;MQRankSum=1.256;NCC=0;QD=13.95;ReadPosRankSum=0.004;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:50,38:0:0,0:0,0:99:0:0,0:0:0:1256,0,1768:0,0,0,0:0 +20 10051448 . T C 1134.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-0.289;ClippingRankSum=0.000;DP=71;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.41;MQ0=0;MQRankSum=-1.424;NCC=0;QD=15.98;ReadPosRankSum=-0.719;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:36,35:0:0,0:0,0:99:0:0,0:0:0:1163,0,1150:0,0,0,0:0 +20 10052688 . C A 1062.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=0.180;ClippingRankSum=0.000;DP=77;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.76;MQ0=0;MQRankSum=0.870;NCC=0;QD=13.80;ReadPosRankSum=1.412;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:45,32:0:0,0:0,0:99:0:0,0:0:0:1091,0,1645:0,0,0,0:0 +20 10058022 . T C 975.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-2.105;ClippingRankSum=0.000;DP=73;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=57.81;MQ0=0;MQRankSum=0.931;NCC=0;QD=13.37;ReadPosRankSum=0.039;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:39,34:0:0,0:0,0:99:0:0,0:0:0:1004,0,1261:0,0,0,0:0 +20 10062935 . C CA 92.84 . AC=1;AF=0.500;AN=2;AS_MQ;DP=67;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=52.53;MQ0=1;NCC=0;QD=1.39;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:0,0:0:0,0:0,0:99:0:0,0:0:0:130,0,101:0,0,0,0:0 +20 10067049 . TAAAAAAAA T,TA 614.73 . AC=1,1;AF=0.500,0.500;AN=2;AS_MQ;DP=54;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=52.36;MQ0=1;NCC=0;QD=11.38;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/2:0,0,0:0:0,0,0:0,0,0:99:0,0:0,0,0:0,0:0,0:652,164,339,135,0,106:0,0,0,0:0 +20 10067090 . C A 2004.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=58;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=53.81;MQ0=0;NCC=0;QD=34.57;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:1,57:0:0,0:0,0:99:0:0,0:0:0:2033,164,0:0,0,0,0:0 +20 10067264 . G A 2922.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=76;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.39;MQ0=0;NCC=0;QD=29.41;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,76:0:0,0:0,0:99:0:0,0:0:0:2951,219,0:0,0,0,0:0 +20 10067722 . A C 2146.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=54;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=60.00;MQ0=0;NCC=0;QD=31.11;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,54:0:0,0:0,0:99:0:0,0:0:0:2175,163,0:0,0,0,0:0 +20 10068158 . GTGTATATATATA G 66.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=27;ExcessHet=3.0103;FS=0.000;GQ_MEAN=57.00;MQ=57.39;MQ0=0;NCC=0;QD=2.47;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:0,0:0:0,0:0,0:57:0:0,0:0:0:104,0,57:0,0,0,0:0 +20 10068981 . G A 2503.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=64;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.20;MQ0=0;NCC=0;QD=34.66;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,64:0:0,0:0,0:99:0:0,0:0:0:2532,184,0:0,0,0,0:0 +20 10070602 . T C 2691.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=73;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=58.73;MQ0=0;NCC=0;QD=29.40;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,73:0:0,0:0,0:99:0:0,0:0:0:2720,216,0:0,0,0,0:0 +20 10070936 . T A 3631.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=85;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=57.98;MQ0=0;NCC=0;QD=36.76;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,85:0:0,0:0,0:99:0:0,0:0:0:3660,247,0:0,0,0,0:0 +20 10070938 . G GA 3656.73 . AC=2;AF=1.00;AN=2;AS_MQ;DP=84;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=58.09;MQ0=0;NCC=0;QD=30.54;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,0:0:0,0:0,0:99:0:0,0:0:0:3694,250,0:0,0,0,0:0 +20 10071135 . C T 3257.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=80;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.13;MQ0=0;NCC=0;QD=21.53;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,80:0:0,0:0,0:99:0:0,0:0:0:3286,238,0:0,0,0,0:0 +20 10071187 . G A 3410.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=84;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.73;MQ0=0;NCC=0;QD=34.87;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,84:0:0,0:0,0:99:0:0,0:0:0:3439,246,0:0,0,0,0:0 +20 10071890 . T C 1974.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=57;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.67;MQ0=0;NCC=0;QD=34.65;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,57:0:0,0:0,0:99:0:0,0:0:0:2003,171,0:0,0,0,0:0 +20 10072505 . A G 2099.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=66;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.58;MQ0=0;NCC=0;QD=31.81;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:1,65:0:0,0:0,0:99:0:0,0:0:0:2128,191,0:0,0,0,0:0 +20 10074187 . A G 3101.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=79;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.12;MQ0=0;NCC=0;QD=31.04;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,79:0:0,0:0,0:99:0:0,0:0:0:3130,238,0:0,0,0,0:0 +20 10074240 . T C 3406.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=87;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.79;MQ0=0;NCC=0;QD=27.86;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,86:0:0,0:0,0:99:0:0,0:0:0:3435,255,0:0,0,0,0:0 +20 10074716 . G A 2400.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=68;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.66;MQ0=0;NCC=0;QD=34.17;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,68:0:0,0:0,0:99:0:0,0:0:0:2429,192,0:0,0,0,0:0 +20 10074806 . G A 2817.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=74;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.37;MQ0=0;NCC=0;QD=28.60;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,73:0:0,0:0,0:99:0:0,0:0:0:2846,213,0:0,0,0,0:0 +20 10075043 . T C 2405.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=63;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.27;MQ0=0;NCC=0;QD=25.57;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,63:0:0,0:0,0:99:0:0,0:0:0:2434,184,0:0,0,0,0:0 +20 10075168 . C T 3612.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=89;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.10;MQ0=0;NCC=0;QD=33.11;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,89:0:0,0:0,0:99:0:0,0:0:0:3641,264,0:0,0,0,0:0 +20 10075508 . GA G 1928.73 . AC=2;AF=1.00;AN=2;AS_MQ;DP=81;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=60.40;MQ0=0;NCC=0;QD=23.81;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,0:0:0,0:0,0:99:0:0,0:0:0:1966,210,0:0,0,0,0:0 +20 10076250 . A G 1107.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-3.491;ClippingRankSum=0.000;DP=80;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.40;MQ0=0;MQRankSum=-1.441;NCC=0;QD=13.85;ReadPosRankSum=-0.183;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:41,39:0:0,0:0,0:99:0:0,0:0:0:1136,0,1339:0,0,0,0:0 +20 10076339 . A G 1309.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=0.067;ClippingRankSum=0.000;DP=73;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.37;MQ0=0;MQRankSum=0.157;NCC=0;QD=17.94;ReadPosRankSum=0.821;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:33,40:0:0,0:0,0:99:0:0,0:0:0:1338,0,1035:0,0,0,0:0 +20 10076399 . G A 1807.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=4.274;ClippingRankSum=0.000;DP=95;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=60.00;MQ0=0;MQRankSum=0.000;NCC=0;QD=19.03;ReadPosRankSum=-0.951;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:45,50:0:0,0:0,0:99:0:0,0:0:0:1836,0,1544:0,0,0,0:0 +20 10076989 . CA C 221.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=72;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=57.32;MQ0=0;NCC=0;QD=3.08;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:0,0:0:0,0:0,0:99:0:0,0:0:0:218,0,332:0,0,0,0:0 +20 10077752 . T C 1345.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-6.503;ClippingRankSum=0.000;DP=79;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=60.00;MQ0=0;MQRankSum=0.000;NCC=0;QD=17.04;ReadPosRankSum=-0.367;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:34,45:0:0,0:0,0:99:0:0,0:0:0:1374,0,1187:0,0,0,0:0 +20 10079476 . T G 11.12 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-4.512;ClippingRankSum=0.000;DP=52;ExcessHet=3.0103;FS=0.000;GQ_MEAN=39.00;MQ=58.21;MQ0=0;MQRankSum=-1.771;NCC=0;QD=0.21;ReadPosRankSum=-4.216;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:34,18:0:0,0:0,0:39:0:0,0:0:0:39,0,1137:0,0,0,0:0 +20 10081750 . C A 1353.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=2.670;ClippingRankSum=0.000;DP=83;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=60.00;MQ0=0;MQRankSum=0.000;NCC=0;QD=16.31;ReadPosRankSum=-0.420;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:44,39:0:0,0:0,0:99:0:0,0:0:0:1382,0,1525:0,0,0,0:0 +20 10081800 . C T 1109.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=0.241;ClippingRankSum=0.000;DP=70;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=60.00;MQ0=0;MQRankSum=0.000;NCC=0;QD=15.85;ReadPosRankSum=-2.449;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:36,34:0:0,0:0,0:99:0:0,0:0:0:1138,0,1222:0,0,0,0:0 +20 10082892 . C T 1712.77 . AC=2;AF=1.00;AN=2;AS_MQ;DP=44;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.48;MQ0=0;NCC=0;QD=30.20;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 1/1:0,44:0:0,0:0,0:99:0:0,0:0:0:1741,132,0:0,0,0,0:0 +20 10085211 . A T 1210.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-1.293;ClippingRankSum=0.000;DP=77;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.46;MQ0=0;MQRankSum=-0.093;NCC=0;QD=15.72;ReadPosRankSum=-1.226;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:41,36:0:0,0:0,0:99:0:0,0:0:0:1239,0,1443:0,0,0,0:0 +20 10086110 . G A 1274.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-0.545;ClippingRankSum=0.000;DP=84;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=58.89;MQ0=0;MQRankSum=-0.657;NCC=0;QD=15.18;ReadPosRankSum=0.172;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:44,40:0:0,0:0,0:99:0:0,0:0:0:1303,0,1506:0,0,0,0:0 +20 10086283 . G T 1025.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=2.379;ClippingRankSum=0.000;DP=85;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=60.00;MQ0=0;MQRankSum=0.000;NCC=0;QD=12.07;ReadPosRankSum=2.071;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:52,33:0:0,0:0,0:99:0:0,0:0:0:1054,0,1771:0,0,0,0:0 +20 10086619 . T A 796.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=0.487;ClippingRankSum=0.000;DP=74;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.31;MQ0=0;MQRankSum=-0.387;NCC=0;QD=10.77;ReadPosRankSum=0.340;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:47,27:0:0,0:0,0:99:0:0,0:0:0:825,0,1603:0,0,0,0:0 +20 10086853 . G A 1002.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=3.915;ClippingRankSum=0.000;DP=77;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=58.79;MQ0=0;MQRankSum=-0.177;NCC=0;QD=13.02;ReadPosRankSum=-0.245;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:43,34:0:0,0:0,0:99:0:0,0:0:0:1031,0,1280:0,0,0,0:0 +20 10086954 . G A 1095.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=2.606;ClippingRankSum=0.000;DP=69;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=60.00;MQ0=0;MQRankSum=0.000;NCC=0;QD=15.88;ReadPosRankSum=-0.657;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:34,35:0:0,0:0,0:99:0:0,0:0:0:1124,0,1051:0,0,0,0:0 +20 10087230 . A G 1842.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-2.407;ClippingRankSum=0.000;DP=96;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=58.88;MQ0=0;MQRankSum=1.707;NCC=0;QD=19.20;ReadPosRankSum=0.484;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:42,54:0:0,0:0,0:99:0:0,0:0:0:1871,0,1428:0,0,0,0:0 +20 10087394 . T G 1688.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-2.437;ClippingRankSum=0.000;DP=85;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.73;MQ0=0;MQRankSum=1.190;NCC=0;QD=19.87;ReadPosRankSum=0.983;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:36,49:0:0,0:0,0:99:0:0,0:0:0:1717,0,1186:0,0,0,0:0 +20 10087754 . T G 1347.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=0.054;ClippingRankSum=0.000;DP=82;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=60.38;MQ0=0;MQRankSum=2.140;NCC=0;QD=16.64;ReadPosRankSum=-0.768;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:37,44:0:0,0:0,0:99:0:0,0:0:0:1376,0,1239:0,0,0,0:0 +20 10087804 . C T 1619.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=1.940;ClippingRankSum=0.000;DP=102;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=60.36;MQ0=0;MQRankSum=2.618;NCC=0;QD=15.88;ReadPosRankSum=0.893;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:51,51:0:0,0:0,0:99:0:0,0:0:0:1648,0,1511:0,0,0,0:0 +20 10087820 . C CAG 428.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=96;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=60.31;MQ0=0;NCC=0;QD=4.47;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:0,0:0:0,0:0,0:99:0:0,0:0:0:466,0,1169:0,0,0,0:0 +20 10088063 . C T 1417.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=3.214;ClippingRankSum=0.000;DP=95;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.17;MQ0=0;MQRankSum=0.503;NCC=0;QD=14.92;ReadPosRankSum=0.662;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:51,44:0:0,0:0,0:99:0:0,0:0:0:1446,0,1403:0,0,0,0:0 +20 10088699 . C T 776.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=4.018;ClippingRankSum=0.000;DP=69;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=54.23;MQ0=0;MQRankSum=-2.897;NCC=0;QD=11.26;ReadPosRankSum=-0.883;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:41,28:0:0,0:0,0:99:0:0,0:0:0:805,0,1088:0,0,0,0:0 +20 10088730 . G A 972.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-0.123;ClippingRankSum=0.000;DP=59;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=51.33;MQ0=0;MQRankSum=-5.029;NCC=0;QD=17.07;ReadPosRankSum=0.399;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:30,27:0:0,0:0,0:99:0:0,0:0:0:1001,0,1152:0,0,0,0:0 +20 10088736 . A C 1081.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=0.079;ClippingRankSum=0.000;DP=60;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=50.85;MQ0=0;MQRankSum=-5.075;NCC=0;QD=18.34;ReadPosRankSum=0.249;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:30,29:0:0,0:0,0:99:0:0,0:0:0:1110,0,1194:0,0,0,0:0 +20 10088747 . A G 1111.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-3.578;ClippingRankSum=0.000;DP=56;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=51.12;MQ0=0;MQRankSum=-4.708;NCC=0;QD=19.85;ReadPosRankSum=-0.058;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:26,30:0:0,0:0,0:99:0:0,0:0:0:1140,0,995:0,0,0,0:0 +20 10088799 . G A 1018.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=5.675;ClippingRankSum=0.000;DP=56;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=52.08;MQ0=0;MQRankSum=-1.830;NCC=0;QD=18.19;ReadPosRankSum=1.503;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:24,32:0:0,0:0,0:99:0:0,0:0:0:1047,0,617:0,0,0,0:0 +20 10088895 . C T 532.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=2.462;ClippingRankSum=0.000;DP=43;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=56.09;MQ0=1;MQRankSum=0.577;NCC=0;QD=12.39;ReadPosRankSum=0.933;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:25,18:0:0,0:0,0:99:0:0,0:0:0:561,0,673:0,0,0,0:0 +20 10088968 . C CAAA 1175.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=71;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=52.38;MQ0=0;NCC=0;QD=16.56;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:0,0:0:0,0:0,0:99:0:0,0:0:0:1213,0,1367:0,0,0,0:0 +20 10088980 . T C 1247.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-1.957;ClippingRankSum=0.000;DP=82;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=49.88;MQ0=0;MQRankSum=-5.210;NCC=0;QD=17.09;ReadPosRankSum=1.103;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:39,34:0:0,0:0,0:99:0:0,0:0:0:1276,0,1627:0,0,0,0:0 +20 10088985 . T C 1178.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-0.612;ClippingRankSum=0.000;DP=85;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=49.54;MQ0=0;MQRankSum=-5.309;NCC=0;QD=14.03;ReadPosRankSum=1.491;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:46,38:0:0,0:0,0:99:0:0,0:0:0:1207,0,1729:0,0,0,0:0 +20 10089441 . A G 1179.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-4.874;ClippingRankSum=0.000;DP=79;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.12;MQ0=0;MQRankSum=-0.948;NCC=0;QD=15.13;ReadPosRankSum=-0.286;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:38,40:0:0,0:0,0:99:0:0,0:0:0:1208,0,1313:0,0,0,0:0 +20 10089525 . C T 1548.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=5.738;ClippingRankSum=0.000;DP=85;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=58.96;MQ0=0;MQRankSum=0.160;NCC=0;QD=18.22;ReadPosRankSum=0.960;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:39,46:0:0,0:0,0:99:0:0,0:0:0:1577,0,1088:0,0,0,0:0 +20 10090289 . CA C 384.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=78;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.88;MQ0=0;NCC=0;QD=4.93;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:0,0:0:0,0:0,0:99:0:0,0:0:0:422,0,230:0,0,0,0:0 +20 10090764 . A G 840.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-2.561;ClippingRankSum=0.000;DP=65;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=60.00;MQ0=0;MQRankSum=0.000;NCC=0;QD=12.93;ReadPosRankSum=0.803;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:35,30:0:0,0:0,0:99:0:0,0:0:0:869,0,1207:0,0,0,0:0 +20 10090970 . T C 1257.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-0.297;ClippingRankSum=0.000;DP=71;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.47;MQ0=0;MQRankSum=1.486;NCC=0;QD=17.72;ReadPosRankSum=-0.123;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:34,37:0:0,0:0,0:99:0:0,0:0:0:1286,0,1092:0,0,0,0:0 +20 10091214 . C T 1249.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=0.184;ClippingRankSum=0.000;DP=76;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.75;MQ0=0;MQRankSum=-0.934;NCC=0;QD=16.44;ReadPosRankSum=-0.149;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:36,40:0:0,0:0,0:99:0:0,0:0:0:1278,0,1110:0,0,0,0:0 +20 10092415 . A G 1635.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-6.731;ClippingRankSum=0.000;DP=102;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.77;MQ0=0;MQRankSum=0.000;NCC=0;QD=16.04;ReadPosRankSum=0.510;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:52,50:0:0,0:0,0:99:0:0,0:0:0:1664,0,1902:0,0,0,0:0 +20 10092927 . G T 106.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-2.507;ClippingRankSum=0.000;DP=78;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.11;MQ0=0;MQRankSum=-3.009;NCC=0;QD=1.39;ReadPosRankSum=-3.684;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:61,16:0:0,0:0,0:99:0:0,0:0:0:135,0,1864:0,0,0,0:0 +20 10093568 . GT G 326.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=62;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=58.30;MQ0=1;NCC=0;QD=5.27;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:0,0:0:0,0:0,0:99:0:0,0:0:0:364,0,386:0,0,0,0:0 +20 10093923 . T A 1075.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-0.667;ClippingRankSum=0.000;DP=67;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.19;MQ0=0;MQRankSum=0.358;NCC=0;QD=16.06;ReadPosRankSum=-1.689;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:35,32:0:0,0:0,0:99:0:0,0:0:0:1104,0,1257:0,0,0,0:0 +20 10094251 . T A 1270.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=0.502;ClippingRankSum=0.000;DP=64;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=60.00;MQ0=0;MQRankSum=0.000;NCC=0;QD=19.86;ReadPosRankSum=2.029;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:27,37:0:0,0:0,0:99:0:0,0:0:0:1299,0,781:0,0,0,0:0 +20 10094582 . A G 923.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-1.388;ClippingRankSum=0.000;DP=70;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.07;MQ0=0;MQRankSum=1.270;NCC=0;QD=13.39;ReadPosRankSum=-0.151;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:39,30:0:0,0:0,0:99:0:0,0:0:0:952,0,1350:0,0,0,0:0 +20 10094774 . C T 1036.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-1.036;ClippingRankSum=0.000;DP=78;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.41;MQ0=0;MQRankSum=-0.018;NCC=0;QD=13.29;ReadPosRankSum=0.620;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:40,38:0:0,0:0,0:99:0:0,0:0:0:1065,0,1282:0,0,0,0:0 +20 10095432 . GTGATGATGA G 839.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=76;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=53.88;MQ0=0;NCC=0;QD=11.05;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:0,0:0:0,0:0,0:99:0:0,0:0:0:877,0,2108:0,0,0,0:0 +20 10095741 . A G 1075.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-0.346;ClippingRankSum=0.000;DP=73;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=57.10;MQ0=0;MQRankSum=-2.354;NCC=0;QD=14.94;ReadPosRankSum=-0.081;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:37,35:0:0,0:0,0:99:0:0,0:0:0:1104,0,1233:0,0,0,0:0 +20 10096293 . C T 1355.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=4.580;ClippingRankSum=0.000;DP=78;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=58.62;MQ0=0;MQRankSum=1.396;NCC=0;QD=17.38;ReadPosRankSum=-0.821;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:39,39:0:0,0:0,0:99:0:0,0:0:0:1384,0,1258:0,0,0,0:0 +20 10096596 . C T 1562.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=3.048;ClippingRankSum=0.000;DP=87;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=58.77;MQ0=0;MQRankSum=0.612;NCC=0;QD=17.96;ReadPosRankSum=0.017;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:40,47:0:0,0:0,0:99:0:0,0:0:0:1591,0,1273:0,0,0,0:0 +20 10096768 . A C 1682.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-2.764;ClippingRankSum=0.000;DP=91;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.24;MQ0=0;MQRankSum=-1.609;NCC=0;QD=18.49;ReadPosRankSum=0.526;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:42,49:0:0,0:0,0:99:0:0,0:0:0:1711,0,1452:0,0,0,0:0 +20 10096899 . G T 1614.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=2.809;ClippingRankSum=0.000;DP=81;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.25;MQ0=0;MQRankSum=-0.541;NCC=0;QD=19.94;ReadPosRankSum=0.558;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:40,41:0:0,0:0,0:99:0:0,0:0:0:1643,0,1520:0,0,0,0:0 +20 10096905 . TA T 1600.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=84;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.00;MQ0=0;NCC=0;QD=19.06;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:0,0:0:0,0:0,0:99:0:0,0:0:0:1638,0,1623:0,0,0,0:0 +20 10096933 . G C 1511.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-1.914;ClippingRankSum=0.000;DP=88;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=58.83;MQ0=0;MQRankSum=-1.802;NCC=0;QD=17.38;ReadPosRankSum=0.264;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:46,41:0:0,0:0,0:99:0:0,0:0:0:1540,0,1770:0,0,0,0:0 +20 10096958 . G A 1766.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=2.968;ClippingRankSum=0.000;DP=94;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=58.91;MQ0=0;MQRankSum=-0.962;NCC=0;QD=18.80;ReadPosRankSum=-1.953;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:47,47:0:0,0:0,0:99:0:0,0:0:0:1795,0,1629:0,0,0,0:0 +20 10097075 . T G 1445.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-2.641;ClippingRankSum=0.000;DP=94;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=58.35;MQ0=0;MQRankSum=-1.604;NCC=0;QD=15.38;ReadPosRankSum=-0.200;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:45,49:0:0,0:0,0:99:0:0,0:0:0:1474,0,1482:0,0,0,0:0 +20 10097101 . C CTTT 1091.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=80;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=57.36;MQ0=0;NCC=0;QD=13.65;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:0,0:0:0,0:0,0:99:0:0,0:0:0:1129,0,1306:0,0,0,0:0 +20 10097436 . CTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT C 1054.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=65;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=55.82;MQ0=0;NCC=0;QD=16.23;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:0,0:0:0,0:0,0:99:0:0,0:0:0:1092,0,2241:0,0,0,0:0 +20 10097437 . TTTTC T 796.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=66;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=55.92;MQ0=0;NCC=0;QD=12.07;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:0,0:0:0,0:0,0:99:0:0,0:0:0:834,0,1193:0,0,0,0:0 +20 10097626 . C A 626.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=1.128;ClippingRankSum=0.000;DP=49;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=58.28;MQ0=0;MQRankSum=-1.371;NCC=0;QD=12.79;ReadPosRankSum=1.079;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:29,20:0:0,0:0,0:99:0:0,0:0:0:655,0,957:0,0,0,0:0 +20 10097789 . T C 688.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-1.396;ClippingRankSum=0.000;DP=59;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=58.02;MQ0=0;MQRankSum=-2.744;NCC=0;QD=11.67;ReadPosRankSum=0.134;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:35,24:0:0,0:0,0:99:0:0,0:0:0:717,0,1190:0,0,0,0:0 +20 10097928 . G A 570.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-1.621;ClippingRankSum=0.000;DP=39;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=56.79;MQ0=1;MQRankSum=-1.850;NCC=0;QD=14.64;ReadPosRankSum=-0.309;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:18,21:0:0,0:0,0:99:0:0,0:0:0:599,0,586:0,0,0,0:0 +20 10098110 . G C 586.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=2.510;ClippingRankSum=0.000;DP=37;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=58.11;MQ0=0;MQRankSum=-1.477;NCC=0;QD=15.86;ReadPosRankSum=-0.714;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:20,17:0:0,0:0,0:99:0:0,0:0:0:615,0,727:0,0,0,0:0 +20 10098135 . C A 471.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-1.155;ClippingRankSum=0.000;DP=39;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.06;MQ0=0;MQRankSum=1.546;NCC=0;QD=12.10;ReadPosRankSum=-0.591;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:25,14:0:0,0:0,0:99:0:0,0:0:0:500,0,964:0,0,0,0:0 +20 10098219 . TATATATA T 295.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=21;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=55.94;MQ0=0;NCC=0;QD=14.08;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:0,0:0:0,0:0,0:99:0:0,0:0:0:333,0,461:0,0,0,0:0 +20 10098237 . A T 244.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=0.527;ClippingRankSum=0.000;DP=12;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=52.81;MQ0=0;MQRankSum=-2.347;NCC=0;QD=20.40;ReadPosRankSum=1.188;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:7,5:0:0,0:0,0:99:0:0,0:0:0:273,0,273:0,0,0,0:0 +20 10098265 . T C 133.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=1.645;ClippingRankSum=0.000;DP=6;ExcessHet=3.0103;FS=0.000;GQ_MEAN=59.00;MQ=41.96;MQ0=0;MQRankSum=-1.645;NCC=0;QD=22.30;ReadPosRankSum=0.524;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:2,4:0:0,0:0,0:59:0:0,0:0:0:162,0,59:0,0,0,0:0 +20 10098885 . C CA 433.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=32;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=49.27;MQ0=1;NCC=0;QD=13.55;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:0,0:0:0,0:0,0:99:0:0,0:0:0:471,0,572:0,0,0,0:0 +20 10098945 . T C 407.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=1.225;ClippingRankSum=0.000;DP=23;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=50.09;MQ0=0;MQRankSum=-2.636;NCC=0;QD=17.73;ReadPosRankSum=1.042;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:9,14:0:0,0:0,0:99:0:0,0:0:0:436,0,248:0,0,0,0:0 +20 10098987 . C T 379.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=2.922;ClippingRankSum=0.000;DP=25;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=50.88;MQ0=0;MQRankSum=-2.877;NCC=0;QD=15.19;ReadPosRankSum=0.329;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:11,14:0:0,0:0,0:99:0:0,0:0:0:408,0,350:0,0,0,0:0 +20 10099029 . T C 334.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-1.864;ClippingRankSum=0.000;DP=28;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=53.32;MQ0=0;MQRankSum=-3.439;NCC=0;QD=11.96;ReadPosRankSum=-0.361;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:18,10:0:0,0:0,0:99:0:0,0:0:0:363,0,768:0,0,0,0:0 +20 10099034 . C A 334.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=2.757;ClippingRankSum=0.000;DP=28;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=53.32;MQ0=0;MQRankSum=-3.641;NCC=0;QD=11.96;ReadPosRankSum=-1.515;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:18,10:0:0,0:0,0:99:0:0,0:0:0:363,0,768:0,0,0,0:0 +20 10099044 . A C 334.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-0.861;ClippingRankSum=0.000;DP=23;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=51.54;MQ0=0;MQRankSum=-4.268;NCC=0;QD=14.56;ReadPosRankSum=-2.046;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:16,7:0:0,0:0,0:99:0:0,0:0:0:363,0,768:0,0,0,0:0 +20 10099046 . T C 304.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-1.984;ClippingRankSum=0.000;DP=22;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=51.12;MQ0=0;MQRankSum=-4.268;NCC=0;QD=13.85;ReadPosRankSum=-2.117;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:15,7:0:0,0:0,0:99:0:0,0:0:0:333,0,603:0,0,0,0:0 +20 10099055 . T C 256.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-1.788;ClippingRankSum=0.000;DP=27;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=49.71;MQ0=0;MQRankSum=-4.432;NCC=0;QD=9.51;ReadPosRankSum=-2.657;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:16,11:0:0,0:0,0:99:0:0,0:0:0:285,0,673:0,0,0,0:0 +20 10099079 . C T 116.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=1.336;ClippingRankSum=0.000;DP=34;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=50.38;MQ0=0;MQRankSum=-4.225;NCC=0;QD=3.43;ReadPosRankSum=1.168;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:20,14:0:0,0:0,0:99:0:0,0:0:0:145,0,886:0,0,0,0:0 +20 10099111 . T TTTTGTTTG 656.73 . AC=1;AF=0.500;AN=2;AS_MQ;DP=48;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=49.62;MQ0=0;NCC=0;QD=13.68;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:0,0:0:0,0:0,0:99:0:0,0:0:0:694,0,802:0,0,0,0:0 +20 10099140 . G T 1005.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=0.536;ClippingRankSum=0.000;DP=62;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=55.53;MQ0=0;MQRankSum=-1.610;NCC=0;QD=16.22;ReadPosRankSum=0.896;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:32,30:0:0,0:0,0:99:0:0,0:0:0:1034,0,931:0,0,0,0:0 +20 10099190 . G T 1034.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-0.035;ClippingRankSum=0.000;DP=64;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=57.89;MQ0=0;MQRankSum=-1.485;NCC=0;QD=16.17;ReadPosRankSum=-0.491;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:33,31:0:0,0:0,0:99:0:0,0:0:0:1063,0,1154:0,0,0,0:0 +20 10099220 . A G 577.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=-1.426;ClippingRankSum=0.000;DP=46;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=57.00;MQ0=1;MQRankSum=-2.352;NCC=0;QD=12.56;ReadPosRankSum=0.119;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:26,20:0:0,0:0,0:99:0:0,0:0:0:606,0,873:0,0,0,0:0 +20 10099250 . G A 699.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=2.980;ClippingRankSum=0.000;DP=38;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=56.00;MQ0=0;MQRankSum=-2.203;NCC=0;QD=18.42;ReadPosRankSum=0.096;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:16,22:0:0,0:0,0:99:0:0,0:0:0:728,0,424:0,0,0,0:0 +20 10099535 . G A 1335.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=5.034;ClippingRankSum=0.000;DP=66;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.01;MQ0=0;MQRankSum=-1.418;NCC=0;QD=20.55;ReadPosRankSum=-0.771;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:26,39:0:0,0:0,0:99:0:0,0:0:0:1364,0,686:0,0,0,0:0 +20 10099565 . C T 1346.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=4.595;ClippingRankSum=0.000;DP=69;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=59.39;MQ0=0;MQRankSum=-1.266;NCC=0;QD=19.52;ReadPosRankSum=1.454;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:31,38:0:0,0:0,0:99:0:0,0:0:0:1375,0,994:0,0,0,0:0 +20 10099755 . C T 1098.77 . AC=1;AF=0.500;AN=2;AS_MQ;BaseQRankSum=1.866;ClippingRankSum=0.000;DP=68;ExcessHet=3.0103;FS=0.000;GQ_MEAN=99.00;MQ=58.35;MQ0=0;MQRankSum=-0.046;NCC=0;QD=16.16;ReadPosRankSum=-0.245;SOR=0.693;Samples=NA12878 GT:AD:DP:F1R2:F2R1:GQ:MBQ:MFRL:MMQ:MPOS:PL:SB:UNIQ_ALT_READ_COUNT 0/1:34,34:0:0,0:0,0:99:0:0,0:0:0:1127,0,1148:0,0,0,0:0 +20 10099832 . A G 1073.77 . 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AF=0.06,0.00;AFrange=0.01-0.13,95%;AlleleBalance=0.73;DoC=156;FisherStrand=9.4;HomopolymerRun=1;MAPQ0=0;NS=60;OnOffGenotype=0.97;RMSMAPQ=167.02;SB=-0.33;SpanningDeletions=0 GT:RD:GQ 1/0:6:1.72 0/0:5:1.50 ./. 0/0:3:0.90 0/0:2:0.60 ./. 0/0:3:0.89 ./. 0/0:5:1.50 0/0:2:0.60 0/0:11:3.30 0/0:2:0.60 ./. 0/0:2:0.60 1/0:4:2.62 0/0:1:0.30 0/0:7:2.10 ./. 0/0:4:1.19 0/0:4:1.20 ./. ./. 0/0:1:0.30 0/0:3:0.90 0/0:1:0.30 0/0:3:0.90 ./. 0/0:2:0.60 ./. 1/0:8:1.52 0/0:4:1.19 0/0:3:0.90 0/0:3:0.90 0/0:1:0.30 0/0:2:0.60 0/0:5:0.90 0/0:5:1.36 0/0:1:0.30 0/0:3:0.90 0/0:6:1.81 0/0:1:0.30 1/0:3:2.54 0/0:1:0.29 0/0:2:0.60 0/0:1:0.30 1/0:6:1.92 0/0:1:0.30 0/0:1:0.30 0/0:4:1.20 2/2:2:0.00 0/0:2:0.60 ./. 0/0:2:0.60 0/0:3:0.90 2/2:2:0.00 1/0:4:2.47 0/0:4:1.20 0/0:1:0.30 0/0:2:0.60 0/0:2:0.59 +20 10020447 . C T 68.03 . AF=0.06;AFrange=0.01-0.14,95%;AlleleBalance=0.72;DoC=140;FisherStrand=9.4;HomopolymerRun=0;MAPQ0=0;NS=60;OnOffGenotype=0.98;RMSMAPQ=166.27;SB=-0.62;SpanningDeletions=0 GT:RD:GQ 0/1:5:2.27 0/0:2:0.59 ./. 0/0:3:0.90 1/1:1:0.00 ./. 0/0:3:0.41 ./. 0/0:5:1.50 0/0:2:0.60 0/0:7:2.10 0/0:2:0.60 ./. 0/0:2:0.60 0/1:4:2.67 0/0:1:0.30 0/0:7:1.77 ./. 0/0:3:0.89 0/0:4:1.20 ./. ./. ./. 0/0:3:0.89 0/0:1:0.30 0/0:1:0.30 ./. 0/0:2:0.60 0/0:1:0.30 0/1:7:1.57 0/0:5:1.20 0/0:4:1.20 0/0:2:0.60 0/0:2:0.60 ./. 0/0:5:1.50 0/0:5:1.50 0/0:1:0.30 0/0:3:0.90 0/0:5:1.43 ./. 0/1:3:2.44 0/0:1:0.30 0/0:2:0.55 0/0:1:0.30 0/1:6:1.97 0/0:2:0.57 0/0:1:0.30 0/0:5:1.50 0/0:1:0.30 0/0:2:0.60 ./. ./. 0/0:2:0.60 0/0:1:0.30 0/1:4:2.52 0/0:2:0.60 0/0:3:0.90 0/0:4:1.20 0/0:2:0.58 +20 10020452 . T C 32.71 . AF=0.05;AFrange=0.01-0.12,95%;AlleleBalance=0.70;DoC=138;FisherStrand=9.0;HomopolymerRun=0;MAPQ0=0;NS=60;OnOffGenotype=1.00;RMSMAPQ=167.20;SB=-0.03;SpanningDeletions=0 GT:RD:GQ 1/0:5:1.45 1/0:3:1.46 0/0:1:0.30 0/0:3:0.90 ./. ./. 0/0:3:0.60 ./. 0/0:4:1.20 0/0:2:0.60 0/0:6:1.75 0/0:2:0.60 0/0:1:0.30 0/0:3:0.90 1/0:4:2.04 0/0:1:0.30 0/0:8:1.87 ./. 0/0:3:0.89 0/0:3:0.90 ./. ./. 0/0:1:0.30 0/0:3:0.90 0/0:1:0.30 0/0:2:0.60 0/0:1:0.30 0/0:2:0.45 0/0:1:0.30 1/0:7:1.24 0/0:3:0.36 0/0:4:0.80 0/0:1:0.30 0/0:2:0.60 ./. 0/0:3:0.83 0/0:5:1.50 0/0:1:0.30 0/0:3:0.90 0/0:5:1.50 0/0:1:0.30 1/0:3:2.72 0/0:1:0.30 0/0:2:0.60 0/0:1:0.30 1/0:6:1.74 0/0:1:0.28 0/0:2:0.52 0/0:4:1.20 0/0:1:0.30 0/0:2:0.60 ./. ./. 0/0:2:0.60 0/0:1:0.30 0/0:4:1.20 0/0:2:0.60 0/0:3:0.90 0/0:5:1.45 ./. +20 10020453 . G A,T 48.53 . 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AF=0.06;AFrange=0.01-0.13,95%;AlleleBalance=0.74;DoC=152;FisherStrand=20.7;HomopolymerRun=1;MAPQ0=0;NS=60;OnOffGenotype=1.00;RMSMAPQ=170.06;SB=-0.04;SpanningDeletions=0 GT:RD:GQ 0/1:5:2.63 0/0:6:1.80 0/0:1:0.30 0/0:4:1.20 ./. ./. ./. ./. 0/0:3:0.90 0/0:1:0.30 0/0:3:0.90 0/0:4:1.20 0/0:1:0.30 0/0:3:0.90 0/1:4:2.93 0/0:2:0.60 0/0:9:0.25 ./. 0/0:3:0.87 0/0:2:0.60 0/0:1:0.30 ./. 0/0:2:0.60 0/0:3:0.90 0/0:1:0.30 0/0:1:0.30 0/0:2:0.60 0/0:2:0.60 0/0:3:0.90 0/1:5:2.63 0/0:5:1.50 0/0:5:1.50 0/0:3:0.90 0/0:2:0.60 ./. 0/0:1:0.30 0/0:4:1.20 0/0:2:0.59 0/0:4:1.20 0/0:3:0.90 0/0:1:0.27 0/1:4:4.81 0/0:4:1.20 0/0:1:0.30 ./. 0/1:7:2.23 0/0:1:0.30 0/0:7:1.54 0/1:4:1.23 0/0:1:0.30 0/0:1:0.30 ./. 0/0:2:0.30 0/0:2:0.60 0/0:2:0.30 0/0:3:0.90 0/0:1:0.30 0/0:2:0.60 0/0:7:2.06 0/0:2:0.60 +20 10020470 . A G,T 91.66 . AF=0.06,0.00;AFrange=0.01-0.13,95%;AlleleBalance=0.70;DoC=182;FisherStrand=13.9;HomopolymerRun=1;MAPQ0=0;NS=60;OnOffGenotype=0.99;RMSMAPQ=174.37;SB=-0.25;SpanningDeletions=0 GT:RD:GQ 0/1:5:1.74 0/0:6:1.80 0/0:1:0.30 0/0:4:1.20 2/2:1:0.00 ./. ./. ./. 0/0:1:0.29 0/0:1:0.24 0/0:2:0.60 0/0:4:1.20 0/0:1:0.30 0/0:4:1.20 0/1:4:2.24 0/0:2:0.60 0/0:9:2.69 0/0:2:0.60 0/0:3:0.88 0/0:1:0.30 0/0:1:0.30 0/0:1:0.30 0/0:3:0.60 0/0:4:1.20 0/0:1:0.30 0/0:1:0.30 0/0:3:0.90 0/0:3:0.60 0/0:6:1.46 0/1:4:2.24 0/1:5:1.66 0/0:9:2.70 0/0:4:1.20 0/0:2:0.60 0/0:2:0.60 0/0:2:0.60 0/0:5:1.49 0/0:3:0.90 0/0:4:1.20 0/0:4:1.20 0/0:1:0.30 0/1:4:5.78 0/0:6:1.80 0/0:2:0.56 ./. 0/1:6:4.98 0/0:1:0.30 0/0:9:2.29 0/0:4:1.20 0/0:1:0.29 0/0:1:0.30 ./. 0/0:8:1.54 0/0:2:0.60 0/0:1:0.30 0/1:3:2.54 0/0:3:0.90 0/0:3:0.60 0/0:7:2.10 0/0:2:0.60 +20 10020484 . A C,T 55.89 . 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T A 18.59 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. 1/1:2:3:45,3,0 ./. +20 10001617 . C A 12.77 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL 1/1:1:3:39,3,0 ./. ./. +20 10001628 . G A 18.59 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL 1/1:2:3:45,3,0 ./. ./. +20 10001661 . T C 17.49 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=0.500;MQ0=0;OND=0.00 GT:DP:GQ:PL 1/1:2:3:45,3,0 ./. 0/0:1:3:0,3,39 +20 10001670 . T G 14.57 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=0.500;MQ0=0;OND=0.00 GT:DP:GQ:PL 1/1:1:3:42,3,0 ./. 0/0:2:3:0,3,45 +20 10002138 . C G 16.63 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL 1/1:1:3:43,3,0 ./. ./. +20 10002142 . G C 16.63 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL 1/1:1:3:43,3,0 ./. ./. +20 10003021 . C T 12.77 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. 1/1:1:3:39,3,0 ./. +20 10003358 . A C 15.65 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. 1/1:1:3:42,3,0 ./. +20 10003651 . T C 53.42 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=4;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL 1/1:1:3:33,3,0 1/1:2:3:45,3,0 ./. +20 10003692 . A G 12.77 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. 1/1:1:3:39,3,0 ./. +20 10003832 . G A 53.42 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=4;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. 1/1:1:3:39,3,0 1/1:1:3:39,3,0 +20 10004094 . A C 14.68 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. ./. 1/1:1:3:41,3,0 +20 10004351 . C G 56.42 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=4;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. 1/1:1:3:39,3,0 1/1:1:3:42,3,0 +20 10004389 . T G 15.65 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. ./. 1/1:1:3:42,3,0 +20 10004610 . A C 14.68 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. 1/1:1:3:41,3,0 ./. +20 10004725 . A G 14.68 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. 1/1:1:3:41,3,0 ./. +20 10004874 . A C 59.42 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=4;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. 1/1:1:3:42,3,0 1/1:1:3:42,3,0 +20 10004887 . A G 14.57 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=0.500;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. 0/0:1:3:0,3,38 1/1:1:3:42,3,0 +20 10005010 . C T 18.59 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. 1/1:2:3:45,3,0 ./. +20 10005427 . C T 17.49 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=0.500;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. 1/1:2:3:45,3,0 0/0:1:3:0,3,41 +20 10005723 . A G 10.90 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. 1/1:1:3:37,3,0 ./. +20 10006682 . T A 12.77 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. ./. 1/1:1:3:39,3,0 +20 10007352 . C T 204.23 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=6;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL 1/1:1:3:39,3,0 1/1:3:6:79,6,0 1/1:4:9:111,9,0 +20 10008221 . T C 61.42 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=4;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL 1/1:1:3:41,3,0 ./. 1/1:2:3:45,3,0 +20 10009227 . A G 18.59 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. ./. 1/1:2:3:45,3,0 +20 10009246 . A G 18.59 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. ./. 1/1:2:3:45,3,0 +20 10009446 . G T 12.77 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. ./. 1/1:1:3:39,3,0 +20 10009512 . C G 15.65 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. ./. 1/1:1:3:42,3,0 +20 10009795 . A G 13.72 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL 1/1:1:3:40,3,0 ./. ./. +20 10011075 . C T 17.49 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=0.500;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. 1/1:2:3:45,3,0 0/0:1:3:0,3,37 +20 10012362 . G T 12.77 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. 1/1:1:3:39,3,0 ./. +20 10019093 . A G 9258.92 . ABHet=0.558;Dels=0.00;FS=0.000;MLEAC=3;MLEAF=0.500;MQ0=0;OND=0.00 GT:DP:GQ:PL 0/1:250:99:3166,0,3854 0/1:250:99:3346,0,3750 0/1:250:99:2777,0,4107 +20 10024107 . C T 26.29 . ABHet=0.778;ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=0.333;MQ0=0;OND=0.00 GT:DP:GQ:PL 0/1:4:27:27,0,101 0/0:6:18:0,18,215 0/1:5:31:31,0,81 +20 10026108 . A G 23.15 . ABHet=0.778;ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=1;MLEAF=0.167;MQ0=0;OND=0.00 GT:DP:GQ:PL 0/0:15:39:0,39,513 0/1:9:54:54,0,255 0/0:14:42:0,42,541 +20 10026357 . T C 3067.16 . ABHet=0.467;ABHom=1.00;Dels=0.00;FS=2.821;MLEAC=2;MLEAF=0.333;MQ0=0;OND=0.00 GT:DP:GQ:PL 0/1:87:99:1310,0,1044 0/0:90:99:0,220,2870 0/1:111:99:1789,0,1374 +20 10026794 . C T 11.83 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL 1/1:1:3:38,3,0 ./. ./. +20 10030188 . T A 3747.16 . ABHet=0.448;ABHom=1.00;Dels=0.00;FS=0.394;MLEAC=2;MLEAF=0.333;MQ0=0;OND=0.00 GT:DP:GQ:PL 0/1:94:99:1333,0,1308 0/0:137:99:0,328,4257 0/1:154:99:2446,0,1566 +20 10030931 . C A 56.23 . ABHet=0.700;ABHom=0.960;Dels=0.00;FS=0.000;MLEAC=1;MLEAF=0.167;MQ0=0;OND=0.029 GT:DP:GQ:PL 0/0:9:24:0,24,299 0/1:10:87:87,0,229 0/0:16:16:0,16,440 +20 10031342 . G A 18.59 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. 1/1:2:3:45,3,0 ./. +20 10031798 . G A 100.34 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=6;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL 1/1:1:3:40,3,0 1/1:2:3:45,3,0 1/1:1:3:39,3,0 +20 10031827 . C T 17.49 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=0.500;MQ0=0;OND=0.00 GT:DP:GQ:PL 1/1:2:3:45,3,0 0/0:1:3:0,3,42 ./. +20 10032413 . T G 3643.16 . ABHet=0.512;ABHom=1.00;Dels=0.00;FS=0.435;MLEAC=2;MLEAF=0.333;MQ0=0;OND=0.00 GT:DP:GQ:PL 0/1:124:99:2087,0,1530 0/0:97:99:0,250,3265 0/1:134:99:1588,0,2067 +20 10034546 . T C 11.83 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL 1/1:1:3:38,3,0 ./. ./. +20 10036107 . T G 12.39 . ABHet=0.477;ABHom=0.630;Dels=0.00;FS=5.027;MLEAC=1;MLEAF=0.167;MQ0=0;OND=0.231 GT:DP:GQ:PL 0/0:49:28:0,28,561 0/0:24:39:0,39,462 0/1:44:43:43,0,518 +20 10037877 . G C 16.67 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=0.333;MQ0=0;OND=0.00 GT:DP:GQ:PL 1/1:2:3:45,3,0 0/0:3:3:0,3,45 0/0:2:3:0,3,45 +20 10043441 . T A 11.12 . ABHet=0.500;Dels=0.00;FS=0.000;MLEAC=1;MLEAF=0.500;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. 0/1:4:38:39,0,38 ./. +20 10044282 . T C 150.42 . ABHet=0.111;ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=1;MLEAF=0.167;MQ0=0;OND=0.00 GT:DP:GQ:PL 0/0:2:6:0,6,74 0/1:9:18:180,0,18 0/0:3:9:0,9,108 +20 10044849 . A G 57.17 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=0.500;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. 0/0:2:3:0,3,45 1/1:3:6:86,6,0 +20 10045078 . G T 12.77 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. 1/1:1:3:39,3,0 ./. +20 10046489 . C T 11.83 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. ./. 1/1:1:3:38,3,0 +20 10047597 . C A 12.77 . ABHom=1.00;Dels=0.00;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;OND=0.00 GT:DP:GQ:PL ./. ./. 1/1:1:3:39,3,0 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/vcfexamplemultisample.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/vcfexamplemultisample.vcf.idx new file mode 100644 index 0000000000000000000000000000000000000000..f963a8368141e24ffc0623b47ad2c7d3ae44afa6 GIT binary patch literal 433 zcmb`D&q~8U5XMIY4_7x7OXswcpZl^;+v~*D6^nR2XXP!+uK7)Q$D$1Uk@uHB@T5#w0iJ91Gv%;XMDsMt zVs_{ZFuu<-4q*UE8uMA;!R3V)grPIvz=!d~52ll82z?gE;o}TWogJc$o&RqQKllPT C5n&_% literal 0 HcmV?d00001 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/vcfexamplemultisampleempty.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/vcfexamplemultisampleempty.vcf new file mode 100644 index 00000000000..5697b097312 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/vcfexamplemultisampleempty.vcf @@ -0,0 +1,66 @@ +##fileformat=VCFv4.2 +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##GATKCommandLine.UnifiedGenotyper= +##INFO= +##INFO= +##INFO= +##contig= +##contig= +##reference=file:///Users/emeryj/hellbender/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 NA12891 NA12892 +20 10000598 . T A 18.59 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL ./. 1/1:2:3:45,3,0 ./. +20 10001617 . C A 12.77 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL 1/1:1:3:39,3,0 ./. ./. +20 10001628 . G A 18.59 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL 1/1:2:3:45,3,0 ./. ./. +20 10001661 . T C 17.49 . MLEAC=2;MLEAF=0.500 GT:DP:GQ:PL 1/1:2:3:45,3,0 ./. 0/0:1:3:0,3,39 +20 10001670 . T G 14.57 . MLEAC=2;MLEAF=0.500 GT:DP:GQ:PL 1/1:1:3:42,3,0 ./. 0/0:2:3:0,3,45 +20 10002138 . C G 16.63 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL 1/1:1:3:43,3,0 ./. ./. +20 10002142 . G C 16.63 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL 1/1:1:3:43,3,0 ./. ./. +20 10003021 . C T 12.77 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL ./. 1/1:1:3:39,3,0 ./. +20 10003358 . A C 15.65 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL ./. 1/1:1:3:42,3,0 ./. +20 10003651 . T C 53.42 . MLEAC=4;MLEAF=1.00 GT:DP:GQ:PL 1/1:1:3:33,3,0 1/1:2:3:45,3,0 ./. +20 10003692 . A G 12.77 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL ./. 1/1:1:3:39,3,0 ./. +20 10003832 . G A 53.42 . MLEAC=4;MLEAF=1.00 GT:DP:GQ:PL ./. 1/1:1:3:39,3,0 1/1:1:3:39,3,0 +20 10004094 . A C 14.68 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL ./. ./. 1/1:1:3:41,3,0 +20 10004351 . C G 56.42 . MLEAC=4;MLEAF=1.00 GT:DP:GQ:PL ./. 1/1:1:3:39,3,0 1/1:1:3:42,3,0 +20 10004389 . T G 15.65 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL ./. ./. 1/1:1:3:42,3,0 +20 10004610 . A C 14.68 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL ./. 1/1:1:3:41,3,0 ./. +20 10004725 . A G 14.68 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL ./. 1/1:1:3:41,3,0 ./. +20 10004874 . A C 59.42 . MLEAC=4;MLEAF=1.00 GT:DP:GQ:PL ./. 1/1:1:3:42,3,0 1/1:1:3:42,3,0 +20 10004887 . A G 14.57 . MLEAC=2;MLEAF=0.500 GT:DP:GQ:PL ./. 0/0:1:3:0,3,38 1/1:1:3:42,3,0 +20 10005010 . C T 18.59 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL ./. 1/1:2:3:45,3,0 ./. +20 10005427 . C T 17.49 . MLEAC=2;MLEAF=0.500 GT:DP:GQ:PL ./. 1/1:2:3:45,3,0 0/0:1:3:0,3,41 +20 10005723 . A G 10.90 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL ./. 1/1:1:3:37,3,0 ./. +20 10006682 . T A 12.77 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL ./. ./. 1/1:1:3:39,3,0 +20 10007352 . C T 204.23 . MLEAC=6;MLEAF=1.00 GT:DP:GQ:PL 1/1:1:3:39,3,0 1/1:3:6:79,6,0 1/1:4:9:111,9,0 +20 10008221 . T C 61.42 . MLEAC=4;MLEAF=1.00 GT:DP:GQ:PL 1/1:1:3:41,3,0 ./. 1/1:2:3:45,3,0 +20 10009227 . A G 18.59 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL ./. ./. 1/1:2:3:45,3,0 +20 10009246 . A G 18.59 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL ./. ./. 1/1:2:3:45,3,0 +20 10009446 . G T 12.77 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL ./. ./. 1/1:1:3:39,3,0 +20 10009512 . C G 15.65 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL ./. ./. 1/1:1:3:42,3,0 +20 10009795 . A G 13.72 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL 1/1:1:3:40,3,0 ./. ./. +20 10011075 . C T 17.49 . MLEAC=2;MLEAF=0.500 GT:DP:GQ:PL ./. 1/1:2:3:45,3,0 0/0:1:3:0,3,37 +20 10012362 . G T 12.77 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL ./. 1/1:1:3:39,3,0 ./. +20 10019093 . A G 9258.92 . MLEAC=3;MLEAF=0.500 GT:DP:GQ:PL 0/1:250:99:3166,0,3854 0/1:250:99:3346,0,3750 0/1:250:99:2777,0,4107 +20 10024107 . C T 26.29 . MLEAC=2;MLEAF=0.333 GT:DP:GQ:PL 0/1:4:27:27,0,101 0/0:6:18:0,18,215 0/1:5:31:31,0,81 +20 10026108 . A G 23.15 . MLEAC=1;MLEAF=0.167 GT:DP:GQ:PL 0/0:15:39:0,39,513 0/1:9:54:54,0,255 0/0:14:42:0,42,541 +20 10026357 . T C 3067.16 . MLEAC=2;MLEAF=0.333 GT:DP:GQ:PL 0/1:87:99:1310,0,1044 0/0:90:99:0,220,2870 0/1:111:99:1789,0,1374 +20 10026794 . C T 11.83 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL 1/1:1:3:38,3,0 ./. ./. +20 10030188 . T A 3747.16 . MLEAC=2;MLEAF=0.333 GT:DP:GQ:PL 0/1:94:99:1333,0,1308 0/0:137:99:0,328,4257 0/1:154:99:2446,0,1566 +20 10030931 . C A 56.23 . MLEAC=1;MLEAF=0.167 GT:DP:GQ:PL 0/0:9:24:0,24,299 0/1:10:87:87,0,229 0/0:16:16:0,16,440 +20 10031342 . G A 18.59 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL ./. 1/1:2:3:45,3,0 ./. +20 10031798 . G A 100.34 . MLEAC=6;MLEAF=1.00 GT:DP:GQ:PL 1/1:1:3:40,3,0 1/1:2:3:45,3,0 1/1:1:3:39,3,0 +20 10031827 . C T 17.49 . MLEAC=2;MLEAF=0.500 GT:DP:GQ:PL 1/1:2:3:45,3,0 0/0:1:3:0,3,42 ./. +20 10032413 . T G 3643.16 . MLEAC=2;MLEAF=0.333 GT:DP:GQ:PL 0/1:124:99:2087,0,1530 0/0:97:99:0,250,3265 0/1:134:99:1588,0,2067 +20 10034546 . T C 11.83 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL 1/1:1:3:38,3,0 ./. ./. +20 10036107 . T G 12.39 . MLEAC=1;MLEAF=0.167 GT:DP:GQ:PL 0/0:49:28:0,28,561 0/0:24:39:0,39,462 0/1:44:43:43,0,518 +20 10037877 . G C 16.67 . MLEAC=2;MLEAF=0.333 GT:DP:GQ:PL 1/1:2:3:45,3,0 0/0:3:3:0,3,45 0/0:2:3:0,3,45 +20 10043441 . T A 11.12 . MLEAC=1;MLEAF=0.500 GT:DP:GQ:PL ./. 0/1:4:38:39,0,38 ./. +20 10044282 . T C 150.42 . MLEAC=1;MLEAF=0.167 GT:DP:GQ:PL 0/0:2:6:0,6,74 0/1:9:18:180,0,18 0/0:3:9:0,9,108 +20 10044849 . A G 57.17 . MLEAC=2;MLEAF=0.500 GT:DP:GQ:PL ./. 0/0:2:3:0,3,45 1/1:3:6:86,6,0 +20 10045078 . G T 12.77 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL ./. 1/1:1:3:39,3,0 ./. +20 10046489 . C T 11.83 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL ./. ./. 1/1:1:3:38,3,0 +20 10047597 . C A 12.77 . MLEAC=2;MLEAF=1.00 GT:DP:GQ:PL ./. ./. 1/1:1:3:39,3,0 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/vcfexamplemultisampleempty.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator/vcfexamplemultisampleempty.vcf.idx new file mode 100644 index 0000000000000000000000000000000000000000..9afdf7b8ff6583eea97829566a084c0e626c8ab6 GIT binary patch literal 438 zcmb_YQA)!=5FHWx@JH|tf*;aJVk2$;LJ~Eg5$Y!R7q;oN#%{7@ccbk!Jb~BnHr~K1 zxT!?MZwF@Q@!q`M$Fd}P*aLul+lxxj1Q9b$N+Z>zwomv-Ld>X{lfor8E7Yn)L)xGs zEn8KRMyZxKQN z(mP1?+H40_g0mAF(bmW5=WEeL?&`pHl!R>JIdF0Ac)oAJH{rr?