From aa2f2bafb641d037263e43e107ee2c3ae866852b Mon Sep 17 00:00:00 2001 From: David Benjamin Date: Wed, 4 Mar 2020 10:09:26 -0500 Subject: [PATCH] rewrote getReadCoordinateForReferenceCoordinate --- .../tools/walkers/annotator/BaseQuality.java | 2 +- .../annotator/BaseQualityRankSumTest.java | 13 +- .../annotator/ClippingRankSumTest.java | 3 +- .../tools/walkers/annotator/CountNs.java | 16 +- .../annotator/LikelihoodRankSumTest.java | 5 +- .../annotator/MappingQualityRankSumTest.java | 3 +- .../annotator/OrientationBiasReadCounts.java | 8 +- .../tools/walkers/annotator/RankSumTest.java | 26 +- .../walkers/annotator/ReadPosRankSumTest.java | 43 +- .../tools/walkers/annotator/ReadPosition.java | 2 +- .../AS_BaseQualityRankSumTest.java | 7 +- .../AS_MappingQualityRankSumTest.java | 3 +- .../allelespecific/AS_RankSumTest.java | 10 +- .../allelespecific/AS_ReadPosRankSumTest.java | 10 +- .../realignmentfilter/RealignmentEngine.java | 11 +- .../utils/clipping/ReadClipper.java | 15 +- .../utils/fragments/FragmentUtils.java | 18 +- .../hellbender/utils/haplotype/Haplotype.java | 16 +- .../hellbender/utils/read/ReadUtils.java | 268 +++-------- .../BaseRecalibrationEngine.java | 17 +- .../BaseQualityRankSumTestUnitTest.java | 2 + .../annotator/ReadPosRankSumTestUnitTest.java | 28 +- .../AS_BaseQualityRankSumTestUnitTest.java | 3 + .../AS_ReadPosRankSumTestUnitTest.java | 2 +- .../ReferenceConfidenceModelUnitTest.java | 9 +- .../utils/read/ReadUtilsUnitTest.java | 63 ++- .../BaseRecalibrationEngineUnitTest.java | 1 + ...1k.NA12878.indels_context_size_4.recal.txt | 427 +++++++++--------- ...-1m1k.NA12878.low_quality_tail_5.recal.txt | 427 +++++++++--------- ...A12878.mismatches_context_size_4.recal.txt | 426 +++++++++-------- ...0.1m-1m1k.NA12878.noIndels.noBAQ.recal.txt | 163 ++++--- ...1m1k.NA12878.quantizing_levels_6.recal.txt | 427 +++++++++--------- ...Seq.WGS.b37.ch20.1m-1m1k.NA12878.recal.txt | 427 +++++++++--------- ...ed.testGVCFMode.gatk4.alleleSpecific.g.vcf | 110 ++--- ...estGVCFMode.gatk4.alleleSpecific.g.vcf.idx | Bin 40800 -> 40800 bytes .../expected.testGVCFMode.gatk4.g.vcf | 110 ++--- .../expected.testGVCFMode.gatk4.g.vcf.idx | Bin 40785 -> 40785 bytes .../expected.testLinkedDebruijnMode.gatk4.vcf | 116 ++--- ...ected.testLinkedDebruijnMode.gatk4.vcf.idx | Bin 2919 -> 2919 bytes .../expected.testVCFMode.gatk4.nonstrict.vcf | 100 ++-- .../expected.testVCFMode.gatk4.vcf | 102 ++--- .../walkers/CombineGVCFs/IntervalTest.vcf | 2 +- .../walkers/CombineGVCFs/IntervalTest.vcf.idx | Bin 2144 -> 2144 bytes .../convertToBasePairResolution.vcf | 2 +- .../convertToBasePairResolution.vcf.idx | Bin 2426 -> 2426 bytes ...railingReferenceBlocksBandedExpected.g.vcf | 2 +- ...fWithTrailingReferenceBlocksExpected.g.vcf | 2 +- .../CombineGVCFs/newMQcalc.combined.g.vcf | 94 ++-- .../CombineGVCFs/newMQcalc.combined.g.vcf.idx | Bin 42474 -> 42518 bytes ...ingDeletionBaseExtensionTestExpected.g.vcf | 2 +- ...panningDeletionRestrictToStartExpected.vcf | 2 +- ...ingDeletionRestrictToStartExpected.vcf.idx | Bin 370 -> 370 bytes .../testAlleleSpecificAnnotations.vcf | 2 +- .../testAlleleSpecificAnnotations.vcf.idx | Bin 44870 -> 44870 bytes .../testAlleleSpecificAnnotationsNoGroup.vcf | 2 +- ...stAlleleSpecificAnnotationsNoGroup.vcf.idx | Bin 44877 -> 44877 bytes .../testBasepairResolutionInput.vcf | 2 +- .../testBasepairResolutionInput.vcf.idx | Bin 42144 -> 42144 bytes .../CombineGVCFs/testBreakBandsArgumet.vcf | 2 +- .../testBreakBandsArgumet.vcf.idx | Bin 2158 -> 2158 bytes ...tMultipleSpanningDeletionsForOneSample.vcf | 2 +- ...tipleSpanningDeletionsForOneSample.vcf.idx | Bin 429 -> 429 bytes ...leSpanningDeletionsForOneSampleHaploid.vcf | 2 +- ...anningDeletionsForOneSampleHaploid.vcf.idx | Bin 436 -> 436 bytes ...panningDeletionsForOneSampleTetraploid.vcf | 2 +- ...ingDeletionsForOneSampleTetraploid.vcf.idx | Bin 439 -> 439 bytes .../testWrongReferenceBaseBugFix.vcf | 2 +- .../testWrongReferenceBaseBugFix.vcf.idx | Bin 2117 -> 2117 bytes .../newMQcalc.combined.genotyped.vcf | 90 ++-- .../newMQcalc.combined.genotyped.vcf.idx | Bin 12144 -> 12142 bytes 70 files changed, 1770 insertions(+), 1881 deletions(-) diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/BaseQuality.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/BaseQuality.java index 3fbe2b2f799..14f9ae8dd08 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/BaseQuality.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/BaseQuality.java @@ -47,7 +47,7 @@ public static OptionalInt getBaseQuality(final GATKRead read, final VariantConte if (vc.getStart() < read.getStart() || read.getEnd() < vc.getStart()) { return OptionalInt.empty(); } - final OptionalDouble result = BaseQualityRankSumTest.getReadBaseQuality(read, vc.getStart()); + final OptionalDouble result = BaseQualityRankSumTest.getReadBaseQuality(read, vc); return result.isPresent() ? OptionalInt.of((int) FastMath.round(result.getAsDouble())) : OptionalInt.empty(); } } 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 b782a0164a9..1d1b983bc72 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 @@ -1,5 +1,6 @@ package org.broadinstitute.hellbender.tools.walkers.annotator; +import htsjdk.variant.variantcontext.VariantContext; import org.broadinstitute.barclay.help.DocumentedFeature; import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.utils.help.HelpConstants; @@ -10,6 +11,7 @@ import java.util.Collections; import java.util.List; +import java.util.Optional; import java.util.OptionalDouble; @@ -32,14 +34,13 @@ public final class BaseQualityRankSumTest extends RankSumTest implements Standar public List getKeyNames() { return Collections.singletonList(GATKVCFConstants.BASE_QUAL_RANK_SUM_KEY); } @Override - protected OptionalDouble getElementForRead(final GATKRead read, final int refLoc) { - return getReadBaseQuality(read, refLoc); + protected OptionalDouble getElementForRead(final GATKRead read, final VariantContext vc) { + return getReadBaseQuality(read, vc); } - public static OptionalDouble getReadBaseQuality(final GATKRead read, final int refLoc) { + public static OptionalDouble getReadBaseQuality(final GATKRead read, final VariantContext vc) { Utils.nonNull(read); - - final int readCoordinate = ReadUtils.getReadCoordinateForReferenceCoordinateUpToEndOfRead(read, refLoc, ClippingTail.RIGHT_TAIL, true); - return readCoordinate == ReadUtils.CLIPPING_GOAL_NOT_REACHED || readCoordinate < 0 || readCoordinate >= read.getLength() ? OptionalDouble.empty() : OptionalDouble.of(read.getBaseQuality(readCoordinate)); + final Optional readBaseQuality = ReadUtils.getReadBaseQualityAtReferenceCoordinate(read, vc.getStart()); + return readBaseQuality.isPresent() ? OptionalDouble.of(readBaseQuality.get()) : OptionalDouble.empty(); } } 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 8c91fa6e7bc..955c6cfca12 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 @@ -1,5 +1,6 @@ package org.broadinstitute.hellbender.tools.walkers.annotator; +import htsjdk.variant.variantcontext.VariantContext; import org.broadinstitute.barclay.help.DocumentedFeature; import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.utils.help.HelpConstants; @@ -33,7 +34,7 @@ public final class ClippingRankSumTest extends RankSumTest { public List getKeyNames() { return Collections.singletonList(GATKVCFConstants.CLIPPING_RANK_SUM_KEY); } @Override - protected OptionalDouble getElementForRead(final GATKRead read, final int refLoc) { + protected OptionalDouble getElementForRead(final GATKRead read, final VariantContext vc) { Utils.nonNull(read); return OptionalDouble.of(AlignmentUtils.getNumHardClippedBases(read)); } diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/CountNs.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/CountNs.java index 174a0c1e4e4..48ba70f097d 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/CountNs.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/CountNs.java @@ -56,19 +56,7 @@ public List getDescriptions() { @VisibleForTesting static Boolean doesReadHaveN(final GATKRead read, final VariantContext vc) { - - if (vc.getStart() < read.getStart() || read.getEnd() < vc.getStart()) { - return false; - } - - final Pair offsetAndInsideDeletion = ReadUtils.getReadCoordinateForReferenceCoordinate(read, vc.getStart(), true); - - if (offsetAndInsideDeletion.getRight()) { - return false; - } else { - final int offset = offsetAndInsideDeletion.getLeft(); - return !(offset == ReadUtils.CLIPPING_GOAL_NOT_REACHED || offset < 0 || offset >= read.getLength() || AlignmentUtils.isInsideDeletion(read.getCigar(), offset)) - && read.getBase(offset) == 'N'; - } + final Optional readBase = ReadUtils.getReadBaseAtReferenceCoordinate(read, vc.getStart()); + return readBase.isPresent() && readBase.get() == 'N'; } } 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 a7cb489016d..19c42b75eb1 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 @@ -1,6 +1,7 @@ package org.broadinstitute.hellbender.tools.walkers.annotator; import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.VariantContext; import org.broadinstitute.barclay.help.DocumentedFeature; import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods; @@ -31,7 +32,7 @@ public final class LikelihoodRankSumTest extends RankSumTest { public List getKeyNames() { return Collections.singletonList(GATKVCFConstants.LIKELIHOOD_RANK_SUM_KEY); } @Override - protected OptionalDouble getElementForRead(final GATKRead read, final int refLoc, final AlleleLikelihoods.BestAllele bestAllele) { + protected OptionalDouble getElementForRead(final GATKRead read, final VariantContext vc, final AlleleLikelihoods.BestAllele bestAllele) { Utils.nonNull(read, "read is null"); Utils.nonNull(bestAllele, "mostLikelyAllele is null"); if ( ! bestAllele.isInformative() ) { @@ -41,7 +42,7 @@ protected OptionalDouble getElementForRead(final GATKRead read, final int refLoc } @Override - protected OptionalDouble getElementForRead(final GATKRead read, final int refLoc) { + protected OptionalDouble getElementForRead(final GATKRead read, final VariantContext vc) { // 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 a74f98f18be..035e1de78a3 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 @@ -1,5 +1,6 @@ package org.broadinstitute.hellbender.tools.walkers.annotator; +import htsjdk.variant.variantcontext.VariantContext; import org.broadinstitute.barclay.help.DocumentedFeature; import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.utils.help.HelpConstants; @@ -36,7 +37,7 @@ public final class MappingQualityRankSumTest extends RankSumTest implements Stan public List getKeyNames() { return Collections.singletonList(GATKVCFConstants.MAP_QUAL_RANK_SUM_KEY); } @Override - protected OptionalDouble getElementForRead(final GATKRead read, final int refLoc) { + protected OptionalDouble getElementForRead(final GATKRead read, final VariantContext vc) { Utils.nonNull(read); return OptionalDouble.of(read.getMappingQuality()); } diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/OrientationBiasReadCounts.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/OrientationBiasReadCounts.java index 4f965af6a50..c675a67262d 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/OrientationBiasReadCounts.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/OrientationBiasReadCounts.java @@ -16,7 +16,6 @@ import org.broadinstitute.hellbender.utils.help.HelpConstants; import org.broadinstitute.hellbender.utils.pileup.PileupElement; import org.broadinstitute.hellbender.utils.pileup.ReadPileup; -import org.broadinstitute.hellbender.utils.read.ClippingTail; import org.broadinstitute.hellbender.utils.read.GATKRead; import org.broadinstitute.hellbender.utils.read.ReadUtils; import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; @@ -78,7 +77,7 @@ public void annotate(final ReferenceContext refContext, .collect(Collectors.toMap(a -> a, a -> new MutableInt(0))); Utils.stream(likelihoods.bestAllelesBreakingTies(g.getSampleName())) - .filter(ba -> ba.isInformative() && isUsableRead(ba.evidence) && getReadBaseQuality(ba.evidence, vc.getStart()).orElse(0) >= MINIMUM_BASE_QUALITY) + .filter(ba -> ba.isInformative() && isUsableRead(ba.evidence) && BaseQualityRankSumTest.getReadBaseQuality(ba.evidence, vc).orElse(0) >= MINIMUM_BASE_QUALITY) .forEach(ba -> (ReadUtils.isF2R1(ba.evidence) ? f2r1Counts : f1r2Counts).get(ba.allele).increment()); final int[] f1r2 = vc.getAlleles().stream().mapToInt(a -> f1r2Counts.get(a).intValue()).toArray(); @@ -170,9 +169,4 @@ protected static boolean isUsableRead(final GATKRead read) { return read.getMappingQuality() != 0 && read.getMappingQuality() != QualityUtils.MAPPING_QUALITY_UNAVAILABLE; } - private static OptionalDouble getReadBaseQuality(final GATKRead read, final int refLoc) { - Utils.nonNull(read); - final int readCoord = ReadUtils.getReadCoordinateForReferenceCoordinate(read.getSoftStart(), read.getCigar(), refLoc, ClippingTail.RIGHT_TAIL, true); - return readCoord < 0 || readCoord >= read.getLength() ? OptionalDouble.empty() : OptionalDouble.of(read.getBaseQuality(readCoord)); - } } \ No newline at end of file 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 41872a3d541..a15d98ba727 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 @@ -9,11 +9,9 @@ import org.broadinstitute.hellbender.utils.QualityUtils; import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods; -import org.broadinstitute.hellbender.utils.pileup.PileupElement; import org.broadinstitute.hellbender.utils.read.GATKRead; import java.util.*; -import java.util.stream.Collectors; /** @@ -36,10 +34,8 @@ public Map annotate(final ReferenceContext ref, final List refQuals = new ArrayList<>(); final List altQuals = new ArrayList<>(); - final int refLoc = vc.getStart(); - if( likelihoods != null) { - fillQualsFromLikelihood(vc, likelihoods, refQuals, altQuals, refLoc); + fillQualsFromLikelihood(vc, likelihoods, refQuals, altQuals); } @@ -60,12 +56,12 @@ public Map annotate(final ReferenceContext ref, } } - protected void fillQualsFromLikelihood(VariantContext vc, AlleleLikelihoods likelihoods, List refQuals, List altQuals, int refLoc) { + protected void fillQualsFromLikelihood(VariantContext vc, AlleleLikelihoods likelihoods, List refQuals, List altQuals) { for (final AlleleLikelihoods.BestAllele bestAllele : likelihoods.bestAllelesBreakingTies()) { final GATKRead read = bestAllele.evidence; final Allele allele = bestAllele.allele; - if (bestAllele.isInformative() && isUsableRead(read, refLoc)) { - final OptionalDouble value = getElementForRead(read, refLoc, bestAllele); + if (bestAllele.isInformative() && isUsableRead(read, vc)) { + final OptionalDouble value = getElementForRead(read, vc, 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()) { @@ -82,31 +78,31 @@ protected void fillQualsFromLikelihood(VariantContext vc, AlleleLikelihoods.BestAllele bestAllele) { - return getElementForRead(read, refLoc); + protected OptionalDouble getElementForRead(final GATKRead read, final VariantContext vc, final AlleleLikelihoods.BestAllele bestAllele) { + return getElementForRead(read, vc); } /** * Get the element for the given read at the given reference position * * @param read the read - * @param refLoc the reference position + * @param vc the variant to be annotated * @return an OptionalDouble representing the element to be used in the rank sum test, empty if it should not be used */ - protected abstract OptionalDouble getElementForRead(final GATKRead read, final int refLoc); + protected abstract OptionalDouble getElementForRead(final GATKRead read, final VariantContext vc); /** * Can the read be used in comparative tests between ref / alt bases? * * @param read the read to consider - * @param refLoc the reference location + * @param vc the variant to be annotated * @return true if this read is meaningful for comparison, false otherwise */ - protected boolean isUsableRead(final GATKRead read, final int refLoc) { + protected boolean isUsableRead(final GATKRead read, final VariantContext vc) { Utils.nonNull(read); return read.getMappingQuality() != 0 && read.getMappingQuality() != QualityUtils.MAPPING_QUALITY_UNAVAILABLE; } 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 6aff720c5d7..f87486b4a8d 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 @@ -3,6 +3,8 @@ import htsjdk.samtools.Cigar; import htsjdk.samtools.CigarElement; import htsjdk.samtools.CigarOperator; +import htsjdk.variant.variantcontext.VariantContext; +import org.apache.commons.lang3.tuple.Pair; import org.broadinstitute.barclay.help.DocumentedFeature; import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.utils.help.HelpConstants; @@ -39,26 +41,31 @@ public final class ReadPosRankSumTest extends RankSumTest implements StandardAnn public List getKeyNames() { return Collections.singletonList(GATKVCFConstants.READ_POS_RANK_SUM_KEY); } @Override - protected OptionalDouble getElementForRead(final GATKRead read, final int refLoc) { - return getReadPosition(read, refLoc); + protected OptionalDouble getElementForRead(final GATKRead read, final VariantContext vc) { + return getReadPosition(read, vc); } @Override - public boolean isUsableRead(final GATKRead read, final int refLoc) { + public boolean isUsableRead(final GATKRead read, final VariantContext vc) { Utils.nonNull(read); - return super.isUsableRead(read, refLoc) && read.getSoftEnd() >= refLoc; + // we use vc.getEnd() + 1 in case of a leading indel -- if this isn't relevant getReadPosition will return empty + return super.isUsableRead(read, vc) && read.getSoftStart() <= vc.getEnd() + 1 && read.getSoftEnd() >= vc.getStart(); } - public static OptionalDouble getReadPosition(final GATKRead read, final int refLoc) { + public static OptionalDouble getReadPosition(final GATKRead read, final VariantContext vc) { Utils.nonNull(read); - final int offset = ReadUtils.getReadCoordinateForReferenceCoordinate(read.getSoftStart(), read.getCigar(), refLoc, ClippingTail.RIGHT_TAIL, true); - if ( offset == ReadUtils.CLIPPING_GOAL_NOT_REACHED ) { - return OptionalDouble.empty(); + + // edge case: if a read starts with an insertion then the variant context's end is the reference base BEFORE the read start, + // which appears like no overlap + if (read.getStart() == vc.getEnd() + 1 && read.getCigarElements().stream().map(CigarElement::getOperator) + .filter(o -> !o.isClipping()).findFirst().orElse(null) == CigarOperator.INSERTION) { + return OptionalDouble.of(0); } - // If the offset inside a deletion, it does not lie on a read. - if ( AlignmentUtils.isInsideDeletion(read.getCigar(), offset) ) { - return OptionalDouble.of(INVALID_ELEMENT_FROM_READ); + final Pair offset = ReadUtils.getReadCoordinateForReferenceCoordinate(read, vc.getStart()); + + if (offset.getLeft() == ReadUtils.CLIPPING_GOAL_NOT_REACHED) { + return OptionalDouble.empty(); } // hard clips at this point in the code are perfectly good bases that were clipped to make the read fit the assembly region @@ -68,17 +75,9 @@ public static OptionalDouble getReadPosition(final GATKRead read, final int refL final int leadingHardClips = firstElement.getOperator() == CigarOperator.HARD_CLIP ? firstElement.getLength() : 0; final int trailingHardClips = lastElement.getOperator() == CigarOperator.HARD_CLIP ? lastElement.getLength() : 0; - if (offset >= cigar.getReadLength()) { - return OptionalDouble.empty(); - } - int readPos = leadingHardClips + AlignmentUtils.calcAlignmentByteArrayOffset(read.getCigar(), offset, false, 0, 0); - final int numAlignedBases = AlignmentUtils.getNumAlignedBasesCountingSoftClips( read ); - final int numOriginalBases = numAlignedBases + leadingHardClips + trailingHardClips; - //After the middle of the read, we compute the postion from the end of the read. - if (readPos > numOriginalBases / 2) { - readPos = numOriginalBases - (readPos + 1); - } - return OptionalDouble.of(readPos); + final int leftDistance = leadingHardClips + offset.getLeft(); + final int rightDistance = read.getLength() - 1 - offset.getLeft() + trailingHardClips; + return OptionalDouble.of(Math.min(leftDistance, rightDistance)); } } diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/ReadPosition.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/ReadPosition.java index f5866f36ce2..5ef938e40a5 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/ReadPosition.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/ReadPosition.java @@ -53,7 +53,7 @@ protected OptionalInt getValueForRead(final GATKRead read, final VariantContext if (vc.getStart() < read.getStart() || read.getEnd() < vc.getStart()) { return OptionalInt.empty(); } - final OptionalDouble valueAsDouble = ReadPosRankSumTest.getReadPosition(read, vc.getStart()); + final OptionalDouble valueAsDouble = ReadPosRankSumTest.getReadPosition(read, vc); return valueAsDouble.isPresent() ? OptionalInt.of((int) valueAsDouble.getAsDouble()) : OptionalInt.empty(); } } diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_BaseQualityRankSumTest.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_BaseQualityRankSumTest.java index c4219c0ed81..44f82c6edd7 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_BaseQualityRankSumTest.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_BaseQualityRankSumTest.java @@ -1,5 +1,6 @@ package org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific; +import htsjdk.variant.variantcontext.VariantContext; import org.broadinstitute.barclay.help.DocumentedFeature; import org.broadinstitute.hellbender.tools.walkers.annotator.BaseQualityRankSumTest; import org.broadinstitute.hellbender.utils.help.HelpConstants; @@ -74,12 +75,12 @@ public List getSecondaryRawKeys() { * Get the element for the given read at the given reference position * * @param read the read - * @param refLoc the reference position + * @param vc the variant to be annotated * @return a Double representing the element to be used in the rank sum test, or null if it should not be used */ @Override - protected OptionalDouble getElementForRead(final GATKRead read, final int refLoc) { - return BaseQualityRankSumTest.getReadBaseQuality(read, refLoc); + protected OptionalDouble getElementForRead(final GATKRead read, final VariantContext vc) { + return BaseQualityRankSumTest.getReadBaseQuality(read, vc); } } diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_MappingQualityRankSumTest.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_MappingQualityRankSumTest.java index 35757841b6e..d1e0740db8e 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_MappingQualityRankSumTest.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_MappingQualityRankSumTest.java @@ -1,5 +1,6 @@ package org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific; +import htsjdk.variant.variantcontext.VariantContext; import org.broadinstitute.barclay.help.DocumentedFeature; import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.utils.help.HelpConstants; @@ -68,7 +69,7 @@ public List getSecondaryRawKeys() { } @Override - protected OptionalDouble getElementForRead(final GATKRead read, final int refLoc) { + protected OptionalDouble getElementForRead(final GATKRead read, final VariantContext vc) { Utils.nonNull(read); return OptionalDouble.of(read.getMappingQuality()); } 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 ebf2dea76b1..7396c3ddda6 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 @@ -40,10 +40,8 @@ public Map annotate(final ReferenceContext ref, final List refQuals = new ArrayList<>(); final List altQuals = new ArrayList<>(); - final int refLoc = vc.getStart(); - if( likelihoods != null) { - fillQualsFromLikelihood(vc, likelihoods, refQuals, altQuals, refLoc); + fillQualsFromLikelihood(vc, likelihoods, refQuals, altQuals); } if ( refQuals.isEmpty() && altQuals.isEmpty() ) { @@ -153,12 +151,10 @@ private void calculateRawData(VariantContext vc, final AlleleLikelihoods> perAlleleValues = myData.getAttributeMap(); for ( final AlleleLikelihoods.BestAllele bestAllele : likelihoods.bestAllelesBreakingTies() ) { - if (bestAllele.isInformative() && isUsableRead(bestAllele.evidence, refLoc)) { - final OptionalDouble value = getElementForRead(bestAllele.evidence, refLoc, bestAllele); + if (bestAllele.isInformative() && isUsableRead(bestAllele.evidence, vc)) { + final OptionalDouble value = getElementForRead(bestAllele.evidence, vc, bestAllele); if (value.isPresent() && value.getAsDouble() != INVALID_ELEMENT_FROM_READ && perAlleleValues.containsKey(bestAllele.allele)) { perAlleleValues.get(bestAllele.allele).add((int) value.getAsDouble()); } 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 340be1c5910..298a0a156a2 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 @@ -1,6 +1,7 @@ package org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific; +import htsjdk.variant.variantcontext.VariantContext; import org.broadinstitute.barclay.help.DocumentedFeature; import org.broadinstitute.hellbender.tools.walkers.annotator.ReadPosRankSumTest; import org.broadinstitute.hellbender.utils.Utils; @@ -71,13 +72,14 @@ public List getSecondaryRawKeys() { } @Override - protected OptionalDouble getElementForRead(final GATKRead read, final int refLoc) { - return ReadPosRankSumTest.getReadPosition(read, refLoc); + protected OptionalDouble getElementForRead(final GATKRead read, final VariantContext vc) { + return ReadPosRankSumTest.getReadPosition(read, vc); } @Override - public boolean isUsableRead(final GATKRead read, final int refLoc) { + public boolean isUsableRead(final GATKRead read, final VariantContext vc) { Utils.nonNull(read); - return super.isUsableRead(read, refLoc) && read.getSoftEnd() >= refLoc; + // we use vc.getEnd() + 1 in case of a leading indel -- if this isn't relevant getReadPosition will return empty + return super.isUsableRead(read, vc) && read.getSoftStart() <= vc.getEnd() + 1 && read.getSoftEnd() >= vc.getStart(); } } diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/realignmentfilter/RealignmentEngine.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/realignmentfilter/RealignmentEngine.java index 74aff83be42..ba8cd7d791d 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/realignmentfilter/RealignmentEngine.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/realignmentfilter/RealignmentEngine.java @@ -8,6 +8,7 @@ import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.VariantContext; import org.apache.commons.lang.ArrayUtils; +import org.apache.commons.lang3.tuple.Pair; import org.broadinstitute.hellbender.tools.spark.sv.utils.Strand; import org.broadinstitute.hellbender.utils.SimpleInterval; import org.broadinstitute.hellbender.utils.bwa.BwaMemAligner; @@ -38,12 +39,16 @@ public RealignmentEngine(final RealignmentArgumentCollection rfac) { public static boolean supportsVariant(final GATKRead read, final VariantContext vc, int indelStartTolerance) { final byte[] readBases = read.getBasesNoCopy(); - final int variantPositionInRead = ReadUtils.getReadCoordinateForReferenceCoordinate(read.getSoftStart(), read.getCigar(), - vc.getStart(), ClippingTail.RIGHT_TAIL, true); - if ( variantPositionInRead == ReadUtils.CLIPPING_GOAL_NOT_REACHED || AlignmentUtils.isInsideDeletion(read.getCigar(), variantPositionInRead)) { + final Pair offsetAndOperatorInRead = ReadUtils.getReadCoordinateForReferenceCoordinate(read, vc.getStart()); + + if ( offsetAndOperatorInRead.getLeft() == ReadUtils.CLIPPING_GOAL_NOT_REACHED) { + return false; + } else if (vc.isSNP() && offsetAndOperatorInRead.getRight() == CigarOperator.DELETION) { return false; } + final int variantPositionInRead = offsetAndOperatorInRead.getLeft(); + for (final Allele allele : vc.getAlternateAlleles()) { final int referenceLength = vc.getReference().length(); if (allele.length() == referenceLength) { // SNP or MNP -- check whether read bases match variant allele bases diff --git a/src/main/java/org/broadinstitute/hellbender/utils/clipping/ReadClipper.java b/src/main/java/org/broadinstitute/hellbender/utils/clipping/ReadClipper.java index bb4cec7a0eb..3f8eebcef77 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/clipping/ReadClipper.java +++ b/src/main/java/org/broadinstitute/hellbender/utils/clipping/ReadClipper.java @@ -2,6 +2,7 @@ import htsjdk.samtools.CigarElement; import htsjdk.samtools.CigarOperator; +import org.apache.commons.lang3.tuple.Pair; import org.apache.logging.log4j.LogManager; import org.apache.logging.log4j.Logger; import org.broadinstitute.hellbender.exceptions.GATKException; @@ -417,16 +418,26 @@ protected GATKRead clipByReferenceCoordinates(final int refStart, final int refS throw new GATKException("Only one of refStart or refStop must be < 0, not both (" + refStart + ", " + refStop + ")"); } start = 0; - stop = ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStop, ClippingTail.LEFT_TAIL); + + final Pair stopPosAndOperator = ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStop); + + // if the refStop falls in a deletion, the above method returns the position after the deletion. Since the stop we return here + // is inclusive, we decrement the stop to avoid overclipping by one base. As a result we do not clip the deletion, which is fine. + stop = stopPosAndOperator.getLeft() - (stopPosAndOperator.getRight().consumesReadBases() ? 0 : 1); } else { if (refStop >= 0) { throw new GATKException("Either refStart or refStop must be < 0 (" + refStart + ", " + refStop + ")"); } - start = ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStart, ClippingTail.RIGHT_TAIL); + // unlike the above case where we clip the start fo the read, here we clip the end and returning the base to the right of a deletion avoids overclipping + start = ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStart).getLeft(); stop = read.getLength() - 1; } + if (start == ReadUtils.CLIPPING_GOAL_NOT_REACHED || stop == ReadUtils.CLIPPING_GOAL_NOT_REACHED) { + return read; + } + if (start < 0 || stop > read.getLength() - 1) { throw new GATKException("Trying to clip before the start or after the end of a read"); } diff --git a/src/main/java/org/broadinstitute/hellbender/utils/fragments/FragmentUtils.java b/src/main/java/org/broadinstitute/hellbender/utils/fragments/FragmentUtils.java index 624a3bf88ae..b3ac4d15dc9 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/fragments/FragmentUtils.java +++ b/src/main/java/org/broadinstitute/hellbender/utils/fragments/FragmentUtils.java @@ -1,5 +1,6 @@ package org.broadinstitute.hellbender.utils.fragments; +import htsjdk.samtools.CigarOperator; import htsjdk.samtools.util.QualityUtil; import org.apache.commons.lang3.tuple.Pair; import org.broadinstitute.hellbender.utils.Utils; @@ -44,8 +45,21 @@ public static void adjustQualsOfOverlappingPairedFragments(final Pair offset = ReadUtils.getReadCoordinateForReferenceCoordinate(firstRead, secondRead.getStart(), false); - final int firstReadStop = (offset.getRight() ? offset.getLeft() + 1 : offset.getLeft()); + // the offset and cigar operator in the first read at the start of the left read + final Pair offsetAndOperator = ReadUtils.getReadCoordinateForReferenceCoordinate(firstRead, secondRead.getStart()); + final CigarOperator operator = offsetAndOperator.getRight(); + final int offset = offsetAndOperator.getLeft(); + if (offset == ReadUtils.CLIPPING_GOAL_NOT_REACHED) { // no overlap + return; + } + + + // TODO: we should be careful about the case where {@code operator} is a deletion; that is, when the second read start falls in a deletion of the first read + // TODO: however, the issue is bigger than simply getting the start correctly, because the code below assumes that all bases of both reads are aligned in their overlap. + // TODO: Any indel that occurs in one read and not the other will spoil things. Really, the correct thing to do is a Smith-Waterman (or other) alignment of the reads + // TODO: in their overlap and correct the double-counting for all aligned bases. + // TODO: a cheaper solution would be to cap all quals in the overlap region by half of the PCR qual. + final int firstReadStop = offset; final int numOverlappingBases = Math.min(firstRead.getLength() - firstReadStop, secondRead.getLength()); final byte[] firstReadBases = firstRead.getBases(); diff --git a/src/main/java/org/broadinstitute/hellbender/utils/haplotype/Haplotype.java b/src/main/java/org/broadinstitute/hellbender/utils/haplotype/Haplotype.java index dc69ff0b943..fb9db395f70 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/haplotype/Haplotype.java +++ b/src/main/java/org/broadinstitute/hellbender/utils/haplotype/Haplotype.java @@ -6,10 +6,10 @@ import htsjdk.samtools.util.Locatable; import htsjdk.variant.variantcontext.Allele; import org.apache.commons.lang3.ArrayUtils; +import org.apache.commons.lang3.tuple.Pair; import org.broadinstitute.hellbender.utils.SimpleInterval; import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.utils.read.AlignmentUtils; -import org.broadinstitute.hellbender.utils.read.ClippingTail; import org.broadinstitute.hellbender.utils.read.ReadUtils; import java.util.Arrays; @@ -197,9 +197,17 @@ public void setCigar( final Cigar cigar ) { public Haplotype insertAllele( final Allele refAllele, final Allele altAllele, final int refInsertLocation, final int genomicInsertLocation ) { // refInsertLocation is in ref haplotype offset coordinates NOT genomic coordinates - final int haplotypeInsertLocation = ReadUtils.getReadCoordinateForReferenceCoordinate(alignmentStartHapwrtRef, cigar, refInsertLocation, ClippingTail.RIGHT_TAIL, true); - final byte[] myBases = this.getBases(); - if( haplotypeInsertLocation == -1 || haplotypeInsertLocation + refAllele.length() >= myBases.length ) { // desired change falls inside deletion so don't bother creating a new haplotype + final Pair haplotypeInsertLocationAndOperator = ReadUtils.getReadCoordinateForReferenceCoordinate(alignmentStartHapwrtRef, cigar, refInsertLocation); + + // can't insert outside the haplotype or into a deletion + if( haplotypeInsertLocationAndOperator.getLeft() == ReadUtils.CLIPPING_GOAL_NOT_REACHED || !haplotypeInsertLocationAndOperator.getRight().consumesReadBases() ) { + return null; + } + final int haplotypeInsertLocation = haplotypeInsertLocationAndOperator.getLeft(); + final byte[] myBases = getBases(); + + // can't insert if we don't have any sequence after the inserted alt allele to span the new variant + if (haplotypeInsertLocation + refAllele.length() >= myBases.length) { return null; } diff --git a/src/main/java/org/broadinstitute/hellbender/utils/read/ReadUtils.java b/src/main/java/org/broadinstitute/hellbender/utils/read/ReadUtils.java index c0dc35a13aa..79a8504d2c9 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/read/ReadUtils.java +++ b/src/main/java/org/broadinstitute/hellbender/utils/read/ReadUtils.java @@ -666,205 +666,72 @@ public static int getSoftEnd(final GATKRead read) { return softEnd; } - public static int getReadCoordinateForReferenceCoordinateUpToEndOfRead(final GATKRead read, final int refCoord, final ClippingTail tail) { - return getReadCoordinateForReferenceCoordinateUpToEndOfRead(read, refCoord, tail, false); - } - - public static int getReadCoordinateForReferenceCoordinateUpToEndOfRead(final GATKRead read, final int refCoord, final ClippingTail tail, final boolean allowGoalNotReached) { - final int leftmostSafeVariantPosition = Math.max(read.getSoftStart(), refCoord); - return getReadCoordinateForReferenceCoordinate(read.getSoftStart(), read.getCigar(), leftmostSafeVariantPosition, tail, allowGoalNotReached); - } - /** - * Pre-processes the results of {@link #getReadCoordinateForReferenceCoordinate(int, Cigar, int, boolean)} to take care of - * two corner cases: - * - * 1. If clipping the right tail (end of the read) getReadCoordinateForReferenceCoordinate and fall inside - * a deletion return the base after the deletion. If clipping the left tail (beginning of the read) it - * doesn't matter because it already returns the previous base by default. - * - * 2. If clipping the left tail (beginning of the read) getReadCoordinateForReferenceCoordinate and the - * read starts with an insertion, and you're requesting the first read based coordinate, it will skip - * the leading insertion (because it has the same reference coordinate as the following base). - * - * @return the read coordinate corresponding to the requested reference coordinate for clipping. - */ - public static int getReadCoordinateForReferenceCoordinate(final GATKRead read, final int refCoord, final ClippingTail tail) { - return getReadCoordinateForReferenceCoordinate(read.getSoftStart(), read.getCigar(), refCoord, tail, false); + * Find the index within a read's bases corresponding to a given position in the reference, along with the cigar operator of + * the element containing that base. If the reference coordinate occurs within a deletion, the first index after the deletion is returned. + * Note that this treats soft-clipped bases as if they align with the reference, which is useful for hard-clipping reads with soft clips. + * + * @param alignmentStart The soft start of the read on the reference + * @param cigar The read's cigar + * @param refCoord The target reference coordinate + * @return If the reference coordinate occurs before the read start or after the read end {@code CLIPPING_GOAL_NOT_REACHED}; + * if the reference coordinate falls within an alignment block of the read's cigar, the corresponding read coordinate; + * if the reference coordinate falls within a deletion, the first read coordinate after the deletion. Note: if the last cigar element is + * a deletion (which isn't meaningful), it returns {@code CLIPPING_GOAL_NOT_REACHED}. + */ + public static Pair getReadCoordinateForReferenceCoordinate(final int alignmentStart, final Cigar cigar, final int refCoord) { + if (refCoord < alignmentStart) { + return new MutablePair<>(CLIPPING_GOAL_NOT_REACHED, null); + } + int firstReadPosOfElement = 0; //inclusive + int firstRefPosOfElement = alignmentStart; //inclusive + int lastReadPosOfElement = 0; //exclusive + int lastRefPosOfElement = alignmentStart; //exclusive + + // advance forward through all the cigar elements until we bracket the reference coordinate + for (final CigarElement element : cigar) { + final CigarOperator operator = element.getOperator(); + firstReadPosOfElement = lastReadPosOfElement; + firstRefPosOfElement = lastRefPosOfElement; + lastReadPosOfElement += operator.consumesReadBases() ? element.getLength() : 0; + lastRefPosOfElement += operator.consumesReferenceBases() || operator == CigarOperator.S ? element.getLength() : 0; + + if (firstRefPosOfElement <= refCoord && refCoord < lastRefPosOfElement) { // refCoord falls within this cigar element + final int readPosAtRefCoord = firstReadPosOfElement + (operator.consumesReadBases() ? ( refCoord - firstRefPosOfElement) : 0); + return Pair.of(readPosAtRefCoord, operator); + } + } + return new MutablePair<>(CLIPPING_GOAL_NOT_REACHED, null); } - /** - * Returns the read coordinate corresponding to the requested reference coordinate. - * - * WARNING: if the requested reference coordinate happens to fall inside or just before a deletion (or skipped region) in the read, this function - * will return the last read base before the deletion (or skipped region). This function returns a - * Pair(int readCoord, boolean fallsInsideOrJustBeforeDeletionOrSkippedRegion) so you can choose which readCoordinate to use when faced with - * a deletion (or skipped region). - * - * SUGGESTION: Use getReadCoordinateForReferenceCoordinate(GATKSAMRecord, int, ClippingTail) instead to get a - * pre-processed result according to normal clipping needs. Or you can use this function and tailor the - * behavior to your needs. - * - * @param read - * @param refCoord the requested reference coordinate - * @param allowGoalNotReached if true, will return a pair of CLIPPING_GOAL_NOT_REACHED and false a refCoord that doesn't exist on the read is requested, otherwise an exception will be thrown - * @return the read coordinate corresponding to the requested reference coordinate. (see warning!) - */ - public static Pair getReadCoordinateForReferenceCoordinate(GATKRead read, int refCoord, boolean allowGoalNotReached) { - return getReadCoordinateForReferenceCoordinate(read.getSoftStart(), read.getCigar(), refCoord, allowGoalNotReached); - } /** - * Returns the read coordinate corresponding to the requested reference coordinate for a given alignmentStart/Cigar combination. - * - * WARNING: if the requested reference coordinate happens to fall inside or just before a deletion (or skipped region) in the read, this function - * will return the last read base before the deletion (or skipped region). This function returns a - * Pair(int readCoord, boolean fallsInsideOrJustBeforeDeletionOrSkippedRegion) so you can choose which readCoordinate to use when faced with - * a deletion (or skipped region). - * - * SUGGESTION: Use getReadCoordinateForReferenceCoordinate(GATKSAMRecord, int, ClippingTail) instead to get a - * pre-processed result according to normal clipping needs. Or you can use this function and tailor the - * behavior to your needs. - * - * @param alignmentStart alignment start of the cigar to the reference - * @param cigar cigar with which to compute the offset - * @param refCoord the requested reference coordinate - * @param tail controls whether the the preceding or following base of a deletion/insertion is returned - * @param allowGoalNotReached if true, will return a pair of CLIPPING_GOAL_NOT_REACHED and false a refCoord that doesn't exist on the read is requested, otherwise an exception will be thrown - * @return the read coordinate corresponding to the requested reference coordinate. (see warning!) + * Returns the read coordinate corresponding to the requested reference coordinate -- or the read coordinate immediately preceding + * a deletion in which the reference coordinate falls -- along with the cigar operator in which the reference coordinate occurs. */ - public static int getReadCoordinateForReferenceCoordinate(final int alignmentStart, final Cigar cigar, final int refCoord, final ClippingTail tail, final boolean allowGoalNotReached) { - final Pair result = getReadCoordinateForReferenceCoordinate(alignmentStart, cigar, refCoord, allowGoalNotReached); - int readCoord = result.getLeft(); - - // Corner case one: clipping the right tail and falls on deletion, move to the next - // read coordinate. It is not a problem for the left tail because the default answer - // from getReadCoordinateForReferenceCoordinate is to give the previous read coordinate. - if (result.getRight() && tail == ClippingTail.RIGHT_TAIL) { - readCoord++; - } - - // clipping the left tail and first base is insertion, go to the next read coordinate - // with the same reference coordinate. Advance to the next cigar element, or to the - // end of the read if there is no next element. - final CigarElement firstElementIsInsertion = readStartsWithInsertion(cigar); - if (readCoord == 0 && tail == ClippingTail.LEFT_TAIL && firstElementIsInsertion != null) { - readCoord = Math.min(firstElementIsInsertion.getLength(), cigar.getReadLength() - 1); - } - - return readCoord; + public static Pair getReadCoordinateForReferenceCoordinate(final GATKRead read, final int refCoord) { + return getReadCoordinateForReferenceCoordinate(read.getSoftStart(), read.getCigar(), refCoord); } - private static Pair getReadCoordinateForReferenceCoordinate(final int alignmentStart, final Cigar cigar, final int refCoord, final boolean allowGoalNotReached) { - int readBases = 0; - int refBases = 0; - boolean fallsInsideDeletionOrSkippedRegion = false; - boolean endJustBeforeDeletionOrSkippedRegion = false; - boolean fallsInsideOrJustBeforeDeletionOrSkippedRegion = false; - - final int goal = refCoord - alignmentStart; // The goal is to move this many reference bases - if (goal < 0) { - if (allowGoalNotReached) { - return new MutablePair<>(CLIPPING_GOAL_NOT_REACHED, false); - } else { - throw new GATKException(String.format("Somehow the requested coordinate is not covered by the read. Too many deletions? alignment Start: %d, Cigar: %s, refCoord: %s ", - alignmentStart, cigar.toString(), refCoord)); - } - } - boolean goalReached = refBases == goal; - - final Iterator cigarElementIterator = cigar.getCigarElements().iterator(); - while (!goalReached && cigarElementIterator.hasNext()) { - final CigarElement cigarElement = cigarElementIterator.next(); - int shift = 0; - - if (cigarElement.getOperator().consumesReferenceBases() || cigarElement.getOperator() == CigarOperator.SOFT_CLIP) { - if (refBases + cigarElement.getLength() < goal) { - shift = cigarElement.getLength(); - } else { - shift = goal - refBases; - } - - refBases += shift; - } - goalReached = refBases == goal; - - if (!goalReached && cigarElement.getOperator().consumesReadBases()) { - readBases += cigarElement.getLength(); - } - - if (goalReached) { - // Is this base's reference position within this cigar element? Or did we use it all? - final boolean endsWithinCigar = shift < cigarElement.getLength(); - - // If it isn't, we need to check the next one. There should *ALWAYS* be a next one - // since we checked if the goal coordinate is within the read length, so this is just a sanity check. - if (!endsWithinCigar && !cigarElementIterator.hasNext()) { - if (allowGoalNotReached) { - return new MutablePair<>(CLIPPING_GOAL_NOT_REACHED, false); - } else { - throw new GATKException(String.format("Reference coordinate corresponds to a non-existent base in the read. This should never happen -- check read with alignment start: %s and cigar: %s", alignmentStart, cigar)); - } - } - - CigarElement nextCigarElement = null; - - // if we end inside the current cigar element, we just have to check if it is a deletion (or skipped region) - if (endsWithinCigar) { - fallsInsideDeletionOrSkippedRegion = (cigarElement.getOperator() == CigarOperator.DELETION || cigarElement.getOperator() == CigarOperator.SKIPPED_REGION); - }// if we end outside the current cigar element, we need to check if the next element is an insertion, deletion or skipped region. - else { - nextCigarElement = cigarElementIterator.next(); - - // if it's an insertion, we need to clip the whole insertion before looking at the next element - if (nextCigarElement.getOperator() == CigarOperator.INSERTION) { - readBases += nextCigarElement.getLength(); - if (!cigarElementIterator.hasNext()) { - if (allowGoalNotReached) { - return new MutablePair<>(CLIPPING_GOAL_NOT_REACHED, false); - } else { - throw new GATKException(String.format("Reference coordinate corresponds to a non-existent base in the read. This should never happen -- check read with alignment start: %s and cigar: %s", alignmentStart, cigar)); - } - } - - nextCigarElement = cigarElementIterator.next(); - } - - // if it's a deletion (or skipped region), we will pass the information on to be handled downstream. - endJustBeforeDeletionOrSkippedRegion = (nextCigarElement.getOperator() == CigarOperator.DELETION || nextCigarElement.getOperator() == CigarOperator.SKIPPED_REGION); - } - - fallsInsideOrJustBeforeDeletionOrSkippedRegion = endJustBeforeDeletionOrSkippedRegion || fallsInsideDeletionOrSkippedRegion; - - // If we reached our goal outside a deletion (or skipped region), add the shift - if (!fallsInsideOrJustBeforeDeletionOrSkippedRegion && cigarElement.getOperator().consumesReadBases()) { - readBases += shift; - }// If we reached our goal just before a deletion (or skipped region) we need - // to add the shift of the current cigar element but go back to it's last element to return the last - // base before the deletion (or skipped region) (see warning in function contracts) - else if (endJustBeforeDeletionOrSkippedRegion && cigarElement.getOperator().consumesReadBases()) { - readBases += shift - 1; - }// If we reached our goal inside a deletion (or skipped region), or just between a deletion and a skipped region, - // then we must backtrack to the last base before the deletion (or skipped region) - else if (fallsInsideDeletionOrSkippedRegion || - (endJustBeforeDeletionOrSkippedRegion && nextCigarElement.getOperator().equals(CigarOperator.N)) || - (endJustBeforeDeletionOrSkippedRegion && nextCigarElement.getOperator().equals(CigarOperator.D))) { - readBases--; - } - } + public static Optional getReadBaseAtReferenceCoordinate(final GATKRead read, final int refCoord) { + if (refCoord < read.getStart() || read.getEnd() < refCoord) { + return Optional.empty(); } + final Pair offsetAndOperator = getReadCoordinateForReferenceCoordinate(read, refCoord); + return (offsetAndOperator.getLeft() != CLIPPING_GOAL_NOT_REACHED && offsetAndOperator.getRight().consumesReadBases()) ? + Optional.of(read.getBase(offsetAndOperator.getLeft())) : Optional.empty(); + } - if (!goalReached) { - if (allowGoalNotReached) { - return new MutablePair<>(CLIPPING_GOAL_NOT_REACHED, false); - } else { - throw new GATKException("Somehow the requested coordinate is not covered by the read. Alignment " + alignmentStart + " | " + cigar); - } + public static Optional getReadBaseQualityAtReferenceCoordinate(final GATKRead read, final int refCoord) { + if (refCoord < read.getStart() || read.getEnd() < refCoord) { + return Optional.empty(); } - - return Pair.of(readBases, fallsInsideOrJustBeforeDeletionOrSkippedRegion); + final Pair offsetAndOperator = getReadCoordinateForReferenceCoordinate(read.getSoftStart(), read.getCigar(), refCoord); + return (offsetAndOperator.getRight() != null && offsetAndOperator.getRight().consumesReadBases()) ? + Optional.of(read.getBaseQuality(offsetAndOperator.getLeft())) : Optional.empty(); } + /** * Is a base inside a read? * @@ -876,35 +743,6 @@ public static boolean isInsideRead(final GATKRead read, final int referenceCoord return referenceCoordinate >= read.getStart() && referenceCoordinate <= read.getEnd(); } - /** - * @see #readStartsWithInsertion(Cigar, boolean) with ignoreClipOps set to true - */ - public static CigarElement readStartsWithInsertion(final Cigar cigarForRead) { - return readStartsWithInsertion(cigarForRead, true); - } - - public static CigarElement readStartsWithInsertion(final Cigar cigarForRead, final boolean ignoreSoftClipOps) { - return readStartsWithInsertion(cigarForRead.getCigarElements(), ignoreSoftClipOps); - } - - /** - * Checks if a read starts with an insertion. - * - * @param cigarElementsForRead the CIGAR to evaluate - * @param ignoreSoftClipOps should we ignore S operators when evaluating whether an I operator is at the beginning? Note that H operators are always ignored. - * @return the element if it's a leading insertion or null otherwise - */ - public static CigarElement readStartsWithInsertion(final List cigarElementsForRead, final boolean ignoreSoftClipOps) { - for ( final CigarElement cigarElement : cigarElementsForRead ) { - if ( cigarElement.getOperator() == CigarOperator.INSERTION ) { - return cigarElement; - } else if ( cigarElement.getOperator() != CigarOperator.HARD_CLIP && ( !ignoreSoftClipOps || cigarElement.getOperator() != CigarOperator.SOFT_CLIP) ) { - break; - } - } - return null; - } - /** * Returns the reverse complement of the read bases * diff --git a/src/main/java/org/broadinstitute/hellbender/utils/recalibration/BaseRecalibrationEngine.java b/src/main/java/org/broadinstitute/hellbender/utils/recalibration/BaseRecalibrationEngine.java index be1eab77a30..4d4976b7437 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/recalibration/BaseRecalibrationEngine.java +++ b/src/main/java/org/broadinstitute/hellbender/utils/recalibration/BaseRecalibrationEngine.java @@ -1,5 +1,7 @@ package org.broadinstitute.hellbender.utils.recalibration; +import htsjdk.samtools.CigarOperator; +import org.apache.commons.lang3.tuple.Pair; import org.broadinstitute.hellbender.utils.SerializableFunction; import htsjdk.samtools.Cigar; import htsjdk.samtools.CigarElement; @@ -327,7 +329,7 @@ private boolean[] calculateSkipArray( final GATKRead read, final Iterable knownSites ) { + protected static boolean[] calculateKnownSites( final GATKRead read, final Iterable knownSites ) { final int readLength = read.getLength(); final boolean[] knownSitesArray = new boolean[readLength];//initializes to all false final Cigar cigar = read.getCigar(); @@ -338,15 +340,14 @@ protected boolean[] calculateKnownSites( final GATKRead read, final Iterable featureStartAndOperatorOnRead = ReadUtils.getReadCoordinateForReferenceCoordinate(read, knownSite.getStart()); + int featureStartOnRead = featureStartAndOperatorOnRead.getLeft() == ReadUtils.CLIPPING_GOAL_NOT_REACHED ? 0 : featureStartAndOperatorOnRead.getLeft(); + if (featureStartAndOperatorOnRead.getRight() == CigarOperator.DELETION) { + featureStartOnRead--; } - int featureEndOnRead = ReadUtils.getReadCoordinateForReferenceCoordinate(softStart, cigar, knownSite.getEnd(), ClippingTail.LEFT_TAIL, true); - if( featureEndOnRead == ReadUtils.CLIPPING_GOAL_NOT_REACHED ) { - featureEndOnRead = readLength; - } + final Pair featureEndAndOperatorOnRead = ReadUtils.getReadCoordinateForReferenceCoordinate(read, knownSite.getEnd()); + int featureEndOnRead = featureEndAndOperatorOnRead.getLeft() == ReadUtils.CLIPPING_GOAL_NOT_REACHED ? readLength : featureEndAndOperatorOnRead.getLeft(); if( featureStartOnRead > readLength ) { featureStartOnRead = featureEndOnRead = readLength; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/BaseQualityRankSumTestUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/BaseQualityRankSumTestUnitTest.java index f3f4aca5cff..5a921e56a90 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/BaseQualityRankSumTestUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/BaseQualityRankSumTestUnitTest.java @@ -55,6 +55,8 @@ public void testBaseQual() { final int[] refBaseQuals = {50, 60}; final List refReads = Arrays.stream(refBaseQuals).mapToObj(i -> makeRead(i)).collect(Collectors.toList()); final List altReads = Arrays.stream(altBaseQuals).mapToObj(i -> makeRead(i)).collect(Collectors.toList()); + refReads.forEach(read -> read.setPosition("1", 10)); + altReads.forEach(read -> read.setPosition("1", 10)); final AlleleLikelihoods likelihoods = ArtificialAnnotationUtils.makeLikelihoods(SAMPLE_1, refReads, altReads, -100.0, -100.0, REF, ALT); 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 884c595c790..2c1189132ed 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 @@ -28,6 +28,7 @@ public final class ReadPosRankSumTestUnitTest extends GATKBaseTest { private static final Allele REF = Allele.create("T", true); private static final Allele ALT = Allele.create("A", false); + private static final Allele ALT_INSERTION = Allele.create("TTTTT", false); private VariantContext makeVC(final long position) { final double[] genotypeLikelihoods1 = {30,0,190}; @@ -77,7 +78,7 @@ public void testReadPos(){ final String zScoreStr = String.format("%.3f", zScore); Assert.assertEquals(annotate.get(key), zScoreStr); - final long positionEnd = 8L; //past middle + final long positionEnd = 9L; //past middle final VariantContext vcEnd= makeVC(positionEnd); //Note: past the middle of the read we compute the position from the end. @@ -116,7 +117,7 @@ public void testIsUsableRead(final String cigarString, final int mappingQuality, final GATKRead read = ArtificialReadUtils.createArtificialRead(cigar); read.setMappingQuality(mappingQuality); read.setPosition(CONTIG, start); - Assert.assertEquals(readPosRankSumTest.isUsableRead(read, refLoc), isUsable); + Assert.assertEquals(readPosRankSumTest.isUsableRead(read, makeVC(refLoc)), isUsable); } //Basic aligned read @@ -183,6 +184,29 @@ public void init() { 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"); + } + + @Test + public void testLeadingInsertion(){ + final int start = 100; + final VariantContext vc = new VariantContextBuilder().alleles(Arrays.asList(REF, ALT_INSERTION)).chr(CONTIG).start(start-1).stop(start-1).make(); + + final Cigar cigar = TextCigarCodec.decode("10I10M"); + final GATKRead read = ArtificialReadUtils.createArtificialRead(cigar); + + read.setPosition("CONTIG", start); + + Assert.assertEquals(ReadPosRankSumTest.getReadPosition(read, vc).getAsDouble(), 0.0); + } + + @Test + public void testSNPBetweenTwoDeletions(){ + final Cigar cigar = TextCigarCodec.decode("10M10D1M10D10M"); + final GATKRead read = ArtificialReadUtils.createArtificialRead(cigar); + final int start = 100; + read.setPosition("CONTIG", start); + Assert.assertEquals(ReadPosRankSumTest.getReadPosition(read, makeVC(start + 20)).getAsDouble(), 10.0); + Assert.assertEquals(ReadPosRankSumTest.getReadPosition(read, makeVC(start + 19)).getAsDouble(), 10.0); } } 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 5f4a2bac83b..cb19876c25c 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 @@ -68,6 +68,9 @@ public void testBaseQualRawAnnotate() { final List refReads = Arrays.stream(refBaseQuals).mapToObj(i -> BaseQualityRankSumTestUnitTest.makeRead(i)).collect(Collectors.toList()); final List alt1Reads = Arrays.stream(alt1BaseQuals).mapToObj(i -> BaseQualityRankSumTestUnitTest.makeRead(i)).collect(Collectors.toList()); final List alt2Reads = Arrays.stream(alt2BaseQuals).mapToObj(i -> BaseQualityRankSumTestUnitTest.makeRead(i)).collect(Collectors.toList()); + refReads.forEach(read -> read.setPosition("1", 10)); + alt1Reads.forEach(read -> read.setPosition("1", 10)); + alt2Reads.forEach(read -> read.setPosition("1", 10)); final AlleleLikelihoods likelihoods = ArtificialAnnotationUtils.makeTriAllelicLikelihoods(SAMPLE_1, refReads, alt1Reads, alt2Reads, new ArrayList(), -100.0, -100.0, -100,0, REF, ALT1, ALT2); 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 3bbe16c8867..b91ab129e8f 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 @@ -69,7 +69,7 @@ public void testIsUsableRead(final String cigarString, final int mappingQuality, final GATKRead read = ArtificialReadUtils.createArtificialRead(cigar); read.setMappingQuality(mappingQuality); read.setPosition("1", start); - Assert.assertEquals(as_readPosRankSumTest.isUsableRead(read, refLoc), isUsable); + Assert.assertEquals(as_readPosRankSumTest.isUsableRead(read, makeVC(refLoc)), isUsable); } @Test diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java index c9a97de6c94..a8ffbcdf4dc 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java @@ -1,6 +1,7 @@ package org.broadinstitute.hellbender.tools.walkers.haplotypecaller; import com.google.common.base.Strings; +import htsjdk.samtools.CigarOperator; import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SAMReadGroupRecord; import htsjdk.variant.variantcontext.*; @@ -325,13 +326,13 @@ public void testCalcNIndelInformativeReads(final String readBases, final String final GATKRead readCache = ArtificialReadUtils.createArtificialRead(readBases.getBytes(), quals, cigar); for ( int i = 0; i < readBases.getBytes().length; i++ ) { - final Pair readCoordinateForReferenceCoordinate = ReadUtils.getReadCoordinateForReferenceCoordinate(readCache, readCache.getStart() + i, true); + final Pair readCoordinateForReferenceCoordinate = ReadUtils.getReadCoordinateForReferenceCoordinate(readCache, readCache.getStart() + i); - if (!readCoordinateForReferenceCoordinate.getValue() && readCoordinateForReferenceCoordinate.getKey() != -1) { + if (readCoordinateForReferenceCoordinate.getRight() != null && readCoordinateForReferenceCoordinate.getRight().consumesReadBases()) { final GATKRead readNoCache = ArtificialReadUtils.createArtificialRead(readBases.getBytes(), quals, cigar); final SimpleInterval loc = new SimpleInterval("20", i + 1 + readStartIntoRef, i + 1 + readStartIntoRef); - final ReadPileup pileupCache = new ReadPileup(loc, Collections.singletonList(readCache), readCoordinateForReferenceCoordinate.getKey()); - final ReadPileup pileupNoCache = new ReadPileup(loc, Collections.singletonList(readNoCache), ReadUtils.getReadCoordinateForReferenceCoordinate(readNoCache, readNoCache.getStart() + i, false).getKey()); + final ReadPileup pileupCache = new ReadPileup(loc, Collections.singletonList(readCache), readCoordinateForReferenceCoordinate.getLeft()); + final ReadPileup pileupNoCache = new ReadPileup(loc, Collections.singletonList(readNoCache), ReadUtils.getReadCoordinateForReferenceCoordinate(readNoCache, readNoCache.getStart() + i).getKey()); final int actualCache = model.calcNReadsWithNoPlausibleIndelsReads(pileupCache, i + readStartIntoRef, ref.getBytes(), maxIndelSize); final int actualNoCache = model.calcNReadsWithNoPlausibleIndelsReads(pileupNoCache, i + readStartIntoRef, ref.getBytes(), maxIndelSize); Assert.assertEquals(actualCache, (int)expected.get(i), "cached result failed at position " + i); diff --git a/src/test/java/org/broadinstitute/hellbender/utils/read/ReadUtilsUnitTest.java b/src/test/java/org/broadinstitute/hellbender/utils/read/ReadUtilsUnitTest.java index 25271a753ce..b10c1956a2f 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/read/ReadUtilsUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/utils/read/ReadUtilsUnitTest.java @@ -5,6 +5,7 @@ import htsjdk.samtools.*; import htsjdk.samtools.reference.ReferenceSequenceFile; import htsjdk.samtools.reference.ReferenceSequenceFileFactory; +import org.apache.commons.lang3.tuple.Pair; import org.broadinstitute.hellbender.GATKBaseTest; import org.broadinstitute.hellbender.engine.ReadsContext; import org.broadinstitute.hellbender.engine.ReadsDataSource; @@ -193,38 +194,56 @@ public void testGetBasesReverseComplement() { } } + @DataProvider(name = "readCoordinateForReferenceCoordinate") + public Object[][] readCoordinateForReferenceCoordinate() throws Exception { + return new Object[][] { + {"10M", 1, 1, 0, CigarOperator.M}, + {"10M", 5, 5, 0, CigarOperator.M}, + {"10M", 1, 10, 9, CigarOperator.M}, + {"10M", 1, 5, 4, CigarOperator.M}, + {"10M", 1, 0, ReadUtils.CLIPPING_GOAL_NOT_REACHED, null}, + {"10M", 1, 11, ReadUtils.CLIPPING_GOAL_NOT_REACHED, null}, + + {"5M5D5M", 1, 1, 0, CigarOperator.M}, + {"5M5D5M", 1, 5, 4, CigarOperator.M}, + {"5M5D5M", 1, 6, 5, CigarOperator.D}, + {"5M5D5M", 1, 10, 5, CigarOperator.D}, + {"5M5D5M", 1, 11, 5, CigarOperator.M}, + {"5M5D5M", 1, 15, 9, CigarOperator.M}, + {"5M5D5M", 1, 16, ReadUtils.CLIPPING_GOAL_NOT_REACHED, null}, + + {"5M5I5M", 1, 1, 0, CigarOperator.M}, + {"5M5I5M", 1, 5, 4, CigarOperator.M}, + {"5M5I5M", 1, 6, 10, CigarOperator.M}, + {"5M5I5M", 1, 10, 14, CigarOperator.M}, + {"5M5I5M", 1, 11, ReadUtils.CLIPPING_GOAL_NOT_REACHED, null} + }; + } + + @Test(dataProvider = "readCoordinateForReferenceCoordinate") + public void testGetReadCoordinateForReferenceCoordinate(final String cigar, final int start, final int refCoord, final int expected, final CigarOperator op) { + final Pair result = ReadUtils.getReadCoordinateForReferenceCoordinate(start, TextCigarCodec.decode(cigar), refCoord); + Assert.assertEquals(result.getLeft().intValue(), expected); + Assert.assertEquals(result.getRight(), op); + } + @Test - public void testReadWithNsRefIndexInDeletion() throws FileNotFoundException { + public void testReadWithNsRefIndexInDeletion( ) throws FileNotFoundException { final SAMFileHeader header; try(final CachingIndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(IOUtils.getPath(exampleReference))) { header = ArtificialReadUtils.createArtificialSamHeader(seq.getSequenceDictionary()); } final int readLength = 76; - final GATKRead read = ArtificialReadUtils.createArtificialRead(header, "myRead", 0, 8975, readLength); + final GATKRead read = ArtificialReadUtils.createArtificialRead(header, "myRead", 0, 100, readLength); read.setBases(Utils.dupBytes((byte) 'A', readLength)); read.setBaseQualities(Utils.dupBytes((byte)30, readLength)); - read.setCigar("3M414N1D73M"); - - final int result = ReadUtils.getReadCoordinateForReferenceCoordinateUpToEndOfRead(read, 9392, ClippingTail.LEFT_TAIL); - Assert.assertEquals(result, 2); - } + read.setCigar("3M100N1D73M"); - @Test - public void testReadWithNsRefAfterDeletion() throws IOException { - try(final ReferenceSequenceFile seq = new CachingIndexedFastaSequenceFile(IOUtils.getPath(exampleReference))) { - final SAMFileHeader header = ArtificialReadUtils.createArtificialSamHeader(seq.getSequenceDictionary()); - final int readLength = 76; - - final GATKRead read = ArtificialReadUtils.createArtificialRead(header, "myRead", 0, 8975, readLength); - read.setBases(Utils.dupBytes((byte) 'A', readLength)); - read.setBaseQualities(Utils.dupBytes((byte) 30, readLength)); - read.setCigar("3M414N1D73M"); - - final int result = ReadUtils.getReadCoordinateForReferenceCoordinateUpToEndOfRead(read, 9393, - ClippingTail.LEFT_TAIL); - Assert.assertEquals(result, 3); - } + Assert.assertEquals(ReadUtils.getReadCoordinateForReferenceCoordinate(read, 102).getLeft().intValue(), 2); + Assert.assertEquals(ReadUtils.getReadCoordinateForReferenceCoordinate(read, 103).getLeft().intValue(), 3); // the first N base + Assert.assertEquals(ReadUtils.getReadCoordinateForReferenceCoordinate(read, 202).getLeft().intValue(), 3); // the last N base + Assert.assertEquals(ReadUtils.getReadCoordinateForReferenceCoordinate(read, 203).getLeft().intValue(), 3); // the first D base } @DataProvider(name = "HasWellDefinedFragmentSizeData") diff --git a/src/test/java/org/broadinstitute/hellbender/utils/recalibration/BaseRecalibrationEngineUnitTest.java b/src/test/java/org/broadinstitute/hellbender/utils/recalibration/BaseRecalibrationEngineUnitTest.java index bb4f95e3a6a..b00b2c47589 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/recalibration/BaseRecalibrationEngineUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/utils/recalibration/BaseRecalibrationEngineUnitTest.java @@ -14,6 +14,7 @@ import java.util.ArrayList; import java.util.Arrays; +import java.util.Collections; import java.util.List; public final class BaseRecalibrationEngineUnitTest { diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.indels_context_size_4.recal.txt b/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.indels_context_size_4.recal.txt index 3a4bb555094..9ed7cf09e72 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.indels_context_size_4.recal.txt +++ b/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.indels_context_size_4.recal.txt @@ -48,27 +48,27 @@ QualityScore Count QuantizedScore 22 750 24 23 853 24 24 997 24 - 25 1228 24 + 25 1227 24 26 1491 27 - 27 1728 27 + 27 1727 27 28 1781 29 29 2284 29 30 2439 30 - 31 2537 30 + 31 2536 30 32 3565 32 - 33 4141 32 + 33 4139 32 34 5194 34 - 35 7518 35 - 36 11939 36 - 37 28884 37 - 38 27993 38 - 39 15115 39 + 35 7517 35 + 36 11937 36 + 37 28883 37 + 38 27987 38 + 39 15108 39 40 778 39 41 53 39 42 0 39 43 0 39 - 44 15761 44 - 45 234039 45 + 44 9294 44 + 45 240462 45 46 0 93 47 0 93 48 0 93 @@ -121,51 +121,51 @@ QualityScore Count QuantizedScore #:GATKTable:6:48:%s:%s:%.4f:%.4f:%d:%.2f:; #:GATKTable:RecalTable0: ReadGroup EventType EmpiricalQuality EstimatedQReported Observations Errors -20FUKAAXX100202.1 D 45.0000 45.0000 7293 3.86 -20FUKAAXX100202.1 I 45.0000 45.0000 7293 0.00 -20FUKAAXX100202.1 M 27.0000 27.0392 7293 15.67 -20FUKAAXX100202.2 D 44.0000 45.0000 6464 7.56 -20FUKAAXX100202.2 I 45.0000 45.0000 6464 0.00 -20FUKAAXX100202.2 M 29.0000 30.1871 6464 20.60 -20FUKAAXX100202.3 D 45.0000 45.0000 8976 5.73 -20FUKAAXX100202.3 I 45.0000 45.0000 8976 0.00 -20FUKAAXX100202.3 M 27.0000 28.2043 8976 29.75 -20FUKAAXX100202.4 D 45.0000 45.0000 6830 3.75 -20FUKAAXX100202.4 I 45.0000 45.0000 6830 0.00 -20FUKAAXX100202.4 M 29.0000 29.0885 6830 13.00 -20FUKAAXX100202.5 D 45.0000 45.0000 7471 2.86 -20FUKAAXX100202.5 I 45.0000 45.0000 7471 0.00 -20FUKAAXX100202.5 M 28.0000 29.7339 7471 26.67 -20FUKAAXX100202.6 D 45.0000 45.0000 10026 8.40 -20FUKAAXX100202.6 I 45.0000 45.0000 10026 0.00 -20FUKAAXX100202.6 M 27.0000 28.7545 10026 27.25 -20FUKAAXX100202.7 D 45.0000 45.0000 9347 2.78 -20FUKAAXX100202.7 I 45.0000 45.0000 9347 0.00 -20FUKAAXX100202.7 M 26.0000 27.7419 9347 30.67 +20FUKAAXX100202.1 D 45.0000 45.0000 7292 3.71 +20FUKAAXX100202.1 I 45.0000 45.0000 7292 0.00 +20FUKAAXX100202.1 M 27.0000 27.0386 7292 15.67 +20FUKAAXX100202.2 D 45.0000 45.0000 6462 7.33 +20FUKAAXX100202.2 I 45.0000 45.0000 6462 0.00 +20FUKAAXX100202.2 M 29.0000 30.1859 6462 20.60 +20FUKAAXX100202.3 D 45.0000 45.0000 8974 5.46 +20FUKAAXX100202.3 I 45.0000 45.0000 8974 0.00 +20FUKAAXX100202.3 M 27.0000 28.2034 8974 29.75 +20FUKAAXX100202.4 D 45.0000 45.0000 6828 3.50 +20FUKAAXX100202.4 I 45.0000 45.0000 6828 0.00 +20FUKAAXX100202.4 M 29.0000 29.0874 6828 13.00 +20FUKAAXX100202.5 D 45.0000 45.0000 7470 2.71 +20FUKAAXX100202.5 I 45.0000 45.0000 7470 0.00 +20FUKAAXX100202.5 M 28.0000 29.7334 7470 26.67 +20FUKAAXX100202.6 D 45.0000 45.0000 10023 7.95 +20FUKAAXX100202.6 I 45.0000 45.0000 10023 0.00 +20FUKAAXX100202.6 M 27.0000 28.7535 10023 27.25 +20FUKAAXX100202.7 D 45.0000 45.0000 9345 2.57 +20FUKAAXX100202.7 I 45.0000 45.0000 9345 0.00 +20FUKAAXX100202.7 M 26.0000 27.7411 9345 30.67 20FUKAAXX100202.8 D 45.0000 45.0000 8152 3.75 20FUKAAXX100202.8 I 45.0000 45.0000 8152 0.00 20FUKAAXX100202.8 M 28.0000 29.0288 8152 24.00 -20GAVAAXX100126.1 D 44.0000 45.0000 9297 9.12 -20GAVAAXX100126.1 I 45.0000 45.0000 9297 1.00 -20GAVAAXX100126.1 M 26.0000 27.6243 9297 29.75 -20GAVAAXX100126.2 D 45.0000 45.0000 8155 4.86 -20GAVAAXX100126.2 I 45.0000 45.0000 8155 0.00 -20GAVAAXX100126.2 M 26.0000 27.3758 8155 34.42 +20GAVAAXX100126.1 D 44.0000 45.0000 9294 8.52 +20GAVAAXX100126.1 I 45.0000 45.0000 9294 1.00 +20GAVAAXX100126.1 M 26.0000 27.6244 9294 29.75 +20GAVAAXX100126.2 D 45.0000 45.0000 8154 4.71 +20GAVAAXX100126.2 I 45.0000 45.0000 8154 0.00 +20GAVAAXX100126.2 M 26.0000 27.3754 8154 34.42 20GAVAAXX100126.3 D 45.0000 45.0000 6239 3.00 20GAVAAXX100126.3 I 45.0000 45.0000 6239 0.00 20GAVAAXX100126.3 M 26.0000 26.8893 6239 20.57 -20GAVAAXX100126.4 D 45.0000 45.0000 6633 2.86 -20GAVAAXX100126.4 I 45.0000 45.0000 6633 0.00 -20GAVAAXX100126.4 M 26.0000 27.0432 6633 29.33 -20GAVAAXX100126.5 D 45.0000 45.0000 5884 0.86 -20GAVAAXX100126.5 I 45.0000 45.0000 5884 0.00 -20GAVAAXX100126.5 M 27.0000 28.0717 5884 21.33 -20GAVAAXX100126.6 D 45.0000 45.0000 8002 3.69 -20GAVAAXX100126.6 I 45.0000 45.0000 8002 0.00 -20GAVAAXX100126.6 M 27.0000 28.4682 8002 27.00 -20GAVAAXX100126.7 D 45.0000 45.0000 7598 2.88 -20GAVAAXX100126.7 I 45.0000 45.0000 7598 0.00 -20GAVAAXX100126.7 M 25.0000 25.6878 7598 27.75 +20GAVAAXX100126.4 D 45.0000 45.0000 6632 2.71 +20GAVAAXX100126.4 I 45.0000 45.0000 6632 0.00 +20GAVAAXX100126.4 M 26.0000 27.0426 6632 29.33 +20GAVAAXX100126.5 D 45.0000 45.0000 5883 0.71 +20GAVAAXX100126.5 I 45.0000 45.0000 5883 0.00 +20GAVAAXX100126.5 M 27.0000 28.0710 5883 21.33 +20GAVAAXX100126.6 D 45.0000 45.0000 8000 3.38 +20GAVAAXX100126.6 I 45.0000 45.0000 8000 0.00 +20GAVAAXX100126.6 M 27.0000 28.4675 8000 27.00 +20GAVAAXX100126.7 D 45.0000 45.0000 7597 2.75 +20GAVAAXX100126.7 I 45.0000 45.0000 7597 0.00 +20GAVAAXX100126.7 M 25.0000 25.6874 7597 27.75 20GAVAAXX100126.8 D 45.0000 45.0000 8533 5.69 20GAVAAXX100126.8 I 45.0000 45.0000 8533 1.00 20GAVAAXX100126.8 M 26.0000 27.3594 8533 29.25 @@ -204,12 +204,12 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20FUKAAXX100202.1 34 M 34.0000 217 0.20 20FUKAAXX100202.1 35 M 35.0000 347 1.07 20FUKAAXX100202.1 36 M 36.0000 599 1.00 -20FUKAAXX100202.1 37 M 37.0000 1407 1.33 +20FUKAAXX100202.1 37 M 37.0000 1406 1.33 20FUKAAXX100202.1 38 M 38.0000 2058 0.33 20FUKAAXX100202.1 39 M 39.0000 741 0.00 20FUKAAXX100202.1 40 M 40.0000 16 0.00 -20FUKAAXX100202.1 45 D 45.0000 7293 3.86 -20FUKAAXX100202.1 45 I 45.0000 7293 0.00 +20FUKAAXX100202.1 45 D 45.0000 7292 3.71 +20FUKAAXX100202.1 45 I 45.0000 7292 0.00 20FUKAAXX100202.2 6 M 6.0000 1 0.00 20FUKAAXX100202.2 7 M 7.0000 1 0.00 20FUKAAXX100202.2 8 M 8.0000 3 0.00 @@ -243,10 +243,10 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20FUKAAXX100202.2 36 M 36.0000 580 4.00 20FUKAAXX100202.2 37 M 37.0000 1371 2.00 20FUKAAXX100202.2 38 M 38.0000 2181 6.00 -20FUKAAXX100202.2 39 M 39.0000 667 1.00 +20FUKAAXX100202.2 39 M 39.0000 665 1.00 20FUKAAXX100202.2 40 M 40.0000 27 0.00 -20FUKAAXX100202.2 45 D 44.0000 6464 7.56 -20FUKAAXX100202.2 45 I 45.0000 6464 0.00 +20FUKAAXX100202.2 45 D 45.0000 6462 7.33 +20FUKAAXX100202.2 45 I 45.0000 6462 0.00 20FUKAAXX100202.3 6 M 6.0000 1 1.00 20FUKAAXX100202.3 7 M 7.0000 4 0.00 20FUKAAXX100202.3 8 M 8.0000 8 0.00 @@ -277,13 +277,13 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20FUKAAXX100202.3 33 M 33.0000 245 0.00 20FUKAAXX100202.3 34 M 34.0000 262 0.00 20FUKAAXX100202.3 35 M 35.0000 463 1.00 -20FUKAAXX100202.3 36 M 36.0000 944 6.25 +20FUKAAXX100202.3 36 M 36.0000 943 6.25 20FUKAAXX100202.3 37 M 37.0000 1649 4.25 20FUKAAXX100202.3 38 M 37.0000 2837 11.25 -20FUKAAXX100202.3 39 M 39.0000 976 0.00 +20FUKAAXX100202.3 39 M 39.0000 975 0.00 20FUKAAXX100202.3 40 M 40.0000 28 0.00 -20FUKAAXX100202.3 45 D 45.0000 8976 5.73 -20FUKAAXX100202.3 45 I 45.0000 8976 0.00 +20FUKAAXX100202.3 45 D 45.0000 8974 5.46 +20FUKAAXX100202.3 45 I 45.0000 8974 0.00 20FUKAAXX100202.4 6 M 6.0000 1 0.00 20FUKAAXX100202.4 7 M 7.0000 2 1.00 20FUKAAXX100202.4 8 M 8.0000 3 1.00 @@ -317,10 +317,10 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20FUKAAXX100202.4 36 M 36.0000 633 0.00 20FUKAAXX100202.4 37 M 37.0000 1408 3.25 20FUKAAXX100202.4 38 M 38.0000 2074 3.50 -20FUKAAXX100202.4 39 M 39.0000 662 1.00 +20FUKAAXX100202.4 39 M 39.0000 660 1.00 20FUKAAXX100202.4 40 M 40.0000 20 0.00 -20FUKAAXX100202.4 45 D 45.0000 6830 3.75 -20FUKAAXX100202.4 45 I 45.0000 6830 0.00 +20FUKAAXX100202.4 45 D 45.0000 6828 3.50 +20FUKAAXX100202.4 45 I 45.0000 6828 0.00 20FUKAAXX100202.5 6 M 6.0000 1 0.00 20FUKAAXX100202.5 7 M 7.0000 3 0.00 20FUKAAXX100202.5 8 M 8.0000 2 1.00 @@ -354,10 +354,10 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20FUKAAXX100202.5 36 M 36.0000 695 2.33 20FUKAAXX100202.5 37 M 37.0000 1329 2.00 20FUKAAXX100202.5 38 M 37.0000 2579 9.80 -20FUKAAXX100202.5 39 M 39.0000 907 1.00 +20FUKAAXX100202.5 39 M 39.0000 906 1.00 20FUKAAXX100202.5 40 M 40.0000 67 0.20 -20FUKAAXX100202.5 45 D 45.0000 7471 2.86 -20FUKAAXX100202.5 45 I 45.0000 7471 0.00 +20FUKAAXX100202.5 45 D 45.0000 7470 2.71 +20FUKAAXX100202.5 45 I 45.0000 7470 0.00 20FUKAAXX100202.6 6 M 6.0000 7 4.00 20FUKAAXX100202.6 7 M 7.0000 4 2.00 20FUKAAXX100202.6 8 M 8.0000 5 0.00 @@ -387,14 +387,14 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20FUKAAXX100202.6 32 M 32.0000 226 1.00 20FUKAAXX100202.6 33 M 33.0000 231 2.00 20FUKAAXX100202.6 34 M 34.0000 302 0.00 -20FUKAAXX100202.6 35 M 35.0000 579 2.17 +20FUKAAXX100202.6 35 M 35.0000 578 2.17 20FUKAAXX100202.6 36 M 36.0000 975 2.33 20FUKAAXX100202.6 37 M 37.0000 1959 1.17 -20FUKAAXX100202.6 38 M 38.0000 3301 6.00 +20FUKAAXX100202.6 38 M 38.0000 3299 6.00 20FUKAAXX100202.6 39 M 39.0000 1111 1.00 20FUKAAXX100202.6 40 M 40.0000 43 0.00 -20FUKAAXX100202.6 45 D 45.0000 10026 8.40 -20FUKAAXX100202.6 45 I 45.0000 10026 0.00 +20FUKAAXX100202.6 45 D 45.0000 10023 7.95 +20FUKAAXX100202.6 45 I 45.0000 10023 0.00 20FUKAAXX100202.7 6 M 6.0000 5 2.00 20FUKAAXX100202.7 7 M 7.0000 5 1.00 20FUKAAXX100202.7 8 M 8.0000 9 3.33 @@ -425,13 +425,13 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20FUKAAXX100202.7 33 M 33.0000 197 0.00 20FUKAAXX100202.7 34 M 34.0000 251 0.00 20FUKAAXX100202.7 35 M 35.0000 441 1.92 -20FUKAAXX100202.7 36 M 36.0000 955 3.33 +20FUKAAXX100202.7 36 M 36.0000 954 3.33 20FUKAAXX100202.7 37 M 37.0000 1600 2.67 -20FUKAAXX100202.7 38 M 38.0000 3286 3.92 +20FUKAAXX100202.7 38 M 38.0000 3285 3.92 20FUKAAXX100202.7 39 M 39.0000 1063 1.25 20FUKAAXX100202.7 40 M 40.0000 43 0.00 -20FUKAAXX100202.7 45 D 45.0000 9347 2.78 -20FUKAAXX100202.7 45 I 45.0000 9347 0.00 +20FUKAAXX100202.7 45 D 45.0000 9345 2.57 +20FUKAAXX100202.7 45 I 45.0000 9345 0.00 20FUKAAXX100202.8 6 M 6.0000 4 2.00 20FUKAAXX100202.8 7 M 7.0000 5 0.00 20FUKAAXX100202.8 8 M 8.0000 1 0.00 @@ -488,9 +488,9 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.1 22 M 22.0000 43 1.00 20GAVAAXX100126.1 23 M 23.0000 65 0.13 20GAVAAXX100126.1 24 M 24.0000 56 0.00 -20GAVAAXX100126.1 25 M 25.0000 85 0.00 +20GAVAAXX100126.1 25 M 25.0000 84 0.00 20GAVAAXX100126.1 26 M 26.0000 104 0.00 -20GAVAAXX100126.1 27 M 27.0000 114 0.00 +20GAVAAXX100126.1 27 M 27.0000 113 0.00 20GAVAAXX100126.1 28 M 28.0000 149 0.00 20GAVAAXX100126.1 29 M 29.0000 185 1.33 20GAVAAXX100126.1 30 M 30.0000 179 0.00 @@ -502,11 +502,11 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.1 36 M 36.0000 822 2.25 20GAVAAXX100126.1 37 M 37.0000 1759 7.00 20GAVAAXX100126.1 38 M 38.0000 1880 3.25 -20GAVAAXX100126.1 39 M 39.0000 1546 2.00 +20GAVAAXX100126.1 39 M 39.0000 1545 2.00 20GAVAAXX100126.1 40 M 40.0000 243 0.00 20GAVAAXX100126.1 41 M 41.0000 23 0.00 -20GAVAAXX100126.1 45 D 44.0000 9297 9.12 -20GAVAAXX100126.1 45 I 45.0000 9297 1.00 +20GAVAAXX100126.1 45 D 44.0000 9294 8.52 +20GAVAAXX100126.1 45 I 45.0000 9294 1.00 20GAVAAXX100126.2 6 M 6.0000 10 4.00 20GAVAAXX100126.2 7 M 7.0000 8 1.00 20GAVAAXX100126.2 8 M 8.0000 6 0.00 @@ -534,7 +534,7 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.2 30 M 30.0000 169 0.00 20GAVAAXX100126.2 31 M 31.0000 222 1.25 20GAVAAXX100126.2 32 M 32.0000 336 0.00 -20GAVAAXX100126.2 33 M 33.0000 392 6.00 +20GAVAAXX100126.2 33 M 33.0000 391 6.00 20GAVAAXX100126.2 34 M 34.0000 471 0.00 20GAVAAXX100126.2 35 M 35.0000 540 2.00 20GAVAAXX100126.2 36 M 36.0000 685 1.67 @@ -543,8 +543,8 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.2 39 M 39.0000 1127 2.00 20GAVAAXX100126.2 40 M 40.0000 49 0.00 20GAVAAXX100126.2 41 M 41.0000 9 0.00 -20GAVAAXX100126.2 45 D 45.0000 8155 4.86 -20GAVAAXX100126.2 45 I 45.0000 8155 0.00 +20GAVAAXX100126.2 45 D 45.0000 8154 4.71 +20GAVAAXX100126.2 45 I 45.0000 8154 0.00 20GAVAAXX100126.3 6 M 6.0000 2 0.00 20GAVAAXX100126.3 7 M 7.0000 8 2.00 20GAVAAXX100126.3 8 M 8.0000 8 2.00 @@ -615,12 +615,12 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.4 35 M 35.0000 487 2.00 20GAVAAXX100126.4 36 M 36.0000 639 1.25 20GAVAAXX100126.4 37 M 37.0000 1224 5.50 -20GAVAAXX100126.4 38 M 38.0000 1250 4.67 +20GAVAAXX100126.4 38 M 38.0000 1249 4.67 20GAVAAXX100126.4 39 M 39.0000 857 2.00 20GAVAAXX100126.4 40 M 40.0000 33 0.00 20GAVAAXX100126.4 41 M 41.0000 1 0.00 -20GAVAAXX100126.4 45 D 45.0000 6633 2.86 -20GAVAAXX100126.4 45 I 45.0000 6633 0.00 +20GAVAAXX100126.4 45 D 45.0000 6632 2.71 +20GAVAAXX100126.4 45 I 45.0000 6632 0.00 20GAVAAXX100126.5 6 M 6.0000 4 0.00 20GAVAAXX100126.5 7 M 7.0000 8 3.00 20GAVAAXX100126.5 8 M 8.0000 4 1.00 @@ -653,12 +653,12 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.5 35 M 35.0000 328 1.00 20GAVAAXX100126.5 36 M 36.0000 583 0.33 20GAVAAXX100126.5 37 M 37.0000 1187 2.00 -20GAVAAXX100126.5 38 M 38.0000 1446 2.00 +20GAVAAXX100126.5 38 M 38.0000 1445 2.00 20GAVAAXX100126.5 39 M 39.0000 909 2.00 20GAVAAXX100126.5 40 M 40.0000 43 0.00 20GAVAAXX100126.5 41 M 41.0000 5 0.00 -20GAVAAXX100126.5 45 D 45.0000 5884 0.86 -20GAVAAXX100126.5 45 I 45.0000 5884 0.00 +20GAVAAXX100126.5 45 D 45.0000 5883 0.71 +20GAVAAXX100126.5 45 I 45.0000 5883 0.00 20GAVAAXX100126.6 6 M 6.0000 4 2.00 20GAVAAXX100126.6 7 M 7.0000 6 0.00 20GAVAAXX100126.6 8 M 8.0000 9 3.00 @@ -684,18 +684,18 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.6 28 M 28.0000 105 0.00 20GAVAAXX100126.6 29 M 29.0000 158 1.00 20GAVAAXX100126.6 30 M 30.0000 144 0.00 -20GAVAAXX100126.6 31 M 31.0000 194 1.00 +20GAVAAXX100126.6 31 M 31.0000 193 1.00 20GAVAAXX100126.6 32 M 32.0000 239 0.00 20GAVAAXX100126.6 33 M 33.0000 358 0.00 20GAVAAXX100126.6 34 M 34.0000 481 1.00 20GAVAAXX100126.6 35 M 35.0000 578 2.00 20GAVAAXX100126.6 36 M 36.0000 845 2.00 20GAVAAXX100126.6 37 M 37.0000 1617 4.00 -20GAVAAXX100126.6 38 M 38.0000 1661 3.00 +20GAVAAXX100126.6 38 M 38.0000 1660 3.00 20GAVAAXX100126.6 39 M 39.0000 1030 2.00 20GAVAAXX100126.6 40 M 40.0000 35 0.00 -20GAVAAXX100126.6 45 D 45.0000 8002 3.69 -20GAVAAXX100126.6 45 I 45.0000 8002 0.00 +20GAVAAXX100126.6 45 D 45.0000 8000 3.38 +20GAVAAXX100126.6 45 I 45.0000 8000 0.00 20GAVAAXX100126.7 6 M 6.0000 7 1.00 20GAVAAXX100126.7 7 M 7.0000 16 6.00 20GAVAAXX100126.7 8 M 8.0000 16 2.00 @@ -723,7 +723,7 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.7 30 M 30.0000 192 0.00 20GAVAAXX100126.7 31 M 31.0000 200 0.00 20GAVAAXX100126.7 32 M 32.0000 228 1.00 -20GAVAAXX100126.7 33 M 33.0000 382 1.25 +20GAVAAXX100126.7 33 M 33.0000 381 1.25 20GAVAAXX100126.7 34 M 34.0000 412 2.00 20GAVAAXX100126.7 35 M 35.0000 554 0.00 20GAVAAXX100126.7 36 M 36.0000 700 1.50 @@ -732,8 +732,8 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.7 39 M 39.0000 881 1.00 20GAVAAXX100126.7 40 M 40.0000 49 0.00 20GAVAAXX100126.7 41 M 41.0000 6 0.00 -20GAVAAXX100126.7 45 D 45.0000 7598 2.88 -20GAVAAXX100126.7 45 I 45.0000 7598 0.00 +20GAVAAXX100126.7 45 D 45.0000 7597 2.75 +20GAVAAXX100126.7 45 I 45.0000 7597 0.00 20GAVAAXX100126.8 6 M 6.0000 9 1.00 20GAVAAXX100126.8 7 M 7.0000 4 0.00 20GAVAAXX100126.8 8 M 8.0000 7 1.00 @@ -773,7 +773,7 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.8 45 D 45.0000 8533 5.69 20GAVAAXX100126.8 45 I 45.0000 8533 1.00 -#:GATKTable:8:54597:%s:%d:%s:%s:%s:%.4f:%d:%.2f:; +#:GATKTable:8:54594:%s:%d:%s:%s:%s:%.4f:%d:%.2f:; #:GATKTable:RecalTable2: ReadGroup QualityScore CovariateValue CovariateName EventType EmpiricalQuality Observations Errors 20FUKAAXX100202.1 6 -31 Cycle M 6.0000 1 0.00 @@ -2925,7 +2925,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.1 37 -33 Cycle M 37.0000 5 0.00 20FUKAAXX100202.1 37 -34 Cycle M 37.0000 13 0.00 20FUKAAXX100202.1 37 -35 Cycle M 37.0000 12 0.00 -20FUKAAXX100202.1 37 -36 Cycle M 37.0000 14 0.00 +20FUKAAXX100202.1 37 -36 Cycle M 37.0000 13 0.00 20FUKAAXX100202.1 37 -37 Cycle M 37.0000 10 0.00 20FUKAAXX100202.1 37 -38 Cycle M 37.0000 9 0.00 20FUKAAXX100202.1 37 -39 Cycle M 37.0000 9 0.00 @@ -3100,7 +3100,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.1 37 TA Context M 37.0000 42 0.00 20FUKAAXX100202.1 37 TC Context M 37.0000 280 0.00 20FUKAAXX100202.1 37 TG Context M 37.0000 83 1.00 -20FUKAAXX100202.1 37 TT Context M 37.0000 116 0.00 +20FUKAAXX100202.1 37 TT Context M 37.0000 115 0.00 20FUKAAXX100202.1 38 -10 Cycle M 38.0000 2 0.00 20FUKAAXX100202.1 38 -100 Cycle M 38.0000 3 0.00 20FUKAAXX100202.1 38 -101 Cycle M 38.0000 4 0.00 @@ -3545,8 +3545,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.1 45 -34 Cycle I 45.0000 37 0.00 20FUKAAXX100202.1 45 -35 Cycle D 45.0000 37 0.00 20FUKAAXX100202.1 45 -35 Cycle I 45.0000 37 0.00 -20FUKAAXX100202.1 45 -36 Cycle D 45.0000 37 0.14 -20FUKAAXX100202.1 45 -36 Cycle I 45.0000 37 0.00 +20FUKAAXX100202.1 45 -36 Cycle D 45.0000 36 0.00 +20FUKAAXX100202.1 45 -36 Cycle I 45.0000 36 0.00 20FUKAAXX100202.1 45 -37 Cycle D 45.0000 37 0.14 20FUKAAXX100202.1 45 -37 Cycle I 45.0000 37 0.00 20FUKAAXX100202.1 45 -38 Cycle D 45.0000 38 0.14 @@ -4299,8 +4299,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.1 45 TCTC Context I 45.0000 44 0.00 20FUKAAXX100202.1 45 TCTG Context D 45.0000 47 0.00 20FUKAAXX100202.1 45 TCTG Context I 45.0000 47 0.00 -20FUKAAXX100202.1 45 TCTT Context D 45.0000 33 0.29 -20FUKAAXX100202.1 45 TCTT Context I 45.0000 33 0.00 +20FUKAAXX100202.1 45 TCTT Context D 45.0000 32 0.14 +20FUKAAXX100202.1 45 TCTT Context I 45.0000 32 0.00 20FUKAAXX100202.1 45 TGAA Context D 45.0000 62 0.29 20FUKAAXX100202.1 45 TGAA Context I 45.0000 62 0.00 20FUKAAXX100202.1 45 TGAC Context D 45.0000 32 0.00 @@ -6319,7 +6319,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.2 39 14 Cycle M 39.0000 3 0.00 20FUKAAXX100202.2 39 15 Cycle M 39.0000 3 0.00 20FUKAAXX100202.2 39 16 Cycle M 39.0000 2 0.00 -20FUKAAXX100202.2 39 17 Cycle M 39.0000 3 0.00 +20FUKAAXX100202.2 39 17 Cycle M 39.0000 2 0.00 20FUKAAXX100202.2 39 18 Cycle M 39.0000 7 0.00 20FUKAAXX100202.2 39 19 Cycle M 39.0000 4 0.00 20FUKAAXX100202.2 39 20 Cycle M 39.0000 3 0.00 @@ -6379,7 +6379,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.2 39 77 Cycle M 39.0000 5 0.00 20FUKAAXX100202.2 39 78 Cycle M 39.0000 2 0.00 20FUKAAXX100202.2 39 79 Cycle M 39.0000 6 0.00 -20FUKAAXX100202.2 39 8 Cycle M 39.0000 4 0.00 +20FUKAAXX100202.2 39 8 Cycle M 39.0000 3 0.00 20FUKAAXX100202.2 39 80 Cycle M 39.0000 2 0.00 20FUKAAXX100202.2 39 81 Cycle M 39.0000 2 0.00 20FUKAAXX100202.2 39 82 Cycle M 39.0000 2 0.00 @@ -6398,7 +6398,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.2 39 95 Cycle M 39.0000 3 0.00 20FUKAAXX100202.2 39 96 Cycle M 39.0000 3 0.00 20FUKAAXX100202.2 39 97 Cycle M 39.0000 1 0.00 -20FUKAAXX100202.2 39 AA Context M 39.0000 241 0.00 +20FUKAAXX100202.2 39 AA Context M 39.0000 239 0.00 20FUKAAXX100202.2 39 AG Context M 39.0000 2 0.00 20FUKAAXX100202.2 39 AT Context M 39.0000 1 0.00 20FUKAAXX100202.2 39 CA Context M 39.0000 81 0.00 @@ -6621,8 +6621,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.2 45 15 Cycle I 45.0000 32 0.00 20FUKAAXX100202.2 45 16 Cycle D 45.0000 32 0.13 20FUKAAXX100202.2 45 16 Cycle I 45.0000 32 0.00 -20FUKAAXX100202.2 45 17 Cycle D 45.0000 32 0.13 -20FUKAAXX100202.2 45 17 Cycle I 45.0000 32 0.00 +20FUKAAXX100202.2 45 17 Cycle D 45.0000 31 0.00 +20FUKAAXX100202.2 45 17 Cycle I 45.0000 31 0.00 20FUKAAXX100202.2 45 18 Cycle D 45.0000 31 0.00 20FUKAAXX100202.2 45 18 Cycle I 45.0000 31 0.00 20FUKAAXX100202.2 45 19 Cycle D 45.0000 32 0.25 @@ -6753,8 +6753,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.2 45 78 Cycle I 45.0000 30 0.00 20FUKAAXX100202.2 45 79 Cycle D 45.0000 29 0.00 20FUKAAXX100202.2 45 79 Cycle I 45.0000 29 0.00 -20FUKAAXX100202.2 45 8 Cycle D 45.0000 32 0.11 -20FUKAAXX100202.2 45 8 Cycle I 45.0000 32 0.00 +20FUKAAXX100202.2 45 8 Cycle D 45.0000 31 0.00 +20FUKAAXX100202.2 45 8 Cycle I 45.0000 31 0.00 20FUKAAXX100202.2 45 80 Cycle D 45.0000 30 0.00 20FUKAAXX100202.2 45 80 Cycle I 45.0000 30 0.00 20FUKAAXX100202.2 45 81 Cycle D 45.0000 29 0.00 @@ -7229,8 +7229,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.2 45 TCTG Context I 45.0000 32 0.00 20FUKAAXX100202.2 45 TCTT Context D 45.0000 34 0.45 20FUKAAXX100202.2 45 TCTT Context I 45.0000 34 0.00 -20FUKAAXX100202.2 45 TGAA Context D 45.0000 52 0.49 -20FUKAAXX100202.2 45 TGAA Context I 45.0000 52 0.00 +20FUKAAXX100202.2 45 TGAA Context D 45.0000 50 0.25 +20FUKAAXX100202.2 45 TGAA Context I 45.0000 50 0.00 20FUKAAXX100202.2 45 TGAC Context D 45.0000 30 0.00 20FUKAAXX100202.2 45 TGAC Context I 45.0000 30 0.00 20FUKAAXX100202.2 45 TGAG Context D 45.0000 49 0.49 @@ -9400,7 +9400,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.3 36 93 Cycle M 36.0000 5 0.00 20FUKAAXX100202.3 36 94 Cycle M 36.0000 4 0.00 20FUKAAXX100202.3 36 95 Cycle M 36.0000 6 0.00 -20FUKAAXX100202.3 36 96 Cycle M 36.0000 6 0.00 +20FUKAAXX100202.3 36 96 Cycle M 36.0000 5 0.00 20FUKAAXX100202.3 36 97 Cycle M 36.0000 3 0.00 20FUKAAXX100202.3 36 98 Cycle M 36.0000 4 0.00 20FUKAAXX100202.3 36 99 Cycle M 36.0000 5 0.00 @@ -9418,7 +9418,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.3 36 TA Context M 36.0000 32 0.00 20FUKAAXX100202.3 36 TC Context M 36.0000 41 0.00 20FUKAAXX100202.3 36 TG Context M 36.0000 56 2.00 -20FUKAAXX100202.3 36 TT Context M 36.0000 50 0.00 +20FUKAAXX100202.3 36 TT Context M 36.0000 49 0.00 20FUKAAXX100202.3 37 -1 Cycle M 37.0000 1 0.00 20FUKAAXX100202.3 37 -10 Cycle M 37.0000 14 0.00 20FUKAAXX100202.3 37 -100 Cycle M 37.0000 6 0.00 @@ -9838,7 +9838,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.3 39 -18 Cycle M 39.0000 6 0.00 20FUKAAXX100202.3 39 -19 Cycle M 39.0000 1 0.00 20FUKAAXX100202.3 39 -20 Cycle M 39.0000 4 0.00 -20FUKAAXX100202.3 39 -21 Cycle M 39.0000 7 0.00 +20FUKAAXX100202.3 39 -21 Cycle M 39.0000 6 0.00 20FUKAAXX100202.3 39 -22 Cycle M 39.0000 10 0.00 20FUKAAXX100202.3 39 -23 Cycle M 39.0000 5 0.00 20FUKAAXX100202.3 39 -25 Cycle M 39.0000 1 0.00 @@ -10008,7 +10008,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.3 39 97 Cycle M 39.0000 3 0.00 20FUKAAXX100202.3 39 98 Cycle M 39.0000 5 0.00 20FUKAAXX100202.3 39 99 Cycle M 39.0000 2 0.00 -20FUKAAXX100202.3 39 AA Context M 39.0000 334 0.00 +20FUKAAXX100202.3 39 AA Context M 39.0000 333 0.00 20FUKAAXX100202.3 39 AG Context M 39.0000 7 0.00 20FUKAAXX100202.3 39 CA Context M 39.0000 170 0.00 20FUKAAXX100202.3 39 CT Context M 39.0000 385 0.00 @@ -10049,8 +10049,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.3 45 -19 Cycle I 45.0000 49 0.00 20FUKAAXX100202.3 45 -20 Cycle D 45.0000 49 0.13 20FUKAAXX100202.3 45 -20 Cycle I 45.0000 49 0.00 -20FUKAAXX100202.3 45 -21 Cycle D 45.0000 49 0.13 -20FUKAAXX100202.3 45 -21 Cycle I 45.0000 49 0.00 +20FUKAAXX100202.3 45 -21 Cycle D 45.0000 48 0.00 +20FUKAAXX100202.3 45 -21 Cycle I 45.0000 48 0.00 20FUKAAXX100202.3 45 -22 Cycle D 45.0000 48 0.00 20FUKAAXX100202.3 45 -22 Cycle I 45.0000 48 0.00 20FUKAAXX100202.3 45 -23 Cycle D 45.0000 49 0.13 @@ -10395,8 +10395,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.3 45 94 Cycle I 45.0000 39 0.00 20FUKAAXX100202.3 45 95 Cycle D 45.0000 38 0.00 20FUKAAXX100202.3 45 95 Cycle I 45.0000 38 0.00 -20FUKAAXX100202.3 45 96 Cycle D 45.0000 39 0.14 -20FUKAAXX100202.3 45 96 Cycle I 45.0000 39 0.00 +20FUKAAXX100202.3 45 96 Cycle D 45.0000 38 0.00 +20FUKAAXX100202.3 45 96 Cycle I 45.0000 38 0.00 20FUKAAXX100202.3 45 97 Cycle D 45.0000 39 0.14 20FUKAAXX100202.3 45 97 Cycle I 45.0000 39 0.00 20FUKAAXX100202.3 45 AAAA Context D 45.0000 45 0.00 @@ -10835,10 +10835,10 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.3 45 TCTC Context I 45.0000 50 0.00 20FUKAAXX100202.3 45 TCTG Context D 45.0000 56 0.00 20FUKAAXX100202.3 45 TCTG Context I 45.0000 56 0.00 -20FUKAAXX100202.3 45 TCTT Context D 45.0000 43 0.29 -20FUKAAXX100202.3 45 TCTT Context I 45.0000 43 0.00 -20FUKAAXX100202.3 45 TGAA Context D 45.0000 77 0.50 -20FUKAAXX100202.3 45 TGAA Context I 45.0000 77 0.00 +20FUKAAXX100202.3 45 TCTT Context D 45.0000 42 0.14 +20FUKAAXX100202.3 45 TCTT Context I 45.0000 42 0.00 +20FUKAAXX100202.3 45 TGAA Context D 45.0000 76 0.38 +20FUKAAXX100202.3 45 TGAA Context I 45.0000 76 0.00 20FUKAAXX100202.3 45 TGAC Context D 45.0000 28 0.00 20FUKAAXX100202.3 45 TGAC Context I 45.0000 28 0.00 20FUKAAXX100202.3 45 TGAG Context D 45.0000 71 0.50 @@ -13155,13 +13155,13 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.4 39 25 Cycle M 39.0000 3 0.00 20FUKAAXX100202.4 39 26 Cycle M 39.0000 1 0.00 20FUKAAXX100202.4 39 27 Cycle M 39.0000 2 0.00 -20FUKAAXX100202.4 39 28 Cycle M 39.0000 3 0.00 +20FUKAAXX100202.4 39 28 Cycle M 39.0000 2 0.00 20FUKAAXX100202.4 39 29 Cycle M 39.0000 3 0.00 20FUKAAXX100202.4 39 30 Cycle M 39.0000 4 0.00 20FUKAAXX100202.4 39 31 Cycle M 39.0000 4 0.00 20FUKAAXX100202.4 39 32 Cycle M 39.0000 7 0.00 20FUKAAXX100202.4 39 33 Cycle M 39.0000 3 0.00 -20FUKAAXX100202.4 39 34 Cycle M 39.0000 5 0.00 +20FUKAAXX100202.4 39 34 Cycle M 39.0000 4 0.00 20FUKAAXX100202.4 39 35 Cycle M 39.0000 2 0.00 20FUKAAXX100202.4 39 36 Cycle M 39.0000 1 0.00 20FUKAAXX100202.4 39 37 Cycle M 39.0000 3 0.00 @@ -13225,7 +13225,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.4 39 96 Cycle M 39.0000 2 0.00 20FUKAAXX100202.4 39 97 Cycle M 39.0000 4 0.00 20FUKAAXX100202.4 39 98 Cycle M 39.0000 2 0.00 -20FUKAAXX100202.4 39 AA Context M 39.0000 193 0.00 +20FUKAAXX100202.4 39 AA Context M 39.0000 191 0.00 20FUKAAXX100202.4 39 AG Context M 39.0000 1 0.00 20FUKAAXX100202.4 39 AT Context M 39.0000 2 0.00 20FUKAAXX100202.4 39 CA Context M 39.0000 109 1.00 @@ -13471,8 +13471,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.4 45 26 Cycle I 45.0000 32 0.00 20FUKAAXX100202.4 45 27 Cycle D 45.0000 32 0.13 20FUKAAXX100202.4 45 27 Cycle I 45.0000 32 0.00 -20FUKAAXX100202.4 45 28 Cycle D 45.0000 32 0.13 -20FUKAAXX100202.4 45 28 Cycle I 45.0000 32 0.00 +20FUKAAXX100202.4 45 28 Cycle D 45.0000 31 0.00 +20FUKAAXX100202.4 45 28 Cycle I 45.0000 31 0.00 20FUKAAXX100202.4 45 29 Cycle D 45.0000 31 0.13 20FUKAAXX100202.4 45 29 Cycle I 45.0000 31 0.00 20FUKAAXX100202.4 45 30 Cycle D 45.0000 31 0.25 @@ -13483,8 +13483,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.4 45 32 Cycle I 45.0000 32 0.00 20FUKAAXX100202.4 45 33 Cycle D 45.0000 32 0.13 20FUKAAXX100202.4 45 33 Cycle I 45.0000 32 0.00 -20FUKAAXX100202.4 45 34 Cycle D 45.0000 32 0.13 -20FUKAAXX100202.4 45 34 Cycle I 45.0000 32 0.00 +20FUKAAXX100202.4 45 34 Cycle D 45.0000 31 0.00 +20FUKAAXX100202.4 45 34 Cycle I 45.0000 31 0.00 20FUKAAXX100202.4 45 35 Cycle D 45.0000 31 0.00 20FUKAAXX100202.4 45 35 Cycle I 45.0000 31 0.00 20FUKAAXX100202.4 45 36 Cycle D 45.0000 32 0.13 @@ -14059,8 +14059,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.4 45 TCTG Context I 45.0000 45 0.00 20FUKAAXX100202.4 45 TCTT Context D 45.0000 35 0.14 20FUKAAXX100202.4 45 TCTT Context I 45.0000 35 0.00 -20FUKAAXX100202.4 45 TGAA Context D 45.0000 49 0.38 -20FUKAAXX100202.4 45 TGAA Context I 45.0000 49 0.00 +20FUKAAXX100202.4 45 TGAA Context D 45.0000 47 0.13 +20FUKAAXX100202.4 45 TGAA Context I 45.0000 47 0.00 20FUKAAXX100202.4 45 TGAC Context D 45.0000 34 0.00 20FUKAAXX100202.4 45 TGAC Context I 45.0000 34 0.00 20FUKAAXX100202.4 45 TGAG Context D 45.0000 58 0.38 @@ -16254,7 +16254,6 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.5 38 TT Context M 38.0000 221 0.00 20FUKAAXX100202.5 39 -100 Cycle M 39.0000 1 0.00 20FUKAAXX100202.5 39 -14 Cycle M 39.0000 2 0.00 -20FUKAAXX100202.5 39 -15 Cycle M 39.0000 1 0.00 20FUKAAXX100202.5 39 -16 Cycle M 39.0000 6 0.00 20FUKAAXX100202.5 39 -17 Cycle M 39.0000 4 0.00 20FUKAAXX100202.5 39 -18 Cycle M 39.0000 4 0.00 @@ -16431,7 +16430,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.5 39 97 Cycle M 39.0000 3 0.00 20FUKAAXX100202.5 39 98 Cycle M 39.0000 3 0.00 20FUKAAXX100202.5 39 99 Cycle M 39.0000 1 0.00 -20FUKAAXX100202.5 39 AA Context M 39.0000 241 0.00 +20FUKAAXX100202.5 39 AA Context M 39.0000 240 0.00 20FUKAAXX100202.5 39 AG Context M 39.0000 19 0.00 20FUKAAXX100202.5 39 AT Context M 39.0000 3 0.00 20FUKAAXX100202.5 39 CA Context M 39.0000 218 0.00 @@ -16485,8 +16484,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.5 45 -13 Cycle I 45.0000 39 0.00 20FUKAAXX100202.5 45 -14 Cycle D 45.0000 39 0.14 20FUKAAXX100202.5 45 -14 Cycle I 45.0000 39 0.00 -20FUKAAXX100202.5 45 -15 Cycle D 45.0000 39 0.14 -20FUKAAXX100202.5 45 -15 Cycle I 45.0000 39 0.00 +20FUKAAXX100202.5 45 -15 Cycle D 45.0000 38 0.00 +20FUKAAXX100202.5 45 -15 Cycle I 45.0000 38 0.00 20FUKAAXX100202.5 45 -16 Cycle D 45.0000 37 0.00 20FUKAAXX100202.5 45 -16 Cycle I 45.0000 37 0.00 20FUKAAXX100202.5 45 -17 Cycle D 45.0000 39 0.14 @@ -17283,8 +17282,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.5 45 TCTG Context I 45.0000 48 0.00 20FUKAAXX100202.5 45 TCTT Context D 45.0000 27 0.14 20FUKAAXX100202.5 45 TCTT Context I 45.0000 27 0.00 -20FUKAAXX100202.5 45 TGAA Context D 45.0000 62 0.29 -20FUKAAXX100202.5 45 TGAA Context I 45.0000 62 0.00 +20FUKAAXX100202.5 45 TGAA Context D 45.0000 61 0.14 +20FUKAAXX100202.5 45 TGAA Context I 45.0000 61 0.00 20FUKAAXX100202.5 45 TGAC Context D 45.0000 30 0.00 20FUKAAXX100202.5 45 TGAC Context I 45.0000 30 0.00 20FUKAAXX100202.5 45 TGAG Context D 45.0000 61 0.29 @@ -19065,7 +19064,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 35 -94 Cycle M 35.0000 2 0.00 20FUKAAXX100202.6 35 -95 Cycle M 35.0000 5 0.00 20FUKAAXX100202.6 35 -96 Cycle M 35.0000 1 0.00 -20FUKAAXX100202.6 35 -97 Cycle M 35.0000 3 0.00 +20FUKAAXX100202.6 35 -97 Cycle M 35.0000 2 0.00 20FUKAAXX100202.6 35 -98 Cycle M 35.0000 4 0.00 20FUKAAXX100202.6 35 -99 Cycle M 35.0000 2 0.00 20FUKAAXX100202.6 35 1 Cycle M 35.0000 51 0.50 @@ -19152,7 +19151,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 35 TA Context M 35.0000 24 1.00 20FUKAAXX100202.6 35 TC Context M 35.0000 33 0.17 20FUKAAXX100202.6 35 TG Context M 35.0000 59 0.00 -20FUKAAXX100202.6 35 TT Context M 35.0000 53 0.00 +20FUKAAXX100202.6 35 TT Context M 35.0000 52 0.00 20FUKAAXX100202.6 36 -10 Cycle M 36.0000 13 0.00 20FUKAAXX100202.6 36 -100 Cycle M 36.0000 6 0.00 20FUKAAXX100202.6 36 -101 Cycle M 36.0000 2 0.00 @@ -19595,7 +19594,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 38 -42 Cycle M 38.0000 17 0.00 20FUKAAXX100202.6 38 -43 Cycle M 38.0000 15 0.00 20FUKAAXX100202.6 38 -44 Cycle M 38.0000 21 0.00 -20FUKAAXX100202.6 38 -45 Cycle M 38.0000 13 0.00 +20FUKAAXX100202.6 38 -45 Cycle M 38.0000 12 0.00 20FUKAAXX100202.6 38 -46 Cycle M 38.0000 23 0.00 20FUKAAXX100202.6 38 -47 Cycle M 38.0000 19 0.00 20FUKAAXX100202.6 38 -48 Cycle M 38.0000 20 0.00 @@ -19736,7 +19735,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 38 85 Cycle M 38.0000 23 0.00 20FUKAAXX100202.6 38 86 Cycle M 38.0000 23 0.00 20FUKAAXX100202.6 38 87 Cycle M 38.0000 15 0.00 -20FUKAAXX100202.6 38 88 Cycle M 38.0000 18 1.00 +20FUKAAXX100202.6 38 88 Cycle M 38.0000 17 1.00 20FUKAAXX100202.6 38 89 Cycle M 38.0000 19 0.00 20FUKAAXX100202.6 38 9 Cycle M 38.0000 13 0.00 20FUKAAXX100202.6 38 90 Cycle M 38.0000 14 0.00 @@ -19762,7 +19761,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 38 TA Context M 38.0000 167 0.00 20FUKAAXX100202.6 38 TC Context M 38.0000 108 0.00 20FUKAAXX100202.6 38 TG Context M 38.0000 463 3.00 -20FUKAAXX100202.6 38 TT Context M 38.0000 306 1.00 +20FUKAAXX100202.6 38 TT Context M 38.0000 304 1.00 20FUKAAXX100202.6 39 -100 Cycle M 39.0000 2 0.00 20FUKAAXX100202.6 39 -16 Cycle M 39.0000 3 0.00 20FUKAAXX100202.6 39 -17 Cycle M 39.0000 2 0.00 @@ -20037,8 +20036,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 45 -43 Cycle I 45.0000 51 0.00 20FUKAAXX100202.6 45 -44 Cycle D 45.0000 49 0.00 20FUKAAXX100202.6 45 -44 Cycle I 45.0000 49 0.00 -20FUKAAXX100202.6 45 -45 Cycle D 45.0000 51 0.14 -20FUKAAXX100202.6 45 -45 Cycle I 45.0000 51 0.00 +20FUKAAXX100202.6 45 -45 Cycle D 45.0000 50 0.00 +20FUKAAXX100202.6 45 -45 Cycle I 45.0000 50 0.00 20FUKAAXX100202.6 45 -46 Cycle D 45.0000 51 0.14 20FUKAAXX100202.6 45 -46 Cycle I 45.0000 51 0.00 20FUKAAXX100202.6 45 -47 Cycle D 45.0000 51 0.14 @@ -20151,8 +20150,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 45 -95 Cycle I 45.0000 36 0.00 20FUKAAXX100202.6 45 -96 Cycle D 45.0000 35 0.00 20FUKAAXX100202.6 45 -96 Cycle I 45.0000 35 0.00 -20FUKAAXX100202.6 45 -97 Cycle D 45.0000 36 0.17 -20FUKAAXX100202.6 45 -97 Cycle I 45.0000 36 0.00 +20FUKAAXX100202.6 45 -97 Cycle D 45.0000 35 0.00 +20FUKAAXX100202.6 45 -97 Cycle I 45.0000 35 0.00 20FUKAAXX100202.6 45 10 Cycle D 45.0000 53 0.00 20FUKAAXX100202.6 45 10 Cycle I 45.0000 53 0.00 20FUKAAXX100202.6 45 11 Cycle D 45.0000 54 0.00 @@ -20317,8 +20316,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 45 86 Cycle I 45.0000 49 0.00 20FUKAAXX100202.6 45 87 Cycle D 45.0000 47 0.00 20FUKAAXX100202.6 45 87 Cycle I 45.0000 47 0.00 -20FUKAAXX100202.6 45 88 Cycle D 45.0000 48 0.14 -20FUKAAXX100202.6 45 88 Cycle I 45.0000 48 0.00 +20FUKAAXX100202.6 45 88 Cycle D 45.0000 47 0.00 +20FUKAAXX100202.6 45 88 Cycle I 45.0000 47 0.00 20FUKAAXX100202.6 45 89 Cycle D 45.0000 47 0.14 20FUKAAXX100202.6 45 89 Cycle I 45.0000 47 0.00 20FUKAAXX100202.6 45 9 Cycle D 45.0000 54 0.00 @@ -20775,8 +20774,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 45 TCTC Context I 45.0000 63 0.00 20FUKAAXX100202.6 45 TCTG Context D 45.0000 57 0.00 20FUKAAXX100202.6 45 TCTG Context I 45.0000 57 0.00 -20FUKAAXX100202.6 45 TCTT Context D 45.0000 57 1.17 -20FUKAAXX100202.6 45 TCTT Context I 45.0000 57 0.00 +20FUKAAXX100202.6 45 TCTT Context D 45.0000 54 0.71 +20FUKAAXX100202.6 45 TCTT Context I 45.0000 54 0.00 20FUKAAXX100202.6 45 TGAA Context D 45.0000 96 0.14 20FUKAAXX100202.6 45 TGAA Context I 45.0000 96 0.00 20FUKAAXX100202.6 45 TGAC Context D 45.0000 36 0.00 @@ -22758,7 +22757,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.7 36 -67 Cycle M 36.0000 3 0.00 20FUKAAXX100202.7 36 -68 Cycle M 36.0000 3 0.00 20FUKAAXX100202.7 36 -69 Cycle M 36.0000 4 0.00 -20FUKAAXX100202.7 36 -7 Cycle M 36.0000 12 0.00 +20FUKAAXX100202.7 36 -7 Cycle M 36.0000 11 0.00 20FUKAAXX100202.7 36 -70 Cycle M 36.0000 4 0.00 20FUKAAXX100202.7 36 -71 Cycle M 36.0000 3 0.00 20FUKAAXX100202.7 36 -72 Cycle M 36.0000 2 0.00 @@ -22888,7 +22887,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.7 36 97 Cycle M 36.0000 5 0.00 20FUKAAXX100202.7 36 98 Cycle M 36.0000 7 0.00 20FUKAAXX100202.7 36 99 Cycle M 36.0000 4 0.00 -20FUKAAXX100202.7 36 AA Context M 36.0000 58 0.00 +20FUKAAXX100202.7 36 AA Context M 36.0000 57 0.00 20FUKAAXX100202.7 36 AC Context M 36.0000 328 2.00 20FUKAAXX100202.7 36 AG Context M 36.0000 72 0.00 20FUKAAXX100202.7 36 AT Context M 36.0000 43 0.00 @@ -23287,7 +23286,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.7 38 90 Cycle M 38.0000 19 0.00 20FUKAAXX100202.7 38 91 Cycle M 38.0000 15 0.00 20FUKAAXX100202.7 38 92 Cycle M 38.0000 21 0.00 -20FUKAAXX100202.7 38 93 Cycle M 38.0000 17 0.00 +20FUKAAXX100202.7 38 93 Cycle M 38.0000 16 0.00 20FUKAAXX100202.7 38 94 Cycle M 38.0000 13 0.00 20FUKAAXX100202.7 38 95 Cycle M 38.0000 17 0.00 20FUKAAXX100202.7 38 96 Cycle M 38.0000 14 1.00 @@ -23307,7 +23306,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.7 38 TA Context M 38.0000 162 0.00 20FUKAAXX100202.7 38 TC Context M 38.0000 131 0.00 20FUKAAXX100202.7 38 TG Context M 38.0000 456 1.33 -20FUKAAXX100202.7 38 TT Context M 38.0000 262 1.00 +20FUKAAXX100202.7 38 TT Context M 38.0000 261 1.00 20FUKAAXX100202.7 39 -100 Cycle M 39.0000 1 0.00 20FUKAAXX100202.7 39 -14 Cycle M 39.0000 3 0.00 20FUKAAXX100202.7 39 -15 Cycle M 39.0000 2 0.00 @@ -23637,8 +23636,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.7 45 -68 Cycle I 45.0000 46 0.00 20FUKAAXX100202.7 45 -69 Cycle D 45.0000 46 0.00 20FUKAAXX100202.7 45 -69 Cycle I 45.0000 46 0.00 -20FUKAAXX100202.7 45 -7 Cycle D 45.0000 51 0.25 -20FUKAAXX100202.7 45 -7 Cycle I 45.0000 51 0.00 +20FUKAAXX100202.7 45 -7 Cycle D 45.0000 50 0.13 +20FUKAAXX100202.7 45 -7 Cycle I 45.0000 50 0.00 20FUKAAXX100202.7 45 -70 Cycle D 45.0000 46 0.00 20FUKAAXX100202.7 45 -70 Cycle I 45.0000 46 0.00 20FUKAAXX100202.7 45 -71 Cycle D 45.0000 46 0.00 @@ -23875,8 +23874,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.7 45 91 Cycle I 45.0000 40 0.00 20FUKAAXX100202.7 45 92 Cycle D 45.0000 40 0.00 20FUKAAXX100202.7 45 92 Cycle I 45.0000 40 0.00 -20FUKAAXX100202.7 45 93 Cycle D 45.0000 41 0.09 -20FUKAAXX100202.7 45 93 Cycle I 45.0000 41 0.00 +20FUKAAXX100202.7 45 93 Cycle D 45.0000 40 0.00 +20FUKAAXX100202.7 45 93 Cycle I 45.0000 40 0.00 20FUKAAXX100202.7 45 94 Cycle D 45.0000 41 0.09 20FUKAAXX100202.7 45 94 Cycle I 45.0000 41 0.00 20FUKAAXX100202.7 45 95 Cycle D 45.0000 41 0.09 @@ -24321,10 +24320,10 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.7 45 TCTC Context I 45.0000 44 0.00 20FUKAAXX100202.7 45 TCTG Context D 45.0000 55 0.00 20FUKAAXX100202.7 45 TCTG Context I 45.0000 55 0.00 -20FUKAAXX100202.7 45 TCTT Context D 45.0000 28 0.09 -20FUKAAXX100202.7 45 TCTT Context I 45.0000 28 0.00 -20FUKAAXX100202.7 45 TGAA Context D 45.0000 99 0.13 -20FUKAAXX100202.7 45 TGAA Context I 45.0000 99 0.00 +20FUKAAXX100202.7 45 TCTT Context D 45.0000 27 0.00 +20FUKAAXX100202.7 45 TCTT Context I 45.0000 27 0.00 +20FUKAAXX100202.7 45 TGAA Context D 45.0000 98 0.00 +20FUKAAXX100202.7 45 TGAA Context I 45.0000 98 0.00 20FUKAAXX100202.7 45 TGAC Context D 45.0000 34 0.00 20FUKAAXX100202.7 45 TGAC Context I 45.0000 34 0.00 20FUKAAXX100202.7 45 TGAG Context D 45.0000 89 0.00 @@ -28345,7 +28344,6 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 24 TC Context M 24.0000 4 0.00 20GAVAAXX100126.1 24 TG Context M 24.0000 1 0.00 20GAVAAXX100126.1 24 TT Context M 24.0000 1 0.00 -20GAVAAXX100126.1 25 -10 Cycle M 25.0000 1 0.00 20GAVAAXX100126.1 25 -12 Cycle M 25.0000 1 0.00 20GAVAAXX100126.1 25 -15 Cycle M 25.0000 1 0.00 20GAVAAXX100126.1 25 -17 Cycle M 25.0000 1 0.00 @@ -28424,7 +28422,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 25 GT Context M 25.0000 7 0.00 20GAVAAXX100126.1 25 TA Context M 25.0000 5 0.00 20GAVAAXX100126.1 25 TC Context M 25.0000 10 0.00 -20GAVAAXX100126.1 25 TG Context M 25.0000 9 0.00 +20GAVAAXX100126.1 25 TG Context M 25.0000 8 0.00 20GAVAAXX100126.1 25 TT Context M 25.0000 5 0.00 20GAVAAXX100126.1 26 -101 Cycle M 26.0000 1 0.00 20GAVAAXX100126.1 26 -18 Cycle M 26.0000 1 0.00 @@ -28584,7 +28582,6 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 27 61 Cycle M 27.0000 1 0.00 20GAVAAXX100126.1 27 63 Cycle M 27.0000 1 0.00 20GAVAAXX100126.1 27 65 Cycle M 27.0000 1 0.00 -20GAVAAXX100126.1 27 66 Cycle M 27.0000 1 0.00 20GAVAAXX100126.1 27 68 Cycle M 27.0000 1 0.00 20GAVAAXX100126.1 27 70 Cycle M 27.0000 2 0.00 20GAVAAXX100126.1 27 71 Cycle M 27.0000 1 0.00 @@ -28604,7 +28601,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 27 91 Cycle M 27.0000 1 0.00 20GAVAAXX100126.1 27 93 Cycle M 27.0000 2 0.00 20GAVAAXX100126.1 27 99 Cycle M 27.0000 2 0.00 -20GAVAAXX100126.1 27 AA Context M 27.0000 8 0.00 +20GAVAAXX100126.1 27 AA Context M 27.0000 7 0.00 20GAVAAXX100126.1 27 AC Context M 27.0000 3 0.00 20GAVAAXX100126.1 27 AG Context M 27.0000 9 0.00 20GAVAAXX100126.1 27 AT Context M 27.0000 3 0.00 @@ -30512,7 +30509,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 39 39 Cycle M 39.0000 16 0.00 20GAVAAXX100126.1 39 40 Cycle M 39.0000 23 0.00 20GAVAAXX100126.1 39 41 Cycle M 39.0000 8 0.00 -20GAVAAXX100126.1 39 42 Cycle M 39.0000 20 0.00 +20GAVAAXX100126.1 39 42 Cycle M 39.0000 19 0.00 20GAVAAXX100126.1 39 43 Cycle M 39.0000 13 0.00 20GAVAAXX100126.1 39 44 Cycle M 39.0000 15 0.00 20GAVAAXX100126.1 39 45 Cycle M 39.0000 11 0.00 @@ -30573,7 +30570,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 39 97 Cycle M 39.0000 10 0.00 20GAVAAXX100126.1 39 98 Cycle M 39.0000 8 0.00 20GAVAAXX100126.1 39 99 Cycle M 39.0000 3 0.00 -20GAVAAXX100126.1 39 AA Context M 39.0000 211 0.00 +20GAVAAXX100126.1 39 AA Context M 39.0000 210 0.00 20GAVAAXX100126.1 39 AG Context M 39.0000 26 0.00 20GAVAAXX100126.1 39 AT Context M 39.0000 49 0.00 20GAVAAXX100126.1 39 CA Context M 39.0000 413 2.00 @@ -30695,8 +30692,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 41 -76 Cycle M 41.0000 1 0.00 20GAVAAXX100126.1 41 AA Context M 41.0000 6 0.00 20GAVAAXX100126.1 41 CT Context M 41.0000 17 0.00 -20GAVAAXX100126.1 45 -10 Cycle D 45.0000 47 0.41 -20GAVAAXX100126.1 45 -10 Cycle I 45.0000 47 0.00 +20GAVAAXX100126.1 45 -10 Cycle D 45.0000 46 0.13 +20GAVAAXX100126.1 45 -10 Cycle I 45.0000 46 0.00 20GAVAAXX100126.1 45 -11 Cycle D 45.0000 46 0.13 20GAVAAXX100126.1 45 -11 Cycle I 45.0000 46 0.00 20GAVAAXX100126.1 45 -12 Cycle D 45.0000 46 0.13 @@ -30945,8 +30942,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 45 40 Cycle I 45.0000 53 0.00 20GAVAAXX100126.1 45 41 Cycle D 45.0000 53 0.14 20GAVAAXX100126.1 45 41 Cycle I 45.0000 53 0.00 -20GAVAAXX100126.1 45 42 Cycle D 45.0000 53 0.14 -20GAVAAXX100126.1 45 42 Cycle I 45.0000 53 0.00 +20GAVAAXX100126.1 45 42 Cycle D 45.0000 52 0.00 +20GAVAAXX100126.1 45 42 Cycle I 45.0000 52 0.00 20GAVAAXX100126.1 45 43 Cycle D 45.0000 52 0.00 20GAVAAXX100126.1 45 43 Cycle I 45.0000 52 0.00 20GAVAAXX100126.1 45 44 Cycle D 45.0000 52 0.14 @@ -30997,8 +30994,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 45 64 Cycle I 45.0000 52 0.00 20GAVAAXX100126.1 45 65 Cycle D 45.0000 51 0.17 20GAVAAXX100126.1 45 65 Cycle I 45.0000 51 0.00 -20GAVAAXX100126.1 45 66 Cycle D 45.0000 52 0.17 -20GAVAAXX100126.1 45 66 Cycle I 45.0000 52 0.00 +20GAVAAXX100126.1 45 66 Cycle D 45.0000 51 0.00 +20GAVAAXX100126.1 45 66 Cycle I 45.0000 51 0.00 20GAVAAXX100126.1 45 67 Cycle D 45.0000 51 0.00 20GAVAAXX100126.1 45 67 Cycle I 45.0000 51 0.00 20GAVAAXX100126.1 45 68 Cycle D 45.0000 52 0.00 @@ -31159,8 +31156,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 45 AGTA Context I 45.0000 28 0.00 20GAVAAXX100126.1 45 AGTC Context D 45.0000 31 0.00 20GAVAAXX100126.1 45 AGTC Context I 45.0000 31 0.00 -20GAVAAXX100126.1 45 AGTG Context D 45.0000 49 0.72 -20GAVAAXX100126.1 45 AGTG Context I 45.0000 49 0.00 +20GAVAAXX100126.1 45 AGTG Context D 45.0000 48 0.43 +20GAVAAXX100126.1 45 AGTG Context I 45.0000 48 0.00 20GAVAAXX100126.1 45 AGTT Context D 45.0000 39 0.00 20GAVAAXX100126.1 45 AGTT Context I 45.0000 39 0.00 20GAVAAXX100126.1 45 ATAA Context D 45.0000 21 0.00 @@ -31505,8 +31502,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 45 TCTG Context I 45.0000 53 0.00 20GAVAAXX100126.1 45 TCTT Context D 45.0000 46 0.70 20GAVAAXX100126.1 45 TCTT Context I 45.0000 46 0.00 -20GAVAAXX100126.1 45 TGAA Context D 45.0000 70 0.31 -20GAVAAXX100126.1 45 TGAA Context I 45.0000 70 0.00 +20GAVAAXX100126.1 45 TGAA Context D 45.0000 68 0.00 +20GAVAAXX100126.1 45 TGAA Context I 45.0000 68 0.00 20GAVAAXX100126.1 45 TGAC Context D 45.0000 50 0.00 20GAVAAXX100126.1 45 TGAC Context I 45.0000 50 0.00 20GAVAAXX100126.1 45 TGAG Context D 45.0000 69 0.43 @@ -33072,7 +33069,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.2 33 -68 Cycle M 33.0000 4 0.00 20GAVAAXX100126.2 33 -69 Cycle M 33.0000 3 0.00 20GAVAAXX100126.2 33 -7 Cycle M 33.0000 4 0.00 -20GAVAAXX100126.2 33 -70 Cycle M 33.0000 2 0.00 +20GAVAAXX100126.2 33 -70 Cycle M 33.0000 1 0.00 20GAVAAXX100126.2 33 -71 Cycle M 33.0000 9 0.00 20GAVAAXX100126.2 33 -72 Cycle M 33.0000 8 0.00 20GAVAAXX100126.2 33 -73 Cycle M 33.0000 4 0.00 @@ -33162,7 +33159,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.2 33 97 Cycle M 33.0000 1 0.00 20GAVAAXX100126.2 33 98 Cycle M 33.0000 4 0.00 20GAVAAXX100126.2 33 99 Cycle M 33.0000 2 0.00 -20GAVAAXX100126.2 33 AA Context M 33.0000 19 0.00 +20GAVAAXX100126.2 33 AA Context M 33.0000 18 0.00 20GAVAAXX100126.2 33 AC Context M 33.0000 25 0.00 20GAVAAXX100126.2 33 AG Context M 33.0000 32 0.00 20GAVAAXX100126.2 33 AT Context M 33.0000 16 0.00 @@ -34374,8 +34371,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.2 45 -69 Cycle I 45.0000 36 0.00 20GAVAAXX100126.2 45 -7 Cycle D 45.0000 41 0.00 20GAVAAXX100126.2 45 -7 Cycle I 45.0000 41 0.00 -20GAVAAXX100126.2 45 -70 Cycle D 45.0000 37 0.14 -20GAVAAXX100126.2 45 -70 Cycle I 45.0000 37 0.00 +20GAVAAXX100126.2 45 -70 Cycle D 45.0000 36 0.00 +20GAVAAXX100126.2 45 -70 Cycle I 45.0000 36 0.00 20GAVAAXX100126.2 45 -71 Cycle D 45.0000 35 0.00 20GAVAAXX100126.2 45 -71 Cycle I 45.0000 35 0.00 20GAVAAXX100126.2 45 -72 Cycle D 45.0000 36 0.14 @@ -34922,8 +34919,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.2 45 GCTG Context I 45.0000 29 0.00 20GAVAAXX100126.2 45 GCTT Context D 45.0000 44 0.00 20GAVAAXX100126.2 45 GCTT Context I 45.0000 44 0.00 -20GAVAAXX100126.2 45 GGAA Context D 45.0000 28 0.14 -20GAVAAXX100126.2 45 GGAA Context I 45.0000 28 0.00 +20GAVAAXX100126.2 45 GGAA Context D 45.0000 27 0.00 +20GAVAAXX100126.2 45 GGAA Context I 45.0000 27 0.00 20GAVAAXX100126.2 45 GGAC Context D 45.0000 31 0.00 20GAVAAXX100126.2 45 GGAC Context I 45.0000 31 0.00 20GAVAAXX100126.2 45 GGAG Context D 45.0000 66 0.00 @@ -40596,7 +40593,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.4 38 10 Cycle M 38.0000 10 0.00 20GAVAAXX100126.4 38 100 Cycle M 38.0000 4 0.00 20GAVAAXX100126.4 38 101 Cycle M 38.0000 5 0.00 -20GAVAAXX100126.4 38 11 Cycle M 38.0000 9 0.00 +20GAVAAXX100126.4 38 11 Cycle M 38.0000 8 0.00 20GAVAAXX100126.4 38 12 Cycle M 38.0000 8 0.00 20GAVAAXX100126.4 38 13 Cycle M 38.0000 9 0.00 20GAVAAXX100126.4 38 14 Cycle M 38.0000 11 0.00 @@ -40703,7 +40700,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.4 38 TA Context M 38.0000 97 0.00 20GAVAAXX100126.4 38 TC Context M 38.0000 29 0.00 20GAVAAXX100126.4 38 TG Context M 38.0000 196 3.00 -20GAVAAXX100126.4 38 TT Context M 38.0000 99 0.00 +20GAVAAXX100126.4 38 TT Context M 38.0000 98 0.00 20GAVAAXX100126.4 39 -13 Cycle M 39.0000 4 0.00 20GAVAAXX100126.4 39 -14 Cycle M 39.0000 3 0.00 20GAVAAXX100126.4 39 -15 Cycle M 39.0000 2 0.00 @@ -41063,8 +41060,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.4 45 -97 Cycle I 45.0000 25 0.00 20GAVAAXX100126.4 45 10 Cycle D 45.0000 33 0.00 20GAVAAXX100126.4 45 10 Cycle I 45.0000 33 0.00 -20GAVAAXX100126.4 45 11 Cycle D 45.0000 34 0.14 -20GAVAAXX100126.4 45 11 Cycle I 45.0000 34 0.00 +20GAVAAXX100126.4 45 11 Cycle D 45.0000 33 0.00 +20GAVAAXX100126.4 45 11 Cycle I 45.0000 33 0.00 20GAVAAXX100126.4 45 12 Cycle D 45.0000 34 0.14 20GAVAAXX100126.4 45 12 Cycle I 45.0000 34 0.00 20GAVAAXX100126.4 45 13 Cycle D 45.0000 34 0.14 @@ -41683,8 +41680,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.4 45 TCTC Context I 45.0000 28 0.00 20GAVAAXX100126.4 45 TCTG Context D 45.0000 37 0.00 20GAVAAXX100126.4 45 TCTG Context I 45.0000 37 0.00 -20GAVAAXX100126.4 45 TCTT Context D 45.0000 35 0.45 -20GAVAAXX100126.4 45 TCTT Context I 45.0000 35 0.00 +20GAVAAXX100126.4 45 TCTT Context D 45.0000 34 0.31 +20GAVAAXX100126.4 45 TCTT Context I 45.0000 34 0.00 20GAVAAXX100126.4 45 TGAA Context D 45.0000 59 0.00 20GAVAAXX100126.4 45 TGAA Context I 45.0000 59 0.00 20GAVAAXX100126.4 45 TGAC Context D 45.0000 28 0.00 @@ -43695,7 +43692,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.5 38 20 Cycle M 38.0000 11 0.00 20GAVAAXX100126.5 38 21 Cycle M 38.0000 17 1.00 20GAVAAXX100126.5 38 22 Cycle M 38.0000 13 0.00 -20GAVAAXX100126.5 38 23 Cycle M 38.0000 11 0.00 +20GAVAAXX100126.5 38 23 Cycle M 38.0000 10 0.00 20GAVAAXX100126.5 38 24 Cycle M 38.0000 10 0.00 20GAVAAXX100126.5 38 25 Cycle M 38.0000 12 0.00 20GAVAAXX100126.5 38 26 Cycle M 38.0000 15 0.00 @@ -43791,7 +43788,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.5 38 TA Context M 38.0000 89 0.00 20GAVAAXX100126.5 38 TC Context M 38.0000 51 0.00 20GAVAAXX100126.5 38 TG Context M 38.0000 268 1.00 -20GAVAAXX100126.5 38 TT Context M 38.0000 169 0.00 +20GAVAAXX100126.5 38 TT Context M 38.0000 168 0.00 20GAVAAXX100126.5 39 -11 Cycle M 39.0000 1 0.00 20GAVAAXX100126.5 39 -12 Cycle M 39.0000 3 0.00 20GAVAAXX100126.5 39 -14 Cycle M 39.0000 1 0.00 @@ -44217,8 +44214,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.5 45 21 Cycle I 45.0000 33 0.00 20GAVAAXX100126.5 45 22 Cycle D 45.0000 32 0.00 20GAVAAXX100126.5 45 22 Cycle I 45.0000 32 0.00 -20GAVAAXX100126.5 45 23 Cycle D 45.0000 33 0.14 -20GAVAAXX100126.5 45 23 Cycle I 45.0000 33 0.00 +20GAVAAXX100126.5 45 23 Cycle D 45.0000 32 0.00 +20GAVAAXX100126.5 45 23 Cycle I 45.0000 32 0.00 20GAVAAXX100126.5 45 24 Cycle D 45.0000 33 0.14 20GAVAAXX100126.5 45 24 Cycle I 45.0000 33 0.00 20GAVAAXX100126.5 45 25 Cycle D 45.0000 32 0.14 @@ -44807,8 +44804,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.5 45 TCTC Context I 45.0000 16 0.00 20GAVAAXX100126.5 45 TCTG Context D 45.0000 38 0.00 20GAVAAXX100126.5 45 TCTG Context I 45.0000 38 0.00 -20GAVAAXX100126.5 45 TCTT Context D 45.0000 21 0.14 -20GAVAAXX100126.5 45 TCTT Context I 45.0000 21 0.00 +20GAVAAXX100126.5 45 TCTT Context D 45.0000 20 0.00 +20GAVAAXX100126.5 45 TCTT Context I 45.0000 20 0.00 20GAVAAXX100126.5 45 TGAA Context D 45.0000 71 0.00 20GAVAAXX100126.5 45 TGAA Context I 45.0000 71 0.00 20GAVAAXX100126.5 45 TGAC Context D 45.0000 17 0.00 @@ -45876,7 +45873,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.6 31 -46 Cycle M 31.0000 2 0.00 20GAVAAXX100126.6 31 -47 Cycle M 31.0000 2 0.00 20GAVAAXX100126.6 31 -48 Cycle M 31.0000 3 0.00 -20GAVAAXX100126.6 31 -5 Cycle M 31.0000 6 0.00 +20GAVAAXX100126.6 31 -5 Cycle M 31.0000 5 0.00 20GAVAAXX100126.6 31 -50 Cycle M 31.0000 4 0.00 20GAVAAXX100126.6 31 -51 Cycle M 31.0000 1 0.00 20GAVAAXX100126.6 31 -52 Cycle M 31.0000 1 0.00 @@ -45952,7 +45949,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.6 31 94 Cycle M 31.0000 1 0.00 20GAVAAXX100126.6 31 97 Cycle M 31.0000 2 0.00 20GAVAAXX100126.6 31 99 Cycle M 31.0000 1 0.00 -20GAVAAXX100126.6 31 AA Context M 31.0000 14 0.00 +20GAVAAXX100126.6 31 AA Context M 31.0000 13 0.00 20GAVAAXX100126.6 31 AC Context M 31.0000 17 0.00 20GAVAAXX100126.6 31 AG Context M 31.0000 16 0.00 20GAVAAXX100126.6 31 AT Context M 31.0000 6 0.00 @@ -47054,7 +47051,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.6 38 40 Cycle M 38.0000 13 0.00 20GAVAAXX100126.6 38 41 Cycle M 38.0000 9 0.00 20GAVAAXX100126.6 38 42 Cycle M 38.0000 13 0.00 -20GAVAAXX100126.6 38 43 Cycle M 38.0000 17 0.00 +20GAVAAXX100126.6 38 43 Cycle M 38.0000 16 0.00 20GAVAAXX100126.6 38 44 Cycle M 38.0000 14 0.00 20GAVAAXX100126.6 38 45 Cycle M 38.0000 14 0.00 20GAVAAXX100126.6 38 46 Cycle M 38.0000 10 0.00 @@ -47130,7 +47127,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.6 38 TA Context M 38.0000 105 0.00 20GAVAAXX100126.6 38 TC Context M 38.0000 12 0.00 20GAVAAXX100126.6 38 TG Context M 38.0000 263 2.00 -20GAVAAXX100126.6 38 TT Context M 38.0000 214 0.00 +20GAVAAXX100126.6 38 TT Context M 38.0000 213 0.00 20GAVAAXX100126.6 39 -12 Cycle M 39.0000 2 0.00 20GAVAAXX100126.6 39 -13 Cycle M 39.0000 1 0.00 20GAVAAXX100126.6 39 -14 Cycle M 39.0000 3 0.00 @@ -47378,8 +47375,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.6 45 -48 Cycle I 45.0000 39 0.00 20GAVAAXX100126.6 45 -49 Cycle D 45.0000 38 0.00 20GAVAAXX100126.6 45 -49 Cycle I 45.0000 38 0.00 -20GAVAAXX100126.6 45 -5 Cycle D 45.0000 40 0.17 -20GAVAAXX100126.6 45 -5 Cycle I 45.0000 40 0.00 +20GAVAAXX100126.6 45 -5 Cycle D 45.0000 39 0.00 +20GAVAAXX100126.6 45 -5 Cycle I 45.0000 39 0.00 20GAVAAXX100126.6 45 -50 Cycle D 45.0000 38 0.00 20GAVAAXX100126.6 45 -50 Cycle I 45.0000 38 0.00 20GAVAAXX100126.6 45 -51 Cycle D 45.0000 38 0.00 @@ -47550,8 +47547,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.6 45 41 Cycle I 45.0000 41 0.00 20GAVAAXX100126.6 45 42 Cycle D 45.0000 40 0.14 20GAVAAXX100126.6 45 42 Cycle I 45.0000 40 0.00 -20GAVAAXX100126.6 45 43 Cycle D 45.0000 41 0.29 -20GAVAAXX100126.6 45 43 Cycle I 45.0000 41 0.00 +20GAVAAXX100126.6 45 43 Cycle D 45.0000 40 0.14 +20GAVAAXX100126.6 45 43 Cycle I 45.0000 40 0.00 20GAVAAXX100126.6 45 44 Cycle D 45.0000 41 0.29 20GAVAAXX100126.6 45 44 Cycle I 45.0000 41 0.00 20GAVAAXX100126.6 45 45 Cycle D 45.0000 41 0.29 @@ -48102,10 +48099,10 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.6 45 TCTC Context I 45.0000 45 0.00 20GAVAAXX100126.6 45 TCTG Context D 45.0000 58 0.00 20GAVAAXX100126.6 45 TCTG Context I 45.0000 58 0.00 -20GAVAAXX100126.6 45 TCTT Context D 45.0000 39 0.43 -20GAVAAXX100126.6 45 TCTT Context I 45.0000 39 0.00 -20GAVAAXX100126.6 45 TGAA Context D 45.0000 78 0.17 -20GAVAAXX100126.6 45 TGAA Context I 45.0000 78 0.00 +20GAVAAXX100126.6 45 TCTT Context D 45.0000 38 0.29 +20GAVAAXX100126.6 45 TCTT Context I 45.0000 38 0.00 +20GAVAAXX100126.6 45 TGAA Context D 45.0000 77 0.00 +20GAVAAXX100126.6 45 TGAA Context I 45.0000 77 0.00 20GAVAAXX100126.6 45 TGAC Context D 45.0000 36 0.00 20GAVAAXX100126.6 45 TGAC Context I 45.0000 36 0.00 20GAVAAXX100126.6 45 TGAG Context D 45.0000 55 0.00 @@ -49792,7 +49789,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.7 33 -32 Cycle M 33.0000 1 0.00 20GAVAAXX100126.7 33 -33 Cycle M 33.0000 3 0.00 20GAVAAXX100126.7 33 -34 Cycle M 33.0000 3 0.00 -20GAVAAXX100126.7 33 -35 Cycle M 33.0000 3 0.00 +20GAVAAXX100126.7 33 -35 Cycle M 33.0000 2 0.00 20GAVAAXX100126.7 33 -37 Cycle M 33.0000 4 0.00 20GAVAAXX100126.7 33 -38 Cycle M 33.0000 1 0.00 20GAVAAXX100126.7 33 -39 Cycle M 33.0000 5 0.00 @@ -49905,7 +49902,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.7 33 96 Cycle M 33.0000 1 0.00 20GAVAAXX100126.7 33 98 Cycle M 33.0000 3 0.00 20GAVAAXX100126.7 33 99 Cycle M 33.0000 2 0.00 -20GAVAAXX100126.7 33 AA Context M 33.0000 15 0.00 +20GAVAAXX100126.7 33 AA Context M 33.0000 14 0.00 20GAVAAXX100126.7 33 AC Context M 33.0000 16 0.00 20GAVAAXX100126.7 33 AG Context M 33.0000 31 0.25 20GAVAAXX100126.7 33 AT Context M 33.0000 18 0.00 @@ -51025,8 +51022,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.7 45 -33 Cycle I 45.0000 39 0.00 20GAVAAXX100126.7 45 -34 Cycle D 45.0000 39 0.13 20GAVAAXX100126.7 45 -34 Cycle I 45.0000 39 0.00 -20GAVAAXX100126.7 45 -35 Cycle D 45.0000 39 0.13 -20GAVAAXX100126.7 45 -35 Cycle I 45.0000 39 0.00 +20GAVAAXX100126.7 45 -35 Cycle D 45.0000 38 0.00 +20GAVAAXX100126.7 45 -35 Cycle I 45.0000 38 0.00 20GAVAAXX100126.7 45 -36 Cycle D 45.0000 38 0.00 20GAVAAXX100126.7 45 -36 Cycle I 45.0000 38 0.00 20GAVAAXX100126.7 45 -37 Cycle D 45.0000 39 0.13 @@ -51783,8 +51780,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.7 45 TCTG Context I 45.0000 42 0.00 20GAVAAXX100126.7 45 TCTT Context D 45.0000 32 0.14 20GAVAAXX100126.7 45 TCTT Context I 45.0000 32 0.00 -20GAVAAXX100126.7 45 TGAA Context D 45.0000 64 0.25 -20GAVAAXX100126.7 45 TGAA Context I 45.0000 64 0.00 +20GAVAAXX100126.7 45 TGAA Context D 45.0000 63 0.13 +20GAVAAXX100126.7 45 TGAA Context I 45.0000 63 0.00 20GAVAAXX100126.7 45 TGAC Context D 45.0000 40 0.00 20GAVAAXX100126.7 45 TGAC Context I 45.0000 40 0.00 20GAVAAXX100126.7 45 TGAG Context D 45.0000 63 0.25 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.low_quality_tail_5.recal.txt b/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.low_quality_tail_5.recal.txt index d7e7ca49ab4..ce27be0d89d 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.low_quality_tail_5.recal.txt +++ b/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.low_quality_tail_5.recal.txt @@ -48,27 +48,27 @@ QualityScore Count QuantizedScore 22 750 24 23 853 24 24 997 24 - 25 1228 24 + 25 1227 24 26 1491 27 - 27 1728 27 + 27 1727 27 28 1781 29 29 2284 29 30 2439 30 - 31 2537 30 + 31 2536 30 32 3565 32 - 33 4141 32 + 33 4139 32 34 5194 34 - 35 7518 35 - 36 11939 36 - 37 28884 37 - 38 27993 38 - 39 15115 39 + 35 7517 35 + 36 11937 36 + 37 28883 37 + 38 27987 38 + 39 15108 39 40 778 39 41 53 39 42 0 39 43 0 39 - 44 15761 44 - 45 234039 45 + 44 9294 44 + 45 240462 45 46 0 93 47 0 93 48 0 93 @@ -121,51 +121,51 @@ QualityScore Count QuantizedScore #:GATKTable:6:48:%s:%s:%.4f:%.4f:%d:%.2f:; #:GATKTable:RecalTable0: ReadGroup EventType EmpiricalQuality EstimatedQReported Observations Errors -20FUKAAXX100202.1 D 45.0000 45.0000 7293 3.86 -20FUKAAXX100202.1 I 45.0000 45.0000 7293 0.00 -20FUKAAXX100202.1 M 27.0000 27.0392 7293 15.67 -20FUKAAXX100202.2 D 44.0000 45.0000 6464 7.56 -20FUKAAXX100202.2 I 45.0000 45.0000 6464 0.00 -20FUKAAXX100202.2 M 29.0000 30.1871 6464 20.60 -20FUKAAXX100202.3 D 45.0000 45.0000 8976 5.73 -20FUKAAXX100202.3 I 45.0000 45.0000 8976 0.00 -20FUKAAXX100202.3 M 27.0000 28.2043 8976 29.75 -20FUKAAXX100202.4 D 45.0000 45.0000 6830 3.75 -20FUKAAXX100202.4 I 45.0000 45.0000 6830 0.00 -20FUKAAXX100202.4 M 29.0000 29.0885 6830 13.00 -20FUKAAXX100202.5 D 45.0000 45.0000 7471 2.86 -20FUKAAXX100202.5 I 45.0000 45.0000 7471 0.00 -20FUKAAXX100202.5 M 28.0000 29.7339 7471 26.67 -20FUKAAXX100202.6 D 45.0000 45.0000 10026 8.40 -20FUKAAXX100202.6 I 45.0000 45.0000 10026 0.00 -20FUKAAXX100202.6 M 27.0000 28.7545 10026 27.25 -20FUKAAXX100202.7 D 45.0000 45.0000 9347 2.78 -20FUKAAXX100202.7 I 45.0000 45.0000 9347 0.00 -20FUKAAXX100202.7 M 26.0000 27.7419 9347 30.67 +20FUKAAXX100202.1 D 45.0000 45.0000 7292 3.71 +20FUKAAXX100202.1 I 45.0000 45.0000 7292 0.00 +20FUKAAXX100202.1 M 27.0000 27.0386 7292 15.67 +20FUKAAXX100202.2 D 45.0000 45.0000 6462 7.33 +20FUKAAXX100202.2 I 45.0000 45.0000 6462 0.00 +20FUKAAXX100202.2 M 29.0000 30.1859 6462 20.60 +20FUKAAXX100202.3 D 45.0000 45.0000 8974 5.46 +20FUKAAXX100202.3 I 45.0000 45.0000 8974 0.00 +20FUKAAXX100202.3 M 27.0000 28.2034 8974 29.75 +20FUKAAXX100202.4 D 45.0000 45.0000 6828 3.50 +20FUKAAXX100202.4 I 45.0000 45.0000 6828 0.00 +20FUKAAXX100202.4 M 29.0000 29.0874 6828 13.00 +20FUKAAXX100202.5 D 45.0000 45.0000 7470 2.71 +20FUKAAXX100202.5 I 45.0000 45.0000 7470 0.00 +20FUKAAXX100202.5 M 28.0000 29.7334 7470 26.67 +20FUKAAXX100202.6 D 45.0000 45.0000 10023 7.95 +20FUKAAXX100202.6 I 45.0000 45.0000 10023 0.00 +20FUKAAXX100202.6 M 27.0000 28.7535 10023 27.25 +20FUKAAXX100202.7 D 45.0000 45.0000 9345 2.57 +20FUKAAXX100202.7 I 45.0000 45.0000 9345 0.00 +20FUKAAXX100202.7 M 26.0000 27.7411 9345 30.67 20FUKAAXX100202.8 D 45.0000 45.0000 8152 3.75 20FUKAAXX100202.8 I 45.0000 45.0000 8152 0.00 20FUKAAXX100202.8 M 28.0000 29.0288 8152 24.00 -20GAVAAXX100126.1 D 44.0000 45.0000 9297 9.12 -20GAVAAXX100126.1 I 45.0000 45.0000 9297 1.00 -20GAVAAXX100126.1 M 26.0000 27.6243 9297 29.75 -20GAVAAXX100126.2 D 45.0000 45.0000 8155 4.86 -20GAVAAXX100126.2 I 45.0000 45.0000 8155 0.00 -20GAVAAXX100126.2 M 26.0000 27.3758 8155 34.42 +20GAVAAXX100126.1 D 44.0000 45.0000 9294 8.52 +20GAVAAXX100126.1 I 45.0000 45.0000 9294 1.00 +20GAVAAXX100126.1 M 26.0000 27.6244 9294 29.75 +20GAVAAXX100126.2 D 45.0000 45.0000 8154 4.71 +20GAVAAXX100126.2 I 45.0000 45.0000 8154 0.00 +20GAVAAXX100126.2 M 26.0000 27.3754 8154 34.42 20GAVAAXX100126.3 D 45.0000 45.0000 6239 3.00 20GAVAAXX100126.3 I 45.0000 45.0000 6239 0.00 20GAVAAXX100126.3 M 26.0000 26.8893 6239 20.57 -20GAVAAXX100126.4 D 45.0000 45.0000 6633 2.86 -20GAVAAXX100126.4 I 45.0000 45.0000 6633 0.00 -20GAVAAXX100126.4 M 26.0000 27.0432 6633 29.33 -20GAVAAXX100126.5 D 45.0000 45.0000 5884 0.86 -20GAVAAXX100126.5 I 45.0000 45.0000 5884 0.00 -20GAVAAXX100126.5 M 27.0000 28.0717 5884 21.33 -20GAVAAXX100126.6 D 45.0000 45.0000 8002 3.69 -20GAVAAXX100126.6 I 45.0000 45.0000 8002 0.00 -20GAVAAXX100126.6 M 27.0000 28.4682 8002 27.00 -20GAVAAXX100126.7 D 45.0000 45.0000 7598 2.88 -20GAVAAXX100126.7 I 45.0000 45.0000 7598 0.00 -20GAVAAXX100126.7 M 25.0000 25.6878 7598 27.75 +20GAVAAXX100126.4 D 45.0000 45.0000 6632 2.71 +20GAVAAXX100126.4 I 45.0000 45.0000 6632 0.00 +20GAVAAXX100126.4 M 26.0000 27.0426 6632 29.33 +20GAVAAXX100126.5 D 45.0000 45.0000 5883 0.71 +20GAVAAXX100126.5 I 45.0000 45.0000 5883 0.00 +20GAVAAXX100126.5 M 27.0000 28.0710 5883 21.33 +20GAVAAXX100126.6 D 45.0000 45.0000 8000 3.38 +20GAVAAXX100126.6 I 45.0000 45.0000 8000 0.00 +20GAVAAXX100126.6 M 27.0000 28.4675 8000 27.00 +20GAVAAXX100126.7 D 45.0000 45.0000 7597 2.75 +20GAVAAXX100126.7 I 45.0000 45.0000 7597 0.00 +20GAVAAXX100126.7 M 25.0000 25.6874 7597 27.75 20GAVAAXX100126.8 D 45.0000 45.0000 8533 5.69 20GAVAAXX100126.8 I 45.0000 45.0000 8533 1.00 20GAVAAXX100126.8 M 26.0000 27.3594 8533 29.25 @@ -204,12 +204,12 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20FUKAAXX100202.1 34 M 34.0000 217 0.20 20FUKAAXX100202.1 35 M 35.0000 347 1.07 20FUKAAXX100202.1 36 M 36.0000 599 1.00 -20FUKAAXX100202.1 37 M 37.0000 1407 1.33 +20FUKAAXX100202.1 37 M 37.0000 1406 1.33 20FUKAAXX100202.1 38 M 38.0000 2058 0.33 20FUKAAXX100202.1 39 M 39.0000 741 0.00 20FUKAAXX100202.1 40 M 40.0000 16 0.00 -20FUKAAXX100202.1 45 D 45.0000 7293 3.86 -20FUKAAXX100202.1 45 I 45.0000 7293 0.00 +20FUKAAXX100202.1 45 D 45.0000 7292 3.71 +20FUKAAXX100202.1 45 I 45.0000 7292 0.00 20FUKAAXX100202.2 6 M 6.0000 1 0.00 20FUKAAXX100202.2 7 M 7.0000 1 0.00 20FUKAAXX100202.2 8 M 8.0000 3 0.00 @@ -243,10 +243,10 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20FUKAAXX100202.2 36 M 36.0000 580 4.00 20FUKAAXX100202.2 37 M 37.0000 1371 2.00 20FUKAAXX100202.2 38 M 38.0000 2181 6.00 -20FUKAAXX100202.2 39 M 39.0000 667 1.00 +20FUKAAXX100202.2 39 M 39.0000 665 1.00 20FUKAAXX100202.2 40 M 40.0000 27 0.00 -20FUKAAXX100202.2 45 D 44.0000 6464 7.56 -20FUKAAXX100202.2 45 I 45.0000 6464 0.00 +20FUKAAXX100202.2 45 D 45.0000 6462 7.33 +20FUKAAXX100202.2 45 I 45.0000 6462 0.00 20FUKAAXX100202.3 6 M 6.0000 1 1.00 20FUKAAXX100202.3 7 M 7.0000 4 0.00 20FUKAAXX100202.3 8 M 8.0000 8 0.00 @@ -277,13 +277,13 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20FUKAAXX100202.3 33 M 33.0000 245 0.00 20FUKAAXX100202.3 34 M 34.0000 262 0.00 20FUKAAXX100202.3 35 M 35.0000 463 1.00 -20FUKAAXX100202.3 36 M 36.0000 944 6.25 +20FUKAAXX100202.3 36 M 36.0000 943 6.25 20FUKAAXX100202.3 37 M 37.0000 1649 4.25 20FUKAAXX100202.3 38 M 37.0000 2837 11.25 -20FUKAAXX100202.3 39 M 39.0000 976 0.00 +20FUKAAXX100202.3 39 M 39.0000 975 0.00 20FUKAAXX100202.3 40 M 40.0000 28 0.00 -20FUKAAXX100202.3 45 D 45.0000 8976 5.73 -20FUKAAXX100202.3 45 I 45.0000 8976 0.00 +20FUKAAXX100202.3 45 D 45.0000 8974 5.46 +20FUKAAXX100202.3 45 I 45.0000 8974 0.00 20FUKAAXX100202.4 6 M 6.0000 1 0.00 20FUKAAXX100202.4 7 M 7.0000 2 1.00 20FUKAAXX100202.4 8 M 8.0000 3 1.00 @@ -317,10 +317,10 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20FUKAAXX100202.4 36 M 36.0000 633 0.00 20FUKAAXX100202.4 37 M 37.0000 1408 3.25 20FUKAAXX100202.4 38 M 38.0000 2074 3.50 -20FUKAAXX100202.4 39 M 39.0000 662 1.00 +20FUKAAXX100202.4 39 M 39.0000 660 1.00 20FUKAAXX100202.4 40 M 40.0000 20 0.00 -20FUKAAXX100202.4 45 D 45.0000 6830 3.75 -20FUKAAXX100202.4 45 I 45.0000 6830 0.00 +20FUKAAXX100202.4 45 D 45.0000 6828 3.50 +20FUKAAXX100202.4 45 I 45.0000 6828 0.00 20FUKAAXX100202.5 6 M 6.0000 1 0.00 20FUKAAXX100202.5 7 M 7.0000 3 0.00 20FUKAAXX100202.5 8 M 8.0000 2 1.00 @@ -354,10 +354,10 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20FUKAAXX100202.5 36 M 36.0000 695 2.33 20FUKAAXX100202.5 37 M 37.0000 1329 2.00 20FUKAAXX100202.5 38 M 37.0000 2579 9.80 -20FUKAAXX100202.5 39 M 39.0000 907 1.00 +20FUKAAXX100202.5 39 M 39.0000 906 1.00 20FUKAAXX100202.5 40 M 40.0000 67 0.20 -20FUKAAXX100202.5 45 D 45.0000 7471 2.86 -20FUKAAXX100202.5 45 I 45.0000 7471 0.00 +20FUKAAXX100202.5 45 D 45.0000 7470 2.71 +20FUKAAXX100202.5 45 I 45.0000 7470 0.00 20FUKAAXX100202.6 6 M 6.0000 7 4.00 20FUKAAXX100202.6 7 M 7.0000 4 2.00 20FUKAAXX100202.6 8 M 8.0000 5 0.00 @@ -387,14 +387,14 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20FUKAAXX100202.6 32 M 32.0000 226 1.00 20FUKAAXX100202.6 33 M 33.0000 231 2.00 20FUKAAXX100202.6 34 M 34.0000 302 0.00 -20FUKAAXX100202.6 35 M 35.0000 579 2.17 +20FUKAAXX100202.6 35 M 35.0000 578 2.17 20FUKAAXX100202.6 36 M 36.0000 975 2.33 20FUKAAXX100202.6 37 M 37.0000 1959 1.17 -20FUKAAXX100202.6 38 M 38.0000 3301 6.00 +20FUKAAXX100202.6 38 M 38.0000 3299 6.00 20FUKAAXX100202.6 39 M 39.0000 1111 1.00 20FUKAAXX100202.6 40 M 40.0000 43 0.00 -20FUKAAXX100202.6 45 D 45.0000 10026 8.40 -20FUKAAXX100202.6 45 I 45.0000 10026 0.00 +20FUKAAXX100202.6 45 D 45.0000 10023 7.95 +20FUKAAXX100202.6 45 I 45.0000 10023 0.00 20FUKAAXX100202.7 6 M 6.0000 5 2.00 20FUKAAXX100202.7 7 M 7.0000 5 1.00 20FUKAAXX100202.7 8 M 8.0000 9 3.33 @@ -425,13 +425,13 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20FUKAAXX100202.7 33 M 33.0000 197 0.00 20FUKAAXX100202.7 34 M 34.0000 251 0.00 20FUKAAXX100202.7 35 M 35.0000 441 1.92 -20FUKAAXX100202.7 36 M 36.0000 955 3.33 +20FUKAAXX100202.7 36 M 36.0000 954 3.33 20FUKAAXX100202.7 37 M 37.0000 1600 2.67 -20FUKAAXX100202.7 38 M 38.0000 3286 3.92 +20FUKAAXX100202.7 38 M 38.0000 3285 3.92 20FUKAAXX100202.7 39 M 39.0000 1063 1.25 20FUKAAXX100202.7 40 M 40.0000 43 0.00 -20FUKAAXX100202.7 45 D 45.0000 9347 2.78 -20FUKAAXX100202.7 45 I 45.0000 9347 0.00 +20FUKAAXX100202.7 45 D 45.0000 9345 2.57 +20FUKAAXX100202.7 45 I 45.0000 9345 0.00 20FUKAAXX100202.8 6 M 6.0000 4 2.00 20FUKAAXX100202.8 7 M 7.0000 5 0.00 20FUKAAXX100202.8 8 M 8.0000 1 0.00 @@ -488,9 +488,9 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.1 22 M 22.0000 43 1.00 20GAVAAXX100126.1 23 M 23.0000 65 0.13 20GAVAAXX100126.1 24 M 24.0000 56 0.00 -20GAVAAXX100126.1 25 M 25.0000 85 0.00 +20GAVAAXX100126.1 25 M 25.0000 84 0.00 20GAVAAXX100126.1 26 M 26.0000 104 0.00 -20GAVAAXX100126.1 27 M 27.0000 114 0.00 +20GAVAAXX100126.1 27 M 27.0000 113 0.00 20GAVAAXX100126.1 28 M 28.0000 149 0.00 20GAVAAXX100126.1 29 M 29.0000 185 1.33 20GAVAAXX100126.1 30 M 30.0000 179 0.00 @@ -502,11 +502,11 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.1 36 M 36.0000 822 2.25 20GAVAAXX100126.1 37 M 37.0000 1759 7.00 20GAVAAXX100126.1 38 M 38.0000 1880 3.25 -20GAVAAXX100126.1 39 M 39.0000 1546 2.00 +20GAVAAXX100126.1 39 M 39.0000 1545 2.00 20GAVAAXX100126.1 40 M 40.0000 243 0.00 20GAVAAXX100126.1 41 M 41.0000 23 0.00 -20GAVAAXX100126.1 45 D 44.0000 9297 9.12 -20GAVAAXX100126.1 45 I 45.0000 9297 1.00 +20GAVAAXX100126.1 45 D 44.0000 9294 8.52 +20GAVAAXX100126.1 45 I 45.0000 9294 1.00 20GAVAAXX100126.2 6 M 6.0000 10 4.00 20GAVAAXX100126.2 7 M 7.0000 8 1.00 20GAVAAXX100126.2 8 M 8.0000 6 0.00 @@ -534,7 +534,7 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.2 30 M 30.0000 169 0.00 20GAVAAXX100126.2 31 M 31.0000 222 1.25 20GAVAAXX100126.2 32 M 32.0000 336 0.00 -20GAVAAXX100126.2 33 M 33.0000 392 6.00 +20GAVAAXX100126.2 33 M 33.0000 391 6.00 20GAVAAXX100126.2 34 M 34.0000 471 0.00 20GAVAAXX100126.2 35 M 35.0000 540 2.00 20GAVAAXX100126.2 36 M 36.0000 685 1.67 @@ -543,8 +543,8 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.2 39 M 39.0000 1127 2.00 20GAVAAXX100126.2 40 M 40.0000 49 0.00 20GAVAAXX100126.2 41 M 41.0000 9 0.00 -20GAVAAXX100126.2 45 D 45.0000 8155 4.86 -20GAVAAXX100126.2 45 I 45.0000 8155 0.00 +20GAVAAXX100126.2 45 D 45.0000 8154 4.71 +20GAVAAXX100126.2 45 I 45.0000 8154 0.00 20GAVAAXX100126.3 6 M 6.0000 2 0.00 20GAVAAXX100126.3 7 M 7.0000 8 2.00 20GAVAAXX100126.3 8 M 8.0000 8 2.00 @@ -615,12 +615,12 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.4 35 M 35.0000 487 2.00 20GAVAAXX100126.4 36 M 36.0000 639 1.25 20GAVAAXX100126.4 37 M 37.0000 1224 5.50 -20GAVAAXX100126.4 38 M 38.0000 1250 4.67 +20GAVAAXX100126.4 38 M 38.0000 1249 4.67 20GAVAAXX100126.4 39 M 39.0000 857 2.00 20GAVAAXX100126.4 40 M 40.0000 33 0.00 20GAVAAXX100126.4 41 M 41.0000 1 0.00 -20GAVAAXX100126.4 45 D 45.0000 6633 2.86 -20GAVAAXX100126.4 45 I 45.0000 6633 0.00 +20GAVAAXX100126.4 45 D 45.0000 6632 2.71 +20GAVAAXX100126.4 45 I 45.0000 6632 0.00 20GAVAAXX100126.5 6 M 6.0000 4 0.00 20GAVAAXX100126.5 7 M 7.0000 8 3.00 20GAVAAXX100126.5 8 M 8.0000 4 1.00 @@ -653,12 +653,12 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.5 35 M 35.0000 328 1.00 20GAVAAXX100126.5 36 M 36.0000 583 0.33 20GAVAAXX100126.5 37 M 37.0000 1187 2.00 -20GAVAAXX100126.5 38 M 38.0000 1446 2.00 +20GAVAAXX100126.5 38 M 38.0000 1445 2.00 20GAVAAXX100126.5 39 M 39.0000 909 2.00 20GAVAAXX100126.5 40 M 40.0000 43 0.00 20GAVAAXX100126.5 41 M 41.0000 5 0.00 -20GAVAAXX100126.5 45 D 45.0000 5884 0.86 -20GAVAAXX100126.5 45 I 45.0000 5884 0.00 +20GAVAAXX100126.5 45 D 45.0000 5883 0.71 +20GAVAAXX100126.5 45 I 45.0000 5883 0.00 20GAVAAXX100126.6 6 M 6.0000 4 2.00 20GAVAAXX100126.6 7 M 7.0000 6 0.00 20GAVAAXX100126.6 8 M 8.0000 9 3.00 @@ -684,18 +684,18 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.6 28 M 28.0000 105 0.00 20GAVAAXX100126.6 29 M 29.0000 158 1.00 20GAVAAXX100126.6 30 M 30.0000 144 0.00 -20GAVAAXX100126.6 31 M 31.0000 194 1.00 +20GAVAAXX100126.6 31 M 31.0000 193 1.00 20GAVAAXX100126.6 32 M 32.0000 239 0.00 20GAVAAXX100126.6 33 M 33.0000 358 0.00 20GAVAAXX100126.6 34 M 34.0000 481 1.00 20GAVAAXX100126.6 35 M 35.0000 578 2.00 20GAVAAXX100126.6 36 M 36.0000 845 2.00 20GAVAAXX100126.6 37 M 37.0000 1617 4.00 -20GAVAAXX100126.6 38 M 38.0000 1661 3.00 +20GAVAAXX100126.6 38 M 38.0000 1660 3.00 20GAVAAXX100126.6 39 M 39.0000 1030 2.00 20GAVAAXX100126.6 40 M 40.0000 35 0.00 -20GAVAAXX100126.6 45 D 45.0000 8002 3.69 -20GAVAAXX100126.6 45 I 45.0000 8002 0.00 +20GAVAAXX100126.6 45 D 45.0000 8000 3.38 +20GAVAAXX100126.6 45 I 45.0000 8000 0.00 20GAVAAXX100126.7 6 M 6.0000 7 1.00 20GAVAAXX100126.7 7 M 7.0000 16 6.00 20GAVAAXX100126.7 8 M 8.0000 16 2.00 @@ -723,7 +723,7 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.7 30 M 30.0000 192 0.00 20GAVAAXX100126.7 31 M 31.0000 200 0.00 20GAVAAXX100126.7 32 M 32.0000 228 1.00 -20GAVAAXX100126.7 33 M 33.0000 382 1.25 +20GAVAAXX100126.7 33 M 33.0000 381 1.25 20GAVAAXX100126.7 34 M 34.0000 412 2.00 20GAVAAXX100126.7 35 M 35.0000 554 0.00 20GAVAAXX100126.7 36 M 36.0000 700 1.50 @@ -732,8 +732,8 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.7 39 M 39.0000 881 1.00 20GAVAAXX100126.7 40 M 40.0000 49 0.00 20GAVAAXX100126.7 41 M 41.0000 6 0.00 -20GAVAAXX100126.7 45 D 45.0000 7598 2.88 -20GAVAAXX100126.7 45 I 45.0000 7598 0.00 +20GAVAAXX100126.7 45 D 45.0000 7597 2.75 +20GAVAAXX100126.7 45 I 45.0000 7597 0.00 20GAVAAXX100126.8 6 M 6.0000 9 1.00 20GAVAAXX100126.8 7 M 7.0000 4 0.00 20GAVAAXX100126.8 8 M 8.0000 7 1.00 @@ -773,7 +773,7 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.8 45 D 45.0000 8533 5.69 20GAVAAXX100126.8 45 I 45.0000 8533 1.00 -#:GATKTable:8:48659:%s:%d:%s:%s:%s:%.4f:%d:%.2f:; +#:GATKTable:8:48656:%s:%d:%s:%s:%s:%.4f:%d:%.2f:; #:GATKTable:RecalTable2: ReadGroup QualityScore CovariateValue CovariateName EventType EmpiricalQuality Observations Errors 20FUKAAXX100202.1 6 -31 Cycle M 6.0000 1 0.00 @@ -2925,7 +2925,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.1 37 -33 Cycle M 37.0000 5 0.00 20FUKAAXX100202.1 37 -34 Cycle M 37.0000 13 0.00 20FUKAAXX100202.1 37 -35 Cycle M 37.0000 12 0.00 -20FUKAAXX100202.1 37 -36 Cycle M 37.0000 14 0.00 +20FUKAAXX100202.1 37 -36 Cycle M 37.0000 13 0.00 20FUKAAXX100202.1 37 -37 Cycle M 37.0000 10 0.00 20FUKAAXX100202.1 37 -38 Cycle M 37.0000 9 0.00 20FUKAAXX100202.1 37 -39 Cycle M 37.0000 9 0.00 @@ -3100,7 +3100,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.1 37 TA Context M 37.0000 42 0.00 20FUKAAXX100202.1 37 TC Context M 37.0000 280 0.00 20FUKAAXX100202.1 37 TG Context M 37.0000 83 1.00 -20FUKAAXX100202.1 37 TT Context M 37.0000 116 0.00 +20FUKAAXX100202.1 37 TT Context M 37.0000 115 0.00 20FUKAAXX100202.1 38 -10 Cycle M 38.0000 2 0.00 20FUKAAXX100202.1 38 -100 Cycle M 38.0000 3 0.00 20FUKAAXX100202.1 38 -101 Cycle M 38.0000 4 0.00 @@ -3545,8 +3545,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.1 45 -34 Cycle I 45.0000 37 0.00 20FUKAAXX100202.1 45 -35 Cycle D 45.0000 37 0.00 20FUKAAXX100202.1 45 -35 Cycle I 45.0000 37 0.00 -20FUKAAXX100202.1 45 -36 Cycle D 45.0000 37 0.14 -20FUKAAXX100202.1 45 -36 Cycle I 45.0000 37 0.00 +20FUKAAXX100202.1 45 -36 Cycle D 45.0000 36 0.00 +20FUKAAXX100202.1 45 -36 Cycle I 45.0000 36 0.00 20FUKAAXX100202.1 45 -37 Cycle D 45.0000 37 0.14 20FUKAAXX100202.1 45 -37 Cycle I 45.0000 37 0.00 20FUKAAXX100202.1 45 -38 Cycle D 45.0000 38 0.14 @@ -3927,8 +3927,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.1 45 CTC Context I 45.0000 165 0.00 20FUKAAXX100202.1 45 CTG Context D 45.0000 167 0.00 20FUKAAXX100202.1 45 CTG Context I 45.0000 167 0.00 -20FUKAAXX100202.1 45 CTT Context D 45.0000 148 0.29 -20FUKAAXX100202.1 45 CTT Context I 45.0000 148 0.00 +20FUKAAXX100202.1 45 CTT Context D 45.0000 147 0.14 +20FUKAAXX100202.1 45 CTT Context I 45.0000 147 0.00 20FUKAAXX100202.1 45 GAA Context D 45.0000 142 0.29 20FUKAAXX100202.1 45 GAA Context I 45.0000 142 0.00 20FUKAAXX100202.1 45 GAC Context D 45.0000 81 0.00 @@ -5947,7 +5947,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.2 39 14 Cycle M 39.0000 3 0.00 20FUKAAXX100202.2 39 15 Cycle M 39.0000 3 0.00 20FUKAAXX100202.2 39 16 Cycle M 39.0000 2 0.00 -20FUKAAXX100202.2 39 17 Cycle M 39.0000 3 0.00 +20FUKAAXX100202.2 39 17 Cycle M 39.0000 2 0.00 20FUKAAXX100202.2 39 18 Cycle M 39.0000 7 0.00 20FUKAAXX100202.2 39 19 Cycle M 39.0000 4 0.00 20FUKAAXX100202.2 39 20 Cycle M 39.0000 3 0.00 @@ -6007,7 +6007,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.2 39 77 Cycle M 39.0000 5 0.00 20FUKAAXX100202.2 39 78 Cycle M 39.0000 2 0.00 20FUKAAXX100202.2 39 79 Cycle M 39.0000 6 0.00 -20FUKAAXX100202.2 39 8 Cycle M 39.0000 4 0.00 +20FUKAAXX100202.2 39 8 Cycle M 39.0000 3 0.00 20FUKAAXX100202.2 39 80 Cycle M 39.0000 2 0.00 20FUKAAXX100202.2 39 81 Cycle M 39.0000 2 0.00 20FUKAAXX100202.2 39 82 Cycle M 39.0000 2 0.00 @@ -6026,7 +6026,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.2 39 95 Cycle M 39.0000 3 0.00 20FUKAAXX100202.2 39 96 Cycle M 39.0000 3 0.00 20FUKAAXX100202.2 39 97 Cycle M 39.0000 1 0.00 -20FUKAAXX100202.2 39 AA Context M 39.0000 241 0.00 +20FUKAAXX100202.2 39 AA Context M 39.0000 239 0.00 20FUKAAXX100202.2 39 AG Context M 39.0000 2 0.00 20FUKAAXX100202.2 39 AT Context M 39.0000 1 0.00 20FUKAAXX100202.2 39 CA Context M 39.0000 81 0.00 @@ -6249,8 +6249,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.2 45 15 Cycle I 45.0000 32 0.00 20FUKAAXX100202.2 45 16 Cycle D 45.0000 32 0.13 20FUKAAXX100202.2 45 16 Cycle I 45.0000 32 0.00 -20FUKAAXX100202.2 45 17 Cycle D 45.0000 32 0.13 -20FUKAAXX100202.2 45 17 Cycle I 45.0000 32 0.00 +20FUKAAXX100202.2 45 17 Cycle D 45.0000 31 0.00 +20FUKAAXX100202.2 45 17 Cycle I 45.0000 31 0.00 20FUKAAXX100202.2 45 18 Cycle D 45.0000 31 0.00 20FUKAAXX100202.2 45 18 Cycle I 45.0000 31 0.00 20FUKAAXX100202.2 45 19 Cycle D 45.0000 32 0.25 @@ -6381,8 +6381,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.2 45 78 Cycle I 45.0000 30 0.00 20FUKAAXX100202.2 45 79 Cycle D 45.0000 29 0.00 20FUKAAXX100202.2 45 79 Cycle I 45.0000 29 0.00 -20FUKAAXX100202.2 45 8 Cycle D 45.0000 32 0.11 -20FUKAAXX100202.2 45 8 Cycle I 45.0000 32 0.00 +20FUKAAXX100202.2 45 8 Cycle D 45.0000 31 0.00 +20FUKAAXX100202.2 45 8 Cycle I 45.0000 31 0.00 20FUKAAXX100202.2 45 80 Cycle D 45.0000 30 0.00 20FUKAAXX100202.2 45 80 Cycle I 45.0000 30 0.00 20FUKAAXX100202.2 45 81 Cycle D 45.0000 29 0.00 @@ -6485,8 +6485,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.2 45 CTG Context I 45.0000 136 0.00 20FUKAAXX100202.2 45 CTT Context D 45.0000 128 0.65 20FUKAAXX100202.2 45 CTT Context I 45.0000 128 0.00 -20FUKAAXX100202.2 45 GAA Context D 45.0000 118 0.49 -20FUKAAXX100202.2 45 GAA Context I 45.0000 118 0.00 +20FUKAAXX100202.2 45 GAA Context D 45.0000 116 0.25 +20FUKAAXX100202.2 45 GAA Context I 45.0000 116 0.00 20FUKAAXX100202.2 45 GAC Context D 45.0000 69 0.00 20FUKAAXX100202.2 45 GAC Context I 45.0000 69 0.00 20FUKAAXX100202.2 45 GAG Context D 45.0000 137 0.49 @@ -8656,7 +8656,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.3 36 93 Cycle M 36.0000 5 0.00 20FUKAAXX100202.3 36 94 Cycle M 36.0000 4 0.00 20FUKAAXX100202.3 36 95 Cycle M 36.0000 6 0.00 -20FUKAAXX100202.3 36 96 Cycle M 36.0000 6 0.00 +20FUKAAXX100202.3 36 96 Cycle M 36.0000 5 0.00 20FUKAAXX100202.3 36 97 Cycle M 36.0000 3 0.00 20FUKAAXX100202.3 36 98 Cycle M 36.0000 4 0.00 20FUKAAXX100202.3 36 99 Cycle M 36.0000 5 0.00 @@ -8674,7 +8674,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.3 36 TA Context M 36.0000 32 0.00 20FUKAAXX100202.3 36 TC Context M 36.0000 41 0.00 20FUKAAXX100202.3 36 TG Context M 36.0000 56 2.00 -20FUKAAXX100202.3 36 TT Context M 36.0000 50 0.00 +20FUKAAXX100202.3 36 TT Context M 36.0000 49 0.00 20FUKAAXX100202.3 37 -1 Cycle M 37.0000 1 0.00 20FUKAAXX100202.3 37 -10 Cycle M 37.0000 14 0.00 20FUKAAXX100202.3 37 -100 Cycle M 37.0000 6 0.00 @@ -9094,7 +9094,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.3 39 -18 Cycle M 39.0000 6 0.00 20FUKAAXX100202.3 39 -19 Cycle M 39.0000 1 0.00 20FUKAAXX100202.3 39 -20 Cycle M 39.0000 4 0.00 -20FUKAAXX100202.3 39 -21 Cycle M 39.0000 7 0.00 +20FUKAAXX100202.3 39 -21 Cycle M 39.0000 6 0.00 20FUKAAXX100202.3 39 -22 Cycle M 39.0000 10 0.00 20FUKAAXX100202.3 39 -23 Cycle M 39.0000 5 0.00 20FUKAAXX100202.3 39 -25 Cycle M 39.0000 1 0.00 @@ -9264,7 +9264,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.3 39 97 Cycle M 39.0000 3 0.00 20FUKAAXX100202.3 39 98 Cycle M 39.0000 5 0.00 20FUKAAXX100202.3 39 99 Cycle M 39.0000 2 0.00 -20FUKAAXX100202.3 39 AA Context M 39.0000 334 0.00 +20FUKAAXX100202.3 39 AA Context M 39.0000 333 0.00 20FUKAAXX100202.3 39 AG Context M 39.0000 7 0.00 20FUKAAXX100202.3 39 CA Context M 39.0000 170 0.00 20FUKAAXX100202.3 39 CT Context M 39.0000 385 0.00 @@ -9305,8 +9305,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.3 45 -19 Cycle I 45.0000 49 0.00 20FUKAAXX100202.3 45 -20 Cycle D 45.0000 49 0.13 20FUKAAXX100202.3 45 -20 Cycle I 45.0000 49 0.00 -20FUKAAXX100202.3 45 -21 Cycle D 45.0000 49 0.13 -20FUKAAXX100202.3 45 -21 Cycle I 45.0000 49 0.00 +20FUKAAXX100202.3 45 -21 Cycle D 45.0000 48 0.00 +20FUKAAXX100202.3 45 -21 Cycle I 45.0000 48 0.00 20FUKAAXX100202.3 45 -22 Cycle D 45.0000 48 0.00 20FUKAAXX100202.3 45 -22 Cycle I 45.0000 48 0.00 20FUKAAXX100202.3 45 -23 Cycle D 45.0000 49 0.13 @@ -9651,8 +9651,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.3 45 94 Cycle I 45.0000 39 0.00 20FUKAAXX100202.3 45 95 Cycle D 45.0000 38 0.00 20FUKAAXX100202.3 45 95 Cycle I 45.0000 38 0.00 -20FUKAAXX100202.3 45 96 Cycle D 45.0000 39 0.14 -20FUKAAXX100202.3 45 96 Cycle I 45.0000 39 0.00 +20FUKAAXX100202.3 45 96 Cycle D 45.0000 38 0.00 +20FUKAAXX100202.3 45 96 Cycle I 45.0000 38 0.00 20FUKAAXX100202.3 45 97 Cycle D 45.0000 39 0.14 20FUKAAXX100202.3 45 97 Cycle I 45.0000 39 0.00 20FUKAAXX100202.3 45 AAA Context D 45.0000 201 0.38 @@ -9717,10 +9717,10 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.3 45 CTC Context I 45.0000 176 0.00 20FUKAAXX100202.3 45 CTG Context D 45.0000 198 0.00 20FUKAAXX100202.3 45 CTG Context I 45.0000 198 0.00 -20FUKAAXX100202.3 45 CTT Context D 45.0000 176 0.29 -20FUKAAXX100202.3 45 CTT Context I 45.0000 176 0.00 -20FUKAAXX100202.3 45 GAA Context D 45.0000 173 0.50 -20FUKAAXX100202.3 45 GAA Context I 45.0000 173 0.00 +20FUKAAXX100202.3 45 CTT Context D 45.0000 175 0.14 +20FUKAAXX100202.3 45 CTT Context I 45.0000 175 0.00 +20FUKAAXX100202.3 45 GAA Context D 45.0000 172 0.38 +20FUKAAXX100202.3 45 GAA Context I 45.0000 172 0.00 20FUKAAXX100202.3 45 GAC Context D 45.0000 85 0.00 20FUKAAXX100202.3 45 GAC Context I 45.0000 85 0.00 20FUKAAXX100202.3 45 GAG Context D 45.0000 177 0.50 @@ -12039,13 +12039,13 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.4 39 25 Cycle M 39.0000 3 0.00 20FUKAAXX100202.4 39 26 Cycle M 39.0000 1 0.00 20FUKAAXX100202.4 39 27 Cycle M 39.0000 2 0.00 -20FUKAAXX100202.4 39 28 Cycle M 39.0000 3 0.00 +20FUKAAXX100202.4 39 28 Cycle M 39.0000 2 0.00 20FUKAAXX100202.4 39 29 Cycle M 39.0000 3 0.00 20FUKAAXX100202.4 39 30 Cycle M 39.0000 4 0.00 20FUKAAXX100202.4 39 31 Cycle M 39.0000 4 0.00 20FUKAAXX100202.4 39 32 Cycle M 39.0000 7 0.00 20FUKAAXX100202.4 39 33 Cycle M 39.0000 3 0.00 -20FUKAAXX100202.4 39 34 Cycle M 39.0000 5 0.00 +20FUKAAXX100202.4 39 34 Cycle M 39.0000 4 0.00 20FUKAAXX100202.4 39 35 Cycle M 39.0000 2 0.00 20FUKAAXX100202.4 39 36 Cycle M 39.0000 1 0.00 20FUKAAXX100202.4 39 37 Cycle M 39.0000 3 0.00 @@ -12109,7 +12109,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.4 39 96 Cycle M 39.0000 2 0.00 20FUKAAXX100202.4 39 97 Cycle M 39.0000 4 0.00 20FUKAAXX100202.4 39 98 Cycle M 39.0000 2 0.00 -20FUKAAXX100202.4 39 AA Context M 39.0000 193 0.00 +20FUKAAXX100202.4 39 AA Context M 39.0000 191 0.00 20FUKAAXX100202.4 39 AG Context M 39.0000 1 0.00 20FUKAAXX100202.4 39 AT Context M 39.0000 2 0.00 20FUKAAXX100202.4 39 CA Context M 39.0000 109 1.00 @@ -12355,8 +12355,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.4 45 26 Cycle I 45.0000 32 0.00 20FUKAAXX100202.4 45 27 Cycle D 45.0000 32 0.13 20FUKAAXX100202.4 45 27 Cycle I 45.0000 32 0.00 -20FUKAAXX100202.4 45 28 Cycle D 45.0000 32 0.13 -20FUKAAXX100202.4 45 28 Cycle I 45.0000 32 0.00 +20FUKAAXX100202.4 45 28 Cycle D 45.0000 31 0.00 +20FUKAAXX100202.4 45 28 Cycle I 45.0000 31 0.00 20FUKAAXX100202.4 45 29 Cycle D 45.0000 31 0.13 20FUKAAXX100202.4 45 29 Cycle I 45.0000 31 0.00 20FUKAAXX100202.4 45 30 Cycle D 45.0000 31 0.25 @@ -12367,8 +12367,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.4 45 32 Cycle I 45.0000 32 0.00 20FUKAAXX100202.4 45 33 Cycle D 45.0000 32 0.13 20FUKAAXX100202.4 45 33 Cycle I 45.0000 32 0.00 -20FUKAAXX100202.4 45 34 Cycle D 45.0000 32 0.13 -20FUKAAXX100202.4 45 34 Cycle I 45.0000 32 0.00 +20FUKAAXX100202.4 45 34 Cycle D 45.0000 31 0.00 +20FUKAAXX100202.4 45 34 Cycle I 45.0000 31 0.00 20FUKAAXX100202.4 45 35 Cycle D 45.0000 31 0.00 20FUKAAXX100202.4 45 35 Cycle I 45.0000 31 0.00 20FUKAAXX100202.4 45 36 Cycle D 45.0000 32 0.13 @@ -12569,8 +12569,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.4 45 CTG Context I 45.0000 141 0.00 20FUKAAXX100202.4 45 CTT Context D 45.0000 132 0.14 20FUKAAXX100202.4 45 CTT Context I 45.0000 132 0.00 -20FUKAAXX100202.4 45 GAA Context D 45.0000 103 0.38 -20FUKAAXX100202.4 45 GAA Context I 45.0000 103 0.00 +20FUKAAXX100202.4 45 GAA Context D 45.0000 101 0.13 +20FUKAAXX100202.4 45 GAA Context I 45.0000 101 0.00 20FUKAAXX100202.4 45 GAC Context D 45.0000 80 0.00 20FUKAAXX100202.4 45 GAC Context I 45.0000 80 0.00 20FUKAAXX100202.4 45 GAG Context D 45.0000 155 0.38 @@ -14766,7 +14766,6 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.5 38 TT Context M 38.0000 221 0.00 20FUKAAXX100202.5 39 -100 Cycle M 39.0000 1 0.00 20FUKAAXX100202.5 39 -14 Cycle M 39.0000 2 0.00 -20FUKAAXX100202.5 39 -15 Cycle M 39.0000 1 0.00 20FUKAAXX100202.5 39 -16 Cycle M 39.0000 6 0.00 20FUKAAXX100202.5 39 -17 Cycle M 39.0000 4 0.00 20FUKAAXX100202.5 39 -18 Cycle M 39.0000 4 0.00 @@ -14943,7 +14942,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.5 39 97 Cycle M 39.0000 3 0.00 20FUKAAXX100202.5 39 98 Cycle M 39.0000 3 0.00 20FUKAAXX100202.5 39 99 Cycle M 39.0000 1 0.00 -20FUKAAXX100202.5 39 AA Context M 39.0000 241 0.00 +20FUKAAXX100202.5 39 AA Context M 39.0000 240 0.00 20FUKAAXX100202.5 39 AG Context M 39.0000 19 0.00 20FUKAAXX100202.5 39 AT Context M 39.0000 3 0.00 20FUKAAXX100202.5 39 CA Context M 39.0000 218 0.00 @@ -14997,8 +14996,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.5 45 -13 Cycle I 45.0000 39 0.00 20FUKAAXX100202.5 45 -14 Cycle D 45.0000 39 0.14 20FUKAAXX100202.5 45 -14 Cycle I 45.0000 39 0.00 -20FUKAAXX100202.5 45 -15 Cycle D 45.0000 39 0.14 -20FUKAAXX100202.5 45 -15 Cycle I 45.0000 39 0.00 +20FUKAAXX100202.5 45 -15 Cycle D 45.0000 38 0.00 +20FUKAAXX100202.5 45 -15 Cycle I 45.0000 38 0.00 20FUKAAXX100202.5 45 -16 Cycle D 45.0000 37 0.00 20FUKAAXX100202.5 45 -16 Cycle I 45.0000 37 0.00 20FUKAAXX100202.5 45 -17 Cycle D 45.0000 39 0.14 @@ -15423,8 +15422,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.5 45 CTG Context I 45.0000 154 0.00 20FUKAAXX100202.5 45 CTT Context D 45.0000 121 0.14 20FUKAAXX100202.5 45 CTT Context I 45.0000 121 0.00 -20FUKAAXX100202.5 45 GAA Context D 45.0000 162 0.29 -20FUKAAXX100202.5 45 GAA Context I 45.0000 162 0.00 +20FUKAAXX100202.5 45 GAA Context D 45.0000 161 0.14 +20FUKAAXX100202.5 45 GAA Context I 45.0000 161 0.00 20FUKAAXX100202.5 45 GAC Context D 45.0000 76 0.00 20FUKAAXX100202.5 45 GAC Context I 45.0000 76 0.00 20FUKAAXX100202.5 45 GAG Context D 45.0000 173 0.29 @@ -17205,7 +17204,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 35 -94 Cycle M 35.0000 2 0.00 20FUKAAXX100202.6 35 -95 Cycle M 35.0000 5 0.00 20FUKAAXX100202.6 35 -96 Cycle M 35.0000 1 0.00 -20FUKAAXX100202.6 35 -97 Cycle M 35.0000 3 0.00 +20FUKAAXX100202.6 35 -97 Cycle M 35.0000 2 0.00 20FUKAAXX100202.6 35 -98 Cycle M 35.0000 4 0.00 20FUKAAXX100202.6 35 -99 Cycle M 35.0000 2 0.00 20FUKAAXX100202.6 35 1 Cycle M 35.0000 51 0.50 @@ -17292,7 +17291,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 35 TA Context M 35.0000 24 1.00 20FUKAAXX100202.6 35 TC Context M 35.0000 33 0.17 20FUKAAXX100202.6 35 TG Context M 35.0000 59 0.00 -20FUKAAXX100202.6 35 TT Context M 35.0000 53 0.00 +20FUKAAXX100202.6 35 TT Context M 35.0000 52 0.00 20FUKAAXX100202.6 36 -10 Cycle M 36.0000 13 0.00 20FUKAAXX100202.6 36 -100 Cycle M 36.0000 6 0.00 20FUKAAXX100202.6 36 -101 Cycle M 36.0000 2 0.00 @@ -17735,7 +17734,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 38 -42 Cycle M 38.0000 17 0.00 20FUKAAXX100202.6 38 -43 Cycle M 38.0000 15 0.00 20FUKAAXX100202.6 38 -44 Cycle M 38.0000 21 0.00 -20FUKAAXX100202.6 38 -45 Cycle M 38.0000 13 0.00 +20FUKAAXX100202.6 38 -45 Cycle M 38.0000 12 0.00 20FUKAAXX100202.6 38 -46 Cycle M 38.0000 23 0.00 20FUKAAXX100202.6 38 -47 Cycle M 38.0000 19 0.00 20FUKAAXX100202.6 38 -48 Cycle M 38.0000 20 0.00 @@ -17876,7 +17875,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 38 85 Cycle M 38.0000 23 0.00 20FUKAAXX100202.6 38 86 Cycle M 38.0000 23 0.00 20FUKAAXX100202.6 38 87 Cycle M 38.0000 15 0.00 -20FUKAAXX100202.6 38 88 Cycle M 38.0000 18 1.00 +20FUKAAXX100202.6 38 88 Cycle M 38.0000 17 1.00 20FUKAAXX100202.6 38 89 Cycle M 38.0000 19 0.00 20FUKAAXX100202.6 38 9 Cycle M 38.0000 13 0.00 20FUKAAXX100202.6 38 90 Cycle M 38.0000 14 0.00 @@ -17902,7 +17901,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 38 TA Context M 38.0000 167 0.00 20FUKAAXX100202.6 38 TC Context M 38.0000 108 0.00 20FUKAAXX100202.6 38 TG Context M 38.0000 463 3.00 -20FUKAAXX100202.6 38 TT Context M 38.0000 306 1.00 +20FUKAAXX100202.6 38 TT Context M 38.0000 304 1.00 20FUKAAXX100202.6 39 -100 Cycle M 39.0000 2 0.00 20FUKAAXX100202.6 39 -16 Cycle M 39.0000 3 0.00 20FUKAAXX100202.6 39 -17 Cycle M 39.0000 2 0.00 @@ -18177,8 +18176,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 45 -43 Cycle I 45.0000 51 0.00 20FUKAAXX100202.6 45 -44 Cycle D 45.0000 49 0.00 20FUKAAXX100202.6 45 -44 Cycle I 45.0000 49 0.00 -20FUKAAXX100202.6 45 -45 Cycle D 45.0000 51 0.14 -20FUKAAXX100202.6 45 -45 Cycle I 45.0000 51 0.00 +20FUKAAXX100202.6 45 -45 Cycle D 45.0000 50 0.00 +20FUKAAXX100202.6 45 -45 Cycle I 45.0000 50 0.00 20FUKAAXX100202.6 45 -46 Cycle D 45.0000 51 0.14 20FUKAAXX100202.6 45 -46 Cycle I 45.0000 51 0.00 20FUKAAXX100202.6 45 -47 Cycle D 45.0000 51 0.14 @@ -18291,8 +18290,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 45 -95 Cycle I 45.0000 36 0.00 20FUKAAXX100202.6 45 -96 Cycle D 45.0000 35 0.00 20FUKAAXX100202.6 45 -96 Cycle I 45.0000 35 0.00 -20FUKAAXX100202.6 45 -97 Cycle D 45.0000 36 0.17 -20FUKAAXX100202.6 45 -97 Cycle I 45.0000 36 0.00 +20FUKAAXX100202.6 45 -97 Cycle D 45.0000 35 0.00 +20FUKAAXX100202.6 45 -97 Cycle I 45.0000 35 0.00 20FUKAAXX100202.6 45 10 Cycle D 45.0000 53 0.00 20FUKAAXX100202.6 45 10 Cycle I 45.0000 53 0.00 20FUKAAXX100202.6 45 11 Cycle D 45.0000 54 0.00 @@ -18457,8 +18456,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 45 86 Cycle I 45.0000 49 0.00 20FUKAAXX100202.6 45 87 Cycle D 45.0000 47 0.00 20FUKAAXX100202.6 45 87 Cycle I 45.0000 47 0.00 -20FUKAAXX100202.6 45 88 Cycle D 45.0000 48 0.14 -20FUKAAXX100202.6 45 88 Cycle I 45.0000 48 0.00 +20FUKAAXX100202.6 45 88 Cycle D 45.0000 47 0.00 +20FUKAAXX100202.6 45 88 Cycle I 45.0000 47 0.00 20FUKAAXX100202.6 45 89 Cycle D 45.0000 47 0.14 20FUKAAXX100202.6 45 89 Cycle I 45.0000 47 0.00 20FUKAAXX100202.6 45 9 Cycle D 45.0000 54 0.00 @@ -18541,8 +18540,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 45 CTC Context I 45.0000 221 0.00 20FUKAAXX100202.6 45 CTG Context D 45.0000 209 0.00 20FUKAAXX100202.6 45 CTG Context I 45.0000 209 0.00 -20FUKAAXX100202.6 45 CTT Context D 45.0000 203 1.17 -20FUKAAXX100202.6 45 CTT Context I 45.0000 203 0.00 +20FUKAAXX100202.6 45 CTT Context D 45.0000 200 0.71 +20FUKAAXX100202.6 45 CTT Context I 45.0000 200 0.00 20FUKAAXX100202.6 45 GAA Context D 45.0000 195 0.14 20FUKAAXX100202.6 45 GAA Context I 45.0000 195 0.00 20FUKAAXX100202.6 45 GAC Context D 45.0000 107 0.00 @@ -20524,7 +20523,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.7 36 -67 Cycle M 36.0000 3 0.00 20FUKAAXX100202.7 36 -68 Cycle M 36.0000 3 0.00 20FUKAAXX100202.7 36 -69 Cycle M 36.0000 4 0.00 -20FUKAAXX100202.7 36 -7 Cycle M 36.0000 12 0.00 +20FUKAAXX100202.7 36 -7 Cycle M 36.0000 11 0.00 20FUKAAXX100202.7 36 -70 Cycle M 36.0000 4 0.00 20FUKAAXX100202.7 36 -71 Cycle M 36.0000 3 0.00 20FUKAAXX100202.7 36 -72 Cycle M 36.0000 2 0.00 @@ -20654,7 +20653,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.7 36 97 Cycle M 36.0000 5 0.00 20FUKAAXX100202.7 36 98 Cycle M 36.0000 7 0.00 20FUKAAXX100202.7 36 99 Cycle M 36.0000 4 0.00 -20FUKAAXX100202.7 36 AA Context M 36.0000 58 0.00 +20FUKAAXX100202.7 36 AA Context M 36.0000 57 0.00 20FUKAAXX100202.7 36 AC Context M 36.0000 328 2.00 20FUKAAXX100202.7 36 AG Context M 36.0000 72 0.00 20FUKAAXX100202.7 36 AT Context M 36.0000 43 0.00 @@ -21053,7 +21052,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.7 38 90 Cycle M 38.0000 19 0.00 20FUKAAXX100202.7 38 91 Cycle M 38.0000 15 0.00 20FUKAAXX100202.7 38 92 Cycle M 38.0000 21 0.00 -20FUKAAXX100202.7 38 93 Cycle M 38.0000 17 0.00 +20FUKAAXX100202.7 38 93 Cycle M 38.0000 16 0.00 20FUKAAXX100202.7 38 94 Cycle M 38.0000 13 0.00 20FUKAAXX100202.7 38 95 Cycle M 38.0000 17 0.00 20FUKAAXX100202.7 38 96 Cycle M 38.0000 14 1.00 @@ -21073,7 +21072,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.7 38 TA Context M 38.0000 162 0.00 20FUKAAXX100202.7 38 TC Context M 38.0000 131 0.00 20FUKAAXX100202.7 38 TG Context M 38.0000 456 1.33 -20FUKAAXX100202.7 38 TT Context M 38.0000 262 1.00 +20FUKAAXX100202.7 38 TT Context M 38.0000 261 1.00 20FUKAAXX100202.7 39 -100 Cycle M 39.0000 1 0.00 20FUKAAXX100202.7 39 -14 Cycle M 39.0000 3 0.00 20FUKAAXX100202.7 39 -15 Cycle M 39.0000 2 0.00 @@ -21403,8 +21402,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.7 45 -68 Cycle I 45.0000 46 0.00 20FUKAAXX100202.7 45 -69 Cycle D 45.0000 46 0.00 20FUKAAXX100202.7 45 -69 Cycle I 45.0000 46 0.00 -20FUKAAXX100202.7 45 -7 Cycle D 45.0000 51 0.25 -20FUKAAXX100202.7 45 -7 Cycle I 45.0000 51 0.00 +20FUKAAXX100202.7 45 -7 Cycle D 45.0000 50 0.13 +20FUKAAXX100202.7 45 -7 Cycle I 45.0000 50 0.00 20FUKAAXX100202.7 45 -70 Cycle D 45.0000 46 0.00 20FUKAAXX100202.7 45 -70 Cycle I 45.0000 46 0.00 20FUKAAXX100202.7 45 -71 Cycle D 45.0000 46 0.00 @@ -21641,8 +21640,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.7 45 91 Cycle I 45.0000 40 0.00 20FUKAAXX100202.7 45 92 Cycle D 45.0000 40 0.00 20FUKAAXX100202.7 45 92 Cycle I 45.0000 40 0.00 -20FUKAAXX100202.7 45 93 Cycle D 45.0000 41 0.09 -20FUKAAXX100202.7 45 93 Cycle I 45.0000 41 0.00 +20FUKAAXX100202.7 45 93 Cycle D 45.0000 40 0.00 +20FUKAAXX100202.7 45 93 Cycle I 45.0000 40 0.00 20FUKAAXX100202.7 45 94 Cycle D 45.0000 41 0.09 20FUKAAXX100202.7 45 94 Cycle I 45.0000 41 0.00 20FUKAAXX100202.7 45 95 Cycle D 45.0000 41 0.09 @@ -21713,10 +21712,10 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.7 45 CTC Context I 45.0000 184 0.00 20FUKAAXX100202.7 45 CTG Context D 45.0000 196 0.00 20FUKAAXX100202.7 45 CTG Context I 45.0000 196 0.00 -20FUKAAXX100202.7 45 CTT Context D 45.0000 166 0.09 -20FUKAAXX100202.7 45 CTT Context I 45.0000 166 0.00 -20FUKAAXX100202.7 45 GAA Context D 45.0000 230 0.25 -20FUKAAXX100202.7 45 GAA Context I 45.0000 230 0.00 +20FUKAAXX100202.7 45 CTT Context D 45.0000 165 0.00 +20FUKAAXX100202.7 45 CTT Context I 45.0000 165 0.00 +20FUKAAXX100202.7 45 GAA Context D 45.0000 229 0.13 +20FUKAAXX100202.7 45 GAA Context I 45.0000 229 0.00 20FUKAAXX100202.7 45 GAC Context D 45.0000 82 0.00 20FUKAAXX100202.7 45 GAC Context I 45.0000 82 0.00 20FUKAAXX100202.7 45 GAG Context D 45.0000 219 0.25 @@ -25367,7 +25366,6 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 24 TC Context M 24.0000 4 0.00 20GAVAAXX100126.1 24 TG Context M 24.0000 1 0.00 20GAVAAXX100126.1 24 TT Context M 24.0000 1 0.00 -20GAVAAXX100126.1 25 -10 Cycle M 25.0000 1 0.00 20GAVAAXX100126.1 25 -12 Cycle M 25.0000 1 0.00 20GAVAAXX100126.1 25 -15 Cycle M 25.0000 1 0.00 20GAVAAXX100126.1 25 -17 Cycle M 25.0000 1 0.00 @@ -25446,7 +25444,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 25 GT Context M 25.0000 7 0.00 20GAVAAXX100126.1 25 TA Context M 25.0000 5 0.00 20GAVAAXX100126.1 25 TC Context M 25.0000 10 0.00 -20GAVAAXX100126.1 25 TG Context M 25.0000 9 0.00 +20GAVAAXX100126.1 25 TG Context M 25.0000 8 0.00 20GAVAAXX100126.1 25 TT Context M 25.0000 5 0.00 20GAVAAXX100126.1 26 -101 Cycle M 26.0000 1 0.00 20GAVAAXX100126.1 26 -18 Cycle M 26.0000 1 0.00 @@ -25606,7 +25604,6 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 27 61 Cycle M 27.0000 1 0.00 20GAVAAXX100126.1 27 63 Cycle M 27.0000 1 0.00 20GAVAAXX100126.1 27 65 Cycle M 27.0000 1 0.00 -20GAVAAXX100126.1 27 66 Cycle M 27.0000 1 0.00 20GAVAAXX100126.1 27 68 Cycle M 27.0000 1 0.00 20GAVAAXX100126.1 27 70 Cycle M 27.0000 2 0.00 20GAVAAXX100126.1 27 71 Cycle M 27.0000 1 0.00 @@ -25626,7 +25623,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 27 91 Cycle M 27.0000 1 0.00 20GAVAAXX100126.1 27 93 Cycle M 27.0000 2 0.00 20GAVAAXX100126.1 27 99 Cycle M 27.0000 2 0.00 -20GAVAAXX100126.1 27 AA Context M 27.0000 8 0.00 +20GAVAAXX100126.1 27 AA Context M 27.0000 7 0.00 20GAVAAXX100126.1 27 AC Context M 27.0000 3 0.00 20GAVAAXX100126.1 27 AG Context M 27.0000 9 0.00 20GAVAAXX100126.1 27 AT Context M 27.0000 3 0.00 @@ -27534,7 +27531,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 39 39 Cycle M 39.0000 16 0.00 20GAVAAXX100126.1 39 40 Cycle M 39.0000 23 0.00 20GAVAAXX100126.1 39 41 Cycle M 39.0000 8 0.00 -20GAVAAXX100126.1 39 42 Cycle M 39.0000 20 0.00 +20GAVAAXX100126.1 39 42 Cycle M 39.0000 19 0.00 20GAVAAXX100126.1 39 43 Cycle M 39.0000 13 0.00 20GAVAAXX100126.1 39 44 Cycle M 39.0000 15 0.00 20GAVAAXX100126.1 39 45 Cycle M 39.0000 11 0.00 @@ -27595,7 +27592,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 39 97 Cycle M 39.0000 10 0.00 20GAVAAXX100126.1 39 98 Cycle M 39.0000 8 0.00 20GAVAAXX100126.1 39 99 Cycle M 39.0000 3 0.00 -20GAVAAXX100126.1 39 AA Context M 39.0000 211 0.00 +20GAVAAXX100126.1 39 AA Context M 39.0000 210 0.00 20GAVAAXX100126.1 39 AG Context M 39.0000 26 0.00 20GAVAAXX100126.1 39 AT Context M 39.0000 49 0.00 20GAVAAXX100126.1 39 CA Context M 39.0000 413 2.00 @@ -27717,8 +27714,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 41 -76 Cycle M 41.0000 1 0.00 20GAVAAXX100126.1 41 AA Context M 41.0000 6 0.00 20GAVAAXX100126.1 41 CT Context M 41.0000 17 0.00 -20GAVAAXX100126.1 45 -10 Cycle D 45.0000 47 0.41 -20GAVAAXX100126.1 45 -10 Cycle I 45.0000 47 0.00 +20GAVAAXX100126.1 45 -10 Cycle D 45.0000 46 0.13 +20GAVAAXX100126.1 45 -10 Cycle I 45.0000 46 0.00 20GAVAAXX100126.1 45 -11 Cycle D 45.0000 46 0.13 20GAVAAXX100126.1 45 -11 Cycle I 45.0000 46 0.00 20GAVAAXX100126.1 45 -12 Cycle D 45.0000 46 0.13 @@ -27967,8 +27964,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 45 40 Cycle I 45.0000 53 0.00 20GAVAAXX100126.1 45 41 Cycle D 45.0000 53 0.14 20GAVAAXX100126.1 45 41 Cycle I 45.0000 53 0.00 -20GAVAAXX100126.1 45 42 Cycle D 45.0000 53 0.14 -20GAVAAXX100126.1 45 42 Cycle I 45.0000 53 0.00 +20GAVAAXX100126.1 45 42 Cycle D 45.0000 52 0.00 +20GAVAAXX100126.1 45 42 Cycle I 45.0000 52 0.00 20GAVAAXX100126.1 45 43 Cycle D 45.0000 52 0.00 20GAVAAXX100126.1 45 43 Cycle I 45.0000 52 0.00 20GAVAAXX100126.1 45 44 Cycle D 45.0000 52 0.14 @@ -28019,8 +28016,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 45 64 Cycle I 45.0000 52 0.00 20GAVAAXX100126.1 45 65 Cycle D 45.0000 51 0.17 20GAVAAXX100126.1 45 65 Cycle I 45.0000 51 0.00 -20GAVAAXX100126.1 45 66 Cycle D 45.0000 52 0.17 -20GAVAAXX100126.1 45 66 Cycle I 45.0000 52 0.00 +20GAVAAXX100126.1 45 66 Cycle D 45.0000 51 0.00 +20GAVAAXX100126.1 45 66 Cycle I 45.0000 51 0.00 20GAVAAXX100126.1 45 67 Cycle D 45.0000 51 0.00 20GAVAAXX100126.1 45 67 Cycle I 45.0000 51 0.00 20GAVAAXX100126.1 45 68 Cycle D 45.0000 52 0.00 @@ -28153,8 +28150,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 45 CTG Context I 45.0000 214 0.00 20GAVAAXX100126.1 45 CTT Context D 45.0000 187 0.70 20GAVAAXX100126.1 45 CTT Context I 45.0000 187 0.00 -20GAVAAXX100126.1 45 GAA Context D 45.0000 155 0.31 -20GAVAAXX100126.1 45 GAA Context I 45.0000 155 0.00 +20GAVAAXX100126.1 45 GAA Context D 45.0000 153 0.00 +20GAVAAXX100126.1 45 GAA Context I 45.0000 153 0.00 20GAVAAXX100126.1 45 GAC Context D 45.0000 90 0.00 20GAVAAXX100126.1 45 GAC Context I 45.0000 90 0.00 20GAVAAXX100126.1 45 GAG Context D 45.0000 189 0.43 @@ -28181,8 +28178,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 45 GTA Context I 45.0000 95 0.00 20GAVAAXX100126.1 45 GTC Context D 45.0000 85 0.46 20GAVAAXX100126.1 45 GTC Context I 45.0000 85 0.00 -20GAVAAXX100126.1 45 GTG Context D 45.0000 190 0.72 -20GAVAAXX100126.1 45 GTG Context I 45.0000 190 0.00 +20GAVAAXX100126.1 45 GTG Context D 45.0000 189 0.43 +20GAVAAXX100126.1 45 GTG Context I 45.0000 189 0.00 20GAVAAXX100126.1 45 GTT Context D 45.0000 116 0.00 20GAVAAXX100126.1 45 GTT Context I 45.0000 116 0.00 20GAVAAXX100126.1 45 TAA Context D 45.0000 81 0.00 @@ -29720,7 +29717,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.2 33 -68 Cycle M 33.0000 4 0.00 20GAVAAXX100126.2 33 -69 Cycle M 33.0000 3 0.00 20GAVAAXX100126.2 33 -7 Cycle M 33.0000 4 0.00 -20GAVAAXX100126.2 33 -70 Cycle M 33.0000 2 0.00 +20GAVAAXX100126.2 33 -70 Cycle M 33.0000 1 0.00 20GAVAAXX100126.2 33 -71 Cycle M 33.0000 9 0.00 20GAVAAXX100126.2 33 -72 Cycle M 33.0000 8 0.00 20GAVAAXX100126.2 33 -73 Cycle M 33.0000 4 0.00 @@ -29810,7 +29807,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.2 33 97 Cycle M 33.0000 1 0.00 20GAVAAXX100126.2 33 98 Cycle M 33.0000 4 0.00 20GAVAAXX100126.2 33 99 Cycle M 33.0000 2 0.00 -20GAVAAXX100126.2 33 AA Context M 33.0000 19 0.00 +20GAVAAXX100126.2 33 AA Context M 33.0000 18 0.00 20GAVAAXX100126.2 33 AC Context M 33.0000 25 0.00 20GAVAAXX100126.2 33 AG Context M 33.0000 32 0.00 20GAVAAXX100126.2 33 AT Context M 33.0000 16 0.00 @@ -31022,8 +31019,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.2 45 -69 Cycle I 45.0000 36 0.00 20GAVAAXX100126.2 45 -7 Cycle D 45.0000 41 0.00 20GAVAAXX100126.2 45 -7 Cycle I 45.0000 41 0.00 -20GAVAAXX100126.2 45 -70 Cycle D 45.0000 37 0.14 -20GAVAAXX100126.2 45 -70 Cycle I 45.0000 37 0.00 +20GAVAAXX100126.2 45 -70 Cycle D 45.0000 36 0.00 +20GAVAAXX100126.2 45 -70 Cycle I 45.0000 36 0.00 20GAVAAXX100126.2 45 -71 Cycle D 45.0000 35 0.00 20GAVAAXX100126.2 45 -71 Cycle I 45.0000 35 0.00 20GAVAAXX100126.2 45 -72 Cycle D 45.0000 36 0.14 @@ -31332,8 +31329,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.2 45 CTG Context I 45.0000 154 0.00 20GAVAAXX100126.2 45 CTT Context D 45.0000 141 0.43 20GAVAAXX100126.2 45 CTT Context I 45.0000 141 0.00 -20GAVAAXX100126.2 45 GAA Context D 45.0000 130 0.43 -20GAVAAXX100126.2 45 GAA Context I 45.0000 130 0.00 +20GAVAAXX100126.2 45 GAA Context D 45.0000 129 0.29 +20GAVAAXX100126.2 45 GAA Context I 45.0000 129 0.00 20GAVAAXX100126.2 45 GAC Context D 45.0000 87 0.00 20GAVAAXX100126.2 45 GAC Context I 45.0000 87 0.00 20GAVAAXX100126.2 45 GAG Context D 45.0000 183 0.14 @@ -36512,7 +36509,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.4 38 10 Cycle M 38.0000 10 0.00 20GAVAAXX100126.4 38 100 Cycle M 38.0000 4 0.00 20GAVAAXX100126.4 38 101 Cycle M 38.0000 5 0.00 -20GAVAAXX100126.4 38 11 Cycle M 38.0000 9 0.00 +20GAVAAXX100126.4 38 11 Cycle M 38.0000 8 0.00 20GAVAAXX100126.4 38 12 Cycle M 38.0000 8 0.00 20GAVAAXX100126.4 38 13 Cycle M 38.0000 9 0.00 20GAVAAXX100126.4 38 14 Cycle M 38.0000 11 0.00 @@ -36619,7 +36616,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.4 38 TA Context M 38.0000 97 0.00 20GAVAAXX100126.4 38 TC Context M 38.0000 29 0.00 20GAVAAXX100126.4 38 TG Context M 38.0000 196 3.00 -20GAVAAXX100126.4 38 TT Context M 38.0000 99 0.00 +20GAVAAXX100126.4 38 TT Context M 38.0000 98 0.00 20GAVAAXX100126.4 39 -13 Cycle M 39.0000 4 0.00 20GAVAAXX100126.4 39 -14 Cycle M 39.0000 3 0.00 20GAVAAXX100126.4 39 -15 Cycle M 39.0000 2 0.00 @@ -36979,8 +36976,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.4 45 -97 Cycle I 45.0000 25 0.00 20GAVAAXX100126.4 45 10 Cycle D 45.0000 33 0.00 20GAVAAXX100126.4 45 10 Cycle I 45.0000 33 0.00 -20GAVAAXX100126.4 45 11 Cycle D 45.0000 34 0.14 -20GAVAAXX100126.4 45 11 Cycle I 45.0000 34 0.00 +20GAVAAXX100126.4 45 11 Cycle D 45.0000 33 0.00 +20GAVAAXX100126.4 45 11 Cycle I 45.0000 33 0.00 20GAVAAXX100126.4 45 12 Cycle D 45.0000 34 0.14 20GAVAAXX100126.4 45 12 Cycle I 45.0000 34 0.00 20GAVAAXX100126.4 45 13 Cycle D 45.0000 34 0.14 @@ -37225,8 +37222,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.4 45 CTC Context I 45.0000 139 0.00 20GAVAAXX100126.4 45 CTG Context D 45.0000 154 0.00 20GAVAAXX100126.4 45 CTG Context I 45.0000 154 0.00 -20GAVAAXX100126.4 45 CTT Context D 45.0000 139 0.45 -20GAVAAXX100126.4 45 CTT Context I 45.0000 139 0.00 +20GAVAAXX100126.4 45 CTT Context D 45.0000 138 0.31 +20GAVAAXX100126.4 45 CTT Context I 45.0000 138 0.00 20GAVAAXX100126.4 45 GAA Context D 45.0000 118 0.00 20GAVAAXX100126.4 45 GAA Context I 45.0000 118 0.00 20GAVAAXX100126.4 45 GAC Context D 45.0000 72 0.00 @@ -39237,7 +39234,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.5 38 20 Cycle M 38.0000 11 0.00 20GAVAAXX100126.5 38 21 Cycle M 38.0000 17 1.00 20GAVAAXX100126.5 38 22 Cycle M 38.0000 13 0.00 -20GAVAAXX100126.5 38 23 Cycle M 38.0000 11 0.00 +20GAVAAXX100126.5 38 23 Cycle M 38.0000 10 0.00 20GAVAAXX100126.5 38 24 Cycle M 38.0000 10 0.00 20GAVAAXX100126.5 38 25 Cycle M 38.0000 12 0.00 20GAVAAXX100126.5 38 26 Cycle M 38.0000 15 0.00 @@ -39333,7 +39330,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.5 38 TA Context M 38.0000 89 0.00 20GAVAAXX100126.5 38 TC Context M 38.0000 51 0.00 20GAVAAXX100126.5 38 TG Context M 38.0000 268 1.00 -20GAVAAXX100126.5 38 TT Context M 38.0000 169 0.00 +20GAVAAXX100126.5 38 TT Context M 38.0000 168 0.00 20GAVAAXX100126.5 39 -11 Cycle M 39.0000 1 0.00 20GAVAAXX100126.5 39 -12 Cycle M 39.0000 3 0.00 20GAVAAXX100126.5 39 -14 Cycle M 39.0000 1 0.00 @@ -39759,8 +39756,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.5 45 21 Cycle I 45.0000 33 0.00 20GAVAAXX100126.5 45 22 Cycle D 45.0000 32 0.00 20GAVAAXX100126.5 45 22 Cycle I 45.0000 32 0.00 -20GAVAAXX100126.5 45 23 Cycle D 45.0000 33 0.14 -20GAVAAXX100126.5 45 23 Cycle I 45.0000 33 0.00 +20GAVAAXX100126.5 45 23 Cycle D 45.0000 32 0.00 +20GAVAAXX100126.5 45 23 Cycle I 45.0000 32 0.00 20GAVAAXX100126.5 45 24 Cycle D 45.0000 33 0.14 20GAVAAXX100126.5 45 24 Cycle I 45.0000 33 0.00 20GAVAAXX100126.5 45 25 Cycle D 45.0000 32 0.14 @@ -39981,8 +39978,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.5 45 CTC Context I 45.0000 103 0.00 20GAVAAXX100126.5 45 CTG Context D 45.0000 132 0.00 20GAVAAXX100126.5 45 CTG Context I 45.0000 132 0.00 -20GAVAAXX100126.5 45 CTT Context D 45.0000 102 0.14 -20GAVAAXX100126.5 45 CTT Context I 45.0000 102 0.00 +20GAVAAXX100126.5 45 CTT Context D 45.0000 101 0.00 +20GAVAAXX100126.5 45 CTT Context I 45.0000 101 0.00 20GAVAAXX100126.5 45 GAA Context D 45.0000 148 0.00 20GAVAAXX100126.5 45 GAA Context I 45.0000 148 0.00 20GAVAAXX100126.5 45 GAC Context D 45.0000 56 0.00 @@ -41050,7 +41047,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.6 31 -46 Cycle M 31.0000 2 0.00 20GAVAAXX100126.6 31 -47 Cycle M 31.0000 2 0.00 20GAVAAXX100126.6 31 -48 Cycle M 31.0000 3 0.00 -20GAVAAXX100126.6 31 -5 Cycle M 31.0000 6 0.00 +20GAVAAXX100126.6 31 -5 Cycle M 31.0000 5 0.00 20GAVAAXX100126.6 31 -50 Cycle M 31.0000 4 0.00 20GAVAAXX100126.6 31 -51 Cycle M 31.0000 1 0.00 20GAVAAXX100126.6 31 -52 Cycle M 31.0000 1 0.00 @@ -41126,7 +41123,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.6 31 94 Cycle M 31.0000 1 0.00 20GAVAAXX100126.6 31 97 Cycle M 31.0000 2 0.00 20GAVAAXX100126.6 31 99 Cycle M 31.0000 1 0.00 -20GAVAAXX100126.6 31 AA Context M 31.0000 14 0.00 +20GAVAAXX100126.6 31 AA Context M 31.0000 13 0.00 20GAVAAXX100126.6 31 AC Context M 31.0000 17 0.00 20GAVAAXX100126.6 31 AG Context M 31.0000 16 0.00 20GAVAAXX100126.6 31 AT Context M 31.0000 6 0.00 @@ -42228,7 +42225,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.6 38 40 Cycle M 38.0000 13 0.00 20GAVAAXX100126.6 38 41 Cycle M 38.0000 9 0.00 20GAVAAXX100126.6 38 42 Cycle M 38.0000 13 0.00 -20GAVAAXX100126.6 38 43 Cycle M 38.0000 17 0.00 +20GAVAAXX100126.6 38 43 Cycle M 38.0000 16 0.00 20GAVAAXX100126.6 38 44 Cycle M 38.0000 14 0.00 20GAVAAXX100126.6 38 45 Cycle M 38.0000 14 0.00 20GAVAAXX100126.6 38 46 Cycle M 38.0000 10 0.00 @@ -42304,7 +42301,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.6 38 TA Context M 38.0000 105 0.00 20GAVAAXX100126.6 38 TC Context M 38.0000 12 0.00 20GAVAAXX100126.6 38 TG Context M 38.0000 263 2.00 -20GAVAAXX100126.6 38 TT Context M 38.0000 214 0.00 +20GAVAAXX100126.6 38 TT Context M 38.0000 213 0.00 20GAVAAXX100126.6 39 -12 Cycle M 39.0000 2 0.00 20GAVAAXX100126.6 39 -13 Cycle M 39.0000 1 0.00 20GAVAAXX100126.6 39 -14 Cycle M 39.0000 3 0.00 @@ -42552,8 +42549,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.6 45 -48 Cycle I 45.0000 39 0.00 20GAVAAXX100126.6 45 -49 Cycle D 45.0000 38 0.00 20GAVAAXX100126.6 45 -49 Cycle I 45.0000 38 0.00 -20GAVAAXX100126.6 45 -5 Cycle D 45.0000 40 0.17 -20GAVAAXX100126.6 45 -5 Cycle I 45.0000 40 0.00 +20GAVAAXX100126.6 45 -5 Cycle D 45.0000 39 0.00 +20GAVAAXX100126.6 45 -5 Cycle I 45.0000 39 0.00 20GAVAAXX100126.6 45 -50 Cycle D 45.0000 38 0.00 20GAVAAXX100126.6 45 -50 Cycle I 45.0000 38 0.00 20GAVAAXX100126.6 45 -51 Cycle D 45.0000 38 0.00 @@ -42724,8 +42721,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.6 45 41 Cycle I 45.0000 41 0.00 20GAVAAXX100126.6 45 42 Cycle D 45.0000 40 0.14 20GAVAAXX100126.6 45 42 Cycle I 45.0000 40 0.00 -20GAVAAXX100126.6 45 43 Cycle D 45.0000 41 0.29 -20GAVAAXX100126.6 45 43 Cycle I 45.0000 41 0.00 +20GAVAAXX100126.6 45 43 Cycle D 45.0000 40 0.14 +20GAVAAXX100126.6 45 43 Cycle I 45.0000 40 0.00 20GAVAAXX100126.6 45 44 Cycle D 45.0000 41 0.29 20GAVAAXX100126.6 45 44 Cycle I 45.0000 41 0.00 20GAVAAXX100126.6 45 45 Cycle D 45.0000 41 0.29 @@ -42906,10 +42903,10 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.6 45 CTC Context I 45.0000 187 0.00 20GAVAAXX100126.6 45 CTG Context D 45.0000 189 0.00 20GAVAAXX100126.6 45 CTG Context I 45.0000 189 0.00 -20GAVAAXX100126.6 45 CTT Context D 45.0000 153 0.43 -20GAVAAXX100126.6 45 CTT Context I 45.0000 153 0.00 -20GAVAAXX100126.6 45 GAA Context D 45.0000 149 0.17 -20GAVAAXX100126.6 45 GAA Context I 45.0000 149 0.00 +20GAVAAXX100126.6 45 CTT Context D 45.0000 152 0.29 +20GAVAAXX100126.6 45 CTT Context I 45.0000 152 0.00 +20GAVAAXX100126.6 45 GAA Context D 45.0000 148 0.00 +20GAVAAXX100126.6 45 GAA Context I 45.0000 148 0.00 20GAVAAXX100126.6 45 GAC Context D 45.0000 85 0.00 20GAVAAXX100126.6 45 GAC Context I 45.0000 85 0.00 20GAVAAXX100126.6 45 GAG Context D 45.0000 172 0.00 @@ -44596,7 +44593,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.7 33 -32 Cycle M 33.0000 1 0.00 20GAVAAXX100126.7 33 -33 Cycle M 33.0000 3 0.00 20GAVAAXX100126.7 33 -34 Cycle M 33.0000 3 0.00 -20GAVAAXX100126.7 33 -35 Cycle M 33.0000 3 0.00 +20GAVAAXX100126.7 33 -35 Cycle M 33.0000 2 0.00 20GAVAAXX100126.7 33 -37 Cycle M 33.0000 4 0.00 20GAVAAXX100126.7 33 -38 Cycle M 33.0000 1 0.00 20GAVAAXX100126.7 33 -39 Cycle M 33.0000 5 0.00 @@ -44709,7 +44706,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.7 33 96 Cycle M 33.0000 1 0.00 20GAVAAXX100126.7 33 98 Cycle M 33.0000 3 0.00 20GAVAAXX100126.7 33 99 Cycle M 33.0000 2 0.00 -20GAVAAXX100126.7 33 AA Context M 33.0000 15 0.00 +20GAVAAXX100126.7 33 AA Context M 33.0000 14 0.00 20GAVAAXX100126.7 33 AC Context M 33.0000 16 0.00 20GAVAAXX100126.7 33 AG Context M 33.0000 31 0.25 20GAVAAXX100126.7 33 AT Context M 33.0000 18 0.00 @@ -45829,8 +45826,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.7 45 -33 Cycle I 45.0000 39 0.00 20GAVAAXX100126.7 45 -34 Cycle D 45.0000 39 0.13 20GAVAAXX100126.7 45 -34 Cycle I 45.0000 39 0.00 -20GAVAAXX100126.7 45 -35 Cycle D 45.0000 39 0.13 -20GAVAAXX100126.7 45 -35 Cycle I 45.0000 39 0.00 +20GAVAAXX100126.7 45 -35 Cycle D 45.0000 38 0.00 +20GAVAAXX100126.7 45 -35 Cycle I 45.0000 38 0.00 20GAVAAXX100126.7 45 -36 Cycle D 45.0000 38 0.00 20GAVAAXX100126.7 45 -36 Cycle I 45.0000 38 0.00 20GAVAAXX100126.7 45 -37 Cycle D 45.0000 39 0.13 @@ -46215,8 +46212,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.7 45 CTG Context I 45.0000 180 0.00 20GAVAAXX100126.7 45 CTT Context D 45.0000 128 0.14 20GAVAAXX100126.7 45 CTT Context I 45.0000 128 0.00 -20GAVAAXX100126.7 45 GAA Context D 45.0000 148 0.25 -20GAVAAXX100126.7 45 GAA Context I 45.0000 148 0.00 +20GAVAAXX100126.7 45 GAA Context D 45.0000 147 0.13 +20GAVAAXX100126.7 45 GAA Context I 45.0000 147 0.00 20GAVAAXX100126.7 45 GAC Context D 45.0000 96 0.00 20GAVAAXX100126.7 45 GAC Context I 45.0000 96 0.00 20GAVAAXX100126.7 45 GAG Context D 45.0000 172 0.25 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.mismatches_context_size_4.recal.txt b/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.mismatches_context_size_4.recal.txt index 3e7118075a3..07dddf9f44c 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.mismatches_context_size_4.recal.txt +++ b/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.mismatches_context_size_4.recal.txt @@ -48,27 +48,27 @@ QualityScore Count QuantizedScore 22 750 24 23 853 24 24 997 24 - 25 1228 24 + 25 1227 24 26 1491 27 - 27 1728 27 + 27 1727 27 28 1781 29 29 2284 29 30 2439 30 - 31 2537 30 + 31 2536 30 32 3565 32 - 33 4141 32 + 33 4139 32 34 5194 34 - 35 7518 35 - 36 11939 36 - 37 28884 37 - 38 27993 38 - 39 15115 39 + 35 7517 35 + 36 11937 36 + 37 28883 37 + 38 27987 38 + 39 15108 39 40 778 39 41 53 39 42 0 39 43 0 39 - 44 15761 44 - 45 234039 45 + 44 9294 44 + 45 240462 45 46 0 93 47 0 93 48 0 93 @@ -121,51 +121,51 @@ QualityScore Count QuantizedScore #:GATKTable:6:48:%s:%s:%.4f:%.4f:%d:%.2f:; #:GATKTable:RecalTable0: ReadGroup EventType EmpiricalQuality EstimatedQReported Observations Errors -20FUKAAXX100202.1 D 45.0000 45.0000 7293 3.86 -20FUKAAXX100202.1 I 45.0000 45.0000 7293 0.00 -20FUKAAXX100202.1 M 27.0000 27.0392 7293 15.67 -20FUKAAXX100202.2 D 44.0000 45.0000 6464 7.56 -20FUKAAXX100202.2 I 45.0000 45.0000 6464 0.00 -20FUKAAXX100202.2 M 29.0000 30.1871 6464 20.60 -20FUKAAXX100202.3 D 45.0000 45.0000 8976 5.73 -20FUKAAXX100202.3 I 45.0000 45.0000 8976 0.00 -20FUKAAXX100202.3 M 27.0000 28.2043 8976 29.75 -20FUKAAXX100202.4 D 45.0000 45.0000 6830 3.75 -20FUKAAXX100202.4 I 45.0000 45.0000 6830 0.00 -20FUKAAXX100202.4 M 29.0000 29.0885 6830 13.00 -20FUKAAXX100202.5 D 45.0000 45.0000 7471 2.86 -20FUKAAXX100202.5 I 45.0000 45.0000 7471 0.00 -20FUKAAXX100202.5 M 28.0000 29.7339 7471 26.67 -20FUKAAXX100202.6 D 45.0000 45.0000 10026 8.40 -20FUKAAXX100202.6 I 45.0000 45.0000 10026 0.00 -20FUKAAXX100202.6 M 27.0000 28.7545 10026 27.25 -20FUKAAXX100202.7 D 45.0000 45.0000 9347 2.78 -20FUKAAXX100202.7 I 45.0000 45.0000 9347 0.00 -20FUKAAXX100202.7 M 26.0000 27.7419 9347 30.67 +20FUKAAXX100202.1 D 45.0000 45.0000 7292 3.71 +20FUKAAXX100202.1 I 45.0000 45.0000 7292 0.00 +20FUKAAXX100202.1 M 27.0000 27.0386 7292 15.67 +20FUKAAXX100202.2 D 45.0000 45.0000 6462 7.33 +20FUKAAXX100202.2 I 45.0000 45.0000 6462 0.00 +20FUKAAXX100202.2 M 29.0000 30.1859 6462 20.60 +20FUKAAXX100202.3 D 45.0000 45.0000 8974 5.46 +20FUKAAXX100202.3 I 45.0000 45.0000 8974 0.00 +20FUKAAXX100202.3 M 27.0000 28.2034 8974 29.75 +20FUKAAXX100202.4 D 45.0000 45.0000 6828 3.50 +20FUKAAXX100202.4 I 45.0000 45.0000 6828 0.00 +20FUKAAXX100202.4 M 29.0000 29.0874 6828 13.00 +20FUKAAXX100202.5 D 45.0000 45.0000 7470 2.71 +20FUKAAXX100202.5 I 45.0000 45.0000 7470 0.00 +20FUKAAXX100202.5 M 28.0000 29.7334 7470 26.67 +20FUKAAXX100202.6 D 45.0000 45.0000 10023 7.95 +20FUKAAXX100202.6 I 45.0000 45.0000 10023 0.00 +20FUKAAXX100202.6 M 27.0000 28.7535 10023 27.25 +20FUKAAXX100202.7 D 45.0000 45.0000 9345 2.57 +20FUKAAXX100202.7 I 45.0000 45.0000 9345 0.00 +20FUKAAXX100202.7 M 26.0000 27.7411 9345 30.67 20FUKAAXX100202.8 D 45.0000 45.0000 8152 3.75 20FUKAAXX100202.8 I 45.0000 45.0000 8152 0.00 20FUKAAXX100202.8 M 28.0000 29.0288 8152 24.00 -20GAVAAXX100126.1 D 44.0000 45.0000 9297 9.12 -20GAVAAXX100126.1 I 45.0000 45.0000 9297 1.00 -20GAVAAXX100126.1 M 26.0000 27.6243 9297 29.75 -20GAVAAXX100126.2 D 45.0000 45.0000 8155 4.86 -20GAVAAXX100126.2 I 45.0000 45.0000 8155 0.00 -20GAVAAXX100126.2 M 26.0000 27.3758 8155 34.42 +20GAVAAXX100126.1 D 44.0000 45.0000 9294 8.52 +20GAVAAXX100126.1 I 45.0000 45.0000 9294 1.00 +20GAVAAXX100126.1 M 26.0000 27.6244 9294 29.75 +20GAVAAXX100126.2 D 45.0000 45.0000 8154 4.71 +20GAVAAXX100126.2 I 45.0000 45.0000 8154 0.00 +20GAVAAXX100126.2 M 26.0000 27.3754 8154 34.42 20GAVAAXX100126.3 D 45.0000 45.0000 6239 3.00 20GAVAAXX100126.3 I 45.0000 45.0000 6239 0.00 20GAVAAXX100126.3 M 26.0000 26.8893 6239 20.57 -20GAVAAXX100126.4 D 45.0000 45.0000 6633 2.86 -20GAVAAXX100126.4 I 45.0000 45.0000 6633 0.00 -20GAVAAXX100126.4 M 26.0000 27.0432 6633 29.33 -20GAVAAXX100126.5 D 45.0000 45.0000 5884 0.86 -20GAVAAXX100126.5 I 45.0000 45.0000 5884 0.00 -20GAVAAXX100126.5 M 27.0000 28.0717 5884 21.33 -20GAVAAXX100126.6 D 45.0000 45.0000 8002 3.69 -20GAVAAXX100126.6 I 45.0000 45.0000 8002 0.00 -20GAVAAXX100126.6 M 27.0000 28.4682 8002 27.00 -20GAVAAXX100126.7 D 45.0000 45.0000 7598 2.88 -20GAVAAXX100126.7 I 45.0000 45.0000 7598 0.00 -20GAVAAXX100126.7 M 25.0000 25.6878 7598 27.75 +20GAVAAXX100126.4 D 45.0000 45.0000 6632 2.71 +20GAVAAXX100126.4 I 45.0000 45.0000 6632 0.00 +20GAVAAXX100126.4 M 26.0000 27.0426 6632 29.33 +20GAVAAXX100126.5 D 45.0000 45.0000 5883 0.71 +20GAVAAXX100126.5 I 45.0000 45.0000 5883 0.00 +20GAVAAXX100126.5 M 27.0000 28.0710 5883 21.33 +20GAVAAXX100126.6 D 45.0000 45.0000 8000 3.38 +20GAVAAXX100126.6 I 45.0000 45.0000 8000 0.00 +20GAVAAXX100126.6 M 27.0000 28.4675 8000 27.00 +20GAVAAXX100126.7 D 45.0000 45.0000 7597 2.75 +20GAVAAXX100126.7 I 45.0000 45.0000 7597 0.00 +20GAVAAXX100126.7 M 25.0000 25.6874 7597 27.75 20GAVAAXX100126.8 D 45.0000 45.0000 8533 5.69 20GAVAAXX100126.8 I 45.0000 45.0000 8533 1.00 20GAVAAXX100126.8 M 26.0000 27.3594 8533 29.25 @@ -204,12 +204,12 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20FUKAAXX100202.1 34 M 34.0000 217 0.20 20FUKAAXX100202.1 35 M 35.0000 347 1.07 20FUKAAXX100202.1 36 M 36.0000 599 1.00 -20FUKAAXX100202.1 37 M 37.0000 1407 1.33 +20FUKAAXX100202.1 37 M 37.0000 1406 1.33 20FUKAAXX100202.1 38 M 38.0000 2058 0.33 20FUKAAXX100202.1 39 M 39.0000 741 0.00 20FUKAAXX100202.1 40 M 40.0000 16 0.00 -20FUKAAXX100202.1 45 D 45.0000 7293 3.86 -20FUKAAXX100202.1 45 I 45.0000 7293 0.00 +20FUKAAXX100202.1 45 D 45.0000 7292 3.71 +20FUKAAXX100202.1 45 I 45.0000 7292 0.00 20FUKAAXX100202.2 6 M 6.0000 1 0.00 20FUKAAXX100202.2 7 M 7.0000 1 0.00 20FUKAAXX100202.2 8 M 8.0000 3 0.00 @@ -243,10 +243,10 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20FUKAAXX100202.2 36 M 36.0000 580 4.00 20FUKAAXX100202.2 37 M 37.0000 1371 2.00 20FUKAAXX100202.2 38 M 38.0000 2181 6.00 -20FUKAAXX100202.2 39 M 39.0000 667 1.00 +20FUKAAXX100202.2 39 M 39.0000 665 1.00 20FUKAAXX100202.2 40 M 40.0000 27 0.00 -20FUKAAXX100202.2 45 D 44.0000 6464 7.56 -20FUKAAXX100202.2 45 I 45.0000 6464 0.00 +20FUKAAXX100202.2 45 D 45.0000 6462 7.33 +20FUKAAXX100202.2 45 I 45.0000 6462 0.00 20FUKAAXX100202.3 6 M 6.0000 1 1.00 20FUKAAXX100202.3 7 M 7.0000 4 0.00 20FUKAAXX100202.3 8 M 8.0000 8 0.00 @@ -277,13 +277,13 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20FUKAAXX100202.3 33 M 33.0000 245 0.00 20FUKAAXX100202.3 34 M 34.0000 262 0.00 20FUKAAXX100202.3 35 M 35.0000 463 1.00 -20FUKAAXX100202.3 36 M 36.0000 944 6.25 +20FUKAAXX100202.3 36 M 36.0000 943 6.25 20FUKAAXX100202.3 37 M 37.0000 1649 4.25 20FUKAAXX100202.3 38 M 37.0000 2837 11.25 -20FUKAAXX100202.3 39 M 39.0000 976 0.00 +20FUKAAXX100202.3 39 M 39.0000 975 0.00 20FUKAAXX100202.3 40 M 40.0000 28 0.00 -20FUKAAXX100202.3 45 D 45.0000 8976 5.73 -20FUKAAXX100202.3 45 I 45.0000 8976 0.00 +20FUKAAXX100202.3 45 D 45.0000 8974 5.46 +20FUKAAXX100202.3 45 I 45.0000 8974 0.00 20FUKAAXX100202.4 6 M 6.0000 1 0.00 20FUKAAXX100202.4 7 M 7.0000 2 1.00 20FUKAAXX100202.4 8 M 8.0000 3 1.00 @@ -317,10 +317,10 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20FUKAAXX100202.4 36 M 36.0000 633 0.00 20FUKAAXX100202.4 37 M 37.0000 1408 3.25 20FUKAAXX100202.4 38 M 38.0000 2074 3.50 -20FUKAAXX100202.4 39 M 39.0000 662 1.00 +20FUKAAXX100202.4 39 M 39.0000 660 1.00 20FUKAAXX100202.4 40 M 40.0000 20 0.00 -20FUKAAXX100202.4 45 D 45.0000 6830 3.75 -20FUKAAXX100202.4 45 I 45.0000 6830 0.00 +20FUKAAXX100202.4 45 D 45.0000 6828 3.50 +20FUKAAXX100202.4 45 I 45.0000 6828 0.00 20FUKAAXX100202.5 6 M 6.0000 1 0.00 20FUKAAXX100202.5 7 M 7.0000 3 0.00 20FUKAAXX100202.5 8 M 8.0000 2 1.00 @@ -354,10 +354,10 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20FUKAAXX100202.5 36 M 36.0000 695 2.33 20FUKAAXX100202.5 37 M 37.0000 1329 2.00 20FUKAAXX100202.5 38 M 37.0000 2579 9.80 -20FUKAAXX100202.5 39 M 39.0000 907 1.00 +20FUKAAXX100202.5 39 M 39.0000 906 1.00 20FUKAAXX100202.5 40 M 40.0000 67 0.20 -20FUKAAXX100202.5 45 D 45.0000 7471 2.86 -20FUKAAXX100202.5 45 I 45.0000 7471 0.00 +20FUKAAXX100202.5 45 D 45.0000 7470 2.71 +20FUKAAXX100202.5 45 I 45.0000 7470 0.00 20FUKAAXX100202.6 6 M 6.0000 7 4.00 20FUKAAXX100202.6 7 M 7.0000 4 2.00 20FUKAAXX100202.6 8 M 8.0000 5 0.00 @@ -387,14 +387,14 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20FUKAAXX100202.6 32 M 32.0000 226 1.00 20FUKAAXX100202.6 33 M 33.0000 231 2.00 20FUKAAXX100202.6 34 M 34.0000 302 0.00 -20FUKAAXX100202.6 35 M 35.0000 579 2.17 +20FUKAAXX100202.6 35 M 35.0000 578 2.17 20FUKAAXX100202.6 36 M 36.0000 975 2.33 20FUKAAXX100202.6 37 M 37.0000 1959 1.17 -20FUKAAXX100202.6 38 M 38.0000 3301 6.00 +20FUKAAXX100202.6 38 M 38.0000 3299 6.00 20FUKAAXX100202.6 39 M 39.0000 1111 1.00 20FUKAAXX100202.6 40 M 40.0000 43 0.00 -20FUKAAXX100202.6 45 D 45.0000 10026 8.40 -20FUKAAXX100202.6 45 I 45.0000 10026 0.00 +20FUKAAXX100202.6 45 D 45.0000 10023 7.95 +20FUKAAXX100202.6 45 I 45.0000 10023 0.00 20FUKAAXX100202.7 6 M 6.0000 5 2.00 20FUKAAXX100202.7 7 M 7.0000 5 1.00 20FUKAAXX100202.7 8 M 8.0000 9 3.33 @@ -425,13 +425,13 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20FUKAAXX100202.7 33 M 33.0000 197 0.00 20FUKAAXX100202.7 34 M 34.0000 251 0.00 20FUKAAXX100202.7 35 M 35.0000 441 1.92 -20FUKAAXX100202.7 36 M 36.0000 955 3.33 +20FUKAAXX100202.7 36 M 36.0000 954 3.33 20FUKAAXX100202.7 37 M 37.0000 1600 2.67 -20FUKAAXX100202.7 38 M 38.0000 3286 3.92 +20FUKAAXX100202.7 38 M 38.0000 3285 3.92 20FUKAAXX100202.7 39 M 39.0000 1063 1.25 20FUKAAXX100202.7 40 M 40.0000 43 0.00 -20FUKAAXX100202.7 45 D 45.0000 9347 2.78 -20FUKAAXX100202.7 45 I 45.0000 9347 0.00 +20FUKAAXX100202.7 45 D 45.0000 9345 2.57 +20FUKAAXX100202.7 45 I 45.0000 9345 0.00 20FUKAAXX100202.8 6 M 6.0000 4 2.00 20FUKAAXX100202.8 7 M 7.0000 5 0.00 20FUKAAXX100202.8 8 M 8.0000 1 0.00 @@ -488,9 +488,9 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.1 22 M 22.0000 43 1.00 20GAVAAXX100126.1 23 M 23.0000 65 0.13 20GAVAAXX100126.1 24 M 24.0000 56 0.00 -20GAVAAXX100126.1 25 M 25.0000 85 0.00 +20GAVAAXX100126.1 25 M 25.0000 84 0.00 20GAVAAXX100126.1 26 M 26.0000 104 0.00 -20GAVAAXX100126.1 27 M 27.0000 114 0.00 +20GAVAAXX100126.1 27 M 27.0000 113 0.00 20GAVAAXX100126.1 28 M 28.0000 149 0.00 20GAVAAXX100126.1 29 M 29.0000 185 1.33 20GAVAAXX100126.1 30 M 30.0000 179 0.00 @@ -502,11 +502,11 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.1 36 M 36.0000 822 2.25 20GAVAAXX100126.1 37 M 37.0000 1759 7.00 20GAVAAXX100126.1 38 M 38.0000 1880 3.25 -20GAVAAXX100126.1 39 M 39.0000 1546 2.00 +20GAVAAXX100126.1 39 M 39.0000 1545 2.00 20GAVAAXX100126.1 40 M 40.0000 243 0.00 20GAVAAXX100126.1 41 M 41.0000 23 0.00 -20GAVAAXX100126.1 45 D 44.0000 9297 9.12 -20GAVAAXX100126.1 45 I 45.0000 9297 1.00 +20GAVAAXX100126.1 45 D 44.0000 9294 8.52 +20GAVAAXX100126.1 45 I 45.0000 9294 1.00 20GAVAAXX100126.2 6 M 6.0000 10 4.00 20GAVAAXX100126.2 7 M 7.0000 8 1.00 20GAVAAXX100126.2 8 M 8.0000 6 0.00 @@ -534,7 +534,7 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.2 30 M 30.0000 169 0.00 20GAVAAXX100126.2 31 M 31.0000 222 1.25 20GAVAAXX100126.2 32 M 32.0000 336 0.00 -20GAVAAXX100126.2 33 M 33.0000 392 6.00 +20GAVAAXX100126.2 33 M 33.0000 391 6.00 20GAVAAXX100126.2 34 M 34.0000 471 0.00 20GAVAAXX100126.2 35 M 35.0000 540 2.00 20GAVAAXX100126.2 36 M 36.0000 685 1.67 @@ -543,8 +543,8 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.2 39 M 39.0000 1127 2.00 20GAVAAXX100126.2 40 M 40.0000 49 0.00 20GAVAAXX100126.2 41 M 41.0000 9 0.00 -20GAVAAXX100126.2 45 D 45.0000 8155 4.86 -20GAVAAXX100126.2 45 I 45.0000 8155 0.00 +20GAVAAXX100126.2 45 D 45.0000 8154 4.71 +20GAVAAXX100126.2 45 I 45.0000 8154 0.00 20GAVAAXX100126.3 6 M 6.0000 2 0.00 20GAVAAXX100126.3 7 M 7.0000 8 2.00 20GAVAAXX100126.3 8 M 8.0000 8 2.00 @@ -615,12 +615,12 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.4 35 M 35.0000 487 2.00 20GAVAAXX100126.4 36 M 36.0000 639 1.25 20GAVAAXX100126.4 37 M 37.0000 1224 5.50 -20GAVAAXX100126.4 38 M 38.0000 1250 4.67 +20GAVAAXX100126.4 38 M 38.0000 1249 4.67 20GAVAAXX100126.4 39 M 39.0000 857 2.00 20GAVAAXX100126.4 40 M 40.0000 33 0.00 20GAVAAXX100126.4 41 M 41.0000 1 0.00 -20GAVAAXX100126.4 45 D 45.0000 6633 2.86 -20GAVAAXX100126.4 45 I 45.0000 6633 0.00 +20GAVAAXX100126.4 45 D 45.0000 6632 2.71 +20GAVAAXX100126.4 45 I 45.0000 6632 0.00 20GAVAAXX100126.5 6 M 6.0000 4 0.00 20GAVAAXX100126.5 7 M 7.0000 8 3.00 20GAVAAXX100126.5 8 M 8.0000 4 1.00 @@ -653,12 +653,12 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.5 35 M 35.0000 328 1.00 20GAVAAXX100126.5 36 M 36.0000 583 0.33 20GAVAAXX100126.5 37 M 37.0000 1187 2.00 -20GAVAAXX100126.5 38 M 38.0000 1446 2.00 +20GAVAAXX100126.5 38 M 38.0000 1445 2.00 20GAVAAXX100126.5 39 M 39.0000 909 2.00 20GAVAAXX100126.5 40 M 40.0000 43 0.00 20GAVAAXX100126.5 41 M 41.0000 5 0.00 -20GAVAAXX100126.5 45 D 45.0000 5884 0.86 -20GAVAAXX100126.5 45 I 45.0000 5884 0.00 +20GAVAAXX100126.5 45 D 45.0000 5883 0.71 +20GAVAAXX100126.5 45 I 45.0000 5883 0.00 20GAVAAXX100126.6 6 M 6.0000 4 2.00 20GAVAAXX100126.6 7 M 7.0000 6 0.00 20GAVAAXX100126.6 8 M 8.0000 9 3.00 @@ -684,18 +684,18 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.6 28 M 28.0000 105 0.00 20GAVAAXX100126.6 29 M 29.0000 158 1.00 20GAVAAXX100126.6 30 M 30.0000 144 0.00 -20GAVAAXX100126.6 31 M 31.0000 194 1.00 +20GAVAAXX100126.6 31 M 31.0000 193 1.00 20GAVAAXX100126.6 32 M 32.0000 239 0.00 20GAVAAXX100126.6 33 M 33.0000 358 0.00 20GAVAAXX100126.6 34 M 34.0000 481 1.00 20GAVAAXX100126.6 35 M 35.0000 578 2.00 20GAVAAXX100126.6 36 M 36.0000 845 2.00 20GAVAAXX100126.6 37 M 37.0000 1617 4.00 -20GAVAAXX100126.6 38 M 38.0000 1661 3.00 +20GAVAAXX100126.6 38 M 38.0000 1660 3.00 20GAVAAXX100126.6 39 M 39.0000 1030 2.00 20GAVAAXX100126.6 40 M 40.0000 35 0.00 -20GAVAAXX100126.6 45 D 45.0000 8002 3.69 -20GAVAAXX100126.6 45 I 45.0000 8002 0.00 +20GAVAAXX100126.6 45 D 45.0000 8000 3.38 +20GAVAAXX100126.6 45 I 45.0000 8000 0.00 20GAVAAXX100126.7 6 M 6.0000 7 1.00 20GAVAAXX100126.7 7 M 7.0000 16 6.00 20GAVAAXX100126.7 8 M 8.0000 16 2.00 @@ -723,7 +723,7 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.7 30 M 30.0000 192 0.00 20GAVAAXX100126.7 31 M 31.0000 200 0.00 20GAVAAXX100126.7 32 M 32.0000 228 1.00 -20GAVAAXX100126.7 33 M 33.0000 382 1.25 +20GAVAAXX100126.7 33 M 33.0000 381 1.25 20GAVAAXX100126.7 34 M 34.0000 412 2.00 20GAVAAXX100126.7 35 M 35.0000 554 0.00 20GAVAAXX100126.7 36 M 36.0000 700 1.50 @@ -732,8 +732,8 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.7 39 M 39.0000 881 1.00 20GAVAAXX100126.7 40 M 40.0000 49 0.00 20GAVAAXX100126.7 41 M 41.0000 6 0.00 -20GAVAAXX100126.7 45 D 45.0000 7598 2.88 -20GAVAAXX100126.7 45 I 45.0000 7598 0.00 +20GAVAAXX100126.7 45 D 45.0000 7597 2.75 +20GAVAAXX100126.7 45 I 45.0000 7597 0.00 20GAVAAXX100126.8 6 M 6.0000 9 1.00 20GAVAAXX100126.8 7 M 7.0000 4 0.00 20GAVAAXX100126.8 8 M 8.0000 7 1.00 @@ -773,7 +773,7 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.8 45 D 45.0000 8533 5.69 20GAVAAXX100126.8 45 I 45.0000 8533 1.00 -#:GATKTable:8:76960:%s:%d:%s:%s:%s:%.4f:%d:%.2f:; +#:GATKTable:8:76956:%s:%d:%s:%s:%s:%.4f:%d:%.2f:; #:GATKTable:RecalTable2: ReadGroup QualityScore CovariateValue CovariateName EventType EmpiricalQuality Observations Errors 20FUKAAXX100202.1 6 -31 Cycle M 6.0000 1 0.00 @@ -4264,7 +4264,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.1 37 -33 Cycle M 37.0000 5 0.00 20FUKAAXX100202.1 37 -34 Cycle M 37.0000 13 0.00 20FUKAAXX100202.1 37 -35 Cycle M 37.0000 12 0.00 -20FUKAAXX100202.1 37 -36 Cycle M 37.0000 14 0.00 +20FUKAAXX100202.1 37 -36 Cycle M 37.0000 13 0.00 20FUKAAXX100202.1 37 -37 Cycle M 37.0000 10 0.00 20FUKAAXX100202.1 37 -38 Cycle M 37.0000 9 0.00 20FUKAAXX100202.1 37 -39 Cycle M 37.0000 9 0.00 @@ -4600,7 +4600,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.1 37 TCTA Context M 37.0000 2 0.00 20FUKAAXX100202.1 37 TCTC Context M 37.0000 26 0.00 20FUKAAXX100202.1 37 TCTG Context M 37.0000 5 0.00 -20FUKAAXX100202.1 37 TCTT Context M 37.0000 13 0.00 +20FUKAAXX100202.1 37 TCTT Context M 37.0000 12 0.00 20FUKAAXX100202.1 37 TGAA Context M 37.0000 1 0.00 20FUKAAXX100202.1 37 TGAG Context M 37.0000 6 0.00 20FUKAAXX100202.1 37 TGAT Context M 37.0000 3 0.00 @@ -5328,8 +5328,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.1 45 -34 Cycle I 45.0000 37 0.00 20FUKAAXX100202.1 45 -35 Cycle D 45.0000 37 0.00 20FUKAAXX100202.1 45 -35 Cycle I 45.0000 37 0.00 -20FUKAAXX100202.1 45 -36 Cycle D 45.0000 37 0.14 -20FUKAAXX100202.1 45 -36 Cycle I 45.0000 37 0.00 +20FUKAAXX100202.1 45 -36 Cycle D 45.0000 36 0.00 +20FUKAAXX100202.1 45 -36 Cycle I 45.0000 36 0.00 20FUKAAXX100202.1 45 -37 Cycle D 45.0000 37 0.14 20FUKAAXX100202.1 45 -37 Cycle I 45.0000 37 0.00 20FUKAAXX100202.1 45 -38 Cycle D 45.0000 38 0.14 @@ -5710,8 +5710,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.1 45 CTC Context I 45.0000 165 0.00 20FUKAAXX100202.1 45 CTG Context D 45.0000 167 0.00 20FUKAAXX100202.1 45 CTG Context I 45.0000 167 0.00 -20FUKAAXX100202.1 45 CTT Context D 45.0000 148 0.29 -20FUKAAXX100202.1 45 CTT Context I 45.0000 148 0.00 +20FUKAAXX100202.1 45 CTT Context D 45.0000 147 0.14 +20FUKAAXX100202.1 45 CTT Context I 45.0000 147 0.00 20FUKAAXX100202.1 45 GAA Context D 45.0000 142 0.29 20FUKAAXX100202.1 45 GAA Context I 45.0000 142 0.00 20FUKAAXX100202.1 45 GAC Context D 45.0000 81 0.00 @@ -9028,7 +9028,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.2 39 14 Cycle M 39.0000 3 0.00 20FUKAAXX100202.2 39 15 Cycle M 39.0000 3 0.00 20FUKAAXX100202.2 39 16 Cycle M 39.0000 2 0.00 -20FUKAAXX100202.2 39 17 Cycle M 39.0000 3 0.00 +20FUKAAXX100202.2 39 17 Cycle M 39.0000 2 0.00 20FUKAAXX100202.2 39 18 Cycle M 39.0000 7 0.00 20FUKAAXX100202.2 39 19 Cycle M 39.0000 4 0.00 20FUKAAXX100202.2 39 20 Cycle M 39.0000 3 0.00 @@ -9088,7 +9088,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.2 39 77 Cycle M 39.0000 5 0.00 20FUKAAXX100202.2 39 78 Cycle M 39.0000 2 0.00 20FUKAAXX100202.2 39 79 Cycle M 39.0000 6 0.00 -20FUKAAXX100202.2 39 8 Cycle M 39.0000 4 0.00 +20FUKAAXX100202.2 39 8 Cycle M 39.0000 3 0.00 20FUKAAXX100202.2 39 80 Cycle M 39.0000 2 0.00 20FUKAAXX100202.2 39 81 Cycle M 39.0000 2 0.00 20FUKAAXX100202.2 39 82 Cycle M 39.0000 2 0.00 @@ -9164,7 +9164,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.2 39 TCAA Context M 39.0000 22 0.00 20FUKAAXX100202.2 39 TCCA Context M 39.0000 6 0.00 20FUKAAXX100202.2 39 TCCT Context M 39.0000 24 0.00 -20FUKAAXX100202.2 39 TGAA Context M 39.0000 31 0.00 +20FUKAAXX100202.2 39 TGAA Context M 39.0000 29 0.00 20FUKAAXX100202.2 39 TGCT Context M 39.0000 24 0.00 20FUKAAXX100202.2 39 TGGA Context M 39.0000 3 0.00 20FUKAAXX100202.2 39 TGGG Context M 39.0000 1 0.00 @@ -9398,8 +9398,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.2 45 15 Cycle I 45.0000 32 0.00 20FUKAAXX100202.2 45 16 Cycle D 45.0000 32 0.13 20FUKAAXX100202.2 45 16 Cycle I 45.0000 32 0.00 -20FUKAAXX100202.2 45 17 Cycle D 45.0000 32 0.13 -20FUKAAXX100202.2 45 17 Cycle I 45.0000 32 0.00 +20FUKAAXX100202.2 45 17 Cycle D 45.0000 31 0.00 +20FUKAAXX100202.2 45 17 Cycle I 45.0000 31 0.00 20FUKAAXX100202.2 45 18 Cycle D 45.0000 31 0.00 20FUKAAXX100202.2 45 18 Cycle I 45.0000 31 0.00 20FUKAAXX100202.2 45 19 Cycle D 45.0000 32 0.25 @@ -9530,8 +9530,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.2 45 78 Cycle I 45.0000 30 0.00 20FUKAAXX100202.2 45 79 Cycle D 45.0000 29 0.00 20FUKAAXX100202.2 45 79 Cycle I 45.0000 29 0.00 -20FUKAAXX100202.2 45 8 Cycle D 45.0000 32 0.11 -20FUKAAXX100202.2 45 8 Cycle I 45.0000 32 0.00 +20FUKAAXX100202.2 45 8 Cycle D 45.0000 31 0.00 +20FUKAAXX100202.2 45 8 Cycle I 45.0000 31 0.00 20FUKAAXX100202.2 45 80 Cycle D 45.0000 30 0.00 20FUKAAXX100202.2 45 80 Cycle I 45.0000 30 0.00 20FUKAAXX100202.2 45 81 Cycle D 45.0000 29 0.00 @@ -9634,8 +9634,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.2 45 CTG Context I 45.0000 136 0.00 20FUKAAXX100202.2 45 CTT Context D 45.0000 128 0.65 20FUKAAXX100202.2 45 CTT Context I 45.0000 128 0.00 -20FUKAAXX100202.2 45 GAA Context D 45.0000 118 0.49 -20FUKAAXX100202.2 45 GAA Context I 45.0000 118 0.00 +20FUKAAXX100202.2 45 GAA Context D 45.0000 116 0.25 +20FUKAAXX100202.2 45 GAA Context I 45.0000 116 0.00 20FUKAAXX100202.2 45 GAC Context D 45.0000 69 0.00 20FUKAAXX100202.2 45 GAC Context I 45.0000 69 0.00 20FUKAAXX100202.2 45 GAG Context D 45.0000 137 0.49 @@ -12974,7 +12974,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.3 36 93 Cycle M 36.0000 5 0.00 20FUKAAXX100202.3 36 94 Cycle M 36.0000 4 0.00 20FUKAAXX100202.3 36 95 Cycle M 36.0000 6 0.00 -20FUKAAXX100202.3 36 96 Cycle M 36.0000 6 0.00 +20FUKAAXX100202.3 36 96 Cycle M 36.0000 5 0.00 20FUKAAXX100202.3 36 97 Cycle M 36.0000 3 0.00 20FUKAAXX100202.3 36 98 Cycle M 36.0000 4 0.00 20FUKAAXX100202.3 36 99 Cycle M 36.0000 5 0.00 @@ -13142,7 +13142,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.3 36 TCTA Context M 36.0000 3 0.00 20FUKAAXX100202.3 36 TCTC Context M 36.0000 2 0.00 20FUKAAXX100202.3 36 TCTG Context M 36.0000 4 0.00 -20FUKAAXX100202.3 36 TCTT Context M 36.0000 5 0.00 +20FUKAAXX100202.3 36 TCTT Context M 36.0000 4 0.00 20FUKAAXX100202.3 36 TGAA Context M 36.0000 3 0.00 20FUKAAXX100202.3 36 TGAC Context M 36.0000 15 0.00 20FUKAAXX100202.3 36 TGAG Context M 36.0000 4 0.00 @@ -13967,7 +13967,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.3 39 -18 Cycle M 39.0000 6 0.00 20FUKAAXX100202.3 39 -19 Cycle M 39.0000 1 0.00 20FUKAAXX100202.3 39 -20 Cycle M 39.0000 4 0.00 -20FUKAAXX100202.3 39 -21 Cycle M 39.0000 7 0.00 +20FUKAAXX100202.3 39 -21 Cycle M 39.0000 6 0.00 20FUKAAXX100202.3 39 -22 Cycle M 39.0000 10 0.00 20FUKAAXX100202.3 39 -23 Cycle M 39.0000 5 0.00 20FUKAAXX100202.3 39 -25 Cycle M 39.0000 1 0.00 @@ -14199,7 +14199,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.3 39 TCAG Context M 39.0000 1 0.00 20FUKAAXX100202.3 39 TCCA Context M 39.0000 15 0.00 20FUKAAXX100202.3 39 TCCT Context M 39.0000 36 0.00 -20FUKAAXX100202.3 39 TGAA Context M 39.0000 41 0.00 +20FUKAAXX100202.3 39 TGAA Context M 39.0000 40 0.00 20FUKAAXX100202.3 39 TGCA Context M 39.0000 7 0.00 20FUKAAXX100202.3 39 TGCT Context M 39.0000 16 0.00 20FUKAAXX100202.3 39 TGGA Context M 39.0000 4 0.00 @@ -14254,8 +14254,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.3 45 -19 Cycle I 45.0000 49 0.00 20FUKAAXX100202.3 45 -20 Cycle D 45.0000 49 0.13 20FUKAAXX100202.3 45 -20 Cycle I 45.0000 49 0.00 -20FUKAAXX100202.3 45 -21 Cycle D 45.0000 49 0.13 -20FUKAAXX100202.3 45 -21 Cycle I 45.0000 49 0.00 +20FUKAAXX100202.3 45 -21 Cycle D 45.0000 48 0.00 +20FUKAAXX100202.3 45 -21 Cycle I 45.0000 48 0.00 20FUKAAXX100202.3 45 -22 Cycle D 45.0000 48 0.00 20FUKAAXX100202.3 45 -22 Cycle I 45.0000 48 0.00 20FUKAAXX100202.3 45 -23 Cycle D 45.0000 49 0.13 @@ -14600,8 +14600,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.3 45 94 Cycle I 45.0000 39 0.00 20FUKAAXX100202.3 45 95 Cycle D 45.0000 38 0.00 20FUKAAXX100202.3 45 95 Cycle I 45.0000 38 0.00 -20FUKAAXX100202.3 45 96 Cycle D 45.0000 39 0.14 -20FUKAAXX100202.3 45 96 Cycle I 45.0000 39 0.00 +20FUKAAXX100202.3 45 96 Cycle D 45.0000 38 0.00 +20FUKAAXX100202.3 45 96 Cycle I 45.0000 38 0.00 20FUKAAXX100202.3 45 97 Cycle D 45.0000 39 0.14 20FUKAAXX100202.3 45 97 Cycle I 45.0000 39 0.00 20FUKAAXX100202.3 45 AAA Context D 45.0000 201 0.38 @@ -14666,10 +14666,10 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.3 45 CTC Context I 45.0000 176 0.00 20FUKAAXX100202.3 45 CTG Context D 45.0000 198 0.00 20FUKAAXX100202.3 45 CTG Context I 45.0000 198 0.00 -20FUKAAXX100202.3 45 CTT Context D 45.0000 176 0.29 -20FUKAAXX100202.3 45 CTT Context I 45.0000 176 0.00 -20FUKAAXX100202.3 45 GAA Context D 45.0000 173 0.50 -20FUKAAXX100202.3 45 GAA Context I 45.0000 173 0.00 +20FUKAAXX100202.3 45 CTT Context D 45.0000 175 0.14 +20FUKAAXX100202.3 45 CTT Context I 45.0000 175 0.00 +20FUKAAXX100202.3 45 GAA Context D 45.0000 172 0.38 +20FUKAAXX100202.3 45 GAA Context I 45.0000 172 0.00 20FUKAAXX100202.3 45 GAC Context D 45.0000 85 0.00 20FUKAAXX100202.3 45 GAC Context I 45.0000 85 0.00 20FUKAAXX100202.3 45 GAG Context D 45.0000 177 0.50 @@ -18443,13 +18443,13 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.4 39 25 Cycle M 39.0000 3 0.00 20FUKAAXX100202.4 39 26 Cycle M 39.0000 1 0.00 20FUKAAXX100202.4 39 27 Cycle M 39.0000 2 0.00 -20FUKAAXX100202.4 39 28 Cycle M 39.0000 3 0.00 +20FUKAAXX100202.4 39 28 Cycle M 39.0000 2 0.00 20FUKAAXX100202.4 39 29 Cycle M 39.0000 3 0.00 20FUKAAXX100202.4 39 30 Cycle M 39.0000 4 0.00 20FUKAAXX100202.4 39 31 Cycle M 39.0000 4 0.00 20FUKAAXX100202.4 39 32 Cycle M 39.0000 7 0.00 20FUKAAXX100202.4 39 33 Cycle M 39.0000 3 0.00 -20FUKAAXX100202.4 39 34 Cycle M 39.0000 5 0.00 +20FUKAAXX100202.4 39 34 Cycle M 39.0000 4 0.00 20FUKAAXX100202.4 39 35 Cycle M 39.0000 2 0.00 20FUKAAXX100202.4 39 36 Cycle M 39.0000 1 0.00 20FUKAAXX100202.4 39 37 Cycle M 39.0000 3 0.00 @@ -18569,7 +18569,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.4 39 TCAG Context M 39.0000 1 0.00 20FUKAAXX100202.4 39 TCCA Context M 39.0000 11 0.00 20FUKAAXX100202.4 39 TCCT Context M 39.0000 27 0.00 -20FUKAAXX100202.4 39 TGAA Context M 39.0000 24 0.00 +20FUKAAXX100202.4 39 TGAA Context M 39.0000 22 0.00 20FUKAAXX100202.4 39 TGCA Context M 39.0000 4 0.00 20FUKAAXX100202.4 39 TGCT Context M 39.0000 20 0.00 20FUKAAXX100202.4 39 TGGA Context M 39.0000 2 0.00 @@ -18827,8 +18827,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.4 45 26 Cycle I 45.0000 32 0.00 20FUKAAXX100202.4 45 27 Cycle D 45.0000 32 0.13 20FUKAAXX100202.4 45 27 Cycle I 45.0000 32 0.00 -20FUKAAXX100202.4 45 28 Cycle D 45.0000 32 0.13 -20FUKAAXX100202.4 45 28 Cycle I 45.0000 32 0.00 +20FUKAAXX100202.4 45 28 Cycle D 45.0000 31 0.00 +20FUKAAXX100202.4 45 28 Cycle I 45.0000 31 0.00 20FUKAAXX100202.4 45 29 Cycle D 45.0000 31 0.13 20FUKAAXX100202.4 45 29 Cycle I 45.0000 31 0.00 20FUKAAXX100202.4 45 30 Cycle D 45.0000 31 0.25 @@ -18839,8 +18839,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.4 45 32 Cycle I 45.0000 32 0.00 20FUKAAXX100202.4 45 33 Cycle D 45.0000 32 0.13 20FUKAAXX100202.4 45 33 Cycle I 45.0000 32 0.00 -20FUKAAXX100202.4 45 34 Cycle D 45.0000 32 0.13 -20FUKAAXX100202.4 45 34 Cycle I 45.0000 32 0.00 +20FUKAAXX100202.4 45 34 Cycle D 45.0000 31 0.00 +20FUKAAXX100202.4 45 34 Cycle I 45.0000 31 0.00 20FUKAAXX100202.4 45 35 Cycle D 45.0000 31 0.00 20FUKAAXX100202.4 45 35 Cycle I 45.0000 31 0.00 20FUKAAXX100202.4 45 36 Cycle D 45.0000 32 0.13 @@ -19041,8 +19041,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.4 45 CTG Context I 45.0000 141 0.00 20FUKAAXX100202.4 45 CTT Context D 45.0000 132 0.14 20FUKAAXX100202.4 45 CTT Context I 45.0000 132 0.00 -20FUKAAXX100202.4 45 GAA Context D 45.0000 103 0.38 -20FUKAAXX100202.4 45 GAA Context I 45.0000 103 0.00 +20FUKAAXX100202.4 45 GAA Context D 45.0000 101 0.13 +20FUKAAXX100202.4 45 GAA Context I 45.0000 101 0.00 20FUKAAXX100202.4 45 GAC Context D 45.0000 80 0.00 20FUKAAXX100202.4 45 GAC Context I 45.0000 80 0.00 20FUKAAXX100202.4 45 GAG Context D 45.0000 155 0.38 @@ -22686,7 +22686,6 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.5 38 TTTT Context M 38.0000 13 0.00 20FUKAAXX100202.5 39 -100 Cycle M 39.0000 1 0.00 20FUKAAXX100202.5 39 -14 Cycle M 39.0000 2 0.00 -20FUKAAXX100202.5 39 -15 Cycle M 39.0000 1 0.00 20FUKAAXX100202.5 39 -16 Cycle M 39.0000 6 0.00 20FUKAAXX100202.5 39 -17 Cycle M 39.0000 4 0.00 20FUKAAXX100202.5 39 -18 Cycle M 39.0000 4 0.00 @@ -22939,7 +22938,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.5 39 TCAT Context M 39.0000 1 0.00 20FUKAAXX100202.5 39 TCCA Context M 39.0000 14 0.00 20FUKAAXX100202.5 39 TCCT Context M 39.0000 23 0.00 -20FUKAAXX100202.5 39 TGAA Context M 39.0000 33 0.00 +20FUKAAXX100202.5 39 TGAA Context M 39.0000 32 0.00 20FUKAAXX100202.5 39 TGAG Context M 39.0000 2 0.00 20FUKAAXX100202.5 39 TGCA Context M 39.0000 7 0.00 20FUKAAXX100202.5 39 TGCT Context M 39.0000 13 0.00 @@ -23008,8 +23007,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.5 45 -13 Cycle I 45.0000 39 0.00 20FUKAAXX100202.5 45 -14 Cycle D 45.0000 39 0.14 20FUKAAXX100202.5 45 -14 Cycle I 45.0000 39 0.00 -20FUKAAXX100202.5 45 -15 Cycle D 45.0000 39 0.14 -20FUKAAXX100202.5 45 -15 Cycle I 45.0000 39 0.00 +20FUKAAXX100202.5 45 -15 Cycle D 45.0000 38 0.00 +20FUKAAXX100202.5 45 -15 Cycle I 45.0000 38 0.00 20FUKAAXX100202.5 45 -16 Cycle D 45.0000 37 0.00 20FUKAAXX100202.5 45 -16 Cycle I 45.0000 37 0.00 20FUKAAXX100202.5 45 -17 Cycle D 45.0000 39 0.14 @@ -23434,8 +23433,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.5 45 CTG Context I 45.0000 154 0.00 20FUKAAXX100202.5 45 CTT Context D 45.0000 121 0.14 20FUKAAXX100202.5 45 CTT Context I 45.0000 121 0.00 -20FUKAAXX100202.5 45 GAA Context D 45.0000 162 0.29 -20FUKAAXX100202.5 45 GAA Context I 45.0000 162 0.00 +20FUKAAXX100202.5 45 GAA Context D 45.0000 161 0.14 +20FUKAAXX100202.5 45 GAA Context I 45.0000 161 0.00 20FUKAAXX100202.5 45 GAC Context D 45.0000 76 0.00 20FUKAAXX100202.5 45 GAC Context I 45.0000 76 0.00 20FUKAAXX100202.5 45 GAG Context D 45.0000 173 0.29 @@ -26191,7 +26190,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 35 -94 Cycle M 35.0000 2 0.00 20FUKAAXX100202.6 35 -95 Cycle M 35.0000 5 0.00 20FUKAAXX100202.6 35 -96 Cycle M 35.0000 1 0.00 -20FUKAAXX100202.6 35 -97 Cycle M 35.0000 3 0.00 +20FUKAAXX100202.6 35 -97 Cycle M 35.0000 2 0.00 20FUKAAXX100202.6 35 -98 Cycle M 35.0000 4 0.00 20FUKAAXX100202.6 35 -99 Cycle M 35.0000 2 0.00 20FUKAAXX100202.6 35 1 Cycle M 35.0000 51 0.50 @@ -26416,7 +26415,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 35 TCTA Context M 35.0000 1 0.00 20FUKAAXX100202.6 35 TCTC Context M 35.0000 2 0.00 20FUKAAXX100202.6 35 TCTG Context M 35.0000 1 0.00 -20FUKAAXX100202.6 35 TCTT Context M 35.0000 2 0.00 +20FUKAAXX100202.6 35 TCTT Context M 35.0000 1 0.00 20FUKAAXX100202.6 35 TGAA Context M 35.0000 7 0.00 20FUKAAXX100202.6 35 TGAC Context M 35.0000 3 0.00 20FUKAAXX100202.6 35 TGAG Context M 35.0000 4 0.00 @@ -27260,7 +27259,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 38 -42 Cycle M 38.0000 17 0.00 20FUKAAXX100202.6 38 -43 Cycle M 38.0000 15 0.00 20FUKAAXX100202.6 38 -44 Cycle M 38.0000 21 0.00 -20FUKAAXX100202.6 38 -45 Cycle M 38.0000 13 0.00 +20FUKAAXX100202.6 38 -45 Cycle M 38.0000 12 0.00 20FUKAAXX100202.6 38 -46 Cycle M 38.0000 23 0.00 20FUKAAXX100202.6 38 -47 Cycle M 38.0000 19 0.00 20FUKAAXX100202.6 38 -48 Cycle M 38.0000 20 0.00 @@ -27401,7 +27400,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 38 85 Cycle M 38.0000 23 0.00 20FUKAAXX100202.6 38 86 Cycle M 38.0000 23 0.00 20FUKAAXX100202.6 38 87 Cycle M 38.0000 15 0.00 -20FUKAAXX100202.6 38 88 Cycle M 38.0000 18 1.00 +20FUKAAXX100202.6 38 88 Cycle M 38.0000 17 1.00 20FUKAAXX100202.6 38 89 Cycle M 38.0000 19 0.00 20FUKAAXX100202.6 38 9 Cycle M 38.0000 13 0.00 20FUKAAXX100202.6 38 90 Cycle M 38.0000 14 0.00 @@ -27594,7 +27593,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 38 TCTA Context M 38.0000 14 0.00 20FUKAAXX100202.6 38 TCTC Context M 38.0000 9 0.00 20FUKAAXX100202.6 38 TCTG Context M 38.0000 34 0.00 -20FUKAAXX100202.6 38 TCTT Context M 38.0000 32 0.00 +20FUKAAXX100202.6 38 TCTT Context M 38.0000 30 0.00 20FUKAAXX100202.6 38 TGAA Context M 38.0000 4 0.00 20FUKAAXX100202.6 38 TGAG Context M 38.0000 49 0.00 20FUKAAXX100202.6 38 TGAT Context M 38.0000 35 0.00 @@ -27978,8 +27977,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 45 -43 Cycle I 45.0000 51 0.00 20FUKAAXX100202.6 45 -44 Cycle D 45.0000 49 0.00 20FUKAAXX100202.6 45 -44 Cycle I 45.0000 49 0.00 -20FUKAAXX100202.6 45 -45 Cycle D 45.0000 51 0.14 -20FUKAAXX100202.6 45 -45 Cycle I 45.0000 51 0.00 +20FUKAAXX100202.6 45 -45 Cycle D 45.0000 50 0.00 +20FUKAAXX100202.6 45 -45 Cycle I 45.0000 50 0.00 20FUKAAXX100202.6 45 -46 Cycle D 45.0000 51 0.14 20FUKAAXX100202.6 45 -46 Cycle I 45.0000 51 0.00 20FUKAAXX100202.6 45 -47 Cycle D 45.0000 51 0.14 @@ -28092,8 +28091,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 45 -95 Cycle I 45.0000 36 0.00 20FUKAAXX100202.6 45 -96 Cycle D 45.0000 35 0.00 20FUKAAXX100202.6 45 -96 Cycle I 45.0000 35 0.00 -20FUKAAXX100202.6 45 -97 Cycle D 45.0000 36 0.17 -20FUKAAXX100202.6 45 -97 Cycle I 45.0000 36 0.00 +20FUKAAXX100202.6 45 -97 Cycle D 45.0000 35 0.00 +20FUKAAXX100202.6 45 -97 Cycle I 45.0000 35 0.00 20FUKAAXX100202.6 45 10 Cycle D 45.0000 53 0.00 20FUKAAXX100202.6 45 10 Cycle I 45.0000 53 0.00 20FUKAAXX100202.6 45 11 Cycle D 45.0000 54 0.00 @@ -28258,8 +28257,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 45 86 Cycle I 45.0000 49 0.00 20FUKAAXX100202.6 45 87 Cycle D 45.0000 47 0.00 20FUKAAXX100202.6 45 87 Cycle I 45.0000 47 0.00 -20FUKAAXX100202.6 45 88 Cycle D 45.0000 48 0.14 -20FUKAAXX100202.6 45 88 Cycle I 45.0000 48 0.00 +20FUKAAXX100202.6 45 88 Cycle D 45.0000 47 0.00 +20FUKAAXX100202.6 45 88 Cycle I 45.0000 47 0.00 20FUKAAXX100202.6 45 89 Cycle D 45.0000 47 0.14 20FUKAAXX100202.6 45 89 Cycle I 45.0000 47 0.00 20FUKAAXX100202.6 45 9 Cycle D 45.0000 54 0.00 @@ -28342,8 +28341,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 45 CTC Context I 45.0000 221 0.00 20FUKAAXX100202.6 45 CTG Context D 45.0000 209 0.00 20FUKAAXX100202.6 45 CTG Context I 45.0000 209 0.00 -20FUKAAXX100202.6 45 CTT Context D 45.0000 203 1.17 -20FUKAAXX100202.6 45 CTT Context I 45.0000 203 0.00 +20FUKAAXX100202.6 45 CTT Context D 45.0000 200 0.71 +20FUKAAXX100202.6 45 CTT Context I 45.0000 200 0.00 20FUKAAXX100202.6 45 GAA Context D 45.0000 195 0.14 20FUKAAXX100202.6 45 GAA Context I 45.0000 195 0.00 20FUKAAXX100202.6 45 GAC Context D 45.0000 107 0.00 @@ -31420,7 +31419,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.7 36 -67 Cycle M 36.0000 3 0.00 20FUKAAXX100202.7 36 -68 Cycle M 36.0000 3 0.00 20FUKAAXX100202.7 36 -69 Cycle M 36.0000 4 0.00 -20FUKAAXX100202.7 36 -7 Cycle M 36.0000 12 0.00 +20FUKAAXX100202.7 36 -7 Cycle M 36.0000 11 0.00 20FUKAAXX100202.7 36 -70 Cycle M 36.0000 4 0.00 20FUKAAXX100202.7 36 -71 Cycle M 36.0000 3 0.00 20FUKAAXX100202.7 36 -72 Cycle M 36.0000 2 0.00 @@ -31721,7 +31720,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.7 36 TCTC Context M 36.0000 2 0.00 20FUKAAXX100202.7 36 TCTG Context M 36.0000 3 0.00 20FUKAAXX100202.7 36 TCTT Context M 36.0000 1 0.00 -20FUKAAXX100202.7 36 TGAA Context M 36.0000 11 0.00 +20FUKAAXX100202.7 36 TGAA Context M 36.0000 10 0.00 20FUKAAXX100202.7 36 TGAC Context M 36.0000 27 0.00 20FUKAAXX100202.7 36 TGAG Context M 36.0000 3 0.00 20FUKAAXX100202.7 36 TGAT Context M 36.0000 4 0.00 @@ -32327,7 +32326,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.7 38 90 Cycle M 38.0000 19 0.00 20FUKAAXX100202.7 38 91 Cycle M 38.0000 15 0.00 20FUKAAXX100202.7 38 92 Cycle M 38.0000 21 0.00 -20FUKAAXX100202.7 38 93 Cycle M 38.0000 17 0.00 +20FUKAAXX100202.7 38 93 Cycle M 38.0000 16 0.00 20FUKAAXX100202.7 38 94 Cycle M 38.0000 13 0.00 20FUKAAXX100202.7 38 95 Cycle M 38.0000 17 0.00 20FUKAAXX100202.7 38 96 Cycle M 38.0000 14 1.00 @@ -32517,7 +32516,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.7 38 TCTA Context M 38.0000 13 0.00 20FUKAAXX100202.7 38 TCTC Context M 38.0000 12 0.00 20FUKAAXX100202.7 38 TCTG Context M 38.0000 40 0.00 -20FUKAAXX100202.7 38 TCTT Context M 38.0000 15 0.00 +20FUKAAXX100202.7 38 TCTT Context M 38.0000 14 0.00 20FUKAAXX100202.7 38 TGAA Context M 38.0000 5 0.00 20FUKAAXX100202.7 38 TGAG Context M 38.0000 60 0.00 20FUKAAXX100202.7 38 TGAT Context M 38.0000 28 0.00 @@ -32953,8 +32952,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.7 45 -68 Cycle I 45.0000 46 0.00 20FUKAAXX100202.7 45 -69 Cycle D 45.0000 46 0.00 20FUKAAXX100202.7 45 -69 Cycle I 45.0000 46 0.00 -20FUKAAXX100202.7 45 -7 Cycle D 45.0000 51 0.25 -20FUKAAXX100202.7 45 -7 Cycle I 45.0000 51 0.00 +20FUKAAXX100202.7 45 -7 Cycle D 45.0000 50 0.13 +20FUKAAXX100202.7 45 -7 Cycle I 45.0000 50 0.00 20FUKAAXX100202.7 45 -70 Cycle D 45.0000 46 0.00 20FUKAAXX100202.7 45 -70 Cycle I 45.0000 46 0.00 20FUKAAXX100202.7 45 -71 Cycle D 45.0000 46 0.00 @@ -33191,8 +33190,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.7 45 91 Cycle I 45.0000 40 0.00 20FUKAAXX100202.7 45 92 Cycle D 45.0000 40 0.00 20FUKAAXX100202.7 45 92 Cycle I 45.0000 40 0.00 -20FUKAAXX100202.7 45 93 Cycle D 45.0000 41 0.09 -20FUKAAXX100202.7 45 93 Cycle I 45.0000 41 0.00 +20FUKAAXX100202.7 45 93 Cycle D 45.0000 40 0.00 +20FUKAAXX100202.7 45 93 Cycle I 45.0000 40 0.00 20FUKAAXX100202.7 45 94 Cycle D 45.0000 41 0.09 20FUKAAXX100202.7 45 94 Cycle I 45.0000 41 0.00 20FUKAAXX100202.7 45 95 Cycle D 45.0000 41 0.09 @@ -33263,10 +33262,10 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.7 45 CTC Context I 45.0000 184 0.00 20FUKAAXX100202.7 45 CTG Context D 45.0000 196 0.00 20FUKAAXX100202.7 45 CTG Context I 45.0000 196 0.00 -20FUKAAXX100202.7 45 CTT Context D 45.0000 166 0.09 -20FUKAAXX100202.7 45 CTT Context I 45.0000 166 0.00 -20FUKAAXX100202.7 45 GAA Context D 45.0000 230 0.25 -20FUKAAXX100202.7 45 GAA Context I 45.0000 230 0.00 +20FUKAAXX100202.7 45 CTT Context D 45.0000 165 0.00 +20FUKAAXX100202.7 45 CTT Context I 45.0000 165 0.00 +20FUKAAXX100202.7 45 GAA Context D 45.0000 229 0.13 +20FUKAAXX100202.7 45 GAA Context I 45.0000 229 0.00 20FUKAAXX100202.7 45 GAC Context D 45.0000 82 0.00 20FUKAAXX100202.7 45 GAC Context I 45.0000 82 0.00 20FUKAAXX100202.7 45 GAG Context D 45.0000 219 0.25 @@ -38765,7 +38764,6 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 24 TGTA Context M 24.0000 1 0.00 20GAVAAXX100126.1 24 TTCG Context M 24.0000 1 0.00 20GAVAAXX100126.1 24 TTTC Context M 24.0000 2 0.00 -20GAVAAXX100126.1 25 -10 Cycle M 25.0000 1 0.00 20GAVAAXX100126.1 25 -12 Cycle M 25.0000 1 0.00 20GAVAAXX100126.1 25 -15 Cycle M 25.0000 1 0.00 20GAVAAXX100126.1 25 -17 Cycle M 25.0000 1 0.00 @@ -38840,7 +38838,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 25 AGAT Context M 25.0000 1 0.00 20GAVAAXX100126.1 25 AGGT Context M 25.0000 4 0.00 20GAVAAXX100126.1 25 AGTC Context M 25.0000 1 0.00 -20GAVAAXX100126.1 25 AGTG Context M 25.0000 2 0.00 +20GAVAAXX100126.1 25 AGTG Context M 25.0000 1 0.00 20GAVAAXX100126.1 25 ATCA Context M 25.0000 1 0.00 20GAVAAXX100126.1 25 ATTC Context M 25.0000 1 0.00 20GAVAAXX100126.1 25 CACC Context M 25.0000 2 0.00 @@ -39101,7 +39099,6 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 27 61 Cycle M 27.0000 1 0.00 20GAVAAXX100126.1 27 63 Cycle M 27.0000 1 0.00 20GAVAAXX100126.1 27 65 Cycle M 27.0000 1 0.00 -20GAVAAXX100126.1 27 66 Cycle M 27.0000 1 0.00 20GAVAAXX100126.1 27 68 Cycle M 27.0000 1 0.00 20GAVAAXX100126.1 27 70 Cycle M 27.0000 2 0.00 20GAVAAXX100126.1 27 71 Cycle M 27.0000 1 0.00 @@ -39185,7 +39182,6 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 27 GTTG Context M 27.0000 1 0.00 20GAVAAXX100126.1 27 GTTT Context M 27.0000 1 0.00 20GAVAAXX100126.1 27 TCAG Context M 27.0000 1 0.00 -20GAVAAXX100126.1 27 TGAA Context M 27.0000 1 0.00 20GAVAAXX100126.1 27 TGAC Context M 27.0000 1 0.00 20GAVAAXX100126.1 27 TGCA Context M 27.0000 2 0.00 20GAVAAXX100126.1 27 TGCC Context M 27.0000 1 0.00 @@ -42617,7 +42613,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 39 39 Cycle M 39.0000 16 0.00 20GAVAAXX100126.1 39 40 Cycle M 39.0000 23 0.00 20GAVAAXX100126.1 39 41 Cycle M 39.0000 8 0.00 -20GAVAAXX100126.1 39 42 Cycle M 39.0000 20 0.00 +20GAVAAXX100126.1 39 42 Cycle M 39.0000 19 0.00 20GAVAAXX100126.1 39 43 Cycle M 39.0000 13 0.00 20GAVAAXX100126.1 39 44 Cycle M 39.0000 15 0.00 20GAVAAXX100126.1 39 45 Cycle M 39.0000 11 0.00 @@ -42797,7 +42793,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 39 TCCT Context M 39.0000 37 0.00 20GAVAAXX100126.1 39 TCTA Context M 39.0000 2 0.00 20GAVAAXX100126.1 39 TCTT Context M 39.0000 18 0.00 -20GAVAAXX100126.1 39 TGAA Context M 39.0000 20 0.00 +20GAVAAXX100126.1 39 TGAA Context M 39.0000 19 0.00 20GAVAAXX100126.1 39 TGAG Context M 39.0000 3 0.00 20GAVAAXX100126.1 39 TGAT Context M 39.0000 5 0.00 20GAVAAXX100126.1 39 TGCA Context M 39.0000 13 0.00 @@ -42980,8 +42976,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 41 TCAA Context M 41.0000 1 0.00 20GAVAAXX100126.1 41 TGAA Context M 41.0000 1 0.00 20GAVAAXX100126.1 41 TGCT Context M 41.0000 2 0.00 -20GAVAAXX100126.1 45 -10 Cycle D 45.0000 47 0.41 -20GAVAAXX100126.1 45 -10 Cycle I 45.0000 47 0.00 +20GAVAAXX100126.1 45 -10 Cycle D 45.0000 46 0.13 +20GAVAAXX100126.1 45 -10 Cycle I 45.0000 46 0.00 20GAVAAXX100126.1 45 -11 Cycle D 45.0000 46 0.13 20GAVAAXX100126.1 45 -11 Cycle I 45.0000 46 0.00 20GAVAAXX100126.1 45 -12 Cycle D 45.0000 46 0.13 @@ -43230,8 +43226,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 45 40 Cycle I 45.0000 53 0.00 20GAVAAXX100126.1 45 41 Cycle D 45.0000 53 0.14 20GAVAAXX100126.1 45 41 Cycle I 45.0000 53 0.00 -20GAVAAXX100126.1 45 42 Cycle D 45.0000 53 0.14 -20GAVAAXX100126.1 45 42 Cycle I 45.0000 53 0.00 +20GAVAAXX100126.1 45 42 Cycle D 45.0000 52 0.00 +20GAVAAXX100126.1 45 42 Cycle I 45.0000 52 0.00 20GAVAAXX100126.1 45 43 Cycle D 45.0000 52 0.00 20GAVAAXX100126.1 45 43 Cycle I 45.0000 52 0.00 20GAVAAXX100126.1 45 44 Cycle D 45.0000 52 0.14 @@ -43282,8 +43278,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 45 64 Cycle I 45.0000 52 0.00 20GAVAAXX100126.1 45 65 Cycle D 45.0000 51 0.17 20GAVAAXX100126.1 45 65 Cycle I 45.0000 51 0.00 -20GAVAAXX100126.1 45 66 Cycle D 45.0000 52 0.17 -20GAVAAXX100126.1 45 66 Cycle I 45.0000 52 0.00 +20GAVAAXX100126.1 45 66 Cycle D 45.0000 51 0.00 +20GAVAAXX100126.1 45 66 Cycle I 45.0000 51 0.00 20GAVAAXX100126.1 45 67 Cycle D 45.0000 51 0.00 20GAVAAXX100126.1 45 67 Cycle I 45.0000 51 0.00 20GAVAAXX100126.1 45 68 Cycle D 45.0000 52 0.00 @@ -43416,8 +43412,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 45 CTG Context I 45.0000 214 0.00 20GAVAAXX100126.1 45 CTT Context D 45.0000 188 0.70 20GAVAAXX100126.1 45 CTT Context I 45.0000 188 0.00 -20GAVAAXX100126.1 45 GAA Context D 45.0000 155 0.31 -20GAVAAXX100126.1 45 GAA Context I 45.0000 155 0.00 +20GAVAAXX100126.1 45 GAA Context D 45.0000 153 0.00 +20GAVAAXX100126.1 45 GAA Context I 45.0000 153 0.00 20GAVAAXX100126.1 45 GAC Context D 45.0000 90 0.00 20GAVAAXX100126.1 45 GAC Context I 45.0000 90 0.00 20GAVAAXX100126.1 45 GAG Context D 45.0000 189 0.43 @@ -43444,8 +43440,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 45 GTA Context I 45.0000 95 0.00 20GAVAAXX100126.1 45 GTC Context D 45.0000 85 0.46 20GAVAAXX100126.1 45 GTC Context I 45.0000 85 0.00 -20GAVAAXX100126.1 45 GTG Context D 45.0000 190 0.72 -20GAVAAXX100126.1 45 GTG Context I 45.0000 190 0.00 +20GAVAAXX100126.1 45 GTG Context D 45.0000 189 0.43 +20GAVAAXX100126.1 45 GTG Context I 45.0000 189 0.00 20GAVAAXX100126.1 45 GTT Context D 45.0000 116 0.00 20GAVAAXX100126.1 45 GTT Context I 45.0000 116 0.00 20GAVAAXX100126.1 45 TAA Context D 45.0000 81 0.00 @@ -45870,7 +45866,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.2 33 -68 Cycle M 33.0000 4 0.00 20GAVAAXX100126.2 33 -69 Cycle M 33.0000 3 0.00 20GAVAAXX100126.2 33 -7 Cycle M 33.0000 4 0.00 -20GAVAAXX100126.2 33 -70 Cycle M 33.0000 2 0.00 +20GAVAAXX100126.2 33 -70 Cycle M 33.0000 1 0.00 20GAVAAXX100126.2 33 -71 Cycle M 33.0000 9 0.00 20GAVAAXX100126.2 33 -72 Cycle M 33.0000 8 0.00 20GAVAAXX100126.2 33 -73 Cycle M 33.0000 4 0.00 @@ -46060,7 +46056,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.2 33 GCGG Context M 33.0000 1 0.00 20GAVAAXX100126.2 33 GCTC Context M 33.0000 1 0.00 20GAVAAXX100126.2 33 GCTT Context M 33.0000 2 0.00 -20GAVAAXX100126.2 33 GGAA Context M 33.0000 2 0.00 +20GAVAAXX100126.2 33 GGAA Context M 33.0000 1 0.00 20GAVAAXX100126.2 33 GGAG Context M 33.0000 3 0.00 20GAVAAXX100126.2 33 GGAT Context M 33.0000 1 0.00 20GAVAAXX100126.2 33 GGCA Context M 33.0000 1 0.00 @@ -48313,8 +48309,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.2 45 -69 Cycle I 45.0000 36 0.00 20GAVAAXX100126.2 45 -7 Cycle D 45.0000 41 0.00 20GAVAAXX100126.2 45 -7 Cycle I 45.0000 41 0.00 -20GAVAAXX100126.2 45 -70 Cycle D 45.0000 37 0.14 -20GAVAAXX100126.2 45 -70 Cycle I 45.0000 37 0.00 +20GAVAAXX100126.2 45 -70 Cycle D 45.0000 36 0.00 +20GAVAAXX100126.2 45 -70 Cycle I 45.0000 36 0.00 20GAVAAXX100126.2 45 -71 Cycle D 45.0000 35 0.00 20GAVAAXX100126.2 45 -71 Cycle I 45.0000 35 0.00 20GAVAAXX100126.2 45 -72 Cycle D 45.0000 36 0.14 @@ -48623,8 +48619,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.2 45 CTG Context I 45.0000 154 0.00 20GAVAAXX100126.2 45 CTT Context D 45.0000 141 0.43 20GAVAAXX100126.2 45 CTT Context I 45.0000 141 0.00 -20GAVAAXX100126.2 45 GAA Context D 45.0000 130 0.43 -20GAVAAXX100126.2 45 GAA Context I 45.0000 130 0.00 +20GAVAAXX100126.2 45 GAA Context D 45.0000 129 0.29 +20GAVAAXX100126.2 45 GAA Context I 45.0000 129 0.00 20GAVAAXX100126.2 45 GAC Context D 45.0000 87 0.00 20GAVAAXX100126.2 45 GAC Context I 45.0000 87 0.00 20GAVAAXX100126.2 45 GAG Context D 45.0000 183 0.14 @@ -57067,7 +57063,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.4 38 10 Cycle M 38.0000 10 0.00 20GAVAAXX100126.4 38 100 Cycle M 38.0000 4 0.00 20GAVAAXX100126.4 38 101 Cycle M 38.0000 5 0.00 -20GAVAAXX100126.4 38 11 Cycle M 38.0000 9 0.00 +20GAVAAXX100126.4 38 11 Cycle M 38.0000 8 0.00 20GAVAAXX100126.4 38 12 Cycle M 38.0000 8 0.00 20GAVAAXX100126.4 38 13 Cycle M 38.0000 9 0.00 20GAVAAXX100126.4 38 14 Cycle M 38.0000 11 0.00 @@ -57328,7 +57324,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.4 38 TCTA Context M 38.0000 6 0.00 20GAVAAXX100126.4 38 TCTC Context M 38.0000 1 0.00 20GAVAAXX100126.4 38 TCTG Context M 38.0000 14 0.00 -20GAVAAXX100126.4 38 TCTT Context M 38.0000 11 0.00 +20GAVAAXX100126.4 38 TCTT Context M 38.0000 10 0.00 20GAVAAXX100126.4 38 TGAA Context M 38.0000 3 0.00 20GAVAAXX100126.4 38 TGAC Context M 38.0000 1 0.00 20GAVAAXX100126.4 38 TGAG Context M 38.0000 19 0.00 @@ -57828,8 +57824,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.4 45 -97 Cycle I 45.0000 25 0.00 20GAVAAXX100126.4 45 10 Cycle D 45.0000 33 0.00 20GAVAAXX100126.4 45 10 Cycle I 45.0000 33 0.00 -20GAVAAXX100126.4 45 11 Cycle D 45.0000 34 0.14 -20GAVAAXX100126.4 45 11 Cycle I 45.0000 34 0.00 +20GAVAAXX100126.4 45 11 Cycle D 45.0000 33 0.00 +20GAVAAXX100126.4 45 11 Cycle I 45.0000 33 0.00 20GAVAAXX100126.4 45 12 Cycle D 45.0000 34 0.14 20GAVAAXX100126.4 45 12 Cycle I 45.0000 34 0.00 20GAVAAXX100126.4 45 13 Cycle D 45.0000 34 0.14 @@ -58074,8 +58070,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.4 45 CTC Context I 45.0000 139 0.00 20GAVAAXX100126.4 45 CTG Context D 45.0000 154 0.00 20GAVAAXX100126.4 45 CTG Context I 45.0000 154 0.00 -20GAVAAXX100126.4 45 CTT Context D 45.0000 139 0.45 -20GAVAAXX100126.4 45 CTT Context I 45.0000 139 0.00 +20GAVAAXX100126.4 45 CTT Context D 45.0000 138 0.31 +20GAVAAXX100126.4 45 CTT Context I 45.0000 138 0.00 20GAVAAXX100126.4 45 GAA Context D 45.0000 118 0.00 20GAVAAXX100126.4 45 GAA Context I 45.0000 118 0.00 20GAVAAXX100126.4 45 GAC Context D 45.0000 72 0.00 @@ -61251,7 +61247,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.5 38 20 Cycle M 38.0000 11 0.00 20GAVAAXX100126.5 38 21 Cycle M 38.0000 17 1.00 20GAVAAXX100126.5 38 22 Cycle M 38.0000 13 0.00 -20GAVAAXX100126.5 38 23 Cycle M 38.0000 11 0.00 +20GAVAAXX100126.5 38 23 Cycle M 38.0000 10 0.00 20GAVAAXX100126.5 38 24 Cycle M 38.0000 10 0.00 20GAVAAXX100126.5 38 25 Cycle M 38.0000 12 0.00 20GAVAAXX100126.5 38 26 Cycle M 38.0000 15 0.00 @@ -61507,7 +61503,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.5 38 TCTA Context M 38.0000 3 0.00 20GAVAAXX100126.5 38 TCTC Context M 38.0000 1 0.00 20GAVAAXX100126.5 38 TCTG Context M 38.0000 27 0.00 -20GAVAAXX100126.5 38 TCTT Context M 38.0000 12 0.00 +20GAVAAXX100126.5 38 TCTT Context M 38.0000 11 0.00 20GAVAAXX100126.5 38 TGAA Context M 38.0000 4 0.00 20GAVAAXX100126.5 38 TGAG Context M 38.0000 27 0.00 20GAVAAXX100126.5 38 TGAT Context M 38.0000 5 0.00 @@ -62098,8 +62094,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.5 45 21 Cycle I 45.0000 33 0.00 20GAVAAXX100126.5 45 22 Cycle D 45.0000 32 0.00 20GAVAAXX100126.5 45 22 Cycle I 45.0000 32 0.00 -20GAVAAXX100126.5 45 23 Cycle D 45.0000 33 0.14 -20GAVAAXX100126.5 45 23 Cycle I 45.0000 33 0.00 +20GAVAAXX100126.5 45 23 Cycle D 45.0000 32 0.00 +20GAVAAXX100126.5 45 23 Cycle I 45.0000 32 0.00 20GAVAAXX100126.5 45 24 Cycle D 45.0000 33 0.14 20GAVAAXX100126.5 45 24 Cycle I 45.0000 33 0.00 20GAVAAXX100126.5 45 25 Cycle D 45.0000 32 0.14 @@ -62320,8 +62316,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.5 45 CTC Context I 45.0000 103 0.00 20GAVAAXX100126.5 45 CTG Context D 45.0000 132 0.00 20GAVAAXX100126.5 45 CTG Context I 45.0000 132 0.00 -20GAVAAXX100126.5 45 CTT Context D 45.0000 102 0.14 -20GAVAAXX100126.5 45 CTT Context I 45.0000 102 0.00 +20GAVAAXX100126.5 45 CTT Context D 45.0000 101 0.00 +20GAVAAXX100126.5 45 CTT Context I 45.0000 101 0.00 20GAVAAXX100126.5 45 GAA Context D 45.0000 148 0.00 20GAVAAXX100126.5 45 GAA Context I 45.0000 148 0.00 20GAVAAXX100126.5 45 GAC Context D 45.0000 56 0.00 @@ -63901,7 +63897,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.6 31 -46 Cycle M 31.0000 2 0.00 20GAVAAXX100126.6 31 -47 Cycle M 31.0000 2 0.00 20GAVAAXX100126.6 31 -48 Cycle M 31.0000 3 0.00 -20GAVAAXX100126.6 31 -5 Cycle M 31.0000 6 0.00 +20GAVAAXX100126.6 31 -5 Cycle M 31.0000 5 0.00 20GAVAAXX100126.6 31 -50 Cycle M 31.0000 4 0.00 20GAVAAXX100126.6 31 -51 Cycle M 31.0000 1 0.00 20GAVAAXX100126.6 31 -52 Cycle M 31.0000 1 0.00 @@ -64073,7 +64069,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.6 31 TCTC Context M 31.0000 2 0.00 20GAVAAXX100126.6 31 TCTG Context M 31.0000 2 0.00 20GAVAAXX100126.6 31 TCTT Context M 31.0000 1 0.00 -20GAVAAXX100126.6 31 TGAA Context M 31.0000 4 0.00 +20GAVAAXX100126.6 31 TGAA Context M 31.0000 3 0.00 20GAVAAXX100126.6 31 TGAG Context M 31.0000 2 0.00 20GAVAAXX100126.6 31 TGAT Context M 31.0000 1 0.00 20GAVAAXX100126.6 31 TGCA Context M 31.0000 1 0.00 @@ -66143,7 +66139,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.6 38 40 Cycle M 38.0000 13 0.00 20GAVAAXX100126.6 38 41 Cycle M 38.0000 9 0.00 20GAVAAXX100126.6 38 42 Cycle M 38.0000 13 0.00 -20GAVAAXX100126.6 38 43 Cycle M 38.0000 17 0.00 +20GAVAAXX100126.6 38 43 Cycle M 38.0000 16 0.00 20GAVAAXX100126.6 38 44 Cycle M 38.0000 14 0.00 20GAVAAXX100126.6 38 45 Cycle M 38.0000 14 0.00 20GAVAAXX100126.6 38 46 Cycle M 38.0000 10 0.00 @@ -66368,7 +66364,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.6 38 TCCT Context M 38.0000 7 0.00 20GAVAAXX100126.6 38 TCTA Context M 38.0000 4 0.00 20GAVAAXX100126.6 38 TCTG Context M 38.0000 16 0.00 -20GAVAAXX100126.6 38 TCTT Context M 38.0000 17 0.00 +20GAVAAXX100126.6 38 TCTT Context M 38.0000 16 0.00 20GAVAAXX100126.6 38 TGAA Context M 38.0000 6 0.00 20GAVAAXX100126.6 38 TGAG Context M 38.0000 25 0.00 20GAVAAXX100126.6 38 TGAT Context M 38.0000 16 1.00 @@ -66766,8 +66762,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.6 45 -48 Cycle I 45.0000 39 0.00 20GAVAAXX100126.6 45 -49 Cycle D 45.0000 38 0.00 20GAVAAXX100126.6 45 -49 Cycle I 45.0000 38 0.00 -20GAVAAXX100126.6 45 -5 Cycle D 45.0000 40 0.17 -20GAVAAXX100126.6 45 -5 Cycle I 45.0000 40 0.00 +20GAVAAXX100126.6 45 -5 Cycle D 45.0000 39 0.00 +20GAVAAXX100126.6 45 -5 Cycle I 45.0000 39 0.00 20GAVAAXX100126.6 45 -50 Cycle D 45.0000 38 0.00 20GAVAAXX100126.6 45 -50 Cycle I 45.0000 38 0.00 20GAVAAXX100126.6 45 -51 Cycle D 45.0000 38 0.00 @@ -66938,8 +66934,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.6 45 41 Cycle I 45.0000 41 0.00 20GAVAAXX100126.6 45 42 Cycle D 45.0000 40 0.14 20GAVAAXX100126.6 45 42 Cycle I 45.0000 40 0.00 -20GAVAAXX100126.6 45 43 Cycle D 45.0000 41 0.29 -20GAVAAXX100126.6 45 43 Cycle I 45.0000 41 0.00 +20GAVAAXX100126.6 45 43 Cycle D 45.0000 40 0.14 +20GAVAAXX100126.6 45 43 Cycle I 45.0000 40 0.00 20GAVAAXX100126.6 45 44 Cycle D 45.0000 41 0.29 20GAVAAXX100126.6 45 44 Cycle I 45.0000 41 0.00 20GAVAAXX100126.6 45 45 Cycle D 45.0000 41 0.29 @@ -67120,10 +67116,10 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.6 45 CTC Context I 45.0000 187 0.00 20GAVAAXX100126.6 45 CTG Context D 45.0000 189 0.00 20GAVAAXX100126.6 45 CTG Context I 45.0000 189 0.00 -20GAVAAXX100126.6 45 CTT Context D 45.0000 153 0.43 -20GAVAAXX100126.6 45 CTT Context I 45.0000 153 0.00 -20GAVAAXX100126.6 45 GAA Context D 45.0000 149 0.17 -20GAVAAXX100126.6 45 GAA Context I 45.0000 149 0.00 +20GAVAAXX100126.6 45 CTT Context D 45.0000 152 0.29 +20GAVAAXX100126.6 45 CTT Context I 45.0000 152 0.00 +20GAVAAXX100126.6 45 GAA Context D 45.0000 148 0.00 +20GAVAAXX100126.6 45 GAA Context I 45.0000 148 0.00 20GAVAAXX100126.6 45 GAC Context D 45.0000 85 0.00 20GAVAAXX100126.6 45 GAC Context I 45.0000 85 0.00 20GAVAAXX100126.6 45 GAG Context D 45.0000 172 0.00 @@ -69754,7 +69750,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.7 33 -32 Cycle M 33.0000 1 0.00 20GAVAAXX100126.7 33 -33 Cycle M 33.0000 3 0.00 20GAVAAXX100126.7 33 -34 Cycle M 33.0000 3 0.00 -20GAVAAXX100126.7 33 -35 Cycle M 33.0000 3 0.00 +20GAVAAXX100126.7 33 -35 Cycle M 33.0000 2 0.00 20GAVAAXX100126.7 33 -37 Cycle M 33.0000 4 0.00 20GAVAAXX100126.7 33 -38 Cycle M 33.0000 1 0.00 20GAVAAXX100126.7 33 -39 Cycle M 33.0000 5 0.00 @@ -69997,7 +69993,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.7 33 TCCC Context M 33.0000 2 0.00 20GAVAAXX100126.7 33 TCCT Context M 33.0000 4 0.00 20GAVAAXX100126.7 33 TCTC Context M 33.0000 2 0.00 -20GAVAAXX100126.7 33 TGAA Context M 33.0000 3 0.00 +20GAVAAXX100126.7 33 TGAA Context M 33.0000 2 0.00 20GAVAAXX100126.7 33 TGAC Context M 33.0000 1 0.00 20GAVAAXX100126.7 33 TGAG Context M 33.0000 1 0.00 20GAVAAXX100126.7 33 TGAT Context M 33.0000 3 0.00 @@ -72096,8 +72092,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.7 45 -33 Cycle I 45.0000 39 0.00 20GAVAAXX100126.7 45 -34 Cycle D 45.0000 39 0.13 20GAVAAXX100126.7 45 -34 Cycle I 45.0000 39 0.00 -20GAVAAXX100126.7 45 -35 Cycle D 45.0000 39 0.13 -20GAVAAXX100126.7 45 -35 Cycle I 45.0000 39 0.00 +20GAVAAXX100126.7 45 -35 Cycle D 45.0000 38 0.00 +20GAVAAXX100126.7 45 -35 Cycle I 45.0000 38 0.00 20GAVAAXX100126.7 45 -36 Cycle D 45.0000 38 0.00 20GAVAAXX100126.7 45 -36 Cycle I 45.0000 38 0.00 20GAVAAXX100126.7 45 -37 Cycle D 45.0000 39 0.13 @@ -72482,8 +72478,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.7 45 CTG Context I 45.0000 180 0.00 20GAVAAXX100126.7 45 CTT Context D 45.0000 128 0.14 20GAVAAXX100126.7 45 CTT Context I 45.0000 128 0.00 -20GAVAAXX100126.7 45 GAA Context D 45.0000 148 0.25 -20GAVAAXX100126.7 45 GAA Context I 45.0000 148 0.00 +20GAVAAXX100126.7 45 GAA Context D 45.0000 147 0.13 +20GAVAAXX100126.7 45 GAA Context I 45.0000 147 0.00 20GAVAAXX100126.7 45 GAC Context D 45.0000 96 0.00 20GAVAAXX100126.7 45 GAC Context I 45.0000 96 0.00 20GAVAAXX100126.7 45 GAG Context D 45.0000 172 0.25 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.noIndels.noBAQ.recal.txt b/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.noIndels.noBAQ.recal.txt index 24c74b37358..3f23475c293 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.noIndels.noBAQ.recal.txt +++ b/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.noIndels.noBAQ.recal.txt @@ -48,21 +48,21 @@ QualityScore Count QuantizedScore 22 750 23 23 853 23 24 997 25 - 25 1228 25 + 25 1227 25 26 1491 27 - 27 1728 27 + 27 1727 27 28 1781 29 29 2284 29 30 2439 30 - 31 2537 30 + 31 2536 30 32 3565 32 - 33 4141 33 + 33 4139 33 34 5194 34 - 35 7518 35 - 36 11939 36 - 37 28884 37 - 38 27993 38 - 39 15115 39 + 35 7517 35 + 36 11937 36 + 37 28883 37 + 38 27987 38 + 39 15108 39 40 778 39 41 53 39 42 0 39 @@ -121,21 +121,21 @@ QualityScore Count QuantizedScore #:GATKTable:6:16:%s:%s:%.4f:%.4f:%d:%.2f:; #:GATKTable:RecalTable0: ReadGroup EventType EmpiricalQuality EstimatedQReported Observations Errors -20FUKAAXX100202.1 M 27.0000 27.0392 7293 15.00 -20FUKAAXX100202.2 M 29.0000 30.1871 6464 20.00 -20FUKAAXX100202.3 M 27.0000 28.2043 8976 29.00 -20FUKAAXX100202.4 M 29.0000 29.0885 6830 13.00 -20FUKAAXX100202.5 M 28.0000 29.7339 7471 27.00 -20FUKAAXX100202.6 M 28.0000 28.7545 10026 25.00 -20FUKAAXX100202.7 M 26.0000 27.7419 9347 29.00 +20FUKAAXX100202.1 M 27.0000 27.0386 7292 15.00 +20FUKAAXX100202.2 M 29.0000 30.1859 6462 20.00 +20FUKAAXX100202.3 M 27.0000 28.2034 8974 29.00 +20FUKAAXX100202.4 M 29.0000 29.0874 6828 13.00 +20FUKAAXX100202.5 M 28.0000 29.7334 7470 27.00 +20FUKAAXX100202.6 M 28.0000 28.7535 10023 25.00 +20FUKAAXX100202.7 M 26.0000 27.7411 9345 29.00 20FUKAAXX100202.8 M 28.0000 29.0288 8152 24.00 -20GAVAAXX100126.1 M 26.0000 27.6243 9297 29.00 -20GAVAAXX100126.2 M 26.0000 27.3758 8155 32.00 +20GAVAAXX100126.1 M 26.0000 27.6244 9294 29.00 +20GAVAAXX100126.2 M 26.0000 27.3754 8154 32.00 20GAVAAXX100126.3 M 26.0000 26.8893 6239 18.00 -20GAVAAXX100126.4 M 26.0000 27.0432 6633 28.00 -20GAVAAXX100126.5 M 27.0000 28.0717 5884 21.00 -20GAVAAXX100126.6 M 27.0000 28.4682 8002 27.00 -20GAVAAXX100126.7 M 25.0000 25.6878 7598 27.00 +20GAVAAXX100126.4 M 26.0000 27.0426 6632 28.00 +20GAVAAXX100126.5 M 27.0000 28.0710 5883 21.00 +20GAVAAXX100126.6 M 27.0000 28.4675 8000 27.00 +20GAVAAXX100126.7 M 25.0000 25.6874 7597 27.00 20GAVAAXX100126.8 M 26.0000 27.3594 8533 27.00 #:GATKTable:6:567:%s:%d:%s:%.4f:%d:%.2f:; @@ -172,7 +172,7 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20FUKAAXX100202.1 34 M 34.0000 217 0.00 20FUKAAXX100202.1 35 M 35.0000 347 1.00 20FUKAAXX100202.1 36 M 36.0000 599 1.00 -20FUKAAXX100202.1 37 M 37.0000 1407 1.00 +20FUKAAXX100202.1 37 M 37.0000 1406 1.00 20FUKAAXX100202.1 38 M 38.0000 2058 0.00 20FUKAAXX100202.1 39 M 39.0000 741 0.00 20FUKAAXX100202.1 40 M 40.0000 16 0.00 @@ -209,7 +209,7 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20FUKAAXX100202.2 36 M 36.0000 580 4.00 20FUKAAXX100202.2 37 M 37.0000 1371 2.00 20FUKAAXX100202.2 38 M 38.0000 2181 6.00 -20FUKAAXX100202.2 39 M 39.0000 667 1.00 +20FUKAAXX100202.2 39 M 39.0000 665 1.00 20FUKAAXX100202.2 40 M 40.0000 27 0.00 20FUKAAXX100202.3 6 M 6.0000 1 1.00 20FUKAAXX100202.3 7 M 7.0000 4 0.00 @@ -241,10 +241,10 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20FUKAAXX100202.3 33 M 33.0000 245 0.00 20FUKAAXX100202.3 34 M 34.0000 262 0.00 20FUKAAXX100202.3 35 M 35.0000 463 1.00 -20FUKAAXX100202.3 36 M 36.0000 944 6.00 +20FUKAAXX100202.3 36 M 36.0000 943 6.00 20FUKAAXX100202.3 37 M 37.0000 1649 4.00 20FUKAAXX100202.3 38 M 37.0000 2837 11.00 -20FUKAAXX100202.3 39 M 39.0000 976 0.00 +20FUKAAXX100202.3 39 M 39.0000 975 0.00 20FUKAAXX100202.3 40 M 40.0000 28 0.00 20FUKAAXX100202.4 6 M 6.0000 1 0.00 20FUKAAXX100202.4 7 M 7.0000 2 1.00 @@ -279,7 +279,7 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20FUKAAXX100202.4 36 M 36.0000 633 0.00 20FUKAAXX100202.4 37 M 37.0000 1408 3.00 20FUKAAXX100202.4 38 M 38.0000 2074 3.00 -20FUKAAXX100202.4 39 M 39.0000 662 1.00 +20FUKAAXX100202.4 39 M 39.0000 660 1.00 20FUKAAXX100202.4 40 M 40.0000 20 0.00 20FUKAAXX100202.5 6 M 6.0000 1 0.00 20FUKAAXX100202.5 7 M 7.0000 3 0.00 @@ -314,7 +314,7 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20FUKAAXX100202.5 36 M 36.0000 695 3.00 20FUKAAXX100202.5 37 M 37.0000 1329 2.00 20FUKAAXX100202.5 38 M 37.0000 2579 10.00 -20FUKAAXX100202.5 39 M 39.0000 907 1.00 +20FUKAAXX100202.5 39 M 39.0000 906 1.00 20FUKAAXX100202.5 40 M 40.0000 67 0.00 20FUKAAXX100202.6 6 M 6.0000 7 4.00 20FUKAAXX100202.6 7 M 7.0000 4 2.00 @@ -345,10 +345,10 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20FUKAAXX100202.6 32 M 32.0000 226 1.00 20FUKAAXX100202.6 33 M 33.0000 231 2.00 20FUKAAXX100202.6 34 M 34.0000 302 0.00 -20FUKAAXX100202.6 35 M 35.0000 579 2.00 +20FUKAAXX100202.6 35 M 35.0000 578 2.00 20FUKAAXX100202.6 36 M 36.0000 975 2.00 20FUKAAXX100202.6 37 M 37.0000 1959 1.00 -20FUKAAXX100202.6 38 M 38.0000 3301 5.00 +20FUKAAXX100202.6 38 M 38.0000 3299 5.00 20FUKAAXX100202.6 39 M 39.0000 1111 1.00 20FUKAAXX100202.6 40 M 40.0000 43 0.00 20FUKAAXX100202.7 6 M 6.0000 5 2.00 @@ -381,9 +381,9 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20FUKAAXX100202.7 33 M 33.0000 197 0.00 20FUKAAXX100202.7 34 M 34.0000 251 0.00 20FUKAAXX100202.7 35 M 35.0000 441 1.00 -20FUKAAXX100202.7 36 M 36.0000 955 2.00 +20FUKAAXX100202.7 36 M 36.0000 954 2.00 20FUKAAXX100202.7 37 M 37.0000 1600 2.00 -20FUKAAXX100202.7 38 M 38.0000 3286 4.00 +20FUKAAXX100202.7 38 M 38.0000 3285 4.00 20FUKAAXX100202.7 39 M 39.0000 1063 1.00 20FUKAAXX100202.7 40 M 40.0000 43 0.00 20FUKAAXX100202.8 6 M 6.0000 4 2.00 @@ -440,9 +440,9 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.1 22 M 22.0000 43 1.00 20GAVAAXX100126.1 23 M 23.0000 65 0.00 20GAVAAXX100126.1 24 M 24.0000 56 0.00 -20GAVAAXX100126.1 25 M 25.0000 85 0.00 +20GAVAAXX100126.1 25 M 25.0000 84 0.00 20GAVAAXX100126.1 26 M 26.0000 104 0.00 -20GAVAAXX100126.1 27 M 27.0000 114 0.00 +20GAVAAXX100126.1 27 M 27.0000 113 0.00 20GAVAAXX100126.1 28 M 28.0000 149 0.00 20GAVAAXX100126.1 29 M 29.0000 185 1.00 20GAVAAXX100126.1 30 M 30.0000 179 0.00 @@ -454,7 +454,7 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.1 36 M 36.0000 822 2.00 20GAVAAXX100126.1 37 M 37.0000 1759 7.00 20GAVAAXX100126.1 38 M 38.0000 1880 3.00 -20GAVAAXX100126.1 39 M 39.0000 1546 2.00 +20GAVAAXX100126.1 39 M 39.0000 1545 2.00 20GAVAAXX100126.1 40 M 40.0000 243 0.00 20GAVAAXX100126.1 41 M 41.0000 23 0.00 20GAVAAXX100126.2 6 M 6.0000 10 4.00 @@ -484,7 +484,7 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.2 30 M 30.0000 169 0.00 20GAVAAXX100126.2 31 M 31.0000 222 1.00 20GAVAAXX100126.2 32 M 32.0000 336 0.00 -20GAVAAXX100126.2 33 M 33.0000 392 6.00 +20GAVAAXX100126.2 33 M 33.0000 391 6.00 20GAVAAXX100126.2 34 M 34.0000 471 0.00 20GAVAAXX100126.2 35 M 35.0000 540 2.00 20GAVAAXX100126.2 36 M 36.0000 685 1.00 @@ -561,7 +561,7 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.4 35 M 35.0000 487 2.00 20GAVAAXX100126.4 36 M 36.0000 639 1.00 20GAVAAXX100126.4 37 M 37.0000 1224 5.00 -20GAVAAXX100126.4 38 M 38.0000 1250 4.00 +20GAVAAXX100126.4 38 M 38.0000 1249 4.00 20GAVAAXX100126.4 39 M 39.0000 857 2.00 20GAVAAXX100126.4 40 M 40.0000 33 0.00 20GAVAAXX100126.4 41 M 41.0000 1 0.00 @@ -597,7 +597,7 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.5 35 M 35.0000 328 1.00 20GAVAAXX100126.5 36 M 36.0000 583 0.00 20GAVAAXX100126.5 37 M 37.0000 1187 2.00 -20GAVAAXX100126.5 38 M 38.0000 1446 2.00 +20GAVAAXX100126.5 38 M 38.0000 1445 2.00 20GAVAAXX100126.5 39 M 39.0000 909 2.00 20GAVAAXX100126.5 40 M 40.0000 43 0.00 20GAVAAXX100126.5 41 M 41.0000 5 0.00 @@ -626,14 +626,14 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.6 28 M 28.0000 105 0.00 20GAVAAXX100126.6 29 M 29.0000 158 1.00 20GAVAAXX100126.6 30 M 30.0000 144 0.00 -20GAVAAXX100126.6 31 M 31.0000 194 1.00 +20GAVAAXX100126.6 31 M 31.0000 193 1.00 20GAVAAXX100126.6 32 M 32.0000 239 0.00 20GAVAAXX100126.6 33 M 33.0000 358 0.00 20GAVAAXX100126.6 34 M 34.0000 481 1.00 20GAVAAXX100126.6 35 M 35.0000 578 2.00 20GAVAAXX100126.6 36 M 36.0000 845 2.00 20GAVAAXX100126.6 37 M 37.0000 1617 4.00 -20GAVAAXX100126.6 38 M 38.0000 1661 3.00 +20GAVAAXX100126.6 38 M 38.0000 1660 3.00 20GAVAAXX100126.6 39 M 39.0000 1030 2.00 20GAVAAXX100126.6 40 M 40.0000 35 0.00 20GAVAAXX100126.7 6 M 6.0000 7 1.00 @@ -663,7 +663,7 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.7 30 M 30.0000 192 0.00 20GAVAAXX100126.7 31 M 31.0000 200 0.00 20GAVAAXX100126.7 32 M 32.0000 228 1.00 -20GAVAAXX100126.7 33 M 33.0000 382 1.00 +20GAVAAXX100126.7 33 M 33.0000 381 1.00 20GAVAAXX100126.7 34 M 34.0000 412 2.00 20GAVAAXX100126.7 35 M 35.0000 554 0.00 20GAVAAXX100126.7 36 M 36.0000 700 1.00 @@ -709,7 +709,7 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.8 40 M 40.0000 33 0.00 20GAVAAXX100126.8 41 M 41.0000 4 0.00 -#:GATKTable:8:40659:%s:%d:%s:%s:%s:%.4f:%d:%.2f:; +#:GATKTable:8:40656:%s:%d:%s:%s:%s:%.4f:%d:%.2f:; #:GATKTable:RecalTable2: ReadGroup QualityScore CovariateValue CovariateName EventType EmpiricalQuality Observations Errors 20FUKAAXX100202.1 6 -31 Cycle M 6.0000 1 0.00 @@ -2861,7 +2861,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.1 37 -33 Cycle M 37.0000 5 0.00 20FUKAAXX100202.1 37 -34 Cycle M 37.0000 13 0.00 20FUKAAXX100202.1 37 -35 Cycle M 37.0000 12 0.00 -20FUKAAXX100202.1 37 -36 Cycle M 37.0000 14 0.00 +20FUKAAXX100202.1 37 -36 Cycle M 37.0000 13 0.00 20FUKAAXX100202.1 37 -37 Cycle M 37.0000 10 0.00 20FUKAAXX100202.1 37 -38 Cycle M 37.0000 9 0.00 20FUKAAXX100202.1 37 -39 Cycle M 37.0000 9 0.00 @@ -3036,7 +3036,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.1 37 TA Context M 37.0000 42 0.00 20FUKAAXX100202.1 37 TC Context M 37.0000 280 0.00 20FUKAAXX100202.1 37 TG Context M 37.0000 83 1.00 -20FUKAAXX100202.1 37 TT Context M 37.0000 116 0.00 +20FUKAAXX100202.1 37 TT Context M 37.0000 115 0.00 20FUKAAXX100202.1 38 -10 Cycle M 38.0000 2 0.00 20FUKAAXX100202.1 38 -100 Cycle M 38.0000 3 0.00 20FUKAAXX100202.1 38 -101 Cycle M 38.0000 4 0.00 @@ -5383,7 +5383,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.2 39 14 Cycle M 39.0000 3 0.00 20FUKAAXX100202.2 39 15 Cycle M 39.0000 3 0.00 20FUKAAXX100202.2 39 16 Cycle M 39.0000 2 0.00 -20FUKAAXX100202.2 39 17 Cycle M 39.0000 3 0.00 +20FUKAAXX100202.2 39 17 Cycle M 39.0000 2 0.00 20FUKAAXX100202.2 39 18 Cycle M 39.0000 7 0.00 20FUKAAXX100202.2 39 19 Cycle M 39.0000 4 0.00 20FUKAAXX100202.2 39 20 Cycle M 39.0000 3 0.00 @@ -5443,7 +5443,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.2 39 77 Cycle M 39.0000 5 0.00 20FUKAAXX100202.2 39 78 Cycle M 39.0000 2 0.00 20FUKAAXX100202.2 39 79 Cycle M 39.0000 6 0.00 -20FUKAAXX100202.2 39 8 Cycle M 39.0000 4 0.00 +20FUKAAXX100202.2 39 8 Cycle M 39.0000 3 0.00 20FUKAAXX100202.2 39 80 Cycle M 39.0000 2 0.00 20FUKAAXX100202.2 39 81 Cycle M 39.0000 2 0.00 20FUKAAXX100202.2 39 82 Cycle M 39.0000 2 0.00 @@ -5462,7 +5462,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.2 39 95 Cycle M 39.0000 3 0.00 20FUKAAXX100202.2 39 96 Cycle M 39.0000 3 0.00 20FUKAAXX100202.2 39 97 Cycle M 39.0000 1 0.00 -20FUKAAXX100202.2 39 AA Context M 39.0000 241 0.00 +20FUKAAXX100202.2 39 AA Context M 39.0000 239 0.00 20FUKAAXX100202.2 39 AG Context M 39.0000 2 0.00 20FUKAAXX100202.2 39 AT Context M 39.0000 1 0.00 20FUKAAXX100202.2 39 CA Context M 39.0000 81 0.00 @@ -7592,7 +7592,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.3 36 93 Cycle M 36.0000 5 0.00 20FUKAAXX100202.3 36 94 Cycle M 36.0000 4 0.00 20FUKAAXX100202.3 36 95 Cycle M 36.0000 6 0.00 -20FUKAAXX100202.3 36 96 Cycle M 36.0000 6 0.00 +20FUKAAXX100202.3 36 96 Cycle M 36.0000 5 0.00 20FUKAAXX100202.3 36 97 Cycle M 36.0000 3 0.00 20FUKAAXX100202.3 36 98 Cycle M 36.0000 4 0.00 20FUKAAXX100202.3 36 99 Cycle M 36.0000 5 0.00 @@ -7610,7 +7610,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.3 36 TA Context M 36.0000 32 0.00 20FUKAAXX100202.3 36 TC Context M 36.0000 41 0.00 20FUKAAXX100202.3 36 TG Context M 36.0000 56 2.00 -20FUKAAXX100202.3 36 TT Context M 36.0000 50 0.00 +20FUKAAXX100202.3 36 TT Context M 36.0000 49 0.00 20FUKAAXX100202.3 37 -1 Cycle M 37.0000 1 0.00 20FUKAAXX100202.3 37 -10 Cycle M 37.0000 14 0.00 20FUKAAXX100202.3 37 -100 Cycle M 37.0000 6 0.00 @@ -8030,7 +8030,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.3 39 -18 Cycle M 39.0000 6 0.00 20FUKAAXX100202.3 39 -19 Cycle M 39.0000 1 0.00 20FUKAAXX100202.3 39 -20 Cycle M 39.0000 4 0.00 -20FUKAAXX100202.3 39 -21 Cycle M 39.0000 7 0.00 +20FUKAAXX100202.3 39 -21 Cycle M 39.0000 6 0.00 20FUKAAXX100202.3 39 -22 Cycle M 39.0000 10 0.00 20FUKAAXX100202.3 39 -23 Cycle M 39.0000 5 0.00 20FUKAAXX100202.3 39 -25 Cycle M 39.0000 1 0.00 @@ -8200,7 +8200,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.3 39 97 Cycle M 39.0000 3 0.00 20FUKAAXX100202.3 39 98 Cycle M 39.0000 5 0.00 20FUKAAXX100202.3 39 99 Cycle M 39.0000 2 0.00 -20FUKAAXX100202.3 39 AA Context M 39.0000 334 0.00 +20FUKAAXX100202.3 39 AA Context M 39.0000 333 0.00 20FUKAAXX100202.3 39 AG Context M 39.0000 7 0.00 20FUKAAXX100202.3 39 CA Context M 39.0000 170 0.00 20FUKAAXX100202.3 39 CT Context M 39.0000 385 0.00 @@ -10475,13 +10475,13 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.4 39 25 Cycle M 39.0000 3 0.00 20FUKAAXX100202.4 39 26 Cycle M 39.0000 1 0.00 20FUKAAXX100202.4 39 27 Cycle M 39.0000 2 0.00 -20FUKAAXX100202.4 39 28 Cycle M 39.0000 3 0.00 +20FUKAAXX100202.4 39 28 Cycle M 39.0000 2 0.00 20FUKAAXX100202.4 39 29 Cycle M 39.0000 3 0.00 20FUKAAXX100202.4 39 30 Cycle M 39.0000 4 0.00 20FUKAAXX100202.4 39 31 Cycle M 39.0000 4 0.00 20FUKAAXX100202.4 39 32 Cycle M 39.0000 7 0.00 20FUKAAXX100202.4 39 33 Cycle M 39.0000 3 0.00 -20FUKAAXX100202.4 39 34 Cycle M 39.0000 5 0.00 +20FUKAAXX100202.4 39 34 Cycle M 39.0000 4 0.00 20FUKAAXX100202.4 39 35 Cycle M 39.0000 2 0.00 20FUKAAXX100202.4 39 36 Cycle M 39.0000 1 0.00 20FUKAAXX100202.4 39 37 Cycle M 39.0000 3 0.00 @@ -10545,7 +10545,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.4 39 96 Cycle M 39.0000 2 0.00 20FUKAAXX100202.4 39 97 Cycle M 39.0000 4 0.00 20FUKAAXX100202.4 39 98 Cycle M 39.0000 2 0.00 -20FUKAAXX100202.4 39 AA Context M 39.0000 193 0.00 +20FUKAAXX100202.4 39 AA Context M 39.0000 191 0.00 20FUKAAXX100202.4 39 AG Context M 39.0000 1 0.00 20FUKAAXX100202.4 39 AT Context M 39.0000 2 0.00 20FUKAAXX100202.4 39 CA Context M 39.0000 109 1.00 @@ -12702,7 +12702,6 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.5 38 TT Context M 38.0000 221 0.00 20FUKAAXX100202.5 39 -100 Cycle M 39.0000 1 0.00 20FUKAAXX100202.5 39 -14 Cycle M 39.0000 2 0.00 -20FUKAAXX100202.5 39 -15 Cycle M 39.0000 1 0.00 20FUKAAXX100202.5 39 -16 Cycle M 39.0000 6 0.00 20FUKAAXX100202.5 39 -17 Cycle M 39.0000 4 0.00 20FUKAAXX100202.5 39 -18 Cycle M 39.0000 4 0.00 @@ -12879,7 +12878,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.5 39 97 Cycle M 39.0000 3 0.00 20FUKAAXX100202.5 39 98 Cycle M 39.0000 3 0.00 20FUKAAXX100202.5 39 99 Cycle M 39.0000 1 0.00 -20FUKAAXX100202.5 39 AA Context M 39.0000 241 0.00 +20FUKAAXX100202.5 39 AA Context M 39.0000 240 0.00 20FUKAAXX100202.5 39 AG Context M 39.0000 19 0.00 20FUKAAXX100202.5 39 AT Context M 39.0000 3 0.00 20FUKAAXX100202.5 39 CA Context M 39.0000 218 0.00 @@ -14641,7 +14640,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 35 -94 Cycle M 35.0000 2 0.00 20FUKAAXX100202.6 35 -95 Cycle M 35.0000 5 0.00 20FUKAAXX100202.6 35 -96 Cycle M 35.0000 1 0.00 -20FUKAAXX100202.6 35 -97 Cycle M 35.0000 3 0.00 +20FUKAAXX100202.6 35 -97 Cycle M 35.0000 2 0.00 20FUKAAXX100202.6 35 -98 Cycle M 35.0000 4 0.00 20FUKAAXX100202.6 35 -99 Cycle M 35.0000 2 0.00 20FUKAAXX100202.6 35 1 Cycle M 35.0000 51 1.00 @@ -14728,7 +14727,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 35 TA Context M 35.0000 24 1.00 20FUKAAXX100202.6 35 TC Context M 35.0000 33 0.00 20FUKAAXX100202.6 35 TG Context M 35.0000 59 0.00 -20FUKAAXX100202.6 35 TT Context M 35.0000 53 0.00 +20FUKAAXX100202.6 35 TT Context M 35.0000 52 0.00 20FUKAAXX100202.6 36 -10 Cycle M 36.0000 13 0.00 20FUKAAXX100202.6 36 -100 Cycle M 36.0000 6 0.00 20FUKAAXX100202.6 36 -101 Cycle M 36.0000 2 0.00 @@ -15171,7 +15170,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 38 -42 Cycle M 38.0000 17 0.00 20FUKAAXX100202.6 38 -43 Cycle M 38.0000 15 0.00 20FUKAAXX100202.6 38 -44 Cycle M 38.0000 21 0.00 -20FUKAAXX100202.6 38 -45 Cycle M 38.0000 13 0.00 +20FUKAAXX100202.6 38 -45 Cycle M 38.0000 12 0.00 20FUKAAXX100202.6 38 -46 Cycle M 38.0000 23 0.00 20FUKAAXX100202.6 38 -47 Cycle M 38.0000 19 0.00 20FUKAAXX100202.6 38 -48 Cycle M 38.0000 20 0.00 @@ -15312,7 +15311,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 38 85 Cycle M 38.0000 23 0.00 20FUKAAXX100202.6 38 86 Cycle M 38.0000 23 0.00 20FUKAAXX100202.6 38 87 Cycle M 38.0000 15 0.00 -20FUKAAXX100202.6 38 88 Cycle M 38.0000 18 1.00 +20FUKAAXX100202.6 38 88 Cycle M 38.0000 17 1.00 20FUKAAXX100202.6 38 89 Cycle M 38.0000 19 0.00 20FUKAAXX100202.6 38 9 Cycle M 38.0000 13 0.00 20FUKAAXX100202.6 38 90 Cycle M 38.0000 14 0.00 @@ -15338,7 +15337,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 38 TA Context M 38.0000 167 0.00 20FUKAAXX100202.6 38 TC Context M 38.0000 108 0.00 20FUKAAXX100202.6 38 TG Context M 38.0000 463 3.00 -20FUKAAXX100202.6 38 TT Context M 38.0000 306 1.00 +20FUKAAXX100202.6 38 TT Context M 38.0000 304 1.00 20FUKAAXX100202.6 39 -100 Cycle M 39.0000 2 0.00 20FUKAAXX100202.6 39 -16 Cycle M 39.0000 3 0.00 20FUKAAXX100202.6 39 -17 Cycle M 39.0000 2 0.00 @@ -17460,7 +17459,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.7 36 -67 Cycle M 36.0000 3 0.00 20FUKAAXX100202.7 36 -68 Cycle M 36.0000 3 0.00 20FUKAAXX100202.7 36 -69 Cycle M 36.0000 4 0.00 -20FUKAAXX100202.7 36 -7 Cycle M 36.0000 12 0.00 +20FUKAAXX100202.7 36 -7 Cycle M 36.0000 11 0.00 20FUKAAXX100202.7 36 -70 Cycle M 36.0000 4 0.00 20FUKAAXX100202.7 36 -71 Cycle M 36.0000 3 0.00 20FUKAAXX100202.7 36 -72 Cycle M 36.0000 2 0.00 @@ -17590,7 +17589,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.7 36 97 Cycle M 36.0000 5 0.00 20FUKAAXX100202.7 36 98 Cycle M 36.0000 7 0.00 20FUKAAXX100202.7 36 99 Cycle M 36.0000 4 0.00 -20FUKAAXX100202.7 36 AA Context M 36.0000 58 0.00 +20FUKAAXX100202.7 36 AA Context M 36.0000 57 0.00 20FUKAAXX100202.7 36 AC Context M 36.0000 328 2.00 20FUKAAXX100202.7 36 AG Context M 36.0000 72 0.00 20FUKAAXX100202.7 36 AT Context M 36.0000 43 0.00 @@ -17989,7 +17988,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.7 38 90 Cycle M 38.0000 19 0.00 20FUKAAXX100202.7 38 91 Cycle M 38.0000 15 0.00 20FUKAAXX100202.7 38 92 Cycle M 38.0000 21 0.00 -20FUKAAXX100202.7 38 93 Cycle M 38.0000 17 0.00 +20FUKAAXX100202.7 38 93 Cycle M 38.0000 16 0.00 20FUKAAXX100202.7 38 94 Cycle M 38.0000 13 0.00 20FUKAAXX100202.7 38 95 Cycle M 38.0000 17 0.00 20FUKAAXX100202.7 38 96 Cycle M 38.0000 14 1.00 @@ -18009,7 +18008,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.7 38 TA Context M 38.0000 162 0.00 20FUKAAXX100202.7 38 TC Context M 38.0000 131 0.00 20FUKAAXX100202.7 38 TG Context M 38.0000 456 2.00 -20FUKAAXX100202.7 38 TT Context M 38.0000 262 1.00 +20FUKAAXX100202.7 38 TT Context M 38.0000 261 1.00 20FUKAAXX100202.7 39 -100 Cycle M 39.0000 1 0.00 20FUKAAXX100202.7 39 -14 Cycle M 39.0000 3 0.00 20FUKAAXX100202.7 39 -15 Cycle M 39.0000 2 0.00 @@ -21303,7 +21302,6 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 24 TC Context M 24.0000 4 0.00 20GAVAAXX100126.1 24 TG Context M 24.0000 1 0.00 20GAVAAXX100126.1 24 TT Context M 24.0000 1 0.00 -20GAVAAXX100126.1 25 -10 Cycle M 25.0000 1 0.00 20GAVAAXX100126.1 25 -12 Cycle M 25.0000 1 0.00 20GAVAAXX100126.1 25 -15 Cycle M 25.0000 1 0.00 20GAVAAXX100126.1 25 -17 Cycle M 25.0000 1 0.00 @@ -21382,7 +21380,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 25 GT Context M 25.0000 7 0.00 20GAVAAXX100126.1 25 TA Context M 25.0000 5 0.00 20GAVAAXX100126.1 25 TC Context M 25.0000 10 0.00 -20GAVAAXX100126.1 25 TG Context M 25.0000 9 0.00 +20GAVAAXX100126.1 25 TG Context M 25.0000 8 0.00 20GAVAAXX100126.1 25 TT Context M 25.0000 5 0.00 20GAVAAXX100126.1 26 -101 Cycle M 26.0000 1 0.00 20GAVAAXX100126.1 26 -18 Cycle M 26.0000 1 0.00 @@ -21542,7 +21540,6 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 27 61 Cycle M 27.0000 1 0.00 20GAVAAXX100126.1 27 63 Cycle M 27.0000 1 0.00 20GAVAAXX100126.1 27 65 Cycle M 27.0000 1 0.00 -20GAVAAXX100126.1 27 66 Cycle M 27.0000 1 0.00 20GAVAAXX100126.1 27 68 Cycle M 27.0000 1 0.00 20GAVAAXX100126.1 27 70 Cycle M 27.0000 2 0.00 20GAVAAXX100126.1 27 71 Cycle M 27.0000 1 0.00 @@ -21562,7 +21559,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 27 91 Cycle M 27.0000 1 0.00 20GAVAAXX100126.1 27 93 Cycle M 27.0000 2 0.00 20GAVAAXX100126.1 27 99 Cycle M 27.0000 2 0.00 -20GAVAAXX100126.1 27 AA Context M 27.0000 8 0.00 +20GAVAAXX100126.1 27 AA Context M 27.0000 7 0.00 20GAVAAXX100126.1 27 AC Context M 27.0000 3 0.00 20GAVAAXX100126.1 27 AG Context M 27.0000 9 0.00 20GAVAAXX100126.1 27 AT Context M 27.0000 3 0.00 @@ -23470,7 +23467,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 39 39 Cycle M 39.0000 16 0.00 20GAVAAXX100126.1 39 40 Cycle M 39.0000 23 0.00 20GAVAAXX100126.1 39 41 Cycle M 39.0000 8 0.00 -20GAVAAXX100126.1 39 42 Cycle M 39.0000 20 0.00 +20GAVAAXX100126.1 39 42 Cycle M 39.0000 19 0.00 20GAVAAXX100126.1 39 43 Cycle M 39.0000 13 0.00 20GAVAAXX100126.1 39 44 Cycle M 39.0000 15 0.00 20GAVAAXX100126.1 39 45 Cycle M 39.0000 11 0.00 @@ -23531,7 +23528,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 39 97 Cycle M 39.0000 10 0.00 20GAVAAXX100126.1 39 98 Cycle M 39.0000 8 0.00 20GAVAAXX100126.1 39 99 Cycle M 39.0000 3 0.00 -20GAVAAXX100126.1 39 AA Context M 39.0000 211 0.00 +20GAVAAXX100126.1 39 AA Context M 39.0000 210 0.00 20GAVAAXX100126.1 39 AG Context M 39.0000 26 0.00 20GAVAAXX100126.1 39 AT Context M 39.0000 49 0.00 20GAVAAXX100126.1 39 CA Context M 39.0000 413 2.00 @@ -25156,7 +25153,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.2 33 -68 Cycle M 33.0000 4 0.00 20GAVAAXX100126.2 33 -69 Cycle M 33.0000 3 0.00 20GAVAAXX100126.2 33 -7 Cycle M 33.0000 4 0.00 -20GAVAAXX100126.2 33 -70 Cycle M 33.0000 2 0.00 +20GAVAAXX100126.2 33 -70 Cycle M 33.0000 1 0.00 20GAVAAXX100126.2 33 -71 Cycle M 33.0000 9 0.00 20GAVAAXX100126.2 33 -72 Cycle M 33.0000 8 0.00 20GAVAAXX100126.2 33 -73 Cycle M 33.0000 4 0.00 @@ -25246,7 +25243,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.2 33 97 Cycle M 33.0000 1 0.00 20GAVAAXX100126.2 33 98 Cycle M 33.0000 4 0.00 20GAVAAXX100126.2 33 99 Cycle M 33.0000 2 0.00 -20GAVAAXX100126.2 33 AA Context M 33.0000 19 0.00 +20GAVAAXX100126.2 33 AA Context M 33.0000 18 0.00 20GAVAAXX100126.2 33 AC Context M 33.0000 25 0.00 20GAVAAXX100126.2 33 AG Context M 33.0000 32 0.00 20GAVAAXX100126.2 33 AT Context M 33.0000 16 0.00 @@ -30948,7 +30945,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.4 38 10 Cycle M 38.0000 10 0.00 20GAVAAXX100126.4 38 100 Cycle M 38.0000 4 0.00 20GAVAAXX100126.4 38 101 Cycle M 38.0000 5 0.00 -20GAVAAXX100126.4 38 11 Cycle M 38.0000 9 0.00 +20GAVAAXX100126.4 38 11 Cycle M 38.0000 8 0.00 20GAVAAXX100126.4 38 12 Cycle M 38.0000 8 0.00 20GAVAAXX100126.4 38 13 Cycle M 38.0000 9 0.00 20GAVAAXX100126.4 38 14 Cycle M 38.0000 11 0.00 @@ -31055,7 +31052,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.4 38 TA Context M 38.0000 97 0.00 20GAVAAXX100126.4 38 TC Context M 38.0000 29 0.00 20GAVAAXX100126.4 38 TG Context M 38.0000 196 3.00 -20GAVAAXX100126.4 38 TT Context M 38.0000 99 0.00 +20GAVAAXX100126.4 38 TT Context M 38.0000 98 0.00 20GAVAAXX100126.4 39 -13 Cycle M 39.0000 4 0.00 20GAVAAXX100126.4 39 -14 Cycle M 39.0000 3 0.00 20GAVAAXX100126.4 39 -15 Cycle M 39.0000 2 0.00 @@ -33173,7 +33170,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.5 38 20 Cycle M 38.0000 11 0.00 20GAVAAXX100126.5 38 21 Cycle M 38.0000 17 1.00 20GAVAAXX100126.5 38 22 Cycle M 38.0000 13 0.00 -20GAVAAXX100126.5 38 23 Cycle M 38.0000 11 0.00 +20GAVAAXX100126.5 38 23 Cycle M 38.0000 10 0.00 20GAVAAXX100126.5 38 24 Cycle M 38.0000 10 0.00 20GAVAAXX100126.5 38 25 Cycle M 38.0000 12 0.00 20GAVAAXX100126.5 38 26 Cycle M 38.0000 15 0.00 @@ -33269,7 +33266,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.5 38 TA Context M 38.0000 89 0.00 20GAVAAXX100126.5 38 TC Context M 38.0000 51 0.00 20GAVAAXX100126.5 38 TG Context M 38.0000 268 1.00 -20GAVAAXX100126.5 38 TT Context M 38.0000 169 0.00 +20GAVAAXX100126.5 38 TT Context M 38.0000 168 0.00 20GAVAAXX100126.5 39 -11 Cycle M 39.0000 1 0.00 20GAVAAXX100126.5 39 -12 Cycle M 39.0000 3 0.00 20GAVAAXX100126.5 39 -14 Cycle M 39.0000 1 0.00 @@ -34486,7 +34483,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.6 31 -46 Cycle M 31.0000 2 0.00 20GAVAAXX100126.6 31 -47 Cycle M 31.0000 2 0.00 20GAVAAXX100126.6 31 -48 Cycle M 31.0000 3 0.00 -20GAVAAXX100126.6 31 -5 Cycle M 31.0000 6 0.00 +20GAVAAXX100126.6 31 -5 Cycle M 31.0000 5 0.00 20GAVAAXX100126.6 31 -50 Cycle M 31.0000 4 0.00 20GAVAAXX100126.6 31 -51 Cycle M 31.0000 1 0.00 20GAVAAXX100126.6 31 -52 Cycle M 31.0000 1 0.00 @@ -34562,7 +34559,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.6 31 94 Cycle M 31.0000 1 0.00 20GAVAAXX100126.6 31 97 Cycle M 31.0000 2 0.00 20GAVAAXX100126.6 31 99 Cycle M 31.0000 1 0.00 -20GAVAAXX100126.6 31 AA Context M 31.0000 14 0.00 +20GAVAAXX100126.6 31 AA Context M 31.0000 13 0.00 20GAVAAXX100126.6 31 AC Context M 31.0000 17 0.00 20GAVAAXX100126.6 31 AG Context M 31.0000 16 0.00 20GAVAAXX100126.6 31 AT Context M 31.0000 6 0.00 @@ -35664,7 +35661,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.6 38 40 Cycle M 38.0000 13 0.00 20GAVAAXX100126.6 38 41 Cycle M 38.0000 9 0.00 20GAVAAXX100126.6 38 42 Cycle M 38.0000 13 0.00 -20GAVAAXX100126.6 38 43 Cycle M 38.0000 17 0.00 +20GAVAAXX100126.6 38 43 Cycle M 38.0000 16 0.00 20GAVAAXX100126.6 38 44 Cycle M 38.0000 14 0.00 20GAVAAXX100126.6 38 45 Cycle M 38.0000 14 0.00 20GAVAAXX100126.6 38 46 Cycle M 38.0000 10 0.00 @@ -35740,7 +35737,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.6 38 TA Context M 38.0000 105 0.00 20GAVAAXX100126.6 38 TC Context M 38.0000 12 0.00 20GAVAAXX100126.6 38 TG Context M 38.0000 263 2.00 -20GAVAAXX100126.6 38 TT Context M 38.0000 214 0.00 +20GAVAAXX100126.6 38 TT Context M 38.0000 213 0.00 20GAVAAXX100126.6 39 -12 Cycle M 39.0000 2 0.00 20GAVAAXX100126.6 39 -13 Cycle M 39.0000 1 0.00 20GAVAAXX100126.6 39 -14 Cycle M 39.0000 3 0.00 @@ -37532,7 +37529,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.7 33 -32 Cycle M 33.0000 1 0.00 20GAVAAXX100126.7 33 -33 Cycle M 33.0000 3 0.00 20GAVAAXX100126.7 33 -34 Cycle M 33.0000 3 0.00 -20GAVAAXX100126.7 33 -35 Cycle M 33.0000 3 0.00 +20GAVAAXX100126.7 33 -35 Cycle M 33.0000 2 0.00 20GAVAAXX100126.7 33 -37 Cycle M 33.0000 4 0.00 20GAVAAXX100126.7 33 -38 Cycle M 33.0000 1 0.00 20GAVAAXX100126.7 33 -39 Cycle M 33.0000 5 0.00 @@ -37645,7 +37642,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.7 33 96 Cycle M 33.0000 1 0.00 20GAVAAXX100126.7 33 98 Cycle M 33.0000 3 0.00 20GAVAAXX100126.7 33 99 Cycle M 33.0000 2 0.00 -20GAVAAXX100126.7 33 AA Context M 33.0000 15 0.00 +20GAVAAXX100126.7 33 AA Context M 33.0000 14 0.00 20GAVAAXX100126.7 33 AC Context M 33.0000 16 0.00 20GAVAAXX100126.7 33 AG Context M 33.0000 31 0.00 20GAVAAXX100126.7 33 AT Context M 33.0000 18 0.00 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.quantizing_levels_6.recal.txt b/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.quantizing_levels_6.recal.txt index 329f41c7717..ce3bbb589e1 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.quantizing_levels_6.recal.txt +++ b/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.quantizing_levels_6.recal.txt @@ -48,27 +48,27 @@ QualityScore Count QuantizedScore 22 750 25 23 853 25 24 997 25 - 25 1228 25 + 25 1227 25 26 1491 25 - 27 1728 25 + 27 1727 25 28 1781 25 29 2284 25 30 2439 33 - 31 2537 33 + 31 2536 33 32 3565 33 - 33 4141 33 + 33 4139 33 34 5194 33 - 35 7518 33 - 36 11939 37 - 37 28884 37 - 38 27993 39 - 39 15115 39 + 35 7517 33 + 36 11937 37 + 37 28883 37 + 38 27987 39 + 39 15108 39 40 778 39 41 53 39 42 0 39 43 0 39 - 44 15761 45 - 45 234039 45 + 44 9294 45 + 45 240462 45 46 0 45 47 0 45 48 0 45 @@ -121,51 +121,51 @@ QualityScore Count QuantizedScore #:GATKTable:6:48:%s:%s:%.4f:%.4f:%d:%.2f:; #:GATKTable:RecalTable0: ReadGroup EventType EmpiricalQuality EstimatedQReported Observations Errors -20FUKAAXX100202.1 D 45.0000 45.0000 7293 3.86 -20FUKAAXX100202.1 I 45.0000 45.0000 7293 0.00 -20FUKAAXX100202.1 M 27.0000 27.0392 7293 15.67 -20FUKAAXX100202.2 D 44.0000 45.0000 6464 7.56 -20FUKAAXX100202.2 I 45.0000 45.0000 6464 0.00 -20FUKAAXX100202.2 M 29.0000 30.1871 6464 20.60 -20FUKAAXX100202.3 D 45.0000 45.0000 8976 5.73 -20FUKAAXX100202.3 I 45.0000 45.0000 8976 0.00 -20FUKAAXX100202.3 M 27.0000 28.2043 8976 29.75 -20FUKAAXX100202.4 D 45.0000 45.0000 6830 3.75 -20FUKAAXX100202.4 I 45.0000 45.0000 6830 0.00 -20FUKAAXX100202.4 M 29.0000 29.0885 6830 13.00 -20FUKAAXX100202.5 D 45.0000 45.0000 7471 2.86 -20FUKAAXX100202.5 I 45.0000 45.0000 7471 0.00 -20FUKAAXX100202.5 M 28.0000 29.7339 7471 26.67 -20FUKAAXX100202.6 D 45.0000 45.0000 10026 8.40 -20FUKAAXX100202.6 I 45.0000 45.0000 10026 0.00 -20FUKAAXX100202.6 M 27.0000 28.7545 10026 27.25 -20FUKAAXX100202.7 D 45.0000 45.0000 9347 2.78 -20FUKAAXX100202.7 I 45.0000 45.0000 9347 0.00 -20FUKAAXX100202.7 M 26.0000 27.7419 9347 30.67 +20FUKAAXX100202.1 D 45.0000 45.0000 7292 3.71 +20FUKAAXX100202.1 I 45.0000 45.0000 7292 0.00 +20FUKAAXX100202.1 M 27.0000 27.0386 7292 15.67 +20FUKAAXX100202.2 D 45.0000 45.0000 6462 7.33 +20FUKAAXX100202.2 I 45.0000 45.0000 6462 0.00 +20FUKAAXX100202.2 M 29.0000 30.1859 6462 20.60 +20FUKAAXX100202.3 D 45.0000 45.0000 8974 5.46 +20FUKAAXX100202.3 I 45.0000 45.0000 8974 0.00 +20FUKAAXX100202.3 M 27.0000 28.2034 8974 29.75 +20FUKAAXX100202.4 D 45.0000 45.0000 6828 3.50 +20FUKAAXX100202.4 I 45.0000 45.0000 6828 0.00 +20FUKAAXX100202.4 M 29.0000 29.0874 6828 13.00 +20FUKAAXX100202.5 D 45.0000 45.0000 7470 2.71 +20FUKAAXX100202.5 I 45.0000 45.0000 7470 0.00 +20FUKAAXX100202.5 M 28.0000 29.7334 7470 26.67 +20FUKAAXX100202.6 D 45.0000 45.0000 10023 7.95 +20FUKAAXX100202.6 I 45.0000 45.0000 10023 0.00 +20FUKAAXX100202.6 M 27.0000 28.7535 10023 27.25 +20FUKAAXX100202.7 D 45.0000 45.0000 9345 2.57 +20FUKAAXX100202.7 I 45.0000 45.0000 9345 0.00 +20FUKAAXX100202.7 M 26.0000 27.7411 9345 30.67 20FUKAAXX100202.8 D 45.0000 45.0000 8152 3.75 20FUKAAXX100202.8 I 45.0000 45.0000 8152 0.00 20FUKAAXX100202.8 M 28.0000 29.0288 8152 24.00 -20GAVAAXX100126.1 D 44.0000 45.0000 9297 9.12 -20GAVAAXX100126.1 I 45.0000 45.0000 9297 1.00 -20GAVAAXX100126.1 M 26.0000 27.6243 9297 29.75 -20GAVAAXX100126.2 D 45.0000 45.0000 8155 4.86 -20GAVAAXX100126.2 I 45.0000 45.0000 8155 0.00 -20GAVAAXX100126.2 M 26.0000 27.3758 8155 34.42 +20GAVAAXX100126.1 D 44.0000 45.0000 9294 8.52 +20GAVAAXX100126.1 I 45.0000 45.0000 9294 1.00 +20GAVAAXX100126.1 M 26.0000 27.6244 9294 29.75 +20GAVAAXX100126.2 D 45.0000 45.0000 8154 4.71 +20GAVAAXX100126.2 I 45.0000 45.0000 8154 0.00 +20GAVAAXX100126.2 M 26.0000 27.3754 8154 34.42 20GAVAAXX100126.3 D 45.0000 45.0000 6239 3.00 20GAVAAXX100126.3 I 45.0000 45.0000 6239 0.00 20GAVAAXX100126.3 M 26.0000 26.8893 6239 20.57 -20GAVAAXX100126.4 D 45.0000 45.0000 6633 2.86 -20GAVAAXX100126.4 I 45.0000 45.0000 6633 0.00 -20GAVAAXX100126.4 M 26.0000 27.0432 6633 29.33 -20GAVAAXX100126.5 D 45.0000 45.0000 5884 0.86 -20GAVAAXX100126.5 I 45.0000 45.0000 5884 0.00 -20GAVAAXX100126.5 M 27.0000 28.0717 5884 21.33 -20GAVAAXX100126.6 D 45.0000 45.0000 8002 3.69 -20GAVAAXX100126.6 I 45.0000 45.0000 8002 0.00 -20GAVAAXX100126.6 M 27.0000 28.4682 8002 27.00 -20GAVAAXX100126.7 D 45.0000 45.0000 7598 2.88 -20GAVAAXX100126.7 I 45.0000 45.0000 7598 0.00 -20GAVAAXX100126.7 M 25.0000 25.6878 7598 27.75 +20GAVAAXX100126.4 D 45.0000 45.0000 6632 2.71 +20GAVAAXX100126.4 I 45.0000 45.0000 6632 0.00 +20GAVAAXX100126.4 M 26.0000 27.0426 6632 29.33 +20GAVAAXX100126.5 D 45.0000 45.0000 5883 0.71 +20GAVAAXX100126.5 I 45.0000 45.0000 5883 0.00 +20GAVAAXX100126.5 M 27.0000 28.0710 5883 21.33 +20GAVAAXX100126.6 D 45.0000 45.0000 8000 3.38 +20GAVAAXX100126.6 I 45.0000 45.0000 8000 0.00 +20GAVAAXX100126.6 M 27.0000 28.4675 8000 27.00 +20GAVAAXX100126.7 D 45.0000 45.0000 7597 2.75 +20GAVAAXX100126.7 I 45.0000 45.0000 7597 0.00 +20GAVAAXX100126.7 M 25.0000 25.6874 7597 27.75 20GAVAAXX100126.8 D 45.0000 45.0000 8533 5.69 20GAVAAXX100126.8 I 45.0000 45.0000 8533 1.00 20GAVAAXX100126.8 M 26.0000 27.3594 8533 29.25 @@ -204,12 +204,12 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20FUKAAXX100202.1 34 M 34.0000 217 0.20 20FUKAAXX100202.1 35 M 35.0000 347 1.07 20FUKAAXX100202.1 36 M 36.0000 599 1.00 -20FUKAAXX100202.1 37 M 37.0000 1407 1.33 +20FUKAAXX100202.1 37 M 37.0000 1406 1.33 20FUKAAXX100202.1 38 M 38.0000 2058 0.33 20FUKAAXX100202.1 39 M 39.0000 741 0.00 20FUKAAXX100202.1 40 M 40.0000 16 0.00 -20FUKAAXX100202.1 45 D 45.0000 7293 3.86 -20FUKAAXX100202.1 45 I 45.0000 7293 0.00 +20FUKAAXX100202.1 45 D 45.0000 7292 3.71 +20FUKAAXX100202.1 45 I 45.0000 7292 0.00 20FUKAAXX100202.2 6 M 6.0000 1 0.00 20FUKAAXX100202.2 7 M 7.0000 1 0.00 20FUKAAXX100202.2 8 M 8.0000 3 0.00 @@ -243,10 +243,10 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20FUKAAXX100202.2 36 M 36.0000 580 4.00 20FUKAAXX100202.2 37 M 37.0000 1371 2.00 20FUKAAXX100202.2 38 M 38.0000 2181 6.00 -20FUKAAXX100202.2 39 M 39.0000 667 1.00 +20FUKAAXX100202.2 39 M 39.0000 665 1.00 20FUKAAXX100202.2 40 M 40.0000 27 0.00 -20FUKAAXX100202.2 45 D 44.0000 6464 7.56 -20FUKAAXX100202.2 45 I 45.0000 6464 0.00 +20FUKAAXX100202.2 45 D 45.0000 6462 7.33 +20FUKAAXX100202.2 45 I 45.0000 6462 0.00 20FUKAAXX100202.3 6 M 6.0000 1 1.00 20FUKAAXX100202.3 7 M 7.0000 4 0.00 20FUKAAXX100202.3 8 M 8.0000 8 0.00 @@ -277,13 +277,13 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20FUKAAXX100202.3 33 M 33.0000 245 0.00 20FUKAAXX100202.3 34 M 34.0000 262 0.00 20FUKAAXX100202.3 35 M 35.0000 463 1.00 -20FUKAAXX100202.3 36 M 36.0000 944 6.25 +20FUKAAXX100202.3 36 M 36.0000 943 6.25 20FUKAAXX100202.3 37 M 37.0000 1649 4.25 20FUKAAXX100202.3 38 M 37.0000 2837 11.25 -20FUKAAXX100202.3 39 M 39.0000 976 0.00 +20FUKAAXX100202.3 39 M 39.0000 975 0.00 20FUKAAXX100202.3 40 M 40.0000 28 0.00 -20FUKAAXX100202.3 45 D 45.0000 8976 5.73 -20FUKAAXX100202.3 45 I 45.0000 8976 0.00 +20FUKAAXX100202.3 45 D 45.0000 8974 5.46 +20FUKAAXX100202.3 45 I 45.0000 8974 0.00 20FUKAAXX100202.4 6 M 6.0000 1 0.00 20FUKAAXX100202.4 7 M 7.0000 2 1.00 20FUKAAXX100202.4 8 M 8.0000 3 1.00 @@ -317,10 +317,10 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20FUKAAXX100202.4 36 M 36.0000 633 0.00 20FUKAAXX100202.4 37 M 37.0000 1408 3.25 20FUKAAXX100202.4 38 M 38.0000 2074 3.50 -20FUKAAXX100202.4 39 M 39.0000 662 1.00 +20FUKAAXX100202.4 39 M 39.0000 660 1.00 20FUKAAXX100202.4 40 M 40.0000 20 0.00 -20FUKAAXX100202.4 45 D 45.0000 6830 3.75 -20FUKAAXX100202.4 45 I 45.0000 6830 0.00 +20FUKAAXX100202.4 45 D 45.0000 6828 3.50 +20FUKAAXX100202.4 45 I 45.0000 6828 0.00 20FUKAAXX100202.5 6 M 6.0000 1 0.00 20FUKAAXX100202.5 7 M 7.0000 3 0.00 20FUKAAXX100202.5 8 M 8.0000 2 1.00 @@ -354,10 +354,10 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20FUKAAXX100202.5 36 M 36.0000 695 2.33 20FUKAAXX100202.5 37 M 37.0000 1329 2.00 20FUKAAXX100202.5 38 M 37.0000 2579 9.80 -20FUKAAXX100202.5 39 M 39.0000 907 1.00 +20FUKAAXX100202.5 39 M 39.0000 906 1.00 20FUKAAXX100202.5 40 M 40.0000 67 0.20 -20FUKAAXX100202.5 45 D 45.0000 7471 2.86 -20FUKAAXX100202.5 45 I 45.0000 7471 0.00 +20FUKAAXX100202.5 45 D 45.0000 7470 2.71 +20FUKAAXX100202.5 45 I 45.0000 7470 0.00 20FUKAAXX100202.6 6 M 6.0000 7 4.00 20FUKAAXX100202.6 7 M 7.0000 4 2.00 20FUKAAXX100202.6 8 M 8.0000 5 0.00 @@ -387,14 +387,14 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20FUKAAXX100202.6 32 M 32.0000 226 1.00 20FUKAAXX100202.6 33 M 33.0000 231 2.00 20FUKAAXX100202.6 34 M 34.0000 302 0.00 -20FUKAAXX100202.6 35 M 35.0000 579 2.17 +20FUKAAXX100202.6 35 M 35.0000 578 2.17 20FUKAAXX100202.6 36 M 36.0000 975 2.33 20FUKAAXX100202.6 37 M 37.0000 1959 1.17 -20FUKAAXX100202.6 38 M 38.0000 3301 6.00 +20FUKAAXX100202.6 38 M 38.0000 3299 6.00 20FUKAAXX100202.6 39 M 39.0000 1111 1.00 20FUKAAXX100202.6 40 M 40.0000 43 0.00 -20FUKAAXX100202.6 45 D 45.0000 10026 8.40 -20FUKAAXX100202.6 45 I 45.0000 10026 0.00 +20FUKAAXX100202.6 45 D 45.0000 10023 7.95 +20FUKAAXX100202.6 45 I 45.0000 10023 0.00 20FUKAAXX100202.7 6 M 6.0000 5 2.00 20FUKAAXX100202.7 7 M 7.0000 5 1.00 20FUKAAXX100202.7 8 M 8.0000 9 3.33 @@ -425,13 +425,13 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20FUKAAXX100202.7 33 M 33.0000 197 0.00 20FUKAAXX100202.7 34 M 34.0000 251 0.00 20FUKAAXX100202.7 35 M 35.0000 441 1.92 -20FUKAAXX100202.7 36 M 36.0000 955 3.33 +20FUKAAXX100202.7 36 M 36.0000 954 3.33 20FUKAAXX100202.7 37 M 37.0000 1600 2.67 -20FUKAAXX100202.7 38 M 38.0000 3286 3.92 +20FUKAAXX100202.7 38 M 38.0000 3285 3.92 20FUKAAXX100202.7 39 M 39.0000 1063 1.25 20FUKAAXX100202.7 40 M 40.0000 43 0.00 -20FUKAAXX100202.7 45 D 45.0000 9347 2.78 -20FUKAAXX100202.7 45 I 45.0000 9347 0.00 +20FUKAAXX100202.7 45 D 45.0000 9345 2.57 +20FUKAAXX100202.7 45 I 45.0000 9345 0.00 20FUKAAXX100202.8 6 M 6.0000 4 2.00 20FUKAAXX100202.8 7 M 7.0000 5 0.00 20FUKAAXX100202.8 8 M 8.0000 1 0.00 @@ -488,9 +488,9 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.1 22 M 22.0000 43 1.00 20GAVAAXX100126.1 23 M 23.0000 65 0.13 20GAVAAXX100126.1 24 M 24.0000 56 0.00 -20GAVAAXX100126.1 25 M 25.0000 85 0.00 +20GAVAAXX100126.1 25 M 25.0000 84 0.00 20GAVAAXX100126.1 26 M 26.0000 104 0.00 -20GAVAAXX100126.1 27 M 27.0000 114 0.00 +20GAVAAXX100126.1 27 M 27.0000 113 0.00 20GAVAAXX100126.1 28 M 28.0000 149 0.00 20GAVAAXX100126.1 29 M 29.0000 185 1.33 20GAVAAXX100126.1 30 M 30.0000 179 0.00 @@ -502,11 +502,11 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.1 36 M 36.0000 822 2.25 20GAVAAXX100126.1 37 M 37.0000 1759 7.00 20GAVAAXX100126.1 38 M 38.0000 1880 3.25 -20GAVAAXX100126.1 39 M 39.0000 1546 2.00 +20GAVAAXX100126.1 39 M 39.0000 1545 2.00 20GAVAAXX100126.1 40 M 40.0000 243 0.00 20GAVAAXX100126.1 41 M 41.0000 23 0.00 -20GAVAAXX100126.1 45 D 44.0000 9297 9.12 -20GAVAAXX100126.1 45 I 45.0000 9297 1.00 +20GAVAAXX100126.1 45 D 44.0000 9294 8.52 +20GAVAAXX100126.1 45 I 45.0000 9294 1.00 20GAVAAXX100126.2 6 M 6.0000 10 4.00 20GAVAAXX100126.2 7 M 7.0000 8 1.00 20GAVAAXX100126.2 8 M 8.0000 6 0.00 @@ -534,7 +534,7 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.2 30 M 30.0000 169 0.00 20GAVAAXX100126.2 31 M 31.0000 222 1.25 20GAVAAXX100126.2 32 M 32.0000 336 0.00 -20GAVAAXX100126.2 33 M 33.0000 392 6.00 +20GAVAAXX100126.2 33 M 33.0000 391 6.00 20GAVAAXX100126.2 34 M 34.0000 471 0.00 20GAVAAXX100126.2 35 M 35.0000 540 2.00 20GAVAAXX100126.2 36 M 36.0000 685 1.67 @@ -543,8 +543,8 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.2 39 M 39.0000 1127 2.00 20GAVAAXX100126.2 40 M 40.0000 49 0.00 20GAVAAXX100126.2 41 M 41.0000 9 0.00 -20GAVAAXX100126.2 45 D 45.0000 8155 4.86 -20GAVAAXX100126.2 45 I 45.0000 8155 0.00 +20GAVAAXX100126.2 45 D 45.0000 8154 4.71 +20GAVAAXX100126.2 45 I 45.0000 8154 0.00 20GAVAAXX100126.3 6 M 6.0000 2 0.00 20GAVAAXX100126.3 7 M 7.0000 8 2.00 20GAVAAXX100126.3 8 M 8.0000 8 2.00 @@ -615,12 +615,12 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.4 35 M 35.0000 487 2.00 20GAVAAXX100126.4 36 M 36.0000 639 1.25 20GAVAAXX100126.4 37 M 37.0000 1224 5.50 -20GAVAAXX100126.4 38 M 38.0000 1250 4.67 +20GAVAAXX100126.4 38 M 38.0000 1249 4.67 20GAVAAXX100126.4 39 M 39.0000 857 2.00 20GAVAAXX100126.4 40 M 40.0000 33 0.00 20GAVAAXX100126.4 41 M 41.0000 1 0.00 -20GAVAAXX100126.4 45 D 45.0000 6633 2.86 -20GAVAAXX100126.4 45 I 45.0000 6633 0.00 +20GAVAAXX100126.4 45 D 45.0000 6632 2.71 +20GAVAAXX100126.4 45 I 45.0000 6632 0.00 20GAVAAXX100126.5 6 M 6.0000 4 0.00 20GAVAAXX100126.5 7 M 7.0000 8 3.00 20GAVAAXX100126.5 8 M 8.0000 4 1.00 @@ -653,12 +653,12 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.5 35 M 35.0000 328 1.00 20GAVAAXX100126.5 36 M 36.0000 583 0.33 20GAVAAXX100126.5 37 M 37.0000 1187 2.00 -20GAVAAXX100126.5 38 M 38.0000 1446 2.00 +20GAVAAXX100126.5 38 M 38.0000 1445 2.00 20GAVAAXX100126.5 39 M 39.0000 909 2.00 20GAVAAXX100126.5 40 M 40.0000 43 0.00 20GAVAAXX100126.5 41 M 41.0000 5 0.00 -20GAVAAXX100126.5 45 D 45.0000 5884 0.86 -20GAVAAXX100126.5 45 I 45.0000 5884 0.00 +20GAVAAXX100126.5 45 D 45.0000 5883 0.71 +20GAVAAXX100126.5 45 I 45.0000 5883 0.00 20GAVAAXX100126.6 6 M 6.0000 4 2.00 20GAVAAXX100126.6 7 M 7.0000 6 0.00 20GAVAAXX100126.6 8 M 8.0000 9 3.00 @@ -684,18 +684,18 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.6 28 M 28.0000 105 0.00 20GAVAAXX100126.6 29 M 29.0000 158 1.00 20GAVAAXX100126.6 30 M 30.0000 144 0.00 -20GAVAAXX100126.6 31 M 31.0000 194 1.00 +20GAVAAXX100126.6 31 M 31.0000 193 1.00 20GAVAAXX100126.6 32 M 32.0000 239 0.00 20GAVAAXX100126.6 33 M 33.0000 358 0.00 20GAVAAXX100126.6 34 M 34.0000 481 1.00 20GAVAAXX100126.6 35 M 35.0000 578 2.00 20GAVAAXX100126.6 36 M 36.0000 845 2.00 20GAVAAXX100126.6 37 M 37.0000 1617 4.00 -20GAVAAXX100126.6 38 M 38.0000 1661 3.00 +20GAVAAXX100126.6 38 M 38.0000 1660 3.00 20GAVAAXX100126.6 39 M 39.0000 1030 2.00 20GAVAAXX100126.6 40 M 40.0000 35 0.00 -20GAVAAXX100126.6 45 D 45.0000 8002 3.69 -20GAVAAXX100126.6 45 I 45.0000 8002 0.00 +20GAVAAXX100126.6 45 D 45.0000 8000 3.38 +20GAVAAXX100126.6 45 I 45.0000 8000 0.00 20GAVAAXX100126.7 6 M 6.0000 7 1.00 20GAVAAXX100126.7 7 M 7.0000 16 6.00 20GAVAAXX100126.7 8 M 8.0000 16 2.00 @@ -723,7 +723,7 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.7 30 M 30.0000 192 0.00 20GAVAAXX100126.7 31 M 31.0000 200 0.00 20GAVAAXX100126.7 32 M 32.0000 228 1.00 -20GAVAAXX100126.7 33 M 33.0000 382 1.25 +20GAVAAXX100126.7 33 M 33.0000 381 1.25 20GAVAAXX100126.7 34 M 34.0000 412 2.00 20GAVAAXX100126.7 35 M 35.0000 554 0.00 20GAVAAXX100126.7 36 M 36.0000 700 1.50 @@ -732,8 +732,8 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.7 39 M 39.0000 881 1.00 20GAVAAXX100126.7 40 M 40.0000 49 0.00 20GAVAAXX100126.7 41 M 41.0000 6 0.00 -20GAVAAXX100126.7 45 D 45.0000 7598 2.88 -20GAVAAXX100126.7 45 I 45.0000 7598 0.00 +20GAVAAXX100126.7 45 D 45.0000 7597 2.75 +20GAVAAXX100126.7 45 I 45.0000 7597 0.00 20GAVAAXX100126.8 6 M 6.0000 9 1.00 20GAVAAXX100126.8 7 M 7.0000 4 0.00 20GAVAAXX100126.8 8 M 8.0000 7 1.00 @@ -773,7 +773,7 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.8 45 D 45.0000 8533 5.69 20GAVAAXX100126.8 45 I 45.0000 8533 1.00 -#:GATKTable:8:48659:%s:%d:%s:%s:%s:%.4f:%d:%.2f:; +#:GATKTable:8:48656:%s:%d:%s:%s:%s:%.4f:%d:%.2f:; #:GATKTable:RecalTable2: ReadGroup QualityScore CovariateValue CovariateName EventType EmpiricalQuality Observations Errors 20FUKAAXX100202.1 6 -31 Cycle M 6.0000 1 0.00 @@ -2925,7 +2925,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.1 37 -33 Cycle M 37.0000 5 0.00 20FUKAAXX100202.1 37 -34 Cycle M 37.0000 13 0.00 20FUKAAXX100202.1 37 -35 Cycle M 37.0000 12 0.00 -20FUKAAXX100202.1 37 -36 Cycle M 37.0000 14 0.00 +20FUKAAXX100202.1 37 -36 Cycle M 37.0000 13 0.00 20FUKAAXX100202.1 37 -37 Cycle M 37.0000 10 0.00 20FUKAAXX100202.1 37 -38 Cycle M 37.0000 9 0.00 20FUKAAXX100202.1 37 -39 Cycle M 37.0000 9 0.00 @@ -3100,7 +3100,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.1 37 TA Context M 37.0000 42 0.00 20FUKAAXX100202.1 37 TC Context M 37.0000 280 0.00 20FUKAAXX100202.1 37 TG Context M 37.0000 83 1.00 -20FUKAAXX100202.1 37 TT Context M 37.0000 116 0.00 +20FUKAAXX100202.1 37 TT Context M 37.0000 115 0.00 20FUKAAXX100202.1 38 -10 Cycle M 38.0000 2 0.00 20FUKAAXX100202.1 38 -100 Cycle M 38.0000 3 0.00 20FUKAAXX100202.1 38 -101 Cycle M 38.0000 4 0.00 @@ -3545,8 +3545,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.1 45 -34 Cycle I 45.0000 37 0.00 20FUKAAXX100202.1 45 -35 Cycle D 45.0000 37 0.00 20FUKAAXX100202.1 45 -35 Cycle I 45.0000 37 0.00 -20FUKAAXX100202.1 45 -36 Cycle D 45.0000 37 0.14 -20FUKAAXX100202.1 45 -36 Cycle I 45.0000 37 0.00 +20FUKAAXX100202.1 45 -36 Cycle D 45.0000 36 0.00 +20FUKAAXX100202.1 45 -36 Cycle I 45.0000 36 0.00 20FUKAAXX100202.1 45 -37 Cycle D 45.0000 37 0.14 20FUKAAXX100202.1 45 -37 Cycle I 45.0000 37 0.00 20FUKAAXX100202.1 45 -38 Cycle D 45.0000 38 0.14 @@ -3927,8 +3927,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.1 45 CTC Context I 45.0000 165 0.00 20FUKAAXX100202.1 45 CTG Context D 45.0000 167 0.00 20FUKAAXX100202.1 45 CTG Context I 45.0000 167 0.00 -20FUKAAXX100202.1 45 CTT Context D 45.0000 148 0.29 -20FUKAAXX100202.1 45 CTT Context I 45.0000 148 0.00 +20FUKAAXX100202.1 45 CTT Context D 45.0000 147 0.14 +20FUKAAXX100202.1 45 CTT Context I 45.0000 147 0.00 20FUKAAXX100202.1 45 GAA Context D 45.0000 142 0.29 20FUKAAXX100202.1 45 GAA Context I 45.0000 142 0.00 20FUKAAXX100202.1 45 GAC Context D 45.0000 81 0.00 @@ -5947,7 +5947,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.2 39 14 Cycle M 39.0000 3 0.00 20FUKAAXX100202.2 39 15 Cycle M 39.0000 3 0.00 20FUKAAXX100202.2 39 16 Cycle M 39.0000 2 0.00 -20FUKAAXX100202.2 39 17 Cycle M 39.0000 3 0.00 +20FUKAAXX100202.2 39 17 Cycle M 39.0000 2 0.00 20FUKAAXX100202.2 39 18 Cycle M 39.0000 7 0.00 20FUKAAXX100202.2 39 19 Cycle M 39.0000 4 0.00 20FUKAAXX100202.2 39 20 Cycle M 39.0000 3 0.00 @@ -6007,7 +6007,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.2 39 77 Cycle M 39.0000 5 0.00 20FUKAAXX100202.2 39 78 Cycle M 39.0000 2 0.00 20FUKAAXX100202.2 39 79 Cycle M 39.0000 6 0.00 -20FUKAAXX100202.2 39 8 Cycle M 39.0000 4 0.00 +20FUKAAXX100202.2 39 8 Cycle M 39.0000 3 0.00 20FUKAAXX100202.2 39 80 Cycle M 39.0000 2 0.00 20FUKAAXX100202.2 39 81 Cycle M 39.0000 2 0.00 20FUKAAXX100202.2 39 82 Cycle M 39.0000 2 0.00 @@ -6026,7 +6026,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.2 39 95 Cycle M 39.0000 3 0.00 20FUKAAXX100202.2 39 96 Cycle M 39.0000 3 0.00 20FUKAAXX100202.2 39 97 Cycle M 39.0000 1 0.00 -20FUKAAXX100202.2 39 AA Context M 39.0000 241 0.00 +20FUKAAXX100202.2 39 AA Context M 39.0000 239 0.00 20FUKAAXX100202.2 39 AG Context M 39.0000 2 0.00 20FUKAAXX100202.2 39 AT Context M 39.0000 1 0.00 20FUKAAXX100202.2 39 CA Context M 39.0000 81 0.00 @@ -6249,8 +6249,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.2 45 15 Cycle I 45.0000 32 0.00 20FUKAAXX100202.2 45 16 Cycle D 45.0000 32 0.13 20FUKAAXX100202.2 45 16 Cycle I 45.0000 32 0.00 -20FUKAAXX100202.2 45 17 Cycle D 45.0000 32 0.13 -20FUKAAXX100202.2 45 17 Cycle I 45.0000 32 0.00 +20FUKAAXX100202.2 45 17 Cycle D 45.0000 31 0.00 +20FUKAAXX100202.2 45 17 Cycle I 45.0000 31 0.00 20FUKAAXX100202.2 45 18 Cycle D 45.0000 31 0.00 20FUKAAXX100202.2 45 18 Cycle I 45.0000 31 0.00 20FUKAAXX100202.2 45 19 Cycle D 45.0000 32 0.25 @@ -6381,8 +6381,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.2 45 78 Cycle I 45.0000 30 0.00 20FUKAAXX100202.2 45 79 Cycle D 45.0000 29 0.00 20FUKAAXX100202.2 45 79 Cycle I 45.0000 29 0.00 -20FUKAAXX100202.2 45 8 Cycle D 45.0000 32 0.11 -20FUKAAXX100202.2 45 8 Cycle I 45.0000 32 0.00 +20FUKAAXX100202.2 45 8 Cycle D 45.0000 31 0.00 +20FUKAAXX100202.2 45 8 Cycle I 45.0000 31 0.00 20FUKAAXX100202.2 45 80 Cycle D 45.0000 30 0.00 20FUKAAXX100202.2 45 80 Cycle I 45.0000 30 0.00 20FUKAAXX100202.2 45 81 Cycle D 45.0000 29 0.00 @@ -6485,8 +6485,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.2 45 CTG Context I 45.0000 136 0.00 20FUKAAXX100202.2 45 CTT Context D 45.0000 128 0.65 20FUKAAXX100202.2 45 CTT Context I 45.0000 128 0.00 -20FUKAAXX100202.2 45 GAA Context D 45.0000 118 0.49 -20FUKAAXX100202.2 45 GAA Context I 45.0000 118 0.00 +20FUKAAXX100202.2 45 GAA Context D 45.0000 116 0.25 +20FUKAAXX100202.2 45 GAA Context I 45.0000 116 0.00 20FUKAAXX100202.2 45 GAC Context D 45.0000 69 0.00 20FUKAAXX100202.2 45 GAC Context I 45.0000 69 0.00 20FUKAAXX100202.2 45 GAG Context D 45.0000 137 0.49 @@ -8656,7 +8656,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.3 36 93 Cycle M 36.0000 5 0.00 20FUKAAXX100202.3 36 94 Cycle M 36.0000 4 0.00 20FUKAAXX100202.3 36 95 Cycle M 36.0000 6 0.00 -20FUKAAXX100202.3 36 96 Cycle M 36.0000 6 0.00 +20FUKAAXX100202.3 36 96 Cycle M 36.0000 5 0.00 20FUKAAXX100202.3 36 97 Cycle M 36.0000 3 0.00 20FUKAAXX100202.3 36 98 Cycle M 36.0000 4 0.00 20FUKAAXX100202.3 36 99 Cycle M 36.0000 5 0.00 @@ -8674,7 +8674,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.3 36 TA Context M 36.0000 32 0.00 20FUKAAXX100202.3 36 TC Context M 36.0000 41 0.00 20FUKAAXX100202.3 36 TG Context M 36.0000 56 2.00 -20FUKAAXX100202.3 36 TT Context M 36.0000 50 0.00 +20FUKAAXX100202.3 36 TT Context M 36.0000 49 0.00 20FUKAAXX100202.3 37 -1 Cycle M 37.0000 1 0.00 20FUKAAXX100202.3 37 -10 Cycle M 37.0000 14 0.00 20FUKAAXX100202.3 37 -100 Cycle M 37.0000 6 0.00 @@ -9094,7 +9094,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.3 39 -18 Cycle M 39.0000 6 0.00 20FUKAAXX100202.3 39 -19 Cycle M 39.0000 1 0.00 20FUKAAXX100202.3 39 -20 Cycle M 39.0000 4 0.00 -20FUKAAXX100202.3 39 -21 Cycle M 39.0000 7 0.00 +20FUKAAXX100202.3 39 -21 Cycle M 39.0000 6 0.00 20FUKAAXX100202.3 39 -22 Cycle M 39.0000 10 0.00 20FUKAAXX100202.3 39 -23 Cycle M 39.0000 5 0.00 20FUKAAXX100202.3 39 -25 Cycle M 39.0000 1 0.00 @@ -9264,7 +9264,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.3 39 97 Cycle M 39.0000 3 0.00 20FUKAAXX100202.3 39 98 Cycle M 39.0000 5 0.00 20FUKAAXX100202.3 39 99 Cycle M 39.0000 2 0.00 -20FUKAAXX100202.3 39 AA Context M 39.0000 334 0.00 +20FUKAAXX100202.3 39 AA Context M 39.0000 333 0.00 20FUKAAXX100202.3 39 AG Context M 39.0000 7 0.00 20FUKAAXX100202.3 39 CA Context M 39.0000 170 0.00 20FUKAAXX100202.3 39 CT Context M 39.0000 385 0.00 @@ -9305,8 +9305,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.3 45 -19 Cycle I 45.0000 49 0.00 20FUKAAXX100202.3 45 -20 Cycle D 45.0000 49 0.13 20FUKAAXX100202.3 45 -20 Cycle I 45.0000 49 0.00 -20FUKAAXX100202.3 45 -21 Cycle D 45.0000 49 0.13 -20FUKAAXX100202.3 45 -21 Cycle I 45.0000 49 0.00 +20FUKAAXX100202.3 45 -21 Cycle D 45.0000 48 0.00 +20FUKAAXX100202.3 45 -21 Cycle I 45.0000 48 0.00 20FUKAAXX100202.3 45 -22 Cycle D 45.0000 48 0.00 20FUKAAXX100202.3 45 -22 Cycle I 45.0000 48 0.00 20FUKAAXX100202.3 45 -23 Cycle D 45.0000 49 0.13 @@ -9651,8 +9651,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.3 45 94 Cycle I 45.0000 39 0.00 20FUKAAXX100202.3 45 95 Cycle D 45.0000 38 0.00 20FUKAAXX100202.3 45 95 Cycle I 45.0000 38 0.00 -20FUKAAXX100202.3 45 96 Cycle D 45.0000 39 0.14 -20FUKAAXX100202.3 45 96 Cycle I 45.0000 39 0.00 +20FUKAAXX100202.3 45 96 Cycle D 45.0000 38 0.00 +20FUKAAXX100202.3 45 96 Cycle I 45.0000 38 0.00 20FUKAAXX100202.3 45 97 Cycle D 45.0000 39 0.14 20FUKAAXX100202.3 45 97 Cycle I 45.0000 39 0.00 20FUKAAXX100202.3 45 AAA Context D 45.0000 201 0.38 @@ -9717,10 +9717,10 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.3 45 CTC Context I 45.0000 176 0.00 20FUKAAXX100202.3 45 CTG Context D 45.0000 198 0.00 20FUKAAXX100202.3 45 CTG Context I 45.0000 198 0.00 -20FUKAAXX100202.3 45 CTT Context D 45.0000 176 0.29 -20FUKAAXX100202.3 45 CTT Context I 45.0000 176 0.00 -20FUKAAXX100202.3 45 GAA Context D 45.0000 173 0.50 -20FUKAAXX100202.3 45 GAA Context I 45.0000 173 0.00 +20FUKAAXX100202.3 45 CTT Context D 45.0000 175 0.14 +20FUKAAXX100202.3 45 CTT Context I 45.0000 175 0.00 +20FUKAAXX100202.3 45 GAA Context D 45.0000 172 0.38 +20FUKAAXX100202.3 45 GAA Context I 45.0000 172 0.00 20FUKAAXX100202.3 45 GAC Context D 45.0000 85 0.00 20FUKAAXX100202.3 45 GAC Context I 45.0000 85 0.00 20FUKAAXX100202.3 45 GAG Context D 45.0000 177 0.50 @@ -12039,13 +12039,13 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.4 39 25 Cycle M 39.0000 3 0.00 20FUKAAXX100202.4 39 26 Cycle M 39.0000 1 0.00 20FUKAAXX100202.4 39 27 Cycle M 39.0000 2 0.00 -20FUKAAXX100202.4 39 28 Cycle M 39.0000 3 0.00 +20FUKAAXX100202.4 39 28 Cycle M 39.0000 2 0.00 20FUKAAXX100202.4 39 29 Cycle M 39.0000 3 0.00 20FUKAAXX100202.4 39 30 Cycle M 39.0000 4 0.00 20FUKAAXX100202.4 39 31 Cycle M 39.0000 4 0.00 20FUKAAXX100202.4 39 32 Cycle M 39.0000 7 0.00 20FUKAAXX100202.4 39 33 Cycle M 39.0000 3 0.00 -20FUKAAXX100202.4 39 34 Cycle M 39.0000 5 0.00 +20FUKAAXX100202.4 39 34 Cycle M 39.0000 4 0.00 20FUKAAXX100202.4 39 35 Cycle M 39.0000 2 0.00 20FUKAAXX100202.4 39 36 Cycle M 39.0000 1 0.00 20FUKAAXX100202.4 39 37 Cycle M 39.0000 3 0.00 @@ -12109,7 +12109,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.4 39 96 Cycle M 39.0000 2 0.00 20FUKAAXX100202.4 39 97 Cycle M 39.0000 4 0.00 20FUKAAXX100202.4 39 98 Cycle M 39.0000 2 0.00 -20FUKAAXX100202.4 39 AA Context M 39.0000 193 0.00 +20FUKAAXX100202.4 39 AA Context M 39.0000 191 0.00 20FUKAAXX100202.4 39 AG Context M 39.0000 1 0.00 20FUKAAXX100202.4 39 AT Context M 39.0000 2 0.00 20FUKAAXX100202.4 39 CA Context M 39.0000 109 1.00 @@ -12355,8 +12355,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.4 45 26 Cycle I 45.0000 32 0.00 20FUKAAXX100202.4 45 27 Cycle D 45.0000 32 0.13 20FUKAAXX100202.4 45 27 Cycle I 45.0000 32 0.00 -20FUKAAXX100202.4 45 28 Cycle D 45.0000 32 0.13 -20FUKAAXX100202.4 45 28 Cycle I 45.0000 32 0.00 +20FUKAAXX100202.4 45 28 Cycle D 45.0000 31 0.00 +20FUKAAXX100202.4 45 28 Cycle I 45.0000 31 0.00 20FUKAAXX100202.4 45 29 Cycle D 45.0000 31 0.13 20FUKAAXX100202.4 45 29 Cycle I 45.0000 31 0.00 20FUKAAXX100202.4 45 30 Cycle D 45.0000 31 0.25 @@ -12367,8 +12367,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.4 45 32 Cycle I 45.0000 32 0.00 20FUKAAXX100202.4 45 33 Cycle D 45.0000 32 0.13 20FUKAAXX100202.4 45 33 Cycle I 45.0000 32 0.00 -20FUKAAXX100202.4 45 34 Cycle D 45.0000 32 0.13 -20FUKAAXX100202.4 45 34 Cycle I 45.0000 32 0.00 +20FUKAAXX100202.4 45 34 Cycle D 45.0000 31 0.00 +20FUKAAXX100202.4 45 34 Cycle I 45.0000 31 0.00 20FUKAAXX100202.4 45 35 Cycle D 45.0000 31 0.00 20FUKAAXX100202.4 45 35 Cycle I 45.0000 31 0.00 20FUKAAXX100202.4 45 36 Cycle D 45.0000 32 0.13 @@ -12569,8 +12569,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.4 45 CTG Context I 45.0000 141 0.00 20FUKAAXX100202.4 45 CTT Context D 45.0000 132 0.14 20FUKAAXX100202.4 45 CTT Context I 45.0000 132 0.00 -20FUKAAXX100202.4 45 GAA Context D 45.0000 103 0.38 -20FUKAAXX100202.4 45 GAA Context I 45.0000 103 0.00 +20FUKAAXX100202.4 45 GAA Context D 45.0000 101 0.13 +20FUKAAXX100202.4 45 GAA Context I 45.0000 101 0.00 20FUKAAXX100202.4 45 GAC Context D 45.0000 80 0.00 20FUKAAXX100202.4 45 GAC Context I 45.0000 80 0.00 20FUKAAXX100202.4 45 GAG Context D 45.0000 155 0.38 @@ -14766,7 +14766,6 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.5 38 TT Context M 38.0000 221 0.00 20FUKAAXX100202.5 39 -100 Cycle M 39.0000 1 0.00 20FUKAAXX100202.5 39 -14 Cycle M 39.0000 2 0.00 -20FUKAAXX100202.5 39 -15 Cycle M 39.0000 1 0.00 20FUKAAXX100202.5 39 -16 Cycle M 39.0000 6 0.00 20FUKAAXX100202.5 39 -17 Cycle M 39.0000 4 0.00 20FUKAAXX100202.5 39 -18 Cycle M 39.0000 4 0.00 @@ -14943,7 +14942,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.5 39 97 Cycle M 39.0000 3 0.00 20FUKAAXX100202.5 39 98 Cycle M 39.0000 3 0.00 20FUKAAXX100202.5 39 99 Cycle M 39.0000 1 0.00 -20FUKAAXX100202.5 39 AA Context M 39.0000 241 0.00 +20FUKAAXX100202.5 39 AA Context M 39.0000 240 0.00 20FUKAAXX100202.5 39 AG Context M 39.0000 19 0.00 20FUKAAXX100202.5 39 AT Context M 39.0000 3 0.00 20FUKAAXX100202.5 39 CA Context M 39.0000 218 0.00 @@ -14997,8 +14996,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.5 45 -13 Cycle I 45.0000 39 0.00 20FUKAAXX100202.5 45 -14 Cycle D 45.0000 39 0.14 20FUKAAXX100202.5 45 -14 Cycle I 45.0000 39 0.00 -20FUKAAXX100202.5 45 -15 Cycle D 45.0000 39 0.14 -20FUKAAXX100202.5 45 -15 Cycle I 45.0000 39 0.00 +20FUKAAXX100202.5 45 -15 Cycle D 45.0000 38 0.00 +20FUKAAXX100202.5 45 -15 Cycle I 45.0000 38 0.00 20FUKAAXX100202.5 45 -16 Cycle D 45.0000 37 0.00 20FUKAAXX100202.5 45 -16 Cycle I 45.0000 37 0.00 20FUKAAXX100202.5 45 -17 Cycle D 45.0000 39 0.14 @@ -15423,8 +15422,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.5 45 CTG Context I 45.0000 154 0.00 20FUKAAXX100202.5 45 CTT Context D 45.0000 121 0.14 20FUKAAXX100202.5 45 CTT Context I 45.0000 121 0.00 -20FUKAAXX100202.5 45 GAA Context D 45.0000 162 0.29 -20FUKAAXX100202.5 45 GAA Context I 45.0000 162 0.00 +20FUKAAXX100202.5 45 GAA Context D 45.0000 161 0.14 +20FUKAAXX100202.5 45 GAA Context I 45.0000 161 0.00 20FUKAAXX100202.5 45 GAC Context D 45.0000 76 0.00 20FUKAAXX100202.5 45 GAC Context I 45.0000 76 0.00 20FUKAAXX100202.5 45 GAG Context D 45.0000 173 0.29 @@ -17205,7 +17204,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 35 -94 Cycle M 35.0000 2 0.00 20FUKAAXX100202.6 35 -95 Cycle M 35.0000 5 0.00 20FUKAAXX100202.6 35 -96 Cycle M 35.0000 1 0.00 -20FUKAAXX100202.6 35 -97 Cycle M 35.0000 3 0.00 +20FUKAAXX100202.6 35 -97 Cycle M 35.0000 2 0.00 20FUKAAXX100202.6 35 -98 Cycle M 35.0000 4 0.00 20FUKAAXX100202.6 35 -99 Cycle M 35.0000 2 0.00 20FUKAAXX100202.6 35 1 Cycle M 35.0000 51 0.50 @@ -17292,7 +17291,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 35 TA Context M 35.0000 24 1.00 20FUKAAXX100202.6 35 TC Context M 35.0000 33 0.17 20FUKAAXX100202.6 35 TG Context M 35.0000 59 0.00 -20FUKAAXX100202.6 35 TT Context M 35.0000 53 0.00 +20FUKAAXX100202.6 35 TT Context M 35.0000 52 0.00 20FUKAAXX100202.6 36 -10 Cycle M 36.0000 13 0.00 20FUKAAXX100202.6 36 -100 Cycle M 36.0000 6 0.00 20FUKAAXX100202.6 36 -101 Cycle M 36.0000 2 0.00 @@ -17735,7 +17734,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 38 -42 Cycle M 38.0000 17 0.00 20FUKAAXX100202.6 38 -43 Cycle M 38.0000 15 0.00 20FUKAAXX100202.6 38 -44 Cycle M 38.0000 21 0.00 -20FUKAAXX100202.6 38 -45 Cycle M 38.0000 13 0.00 +20FUKAAXX100202.6 38 -45 Cycle M 38.0000 12 0.00 20FUKAAXX100202.6 38 -46 Cycle M 38.0000 23 0.00 20FUKAAXX100202.6 38 -47 Cycle M 38.0000 19 0.00 20FUKAAXX100202.6 38 -48 Cycle M 38.0000 20 0.00 @@ -17876,7 +17875,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 38 85 Cycle M 38.0000 23 0.00 20FUKAAXX100202.6 38 86 Cycle M 38.0000 23 0.00 20FUKAAXX100202.6 38 87 Cycle M 38.0000 15 0.00 -20FUKAAXX100202.6 38 88 Cycle M 38.0000 18 1.00 +20FUKAAXX100202.6 38 88 Cycle M 38.0000 17 1.00 20FUKAAXX100202.6 38 89 Cycle M 38.0000 19 0.00 20FUKAAXX100202.6 38 9 Cycle M 38.0000 13 0.00 20FUKAAXX100202.6 38 90 Cycle M 38.0000 14 0.00 @@ -17902,7 +17901,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 38 TA Context M 38.0000 167 0.00 20FUKAAXX100202.6 38 TC Context M 38.0000 108 0.00 20FUKAAXX100202.6 38 TG Context M 38.0000 463 3.00 -20FUKAAXX100202.6 38 TT Context M 38.0000 306 1.00 +20FUKAAXX100202.6 38 TT Context M 38.0000 304 1.00 20FUKAAXX100202.6 39 -100 Cycle M 39.0000 2 0.00 20FUKAAXX100202.6 39 -16 Cycle M 39.0000 3 0.00 20FUKAAXX100202.6 39 -17 Cycle M 39.0000 2 0.00 @@ -18177,8 +18176,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 45 -43 Cycle I 45.0000 51 0.00 20FUKAAXX100202.6 45 -44 Cycle D 45.0000 49 0.00 20FUKAAXX100202.6 45 -44 Cycle I 45.0000 49 0.00 -20FUKAAXX100202.6 45 -45 Cycle D 45.0000 51 0.14 -20FUKAAXX100202.6 45 -45 Cycle I 45.0000 51 0.00 +20FUKAAXX100202.6 45 -45 Cycle D 45.0000 50 0.00 +20FUKAAXX100202.6 45 -45 Cycle I 45.0000 50 0.00 20FUKAAXX100202.6 45 -46 Cycle D 45.0000 51 0.14 20FUKAAXX100202.6 45 -46 Cycle I 45.0000 51 0.00 20FUKAAXX100202.6 45 -47 Cycle D 45.0000 51 0.14 @@ -18291,8 +18290,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 45 -95 Cycle I 45.0000 36 0.00 20FUKAAXX100202.6 45 -96 Cycle D 45.0000 35 0.00 20FUKAAXX100202.6 45 -96 Cycle I 45.0000 35 0.00 -20FUKAAXX100202.6 45 -97 Cycle D 45.0000 36 0.17 -20FUKAAXX100202.6 45 -97 Cycle I 45.0000 36 0.00 +20FUKAAXX100202.6 45 -97 Cycle D 45.0000 35 0.00 +20FUKAAXX100202.6 45 -97 Cycle I 45.0000 35 0.00 20FUKAAXX100202.6 45 10 Cycle D 45.0000 53 0.00 20FUKAAXX100202.6 45 10 Cycle I 45.0000 53 0.00 20FUKAAXX100202.6 45 11 Cycle D 45.0000 54 0.00 @@ -18457,8 +18456,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 45 86 Cycle I 45.0000 49 0.00 20FUKAAXX100202.6 45 87 Cycle D 45.0000 47 0.00 20FUKAAXX100202.6 45 87 Cycle I 45.0000 47 0.00 -20FUKAAXX100202.6 45 88 Cycle D 45.0000 48 0.14 -20FUKAAXX100202.6 45 88 Cycle I 45.0000 48 0.00 +20FUKAAXX100202.6 45 88 Cycle D 45.0000 47 0.00 +20FUKAAXX100202.6 45 88 Cycle I 45.0000 47 0.00 20FUKAAXX100202.6 45 89 Cycle D 45.0000 47 0.14 20FUKAAXX100202.6 45 89 Cycle I 45.0000 47 0.00 20FUKAAXX100202.6 45 9 Cycle D 45.0000 54 0.00 @@ -18541,8 +18540,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 45 CTC Context I 45.0000 221 0.00 20FUKAAXX100202.6 45 CTG Context D 45.0000 209 0.00 20FUKAAXX100202.6 45 CTG Context I 45.0000 209 0.00 -20FUKAAXX100202.6 45 CTT Context D 45.0000 203 1.17 -20FUKAAXX100202.6 45 CTT Context I 45.0000 203 0.00 +20FUKAAXX100202.6 45 CTT Context D 45.0000 200 0.71 +20FUKAAXX100202.6 45 CTT Context I 45.0000 200 0.00 20FUKAAXX100202.6 45 GAA Context D 45.0000 195 0.14 20FUKAAXX100202.6 45 GAA Context I 45.0000 195 0.00 20FUKAAXX100202.6 45 GAC Context D 45.0000 107 0.00 @@ -20524,7 +20523,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.7 36 -67 Cycle M 36.0000 3 0.00 20FUKAAXX100202.7 36 -68 Cycle M 36.0000 3 0.00 20FUKAAXX100202.7 36 -69 Cycle M 36.0000 4 0.00 -20FUKAAXX100202.7 36 -7 Cycle M 36.0000 12 0.00 +20FUKAAXX100202.7 36 -7 Cycle M 36.0000 11 0.00 20FUKAAXX100202.7 36 -70 Cycle M 36.0000 4 0.00 20FUKAAXX100202.7 36 -71 Cycle M 36.0000 3 0.00 20FUKAAXX100202.7 36 -72 Cycle M 36.0000 2 0.00 @@ -20654,7 +20653,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.7 36 97 Cycle M 36.0000 5 0.00 20FUKAAXX100202.7 36 98 Cycle M 36.0000 7 0.00 20FUKAAXX100202.7 36 99 Cycle M 36.0000 4 0.00 -20FUKAAXX100202.7 36 AA Context M 36.0000 58 0.00 +20FUKAAXX100202.7 36 AA Context M 36.0000 57 0.00 20FUKAAXX100202.7 36 AC Context M 36.0000 328 2.00 20FUKAAXX100202.7 36 AG Context M 36.0000 72 0.00 20FUKAAXX100202.7 36 AT Context M 36.0000 43 0.00 @@ -21053,7 +21052,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.7 38 90 Cycle M 38.0000 19 0.00 20FUKAAXX100202.7 38 91 Cycle M 38.0000 15 0.00 20FUKAAXX100202.7 38 92 Cycle M 38.0000 21 0.00 -20FUKAAXX100202.7 38 93 Cycle M 38.0000 17 0.00 +20FUKAAXX100202.7 38 93 Cycle M 38.0000 16 0.00 20FUKAAXX100202.7 38 94 Cycle M 38.0000 13 0.00 20FUKAAXX100202.7 38 95 Cycle M 38.0000 17 0.00 20FUKAAXX100202.7 38 96 Cycle M 38.0000 14 1.00 @@ -21073,7 +21072,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.7 38 TA Context M 38.0000 162 0.00 20FUKAAXX100202.7 38 TC Context M 38.0000 131 0.00 20FUKAAXX100202.7 38 TG Context M 38.0000 456 1.33 -20FUKAAXX100202.7 38 TT Context M 38.0000 262 1.00 +20FUKAAXX100202.7 38 TT Context M 38.0000 261 1.00 20FUKAAXX100202.7 39 -100 Cycle M 39.0000 1 0.00 20FUKAAXX100202.7 39 -14 Cycle M 39.0000 3 0.00 20FUKAAXX100202.7 39 -15 Cycle M 39.0000 2 0.00 @@ -21403,8 +21402,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.7 45 -68 Cycle I 45.0000 46 0.00 20FUKAAXX100202.7 45 -69 Cycle D 45.0000 46 0.00 20FUKAAXX100202.7 45 -69 Cycle I 45.0000 46 0.00 -20FUKAAXX100202.7 45 -7 Cycle D 45.0000 51 0.25 -20FUKAAXX100202.7 45 -7 Cycle I 45.0000 51 0.00 +20FUKAAXX100202.7 45 -7 Cycle D 45.0000 50 0.13 +20FUKAAXX100202.7 45 -7 Cycle I 45.0000 50 0.00 20FUKAAXX100202.7 45 -70 Cycle D 45.0000 46 0.00 20FUKAAXX100202.7 45 -70 Cycle I 45.0000 46 0.00 20FUKAAXX100202.7 45 -71 Cycle D 45.0000 46 0.00 @@ -21641,8 +21640,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.7 45 91 Cycle I 45.0000 40 0.00 20FUKAAXX100202.7 45 92 Cycle D 45.0000 40 0.00 20FUKAAXX100202.7 45 92 Cycle I 45.0000 40 0.00 -20FUKAAXX100202.7 45 93 Cycle D 45.0000 41 0.09 -20FUKAAXX100202.7 45 93 Cycle I 45.0000 41 0.00 +20FUKAAXX100202.7 45 93 Cycle D 45.0000 40 0.00 +20FUKAAXX100202.7 45 93 Cycle I 45.0000 40 0.00 20FUKAAXX100202.7 45 94 Cycle D 45.0000 41 0.09 20FUKAAXX100202.7 45 94 Cycle I 45.0000 41 0.00 20FUKAAXX100202.7 45 95 Cycle D 45.0000 41 0.09 @@ -21713,10 +21712,10 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.7 45 CTC Context I 45.0000 184 0.00 20FUKAAXX100202.7 45 CTG Context D 45.0000 196 0.00 20FUKAAXX100202.7 45 CTG Context I 45.0000 196 0.00 -20FUKAAXX100202.7 45 CTT Context D 45.0000 166 0.09 -20FUKAAXX100202.7 45 CTT Context I 45.0000 166 0.00 -20FUKAAXX100202.7 45 GAA Context D 45.0000 230 0.25 -20FUKAAXX100202.7 45 GAA Context I 45.0000 230 0.00 +20FUKAAXX100202.7 45 CTT Context D 45.0000 165 0.00 +20FUKAAXX100202.7 45 CTT Context I 45.0000 165 0.00 +20FUKAAXX100202.7 45 GAA Context D 45.0000 229 0.13 +20FUKAAXX100202.7 45 GAA Context I 45.0000 229 0.00 20FUKAAXX100202.7 45 GAC Context D 45.0000 82 0.00 20FUKAAXX100202.7 45 GAC Context I 45.0000 82 0.00 20FUKAAXX100202.7 45 GAG Context D 45.0000 219 0.25 @@ -25367,7 +25366,6 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 24 TC Context M 24.0000 4 0.00 20GAVAAXX100126.1 24 TG Context M 24.0000 1 0.00 20GAVAAXX100126.1 24 TT Context M 24.0000 1 0.00 -20GAVAAXX100126.1 25 -10 Cycle M 25.0000 1 0.00 20GAVAAXX100126.1 25 -12 Cycle M 25.0000 1 0.00 20GAVAAXX100126.1 25 -15 Cycle M 25.0000 1 0.00 20GAVAAXX100126.1 25 -17 Cycle M 25.0000 1 0.00 @@ -25446,7 +25444,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 25 GT Context M 25.0000 7 0.00 20GAVAAXX100126.1 25 TA Context M 25.0000 5 0.00 20GAVAAXX100126.1 25 TC Context M 25.0000 10 0.00 -20GAVAAXX100126.1 25 TG Context M 25.0000 9 0.00 +20GAVAAXX100126.1 25 TG Context M 25.0000 8 0.00 20GAVAAXX100126.1 25 TT Context M 25.0000 5 0.00 20GAVAAXX100126.1 26 -101 Cycle M 26.0000 1 0.00 20GAVAAXX100126.1 26 -18 Cycle M 26.0000 1 0.00 @@ -25606,7 +25604,6 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 27 61 Cycle M 27.0000 1 0.00 20GAVAAXX100126.1 27 63 Cycle M 27.0000 1 0.00 20GAVAAXX100126.1 27 65 Cycle M 27.0000 1 0.00 -20GAVAAXX100126.1 27 66 Cycle M 27.0000 1 0.00 20GAVAAXX100126.1 27 68 Cycle M 27.0000 1 0.00 20GAVAAXX100126.1 27 70 Cycle M 27.0000 2 0.00 20GAVAAXX100126.1 27 71 Cycle M 27.0000 1 0.00 @@ -25626,7 +25623,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 27 91 Cycle M 27.0000 1 0.00 20GAVAAXX100126.1 27 93 Cycle M 27.0000 2 0.00 20GAVAAXX100126.1 27 99 Cycle M 27.0000 2 0.00 -20GAVAAXX100126.1 27 AA Context M 27.0000 8 0.00 +20GAVAAXX100126.1 27 AA Context M 27.0000 7 0.00 20GAVAAXX100126.1 27 AC Context M 27.0000 3 0.00 20GAVAAXX100126.1 27 AG Context M 27.0000 9 0.00 20GAVAAXX100126.1 27 AT Context M 27.0000 3 0.00 @@ -27534,7 +27531,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 39 39 Cycle M 39.0000 16 0.00 20GAVAAXX100126.1 39 40 Cycle M 39.0000 23 0.00 20GAVAAXX100126.1 39 41 Cycle M 39.0000 8 0.00 -20GAVAAXX100126.1 39 42 Cycle M 39.0000 20 0.00 +20GAVAAXX100126.1 39 42 Cycle M 39.0000 19 0.00 20GAVAAXX100126.1 39 43 Cycle M 39.0000 13 0.00 20GAVAAXX100126.1 39 44 Cycle M 39.0000 15 0.00 20GAVAAXX100126.1 39 45 Cycle M 39.0000 11 0.00 @@ -27595,7 +27592,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 39 97 Cycle M 39.0000 10 0.00 20GAVAAXX100126.1 39 98 Cycle M 39.0000 8 0.00 20GAVAAXX100126.1 39 99 Cycle M 39.0000 3 0.00 -20GAVAAXX100126.1 39 AA Context M 39.0000 211 0.00 +20GAVAAXX100126.1 39 AA Context M 39.0000 210 0.00 20GAVAAXX100126.1 39 AG Context M 39.0000 26 0.00 20GAVAAXX100126.1 39 AT Context M 39.0000 49 0.00 20GAVAAXX100126.1 39 CA Context M 39.0000 413 2.00 @@ -27717,8 +27714,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 41 -76 Cycle M 41.0000 1 0.00 20GAVAAXX100126.1 41 AA Context M 41.0000 6 0.00 20GAVAAXX100126.1 41 CT Context M 41.0000 17 0.00 -20GAVAAXX100126.1 45 -10 Cycle D 45.0000 47 0.41 -20GAVAAXX100126.1 45 -10 Cycle I 45.0000 47 0.00 +20GAVAAXX100126.1 45 -10 Cycle D 45.0000 46 0.13 +20GAVAAXX100126.1 45 -10 Cycle I 45.0000 46 0.00 20GAVAAXX100126.1 45 -11 Cycle D 45.0000 46 0.13 20GAVAAXX100126.1 45 -11 Cycle I 45.0000 46 0.00 20GAVAAXX100126.1 45 -12 Cycle D 45.0000 46 0.13 @@ -27967,8 +27964,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 45 40 Cycle I 45.0000 53 0.00 20GAVAAXX100126.1 45 41 Cycle D 45.0000 53 0.14 20GAVAAXX100126.1 45 41 Cycle I 45.0000 53 0.00 -20GAVAAXX100126.1 45 42 Cycle D 45.0000 53 0.14 -20GAVAAXX100126.1 45 42 Cycle I 45.0000 53 0.00 +20GAVAAXX100126.1 45 42 Cycle D 45.0000 52 0.00 +20GAVAAXX100126.1 45 42 Cycle I 45.0000 52 0.00 20GAVAAXX100126.1 45 43 Cycle D 45.0000 52 0.00 20GAVAAXX100126.1 45 43 Cycle I 45.0000 52 0.00 20GAVAAXX100126.1 45 44 Cycle D 45.0000 52 0.14 @@ -28019,8 +28016,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 45 64 Cycle I 45.0000 52 0.00 20GAVAAXX100126.1 45 65 Cycle D 45.0000 51 0.17 20GAVAAXX100126.1 45 65 Cycle I 45.0000 51 0.00 -20GAVAAXX100126.1 45 66 Cycle D 45.0000 52 0.17 -20GAVAAXX100126.1 45 66 Cycle I 45.0000 52 0.00 +20GAVAAXX100126.1 45 66 Cycle D 45.0000 51 0.00 +20GAVAAXX100126.1 45 66 Cycle I 45.0000 51 0.00 20GAVAAXX100126.1 45 67 Cycle D 45.0000 51 0.00 20GAVAAXX100126.1 45 67 Cycle I 45.0000 51 0.00 20GAVAAXX100126.1 45 68 Cycle D 45.0000 52 0.00 @@ -28153,8 +28150,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 45 CTG Context I 45.0000 214 0.00 20GAVAAXX100126.1 45 CTT Context D 45.0000 188 0.70 20GAVAAXX100126.1 45 CTT Context I 45.0000 188 0.00 -20GAVAAXX100126.1 45 GAA Context D 45.0000 155 0.31 -20GAVAAXX100126.1 45 GAA Context I 45.0000 155 0.00 +20GAVAAXX100126.1 45 GAA Context D 45.0000 153 0.00 +20GAVAAXX100126.1 45 GAA Context I 45.0000 153 0.00 20GAVAAXX100126.1 45 GAC Context D 45.0000 90 0.00 20GAVAAXX100126.1 45 GAC Context I 45.0000 90 0.00 20GAVAAXX100126.1 45 GAG Context D 45.0000 189 0.43 @@ -28181,8 +28178,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 45 GTA Context I 45.0000 95 0.00 20GAVAAXX100126.1 45 GTC Context D 45.0000 85 0.46 20GAVAAXX100126.1 45 GTC Context I 45.0000 85 0.00 -20GAVAAXX100126.1 45 GTG Context D 45.0000 190 0.72 -20GAVAAXX100126.1 45 GTG Context I 45.0000 190 0.00 +20GAVAAXX100126.1 45 GTG Context D 45.0000 189 0.43 +20GAVAAXX100126.1 45 GTG Context I 45.0000 189 0.00 20GAVAAXX100126.1 45 GTT Context D 45.0000 116 0.00 20GAVAAXX100126.1 45 GTT Context I 45.0000 116 0.00 20GAVAAXX100126.1 45 TAA Context D 45.0000 81 0.00 @@ -29720,7 +29717,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.2 33 -68 Cycle M 33.0000 4 0.00 20GAVAAXX100126.2 33 -69 Cycle M 33.0000 3 0.00 20GAVAAXX100126.2 33 -7 Cycle M 33.0000 4 0.00 -20GAVAAXX100126.2 33 -70 Cycle M 33.0000 2 0.00 +20GAVAAXX100126.2 33 -70 Cycle M 33.0000 1 0.00 20GAVAAXX100126.2 33 -71 Cycle M 33.0000 9 0.00 20GAVAAXX100126.2 33 -72 Cycle M 33.0000 8 0.00 20GAVAAXX100126.2 33 -73 Cycle M 33.0000 4 0.00 @@ -29810,7 +29807,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.2 33 97 Cycle M 33.0000 1 0.00 20GAVAAXX100126.2 33 98 Cycle M 33.0000 4 0.00 20GAVAAXX100126.2 33 99 Cycle M 33.0000 2 0.00 -20GAVAAXX100126.2 33 AA Context M 33.0000 19 0.00 +20GAVAAXX100126.2 33 AA Context M 33.0000 18 0.00 20GAVAAXX100126.2 33 AC Context M 33.0000 25 0.00 20GAVAAXX100126.2 33 AG Context M 33.0000 32 0.00 20GAVAAXX100126.2 33 AT Context M 33.0000 16 0.00 @@ -31022,8 +31019,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.2 45 -69 Cycle I 45.0000 36 0.00 20GAVAAXX100126.2 45 -7 Cycle D 45.0000 41 0.00 20GAVAAXX100126.2 45 -7 Cycle I 45.0000 41 0.00 -20GAVAAXX100126.2 45 -70 Cycle D 45.0000 37 0.14 -20GAVAAXX100126.2 45 -70 Cycle I 45.0000 37 0.00 +20GAVAAXX100126.2 45 -70 Cycle D 45.0000 36 0.00 +20GAVAAXX100126.2 45 -70 Cycle I 45.0000 36 0.00 20GAVAAXX100126.2 45 -71 Cycle D 45.0000 35 0.00 20GAVAAXX100126.2 45 -71 Cycle I 45.0000 35 0.00 20GAVAAXX100126.2 45 -72 Cycle D 45.0000 36 0.14 @@ -31332,8 +31329,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.2 45 CTG Context I 45.0000 154 0.00 20GAVAAXX100126.2 45 CTT Context D 45.0000 141 0.43 20GAVAAXX100126.2 45 CTT Context I 45.0000 141 0.00 -20GAVAAXX100126.2 45 GAA Context D 45.0000 130 0.43 -20GAVAAXX100126.2 45 GAA Context I 45.0000 130 0.00 +20GAVAAXX100126.2 45 GAA Context D 45.0000 129 0.29 +20GAVAAXX100126.2 45 GAA Context I 45.0000 129 0.00 20GAVAAXX100126.2 45 GAC Context D 45.0000 87 0.00 20GAVAAXX100126.2 45 GAC Context I 45.0000 87 0.00 20GAVAAXX100126.2 45 GAG Context D 45.0000 183 0.14 @@ -36512,7 +36509,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.4 38 10 Cycle M 38.0000 10 0.00 20GAVAAXX100126.4 38 100 Cycle M 38.0000 4 0.00 20GAVAAXX100126.4 38 101 Cycle M 38.0000 5 0.00 -20GAVAAXX100126.4 38 11 Cycle M 38.0000 9 0.00 +20GAVAAXX100126.4 38 11 Cycle M 38.0000 8 0.00 20GAVAAXX100126.4 38 12 Cycle M 38.0000 8 0.00 20GAVAAXX100126.4 38 13 Cycle M 38.0000 9 0.00 20GAVAAXX100126.4 38 14 Cycle M 38.0000 11 0.00 @@ -36619,7 +36616,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.4 38 TA Context M 38.0000 97 0.00 20GAVAAXX100126.4 38 TC Context M 38.0000 29 0.00 20GAVAAXX100126.4 38 TG Context M 38.0000 196 3.00 -20GAVAAXX100126.4 38 TT Context M 38.0000 99 0.00 +20GAVAAXX100126.4 38 TT Context M 38.0000 98 0.00 20GAVAAXX100126.4 39 -13 Cycle M 39.0000 4 0.00 20GAVAAXX100126.4 39 -14 Cycle M 39.0000 3 0.00 20GAVAAXX100126.4 39 -15 Cycle M 39.0000 2 0.00 @@ -36979,8 +36976,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.4 45 -97 Cycle I 45.0000 25 0.00 20GAVAAXX100126.4 45 10 Cycle D 45.0000 33 0.00 20GAVAAXX100126.4 45 10 Cycle I 45.0000 33 0.00 -20GAVAAXX100126.4 45 11 Cycle D 45.0000 34 0.14 -20GAVAAXX100126.4 45 11 Cycle I 45.0000 34 0.00 +20GAVAAXX100126.4 45 11 Cycle D 45.0000 33 0.00 +20GAVAAXX100126.4 45 11 Cycle I 45.0000 33 0.00 20GAVAAXX100126.4 45 12 Cycle D 45.0000 34 0.14 20GAVAAXX100126.4 45 12 Cycle I 45.0000 34 0.00 20GAVAAXX100126.4 45 13 Cycle D 45.0000 34 0.14 @@ -37225,8 +37222,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.4 45 CTC Context I 45.0000 139 0.00 20GAVAAXX100126.4 45 CTG Context D 45.0000 154 0.00 20GAVAAXX100126.4 45 CTG Context I 45.0000 154 0.00 -20GAVAAXX100126.4 45 CTT Context D 45.0000 139 0.45 -20GAVAAXX100126.4 45 CTT Context I 45.0000 139 0.00 +20GAVAAXX100126.4 45 CTT Context D 45.0000 138 0.31 +20GAVAAXX100126.4 45 CTT Context I 45.0000 138 0.00 20GAVAAXX100126.4 45 GAA Context D 45.0000 118 0.00 20GAVAAXX100126.4 45 GAA Context I 45.0000 118 0.00 20GAVAAXX100126.4 45 GAC Context D 45.0000 72 0.00 @@ -39237,7 +39234,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.5 38 20 Cycle M 38.0000 11 0.00 20GAVAAXX100126.5 38 21 Cycle M 38.0000 17 1.00 20GAVAAXX100126.5 38 22 Cycle M 38.0000 13 0.00 -20GAVAAXX100126.5 38 23 Cycle M 38.0000 11 0.00 +20GAVAAXX100126.5 38 23 Cycle M 38.0000 10 0.00 20GAVAAXX100126.5 38 24 Cycle M 38.0000 10 0.00 20GAVAAXX100126.5 38 25 Cycle M 38.0000 12 0.00 20GAVAAXX100126.5 38 26 Cycle M 38.0000 15 0.00 @@ -39333,7 +39330,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.5 38 TA Context M 38.0000 89 0.00 20GAVAAXX100126.5 38 TC Context M 38.0000 51 0.00 20GAVAAXX100126.5 38 TG Context M 38.0000 268 1.00 -20GAVAAXX100126.5 38 TT Context M 38.0000 169 0.00 +20GAVAAXX100126.5 38 TT Context M 38.0000 168 0.00 20GAVAAXX100126.5 39 -11 Cycle M 39.0000 1 0.00 20GAVAAXX100126.5 39 -12 Cycle M 39.0000 3 0.00 20GAVAAXX100126.5 39 -14 Cycle M 39.0000 1 0.00 @@ -39759,8 +39756,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.5 45 21 Cycle I 45.0000 33 0.00 20GAVAAXX100126.5 45 22 Cycle D 45.0000 32 0.00 20GAVAAXX100126.5 45 22 Cycle I 45.0000 32 0.00 -20GAVAAXX100126.5 45 23 Cycle D 45.0000 33 0.14 -20GAVAAXX100126.5 45 23 Cycle I 45.0000 33 0.00 +20GAVAAXX100126.5 45 23 Cycle D 45.0000 32 0.00 +20GAVAAXX100126.5 45 23 Cycle I 45.0000 32 0.00 20GAVAAXX100126.5 45 24 Cycle D 45.0000 33 0.14 20GAVAAXX100126.5 45 24 Cycle I 45.0000 33 0.00 20GAVAAXX100126.5 45 25 Cycle D 45.0000 32 0.14 @@ -39981,8 +39978,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.5 45 CTC Context I 45.0000 103 0.00 20GAVAAXX100126.5 45 CTG Context D 45.0000 132 0.00 20GAVAAXX100126.5 45 CTG Context I 45.0000 132 0.00 -20GAVAAXX100126.5 45 CTT Context D 45.0000 102 0.14 -20GAVAAXX100126.5 45 CTT Context I 45.0000 102 0.00 +20GAVAAXX100126.5 45 CTT Context D 45.0000 101 0.00 +20GAVAAXX100126.5 45 CTT Context I 45.0000 101 0.00 20GAVAAXX100126.5 45 GAA Context D 45.0000 148 0.00 20GAVAAXX100126.5 45 GAA Context I 45.0000 148 0.00 20GAVAAXX100126.5 45 GAC Context D 45.0000 56 0.00 @@ -41050,7 +41047,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.6 31 -46 Cycle M 31.0000 2 0.00 20GAVAAXX100126.6 31 -47 Cycle M 31.0000 2 0.00 20GAVAAXX100126.6 31 -48 Cycle M 31.0000 3 0.00 -20GAVAAXX100126.6 31 -5 Cycle M 31.0000 6 0.00 +20GAVAAXX100126.6 31 -5 Cycle M 31.0000 5 0.00 20GAVAAXX100126.6 31 -50 Cycle M 31.0000 4 0.00 20GAVAAXX100126.6 31 -51 Cycle M 31.0000 1 0.00 20GAVAAXX100126.6 31 -52 Cycle M 31.0000 1 0.00 @@ -41126,7 +41123,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.6 31 94 Cycle M 31.0000 1 0.00 20GAVAAXX100126.6 31 97 Cycle M 31.0000 2 0.00 20GAVAAXX100126.6 31 99 Cycle M 31.0000 1 0.00 -20GAVAAXX100126.6 31 AA Context M 31.0000 14 0.00 +20GAVAAXX100126.6 31 AA Context M 31.0000 13 0.00 20GAVAAXX100126.6 31 AC Context M 31.0000 17 0.00 20GAVAAXX100126.6 31 AG Context M 31.0000 16 0.00 20GAVAAXX100126.6 31 AT Context M 31.0000 6 0.00 @@ -42228,7 +42225,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.6 38 40 Cycle M 38.0000 13 0.00 20GAVAAXX100126.6 38 41 Cycle M 38.0000 9 0.00 20GAVAAXX100126.6 38 42 Cycle M 38.0000 13 0.00 -20GAVAAXX100126.6 38 43 Cycle M 38.0000 17 0.00 +20GAVAAXX100126.6 38 43 Cycle M 38.0000 16 0.00 20GAVAAXX100126.6 38 44 Cycle M 38.0000 14 0.00 20GAVAAXX100126.6 38 45 Cycle M 38.0000 14 0.00 20GAVAAXX100126.6 38 46 Cycle M 38.0000 10 0.00 @@ -42304,7 +42301,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.6 38 TA Context M 38.0000 105 0.00 20GAVAAXX100126.6 38 TC Context M 38.0000 12 0.00 20GAVAAXX100126.6 38 TG Context M 38.0000 263 2.00 -20GAVAAXX100126.6 38 TT Context M 38.0000 214 0.00 +20GAVAAXX100126.6 38 TT Context M 38.0000 213 0.00 20GAVAAXX100126.6 39 -12 Cycle M 39.0000 2 0.00 20GAVAAXX100126.6 39 -13 Cycle M 39.0000 1 0.00 20GAVAAXX100126.6 39 -14 Cycle M 39.0000 3 0.00 @@ -42552,8 +42549,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.6 45 -48 Cycle I 45.0000 39 0.00 20GAVAAXX100126.6 45 -49 Cycle D 45.0000 38 0.00 20GAVAAXX100126.6 45 -49 Cycle I 45.0000 38 0.00 -20GAVAAXX100126.6 45 -5 Cycle D 45.0000 40 0.17 -20GAVAAXX100126.6 45 -5 Cycle I 45.0000 40 0.00 +20GAVAAXX100126.6 45 -5 Cycle D 45.0000 39 0.00 +20GAVAAXX100126.6 45 -5 Cycle I 45.0000 39 0.00 20GAVAAXX100126.6 45 -50 Cycle D 45.0000 38 0.00 20GAVAAXX100126.6 45 -50 Cycle I 45.0000 38 0.00 20GAVAAXX100126.6 45 -51 Cycle D 45.0000 38 0.00 @@ -42724,8 +42721,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.6 45 41 Cycle I 45.0000 41 0.00 20GAVAAXX100126.6 45 42 Cycle D 45.0000 40 0.14 20GAVAAXX100126.6 45 42 Cycle I 45.0000 40 0.00 -20GAVAAXX100126.6 45 43 Cycle D 45.0000 41 0.29 -20GAVAAXX100126.6 45 43 Cycle I 45.0000 41 0.00 +20GAVAAXX100126.6 45 43 Cycle D 45.0000 40 0.14 +20GAVAAXX100126.6 45 43 Cycle I 45.0000 40 0.00 20GAVAAXX100126.6 45 44 Cycle D 45.0000 41 0.29 20GAVAAXX100126.6 45 44 Cycle I 45.0000 41 0.00 20GAVAAXX100126.6 45 45 Cycle D 45.0000 41 0.29 @@ -42906,10 +42903,10 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.6 45 CTC Context I 45.0000 187 0.00 20GAVAAXX100126.6 45 CTG Context D 45.0000 189 0.00 20GAVAAXX100126.6 45 CTG Context I 45.0000 189 0.00 -20GAVAAXX100126.6 45 CTT Context D 45.0000 153 0.43 -20GAVAAXX100126.6 45 CTT Context I 45.0000 153 0.00 -20GAVAAXX100126.6 45 GAA Context D 45.0000 149 0.17 -20GAVAAXX100126.6 45 GAA Context I 45.0000 149 0.00 +20GAVAAXX100126.6 45 CTT Context D 45.0000 152 0.29 +20GAVAAXX100126.6 45 CTT Context I 45.0000 152 0.00 +20GAVAAXX100126.6 45 GAA Context D 45.0000 148 0.00 +20GAVAAXX100126.6 45 GAA Context I 45.0000 148 0.00 20GAVAAXX100126.6 45 GAC Context D 45.0000 85 0.00 20GAVAAXX100126.6 45 GAC Context I 45.0000 85 0.00 20GAVAAXX100126.6 45 GAG Context D 45.0000 172 0.00 @@ -44596,7 +44593,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.7 33 -32 Cycle M 33.0000 1 0.00 20GAVAAXX100126.7 33 -33 Cycle M 33.0000 3 0.00 20GAVAAXX100126.7 33 -34 Cycle M 33.0000 3 0.00 -20GAVAAXX100126.7 33 -35 Cycle M 33.0000 3 0.00 +20GAVAAXX100126.7 33 -35 Cycle M 33.0000 2 0.00 20GAVAAXX100126.7 33 -37 Cycle M 33.0000 4 0.00 20GAVAAXX100126.7 33 -38 Cycle M 33.0000 1 0.00 20GAVAAXX100126.7 33 -39 Cycle M 33.0000 5 0.00 @@ -44709,7 +44706,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.7 33 96 Cycle M 33.0000 1 0.00 20GAVAAXX100126.7 33 98 Cycle M 33.0000 3 0.00 20GAVAAXX100126.7 33 99 Cycle M 33.0000 2 0.00 -20GAVAAXX100126.7 33 AA Context M 33.0000 15 0.00 +20GAVAAXX100126.7 33 AA Context M 33.0000 14 0.00 20GAVAAXX100126.7 33 AC Context M 33.0000 16 0.00 20GAVAAXX100126.7 33 AG Context M 33.0000 31 0.25 20GAVAAXX100126.7 33 AT Context M 33.0000 18 0.00 @@ -45829,8 +45826,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.7 45 -33 Cycle I 45.0000 39 0.00 20GAVAAXX100126.7 45 -34 Cycle D 45.0000 39 0.13 20GAVAAXX100126.7 45 -34 Cycle I 45.0000 39 0.00 -20GAVAAXX100126.7 45 -35 Cycle D 45.0000 39 0.13 -20GAVAAXX100126.7 45 -35 Cycle I 45.0000 39 0.00 +20GAVAAXX100126.7 45 -35 Cycle D 45.0000 38 0.00 +20GAVAAXX100126.7 45 -35 Cycle I 45.0000 38 0.00 20GAVAAXX100126.7 45 -36 Cycle D 45.0000 38 0.00 20GAVAAXX100126.7 45 -36 Cycle I 45.0000 38 0.00 20GAVAAXX100126.7 45 -37 Cycle D 45.0000 39 0.13 @@ -46215,8 +46212,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.7 45 CTG Context I 45.0000 180 0.00 20GAVAAXX100126.7 45 CTT Context D 45.0000 128 0.14 20GAVAAXX100126.7 45 CTT Context I 45.0000 128 0.00 -20GAVAAXX100126.7 45 GAA Context D 45.0000 148 0.25 -20GAVAAXX100126.7 45 GAA Context I 45.0000 148 0.00 +20GAVAAXX100126.7 45 GAA Context D 45.0000 147 0.13 +20GAVAAXX100126.7 45 GAA Context I 45.0000 147 0.00 20GAVAAXX100126.7 45 GAC Context D 45.0000 96 0.00 20GAVAAXX100126.7 45 GAC Context I 45.0000 96 0.00 20GAVAAXX100126.7 45 GAG Context D 45.0000 172 0.25 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.recal.txt b/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.recal.txt index f02981072df..b929587973c 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.recal.txt +++ b/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.recal.txt @@ -48,27 +48,27 @@ QualityScore Count QuantizedScore 22 750 24 23 853 24 24 997 24 - 25 1228 24 + 25 1227 24 26 1491 27 - 27 1728 27 + 27 1727 27 28 1781 29 29 2284 29 30 2439 30 - 31 2537 30 + 31 2536 30 32 3565 32 - 33 4141 32 + 33 4139 32 34 5194 34 - 35 7518 35 - 36 11939 36 - 37 28884 37 - 38 27993 38 - 39 15115 39 + 35 7517 35 + 36 11937 36 + 37 28883 37 + 38 27987 38 + 39 15108 39 40 778 39 41 53 39 42 0 39 43 0 39 - 44 15761 44 - 45 234039 45 + 44 9294 44 + 45 240462 45 46 0 93 47 0 93 48 0 93 @@ -121,51 +121,51 @@ QualityScore Count QuantizedScore #:GATKTable:6:48:%s:%s:%.4f:%.4f:%d:%.2f:; #:GATKTable:RecalTable0: ReadGroup EventType EmpiricalQuality EstimatedQReported Observations Errors -20FUKAAXX100202.1 D 45.0000 45.0000 7293 3.86 -20FUKAAXX100202.1 I 45.0000 45.0000 7293 0.00 -20FUKAAXX100202.1 M 27.0000 27.0392 7293 15.67 -20FUKAAXX100202.2 D 44.0000 45.0000 6464 7.56 -20FUKAAXX100202.2 I 45.0000 45.0000 6464 0.00 -20FUKAAXX100202.2 M 29.0000 30.1871 6464 20.60 -20FUKAAXX100202.3 D 45.0000 45.0000 8976 5.73 -20FUKAAXX100202.3 I 45.0000 45.0000 8976 0.00 -20FUKAAXX100202.3 M 27.0000 28.2043 8976 29.75 -20FUKAAXX100202.4 D 45.0000 45.0000 6830 3.75 -20FUKAAXX100202.4 I 45.0000 45.0000 6830 0.00 -20FUKAAXX100202.4 M 29.0000 29.0885 6830 13.00 -20FUKAAXX100202.5 D 45.0000 45.0000 7471 2.86 -20FUKAAXX100202.5 I 45.0000 45.0000 7471 0.00 -20FUKAAXX100202.5 M 28.0000 29.7339 7471 26.67 -20FUKAAXX100202.6 D 45.0000 45.0000 10026 8.40 -20FUKAAXX100202.6 I 45.0000 45.0000 10026 0.00 -20FUKAAXX100202.6 M 27.0000 28.7545 10026 27.25 -20FUKAAXX100202.7 D 45.0000 45.0000 9347 2.78 -20FUKAAXX100202.7 I 45.0000 45.0000 9347 0.00 -20FUKAAXX100202.7 M 26.0000 27.7419 9347 30.67 +20FUKAAXX100202.1 D 45.0000 45.0000 7292 3.71 +20FUKAAXX100202.1 I 45.0000 45.0000 7292 0.00 +20FUKAAXX100202.1 M 27.0000 27.0386 7292 15.67 +20FUKAAXX100202.2 D 45.0000 45.0000 6462 7.33 +20FUKAAXX100202.2 I 45.0000 45.0000 6462 0.00 +20FUKAAXX100202.2 M 29.0000 30.1859 6462 20.60 +20FUKAAXX100202.3 D 45.0000 45.0000 8974 5.46 +20FUKAAXX100202.3 I 45.0000 45.0000 8974 0.00 +20FUKAAXX100202.3 M 27.0000 28.2034 8974 29.75 +20FUKAAXX100202.4 D 45.0000 45.0000 6828 3.50 +20FUKAAXX100202.4 I 45.0000 45.0000 6828 0.00 +20FUKAAXX100202.4 M 29.0000 29.0874 6828 13.00 +20FUKAAXX100202.5 D 45.0000 45.0000 7470 2.71 +20FUKAAXX100202.5 I 45.0000 45.0000 7470 0.00 +20FUKAAXX100202.5 M 28.0000 29.7334 7470 26.67 +20FUKAAXX100202.6 D 45.0000 45.0000 10023 7.95 +20FUKAAXX100202.6 I 45.0000 45.0000 10023 0.00 +20FUKAAXX100202.6 M 27.0000 28.7535 10023 27.25 +20FUKAAXX100202.7 D 45.0000 45.0000 9345 2.57 +20FUKAAXX100202.7 I 45.0000 45.0000 9345 0.00 +20FUKAAXX100202.7 M 26.0000 27.7411 9345 30.67 20FUKAAXX100202.8 D 45.0000 45.0000 8152 3.75 20FUKAAXX100202.8 I 45.0000 45.0000 8152 0.00 20FUKAAXX100202.8 M 28.0000 29.0288 8152 24.00 -20GAVAAXX100126.1 D 44.0000 45.0000 9297 9.12 -20GAVAAXX100126.1 I 45.0000 45.0000 9297 1.00 -20GAVAAXX100126.1 M 26.0000 27.6243 9297 29.75 -20GAVAAXX100126.2 D 45.0000 45.0000 8155 4.86 -20GAVAAXX100126.2 I 45.0000 45.0000 8155 0.00 -20GAVAAXX100126.2 M 26.0000 27.3758 8155 34.42 +20GAVAAXX100126.1 D 44.0000 45.0000 9294 8.52 +20GAVAAXX100126.1 I 45.0000 45.0000 9294 1.00 +20GAVAAXX100126.1 M 26.0000 27.6244 9294 29.75 +20GAVAAXX100126.2 D 45.0000 45.0000 8154 4.71 +20GAVAAXX100126.2 I 45.0000 45.0000 8154 0.00 +20GAVAAXX100126.2 M 26.0000 27.3754 8154 34.42 20GAVAAXX100126.3 D 45.0000 45.0000 6239 3.00 20GAVAAXX100126.3 I 45.0000 45.0000 6239 0.00 20GAVAAXX100126.3 M 26.0000 26.8893 6239 20.57 -20GAVAAXX100126.4 D 45.0000 45.0000 6633 2.86 -20GAVAAXX100126.4 I 45.0000 45.0000 6633 0.00 -20GAVAAXX100126.4 M 26.0000 27.0432 6633 29.33 -20GAVAAXX100126.5 D 45.0000 45.0000 5884 0.86 -20GAVAAXX100126.5 I 45.0000 45.0000 5884 0.00 -20GAVAAXX100126.5 M 27.0000 28.0717 5884 21.33 -20GAVAAXX100126.6 D 45.0000 45.0000 8002 3.69 -20GAVAAXX100126.6 I 45.0000 45.0000 8002 0.00 -20GAVAAXX100126.6 M 27.0000 28.4682 8002 27.00 -20GAVAAXX100126.7 D 45.0000 45.0000 7598 2.88 -20GAVAAXX100126.7 I 45.0000 45.0000 7598 0.00 -20GAVAAXX100126.7 M 25.0000 25.6878 7598 27.75 +20GAVAAXX100126.4 D 45.0000 45.0000 6632 2.71 +20GAVAAXX100126.4 I 45.0000 45.0000 6632 0.00 +20GAVAAXX100126.4 M 26.0000 27.0426 6632 29.33 +20GAVAAXX100126.5 D 45.0000 45.0000 5883 0.71 +20GAVAAXX100126.5 I 45.0000 45.0000 5883 0.00 +20GAVAAXX100126.5 M 27.0000 28.0710 5883 21.33 +20GAVAAXX100126.6 D 45.0000 45.0000 8000 3.38 +20GAVAAXX100126.6 I 45.0000 45.0000 8000 0.00 +20GAVAAXX100126.6 M 27.0000 28.4675 8000 27.00 +20GAVAAXX100126.7 D 45.0000 45.0000 7597 2.75 +20GAVAAXX100126.7 I 45.0000 45.0000 7597 0.00 +20GAVAAXX100126.7 M 25.0000 25.6874 7597 27.75 20GAVAAXX100126.8 D 45.0000 45.0000 8533 5.69 20GAVAAXX100126.8 I 45.0000 45.0000 8533 1.00 20GAVAAXX100126.8 M 26.0000 27.3594 8533 29.25 @@ -204,12 +204,12 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20FUKAAXX100202.1 34 M 34.0000 217 0.20 20FUKAAXX100202.1 35 M 35.0000 347 1.07 20FUKAAXX100202.1 36 M 36.0000 599 1.00 -20FUKAAXX100202.1 37 M 37.0000 1407 1.33 +20FUKAAXX100202.1 37 M 37.0000 1406 1.33 20FUKAAXX100202.1 38 M 38.0000 2058 0.33 20FUKAAXX100202.1 39 M 39.0000 741 0.00 20FUKAAXX100202.1 40 M 40.0000 16 0.00 -20FUKAAXX100202.1 45 D 45.0000 7293 3.86 -20FUKAAXX100202.1 45 I 45.0000 7293 0.00 +20FUKAAXX100202.1 45 D 45.0000 7292 3.71 +20FUKAAXX100202.1 45 I 45.0000 7292 0.00 20FUKAAXX100202.2 6 M 6.0000 1 0.00 20FUKAAXX100202.2 7 M 7.0000 1 0.00 20FUKAAXX100202.2 8 M 8.0000 3 0.00 @@ -243,10 +243,10 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20FUKAAXX100202.2 36 M 36.0000 580 4.00 20FUKAAXX100202.2 37 M 37.0000 1371 2.00 20FUKAAXX100202.2 38 M 38.0000 2181 6.00 -20FUKAAXX100202.2 39 M 39.0000 667 1.00 +20FUKAAXX100202.2 39 M 39.0000 665 1.00 20FUKAAXX100202.2 40 M 40.0000 27 0.00 -20FUKAAXX100202.2 45 D 44.0000 6464 7.56 -20FUKAAXX100202.2 45 I 45.0000 6464 0.00 +20FUKAAXX100202.2 45 D 45.0000 6462 7.33 +20FUKAAXX100202.2 45 I 45.0000 6462 0.00 20FUKAAXX100202.3 6 M 6.0000 1 1.00 20FUKAAXX100202.3 7 M 7.0000 4 0.00 20FUKAAXX100202.3 8 M 8.0000 8 0.00 @@ -277,13 +277,13 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20FUKAAXX100202.3 33 M 33.0000 245 0.00 20FUKAAXX100202.3 34 M 34.0000 262 0.00 20FUKAAXX100202.3 35 M 35.0000 463 1.00 -20FUKAAXX100202.3 36 M 36.0000 944 6.25 +20FUKAAXX100202.3 36 M 36.0000 943 6.25 20FUKAAXX100202.3 37 M 37.0000 1649 4.25 20FUKAAXX100202.3 38 M 37.0000 2837 11.25 -20FUKAAXX100202.3 39 M 39.0000 976 0.00 +20FUKAAXX100202.3 39 M 39.0000 975 0.00 20FUKAAXX100202.3 40 M 40.0000 28 0.00 -20FUKAAXX100202.3 45 D 45.0000 8976 5.73 -20FUKAAXX100202.3 45 I 45.0000 8976 0.00 +20FUKAAXX100202.3 45 D 45.0000 8974 5.46 +20FUKAAXX100202.3 45 I 45.0000 8974 0.00 20FUKAAXX100202.4 6 M 6.0000 1 0.00 20FUKAAXX100202.4 7 M 7.0000 2 1.00 20FUKAAXX100202.4 8 M 8.0000 3 1.00 @@ -317,10 +317,10 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20FUKAAXX100202.4 36 M 36.0000 633 0.00 20FUKAAXX100202.4 37 M 37.0000 1408 3.25 20FUKAAXX100202.4 38 M 38.0000 2074 3.50 -20FUKAAXX100202.4 39 M 39.0000 662 1.00 +20FUKAAXX100202.4 39 M 39.0000 660 1.00 20FUKAAXX100202.4 40 M 40.0000 20 0.00 -20FUKAAXX100202.4 45 D 45.0000 6830 3.75 -20FUKAAXX100202.4 45 I 45.0000 6830 0.00 +20FUKAAXX100202.4 45 D 45.0000 6828 3.50 +20FUKAAXX100202.4 45 I 45.0000 6828 0.00 20FUKAAXX100202.5 6 M 6.0000 1 0.00 20FUKAAXX100202.5 7 M 7.0000 3 0.00 20FUKAAXX100202.5 8 M 8.0000 2 1.00 @@ -354,10 +354,10 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20FUKAAXX100202.5 36 M 36.0000 695 2.33 20FUKAAXX100202.5 37 M 37.0000 1329 2.00 20FUKAAXX100202.5 38 M 37.0000 2579 9.80 -20FUKAAXX100202.5 39 M 39.0000 907 1.00 +20FUKAAXX100202.5 39 M 39.0000 906 1.00 20FUKAAXX100202.5 40 M 40.0000 67 0.20 -20FUKAAXX100202.5 45 D 45.0000 7471 2.86 -20FUKAAXX100202.5 45 I 45.0000 7471 0.00 +20FUKAAXX100202.5 45 D 45.0000 7470 2.71 +20FUKAAXX100202.5 45 I 45.0000 7470 0.00 20FUKAAXX100202.6 6 M 6.0000 7 4.00 20FUKAAXX100202.6 7 M 7.0000 4 2.00 20FUKAAXX100202.6 8 M 8.0000 5 0.00 @@ -387,14 +387,14 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20FUKAAXX100202.6 32 M 32.0000 226 1.00 20FUKAAXX100202.6 33 M 33.0000 231 2.00 20FUKAAXX100202.6 34 M 34.0000 302 0.00 -20FUKAAXX100202.6 35 M 35.0000 579 2.17 +20FUKAAXX100202.6 35 M 35.0000 578 2.17 20FUKAAXX100202.6 36 M 36.0000 975 2.33 20FUKAAXX100202.6 37 M 37.0000 1959 1.17 -20FUKAAXX100202.6 38 M 38.0000 3301 6.00 +20FUKAAXX100202.6 38 M 38.0000 3299 6.00 20FUKAAXX100202.6 39 M 39.0000 1111 1.00 20FUKAAXX100202.6 40 M 40.0000 43 0.00 -20FUKAAXX100202.6 45 D 45.0000 10026 8.40 -20FUKAAXX100202.6 45 I 45.0000 10026 0.00 +20FUKAAXX100202.6 45 D 45.0000 10023 7.95 +20FUKAAXX100202.6 45 I 45.0000 10023 0.00 20FUKAAXX100202.7 6 M 6.0000 5 2.00 20FUKAAXX100202.7 7 M 7.0000 5 1.00 20FUKAAXX100202.7 8 M 8.0000 9 3.33 @@ -425,13 +425,13 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20FUKAAXX100202.7 33 M 33.0000 197 0.00 20FUKAAXX100202.7 34 M 34.0000 251 0.00 20FUKAAXX100202.7 35 M 35.0000 441 1.92 -20FUKAAXX100202.7 36 M 36.0000 955 3.33 +20FUKAAXX100202.7 36 M 36.0000 954 3.33 20FUKAAXX100202.7 37 M 37.0000 1600 2.67 -20FUKAAXX100202.7 38 M 38.0000 3286 3.92 +20FUKAAXX100202.7 38 M 38.0000 3285 3.92 20FUKAAXX100202.7 39 M 39.0000 1063 1.25 20FUKAAXX100202.7 40 M 40.0000 43 0.00 -20FUKAAXX100202.7 45 D 45.0000 9347 2.78 -20FUKAAXX100202.7 45 I 45.0000 9347 0.00 +20FUKAAXX100202.7 45 D 45.0000 9345 2.57 +20FUKAAXX100202.7 45 I 45.0000 9345 0.00 20FUKAAXX100202.8 6 M 6.0000 4 2.00 20FUKAAXX100202.8 7 M 7.0000 5 0.00 20FUKAAXX100202.8 8 M 8.0000 1 0.00 @@ -488,9 +488,9 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.1 22 M 22.0000 43 1.00 20GAVAAXX100126.1 23 M 23.0000 65 0.13 20GAVAAXX100126.1 24 M 24.0000 56 0.00 -20GAVAAXX100126.1 25 M 25.0000 85 0.00 +20GAVAAXX100126.1 25 M 25.0000 84 0.00 20GAVAAXX100126.1 26 M 26.0000 104 0.00 -20GAVAAXX100126.1 27 M 27.0000 114 0.00 +20GAVAAXX100126.1 27 M 27.0000 113 0.00 20GAVAAXX100126.1 28 M 28.0000 149 0.00 20GAVAAXX100126.1 29 M 29.0000 185 1.33 20GAVAAXX100126.1 30 M 30.0000 179 0.00 @@ -502,11 +502,11 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.1 36 M 36.0000 822 2.25 20GAVAAXX100126.1 37 M 37.0000 1759 7.00 20GAVAAXX100126.1 38 M 38.0000 1880 3.25 -20GAVAAXX100126.1 39 M 39.0000 1546 2.00 +20GAVAAXX100126.1 39 M 39.0000 1545 2.00 20GAVAAXX100126.1 40 M 40.0000 243 0.00 20GAVAAXX100126.1 41 M 41.0000 23 0.00 -20GAVAAXX100126.1 45 D 44.0000 9297 9.12 -20GAVAAXX100126.1 45 I 45.0000 9297 1.00 +20GAVAAXX100126.1 45 D 44.0000 9294 8.52 +20GAVAAXX100126.1 45 I 45.0000 9294 1.00 20GAVAAXX100126.2 6 M 6.0000 10 4.00 20GAVAAXX100126.2 7 M 7.0000 8 1.00 20GAVAAXX100126.2 8 M 8.0000 6 0.00 @@ -534,7 +534,7 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.2 30 M 30.0000 169 0.00 20GAVAAXX100126.2 31 M 31.0000 222 1.25 20GAVAAXX100126.2 32 M 32.0000 336 0.00 -20GAVAAXX100126.2 33 M 33.0000 392 6.00 +20GAVAAXX100126.2 33 M 33.0000 391 6.00 20GAVAAXX100126.2 34 M 34.0000 471 0.00 20GAVAAXX100126.2 35 M 35.0000 540 2.00 20GAVAAXX100126.2 36 M 36.0000 685 1.67 @@ -543,8 +543,8 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.2 39 M 39.0000 1127 2.00 20GAVAAXX100126.2 40 M 40.0000 49 0.00 20GAVAAXX100126.2 41 M 41.0000 9 0.00 -20GAVAAXX100126.2 45 D 45.0000 8155 4.86 -20GAVAAXX100126.2 45 I 45.0000 8155 0.00 +20GAVAAXX100126.2 45 D 45.0000 8154 4.71 +20GAVAAXX100126.2 45 I 45.0000 8154 0.00 20GAVAAXX100126.3 6 M 6.0000 2 0.00 20GAVAAXX100126.3 7 M 7.0000 8 2.00 20GAVAAXX100126.3 8 M 8.0000 8 2.00 @@ -615,12 +615,12 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.4 35 M 35.0000 487 2.00 20GAVAAXX100126.4 36 M 36.0000 639 1.25 20GAVAAXX100126.4 37 M 37.0000 1224 5.50 -20GAVAAXX100126.4 38 M 38.0000 1250 4.67 +20GAVAAXX100126.4 38 M 38.0000 1249 4.67 20GAVAAXX100126.4 39 M 39.0000 857 2.00 20GAVAAXX100126.4 40 M 40.0000 33 0.00 20GAVAAXX100126.4 41 M 41.0000 1 0.00 -20GAVAAXX100126.4 45 D 45.0000 6633 2.86 -20GAVAAXX100126.4 45 I 45.0000 6633 0.00 +20GAVAAXX100126.4 45 D 45.0000 6632 2.71 +20GAVAAXX100126.4 45 I 45.0000 6632 0.00 20GAVAAXX100126.5 6 M 6.0000 4 0.00 20GAVAAXX100126.5 7 M 7.0000 8 3.00 20GAVAAXX100126.5 8 M 8.0000 4 1.00 @@ -653,12 +653,12 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.5 35 M 35.0000 328 1.00 20GAVAAXX100126.5 36 M 36.0000 583 0.33 20GAVAAXX100126.5 37 M 37.0000 1187 2.00 -20GAVAAXX100126.5 38 M 38.0000 1446 2.00 +20GAVAAXX100126.5 38 M 38.0000 1445 2.00 20GAVAAXX100126.5 39 M 39.0000 909 2.00 20GAVAAXX100126.5 40 M 40.0000 43 0.00 20GAVAAXX100126.5 41 M 41.0000 5 0.00 -20GAVAAXX100126.5 45 D 45.0000 5884 0.86 -20GAVAAXX100126.5 45 I 45.0000 5884 0.00 +20GAVAAXX100126.5 45 D 45.0000 5883 0.71 +20GAVAAXX100126.5 45 I 45.0000 5883 0.00 20GAVAAXX100126.6 6 M 6.0000 4 2.00 20GAVAAXX100126.6 7 M 7.0000 6 0.00 20GAVAAXX100126.6 8 M 8.0000 9 3.00 @@ -684,18 +684,18 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.6 28 M 28.0000 105 0.00 20GAVAAXX100126.6 29 M 29.0000 158 1.00 20GAVAAXX100126.6 30 M 30.0000 144 0.00 -20GAVAAXX100126.6 31 M 31.0000 194 1.00 +20GAVAAXX100126.6 31 M 31.0000 193 1.00 20GAVAAXX100126.6 32 M 32.0000 239 0.00 20GAVAAXX100126.6 33 M 33.0000 358 0.00 20GAVAAXX100126.6 34 M 34.0000 481 1.00 20GAVAAXX100126.6 35 M 35.0000 578 2.00 20GAVAAXX100126.6 36 M 36.0000 845 2.00 20GAVAAXX100126.6 37 M 37.0000 1617 4.00 -20GAVAAXX100126.6 38 M 38.0000 1661 3.00 +20GAVAAXX100126.6 38 M 38.0000 1660 3.00 20GAVAAXX100126.6 39 M 39.0000 1030 2.00 20GAVAAXX100126.6 40 M 40.0000 35 0.00 -20GAVAAXX100126.6 45 D 45.0000 8002 3.69 -20GAVAAXX100126.6 45 I 45.0000 8002 0.00 +20GAVAAXX100126.6 45 D 45.0000 8000 3.38 +20GAVAAXX100126.6 45 I 45.0000 8000 0.00 20GAVAAXX100126.7 6 M 6.0000 7 1.00 20GAVAAXX100126.7 7 M 7.0000 16 6.00 20GAVAAXX100126.7 8 M 8.0000 16 2.00 @@ -723,7 +723,7 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.7 30 M 30.0000 192 0.00 20GAVAAXX100126.7 31 M 31.0000 200 0.00 20GAVAAXX100126.7 32 M 32.0000 228 1.00 -20GAVAAXX100126.7 33 M 33.0000 382 1.25 +20GAVAAXX100126.7 33 M 33.0000 381 1.25 20GAVAAXX100126.7 34 M 34.0000 412 2.00 20GAVAAXX100126.7 35 M 35.0000 554 0.00 20GAVAAXX100126.7 36 M 36.0000 700 1.50 @@ -732,8 +732,8 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.7 39 M 39.0000 881 1.00 20GAVAAXX100126.7 40 M 40.0000 49 0.00 20GAVAAXX100126.7 41 M 41.0000 6 0.00 -20GAVAAXX100126.7 45 D 45.0000 7598 2.88 -20GAVAAXX100126.7 45 I 45.0000 7598 0.00 +20GAVAAXX100126.7 45 D 45.0000 7597 2.75 +20GAVAAXX100126.7 45 I 45.0000 7597 0.00 20GAVAAXX100126.8 6 M 6.0000 9 1.00 20GAVAAXX100126.8 7 M 7.0000 4 0.00 20GAVAAXX100126.8 8 M 8.0000 7 1.00 @@ -773,7 +773,7 @@ ReadGroup QualityScore EventType EmpiricalQuality Observations Erro 20GAVAAXX100126.8 45 D 45.0000 8533 5.69 20GAVAAXX100126.8 45 I 45.0000 8533 1.00 -#:GATKTable:8:48659:%s:%d:%s:%s:%s:%.4f:%d:%.2f:; +#:GATKTable:8:48656:%s:%d:%s:%s:%s:%.4f:%d:%.2f:; #:GATKTable:RecalTable2: ReadGroup QualityScore CovariateValue CovariateName EventType EmpiricalQuality Observations Errors 20FUKAAXX100202.1 6 -31 Cycle M 6.0000 1 0.00 @@ -2925,7 +2925,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.1 37 -33 Cycle M 37.0000 5 0.00 20FUKAAXX100202.1 37 -34 Cycle M 37.0000 13 0.00 20FUKAAXX100202.1 37 -35 Cycle M 37.0000 12 0.00 -20FUKAAXX100202.1 37 -36 Cycle M 37.0000 14 0.00 +20FUKAAXX100202.1 37 -36 Cycle M 37.0000 13 0.00 20FUKAAXX100202.1 37 -37 Cycle M 37.0000 10 0.00 20FUKAAXX100202.1 37 -38 Cycle M 37.0000 9 0.00 20FUKAAXX100202.1 37 -39 Cycle M 37.0000 9 0.00 @@ -3100,7 +3100,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.1 37 TA Context M 37.0000 42 0.00 20FUKAAXX100202.1 37 TC Context M 37.0000 280 0.00 20FUKAAXX100202.1 37 TG Context M 37.0000 83 1.00 -20FUKAAXX100202.1 37 TT Context M 37.0000 116 0.00 +20FUKAAXX100202.1 37 TT Context M 37.0000 115 0.00 20FUKAAXX100202.1 38 -10 Cycle M 38.0000 2 0.00 20FUKAAXX100202.1 38 -100 Cycle M 38.0000 3 0.00 20FUKAAXX100202.1 38 -101 Cycle M 38.0000 4 0.00 @@ -3545,8 +3545,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.1 45 -34 Cycle I 45.0000 37 0.00 20FUKAAXX100202.1 45 -35 Cycle D 45.0000 37 0.00 20FUKAAXX100202.1 45 -35 Cycle I 45.0000 37 0.00 -20FUKAAXX100202.1 45 -36 Cycle D 45.0000 37 0.14 -20FUKAAXX100202.1 45 -36 Cycle I 45.0000 37 0.00 +20FUKAAXX100202.1 45 -36 Cycle D 45.0000 36 0.00 +20FUKAAXX100202.1 45 -36 Cycle I 45.0000 36 0.00 20FUKAAXX100202.1 45 -37 Cycle D 45.0000 37 0.14 20FUKAAXX100202.1 45 -37 Cycle I 45.0000 37 0.00 20FUKAAXX100202.1 45 -38 Cycle D 45.0000 38 0.14 @@ -3927,8 +3927,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.1 45 CTC Context I 45.0000 165 0.00 20FUKAAXX100202.1 45 CTG Context D 45.0000 167 0.00 20FUKAAXX100202.1 45 CTG Context I 45.0000 167 0.00 -20FUKAAXX100202.1 45 CTT Context D 45.0000 148 0.29 -20FUKAAXX100202.1 45 CTT Context I 45.0000 148 0.00 +20FUKAAXX100202.1 45 CTT Context D 45.0000 147 0.14 +20FUKAAXX100202.1 45 CTT Context I 45.0000 147 0.00 20FUKAAXX100202.1 45 GAA Context D 45.0000 142 0.29 20FUKAAXX100202.1 45 GAA Context I 45.0000 142 0.00 20FUKAAXX100202.1 45 GAC Context D 45.0000 81 0.00 @@ -5947,7 +5947,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.2 39 14 Cycle M 39.0000 3 0.00 20FUKAAXX100202.2 39 15 Cycle M 39.0000 3 0.00 20FUKAAXX100202.2 39 16 Cycle M 39.0000 2 0.00 -20FUKAAXX100202.2 39 17 Cycle M 39.0000 3 0.00 +20FUKAAXX100202.2 39 17 Cycle M 39.0000 2 0.00 20FUKAAXX100202.2 39 18 Cycle M 39.0000 7 0.00 20FUKAAXX100202.2 39 19 Cycle M 39.0000 4 0.00 20FUKAAXX100202.2 39 20 Cycle M 39.0000 3 0.00 @@ -6007,7 +6007,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.2 39 77 Cycle M 39.0000 5 0.00 20FUKAAXX100202.2 39 78 Cycle M 39.0000 2 0.00 20FUKAAXX100202.2 39 79 Cycle M 39.0000 6 0.00 -20FUKAAXX100202.2 39 8 Cycle M 39.0000 4 0.00 +20FUKAAXX100202.2 39 8 Cycle M 39.0000 3 0.00 20FUKAAXX100202.2 39 80 Cycle M 39.0000 2 0.00 20FUKAAXX100202.2 39 81 Cycle M 39.0000 2 0.00 20FUKAAXX100202.2 39 82 Cycle M 39.0000 2 0.00 @@ -6026,7 +6026,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.2 39 95 Cycle M 39.0000 3 0.00 20FUKAAXX100202.2 39 96 Cycle M 39.0000 3 0.00 20FUKAAXX100202.2 39 97 Cycle M 39.0000 1 0.00 -20FUKAAXX100202.2 39 AA Context M 39.0000 241 0.00 +20FUKAAXX100202.2 39 AA Context M 39.0000 239 0.00 20FUKAAXX100202.2 39 AG Context M 39.0000 2 0.00 20FUKAAXX100202.2 39 AT Context M 39.0000 1 0.00 20FUKAAXX100202.2 39 CA Context M 39.0000 81 0.00 @@ -6249,8 +6249,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.2 45 15 Cycle I 45.0000 32 0.00 20FUKAAXX100202.2 45 16 Cycle D 45.0000 32 0.13 20FUKAAXX100202.2 45 16 Cycle I 45.0000 32 0.00 -20FUKAAXX100202.2 45 17 Cycle D 45.0000 32 0.13 -20FUKAAXX100202.2 45 17 Cycle I 45.0000 32 0.00 +20FUKAAXX100202.2 45 17 Cycle D 45.0000 31 0.00 +20FUKAAXX100202.2 45 17 Cycle I 45.0000 31 0.00 20FUKAAXX100202.2 45 18 Cycle D 45.0000 31 0.00 20FUKAAXX100202.2 45 18 Cycle I 45.0000 31 0.00 20FUKAAXX100202.2 45 19 Cycle D 45.0000 32 0.25 @@ -6381,8 +6381,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.2 45 78 Cycle I 45.0000 30 0.00 20FUKAAXX100202.2 45 79 Cycle D 45.0000 29 0.00 20FUKAAXX100202.2 45 79 Cycle I 45.0000 29 0.00 -20FUKAAXX100202.2 45 8 Cycle D 45.0000 32 0.11 -20FUKAAXX100202.2 45 8 Cycle I 45.0000 32 0.00 +20FUKAAXX100202.2 45 8 Cycle D 45.0000 31 0.00 +20FUKAAXX100202.2 45 8 Cycle I 45.0000 31 0.00 20FUKAAXX100202.2 45 80 Cycle D 45.0000 30 0.00 20FUKAAXX100202.2 45 80 Cycle I 45.0000 30 0.00 20FUKAAXX100202.2 45 81 Cycle D 45.0000 29 0.00 @@ -6485,8 +6485,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.2 45 CTG Context I 45.0000 136 0.00 20FUKAAXX100202.2 45 CTT Context D 45.0000 128 0.65 20FUKAAXX100202.2 45 CTT Context I 45.0000 128 0.00 -20FUKAAXX100202.2 45 GAA Context D 45.0000 118 0.49 -20FUKAAXX100202.2 45 GAA Context I 45.0000 118 0.00 +20FUKAAXX100202.2 45 GAA Context D 45.0000 116 0.25 +20FUKAAXX100202.2 45 GAA Context I 45.0000 116 0.00 20FUKAAXX100202.2 45 GAC Context D 45.0000 69 0.00 20FUKAAXX100202.2 45 GAC Context I 45.0000 69 0.00 20FUKAAXX100202.2 45 GAG Context D 45.0000 137 0.49 @@ -8656,7 +8656,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.3 36 93 Cycle M 36.0000 5 0.00 20FUKAAXX100202.3 36 94 Cycle M 36.0000 4 0.00 20FUKAAXX100202.3 36 95 Cycle M 36.0000 6 0.00 -20FUKAAXX100202.3 36 96 Cycle M 36.0000 6 0.00 +20FUKAAXX100202.3 36 96 Cycle M 36.0000 5 0.00 20FUKAAXX100202.3 36 97 Cycle M 36.0000 3 0.00 20FUKAAXX100202.3 36 98 Cycle M 36.0000 4 0.00 20FUKAAXX100202.3 36 99 Cycle M 36.0000 5 0.00 @@ -8674,7 +8674,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.3 36 TA Context M 36.0000 32 0.00 20FUKAAXX100202.3 36 TC Context M 36.0000 41 0.00 20FUKAAXX100202.3 36 TG Context M 36.0000 56 2.00 -20FUKAAXX100202.3 36 TT Context M 36.0000 50 0.00 +20FUKAAXX100202.3 36 TT Context M 36.0000 49 0.00 20FUKAAXX100202.3 37 -1 Cycle M 37.0000 1 0.00 20FUKAAXX100202.3 37 -10 Cycle M 37.0000 14 0.00 20FUKAAXX100202.3 37 -100 Cycle M 37.0000 6 0.00 @@ -9094,7 +9094,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.3 39 -18 Cycle M 39.0000 6 0.00 20FUKAAXX100202.3 39 -19 Cycle M 39.0000 1 0.00 20FUKAAXX100202.3 39 -20 Cycle M 39.0000 4 0.00 -20FUKAAXX100202.3 39 -21 Cycle M 39.0000 7 0.00 +20FUKAAXX100202.3 39 -21 Cycle M 39.0000 6 0.00 20FUKAAXX100202.3 39 -22 Cycle M 39.0000 10 0.00 20FUKAAXX100202.3 39 -23 Cycle M 39.0000 5 0.00 20FUKAAXX100202.3 39 -25 Cycle M 39.0000 1 0.00 @@ -9264,7 +9264,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.3 39 97 Cycle M 39.0000 3 0.00 20FUKAAXX100202.3 39 98 Cycle M 39.0000 5 0.00 20FUKAAXX100202.3 39 99 Cycle M 39.0000 2 0.00 -20FUKAAXX100202.3 39 AA Context M 39.0000 334 0.00 +20FUKAAXX100202.3 39 AA Context M 39.0000 333 0.00 20FUKAAXX100202.3 39 AG Context M 39.0000 7 0.00 20FUKAAXX100202.3 39 CA Context M 39.0000 170 0.00 20FUKAAXX100202.3 39 CT Context M 39.0000 385 0.00 @@ -9305,8 +9305,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.3 45 -19 Cycle I 45.0000 49 0.00 20FUKAAXX100202.3 45 -20 Cycle D 45.0000 49 0.13 20FUKAAXX100202.3 45 -20 Cycle I 45.0000 49 0.00 -20FUKAAXX100202.3 45 -21 Cycle D 45.0000 49 0.13 -20FUKAAXX100202.3 45 -21 Cycle I 45.0000 49 0.00 +20FUKAAXX100202.3 45 -21 Cycle D 45.0000 48 0.00 +20FUKAAXX100202.3 45 -21 Cycle I 45.0000 48 0.00 20FUKAAXX100202.3 45 -22 Cycle D 45.0000 48 0.00 20FUKAAXX100202.3 45 -22 Cycle I 45.0000 48 0.00 20FUKAAXX100202.3 45 -23 Cycle D 45.0000 49 0.13 @@ -9651,8 +9651,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.3 45 94 Cycle I 45.0000 39 0.00 20FUKAAXX100202.3 45 95 Cycle D 45.0000 38 0.00 20FUKAAXX100202.3 45 95 Cycle I 45.0000 38 0.00 -20FUKAAXX100202.3 45 96 Cycle D 45.0000 39 0.14 -20FUKAAXX100202.3 45 96 Cycle I 45.0000 39 0.00 +20FUKAAXX100202.3 45 96 Cycle D 45.0000 38 0.00 +20FUKAAXX100202.3 45 96 Cycle I 45.0000 38 0.00 20FUKAAXX100202.3 45 97 Cycle D 45.0000 39 0.14 20FUKAAXX100202.3 45 97 Cycle I 45.0000 39 0.00 20FUKAAXX100202.3 45 AAA Context D 45.0000 201 0.38 @@ -9717,10 +9717,10 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.3 45 CTC Context I 45.0000 176 0.00 20FUKAAXX100202.3 45 CTG Context D 45.0000 198 0.00 20FUKAAXX100202.3 45 CTG Context I 45.0000 198 0.00 -20FUKAAXX100202.3 45 CTT Context D 45.0000 176 0.29 -20FUKAAXX100202.3 45 CTT Context I 45.0000 176 0.00 -20FUKAAXX100202.3 45 GAA Context D 45.0000 173 0.50 -20FUKAAXX100202.3 45 GAA Context I 45.0000 173 0.00 +20FUKAAXX100202.3 45 CTT Context D 45.0000 175 0.14 +20FUKAAXX100202.3 45 CTT Context I 45.0000 175 0.00 +20FUKAAXX100202.3 45 GAA Context D 45.0000 172 0.38 +20FUKAAXX100202.3 45 GAA Context I 45.0000 172 0.00 20FUKAAXX100202.3 45 GAC Context D 45.0000 85 0.00 20FUKAAXX100202.3 45 GAC Context I 45.0000 85 0.00 20FUKAAXX100202.3 45 GAG Context D 45.0000 177 0.50 @@ -12039,13 +12039,13 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.4 39 25 Cycle M 39.0000 3 0.00 20FUKAAXX100202.4 39 26 Cycle M 39.0000 1 0.00 20FUKAAXX100202.4 39 27 Cycle M 39.0000 2 0.00 -20FUKAAXX100202.4 39 28 Cycle M 39.0000 3 0.00 +20FUKAAXX100202.4 39 28 Cycle M 39.0000 2 0.00 20FUKAAXX100202.4 39 29 Cycle M 39.0000 3 0.00 20FUKAAXX100202.4 39 30 Cycle M 39.0000 4 0.00 20FUKAAXX100202.4 39 31 Cycle M 39.0000 4 0.00 20FUKAAXX100202.4 39 32 Cycle M 39.0000 7 0.00 20FUKAAXX100202.4 39 33 Cycle M 39.0000 3 0.00 -20FUKAAXX100202.4 39 34 Cycle M 39.0000 5 0.00 +20FUKAAXX100202.4 39 34 Cycle M 39.0000 4 0.00 20FUKAAXX100202.4 39 35 Cycle M 39.0000 2 0.00 20FUKAAXX100202.4 39 36 Cycle M 39.0000 1 0.00 20FUKAAXX100202.4 39 37 Cycle M 39.0000 3 0.00 @@ -12109,7 +12109,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.4 39 96 Cycle M 39.0000 2 0.00 20FUKAAXX100202.4 39 97 Cycle M 39.0000 4 0.00 20FUKAAXX100202.4 39 98 Cycle M 39.0000 2 0.00 -20FUKAAXX100202.4 39 AA Context M 39.0000 193 0.00 +20FUKAAXX100202.4 39 AA Context M 39.0000 191 0.00 20FUKAAXX100202.4 39 AG Context M 39.0000 1 0.00 20FUKAAXX100202.4 39 AT Context M 39.0000 2 0.00 20FUKAAXX100202.4 39 CA Context M 39.0000 109 1.00 @@ -12355,8 +12355,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.4 45 26 Cycle I 45.0000 32 0.00 20FUKAAXX100202.4 45 27 Cycle D 45.0000 32 0.13 20FUKAAXX100202.4 45 27 Cycle I 45.0000 32 0.00 -20FUKAAXX100202.4 45 28 Cycle D 45.0000 32 0.13 -20FUKAAXX100202.4 45 28 Cycle I 45.0000 32 0.00 +20FUKAAXX100202.4 45 28 Cycle D 45.0000 31 0.00 +20FUKAAXX100202.4 45 28 Cycle I 45.0000 31 0.00 20FUKAAXX100202.4 45 29 Cycle D 45.0000 31 0.13 20FUKAAXX100202.4 45 29 Cycle I 45.0000 31 0.00 20FUKAAXX100202.4 45 30 Cycle D 45.0000 31 0.25 @@ -12367,8 +12367,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.4 45 32 Cycle I 45.0000 32 0.00 20FUKAAXX100202.4 45 33 Cycle D 45.0000 32 0.13 20FUKAAXX100202.4 45 33 Cycle I 45.0000 32 0.00 -20FUKAAXX100202.4 45 34 Cycle D 45.0000 32 0.13 -20FUKAAXX100202.4 45 34 Cycle I 45.0000 32 0.00 +20FUKAAXX100202.4 45 34 Cycle D 45.0000 31 0.00 +20FUKAAXX100202.4 45 34 Cycle I 45.0000 31 0.00 20FUKAAXX100202.4 45 35 Cycle D 45.0000 31 0.00 20FUKAAXX100202.4 45 35 Cycle I 45.0000 31 0.00 20FUKAAXX100202.4 45 36 Cycle D 45.0000 32 0.13 @@ -12569,8 +12569,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.4 45 CTG Context I 45.0000 141 0.00 20FUKAAXX100202.4 45 CTT Context D 45.0000 132 0.14 20FUKAAXX100202.4 45 CTT Context I 45.0000 132 0.00 -20FUKAAXX100202.4 45 GAA Context D 45.0000 103 0.38 -20FUKAAXX100202.4 45 GAA Context I 45.0000 103 0.00 +20FUKAAXX100202.4 45 GAA Context D 45.0000 101 0.13 +20FUKAAXX100202.4 45 GAA Context I 45.0000 101 0.00 20FUKAAXX100202.4 45 GAC Context D 45.0000 80 0.00 20FUKAAXX100202.4 45 GAC Context I 45.0000 80 0.00 20FUKAAXX100202.4 45 GAG Context D 45.0000 155 0.38 @@ -14766,7 +14766,6 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.5 38 TT Context M 38.0000 221 0.00 20FUKAAXX100202.5 39 -100 Cycle M 39.0000 1 0.00 20FUKAAXX100202.5 39 -14 Cycle M 39.0000 2 0.00 -20FUKAAXX100202.5 39 -15 Cycle M 39.0000 1 0.00 20FUKAAXX100202.5 39 -16 Cycle M 39.0000 6 0.00 20FUKAAXX100202.5 39 -17 Cycle M 39.0000 4 0.00 20FUKAAXX100202.5 39 -18 Cycle M 39.0000 4 0.00 @@ -14943,7 +14942,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.5 39 97 Cycle M 39.0000 3 0.00 20FUKAAXX100202.5 39 98 Cycle M 39.0000 3 0.00 20FUKAAXX100202.5 39 99 Cycle M 39.0000 1 0.00 -20FUKAAXX100202.5 39 AA Context M 39.0000 241 0.00 +20FUKAAXX100202.5 39 AA Context M 39.0000 240 0.00 20FUKAAXX100202.5 39 AG Context M 39.0000 19 0.00 20FUKAAXX100202.5 39 AT Context M 39.0000 3 0.00 20FUKAAXX100202.5 39 CA Context M 39.0000 218 0.00 @@ -14997,8 +14996,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.5 45 -13 Cycle I 45.0000 39 0.00 20FUKAAXX100202.5 45 -14 Cycle D 45.0000 39 0.14 20FUKAAXX100202.5 45 -14 Cycle I 45.0000 39 0.00 -20FUKAAXX100202.5 45 -15 Cycle D 45.0000 39 0.14 -20FUKAAXX100202.5 45 -15 Cycle I 45.0000 39 0.00 +20FUKAAXX100202.5 45 -15 Cycle D 45.0000 38 0.00 +20FUKAAXX100202.5 45 -15 Cycle I 45.0000 38 0.00 20FUKAAXX100202.5 45 -16 Cycle D 45.0000 37 0.00 20FUKAAXX100202.5 45 -16 Cycle I 45.0000 37 0.00 20FUKAAXX100202.5 45 -17 Cycle D 45.0000 39 0.14 @@ -15423,8 +15422,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.5 45 CTG Context I 45.0000 154 0.00 20FUKAAXX100202.5 45 CTT Context D 45.0000 121 0.14 20FUKAAXX100202.5 45 CTT Context I 45.0000 121 0.00 -20FUKAAXX100202.5 45 GAA Context D 45.0000 162 0.29 -20FUKAAXX100202.5 45 GAA Context I 45.0000 162 0.00 +20FUKAAXX100202.5 45 GAA Context D 45.0000 161 0.14 +20FUKAAXX100202.5 45 GAA Context I 45.0000 161 0.00 20FUKAAXX100202.5 45 GAC Context D 45.0000 76 0.00 20FUKAAXX100202.5 45 GAC Context I 45.0000 76 0.00 20FUKAAXX100202.5 45 GAG Context D 45.0000 173 0.29 @@ -17205,7 +17204,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 35 -94 Cycle M 35.0000 2 0.00 20FUKAAXX100202.6 35 -95 Cycle M 35.0000 5 0.00 20FUKAAXX100202.6 35 -96 Cycle M 35.0000 1 0.00 -20FUKAAXX100202.6 35 -97 Cycle M 35.0000 3 0.00 +20FUKAAXX100202.6 35 -97 Cycle M 35.0000 2 0.00 20FUKAAXX100202.6 35 -98 Cycle M 35.0000 4 0.00 20FUKAAXX100202.6 35 -99 Cycle M 35.0000 2 0.00 20FUKAAXX100202.6 35 1 Cycle M 35.0000 51 0.50 @@ -17292,7 +17291,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 35 TA Context M 35.0000 24 1.00 20FUKAAXX100202.6 35 TC Context M 35.0000 33 0.17 20FUKAAXX100202.6 35 TG Context M 35.0000 59 0.00 -20FUKAAXX100202.6 35 TT Context M 35.0000 53 0.00 +20FUKAAXX100202.6 35 TT Context M 35.0000 52 0.00 20FUKAAXX100202.6 36 -10 Cycle M 36.0000 13 0.00 20FUKAAXX100202.6 36 -100 Cycle M 36.0000 6 0.00 20FUKAAXX100202.6 36 -101 Cycle M 36.0000 2 0.00 @@ -17735,7 +17734,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 38 -42 Cycle M 38.0000 17 0.00 20FUKAAXX100202.6 38 -43 Cycle M 38.0000 15 0.00 20FUKAAXX100202.6 38 -44 Cycle M 38.0000 21 0.00 -20FUKAAXX100202.6 38 -45 Cycle M 38.0000 13 0.00 +20FUKAAXX100202.6 38 -45 Cycle M 38.0000 12 0.00 20FUKAAXX100202.6 38 -46 Cycle M 38.0000 23 0.00 20FUKAAXX100202.6 38 -47 Cycle M 38.0000 19 0.00 20FUKAAXX100202.6 38 -48 Cycle M 38.0000 20 0.00 @@ -17876,7 +17875,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 38 85 Cycle M 38.0000 23 0.00 20FUKAAXX100202.6 38 86 Cycle M 38.0000 23 0.00 20FUKAAXX100202.6 38 87 Cycle M 38.0000 15 0.00 -20FUKAAXX100202.6 38 88 Cycle M 38.0000 18 1.00 +20FUKAAXX100202.6 38 88 Cycle M 38.0000 17 1.00 20FUKAAXX100202.6 38 89 Cycle M 38.0000 19 0.00 20FUKAAXX100202.6 38 9 Cycle M 38.0000 13 0.00 20FUKAAXX100202.6 38 90 Cycle M 38.0000 14 0.00 @@ -17902,7 +17901,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 38 TA Context M 38.0000 167 0.00 20FUKAAXX100202.6 38 TC Context M 38.0000 108 0.00 20FUKAAXX100202.6 38 TG Context M 38.0000 463 3.00 -20FUKAAXX100202.6 38 TT Context M 38.0000 306 1.00 +20FUKAAXX100202.6 38 TT Context M 38.0000 304 1.00 20FUKAAXX100202.6 39 -100 Cycle M 39.0000 2 0.00 20FUKAAXX100202.6 39 -16 Cycle M 39.0000 3 0.00 20FUKAAXX100202.6 39 -17 Cycle M 39.0000 2 0.00 @@ -18177,8 +18176,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 45 -43 Cycle I 45.0000 51 0.00 20FUKAAXX100202.6 45 -44 Cycle D 45.0000 49 0.00 20FUKAAXX100202.6 45 -44 Cycle I 45.0000 49 0.00 -20FUKAAXX100202.6 45 -45 Cycle D 45.0000 51 0.14 -20FUKAAXX100202.6 45 -45 Cycle I 45.0000 51 0.00 +20FUKAAXX100202.6 45 -45 Cycle D 45.0000 50 0.00 +20FUKAAXX100202.6 45 -45 Cycle I 45.0000 50 0.00 20FUKAAXX100202.6 45 -46 Cycle D 45.0000 51 0.14 20FUKAAXX100202.6 45 -46 Cycle I 45.0000 51 0.00 20FUKAAXX100202.6 45 -47 Cycle D 45.0000 51 0.14 @@ -18291,8 +18290,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 45 -95 Cycle I 45.0000 36 0.00 20FUKAAXX100202.6 45 -96 Cycle D 45.0000 35 0.00 20FUKAAXX100202.6 45 -96 Cycle I 45.0000 35 0.00 -20FUKAAXX100202.6 45 -97 Cycle D 45.0000 36 0.17 -20FUKAAXX100202.6 45 -97 Cycle I 45.0000 36 0.00 +20FUKAAXX100202.6 45 -97 Cycle D 45.0000 35 0.00 +20FUKAAXX100202.6 45 -97 Cycle I 45.0000 35 0.00 20FUKAAXX100202.6 45 10 Cycle D 45.0000 53 0.00 20FUKAAXX100202.6 45 10 Cycle I 45.0000 53 0.00 20FUKAAXX100202.6 45 11 Cycle D 45.0000 54 0.00 @@ -18457,8 +18456,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 45 86 Cycle I 45.0000 49 0.00 20FUKAAXX100202.6 45 87 Cycle D 45.0000 47 0.00 20FUKAAXX100202.6 45 87 Cycle I 45.0000 47 0.00 -20FUKAAXX100202.6 45 88 Cycle D 45.0000 48 0.14 -20FUKAAXX100202.6 45 88 Cycle I 45.0000 48 0.00 +20FUKAAXX100202.6 45 88 Cycle D 45.0000 47 0.00 +20FUKAAXX100202.6 45 88 Cycle I 45.0000 47 0.00 20FUKAAXX100202.6 45 89 Cycle D 45.0000 47 0.14 20FUKAAXX100202.6 45 89 Cycle I 45.0000 47 0.00 20FUKAAXX100202.6 45 9 Cycle D 45.0000 54 0.00 @@ -18541,8 +18540,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.6 45 CTC Context I 45.0000 221 0.00 20FUKAAXX100202.6 45 CTG Context D 45.0000 209 0.00 20FUKAAXX100202.6 45 CTG Context I 45.0000 209 0.00 -20FUKAAXX100202.6 45 CTT Context D 45.0000 203 1.17 -20FUKAAXX100202.6 45 CTT Context I 45.0000 203 0.00 +20FUKAAXX100202.6 45 CTT Context D 45.0000 200 0.71 +20FUKAAXX100202.6 45 CTT Context I 45.0000 200 0.00 20FUKAAXX100202.6 45 GAA Context D 45.0000 195 0.14 20FUKAAXX100202.6 45 GAA Context I 45.0000 195 0.00 20FUKAAXX100202.6 45 GAC Context D 45.0000 107 0.00 @@ -20524,7 +20523,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.7 36 -67 Cycle M 36.0000 3 0.00 20FUKAAXX100202.7 36 -68 Cycle M 36.0000 3 0.00 20FUKAAXX100202.7 36 -69 Cycle M 36.0000 4 0.00 -20FUKAAXX100202.7 36 -7 Cycle M 36.0000 12 0.00 +20FUKAAXX100202.7 36 -7 Cycle M 36.0000 11 0.00 20FUKAAXX100202.7 36 -70 Cycle M 36.0000 4 0.00 20FUKAAXX100202.7 36 -71 Cycle M 36.0000 3 0.00 20FUKAAXX100202.7 36 -72 Cycle M 36.0000 2 0.00 @@ -20654,7 +20653,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.7 36 97 Cycle M 36.0000 5 0.00 20FUKAAXX100202.7 36 98 Cycle M 36.0000 7 0.00 20FUKAAXX100202.7 36 99 Cycle M 36.0000 4 0.00 -20FUKAAXX100202.7 36 AA Context M 36.0000 58 0.00 +20FUKAAXX100202.7 36 AA Context M 36.0000 57 0.00 20FUKAAXX100202.7 36 AC Context M 36.0000 328 2.00 20FUKAAXX100202.7 36 AG Context M 36.0000 72 0.00 20FUKAAXX100202.7 36 AT Context M 36.0000 43 0.00 @@ -21053,7 +21052,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.7 38 90 Cycle M 38.0000 19 0.00 20FUKAAXX100202.7 38 91 Cycle M 38.0000 15 0.00 20FUKAAXX100202.7 38 92 Cycle M 38.0000 21 0.00 -20FUKAAXX100202.7 38 93 Cycle M 38.0000 17 0.00 +20FUKAAXX100202.7 38 93 Cycle M 38.0000 16 0.00 20FUKAAXX100202.7 38 94 Cycle M 38.0000 13 0.00 20FUKAAXX100202.7 38 95 Cycle M 38.0000 17 0.00 20FUKAAXX100202.7 38 96 Cycle M 38.0000 14 1.00 @@ -21073,7 +21072,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.7 38 TA Context M 38.0000 162 0.00 20FUKAAXX100202.7 38 TC Context M 38.0000 131 0.00 20FUKAAXX100202.7 38 TG Context M 38.0000 456 1.33 -20FUKAAXX100202.7 38 TT Context M 38.0000 262 1.00 +20FUKAAXX100202.7 38 TT Context M 38.0000 261 1.00 20FUKAAXX100202.7 39 -100 Cycle M 39.0000 1 0.00 20FUKAAXX100202.7 39 -14 Cycle M 39.0000 3 0.00 20FUKAAXX100202.7 39 -15 Cycle M 39.0000 2 0.00 @@ -21403,8 +21402,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.7 45 -68 Cycle I 45.0000 46 0.00 20FUKAAXX100202.7 45 -69 Cycle D 45.0000 46 0.00 20FUKAAXX100202.7 45 -69 Cycle I 45.0000 46 0.00 -20FUKAAXX100202.7 45 -7 Cycle D 45.0000 51 0.25 -20FUKAAXX100202.7 45 -7 Cycle I 45.0000 51 0.00 +20FUKAAXX100202.7 45 -7 Cycle D 45.0000 50 0.13 +20FUKAAXX100202.7 45 -7 Cycle I 45.0000 50 0.00 20FUKAAXX100202.7 45 -70 Cycle D 45.0000 46 0.00 20FUKAAXX100202.7 45 -70 Cycle I 45.0000 46 0.00 20FUKAAXX100202.7 45 -71 Cycle D 45.0000 46 0.00 @@ -21641,8 +21640,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.7 45 91 Cycle I 45.0000 40 0.00 20FUKAAXX100202.7 45 92 Cycle D 45.0000 40 0.00 20FUKAAXX100202.7 45 92 Cycle I 45.0000 40 0.00 -20FUKAAXX100202.7 45 93 Cycle D 45.0000 41 0.09 -20FUKAAXX100202.7 45 93 Cycle I 45.0000 41 0.00 +20FUKAAXX100202.7 45 93 Cycle D 45.0000 40 0.00 +20FUKAAXX100202.7 45 93 Cycle I 45.0000 40 0.00 20FUKAAXX100202.7 45 94 Cycle D 45.0000 41 0.09 20FUKAAXX100202.7 45 94 Cycle I 45.0000 41 0.00 20FUKAAXX100202.7 45 95 Cycle D 45.0000 41 0.09 @@ -21713,10 +21712,10 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20FUKAAXX100202.7 45 CTC Context I 45.0000 184 0.00 20FUKAAXX100202.7 45 CTG Context D 45.0000 196 0.00 20FUKAAXX100202.7 45 CTG Context I 45.0000 196 0.00 -20FUKAAXX100202.7 45 CTT Context D 45.0000 166 0.09 -20FUKAAXX100202.7 45 CTT Context I 45.0000 166 0.00 -20FUKAAXX100202.7 45 GAA Context D 45.0000 230 0.25 -20FUKAAXX100202.7 45 GAA Context I 45.0000 230 0.00 +20FUKAAXX100202.7 45 CTT Context D 45.0000 165 0.00 +20FUKAAXX100202.7 45 CTT Context I 45.0000 165 0.00 +20FUKAAXX100202.7 45 GAA Context D 45.0000 229 0.13 +20FUKAAXX100202.7 45 GAA Context I 45.0000 229 0.00 20FUKAAXX100202.7 45 GAC Context D 45.0000 82 0.00 20FUKAAXX100202.7 45 GAC Context I 45.0000 82 0.00 20FUKAAXX100202.7 45 GAG Context D 45.0000 219 0.25 @@ -25367,7 +25366,6 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 24 TC Context M 24.0000 4 0.00 20GAVAAXX100126.1 24 TG Context M 24.0000 1 0.00 20GAVAAXX100126.1 24 TT Context M 24.0000 1 0.00 -20GAVAAXX100126.1 25 -10 Cycle M 25.0000 1 0.00 20GAVAAXX100126.1 25 -12 Cycle M 25.0000 1 0.00 20GAVAAXX100126.1 25 -15 Cycle M 25.0000 1 0.00 20GAVAAXX100126.1 25 -17 Cycle M 25.0000 1 0.00 @@ -25446,7 +25444,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 25 GT Context M 25.0000 7 0.00 20GAVAAXX100126.1 25 TA Context M 25.0000 5 0.00 20GAVAAXX100126.1 25 TC Context M 25.0000 10 0.00 -20GAVAAXX100126.1 25 TG Context M 25.0000 9 0.00 +20GAVAAXX100126.1 25 TG Context M 25.0000 8 0.00 20GAVAAXX100126.1 25 TT Context M 25.0000 5 0.00 20GAVAAXX100126.1 26 -101 Cycle M 26.0000 1 0.00 20GAVAAXX100126.1 26 -18 Cycle M 26.0000 1 0.00 @@ -25606,7 +25604,6 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 27 61 Cycle M 27.0000 1 0.00 20GAVAAXX100126.1 27 63 Cycle M 27.0000 1 0.00 20GAVAAXX100126.1 27 65 Cycle M 27.0000 1 0.00 -20GAVAAXX100126.1 27 66 Cycle M 27.0000 1 0.00 20GAVAAXX100126.1 27 68 Cycle M 27.0000 1 0.00 20GAVAAXX100126.1 27 70 Cycle M 27.0000 2 0.00 20GAVAAXX100126.1 27 71 Cycle M 27.0000 1 0.00 @@ -25626,7 +25623,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 27 91 Cycle M 27.0000 1 0.00 20GAVAAXX100126.1 27 93 Cycle M 27.0000 2 0.00 20GAVAAXX100126.1 27 99 Cycle M 27.0000 2 0.00 -20GAVAAXX100126.1 27 AA Context M 27.0000 8 0.00 +20GAVAAXX100126.1 27 AA Context M 27.0000 7 0.00 20GAVAAXX100126.1 27 AC Context M 27.0000 3 0.00 20GAVAAXX100126.1 27 AG Context M 27.0000 9 0.00 20GAVAAXX100126.1 27 AT Context M 27.0000 3 0.00 @@ -27534,7 +27531,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 39 39 Cycle M 39.0000 16 0.00 20GAVAAXX100126.1 39 40 Cycle M 39.0000 23 0.00 20GAVAAXX100126.1 39 41 Cycle M 39.0000 8 0.00 -20GAVAAXX100126.1 39 42 Cycle M 39.0000 20 0.00 +20GAVAAXX100126.1 39 42 Cycle M 39.0000 19 0.00 20GAVAAXX100126.1 39 43 Cycle M 39.0000 13 0.00 20GAVAAXX100126.1 39 44 Cycle M 39.0000 15 0.00 20GAVAAXX100126.1 39 45 Cycle M 39.0000 11 0.00 @@ -27595,7 +27592,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 39 97 Cycle M 39.0000 10 0.00 20GAVAAXX100126.1 39 98 Cycle M 39.0000 8 0.00 20GAVAAXX100126.1 39 99 Cycle M 39.0000 3 0.00 -20GAVAAXX100126.1 39 AA Context M 39.0000 211 0.00 +20GAVAAXX100126.1 39 AA Context M 39.0000 210 0.00 20GAVAAXX100126.1 39 AG Context M 39.0000 26 0.00 20GAVAAXX100126.1 39 AT Context M 39.0000 49 0.00 20GAVAAXX100126.1 39 CA Context M 39.0000 413 2.00 @@ -27717,8 +27714,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 41 -76 Cycle M 41.0000 1 0.00 20GAVAAXX100126.1 41 AA Context M 41.0000 6 0.00 20GAVAAXX100126.1 41 CT Context M 41.0000 17 0.00 -20GAVAAXX100126.1 45 -10 Cycle D 45.0000 47 0.41 -20GAVAAXX100126.1 45 -10 Cycle I 45.0000 47 0.00 +20GAVAAXX100126.1 45 -10 Cycle D 45.0000 46 0.13 +20GAVAAXX100126.1 45 -10 Cycle I 45.0000 46 0.00 20GAVAAXX100126.1 45 -11 Cycle D 45.0000 46 0.13 20GAVAAXX100126.1 45 -11 Cycle I 45.0000 46 0.00 20GAVAAXX100126.1 45 -12 Cycle D 45.0000 46 0.13 @@ -27967,8 +27964,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 45 40 Cycle I 45.0000 53 0.00 20GAVAAXX100126.1 45 41 Cycle D 45.0000 53 0.14 20GAVAAXX100126.1 45 41 Cycle I 45.0000 53 0.00 -20GAVAAXX100126.1 45 42 Cycle D 45.0000 53 0.14 -20GAVAAXX100126.1 45 42 Cycle I 45.0000 53 0.00 +20GAVAAXX100126.1 45 42 Cycle D 45.0000 52 0.00 +20GAVAAXX100126.1 45 42 Cycle I 45.0000 52 0.00 20GAVAAXX100126.1 45 43 Cycle D 45.0000 52 0.00 20GAVAAXX100126.1 45 43 Cycle I 45.0000 52 0.00 20GAVAAXX100126.1 45 44 Cycle D 45.0000 52 0.14 @@ -28019,8 +28016,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 45 64 Cycle I 45.0000 52 0.00 20GAVAAXX100126.1 45 65 Cycle D 45.0000 51 0.17 20GAVAAXX100126.1 45 65 Cycle I 45.0000 51 0.00 -20GAVAAXX100126.1 45 66 Cycle D 45.0000 52 0.17 -20GAVAAXX100126.1 45 66 Cycle I 45.0000 52 0.00 +20GAVAAXX100126.1 45 66 Cycle D 45.0000 51 0.00 +20GAVAAXX100126.1 45 66 Cycle I 45.0000 51 0.00 20GAVAAXX100126.1 45 67 Cycle D 45.0000 51 0.00 20GAVAAXX100126.1 45 67 Cycle I 45.0000 51 0.00 20GAVAAXX100126.1 45 68 Cycle D 45.0000 52 0.00 @@ -28153,8 +28150,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 45 CTG Context I 45.0000 214 0.00 20GAVAAXX100126.1 45 CTT Context D 45.0000 188 0.70 20GAVAAXX100126.1 45 CTT Context I 45.0000 188 0.00 -20GAVAAXX100126.1 45 GAA Context D 45.0000 155 0.31 -20GAVAAXX100126.1 45 GAA Context I 45.0000 155 0.00 +20GAVAAXX100126.1 45 GAA Context D 45.0000 153 0.00 +20GAVAAXX100126.1 45 GAA Context I 45.0000 153 0.00 20GAVAAXX100126.1 45 GAC Context D 45.0000 90 0.00 20GAVAAXX100126.1 45 GAC Context I 45.0000 90 0.00 20GAVAAXX100126.1 45 GAG Context D 45.0000 189 0.43 @@ -28181,8 +28178,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.1 45 GTA Context I 45.0000 95 0.00 20GAVAAXX100126.1 45 GTC Context D 45.0000 85 0.46 20GAVAAXX100126.1 45 GTC Context I 45.0000 85 0.00 -20GAVAAXX100126.1 45 GTG Context D 45.0000 190 0.72 -20GAVAAXX100126.1 45 GTG Context I 45.0000 190 0.00 +20GAVAAXX100126.1 45 GTG Context D 45.0000 189 0.43 +20GAVAAXX100126.1 45 GTG Context I 45.0000 189 0.00 20GAVAAXX100126.1 45 GTT Context D 45.0000 116 0.00 20GAVAAXX100126.1 45 GTT Context I 45.0000 116 0.00 20GAVAAXX100126.1 45 TAA Context D 45.0000 81 0.00 @@ -29720,7 +29717,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.2 33 -68 Cycle M 33.0000 4 0.00 20GAVAAXX100126.2 33 -69 Cycle M 33.0000 3 0.00 20GAVAAXX100126.2 33 -7 Cycle M 33.0000 4 0.00 -20GAVAAXX100126.2 33 -70 Cycle M 33.0000 2 0.00 +20GAVAAXX100126.2 33 -70 Cycle M 33.0000 1 0.00 20GAVAAXX100126.2 33 -71 Cycle M 33.0000 9 0.00 20GAVAAXX100126.2 33 -72 Cycle M 33.0000 8 0.00 20GAVAAXX100126.2 33 -73 Cycle M 33.0000 4 0.00 @@ -29810,7 +29807,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.2 33 97 Cycle M 33.0000 1 0.00 20GAVAAXX100126.2 33 98 Cycle M 33.0000 4 0.00 20GAVAAXX100126.2 33 99 Cycle M 33.0000 2 0.00 -20GAVAAXX100126.2 33 AA Context M 33.0000 19 0.00 +20GAVAAXX100126.2 33 AA Context M 33.0000 18 0.00 20GAVAAXX100126.2 33 AC Context M 33.0000 25 0.00 20GAVAAXX100126.2 33 AG Context M 33.0000 32 0.00 20GAVAAXX100126.2 33 AT Context M 33.0000 16 0.00 @@ -31022,8 +31019,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.2 45 -69 Cycle I 45.0000 36 0.00 20GAVAAXX100126.2 45 -7 Cycle D 45.0000 41 0.00 20GAVAAXX100126.2 45 -7 Cycle I 45.0000 41 0.00 -20GAVAAXX100126.2 45 -70 Cycle D 45.0000 37 0.14 -20GAVAAXX100126.2 45 -70 Cycle I 45.0000 37 0.00 +20GAVAAXX100126.2 45 -70 Cycle D 45.0000 36 0.00 +20GAVAAXX100126.2 45 -70 Cycle I 45.0000 36 0.00 20GAVAAXX100126.2 45 -71 Cycle D 45.0000 35 0.00 20GAVAAXX100126.2 45 -71 Cycle I 45.0000 35 0.00 20GAVAAXX100126.2 45 -72 Cycle D 45.0000 36 0.14 @@ -31332,8 +31329,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.2 45 CTG Context I 45.0000 154 0.00 20GAVAAXX100126.2 45 CTT Context D 45.0000 141 0.43 20GAVAAXX100126.2 45 CTT Context I 45.0000 141 0.00 -20GAVAAXX100126.2 45 GAA Context D 45.0000 130 0.43 -20GAVAAXX100126.2 45 GAA Context I 45.0000 130 0.00 +20GAVAAXX100126.2 45 GAA Context D 45.0000 129 0.29 +20GAVAAXX100126.2 45 GAA Context I 45.0000 129 0.00 20GAVAAXX100126.2 45 GAC Context D 45.0000 87 0.00 20GAVAAXX100126.2 45 GAC Context I 45.0000 87 0.00 20GAVAAXX100126.2 45 GAG Context D 45.0000 183 0.14 @@ -36512,7 +36509,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.4 38 10 Cycle M 38.0000 10 0.00 20GAVAAXX100126.4 38 100 Cycle M 38.0000 4 0.00 20GAVAAXX100126.4 38 101 Cycle M 38.0000 5 0.00 -20GAVAAXX100126.4 38 11 Cycle M 38.0000 9 0.00 +20GAVAAXX100126.4 38 11 Cycle M 38.0000 8 0.00 20GAVAAXX100126.4 38 12 Cycle M 38.0000 8 0.00 20GAVAAXX100126.4 38 13 Cycle M 38.0000 9 0.00 20GAVAAXX100126.4 38 14 Cycle M 38.0000 11 0.00 @@ -36619,7 +36616,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.4 38 TA Context M 38.0000 97 0.00 20GAVAAXX100126.4 38 TC Context M 38.0000 29 0.00 20GAVAAXX100126.4 38 TG Context M 38.0000 196 3.00 -20GAVAAXX100126.4 38 TT Context M 38.0000 99 0.00 +20GAVAAXX100126.4 38 TT Context M 38.0000 98 0.00 20GAVAAXX100126.4 39 -13 Cycle M 39.0000 4 0.00 20GAVAAXX100126.4 39 -14 Cycle M 39.0000 3 0.00 20GAVAAXX100126.4 39 -15 Cycle M 39.0000 2 0.00 @@ -36979,8 +36976,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.4 45 -97 Cycle I 45.0000 25 0.00 20GAVAAXX100126.4 45 10 Cycle D 45.0000 33 0.00 20GAVAAXX100126.4 45 10 Cycle I 45.0000 33 0.00 -20GAVAAXX100126.4 45 11 Cycle D 45.0000 34 0.14 -20GAVAAXX100126.4 45 11 Cycle I 45.0000 34 0.00 +20GAVAAXX100126.4 45 11 Cycle D 45.0000 33 0.00 +20GAVAAXX100126.4 45 11 Cycle I 45.0000 33 0.00 20GAVAAXX100126.4 45 12 Cycle D 45.0000 34 0.14 20GAVAAXX100126.4 45 12 Cycle I 45.0000 34 0.00 20GAVAAXX100126.4 45 13 Cycle D 45.0000 34 0.14 @@ -37225,8 +37222,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.4 45 CTC Context I 45.0000 139 0.00 20GAVAAXX100126.4 45 CTG Context D 45.0000 154 0.00 20GAVAAXX100126.4 45 CTG Context I 45.0000 154 0.00 -20GAVAAXX100126.4 45 CTT Context D 45.0000 139 0.45 -20GAVAAXX100126.4 45 CTT Context I 45.0000 139 0.00 +20GAVAAXX100126.4 45 CTT Context D 45.0000 138 0.31 +20GAVAAXX100126.4 45 CTT Context I 45.0000 138 0.00 20GAVAAXX100126.4 45 GAA Context D 45.0000 118 0.00 20GAVAAXX100126.4 45 GAA Context I 45.0000 118 0.00 20GAVAAXX100126.4 45 GAC Context D 45.0000 72 0.00 @@ -39237,7 +39234,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.5 38 20 Cycle M 38.0000 11 0.00 20GAVAAXX100126.5 38 21 Cycle M 38.0000 17 1.00 20GAVAAXX100126.5 38 22 Cycle M 38.0000 13 0.00 -20GAVAAXX100126.5 38 23 Cycle M 38.0000 11 0.00 +20GAVAAXX100126.5 38 23 Cycle M 38.0000 10 0.00 20GAVAAXX100126.5 38 24 Cycle M 38.0000 10 0.00 20GAVAAXX100126.5 38 25 Cycle M 38.0000 12 0.00 20GAVAAXX100126.5 38 26 Cycle M 38.0000 15 0.00 @@ -39333,7 +39330,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.5 38 TA Context M 38.0000 89 0.00 20GAVAAXX100126.5 38 TC Context M 38.0000 51 0.00 20GAVAAXX100126.5 38 TG Context M 38.0000 268 1.00 -20GAVAAXX100126.5 38 TT Context M 38.0000 169 0.00 +20GAVAAXX100126.5 38 TT Context M 38.0000 168 0.00 20GAVAAXX100126.5 39 -11 Cycle M 39.0000 1 0.00 20GAVAAXX100126.5 39 -12 Cycle M 39.0000 3 0.00 20GAVAAXX100126.5 39 -14 Cycle M 39.0000 1 0.00 @@ -39759,8 +39756,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.5 45 21 Cycle I 45.0000 33 0.00 20GAVAAXX100126.5 45 22 Cycle D 45.0000 32 0.00 20GAVAAXX100126.5 45 22 Cycle I 45.0000 32 0.00 -20GAVAAXX100126.5 45 23 Cycle D 45.0000 33 0.14 -20GAVAAXX100126.5 45 23 Cycle I 45.0000 33 0.00 +20GAVAAXX100126.5 45 23 Cycle D 45.0000 32 0.00 +20GAVAAXX100126.5 45 23 Cycle I 45.0000 32 0.00 20GAVAAXX100126.5 45 24 Cycle D 45.0000 33 0.14 20GAVAAXX100126.5 45 24 Cycle I 45.0000 33 0.00 20GAVAAXX100126.5 45 25 Cycle D 45.0000 32 0.14 @@ -39981,8 +39978,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.5 45 CTC Context I 45.0000 103 0.00 20GAVAAXX100126.5 45 CTG Context D 45.0000 132 0.00 20GAVAAXX100126.5 45 CTG Context I 45.0000 132 0.00 -20GAVAAXX100126.5 45 CTT Context D 45.0000 102 0.14 -20GAVAAXX100126.5 45 CTT Context I 45.0000 102 0.00 +20GAVAAXX100126.5 45 CTT Context D 45.0000 101 0.00 +20GAVAAXX100126.5 45 CTT Context I 45.0000 101 0.00 20GAVAAXX100126.5 45 GAA Context D 45.0000 148 0.00 20GAVAAXX100126.5 45 GAA Context I 45.0000 148 0.00 20GAVAAXX100126.5 45 GAC Context D 45.0000 56 0.00 @@ -41050,7 +41047,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.6 31 -46 Cycle M 31.0000 2 0.00 20GAVAAXX100126.6 31 -47 Cycle M 31.0000 2 0.00 20GAVAAXX100126.6 31 -48 Cycle M 31.0000 3 0.00 -20GAVAAXX100126.6 31 -5 Cycle M 31.0000 6 0.00 +20GAVAAXX100126.6 31 -5 Cycle M 31.0000 5 0.00 20GAVAAXX100126.6 31 -50 Cycle M 31.0000 4 0.00 20GAVAAXX100126.6 31 -51 Cycle M 31.0000 1 0.00 20GAVAAXX100126.6 31 -52 Cycle M 31.0000 1 0.00 @@ -41126,7 +41123,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.6 31 94 Cycle M 31.0000 1 0.00 20GAVAAXX100126.6 31 97 Cycle M 31.0000 2 0.00 20GAVAAXX100126.6 31 99 Cycle M 31.0000 1 0.00 -20GAVAAXX100126.6 31 AA Context M 31.0000 14 0.00 +20GAVAAXX100126.6 31 AA Context M 31.0000 13 0.00 20GAVAAXX100126.6 31 AC Context M 31.0000 17 0.00 20GAVAAXX100126.6 31 AG Context M 31.0000 16 0.00 20GAVAAXX100126.6 31 AT Context M 31.0000 6 0.00 @@ -42228,7 +42225,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.6 38 40 Cycle M 38.0000 13 0.00 20GAVAAXX100126.6 38 41 Cycle M 38.0000 9 0.00 20GAVAAXX100126.6 38 42 Cycle M 38.0000 13 0.00 -20GAVAAXX100126.6 38 43 Cycle M 38.0000 17 0.00 +20GAVAAXX100126.6 38 43 Cycle M 38.0000 16 0.00 20GAVAAXX100126.6 38 44 Cycle M 38.0000 14 0.00 20GAVAAXX100126.6 38 45 Cycle M 38.0000 14 0.00 20GAVAAXX100126.6 38 46 Cycle M 38.0000 10 0.00 @@ -42304,7 +42301,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.6 38 TA Context M 38.0000 105 0.00 20GAVAAXX100126.6 38 TC Context M 38.0000 12 0.00 20GAVAAXX100126.6 38 TG Context M 38.0000 263 2.00 -20GAVAAXX100126.6 38 TT Context M 38.0000 214 0.00 +20GAVAAXX100126.6 38 TT Context M 38.0000 213 0.00 20GAVAAXX100126.6 39 -12 Cycle M 39.0000 2 0.00 20GAVAAXX100126.6 39 -13 Cycle M 39.0000 1 0.00 20GAVAAXX100126.6 39 -14 Cycle M 39.0000 3 0.00 @@ -42552,8 +42549,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.6 45 -48 Cycle I 45.0000 39 0.00 20GAVAAXX100126.6 45 -49 Cycle D 45.0000 38 0.00 20GAVAAXX100126.6 45 -49 Cycle I 45.0000 38 0.00 -20GAVAAXX100126.6 45 -5 Cycle D 45.0000 40 0.17 -20GAVAAXX100126.6 45 -5 Cycle I 45.0000 40 0.00 +20GAVAAXX100126.6 45 -5 Cycle D 45.0000 39 0.00 +20GAVAAXX100126.6 45 -5 Cycle I 45.0000 39 0.00 20GAVAAXX100126.6 45 -50 Cycle D 45.0000 38 0.00 20GAVAAXX100126.6 45 -50 Cycle I 45.0000 38 0.00 20GAVAAXX100126.6 45 -51 Cycle D 45.0000 38 0.00 @@ -42724,8 +42721,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.6 45 41 Cycle I 45.0000 41 0.00 20GAVAAXX100126.6 45 42 Cycle D 45.0000 40 0.14 20GAVAAXX100126.6 45 42 Cycle I 45.0000 40 0.00 -20GAVAAXX100126.6 45 43 Cycle D 45.0000 41 0.29 -20GAVAAXX100126.6 45 43 Cycle I 45.0000 41 0.00 +20GAVAAXX100126.6 45 43 Cycle D 45.0000 40 0.14 +20GAVAAXX100126.6 45 43 Cycle I 45.0000 40 0.00 20GAVAAXX100126.6 45 44 Cycle D 45.0000 41 0.29 20GAVAAXX100126.6 45 44 Cycle I 45.0000 41 0.00 20GAVAAXX100126.6 45 45 Cycle D 45.0000 41 0.29 @@ -42906,10 +42903,10 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.6 45 CTC Context I 45.0000 187 0.00 20GAVAAXX100126.6 45 CTG Context D 45.0000 189 0.00 20GAVAAXX100126.6 45 CTG Context I 45.0000 189 0.00 -20GAVAAXX100126.6 45 CTT Context D 45.0000 153 0.43 -20GAVAAXX100126.6 45 CTT Context I 45.0000 153 0.00 -20GAVAAXX100126.6 45 GAA Context D 45.0000 149 0.17 -20GAVAAXX100126.6 45 GAA Context I 45.0000 149 0.00 +20GAVAAXX100126.6 45 CTT Context D 45.0000 152 0.29 +20GAVAAXX100126.6 45 CTT Context I 45.0000 152 0.00 +20GAVAAXX100126.6 45 GAA Context D 45.0000 148 0.00 +20GAVAAXX100126.6 45 GAA Context I 45.0000 148 0.00 20GAVAAXX100126.6 45 GAC Context D 45.0000 85 0.00 20GAVAAXX100126.6 45 GAC Context I 45.0000 85 0.00 20GAVAAXX100126.6 45 GAG Context D 45.0000 172 0.00 @@ -44596,7 +44593,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.7 33 -32 Cycle M 33.0000 1 0.00 20GAVAAXX100126.7 33 -33 Cycle M 33.0000 3 0.00 20GAVAAXX100126.7 33 -34 Cycle M 33.0000 3 0.00 -20GAVAAXX100126.7 33 -35 Cycle M 33.0000 3 0.00 +20GAVAAXX100126.7 33 -35 Cycle M 33.0000 2 0.00 20GAVAAXX100126.7 33 -37 Cycle M 33.0000 4 0.00 20GAVAAXX100126.7 33 -38 Cycle M 33.0000 1 0.00 20GAVAAXX100126.7 33 -39 Cycle M 33.0000 5 0.00 @@ -44709,7 +44706,7 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.7 33 96 Cycle M 33.0000 1 0.00 20GAVAAXX100126.7 33 98 Cycle M 33.0000 3 0.00 20GAVAAXX100126.7 33 99 Cycle M 33.0000 2 0.00 -20GAVAAXX100126.7 33 AA Context M 33.0000 15 0.00 +20GAVAAXX100126.7 33 AA Context M 33.0000 14 0.00 20GAVAAXX100126.7 33 AC Context M 33.0000 16 0.00 20GAVAAXX100126.7 33 AG Context M 33.0000 31 0.25 20GAVAAXX100126.7 33 AT Context M 33.0000 18 0.00 @@ -45829,8 +45826,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.7 45 -33 Cycle I 45.0000 39 0.00 20GAVAAXX100126.7 45 -34 Cycle D 45.0000 39 0.13 20GAVAAXX100126.7 45 -34 Cycle I 45.0000 39 0.00 -20GAVAAXX100126.7 45 -35 Cycle D 45.0000 39 0.13 -20GAVAAXX100126.7 45 -35 Cycle I 45.0000 39 0.00 +20GAVAAXX100126.7 45 -35 Cycle D 45.0000 38 0.00 +20GAVAAXX100126.7 45 -35 Cycle I 45.0000 38 0.00 20GAVAAXX100126.7 45 -36 Cycle D 45.0000 38 0.00 20GAVAAXX100126.7 45 -36 Cycle I 45.0000 38 0.00 20GAVAAXX100126.7 45 -37 Cycle D 45.0000 39 0.13 @@ -46215,8 +46212,8 @@ ReadGroup QualityScore CovariateValue CovariateName EventType Empir 20GAVAAXX100126.7 45 CTG Context I 45.0000 180 0.00 20GAVAAXX100126.7 45 CTT Context D 45.0000 128 0.14 20GAVAAXX100126.7 45 CTT Context I 45.0000 128 0.00 -20GAVAAXX100126.7 45 GAA Context D 45.0000 148 0.25 -20GAVAAXX100126.7 45 GAA Context I 45.0000 148 0.00 +20GAVAAXX100126.7 45 GAA Context D 45.0000 147 0.13 +20GAVAAXX100126.7 45 GAA Context I 45.0000 147 0.00 20GAVAAXX100126.7 45 GAC Context D 45.0000 96 0.00 20GAVAAXX100126.7 45 GAC Context I 45.0000 96 0.00 20GAVAAXX100126.7 45 GAG Context D 45.0000 172 0.25 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.alleleSpecific.g.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.alleleSpecific.g.vcf index d127ebc7792..e5daad1228c 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.alleleSpecific.g.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.alleleSpecific.g.vcf @@ -208,8 +208,8 @@ 20 10004148 . G . . END=10004192 GT:DP:GQ:MIN_DP:PL 0/0:49:99:45:0,106,1637 20 10004193 . G T, 937.64 . AS_RAW_BaseQRankSum=|-0.4,1|NaN;AS_RAW_MQ=70129.00|109140.00|0.00;AS_RAW_MQRankSum=|3.3,1|NaN;AS_RAW_ReadPosRankSum=|1.7,1|NaN;AS_SB_TABLE=12,11|12,16|0,0;BaseQRankSum=-0.392;DP=54;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=3.385;RAW_MQandDP=188870,54;ReadPosRankSum=1.724 GT:AD:DP:GQ:PL:SB 0/1:23,28,0:51:99:945,0,776,1014,860,1875:12,11,12,16 20 10004194 . C . . END=10004221 GT:DP:GQ:MIN_DP:PL 0/0:50:99:46:0,105,1575 -20 10004222 . C CA, 41.60 . AS_RAW_BaseQRankSum=|0.1,1|NaN;AS_RAW_MQ=133433.00|28232.00|0.00;AS_RAW_MQRankSum=|-2.3,1|NaN;AS_RAW_ReadPosRankSum=|1.2,1|NaN;AS_SB_TABLE=20,15|4,6|0,0;BaseQRankSum=0.124;DP=68;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.220;RAW_MQandDP=230226,68;ReadPosRankSum=1.271 GT:AD:DP:GQ:PL:SB 0/1:35,10,0:45:49:49,0,924,153,952,1105:20,15,4,6 -20 10004223 . A AG, 80.60 . AS_RAW_BaseQRankSum=|-0.8,1|NaN;AS_RAW_MQ=104677.00|44341.00|0.00;AS_RAW_MQRankSum=|2.2,1|NaN;AS_RAW_ReadPosRankSum=|0.4,1|NaN;AS_SB_TABLE=16,19|6,6|0,0;BaseQRankSum=-0.749;DP=68;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=2.272;RAW_MQandDP=230910,68;ReadPosRankSum=0.490 GT:AD:DP:GQ:PL:SB 0/1:35,12,0:47:88:88,0,953,193,987,1180:16,19,6,6 +20 10004222 . C CA, 41.60 . AS_RAW_BaseQRankSum=|0.3,1|NaN;AS_RAW_MQ=133433.00|28232.00|0.00;AS_RAW_MQRankSum=|-2.3,1|NaN;AS_RAW_ReadPosRankSum=|0.1,1|NaN;AS_SB_TABLE=20,15|4,6|0,0;BaseQRankSum=0.335;DP=68;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.220;RAW_MQandDP=230226,68;ReadPosRankSum=0.198 GT:AD:DP:GQ:PL:SB 0/1:35,10,0:45:49:49,0,924,153,952,1105:20,15,4,6 +20 10004223 . A AG, 80.60 . AS_RAW_BaseQRankSum=|-0.8,1|NaN;AS_RAW_MQ=104677.00|44341.00|0.00;AS_RAW_MQRankSum=|2.2,1|NaN;AS_RAW_ReadPosRankSum=|0.1,1|NaN;AS_SB_TABLE=16,19|6,6|0,0;BaseQRankSum=-0.765;DP=68;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=2.272;RAW_MQandDP=230910,68;ReadPosRankSum=0.183 GT:AD:DP:GQ:PL:SB 0/1:35,12,0:47:88:88,0,953,193,987,1180:16,19,6,6 20 10004224 . A . . END=10004224 GT:DP:GQ:MIN_DP:PL 0/0:65:0:65:0,0,1201 20 10004225 . A . . END=10004240 GT:DP:GQ:MIN_DP:PL 0/0:70:99:65:0,117,1755 20 10004241 . G . . END=10004241 GT:DP:GQ:MIN_DP:PL 0/0:66:0:66:0,0,1965 @@ -222,7 +222,7 @@ 20 10004611 . C . . END=10004724 GT:DP:GQ:MIN_DP:PL 0/0:75:99:64:0,120,1800 20 10004725 . A G, 975.64 . AS_RAW_BaseQRankSum=|-2.4,1|NaN;AS_RAW_MQ=91952.00|105769.00|0.00;AS_RAW_MQRankSum=|2.8,1|NaN;AS_RAW_ReadPosRankSum=|1.9,1|NaN;AS_SB_TABLE=10,24|17,13|0,0;BaseQRankSum=-2.393;DP=66;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=2.856;RAW_MQandDP=202162,66;ReadPosRankSum=1.932 GT:AD:DP:GQ:PL:SB 0/1:34,30,0:64:99:983,0,1139,1085,1228,2313:10,24,17,13 20 10004726 . T . . END=10004768 GT:DP:GQ:MIN_DP:PL 0/0:65:99:61:0,120,1800 -20 10004769 . TAAAACTATGC T, 970.60 . AS_RAW_BaseQRankSum=|1.7,1|NaN;AS_RAW_MQ=133200.00|31344.00|0.00;AS_RAW_MQRankSum=|-6.6,1|NaN;AS_RAW_ReadPosRankSum=|1.7,1|NaN;AS_SB_TABLE=14,23|7,19|0,0;BaseQRankSum=1.796;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-6.531;RAW_MQandDP=222144,79;ReadPosRankSum=1.721 GT:AD:DP:GQ:PL:SB 0/1:37,26,0:63:99:978,0,1473,1089,1554,2643:14,23,7,19 +20 10004769 . TAAAACTATGC T, 970.60 . AS_RAW_BaseQRankSum=|0.8,1|NaN;AS_RAW_MQ=133200.00|31344.00|0.00;AS_RAW_MQRankSum=|-6.6,1|NaN;AS_RAW_ReadPosRankSum=|1.7,1|NaN;AS_SB_TABLE=14,23|7,19|0,0;BaseQRankSum=0.807;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-6.531;RAW_MQandDP=222144,79;ReadPosRankSum=1.721 GT:AD:DP:GQ:PL:SB 0/1:37,26,0:63:99:978,0,1473,1089,1554,2643:14,23,7,19 20 10004780 . A . . END=10004873 GT:DP:GQ:MIN_DP:PL 0/0:77:99:69:0,120,1800 20 10004874 . A C, 3617.06 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|306223.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|54,33|0,0;DP=90;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=317023,90 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 1|1:0,87,0:87:99:0|1:10004874_A_C:3631,261,0,3631,261,3631:10004874:0,0,54,33 20 10004875 . T . . END=10004886 GT:DP:GQ:MIN_DP:PL 0/0:86:99:85:0,120,1800 @@ -256,7 +256,7 @@ 20 10007532 . G . . END=10007979 GT:DP:GQ:MIN_DP:PL 0/0:80:99:65:0,120,1800 20 10007980 . A C, 3539.06 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|331800.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|39,51|0,0;DP=92;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=339000,92 GT:AD:DP:GQ:PL:SB 1/1:0,90,0:90:99:3553,270,0,3553,270,3553:0,0,39,51 20 10007981 . A . . END=10008028 GT:DP:GQ:MIN_DP:PL 0/0:86:99:80:0,120,1800 -20 10008029 . T TA, 2009.03 . AS_RAW_BaseQRankSum=|0.4,1|NaN;AS_RAW_MQ=10800.00|278310.00|0.00;AS_RAW_MQRankSum=|0.6,1|NaN;AS_RAW_ReadPosRankSum=|-1.4,1|NaN;AS_SB_TABLE=1,2|28,46|0,0;BaseQRankSum=0.438;DP=97;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=0.651;RAW_MQandDP=362251,97;ReadPosRankSum=-1.326 GT:AD:DP:GQ:PL:SB 1/1:3,74,0:77:99:2023,145,0,2032,222,2109:1,2,28,46 +20 10008029 . T TA, 2009.03 . AS_RAW_BaseQRankSum=|0.4,1|NaN;AS_RAW_MQ=10800.00|278310.00|0.00;AS_RAW_MQRankSum=|0.6,1|NaN;AS_RAW_ReadPosRankSum=|-1.4,1|NaN;AS_SB_TABLE=1,2|28,46|0,0;BaseQRankSum=0.409;DP=97;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=0.651;RAW_MQandDP=362251,97;ReadPosRankSum=-1.357 GT:AD:DP:GQ:PL:SB 1/1:3,74,0:77:99:2023,145,0,2032,222,2109:1,2,28,46 20 10008030 . A . . END=10008145 GT:DP:GQ:MIN_DP:PL 0/0:82:99:76:0,120,1800 20 10008146 . TA T, 2166.03 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|257200.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|38,32|0,0;DP=77;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=282400,77 GT:AD:DP:GQ:PL:SB 1/1:0,70,0:70:99:2180,211,0,2180,211,2180:0,0,38,32 20 10008148 . A . . END=10008220 GT:DP:GQ:MIN_DP:PL 0/0:80:99:72:0,120,1800 @@ -266,22 +266,22 @@ 20 10008459 . A . . END=10008732 GT:DP:GQ:MIN_DP:PL 0/0:70:99:40:0,105,1575 20 10008733 . T . . END=10008733 GT:DP:GQ:MIN_DP:PL 0/0:47:94:47:0,94,1689 20 10008734 . G . . END=10008741 GT:DP:GQ:MIN_DP:PL 0/0:48:99:47:0,120,1800 -20 10008742 . G T, 736.64 . AS_RAW_BaseQRankSum=|3.8,1|NaN;AS_RAW_MQ=37586.00|30288.00|0.00;AS_RAW_MQRankSum=|-1.6,1|NaN;AS_RAW_ReadPosRankSum=|0.1,1|NaN;AS_SB_TABLE=10,13|11,15|0,0;BaseQRankSum=3.893;DP=50;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.502;RAW_MQandDP=68715,50;ReadPosRankSum=0.190 GT:AD:DP:GQ:PL:SB 0/1:23,26,0:49:99:744,0,580,813,658,1471:10,13,11,15 +20 10008742 . G T, 736.64 . AS_RAW_BaseQRankSum=|3.8,1|NaN;AS_RAW_MQ=37586.00|30288.00|0.00;AS_RAW_MQRankSum=|-1.6,1|NaN;AS_RAW_ReadPosRankSum=|0.2,1|NaN;AS_SB_TABLE=10,13|11,15|0,0;BaseQRankSum=3.893;DP=50;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.502;RAW_MQandDP=68715,50;ReadPosRankSum=0.200 GT:AD:DP:GQ:PL:SB 0/1:23,26,0:49:99:744,0,580,813,658,1471:10,13,11,15 20 10008743 . T . . END=10008757 GT:DP:GQ:MIN_DP:PL 0/0:46:99:42:0,99,1485 -20 10008758 . C CA, 706.49 . AS_RAW_BaseQRankSum=|0.1,1|NaN;AS_RAW_MQ=6578.00|43657.00|0.00;AS_RAW_MQRankSum=|-0.9,1|NaN;AS_RAW_ReadPosRankSum=|-0.1,1|NaN;AS_SB_TABLE=3,1|16,18|0,0;BaseQRankSum=0.119;DP=51;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.875;RAW_MQandDP=72567,51;ReadPosRankSum=-0.052 GT:AD:DP:GQ:PL:SB 1/1:4,34,0:38:10:720,10,0,733,102,825:3,1,16,18 +20 10008758 . C CA, 706.49 . AS_RAW_BaseQRankSum=|0.1,1|NaN;AS_RAW_MQ=6578.00|43657.00|0.00;AS_RAW_MQRankSum=|-0.9,1|NaN;AS_RAW_ReadPosRankSum=|-0.3,1|NaN;AS_SB_TABLE=3,1|16,18|0,0;BaseQRankSum=0.130;DP=51;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.875;RAW_MQandDP=72567,51;ReadPosRankSum=-0.262 GT:AD:DP:GQ:PL:SB 1/1:4,34,0:38:10:720,10,0,733,102,825:3,1,16,18 20 10008759 . A . . END=10008772 GT:DP:GQ:MIN_DP:PL 0/0:55:99:53:0,120,1800 20 10008773 . T . . END=10008773 GT:DP:GQ:MIN_DP:PL 0/0:54:0:54:0,0,1660 20 10008774 . T . . END=10008774 GT:DP:GQ:MIN_DP:PL 0/0:55:99:55:0,117,1755 20 10008775 . A . . END=10008775 GT:DP:GQ:MIN_DP:PL 0/0:55:60:55:0,60,1923 20 10008776 . G . . END=10008920 GT:DP:GQ:MIN_DP:PL 0/0:54:99:45:0,99,1480 -20 10008921 . C CA, 283.60 . AS_RAW_BaseQRankSum=|0.5,1|NaN;AS_RAW_MQ=62041.00|48705.00|0.00;AS_RAW_MQRankSum=|-1.4,1|NaN;AS_RAW_ReadPosRankSum=|0.1,1|NaN;AS_SB_TABLE=10,8|8,9|0,0;BaseQRankSum=0.516;DP=60;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.306;RAW_MQandDP=188135,60;ReadPosRankSum=0.173 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:18,17,0:35:99:0|1:10008921_C_CA:291,0,366,345,416,761:10008921:10,8,8,9 +20 10008921 . C CA, 283.60 . AS_RAW_BaseQRankSum=|0.6,1|NaN;AS_RAW_MQ=62041.00|48705.00|0.00;AS_RAW_MQRankSum=|-1.4,1|NaN;AS_RAW_ReadPosRankSum=|-0.1,1|NaN;AS_SB_TABLE=10,8|8,9|0,0;BaseQRankSum=0.610;DP=60;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.306;RAW_MQandDP=188135,60;ReadPosRankSum=-0.017 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:18,17,0:35:99:0|1:10008921_C_CA:291,0,366,345,416,761:10008921:10,8,8,9 20 10008922 . A . . END=10008942 GT:DP:GQ:MIN_DP:PL 0/0:53:99:47:0,114,1710 20 10008943 . A . . END=10008944 GT:DP:GQ:MIN_DP:PL 0/0:47:78:47:0,78,1170 20 10008945 . A . . END=10008947 GT:DP:GQ:MIN_DP:PL 0/0:47:81:46:0,81,1215 -20 10008948 . TA T, 2094.03 . AS_RAW_BaseQRankSum=|0.9,1|NaN;AS_RAW_MQ=625.00|139322.00|0.00;AS_RAW_MQRankSum=|1.9,1|NaN;AS_RAW_ReadPosRankSum=|0.8,1|NaN;AS_SB_TABLE=1,0|36,17|0,0;BaseQRankSum=0.956;DP=56;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=1.946;RAW_MQandDP=147147,56;ReadPosRankSum=0.884 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 1|1:1,53,0:54:99:0|1:10008921_C_CA:2108,117,0,2111,159,2153:10008921:1,0,36,17 +20 10008948 . TA T, 2094.03 . AS_RAW_BaseQRankSum=|0.9,1|NaN;AS_RAW_MQ=625.00|139322.00|0.00;AS_RAW_MQRankSum=|1.9,1|NaN;AS_RAW_ReadPosRankSum=|0.8,1|NaN;AS_SB_TABLE=1,0|36,17|0,0;BaseQRankSum=0.994;DP=56;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=1.946;RAW_MQandDP=147147,56;ReadPosRankSum=0.884 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 1|1:1,53,0:54:99:0|1:10008921_C_CA:2108,117,0,2111,159,2153:10008921:1,0,36,17 20 10008950 . A . . END=10008950 GT:DP:GQ:MIN_DP:PL 0/0:52:96:52:0,96,1440 20 10008951 . A . . END=10008951 GT:DP:GQ:MIN_DP:PL 0/0:51:87:51:0,87,1305 -20 10008952 . CACACACACACACA C,CCA,CCACACACACA,CCACACACACACA, 1702.02 . AS_RAW_BaseQRankSum=|0.3,1|0.3,1|1.3,1|1.9,1|NaN;AS_RAW_MQ=625.00|2523.00|11774.00|12125.00|39600.00|0.00;AS_RAW_MQRankSum=|1.1,1|4.0,1|0.6,1|3.6,1|NaN;AS_RAW_ReadPosRankSum=|0.3,1|1.0,1|-0.3,1|0.8,1|NaN;AS_SB_TABLE=1,0|2,1|8,6|4,1|11,0|0,0;BaseQRankSum=1.046;DP=63;ExcessHet=3.0103;MLEAC=0,1,0,1,0;MLEAF=0.00,0.500,0.00,0.500,0.00;MQRankSum=1.844;RAW_MQandDP=165341,63;ReadPosRankSum=0.716 GT:AD:DP:GQ:PL:SB 2/4:1,3,14,5,11,0:34:99:1719,888,1213,538,767,801,740,494,153,687,597,341,0,444,535,1150,1059,712,761,609,1293:1,0,25,8 +20 10008952 . CACACACACACACA C,CCA,CCACACACACA,CCACACACACACA, 1702.02 . AS_RAW_BaseQRankSum=|0.3,1|0.3,1|1.2,1|1.9,1|NaN;AS_RAW_MQ=625.00|2523.00|11774.00|12125.00|39600.00|0.00;AS_RAW_MQRankSum=|1.1,1|4.0,1|0.6,1|3.6,1|NaN;AS_RAW_ReadPosRankSum=|0.3,1|0.9,1|-0.3,1|0.8,1|NaN;AS_SB_TABLE=1,0|2,1|8,6|4,1|11,0|0,0;BaseQRankSum=1.026;DP=63;ExcessHet=3.0103;MLEAC=0,1,0,1,0;MLEAF=0.00,0.500,0.00,0.500,0.00;MQRankSum=1.844;RAW_MQandDP=165341,63;ReadPosRankSum=0.666 GT:AD:DP:GQ:PL:SB 2/4:1,3,14,5,11,0:34:99:1719,888,1213,538,767,801,740,494,153,687,597,341,0,444,535,1150,1059,712,761,609,1293:1,0,25,8 20 10008966 . C . . END=10008986 GT:DP:GQ:MIN_DP:PL 0/0:58:99:56:0,120,1800 20 10008987 . A . . END=10008989 GT:DP:GQ:MIN_DP:PL 0/0:59:94:59:0,94,2181 20 10008990 . C . . END=10009226 GT:DP:GQ:MIN_DP:PL 0/0:61:99:38:0,102,1530 @@ -299,9 +299,9 @@ 20 10009796 . C . . END=10009832 GT:DP:GQ:MIN_DP:PL 0/0:49:99:44:0,99,1485 20 10009833 . A . . END=10009840 GT:DP:GQ:MIN_DP:PL 0/0:53:63:51:0,63,945 20 10009841 . A . . END=10009841 GT:DP:GQ:MIN_DP:PL 0/0:51:39:51:0,39,585 -20 10009842 . G GAA, 562.60 . AS_RAW_BaseQRankSum=|0.1,1|NaN;AS_RAW_MQ=51846.00|37722.00|0.00;AS_RAW_MQRankSum=|-1.0,1|NaN;AS_RAW_ReadPosRankSum=|1.7,1|NaN;AS_SB_TABLE=9,10|8,8|0,0;BaseQRankSum=0.183;DP=52;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.936;RAW_MQandDP=150768,52;ReadPosRankSum=1.754 GT:AD:DP:GQ:PL:SB 0/1:19,16,0:35:99:570,0,691,628,739,1367:9,10,8,8 +20 10009842 . G GAA, 562.60 . AS_RAW_BaseQRankSum=|0.3,1|NaN;AS_RAW_MQ=51846.00|37722.00|0.00;AS_RAW_MQRankSum=|-1.0,1|NaN;AS_RAW_ReadPosRankSum=|1.7,1|NaN;AS_SB_TABLE=9,10|8,8|0,0;BaseQRankSum=0.383;DP=52;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.936;RAW_MQandDP=150768,52;ReadPosRankSum=1.757 GT:AD:DP:GQ:PL:SB 0/1:19,16,0:35:99:570,0,691,628,739,1367:9,10,8,8 20 10009843 . A . . END=10009843 GT:DP:GQ:MIN_DP:PL 0/0:51:36:51:0,36,540 -20 10009844 . G A, 683.64 . AS_RAW_BaseQRankSum=|0.9,1|NaN;AS_RAW_MQ=37722.00|51846.00|0.00;AS_RAW_MQRankSum=|0.9,1|NaN;AS_RAW_ReadPosRankSum=|-1.6,1|NaN;AS_SB_TABLE=8,8|9,10|0,0;BaseQRankSum=0.998;DP=54;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.975;RAW_MQandDP=155209,54;ReadPosRankSum=-1.575 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:16,19,0:35:99:0|1:10009844_G_A:691,0,585,739,644,1383:10009844:8,8,9,10 +20 10009844 . G A, 683.64 . AS_RAW_BaseQRankSum=|1.1,1|NaN;AS_RAW_MQ=37722.00|51846.00|0.00;AS_RAW_MQRankSum=|0.9,1|NaN;AS_RAW_ReadPosRankSum=|-2.4,1|NaN;AS_SB_TABLE=8,8|9,10|0,0;BaseQRankSum=1.116;DP=54;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.975;RAW_MQandDP=155209,54;ReadPosRankSum=-2.354 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:16,19,0:35:99:0|1:10009844_G_A:691,0,585,739,644,1383:10009844:8,8,9,10 20 10009845 . A . . END=10009847 GT:DP:GQ:MIN_DP:PL 0/0:51:42:51:0,42,630 20 10009848 . G . . END=10009848 GT:DP:GQ:MIN_DP:PL 0/0:54:51:54:0,51,765 20 10009849 . A . . END=10009850 GT:DP:GQ:MIN_DP:PL 0/0:55:57:54:0,57,855 @@ -310,9 +310,9 @@ 20 10009861 . A . . END=10009864 GT:DP:GQ:MIN_DP:PL 0/0:58:84:56:0,84,1260 20 10009865 . A . . END=10009869 GT:DP:GQ:MIN_DP:PL 0/0:57:90:56:0,90,1350 20 10009870 . G . . END=10009870 GT:DP:GQ:MIN_DP:PL 0/0:57:99:57:0,99,1485 -20 10009871 . A G, 679.64 . AS_RAW_BaseQRankSum=|-0.9,1|NaN;AS_RAW_MQ=39404.00|51846.00|0.00;AS_RAW_MQRankSum=|1.3,1|NaN;AS_RAW_ReadPosRankSum=|1.4,1|NaN;AS_SB_TABLE=10,8|9,10|0,0;BaseQRankSum=-0.803;DP=62;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.336;RAW_MQandDP=161937,62;ReadPosRankSum=1.491 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:18,19,0:37:99:0|1:10009844_G_A:687,0,593,740,652,1392:10009844:10,8,9,10 +20 10009871 . A G, 679.64 . AS_RAW_BaseQRankSum=|-0.9,1|NaN;AS_RAW_MQ=39404.00|51846.00|0.00;AS_RAW_MQRankSum=|1.3,1|NaN;AS_RAW_ReadPosRankSum=|0.8,1|NaN;AS_SB_TABLE=10,8|9,10|0,0;BaseQRankSum=-0.803;DP=62;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.336;RAW_MQandDP=161937,62;ReadPosRankSum=0.840 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:18,19,0:37:99:0|1:10009844_G_A:687,0,593,740,652,1392:10009844:10,8,9,10 20 10009872 . G . . END=10009874 GT:DP:GQ:MIN_DP:PL 0/0:57:99:55:0,108,1620 -20 10009875 . A G,AGGGAGG, 2389.06 . AS_RAW_BaseQRankSum=|1.3,1|-0.7,1|NaN;AS_RAW_MQ=1682.00|40205.00|30522.00|0.00;AS_RAW_MQRankSum=|1.8,1|0.9,1|NaN;AS_RAW_ReadPosRankSum=|1.4,1|0.5,1|NaN;AS_SB_TABLE=2,0|6,9|7,7|0,0;BaseQRankSum=0.378;DP=58;ExcessHet=3.0103;MLEAC=1,1,0;MLEAF=0.500,0.500,0.00;MQRankSum=1.413;RAW_MQandDP=147537,58;ReadPosRankSum=1.040 GT:AD:DP:GQ:PL:SB 1/2:2,15,14,0:31:99:2406,645,532,697,0,574,1881,654,701,1805:2,0,13,16 +20 10009875 . A G,AGGGAGG, 2389.06 . AS_RAW_BaseQRankSum=|1.3,1|-0.7,1|NaN;AS_RAW_MQ=1682.00|40205.00|30522.00|0.00;AS_RAW_MQRankSum=|1.8,1|0.9,1|NaN;AS_RAW_ReadPosRankSum=|1.4,1|1.2,1|NaN;AS_SB_TABLE=2,0|6,9|7,7|0,0;BaseQRankSum=0.378;DP=58;ExcessHet=3.0103;MLEAC=1,1,0;MLEAF=0.500,0.500,0.00;MQRankSum=1.413;RAW_MQandDP=147537,58;ReadPosRankSum=1.373 GT:AD:DP:GQ:PL:SB 1/2:2,15,14,0:31:99:2406,645,532,697,0,574,1881,654,701,1805:2,0,13,16 20 10009876 . G . . END=10009878 GT:DP:GQ:MIN_DP:PL 0/0:52:99:51:0,114,1710 20 10009879 . A G, 2259.06 . AS_RAW_BaseQRankSum=|1.5,1|NaN;AS_RAW_MQ=1682.00|133379.00|0.00;AS_RAW_MQRankSum=|1.6,1|NaN;AS_RAW_ReadPosRankSum=|1.1,1|NaN;AS_SB_TABLE=2,0|18,33|0,0;BaseQRankSum=1.534;DP=53;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=1.681;RAW_MQandDP=135061,53;ReadPosRankSum=1.113 GT:AD:DP:GQ:PL:SB 1/1:2,51,0:53:99:2273,150,0,2276,154,2279:2,0,18,33 20 10009880 . G . . END=10009882 GT:DP:GQ:MIN_DP:PL 0/0:49:99:48:0,120,1800 @@ -339,7 +339,7 @@ 20 10011076 . G . . END=10011308 GT:DP:GQ:MIN_DP:PL 0/0:74:99:52:0,120,1800 20 10011309 . T C, 2707.06 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|277200.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|30,47|0,0;DP=80;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=288000,80 GT:AD:DP:GQ:PL:SB 1/1:0,77,0:77:99:2721,231,0,2721,231,2721:0,0,30,47 20 10011310 . G . . END=10011516 GT:DP:GQ:MIN_DP:PL 0/0:80:99:70:0,120,1800 -20 10011517 . GAA G,GA,GAAA, 520.60 . AS_RAW_BaseQRankSum=|-0.9,1|0.9,1|0.2,1|NaN;AS_RAW_MQ=133200.00|7200.00|104700.00|21600.00|0.00;AS_RAW_MQRankSum=|0.0,1|2.0,1|0.0,1|NaN;AS_RAW_ReadPosRankSum=|0.7,1|0.6,1|-1.0,1|NaN;AS_SB_TABLE=23,14|0,2|15,13|4,2|0,0;BaseQRankSum=0.690;DP=99;ExcessHet=3.0103;MLEAC=0,1,0,0;MLEAF=0.00,0.500,0.00,0.00;MQRankSum=1.797;RAW_MQandDP=355310,99;ReadPosRankSum=0.315 GT:AD:DP:GQ:PL:SB 0/2:37,2,28,6,0:73:99:528,611,2117,0,1040,874,605,1499,722,1650,667,1699,965,1470,1638:23,14,19,17 +20 10011517 . GAA G,GA,GAAA, 520.60 . AS_RAW_BaseQRankSum=|-0.9,1|0.9,1|0.2,1|NaN;AS_RAW_MQ=133200.00|7200.00|104700.00|21600.00|0.00;AS_RAW_MQRankSum=|0.0,1|2.0,1|0.0,1|NaN;AS_RAW_ReadPosRankSum=|0.7,1|0.6,1|-0.9,1|NaN;AS_SB_TABLE=23,14|0,2|15,13|4,2|0,0;BaseQRankSum=0.690;DP=99;ExcessHet=3.0103;MLEAC=0,1,0,0;MLEAF=0.00,0.500,0.00,0.00;MQRankSum=1.797;RAW_MQandDP=355310,99;ReadPosRankSum=0.337 GT:AD:DP:GQ:PL:SB 0/2:37,2,28,6,0:73:99:528,611,2117,0,1040,874,605,1499,722,1650,667,1699,965,1470,1638:23,14,19,17 20 10011520 . A . . END=10011665 GT:DP:GQ:MIN_DP:PL 0/0:68:99:62:0,120,1800 20 10011666 . C T, 2976.06 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|254523.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|43,30|0,0;DP=74;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=258123,74 GT:AD:DP:GQ:PL:SB 1/1:0,73,0:73:99:2990,220,0,2990,220,2990:0,0,43,30 20 10011667 . A . . END=10011938 GT:DP:GQ:MIN_DP:PL 0/0:87:99:64:0,111,1665 @@ -497,11 +497,11 @@ 20 10012622 . G . . END=10012624 GT:DP:GQ:MIN_DP:PL 0/0:19:54:19:0,54,810 20 10012625 . C . . END=10012625 GT:DP:GQ:MIN_DP:PL 0/0:20:57:20:0,57,855 20 10012626 . C . . END=10012630 GT:DP:GQ:MIN_DP:PL 0/0:21:60:21:0,60,900 -20 10012631 . C CG, 514.60 . AS_RAW_BaseQRankSum=|-1.1,1|NaN;AS_RAW_MQ=23282.00|25783.00|0.00;AS_RAW_MQRankSum=|-1.7,1|NaN;AS_RAW_ReadPosRankSum=|-1.9,1|NaN;AS_SB_TABLE=8,0|9,4|0,0;BaseQRankSum=-1.030;DP=21;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.670;RAW_MQandDP=49065,21;ReadPosRankSum=-1.813 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:8,13,0:21:99:0|1:10012631_C_CG:522,0,297,546,336,882:10012631:8,0,9,4 +20 10012631 . C CG, 514.60 . AS_RAW_BaseQRankSum=|-1.1,1|NaN;AS_RAW_MQ=23282.00|25783.00|0.00;AS_RAW_MQRankSum=|-1.7,1|NaN;AS_RAW_ReadPosRankSum=|-1.8,1|NaN;AS_SB_TABLE=8,0|9,4|0,0;BaseQRankSum=-1.030;DP=21;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.670;RAW_MQandDP=49065,21;ReadPosRankSum=-1.777 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:8,13,0:21:99:0|1:10012631_C_CG:522,0,297,546,336,882:10012631:8,0,9,4 20 10012632 . G . . END=10012632 GT:DP:GQ:MIN_DP:PL 0/0:21:54:21:0,54,810 20 10012633 . C . . END=10012633 GT:DP:GQ:MIN_DP:PL 0/0:20:51:20:0,51,765 20 10012634 . C . . END=10012635 GT:DP:GQ:MIN_DP:PL 0/0:22:54:22:0,54,810 -20 10012636 . G C, 548.64 . AS_RAW_BaseQRankSum=|2.7,1|NaN;AS_RAW_MQ=23282.00|29383.00|0.00;AS_RAW_MQRankSum=|-1.6,1|NaN;AS_RAW_ReadPosRankSum=|-2.0,1|NaN;AS_SB_TABLE=8,0|10,4|0,0;BaseQRankSum=2.711;DP=22;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.513;RAW_MQandDP=52665,22;ReadPosRankSum=-1.915 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:8,14,0:22:99:0|1:10012631_C_CG:556,0,294,580,336,916:10012631:8,0,10,4 +20 10012636 . G C, 548.64 . AS_RAW_BaseQRankSum=|2.7,1|NaN;AS_RAW_MQ=23282.00|29383.00|0.00;AS_RAW_MQRankSum=|-1.6,1|NaN;AS_RAW_ReadPosRankSum=|-1.8,1|NaN;AS_SB_TABLE=8,0|10,4|0,0;BaseQRankSum=2.711;DP=22;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.513;RAW_MQandDP=52665,22;ReadPosRankSum=-1.777 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:8,14,0:22:99:0|1:10012631_C_CG:556,0,294,580,336,916:10012631:8,0,10,4 20 10012637 . A . . END=10012639 GT:DP:GQ:MIN_DP:PL 0/0:20:54:20:0,54,810 20 10012640 . C . . END=10012640 GT:DP:GQ:MIN_DP:PL 0/0:22:57:22:0,57,855 20 10012641 . T . . END=10012662 GT:DP:GQ:MIN_DP:PL 0/0:24:60:23:0,60,895 @@ -576,7 +576,7 @@ 20 10013575 . T . . END=10014589 GT:DP:GQ:MIN_DP:PL 0/0:72:99:43:0,101,1658 20 10014590 . A . . END=10014590 GT:DP:GQ:MIN_DP:PL 0/0:44:93:44:0,93,1625 20 10014591 . T . . END=10014989 GT:DP:GQ:MIN_DP:PL 0/0:72:99:42:0,116,1732 -20 10014990 . C CAT, 1265.60 . AS_RAW_BaseQRankSum=|1.7,1|NaN;AS_RAW_MQ=134569.00|152100.00|0.00;AS_RAW_MQRankSum=|3.2,1|NaN;AS_RAW_ReadPosRankSum=|-0.5,1|NaN;AS_SB_TABLE=28,10|26,13|0,0;BaseQRankSum=1.756;DP=89;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=3.260;RAW_MQandDP=329869,89;ReadPosRankSum=-0.437 GT:AD:DP:GQ:PL:SB 0/1:38,39,0:77:99:1273,0,1250,1388,1367,2755:28,10,26,13 +20 10014990 . C CAT, 1265.60 . AS_RAW_BaseQRankSum=|1.9,1|NaN;AS_RAW_MQ=134569.00|152100.00|0.00;AS_RAW_MQRankSum=|3.2,1|NaN;AS_RAW_ReadPosRankSum=|-0.4,1|NaN;AS_SB_TABLE=28,10|26,13|0,0;BaseQRankSum=1.930;DP=89;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=3.260;RAW_MQandDP=329869,89;ReadPosRankSum=-0.311 GT:AD:DP:GQ:PL:SB 0/1:38,39,0:77:99:1273,0,1250,1388,1367,2755:28,10,26,13 20 10014991 . A . . END=10015385 GT:DP:GQ:MIN_DP:PL 0/0:73:99:41:0,102,1530 20 10015386 . G . . END=10015388 GT:DP:GQ:MIN_DP:PL 0/0:39:90:39:0,90,1350 20 10015389 . A . . END=10015390 GT:DP:GQ:MIN_DP:PL 0/0:38:81:38:0,81,1215 @@ -711,7 +711,7 @@ 20 10024297 . T . . END=10024297 GT:DP:GQ:MIN_DP:PL 0/0:68:65:68:0,65,2188 20 10024298 . T . . END=10024298 GT:DP:GQ:MIN_DP:PL 0/0:66:59:66:0,59,2080 20 10024299 . C . . END=10024299 GT:DP:GQ:MIN_DP:PL 0/0:62:0:62:0,0,1480 -20 10024300 . CTT C,CT,CTTTT, 126.96 . AS_RAW_BaseQRankSum=|1.9,1|1.3,1|2.3,1|NaN;AS_RAW_MQ=8041.00|6699.00|8882.00|20523.00|0.00;AS_RAW_MQRankSum=|-1.2,1|-0.4,1|-0.1,1|NaN;AS_RAW_ReadPosRankSum=|-1.2,1|-2.2,1|-0.5,1|NaN;AS_SB_TABLE=1,2|3,2|2,2|6,2|0,0;BaseQRankSum=2.384;DP=56;ExcessHet=3.0103;MLEAC=0,1,1,0;MLEAF=0.00,0.500,0.500,0.00;MQRankSum=-0.597;RAW_MQandDP=153536,56;ReadPosRankSum=-1.290 GT:AD:DP:GQ:PL:SB 2/3:3,5,4,8,0:20:9:144,72,401,88,202,222,47,9,0,215,183,284,255,136,369:1,2,11,6 +20 10024300 . CTT C,CT,CTTTT, 126.96 . AS_RAW_BaseQRankSum=|1.9,1|1.3,1|2.2,1|NaN;AS_RAW_MQ=8041.00|6699.00|8882.00|20523.00|0.00;AS_RAW_MQRankSum=|-1.2,1|-0.4,1|-0.1,1|NaN;AS_RAW_ReadPosRankSum=|-1.2,1|-2.2,1|-0.5,1|NaN;AS_SB_TABLE=1,2|3,2|2,2|6,2|0,0;BaseQRankSum=2.355;DP=56;ExcessHet=3.0103;MLEAC=0,1,1,0;MLEAF=0.00,0.500,0.500,0.00;MQRankSum=-0.597;RAW_MQandDP=153536,56;ReadPosRankSum=-1.290 GT:AD:DP:GQ:PL:SB 2/3:3,5,4,8,0:20:9:144,72,401,88,202,222,47,9,0,215,183,284,255,136,369:1,2,11,6 20 10024303 . T . . END=10024303 GT:DP:GQ:MIN_DP:PL 0/0:67:57:67:0,57,855 20 10024304 . T . . END=10024307 GT:DP:GQ:MIN_DP:PL 0/0:69:63:68:0,63,945 20 10024308 . T . . END=10024310 GT:DP:GQ:MIN_DP:PL 0/0:70:78:70:0,78,1170 @@ -730,19 +730,19 @@ 20 10026358 . A . . END=10026793 GT:DP:GQ:MIN_DP:PL 0/0:72:99:41:0,102,1530 20 10026794 . C T, 1105.64 . AS_RAW_BaseQRankSum=|2.8,1|NaN;AS_RAW_MQ=68400.00|116041.00|0.00;AS_RAW_MQRankSum=|-0.8,1|NaN;AS_RAW_ReadPosRankSum=|-0.6,1|NaN;AS_SB_TABLE=7,12|15,18|0,0;BaseQRankSum=2.828;DP=56;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.719;RAW_MQandDP=198841,56;ReadPosRankSum=-0.533 GT:AD:DP:GQ:PL:SB 0/1:19,33,0:52:99:1113,0,529,1170,627,1798:7,12,15,18 20 10026795 . G . . END=10027233 GT:DP:GQ:MIN_DP:PL 0/0:70:99:52:0,115,1800 -20 10027234 . A ATTAG, 1350.60 . AS_RAW_BaseQRankSum=|-0.5,1|NaN;AS_RAW_MQ=119641.00|106210.00|0.00;AS_RAW_MQRankSum=|-0.9,1|NaN;AS_RAW_ReadPosRankSum=|-1.0,1|NaN;AS_SB_TABLE=18,16|15,20|0,0;BaseQRankSum=-0.406;DP=75;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.845;RAW_MQandDP=247451,75;ReadPosRankSum=-0.979 GT:AD:DP:GQ:PL:SB 0/1:34,35,0:69:99:1358,0,1321,1461,1426,2887:18,16,15,20 +20 10027234 . A ATTAG, 1350.60 . AS_RAW_BaseQRankSum=|-0.5,1|NaN;AS_RAW_MQ=119641.00|106210.00|0.00;AS_RAW_MQRankSum=|-0.9,1|NaN;AS_RAW_ReadPosRankSum=|-0.6,1|NaN;AS_SB_TABLE=18,16|15,20|0,0;BaseQRankSum=-0.406;DP=75;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.845;RAW_MQandDP=247451,75;ReadPosRankSum=-0.510 GT:AD:DP:GQ:PL:SB 0/1:34,35,0:69:99:1358,0,1321,1461,1426,2887:18,16,15,20 20 10027235 . T . . END=10027867 GT:DP:GQ:MIN_DP:PL 0/0:78:99:56:0,120,1800 -20 10027868 . A G, 1760.64 . AS_RAW_BaseQRankSum=|-5.8,1|NaN;AS_RAW_MQ=155641.00|162841.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|1.8,1|NaN;AS_SB_TABLE=19,25|27,19|0,0;BaseQRankSum=-5.798;DP=91;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.047;RAW_MQandDP=322082,91;ReadPosRankSum=1.872 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:44,46,0:90:99:0|1:10027868_A_G:1768,0,1671,1901,1810,3710:10027868:19,25,27,19 +20 10027868 . A G, 1760.64 . AS_RAW_BaseQRankSum=|-5.8,1|NaN;AS_RAW_MQ=155641.00|162841.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|1.8,1|NaN;AS_SB_TABLE=19,25|27,19|0,0;BaseQRankSum=-5.793;DP=91;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.047;RAW_MQandDP=322082,91;ReadPosRankSum=1.872 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:44,46,0:90:99:0|1:10027868_A_G:1768,0,1671,1901,1810,3710:10027868:19,25,27,19 20 10027869 . A . . END=10027871 GT:DP:GQ:MIN_DP:PL 0/0:86:99:85:0,120,1800 20 10027872 . A G, 1745.64 . AS_RAW_BaseQRankSum=|-5.5,1|NaN;AS_RAW_MQ=148441.00|159241.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|1.0,1|NaN;AS_SB_TABLE=17,25|26,19|0,0;BaseQRankSum=-5.491;DP=88;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.065;RAW_MQandDP=311282,88;ReadPosRankSum=1.053 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:42,45,0:87:99:0|1:10027868_A_G:1753,0,1606,1879,1742,3621:10027868:17,25,26,19 20 10027873 . G . . END=10028866 GT:DP:GQ:MIN_DP:PL 0/0:80:99:55:0,120,1800 -20 10028867 . A ATG, 1134.60 . AS_RAW_BaseQRankSum=|-0.9,1|NaN;AS_RAW_MQ=115200.00|150800.00|0.00;AS_RAW_MQRankSum=|2.7,1|NaN;AS_RAW_ReadPosRankSum=|0.3,1|NaN;AS_SB_TABLE=11,21|18,21|0,0;BaseQRankSum=-0.874;DP=93;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=2.711;RAW_MQandDP=342441,93;ReadPosRankSum=0.364 GT:AD:DP:GQ:PL:SB 0/1:32,39,0:71:99:1142,0,918,1240,1035,2275:11,21,18,21 +20 10028867 . A ATG, 1134.60 . AS_RAW_BaseQRankSum=|-0.9,1|NaN;AS_RAW_MQ=115200.00|150800.00|0.00;AS_RAW_MQRankSum=|2.7,1|NaN;AS_RAW_ReadPosRankSum=|0.6,1|NaN;AS_SB_TABLE=11,21|18,21|0,0;BaseQRankSum=-0.874;DP=93;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=2.711;RAW_MQandDP=342441,93;ReadPosRankSum=0.630 GT:AD:DP:GQ:PL:SB 0/1:32,39,0:71:99:1142,0,918,1240,1035,2275:11,21,18,21 20 10028868 . T . . END=10030187 GT:DP:GQ:MIN_DP:PL 0/0:80:99:60:0,120,1800 20 10030188 . T A, 1393.64 . AS_RAW_BaseQRankSum=|0.7,1|NaN;AS_RAW_MQ=151200.00|137641.00|0.00;AS_RAW_MQRankSum=|-1.1,1|NaN;AS_RAW_ReadPosRankSum=|-0.6,1|NaN;AS_SB_TABLE=24,18|15,24|0,0;BaseQRankSum=0.711;DP=82;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.013;RAW_MQandDP=290210,82;ReadPosRankSum=-0.553 GT:AD:DP:GQ:PL:SB 0/1:42,39,0:81:99:1401,0,1524,1527,1641,3168:24,18,15,24 20 10030189 . G . . END=10030566 GT:DP:GQ:MIN_DP:PL 0/0:71:99:41:0,103,1575 20 10030567 . G . . END=10030567 GT:DP:GQ:MIN_DP:PL 0/0:41:90:41:0,90,1511 20 10030568 . C . . END=10031253 GT:DP:GQ:MIN_DP:PL 0/0:70:99:42:0,114,1710 -20 10031254 . A AT, 1493.60 . AS_RAW_BaseQRankSum=|-0.1,1|NaN;AS_RAW_MQ=136800.00|168269.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|0.4,1|NaN;AS_SB_TABLE=27,11|25,22|0,0;BaseQRankSum=-0.091;DP=90;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.017;RAW_MQandDP=323069,90;ReadPosRankSum=0.495 GT:AD:DP:GQ:PL:SB 0/1:38,47,0:85:99:1501,0,1159,1615,1300,2916:27,11,25,22 +20 10031254 . A AT, 1493.60 . AS_RAW_BaseQRankSum=|-0.1,1|NaN;AS_RAW_MQ=136800.00|168269.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|0.6,1|NaN;AS_SB_TABLE=27,11|25,22|0,0;BaseQRankSum=-0.091;DP=90;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.017;RAW_MQandDP=323069,90;ReadPosRankSum=0.663 GT:AD:DP:GQ:PL:SB 0/1:38,47,0:85:99:1501,0,1159,1615,1300,2916:27,11,25,22 20 10031255 . T . . END=10031341 GT:DP:GQ:MIN_DP:PL 0/0:95:99:86:0,120,1800 20 10031342 . G A, 1855.64 . AS_RAW_BaseQRankSum=|1.8,1|NaN;AS_RAW_MQ=147600.00|184441.00|0.00;AS_RAW_MQRankSum=|-0.9,1|NaN;AS_RAW_ReadPosRankSum=|-0.1,1|NaN;AS_SB_TABLE=22,19|31,21|0,0;BaseQRankSum=1.833;DP=93;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.866;RAW_MQandDP=332041,93;ReadPosRankSum=-0.012 GT:AD:DP:GQ:PL:SB 0/1:41,52,0:93:99:1863,0,1375,1986,1531,3517:22,19,31,21 20 10031343 . A . . END=10031797 GT:DP:GQ:MIN_DP:PL 0/0:91:99:66:0,120,1800 @@ -756,7 +756,7 @@ 20 10032414 . T . . END=10032881 GT:DP:GQ:MIN_DP:PL 0/0:70:99:55:0,120,1800 20 10032882 . A T, 1223.64 . AS_RAW_BaseQRankSum=|-3.7,1|NaN;AS_RAW_MQ=140400.00|126841.00|0.00;AS_RAW_MQRankSum=|-1.1,1|NaN;AS_RAW_ReadPosRankSum=|0.6,1|NaN;AS_SB_TABLE=28,11|22,14|0,0;BaseQRankSum=-3.697;DP=76;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.014;RAW_MQandDP=270841,76;ReadPosRankSum=0.626 GT:AD:DP:GQ:PL:SB 0/1:39,36,0:75:99:1231,0,1406,1348,1514,2862:28,11,22,14 20 10032883 . A . . END=10032971 GT:DP:GQ:MIN_DP:PL 0/0:67:99:61:0,120,1800 -20 10032972 . C CAT, 1152.60 . AS_RAW_BaseQRankSum=|-0.4,1|NaN;AS_RAW_MQ=118800.00|105241.00|0.00;AS_RAW_MQRankSum=|-1.1,1|NaN;AS_RAW_ReadPosRankSum=|-1.3,1|NaN;AS_SB_TABLE=17,16|11,19|0,0;BaseQRankSum=-0.354;DP=67;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.017;RAW_MQandDP=238441,67;ReadPosRankSum=-1.232 GT:AD:DP:GQ:PL:SB 0/1:33,30,0:63:99:1160,0,1296,1260,1386,2646:17,16,11,19 +20 10032972 . C CAT, 1152.60 . AS_RAW_BaseQRankSum=|-0.4,1|NaN;AS_RAW_MQ=118800.00|105241.00|0.00;AS_RAW_MQRankSum=|-1.1,1|NaN;AS_RAW_ReadPosRankSum=|-0.8,1|NaN;AS_SB_TABLE=17,16|11,19|0,0;BaseQRankSum=-0.354;DP=67;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.017;RAW_MQandDP=238441,67;ReadPosRankSum=-0.723 GT:AD:DP:GQ:PL:SB 0/1:33,30,0:63:99:1160,0,1296,1260,1386,2646:17,16,11,19 20 10032973 . T . . END=10033636 GT:DP:GQ:MIN_DP:PL 0/0:78:99:50:0,120,1800 20 10033637 . C . . END=10033637 GT:DP:GQ:MIN_DP:PL 0/0:58:97:58:0,97,2210 20 10033638 . C . . END=10034305 GT:DP:GQ:MIN_DP:PL 0/0:85:99:53:0,120,1800 @@ -774,7 +774,7 @@ 20 10036158 . T . . END=10036160 GT:DP:GQ:MIN_DP:PL 0/0:42:99:40:0,117,1755 20 10036161 . T . . END=10036161 GT:DP:GQ:MIN_DP:PL 0/0:42:82:42:0,82,1514 20 10036162 . G . . END=10036929 GT:DP:GQ:MIN_DP:PL 0/0:76:99:43:0,113,1513 -20 10036930 . CGATAGCCCTAGCCCTAGATA C, 1070.60 . AS_RAW_BaseQRankSum=|0.2,1|NaN;AS_RAW_MQ=140400.00|58242.00|0.00;AS_RAW_MQRankSum=|-4.1,1|NaN;AS_RAW_ReadPosRankSum=|0.4,1|NaN;AS_SB_TABLE=11,28|15,14|0,0;BaseQRankSum=0.200;DP=98;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.048;RAW_MQandDP=290616,98;ReadPosRankSum=0.460 GT:AD:DP:GQ:PL:SB 0/1:39,29,0:68:99:1078,0,1500,1196,1598,2794:11,28,15,14 +20 10036930 . CGATAGCCCTAGCCCTAGATA C, 1070.60 . AS_RAW_BaseQRankSum=|0.7,1|NaN;AS_RAW_MQ=140400.00|58242.00|0.00;AS_RAW_MQRankSum=|-4.1,1|NaN;AS_RAW_ReadPosRankSum=|0.4,1|NaN;AS_SB_TABLE=11,28|15,14|0,0;BaseQRankSum=0.720;DP=98;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.048;RAW_MQandDP=290616,98;ReadPosRankSum=0.460 GT:AD:DP:GQ:PL:SB 0/1:39,29,0:68:99:1078,0,1500,1196,1598,2794:11,28,15,14 20 10036951 . G . . END=10036956 GT:DP:GQ:MIN_DP:PL 0/0:74:99:70:0,120,1800 20 10036957 . C . . END=10036957 GT:DP:GQ:MIN_DP:PL 0/0:70:37:70:0,37,2472 20 10036958 . C . . END=10036958 GT:DP:GQ:MIN_DP:PL 0/0:70:40:70:0,40,2490 @@ -815,13 +815,13 @@ 20 10040773 . T . . END=10040811 GT:DP:GQ:MIN_DP:PL 0/0:77:99:75:0,120,1800 20 10040812 . AT A, 2631.03 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|174499.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|36,35|0,0;DP=83;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=217699,83 GT:AD:DP:GQ:PL:SB 1/1:0,71,0:71:99:2645,214,0,2645,214,2645:0,0,36,35 20 10040814 . T . . END=10040820 GT:DP:GQ:MIN_DP:PL 0/0:77:99:75:0,120,1800 -20 10040821 . T A, 1166.64 . AS_RAW_BaseQRankSum=|0.1,1|NaN;AS_RAW_MQ=98015.00|98084.00|0.00;AS_RAW_MQRankSum=|-0.2,1|NaN;AS_RAW_ReadPosRankSum=|-1.4,1|NaN;AS_SB_TABLE=20,18|21,18|0,0;BaseQRankSum=0.152;DP=83;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.175;RAW_MQandDP=217699,83;ReadPosRankSum=-1.350 GT:AD:DP:GQ:PL:SB 0/1:38,39,0:77:99:1174,0,1102,1288,1219,2507:20,18,21,18 +20 10040821 . T A, 1166.64 . AS_RAW_BaseQRankSum=|0.1,1|NaN;AS_RAW_MQ=98015.00|98084.00|0.00;AS_RAW_MQRankSum=|-0.2,1|NaN;AS_RAW_ReadPosRankSum=|-1.4,1|NaN;AS_SB_TABLE=20,18|21,18|0,0;BaseQRankSum=0.152;DP=83;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.175;RAW_MQandDP=217699,83;ReadPosRankSum=-1.315 GT:AD:DP:GQ:PL:SB 0/1:38,39,0:77:99:1174,0,1102,1288,1219,2507:20,18,21,18 20 10040822 . A . . END=10041303 GT:DP:GQ:MIN_DP:PL 0/0:71:99:54:0,119,1800 20 10041304 . C T, 2780.06 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|239810.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|34,34|0,0;DP=68;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=239810,68 GT:AD:DP:GQ:PL:SB 1/1:0,68,0:68:99:2794,204,0,2794,204,2794:0,0,34,34 20 10041305 . G . . END=10041697 GT:DP:GQ:MIN_DP:PL 0/0:62:99:48:0,120,1800 -20 10041698 . C CAT, 9.61 . AS_RAW_BaseQRankSum=|1.5,1|NaN;AS_RAW_MQ=156587.00|23121.00|0.00;AS_RAW_MQRankSum=|0.1,1|NaN;AS_RAW_ReadPosRankSum=|0.5,1|NaN;AS_SB_TABLE=21,29|2,5|0,0;BaseQRankSum=1.595;DP=80;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.194;RAW_MQandDP=275031,80;ReadPosRankSum=0.579 GT:AD:DP:GQ:PL:SB 0/1:50,7,0:57:17:17,0,1423,167,1444,1611:21,29,2,5 +20 10041698 . C CAT, 9.61 . AS_RAW_BaseQRankSum=|1.8,1|NaN;AS_RAW_MQ=156587.00|23121.00|0.00;AS_RAW_MQRankSum=|0.1,1|NaN;AS_RAW_ReadPosRankSum=|-0.2,1|NaN;AS_SB_TABLE=21,29|2,5|0,0;BaseQRankSum=1.887;DP=80;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.194;RAW_MQandDP=275031,80;ReadPosRankSum=-0.164 GT:AD:DP:GQ:PL:SB 0/1:50,7,0:57:17:17,0,1423,167,1444,1611:21,29,2,5 20 10041699 . A . . END=10041700 GT:DP:GQ:MIN_DP:PL 0/0:79:99:78:0,120,1800 -20 10041701 . A ATG,ATATG, 1431.60 . AS_RAW_BaseQRankSum=|NaN|0.8,1|NaN;AS_RAW_MQ=23962.00|0.00|149018.00|0.00;AS_RAW_MQRankSum=|NaN|0.3,1|NaN;AS_RAW_ReadPosRankSum=|NaN|-0.3,1|NaN;AS_SB_TABLE=2,6|0,0|21,27|0,0;BaseQRankSum=0.848;DP=80;ExcessHet=3.0103;MLEAC=0,1,0;MLEAF=0.00,0.500,0.00;MQRankSum=0.340;RAW_MQandDP=277790,80;ReadPosRankSum=-0.223 GT:AD:DP:GQ:PL:SB 0/2:8,0,48,0:56:58:1439,1580,2725,0,261,58,1573,2315,265,2200:2,6,21,27 +20 10041701 . A ATG,ATATG, 1431.60 . AS_RAW_BaseQRankSum=|NaN|0.8,1|NaN;AS_RAW_MQ=23962.00|0.00|149018.00|0.00;AS_RAW_MQRankSum=|NaN|0.3,1|NaN;AS_RAW_ReadPosRankSum=|NaN|-0.1,1|NaN;AS_SB_TABLE=2,6|0,0|21,27|0,0;BaseQRankSum=0.848;DP=80;ExcessHet=3.0103;MLEAC=0,1,0;MLEAF=0.00,0.500,0.00;MQRankSum=0.340;RAW_MQandDP=277790,80;ReadPosRankSum=-0.023 GT:AD:DP:GQ:PL:SB 0/2:8,0,48,0:56:58:1439,1580,2725,0,261,58,1573,2315,265,2200:2,6,21,27 20 10041702 . T . . END=10042318 GT:DP:GQ:MIN_DP:PL 0/0:64:99:49:0,117,1800 20 10042319 . C T, 2673.06 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|229851.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|38,28|0,0;DP=69;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=240651,69 GT:AD:DP:GQ:PL:SB 1/1:0,66,0:66:99:2687,199,0,2687,199,2687:0,0,38,28 20 10042320 . C . . END=10042760 GT:DP:GQ:MIN_DP:PL 0/0:74:99:60:0,120,1800 @@ -875,7 +875,7 @@ 20 10052689 . A . . END=10058021 GT:DP:GQ:MIN_DP:PL 0/0:74:99:36:0,99,1485 20 10058022 . T C, 996.64 . AS_RAW_BaseQRankSum=|-2.4,1|NaN;AS_RAW_MQ=125138.00|112441.00|0.00;AS_RAW_MQRankSum=|0.4,1|NaN;AS_RAW_ReadPosRankSum=|0.0,1|NaN;AS_SB_TABLE=16,20|13,19|0,0;BaseQRankSum=-2.346;DP=72;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.466;RAW_MQandDP=251979,72;ReadPosRankSum=0.018 GT:AD:DP:GQ:PL:SB 0/1:36,32,0:68:99:1004,0,1261,1112,1357,2469:16,20,13,19 20 10058023 . A . . END=10062934 GT:DP:GQ:MIN_DP:PL 0/0:76:99:46:0,105,1575 -20 10062935 . CAAA C,CA,CAA,CAAAA, 119.60 . AS_RAW_BaseQRankSum=|0.3,1|-0.2,1|1.4,1|1.3,1|NaN;AS_RAW_MQ=18000.00|4441.00|8041.00|12169.00|24907.00|0.00;AS_RAW_MQRankSum=|-1.1,1|-0.9,1|-0.8,1|-1.6,1|NaN;AS_RAW_ReadPosRankSum=|-1.1,1|-0.5,1|-0.3,1|-1.2,1|NaN;AS_SB_TABLE=2,3|1,1|1,2|3,1|4,6|0,0;BaseQRankSum=1.234;DP=90;ExcessHet=3.0103;MLEAC=0,0,0,1,0;MLEAF=0.00,0.00,0.00,0.500,0.00;MQRankSum=-1.515;RAW_MQandDP=266450,90;ReadPosRankSum=-0.973 GT:AD:DP:GQ:PL:SB 0/4:5,2,3,4,10,0:24:6:127,208,1805,130,1135,1006,104,613,541,490,0,148,50,6,109,237,973,853,595,166,879:2,3,9,10 +20 10062935 . CAAA C,CA,CAA,CAAAA, 119.60 . AS_RAW_BaseQRankSum=|0.3,1|-0.2,1|1.4,1|1.2,1|NaN;AS_RAW_MQ=18000.00|4441.00|8041.00|12169.00|24907.00|0.00;AS_RAW_MQRankSum=|-1.1,1|-0.9,1|-0.8,1|-1.6,1|NaN;AS_RAW_ReadPosRankSum=|-1.1,1|-0.5,1|-0.3,1|-1.2,1|NaN;AS_SB_TABLE=2,3|1,1|1,2|3,1|4,6|0,0;BaseQRankSum=1.237;DP=90;ExcessHet=3.0103;MLEAC=0,0,0,1,0;MLEAF=0.00,0.00,0.00,0.500,0.00;MQRankSum=-1.515;RAW_MQandDP=266450,90;ReadPosRankSum=-0.974 GT:AD:DP:GQ:PL:SB 0/4:5,2,3,4,10,0:24:6:127,208,1805,130,1135,1006,104,613,541,490,0,148,50,6,109,237,973,853,595,166,879:2,3,9,10 20 10062939 . A . . END=10062955 GT:DP:GQ:MIN_DP:PL 0/0:82:99:74:0,120,1800 20 10062956 . T . . END=10062956 GT:DP:GQ:MIN_DP:PL 0/0:69:80:69:0,80,2241 20 10062957 . C . . END=10065775 GT:DP:GQ:MIN_DP:PL 0/0:70:99:42:0,105,1575 @@ -889,7 +889,7 @@ 20 10065803 . G . . END=10065803 GT:DP:GQ:MIN_DP:PL 0/0:59:81:59:0,81,2051 20 10065804 . C . . END=10067046 GT:DP:GQ:MIN_DP:PL 0/0:72:99:48:0,102,1530 20 10067047 . A . . END=10067048 GT:DP:GQ:MIN_DP:PL 0/0:51:96:50:0,96,1440 -20 10067049 . TAAAAAAAAA T,TA,TAA, 639.02 . AS_RAW_BaseQRankSum=|0.0,1|1.0,1|-0.5,1|NaN;AS_RAW_MQ=4441.00|8882.00|14164.00|13087.00|0.00;AS_RAW_MQRankSum=|0.0,1|-0.2,1|-0.7,1|NaN;AS_RAW_ReadPosRankSum=|-1.3,1|-0.7,1|-1.7,1|NaN;AS_SB_TABLE=1,1|3,1|5,2|4,5|0,0;BaseQRankSum=0.177;DP=73;ExcessHet=3.0103;MLEAC=0,1,1,0;MLEAF=0.00,0.500,0.500,0.00;MQRankSum=-0.342;RAW_MQandDP=218656,73;ReadPosRankSum=-1.322 GT:AD:DP:GQ:PL:SB 2/3:2,4,7,9,0:22:99:656,367,923,167,381,339,137,101,0,106,446,592,395,171,628:1,1,12,8 +20 10067049 . TAAAAAAAAA T,TA,TAA, 639.02 . AS_RAW_BaseQRankSum=|0.0,1|0.4,1|-0.7,1|NaN;AS_RAW_MQ=4441.00|8882.00|14164.00|13087.00|0.00;AS_RAW_MQRankSum=|0.0,1|-0.2,1|-0.7,1|NaN;AS_RAW_ReadPosRankSum=|-1.3,1|-0.7,1|-1.7,1|NaN;AS_SB_TABLE=1,1|3,1|5,2|4,5|0,0;BaseQRankSum=-0.086;DP=73;ExcessHet=3.0103;MLEAC=0,1,1,0;MLEAF=0.00,0.500,0.500,0.00;MQRankSum=-0.342;RAW_MQandDP=218656,73;ReadPosRankSum=-1.322 GT:AD:DP:GQ:PL:SB 2/3:2,4,7,9,0:22:99:656,367,923,167,381,339,137,101,0,106,446,592,395,171,628:1,1,12,8 20 10067059 . A . . END=10067067 GT:DP:GQ:MIN_DP:PL 0/0:57:99:50:0,99,1485 20 10067068 . A . . END=10067070 GT:DP:GQ:MIN_DP:PL 0/0:44:96:44:0,96,1440 20 10067071 . A . . END=10067089 GT:DP:GQ:MIN_DP:PL 0/0:48:99:46:0,102,1530 @@ -1003,11 +1003,11 @@ 20 10076340 . A . . END=10076398 GT:DP:GQ:MIN_DP:PL 0/0:88:99:71:0,120,1800 20 10076399 . G A, 1828.64 . AS_RAW_BaseQRankSum=|4.1,1|NaN;AS_RAW_MQ=158400.00|180000.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-1.1,1|NaN;AS_SB_TABLE=22,22|22,28|0,0;BaseQRankSum=4.154;DP=95;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=342000,95;ReadPosRankSum=-1.058 GT:AD:DP:GQ:PL:SB 0/1:44,50,0:94:99:1836,0,1544,1969,1694,3663:22,22,22,28 20 10076400 . G . . END=10076988 GT:DP:GQ:MIN_DP:PL 0/0:73:99:51:0,120,1800 -20 10076989 . CAA C,CA,CAAA, 242.02 . AS_RAW_BaseQRankSum=|-0.6,1|-1.0,1|0.1,1|NaN;AS_RAW_MQ=25200.00|15241.00|46800.00|22441.00|0.00;AS_RAW_MQRankSum=|-0.9,1|0.0,1|-0.7,1|NaN;AS_RAW_ReadPosRankSum=|-1.7,1|-0.8,1|-0.4,1|NaN;AS_SB_TABLE=4,3|2,3|6,7|5,2|0,0;BaseQRankSum=-0.673;DP=83;ExcessHet=3.0103;MLEAC=0,1,1,0;MLEAF=0.00,0.500,0.500,0.00;MQRankSum=-0.706;RAW_MQandDP=279487,83;ReadPosRankSum=-1.056 GT:AD:DP:GQ:PL:SB 2/3:7,5,13,7,0:32:40:259,260,1130,40,436,371,157,266,0,379,329,700,422,328,711:4,3,13,12 +20 10076989 . CAA C,CA,CAAA, 242.02 . AS_RAW_BaseQRankSum=|-0.5,1|-1.0,1|0.3,1|NaN;AS_RAW_MQ=25200.00|15241.00|46800.00|22441.00|0.00;AS_RAW_MQRankSum=|-0.9,1|0.0,1|-0.7,1|NaN;AS_RAW_ReadPosRankSum=|-1.7,1|-0.8,1|-0.1,1|NaN;AS_SB_TABLE=4,3|2,3|6,7|5,2|0,0;BaseQRankSum=-0.600;DP=83;ExcessHet=3.0103;MLEAC=0,1,1,0;MLEAF=0.00,0.500,0.500,0.00;MQRankSum=-0.706;RAW_MQandDP=279487,83;ReadPosRankSum=-0.957 GT:AD:DP:GQ:PL:SB 2/3:7,5,13,7,0:32:40:259,260,1130,40,436,371,157,266,0,379,329,700,422,328,711:4,3,13,12 20 10076992 . A . . END=10077007 GT:DP:GQ:MIN_DP:PL 0/0:70:99:60:0,120,1800 -20 10077008 . T A, 0 . AS_RAW_BaseQRankSum=|-1.8,1|NaN;AS_RAW_MQ=171723.00|11641.00|0.00;AS_RAW_MQRankSum=|-1.4,1|NaN;AS_RAW_ReadPosRankSum=|0.8,1|NaN;AS_SB_TABLE=19,31|4,0|0,0;BaseQRankSum=-1.801;DP=69;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=-1.347;RAW_MQandDP=226328,69;ReadPosRankSum=0.806 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|0:50,4,0:54:45:0|1:10077008_T_A:0,45,2017,151,2029,2135:10077008:19,31,4,0 +20 10077008 . T A, 0 . AS_RAW_BaseQRankSum=|-1.7,1|NaN;AS_RAW_MQ=171723.00|11641.00|0.00;AS_RAW_MQRankSum=|-1.4,1|NaN;AS_RAW_ReadPosRankSum=|0.7,1|NaN;AS_SB_TABLE=19,31|4,0|0,0;BaseQRankSum=-1.698;DP=69;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=-1.347;RAW_MQandDP=226328,69;ReadPosRankSum=0.789 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|0:50,4,0:54:45:0|1:10077008_T_A:0,45,2017,151,2029,2135:10077008:19,31,4,0 20 10077009 . A . . END=10077009 GT:DP:GQ:MIN_DP:PL 0/0:53:99:53:0,120,1800 -20 10077010 . G A, 0 . AS_RAW_BaseQRankSum=|-1.8,1|NaN;AS_RAW_MQ=171723.00|11641.00|0.00;AS_RAW_MQRankSum=|-1.4,1|NaN;AS_RAW_ReadPosRankSum=|0.8,1|NaN;AS_SB_TABLE=19,31|4,0|0,0;BaseQRankSum=-1.733;DP=58;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=-1.347;RAW_MQandDP=197764,58;ReadPosRankSum=0.859 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|0:50,4,0:54:45:0|1:10077008_T_A:0,45,2017,151,2029,2134:10077008:19,31,4,0 +20 10077010 . G A, 0 . AS_RAW_BaseQRankSum=|-1.8,1|NaN;AS_RAW_MQ=171723.00|11641.00|0.00;AS_RAW_MQRankSum=|-1.4,1|NaN;AS_RAW_ReadPosRankSum=|0.9,1|NaN;AS_SB_TABLE=19,31|4,0|0,0;BaseQRankSum=-1.733;DP=58;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=-1.347;RAW_MQandDP=197764,58;ReadPosRankSum=0.943 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|0:50,4,0:54:45:0|1:10077008_T_A:0,45,2017,151,2029,2134:10077008:19,31,4,0 20 10077011 . A . . END=10077751 GT:DP:GQ:MIN_DP:PL 0/0:69:99:44:0,102,1654 20 10077752 . T C, 1366.64 . AS_RAW_BaseQRankSum=|-6.6,1|NaN;AS_RAW_MQ=122400.00|162000.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-0.4,1|NaN;AS_SB_TABLE=16,18|16,29|0,0;BaseQRankSum=-6.503;DP=83;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=298800,83;ReadPosRankSum=-0.352 GT:AD:DP:GQ:PL:SB 0/1:34,45,0:79:99:1374,0,1187,1477,1322,2799:16,18,16,29 20 10077753 . G . . END=10079475 GT:DP:GQ:MIN_DP:PL 0/0:70:99:46:0,108,1620 @@ -1054,7 +1054,7 @@ 20 10087755 . G . . END=10087803 GT:DP:GQ:MIN_DP:PL 0/0:101:99:82:0,120,1800 20 10087804 . C T, 1640.64 . AS_RAW_BaseQRankSum=|1.9,1|NaN;AS_RAW_MQ=178541.00|190769.00|0.00;AS_RAW_MQRankSum=|2.6,1|NaN;AS_RAW_ReadPosRankSum=|0.3,1|NaN;AS_SB_TABLE=33,17|28,22|0,0;BaseQRankSum=1.940;DP=104;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=2.618;RAW_MQandDP=376641,104;ReadPosRankSum=0.341 GT:AD:DP:GQ:PL:SB 0/1:50,50,0:100:99:1648,0,1511,1797,1661,3458:33,17,28,22 20 10087805 . G . . END=10087819 GT:DP:GQ:MIN_DP:PL 0/0:101:99:96:0,120,1800 -20 10087820 . CAG C,CAGAG, 456.60 . AS_RAW_BaseQRankSum=|NaN|-2.0,1|NaN;AS_RAW_MQ=123769.00|0.00|63869.00|0.00;AS_RAW_MQRankSum=|NaN|0.4,1|NaN;AS_RAW_ReadPosRankSum=|NaN|-0.4,1|NaN;AS_SB_TABLE=17,18|0,0|8,10|0,0;BaseQRankSum=-1.974;DP=102;ExcessHet=3.0103;MLEAC=0,1,0;MLEAF=0.00,0.500,0.00;MQRankSum=0.422;RAW_MQandDP=373500,102;ReadPosRankSum=-0.357 GT:AD:DP:GQ:PL:SB 0/2:35,0,18,0:53:99:464,665,2541,0,1195,1170,657,2217,1237,2172:17,18,8,10 +20 10087820 . CAG C,CAGAG, 456.60 . AS_RAW_BaseQRankSum=|NaN|-2.0,1|NaN;AS_RAW_MQ=123769.00|0.00|63869.00|0.00;AS_RAW_MQRankSum=|NaN|0.4,1|NaN;AS_RAW_ReadPosRankSum=|NaN|-0.1,1|NaN;AS_SB_TABLE=17,18|0,0|8,10|0,0;BaseQRankSum=-1.974;DP=102;ExcessHet=3.0103;MLEAC=0,1,0;MLEAF=0.00,0.500,0.00;MQRankSum=0.422;RAW_MQandDP=373500,102;ReadPosRankSum=-0.019 GT:AD:DP:GQ:PL:SB 0/2:35,0,18,0:53:99:464,665,2541,0,1195,1170,657,2217,1237,2172:17,18,8,10 20 10087823 . A . . END=10087841 GT:DP:GQ:MIN_DP:PL 0/0:85:99:82:0,120,1800 20 10087842 . A . . END=10087842 GT:DP:GQ:MIN_DP:PL 0/0:81:0:81:0,0,2313 20 10087843 . A . . END=10087843 GT:DP:GQ:MIN_DP:PL 0/0:81:99:81:0,120,1800 @@ -1064,9 +1064,9 @@ 20 10088064 . G . . END=10088698 GT:DP:GQ:MIN_DP:PL 0/0:87:99:60:0,120,1800 20 10088699 . C T, 797.64 . AS_RAW_BaseQRankSum=|3.8,1|NaN;AS_RAW_MQ=127369.00|71528.00|0.00;AS_RAW_MQRankSum=|-3.2,1|NaN;AS_RAW_ReadPosRankSum=|-1.5,1|NaN;AS_SB_TABLE=15,21|19,7|0,0;BaseQRankSum=3.803;DP=67;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.140;RAW_MQandDP=216897,67;ReadPosRankSum=-1.456 GT:AD:DP:GQ:PL:SB 0/1:36,26,0:62:99:805,0,1088,913,1166,2079:15,21,19,7 20 10088700 . G . . END=10088729 GT:DP:GQ:MIN_DP:PL 0/0:53:99:51:0,120,1800 -20 10088730 . G A, 993.64 . AS_RAW_BaseQRankSum=|-0.1,1|NaN;AS_RAW_MQ=108000.00|48041.00|0.00;AS_RAW_MQRankSum=|-5.3,1|NaN;AS_RAW_ReadPosRankSum=|0.5,1|NaN;AS_SB_TABLE=11,19|16,10|0,0;BaseQRankSum=-0.058;DP=57;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.213;RAW_MQandDP=159641,57;ReadPosRankSum=0.581 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:30,26,0:56:99:0|1:10088730_G_A:1001,0,1152,1092,1231,2322:10088730:11,19,16,10 +20 10088730 . G A, 993.64 . AS_RAW_BaseQRankSum=|0.2,1|NaN;AS_RAW_MQ=108000.00|48041.00|0.00;AS_RAW_MQRankSum=|-5.3,1|NaN;AS_RAW_ReadPosRankSum=|0.5,1|NaN;AS_SB_TABLE=11,19|16,10|0,0;BaseQRankSum=0.224;DP=57;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.213;RAW_MQandDP=159641,57;ReadPosRankSum=0.581 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:30,26,0:56:99:0|1:10088730_G_A:1001,0,1152,1092,1231,2322:10088730:11,19,16,10 20 10088731 . G . . END=10088735 GT:DP:GQ:MIN_DP:PL 0/0:55:99:55:0,120,1800 -20 10088736 . A C, 1102.64 . AS_RAW_BaseQRankSum=|0.0,1|NaN;AS_RAW_MQ=111600.00|56082.00|0.00;AS_RAW_MQRankSum=|-5.2,1|NaN;AS_RAW_ReadPosRankSum=|0.5,1|NaN;AS_SB_TABLE=12,19|17,12|0,0;BaseQRankSum=0.016;DP=60;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.157;RAW_MQandDP=167682,60;ReadPosRankSum=0.573 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:31,29,0:60:99:0|1:10088730_G_A:1110,0,1194,1203,1281,2484:10088730:12,19,17,12 +20 10088736 . A C, 1102.64 . AS_RAW_BaseQRankSum=|0.2,1|NaN;AS_RAW_MQ=111600.00|56082.00|0.00;AS_RAW_MQRankSum=|-5.2,1|NaN;AS_RAW_ReadPosRankSum=|0.5,1|NaN;AS_SB_TABLE=12,19|17,12|0,0;BaseQRankSum=0.282;DP=60;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.157;RAW_MQandDP=167682,60;ReadPosRankSum=0.573 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:31,29,0:60:99:0|1:10088730_G_A:1110,0,1194,1203,1281,2484:10088730:12,19,17,12 20 10088737 . C . . END=10088746 GT:DP:GQ:MIN_DP:PL 0/0:56:99:53:0,120,1800 20 10088747 . A G, 1132.64 . AS_RAW_BaseQRankSum=|-3.9,1|NaN;AS_RAW_MQ=93600.00|58998.00|0.00;AS_RAW_MQRankSum=|-4.9,1|NaN;AS_RAW_ReadPosRankSum=|0.0,1|NaN;AS_SB_TABLE=10,16|19,11|0,0;BaseQRankSum=-3.877;DP=56;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.881;RAW_MQandDP=152598,56;ReadPosRankSum=0.009 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:26,30,0:56:99:0|1:10088730_G_A:1140,0,995,1219,1085,2304:10088730:10,16,19,11 20 10088748 . G . . END=10088798 GT:DP:GQ:MIN_DP:PL 0/0:49:99:46:0,114,1710 @@ -1091,11 +1091,11 @@ 20 10088871 . T . . END=10088894 GT:DP:GQ:MIN_DP:PL 0/0:39:99:33:0,99,1294 20 10088895 . C T, 556.64 . AS_RAW_BaseQRankSum=|2.3,1|NaN;AS_RAW_MQ=72473.00|60377.00|0.00;AS_RAW_MQRankSum=|0.2,1|NaN;AS_RAW_ReadPosRankSum=|1.2,1|NaN;AS_SB_TABLE=10,12|8,10|0,0;BaseQRankSum=2.330;DP=43;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.260;RAW_MQandDP=143650,43;ReadPosRankSum=1.238 GT:AD:DP:GQ:PL:SB 0/1:22,18,0:40:99:564,0,651,630,704,1334:10,12,8,10 20 10088896 . G . . END=10088967 GT:DP:GQ:MIN_DP:PL 0/0:49:99:41:0,107,1668 -20 10088968 . C CAAA, 1289.60 . AS_RAW_BaseQRankSum=|0.1,1|NaN;AS_RAW_MQ=112441.00|59471.00|0.00;AS_RAW_MQRankSum=|-5.4,1|NaN;AS_RAW_ReadPosRankSum=|1.8,1|NaN;AS_SB_TABLE=17,15|19,15|0,0;BaseQRankSum=0.117;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.320;RAW_MQandDP=216408,79;ReadPosRankSum=1.802 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:32,34,0:66:99:0|1:10088968_C_CAAA:1297,0,1230,1394,1333,2726:10088968:17,15,19,15 +20 10088968 . C CAAA, 1289.60 . AS_RAW_BaseQRankSum=|0.3,1|NaN;AS_RAW_MQ=112441.00|59471.00|0.00;AS_RAW_MQRankSum=|-5.4,1|NaN;AS_RAW_ReadPosRankSum=|0.2,1|NaN;AS_SB_TABLE=17,15|19,15|0,0;BaseQRankSum=0.337;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.320;RAW_MQandDP=216408,79;ReadPosRankSum=0.205 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:32,34,0:66:99:0|1:10088968_C_CAAA:1297,0,1230,1394,1333,2726:10088968:17,15,19,15 20 10088969 . A . . END=10088979 GT:DP:GQ:MIN_DP:PL 0/0:73:99:72:0,120,1800 -20 10088980 . T C, 1352.64 . AS_RAW_BaseQRankSum=|-1.8,1|NaN;AS_RAW_MQ=132123.00|63912.00|0.00;AS_RAW_MQRankSum=|-5.3,1|NaN;AS_RAW_ReadPosRankSum=|1.1,1|NaN;AS_SB_TABLE=20,19|20,16|0,0;BaseQRankSum=-1.772;DP=76;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.207;RAW_MQandDP=197331,76;ReadPosRankSum=1.124 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:39,36,0:75:99:0|1:10088968_C_CAAA:1360,0,1491,1478,1599,3077:10088968:20,19,20,16 +20 10088980 . T C, 1352.64 . AS_RAW_BaseQRankSum=|-1.9,1|NaN;AS_RAW_MQ=132123.00|63912.00|0.00;AS_RAW_MQRankSum=|-5.3,1|NaN;AS_RAW_ReadPosRankSum=|1.4,1|NaN;AS_SB_TABLE=20,19|20,16|0,0;BaseQRankSum=-1.845;DP=76;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.207;RAW_MQandDP=197331,76;ReadPosRankSum=1.483 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:39,36,0:75:99:0|1:10088968_C_CAAA:1360,0,1491,1478,1599,3077:10088968:20,19,20,16 20 10088981 . A . . END=10088984 GT:DP:GQ:MIN_DP:PL 0/0:73:99:71:0,120,1800 -20 10088985 . T C, 1283.64 . AS_RAW_BaseQRankSum=|-0.6,1|NaN;AS_RAW_MQ=138965.00|54481.00|0.00;AS_RAW_MQRankSum=|-5.5,1|NaN;AS_RAW_ReadPosRankSum=|1.1,1|NaN;AS_SB_TABLE=22,20|17,17|0,0;BaseQRankSum=-0.525;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.440;RAW_MQandDP=204246,79;ReadPosRankSum=1.155 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:42,34,0:76:99:0|1:10088968_C_CAAA:1291,0,1593,1417,1696,3113:10088968:22,20,17,17 +20 10088985 . T C, 1283.64 . AS_RAW_BaseQRankSum=|-0.6,1|NaN;AS_RAW_MQ=138965.00|54481.00|0.00;AS_RAW_MQRankSum=|-5.5,1|NaN;AS_RAW_ReadPosRankSum=|1.4,1|NaN;AS_SB_TABLE=22,20|17,17|0,0;BaseQRankSum=-0.525;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.440;RAW_MQandDP=204246,79;ReadPosRankSum=1.432 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:42,34,0:76:99:0|1:10088968_C_CAAA:1291,0,1593,1417,1696,3113:10088968:22,20,17,17 20 10088986 . A . . END=10088989 GT:DP:GQ:MIN_DP:PL 0/0:82:99:81:0,120,1800 20 10088990 . A . . END=10088990 GT:DP:GQ:MIN_DP:PL 0/0:84:7:84:0,7,2771 20 10088991 . C . . END=10088991 GT:DP:GQ:MIN_DP:PL 0/0:81:95:81:0,95,2703 @@ -1113,7 +1113,7 @@ 20 10089442 . G . . END=10089524 GT:DP:GQ:MIN_DP:PL 0/0:81:99:74:0,120,1800 20 10089525 . C T, 1569.64 . AS_RAW_BaseQRankSum=|5.8,1|NaN;AS_RAW_MQ=131810.00|154800.00|0.00;AS_RAW_MQRankSum=|1.5,1|NaN;AS_RAW_ReadPosRankSum=|0.8,1|NaN;AS_SB_TABLE=22,16|20,23|0,0;BaseQRankSum=5.859;DP=83;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.531;RAW_MQandDP=293810,83;ReadPosRankSum=0.862 GT:AD:DP:GQ:PL:SB 0/1:38,43,0:81:99:1577,0,1088,1691,1217,2908:22,16,20,23 20 10089526 . G . . END=10090288 GT:DP:GQ:MIN_DP:PL 0/0:72:99:55:0,111,1800 -20 10090289 . CAA C,CA, 405.60 . AS_RAW_BaseQRankSum=|0.7,1|0.1,1|NaN;AS_RAW_MQ=54000.00|10800.00|75900.00|0.00;AS_RAW_MQRankSum=|0.0,1|1.5,1|NaN;AS_RAW_ReadPosRankSum=|-1.0,1|0.7,1|NaN;AS_SB_TABLE=8,7|2,1|8,12|0,0;BaseQRankSum=0.285;DP=88;ExcessHet=3.0103;MLEAC=0,1,0;MLEAF=0.00,0.500,0.00;MQRankSum=1.470;RAW_MQandDP=316482,88;ReadPosRankSum=0.455 GT:AD:DP:GQ:PL:SB 0/2:15,3,20,0:38:99:413,386,1030,0,295,240,474,906,358,938:8,7,10,13 +20 10090289 . CAA C,CA, 405.60 . AS_RAW_BaseQRankSum=|0.7,1|0.1,1|NaN;AS_RAW_MQ=54000.00|10800.00|75900.00|0.00;AS_RAW_MQRankSum=|0.0,1|1.5,1|NaN;AS_RAW_ReadPosRankSum=|-1.0,1|0.7,1|NaN;AS_SB_TABLE=8,7|2,1|8,12|0,0;BaseQRankSum=0.252;DP=88;ExcessHet=3.0103;MLEAC=0,1,0;MLEAF=0.00,0.500,0.00;MQRankSum=1.470;RAW_MQandDP=316482,88;ReadPosRankSum=0.455 GT:AD:DP:GQ:PL:SB 0/2:15,3,20,0:38:99:413,386,1030,0,295,240,474,906,358,938:8,7,10,13 20 10090292 . A . . END=10090763 GT:DP:GQ:MIN_DP:PL 0/0:75:99:61:0,120,1800 20 10090764 . A G, 861.64 . AS_RAW_BaseQRankSum=|-2.7,1|NaN;AS_RAW_MQ=122400.00|104400.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|1.2,1|NaN;AS_SB_TABLE=12,22|14,15|0,0;BaseQRankSum=-2.659;DP=67;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=241200,67;ReadPosRankSum=1.207 GT:AD:DP:GQ:PL:SB 0/1:34,29,0:63:99:869,0,1207,972,1294,2265:12,22,14,15 20 10090765 . A . . END=10090969 GT:DP:GQ:MIN_DP:PL 0/0:75:99:65:0,120,1800 @@ -1135,7 +1135,7 @@ 20 10094583 . T . . END=10094773 GT:DP:GQ:MIN_DP:PL 0/0:78:99:67:0,120,1800 20 10094774 . C T, 1057.64 . AS_RAW_BaseQRankSum=|-0.8,1|NaN;AS_RAW_MQ=141241.00|126000.00|0.00;AS_RAW_MQRankSum=|0.9,1|NaN;AS_RAW_ReadPosRankSum=|0.1,1|NaN;AS_SB_TABLE=24,16|21,14|0,0;BaseQRankSum=-0.784;DP=81;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.962;RAW_MQandDP=286082,81;ReadPosRankSum=0.197 GT:AD:DP:GQ:PL:SB 0/1:40,35,0:75:99:1065,0,1282,1185,1385,2570:24,16,21,14 20 10094775 . A . . END=10095431 GT:DP:GQ:MIN_DP:PL 0/0:77:99:63:0,120,1800 -20 10095432 . GTGATGATGA G, 875.60 . AS_RAW_BaseQRankSum=|1.1,1|NaN;AS_RAW_MQ=93600.00|35579.00|0.00;AS_RAW_MQRankSum=|-4.4,1|NaN;AS_RAW_ReadPosRankSum=|0.3,1|NaN;AS_SB_TABLE=16,10|12,11|0,0;BaseQRankSum=1.109;DP=78;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.378;RAW_MQandDP=231348,78;ReadPosRankSum=0.396 GT:AD:DP:GQ:PL:SB 0/1:26,23,0:49:99:883,0,978,961,1053,2014:16,10,12,11 +20 10095432 . GTGATGATGA G, 875.60 . AS_RAW_BaseQRankSum=|1.0,1|NaN;AS_RAW_MQ=93600.00|35579.00|0.00;AS_RAW_MQRankSum=|-4.4,1|NaN;AS_RAW_ReadPosRankSum=|0.3,1|NaN;AS_SB_TABLE=16,10|12,11|0,0;BaseQRankSum=1.063;DP=78;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.378;RAW_MQandDP=231348,78;ReadPosRankSum=0.396 GT:AD:DP:GQ:PL:SB 0/1:26,23,0:49:99:883,0,978,961,1053,2014:16,10,12,11 20 10095442 . T . . END=10095740 GT:DP:GQ:MIN_DP:PL 0/0:80:99:64:0,120,1800 20 10095741 . A G, 1096.64 . AS_RAW_BaseQRankSum=|-0.6,1|NaN;AS_RAW_MQ=126841.00|103087.00|0.00;AS_RAW_MQRankSum=|-2.4,1|NaN;AS_RAW_ReadPosRankSum=|-0.5,1|NaN;AS_SB_TABLE=14,22|18,16|0,0;BaseQRankSum=-0.534;DP=72;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.313;RAW_MQandDP=237128,72;ReadPosRankSum=-0.500 GT:AD:DP:GQ:PL:SB 0/1:36,34,0:70:99:1104,0,1233,1213,1335,2547:14,22,18,16 20 10095742 . G . . END=10096292 GT:DP:GQ:MIN_DP:PL 0/0:73:99:63:0,120,1800 @@ -1145,19 +1145,19 @@ 20 10096597 . T . . END=10096767 GT:DP:GQ:MIN_DP:PL 0/0:90:99:75:0,120,1800 20 10096768 . A C, 1703.64 . AS_RAW_BaseQRankSum=|-2.8,1|NaN;AS_RAW_MQ=151200.00|168123.00|0.00;AS_RAW_MQRankSum=|-1.7,1|NaN;AS_RAW_ReadPosRankSum=|0.6,1|NaN;AS_SB_TABLE=25,17|24,25|0,0;BaseQRankSum=-2.764;DP=96;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.609;RAW_MQandDP=337323,96;ReadPosRankSum=0.613 GT:AD:DP:GQ:PL:SB 0/1:42,49,0:91:99:1711,0,1452,1838,1600,3437:25,17,24,25 20 10096769 . A . . END=10096898 GT:DP:GQ:MIN_DP:PL 0/0:78:99:65:0,120,1800 -20 10096899 . G T, 1636.64 . AS_RAW_BaseQRankSum=|2.4,1|NaN;AS_RAW_MQ=144000.00|147579.00|0.00;AS_RAW_MQRankSum=|-1.7,1|NaN;AS_RAW_ReadPosRankSum=|0.4,1|NaN;AS_SB_TABLE=20,20|12,31|0,0;BaseQRankSum=2.494;DP=84;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.677;RAW_MQandDP=295179,84;ReadPosRankSum=0.422 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:40,43,0:83:99:0|1:10096899_G_T:1644,0,1519,1764,1649,3413:10096899:20,20,12,31 +20 10096899 . G T, 1636.64 . AS_RAW_BaseQRankSum=|2.7,1|NaN;AS_RAW_MQ=144000.00|147579.00|0.00;AS_RAW_MQRankSum=|-1.7,1|NaN;AS_RAW_ReadPosRankSum=|0.4,1|NaN;AS_SB_TABLE=20,20|12,31|0,0;BaseQRankSum=2.755;DP=84;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.677;RAW_MQandDP=295179,84;ReadPosRankSum=0.422 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:40,43,0:83:99:0|1:10096899_G_T:1644,0,1519,1764,1649,3413:10096899:20,20,12,31 20 10096900 . G . . END=10096904 GT:DP:GQ:MIN_DP:PL 0/0:82:99:78:0,120,1800 20 10096905 . TA T, 1630.60 . AS_RAW_BaseQRankSum=|-0.8,1|NaN;AS_RAW_MQ=154800.00|147579.00|0.00;AS_RAW_MQRankSum=|-1.8,1|NaN;AS_RAW_ReadPosRankSum=|0.4,1|NaN;AS_SB_TABLE=22,21|13,30|0,0;BaseQRankSum=-0.755;DP=86;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.739;RAW_MQandDP=302379,86;ReadPosRankSum=0.461 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:43,43,0:86:99:0|1:10096899_G_T:1638,0,1623,1768,1752,3520:10096899:22,21,13,30 20 10096907 . A . . END=10096932 GT:DP:GQ:MIN_DP:PL 0/0:84:99:82:0,120,1800 -20 10096933 . G C, 1534.64 . AS_RAW_BaseQRankSum=|-1.8,1|NaN;AS_RAW_MQ=169200.00|143979.00|0.00;AS_RAW_MQRankSum=|-1.9,1|NaN;AS_RAW_ReadPosRankSum=|0.3,1|NaN;AS_SB_TABLE=29,18|14,28|0,0;BaseQRankSum=-1.724;DP=89;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.840;RAW_MQandDP=313179,89;ReadPosRankSum=0.334 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:47,42,0:89:99:0|1:10096933_G_C:1542,0,1763,1684,1889,3573:10096933:29,18,14,28 +20 10096933 . G C, 1534.64 . AS_RAW_BaseQRankSum=|-2.0,1|NaN;AS_RAW_MQ=169200.00|143979.00|0.00;AS_RAW_MQRankSum=|-1.9,1|NaN;AS_RAW_ReadPosRankSum=|0.3,1|NaN;AS_SB_TABLE=29,18|14,28|0,0;BaseQRankSum=-1.914;DP=89;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.840;RAW_MQandDP=313179,89;ReadPosRankSum=0.383 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:47,42,0:89:99:0|1:10096933_G_C:1542,0,1763,1684,1889,3573:10096933:29,18,14,28 20 10096934 . T . . END=10096957 GT:DP:GQ:MIN_DP:PL 0/0:89:99:85:0,120,1800 -20 10096958 . G A, 1789.64 . AS_RAW_BaseQRankSum=|2.6,1|NaN;AS_RAW_MQ=158400.00|165579.00|0.00;AS_RAW_MQRankSum=|-1.7,1|NaN;AS_RAW_ReadPosRankSum=|-1.9,1|NaN;AS_SB_TABLE=27,17|16,32|0,0;BaseQRankSum=2.697;DP=93;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.664;RAW_MQandDP=327579,93;ReadPosRankSum=-1.824 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:44,48,0:92:99:0|1:10096933_G_C:1797,0,1622,1929,1766,3695:10096933:27,17,16,32 +20 10096958 . G A, 1789.64 . AS_RAW_BaseQRankSum=|2.6,1|NaN;AS_RAW_MQ=158400.00|165579.00|0.00;AS_RAW_MQRankSum=|-1.7,1|NaN;AS_RAW_ReadPosRankSum=|-1.6,1|NaN;AS_SB_TABLE=27,17|16,32|0,0;BaseQRankSum=2.697;DP=93;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.664;RAW_MQandDP=327579,93;ReadPosRankSum=-1.593 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:44,48,0:92:99:0|1:10096933_G_C:1797,0,1622,1929,1766,3695:10096933:27,17,16,32 20 10096959 . G . . END=10097074 GT:DP:GQ:MIN_DP:PL 0/0:92:99:84:0,120,1800 -20 10097075 . T G, 1466.64 . AS_RAW_BaseQRankSum=|-2.6,1|NaN;AS_RAW_MQ=159700.00|155928.00|0.00;AS_RAW_MQRankSum=|-1.4,1|NaN;AS_RAW_ReadPosRankSum=|0.0,1|NaN;AS_SB_TABLE=18,26|26,22|0,0;BaseQRankSum=-2.533;DP=96;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.389;RAW_MQandDP=324510,96;ReadPosRankSum=0.082 GT:AD:DP:GQ:PL:SB 0/1:44,48,0:92:99:1474,0,1482,1606,1626,3232:18,26,26,22 +20 10097075 . T G, 1466.64 . AS_RAW_BaseQRankSum=|-2.6,1|NaN;AS_RAW_MQ=159700.00|155928.00|0.00;AS_RAW_MQRankSum=|-1.4,1|NaN;AS_RAW_ReadPosRankSum=|0.2,1|NaN;AS_SB_TABLE=18,26|26,22|0,0;BaseQRankSum=-2.533;DP=96;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.389;RAW_MQandDP=324510,96;ReadPosRankSum=0.235 GT:AD:DP:GQ:PL:SB 0/1:44,48,0:92:99:1474,0,1482,1606,1626,3232:18,26,26,22 20 10097076 . A . . END=10097100 GT:DP:GQ:MIN_DP:PL 0/0:91:99:77:0,120,1800 -20 10097101 . C CTTT,CTTTT, 1105.60 . AS_RAW_BaseQRankSum=|-0.9,1|-0.5,1|NaN;AS_RAW_MQ=121504.00|76887.00|5282.00|0.00;AS_RAW_MQRankSum=|-1.8,1|-3.9,1|NaN;AS_RAW_ReadPosRankSum=|2.7,1|-0.7,1|NaN;AS_SB_TABLE=22,12|12,14|2,1|0,0;BaseQRankSum=-0.953;DP=81;ExcessHet=3.0103;MLEAC=1,0,0;MLEAF=0.500,0.00,0.00;MQRankSum=-2.210;RAW_MQandDP=274973,81;ReadPosRankSum=2.373 GT:AD:DP:GQ:PL:SB 0/1:34,26,3,0:63:99:1113,0,1263,585,1269,1857,973,1359,1937,2255:22,12,14,15 +20 10097101 . C CTTT,CTTTT, 1105.60 . AS_RAW_BaseQRankSum=|-0.9,1|-0.5,1|NaN;AS_RAW_MQ=121504.00|76887.00|5282.00|0.00;AS_RAW_MQRankSum=|-1.8,1|-3.9,1|NaN;AS_RAW_ReadPosRankSum=|3.1,1|-0.3,1|NaN;AS_SB_TABLE=22,12|12,14|2,1|0,0;BaseQRankSum=-0.953;DP=81;ExcessHet=3.0103;MLEAC=1,0,0;MLEAF=0.500,0.00,0.00;MQRankSum=-2.210;RAW_MQandDP=274973,81;ReadPosRankSum=2.829 GT:AD:DP:GQ:PL:SB 0/1:34,26,3,0:63:99:1113,0,1263,585,1269,1857,973,1359,1937,2255:22,12,14,15 20 10097102 . T . . END=10097435 GT:DP:GQ:MIN_DP:PL 0/0:70:99:60:0,120,1800 -20 10097436 . CTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT C, 1089.60 . AS_RAW_BaseQRankSum=|1.8,1|NaN;AS_RAW_MQ=204882.00|57261.00|0.00;AS_RAW_MQRankSum=|-6.5,1|NaN;AS_RAW_ReadPosRankSum=|-3.1,1|NaN;AS_SB_TABLE=23,34|11,21|0,0;BaseQRankSum=1.820;DP=90;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-6.464;RAW_MQandDP=265743,90;ReadPosRankSum=-3.097 GT:AD:DP:GQ:PL:SB 0/1:57,32,0:89:99:1097,0,2238,1269,2335,3603:23,34,11,21 +20 10097436 . CTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT C, 1089.60 . AS_RAW_BaseQRankSum=|1.6,1|NaN;AS_RAW_MQ=204882.00|57261.00|0.00;AS_RAW_MQRankSum=|-6.5,1|NaN;AS_RAW_ReadPosRankSum=|-3.1,1|NaN;AS_SB_TABLE=23,34|11,21|0,0;BaseQRankSum=1.650;DP=90;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-6.464;RAW_MQandDP=265743,90;ReadPosRankSum=-3.097 GT:AD:DP:GQ:PL:SB 0/1:57,32,0:89:99:1097,0,2238,1269,2335,3603:23,34,11,21 20 10097437 . TTTTC *,T, 931.01 . AS_RAW_BaseQRankSum=|||;AS_RAW_MQ=0.00|57261.00|84469.00|0.00;AS_RAW_MQRankSum=|||;AS_RAW_ReadPosRankSum=|||;AS_SB_TABLE=0,0|11,21|5,18|0,0;DP=78;ExcessHet=3.0103;MLEAC=1,1,0;MLEAF=0.500,0.500,0.00;RAW_MQandDP=224774,78 GT:AD:DP:GQ:PL:SB 1/2:0,32,23,0:55:99:2133,941,1797,1201,0,1129,2207,1453,1267,2647:0,0,16,39 20 10097442 . T . . END=10097475 GT:DP:GQ:MIN_DP:PL 0/0:78:0:63:0,0,557 20 10097476 . T . . END=10097476 GT:DP:GQ:MIN_DP:PL 0/0:66:11:66:0,11,2255 @@ -1219,13 +1219,13 @@ 20 10098219 . TATATATA T, 325.60 . AS_RAW_BaseQRankSum=|3.1,1|NaN;AS_RAW_MQ=40441.00|25264.00|0.00;AS_RAW_MQRankSum=|-0.3,1|NaN;AS_RAW_ReadPosRankSum=|0.4,1|NaN;AS_SB_TABLE=0,12|0,9|0,0;BaseQRankSum=3.147;DP=21;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.205;RAW_MQandDP=65705,21;ReadPosRankSum=0.427 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:12,9,0:21:99:0|1:10098219_TATATATA_T:333,0,461,369,488,857:10098219:0,12,0,9 20 10098227 . T . . END=10098228 GT:DP:GQ:MIN_DP:PL 0/0:18:30:18:0,30,450 20 10098229 . A . . END=10098236 GT:DP:GQ:MIN_DP:PL 0/0:17:21:13:0,21,315 -20 10098237 . A T, 265.64 . AS_RAW_BaseQRankSum=|0.0,1|NaN;AS_RAW_MQ=25200.00|15464.00|0.00;AS_RAW_MQRankSum=|-1.9,1|NaN;AS_RAW_ReadPosRankSum=|0.2,1|NaN;AS_SB_TABLE=0,7|0,7|0,0;BaseQRankSum=0.006;DP=14;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.885;RAW_MQandDP=40664,14;ReadPosRankSum=0.277 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:7,7,0:14:99:0|1:10098219_TATATATA_T:273,0,273,294,294,588:10098219:0,7,0,7 +20 10098237 . A T, 265.64 . AS_RAW_BaseQRankSum=|0.0,1|NaN;AS_RAW_MQ=25200.00|15464.00|0.00;AS_RAW_MQRankSum=|-1.9,1|NaN;AS_RAW_ReadPosRankSum=|1.1,1|NaN;AS_SB_TABLE=0,7|0,7|0,0;BaseQRankSum=0.006;DP=14;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.885;RAW_MQandDP=40664,14;ReadPosRankSum=1.118 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:7,7,0:14:99:0|1:10098219_TATATATA_T:273,0,273,294,294,588:10098219:0,7,0,7 20 10098238 . A . . END=10098244 GT:DP:GQ:MIN_DP:PL 0/0:10:21:9:0,21,315 20 10098245 . T . . END=10098248 GT:DP:GQ:MIN_DP:PL 0/0:10:24:10:0,24,360 20 10098249 . A . . END=10098250 GT:DP:GQ:MIN_DP:PL 0/0:10:18:9:0,18,270 20 10098251 . A . . END=10098255 GT:DP:GQ:MIN_DP:PL 0/0:8:15:8:0,15,225 20 10098256 . T . . END=10098264 GT:DP:GQ:MIN_DP:PL 0/0:8:9:6:0,9,135 -20 10098265 . T C, 154.64 . AS_RAW_BaseQRankSum=|1.8,1|NaN;AS_RAW_MQ=7200.00|3364.00|0.00;AS_RAW_MQRankSum=|-1.9,1|NaN;AS_RAW_ReadPosRankSum=|0.0,1|NaN;AS_SB_TABLE=0,2|0,4|0,0;BaseQRankSum=1.834;DP=6;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.834;RAW_MQandDP=10564,6;ReadPosRankSum=0.000 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:2,4,0:6:59:0|1:10098219_TATATATA_T:162,0,59,168,71,239:10098219:0,2,0,4 +20 10098265 . T C, 154.64 . AS_RAW_BaseQRankSum=|1.8,1|NaN;AS_RAW_MQ=7200.00|3364.00|0.00;AS_RAW_MQRankSum=|-1.9,1|NaN;AS_RAW_ReadPosRankSum=|0.8,1|NaN;AS_SB_TABLE=0,2|0,4|0,0;BaseQRankSum=1.834;DP=6;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.834;RAW_MQandDP=10564,6;ReadPosRankSum=0.842 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:2,4,0:6:59:0|1:10098219_TATATATA_T:162,0,59,168,71,239:10098219:0,2,0,4 20 10098266 . A . . END=10098272 GT:DP:GQ:MIN_DP:PL 0/0:4:9:4:0,9,135 20 10098273 . A . . END=10098279 GT:DP:GQ:MIN_DP:PL 0/0:3:6:3:0,6,90 20 10098280 . A . . END=10098290 GT:DP:GQ:MIN_DP:PL 0/0:4:9:3:0,9,126 @@ -1300,7 +1300,7 @@ 20 10098882 . C . . END=10098882 GT:DP:GQ:MIN_DP:PL 0/0:32:60:32:0,60,1207 20 10098883 . T . . END=10098883 GT:DP:GQ:MIN_DP:PL 0/0:32:56:32:0,56,1237 20 10098884 . C . . END=10098884 GT:DP:GQ:MIN_DP:PL 0/0:32:84:32:0,84,1260 -20 10098885 . C CA, 463.60 . AS_RAW_BaseQRankSum=|0.1,1|NaN;AS_RAW_MQ=58969.00|18188.00|0.00;AS_RAW_MQRankSum=|-4.5,1|NaN;AS_RAW_ReadPosRankSum=|-1.1,1|NaN;AS_SB_TABLE=16,1|13,1|0,0;BaseQRankSum=0.165;DP=33;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.449;RAW_MQandDP=81598,33;ReadPosRankSum=-1.073 GT:AD:DP:GQ:PL:SB 0/1:17,14,0:31:99:471,0,572,522,615,1137:16,1,13,1 +20 10098885 . C CA, 463.60 . AS_RAW_BaseQRankSum=|0.1,1|NaN;AS_RAW_MQ=58969.00|18188.00|0.00;AS_RAW_MQRankSum=|-4.5,1|NaN;AS_RAW_ReadPosRankSum=|-1.0,1|NaN;AS_SB_TABLE=16,1|13,1|0,0;BaseQRankSum=0.165;DP=33;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.449;RAW_MQandDP=81598,33;ReadPosRankSum=-0.954 GT:AD:DP:GQ:PL:SB 0/1:17,14,0:31:99:471,0,572,522,615,1137:16,1,13,1 20 10098886 . C . . END=10098890 GT:DP:GQ:MIN_DP:PL 0/0:31:84:29:0,84,1260 20 10098891 . C . . END=10098891 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 20 10098892 . G . . END=10098900 GT:DP:GQ:MIN_DP:PL 0/0:31:81:30:0,81,1215 @@ -1333,10 +1333,10 @@ 20 10099022 . C . . END=10099022 GT:DP:GQ:MIN_DP:PL 0/0:25:69:25:0,69,1035 20 10099023 . T . . END=10099027 GT:DP:GQ:MIN_DP:PL 0/0:27:72:26:0,72,1080 20 10099028 . A . . END=10099028 GT:DP:GQ:MIN_DP:PL 0/0:28:69:28:0,69,1035 -20 10099029 . T C, 355.64 . AS_RAW_BaseQRankSum=|-1.6,1|NaN;AS_RAW_MQ=66169.00|17048.00|0.00;AS_RAW_MQRankSum=|-3.8,1|NaN;AS_RAW_ReadPosRankSum=|-1.3,1|NaN;AS_SB_TABLE=14,5|9,1|0,0;BaseQRankSum=-1.518;DP=30;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.731;RAW_MQandDP=84058,30;ReadPosRankSum=-1.224 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:19,10,0:29:99:0|1:10099029_T_C:363,0,768,420,798,1218:10099029:14,5,9,1 +20 10099029 . T C, 355.64 . AS_RAW_BaseQRankSum=|-1.9,1|NaN;AS_RAW_MQ=66169.00|17048.00|0.00;AS_RAW_MQRankSum=|-3.8,1|NaN;AS_RAW_ReadPosRankSum=|-1.3,1|NaN;AS_SB_TABLE=14,5|9,1|0,0;BaseQRankSum=-1.809;DP=30;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.731;RAW_MQandDP=84058,30;ReadPosRankSum=-1.224 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:19,10,0:29:99:0|1:10099029_T_C:363,0,768,420,798,1218:10099029:14,5,9,1 20 10099030 . C . . END=10099031 GT:DP:GQ:MIN_DP:PL 0/0:29:72:28:0,72,1080 20 10099032 . T . . END=10099033 GT:DP:GQ:MIN_DP:PL 0/0:28:63:28:0,63,945 -20 10099034 . C A, 355.64 . AS_RAW_BaseQRankSum=|2.7,1|NaN;AS_RAW_MQ=66169.00|17048.00|0.00;AS_RAW_MQRankSum=|-3.8,1|NaN;AS_RAW_ReadPosRankSum=|-1.9,1|NaN;AS_SB_TABLE=14,5|9,1|0,0;BaseQRankSum=2.752;DP=29;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.731;RAW_MQandDP=83217,29;ReadPosRankSum=-1.850 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:19,10,0:29:99:0|1:10099029_T_C:363,0,768,420,798,1218:10099029:14,5,9,1 +20 10099034 . C A, 355.64 . AS_RAW_BaseQRankSum=|2.7,1|NaN;AS_RAW_MQ=66169.00|17048.00|0.00;AS_RAW_MQRankSum=|-3.8,1|NaN;AS_RAW_ReadPosRankSum=|-1.9,1|NaN;AS_SB_TABLE=14,5|9,1|0,0;BaseQRankSum=2.757;DP=29;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.731;RAW_MQandDP=83217,29;ReadPosRankSum=-1.850 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:19,10,0:29:99:0|1:10099029_T_C:363,0,768,420,798,1218:10099029:14,5,9,1 20 10099035 . G . . END=10099039 GT:DP:GQ:MIN_DP:PL 0/0:29:60:26:0,60,900 20 10099040 . T . . END=10099040 GT:DP:GQ:MIN_DP:PL 0/0:26:51:26:0,51,765 20 10099041 . C . . END=10099041 GT:DP:GQ:MIN_DP:PL 0/0:27:54:27:0,54,810 @@ -1346,13 +1346,13 @@ 20 10099046 . T C, 325.64 . AS_RAW_BaseQRankSum=|-2.2,1|NaN;AS_RAW_MQ=51769.00|8082.00|0.00;AS_RAW_MQRankSum=|-4.5,1|NaN;AS_RAW_ReadPosRankSum=|-2.3,1|NaN;AS_SB_TABLE=12,3|7,2|0,0;BaseQRankSum=-2.165;DP=24;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.418;RAW_MQandDP=59851,24;ReadPosRankSum=-2.297 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:15,9,0:24:99:0|1:10099029_T_C:333,0,603,378,630,1008:10099029:12,3,7,2 20 10099047 . G . . END=10099052 GT:DP:GQ:MIN_DP:PL 0/0:24:57:23:0,57,855 20 10099053 . G . . END=10099054 GT:DP:GQ:MIN_DP:PL 0/0:23:54:23:0,54,810 -20 10099055 . T C, 277.64 . AS_RAW_BaseQRankSum=|-1.0,1|NaN;AS_RAW_MQ=56210.00|6786.00|0.00;AS_RAW_MQRankSum=|-4.2,1|NaN;AS_RAW_ReadPosRankSum=|-2.0,1|NaN;AS_SB_TABLE=12,5|6,2|0,0;BaseQRankSum=-0.996;DP=25;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.179;RAW_MQandDP=62996,25;ReadPosRankSum=-1.970 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:17,8,0:25:99:0|1:10099029_T_C:285,0,673,336,697,1033:10099029:12,5,6,2 +20 10099055 . T C, 277.64 . AS_RAW_BaseQRankSum=|-1.6,1|NaN;AS_RAW_MQ=56210.00|6786.00|0.00;AS_RAW_MQRankSum=|-4.2,1|NaN;AS_RAW_ReadPosRankSum=|-2.0,1|NaN;AS_SB_TABLE=12,5|6,2|0,0;BaseQRankSum=-1.554;DP=25;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.179;RAW_MQandDP=62996,25;ReadPosRankSum=-1.970 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:17,8,0:25:99:0|1:10099029_T_C:285,0,673,336,697,1033:10099029:12,5,6,2 20 10099056 . T . . END=10099061 GT:DP:GQ:MIN_DP:PL 0/0:24:60:23:0,60,900 20 10099062 . A . . END=10099067 GT:DP:GQ:MIN_DP:PL 0/0:25:72:24:0,72,921 20 10099068 . G . . END=10099072 GT:DP:GQ:MIN_DP:PL 0/0:27:81:27:0,81,1042 20 10099073 . T . . END=10099077 GT:DP:GQ:MIN_DP:PL 0/0:27:78:27:0,78,1170 20 10099078 . G . . END=10099078 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 -20 10099079 . C T, 137.64 . AS_RAW_BaseQRankSum=|1.4,1|NaN;AS_RAW_MQ=71054.00|8485.00|0.00;AS_RAW_MQRankSum=|-2.7,1|NaN;AS_RAW_ReadPosRankSum=|0.9,1|NaN;AS_SB_TABLE=12,12|4,2|0,0;BaseQRankSum=1.432;DP=30;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.614;RAW_MQandDP=79539,30;ReadPosRankSum=0.969 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:24,6,0:30:99:0|1:10099029_T_C:145,0,886,217,904,1120:10099029:12,12,4,2 +20 10099079 . C T, 137.64 . AS_RAW_BaseQRankSum=|1.4,1|NaN;AS_RAW_MQ=71054.00|8485.00|0.00;AS_RAW_MQRankSum=|-2.7,1|NaN;AS_RAW_ReadPosRankSum=|0.9,1|NaN;AS_SB_TABLE=12,12|4,2|0,0;BaseQRankSum=1.434;DP=30;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.614;RAW_MQandDP=79539,30;ReadPosRankSum=0.969 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:24,6,0:30:99:0|1:10099029_T_C:145,0,886,217,904,1120:10099029:12,12,4,2 20 10099080 . G . . END=10099089 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,1215 20 10099090 . A . . END=10099095 GT:DP:GQ:MIN_DP:PL 0/0:34:90:31:0,90,1350 20 10099096 . A . . END=10099096 GT:DP:GQ:MIN_DP:PL 0/0:35:74:35:0,74,1310 @@ -1360,9 +1360,9 @@ 20 10099101 . G . . END=10099105 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,99,1485 20 10099106 . T . . END=10099106 GT:DP:GQ:MIN_DP:PL 0/0:36:96:36:0,96,1440 20 10099107 . T . . END=10099110 GT:DP:GQ:MIN_DP:PL 0/0:41:99:39:0,99,1485 -20 10099111 . T TTTTGTTTG, 685.60 . AS_RAW_BaseQRankSum=|-0.7,1|NaN;AS_RAW_MQ=69685.00|45093.00|0.00;AS_RAW_MQRankSum=|-1.0,1|NaN;AS_RAW_ReadPosRankSum=|-0.3,1|NaN;AS_SB_TABLE=13,10|12,7|0,0;BaseQRankSum=-0.622;DP=52;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.973;RAW_MQandDP=150778,52;ReadPosRankSum=-0.273 GT:AD:DP:GQ:PL:SB 0/1:23,19,0:42:99:693,0,802,763,860,1623:13,10,12,7 +20 10099111 . T TTTTGTTTG, 685.60 . AS_RAW_BaseQRankSum=|-1.3,1|NaN;AS_RAW_MQ=69685.00|45093.00|0.00;AS_RAW_MQRankSum=|-1.0,1|NaN;AS_RAW_ReadPosRankSum=|-1.9,1|NaN;AS_SB_TABLE=13,10|12,7|0,0;BaseQRankSum=-1.207;DP=52;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.973;RAW_MQandDP=150778,52;ReadPosRankSum=-1.860 GT:AD:DP:GQ:PL:SB 0/1:23,19,0:42:99:693,0,802,763,860,1623:13,10,12,7 20 10099112 . T . . END=10099139 GT:DP:GQ:MIN_DP:PL 0/0:57:99:49:0,114,1710 -20 10099140 . G T, 1027.64 . AS_RAW_BaseQRankSum=|-0.3,1|NaN;AS_RAW_MQ=104400.00|84512.00|0.00;AS_RAW_MQRankSum=|-2.5,1|NaN;AS_RAW_ReadPosRankSum=|0.1,1|NaN;AS_SB_TABLE=17,12|22,10|0,0;BaseQRankSum=-0.286;DP=63;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.435;RAW_MQandDP=196112,63;ReadPosRankSum=0.116 GT:AD:DP:GQ:PL:SB 0/1:29,32,0:61:99:1035,0,930,1122,1026,2148:17,12,22,10 +20 10099140 . G T, 1027.64 . AS_RAW_BaseQRankSum=|-0.3,1|NaN;AS_RAW_MQ=104400.00|84512.00|0.00;AS_RAW_MQRankSum=|-2.5,1|NaN;AS_RAW_ReadPosRankSum=|0.6,1|NaN;AS_SB_TABLE=17,12|22,10|0,0;BaseQRankSum=-0.286;DP=63;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.435;RAW_MQandDP=196112,63;ReadPosRankSum=0.636 GT:AD:DP:GQ:PL:SB 0/1:29,32,0:61:99:1035,0,930,1122,1026,2148:17,12,22,10 20 10099141 . G . . END=10099189 GT:DP:GQ:MIN_DP:PL 0/0:67:99:64:0,120,1800 20 10099190 . G T, 1030.64 . AS_RAW_BaseQRankSum=|-0.3,1|NaN;AS_RAW_MQ=111600.00|95710.00|0.00;AS_RAW_MQRankSum=|-1.5,1|NaN;AS_RAW_ReadPosRankSum=|-1.6,1|NaN;AS_SB_TABLE=20,11|20,11|0,0;BaseQRankSum=-0.264;DP=62;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.445;RAW_MQandDP=207310,62;ReadPosRankSum=-1.577 GT:AD:DP:GQ:PL:SB 0/1:31,31,0:62:99:1038,0,1088,1131,1182,2313:20,11,20,11 20 10099191 . C . . END=10099219 GT:DP:GQ:MIN_DP:PL 0/0:58:99:46:0,111,1665 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.alleleSpecific.g.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.alleleSpecific.g.vcf.idx index 2e2d0b9c6607132fe18f3187f9990f149235144b..216520bd0679c36f5d67dd7d1b4b538beab4aaab 100644 GIT binary patch delta 396 zcmaE`kLkfarU}b<0$(#RfWU#a}av_GYGBl0Yn!uFf9ED5%Bm2p$&K-L9~qz pLe~gE=wJy5Z7l_%H|Rm=?L+y>?|m>q-AzZ4n440cZl9qR?<2S8|t zU . . END=10004192 GT:DP:GQ:MIN_DP:PL 0/0:49:99:45:0,106,1637 20 10004193 . G T, 937.64 . BaseQRankSum=-0.392;DP=54;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=3.385;RAW_MQandDP=188870,54;ReadPosRankSum=1.724 GT:AD:DP:GQ:PL:SB 0/1:23,28,0:51:99:945,0,776,1014,860,1875:12,11,12,16 20 10004194 . C . . END=10004221 GT:DP:GQ:MIN_DP:PL 0/0:50:99:46:0,105,1575 -20 10004222 . C CA, 41.60 . BaseQRankSum=0.124;DP=68;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.220;RAW_MQandDP=230226,68;ReadPosRankSum=1.271 GT:AD:DP:GQ:PL:SB 0/1:35,10,0:45:49:49,0,924,153,952,1105:20,15,4,6 -20 10004223 . A AG, 80.60 . BaseQRankSum=-0.749;DP=68;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=2.272;RAW_MQandDP=230910,68;ReadPosRankSum=0.490 GT:AD:DP:GQ:PL:SB 0/1:35,12,0:47:88:88,0,953,193,987,1180:16,19,6,6 +20 10004222 . C CA, 41.60 . BaseQRankSum=0.335;DP=68;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.220;RAW_MQandDP=230226,68;ReadPosRankSum=0.198 GT:AD:DP:GQ:PL:SB 0/1:35,10,0:45:49:49,0,924,153,952,1105:20,15,4,6 +20 10004223 . A AG, 80.60 . BaseQRankSum=-0.765;DP=68;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=2.272;RAW_MQandDP=230910,68;ReadPosRankSum=0.183 GT:AD:DP:GQ:PL:SB 0/1:35,12,0:47:88:88,0,953,193,987,1180:16,19,6,6 20 10004224 . A . . END=10004224 GT:DP:GQ:MIN_DP:PL 0/0:65:0:65:0,0,1201 20 10004225 . A . . END=10004240 GT:DP:GQ:MIN_DP:PL 0/0:70:99:65:0,117,1755 20 10004241 . G . . END=10004241 GT:DP:GQ:MIN_DP:PL 0/0:66:0:66:0,0,1965 @@ -215,7 +215,7 @@ 20 10004611 . C . . END=10004724 GT:DP:GQ:MIN_DP:PL 0/0:75:99:64:0,120,1800 20 10004725 . A G, 975.64 . BaseQRankSum=-2.393;DP=66;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=2.856;RAW_MQandDP=202162,66;ReadPosRankSum=1.932 GT:AD:DP:GQ:PL:SB 0/1:34,30,0:64:99:983,0,1139,1085,1228,2313:10,24,17,13 20 10004726 . T . . END=10004768 GT:DP:GQ:MIN_DP:PL 0/0:65:99:61:0,120,1800 -20 10004769 . TAAAACTATGC T, 970.60 . BaseQRankSum=1.796;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-6.531;RAW_MQandDP=222144,79;ReadPosRankSum=1.721 GT:AD:DP:GQ:PL:SB 0/1:37,26,0:63:99:978,0,1473,1089,1554,2643:14,23,7,19 +20 10004769 . TAAAACTATGC T, 970.60 . BaseQRankSum=0.807;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-6.531;RAW_MQandDP=222144,79;ReadPosRankSum=1.721 GT:AD:DP:GQ:PL:SB 0/1:37,26,0:63:99:978,0,1473,1089,1554,2643:14,23,7,19 20 10004780 . A . . END=10004873 GT:DP:GQ:MIN_DP:PL 0/0:77:99:69:0,120,1800 20 10004874 . A C, 3617.06 . DP=90;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=317023,90 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 1|1:0,87,0:87:99:0|1:10004874_A_C:3631,261,0,3631,261,3631:10004874:0,0,54,33 20 10004875 . T . . END=10004886 GT:DP:GQ:MIN_DP:PL 0/0:86:99:85:0,120,1800 @@ -249,7 +249,7 @@ 20 10007532 . G . . END=10007979 GT:DP:GQ:MIN_DP:PL 0/0:80:99:65:0,120,1800 20 10007980 . A C, 3539.06 . DP=92;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=339000,92 GT:AD:DP:GQ:PL:SB 1/1:0,90,0:90:99:3553,270,0,3553,270,3553:0,0,39,51 20 10007981 . A . . END=10008028 GT:DP:GQ:MIN_DP:PL 0/0:86:99:80:0,120,1800 -20 10008029 . T TA, 2009.03 . BaseQRankSum=0.438;DP=97;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=0.651;RAW_MQandDP=362251,97;ReadPosRankSum=-1.326 GT:AD:DP:GQ:PL:SB 1/1:3,74,0:77:99:2023,145,0,2032,222,2109:1,2,28,46 +20 10008029 . T TA, 2009.03 . BaseQRankSum=0.409;DP=97;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=0.651;RAW_MQandDP=362251,97;ReadPosRankSum=-1.357 GT:AD:DP:GQ:PL:SB 1/1:3,74,0:77:99:2023,145,0,2032,222,2109:1,2,28,46 20 10008030 . A . . END=10008145 GT:DP:GQ:MIN_DP:PL 0/0:82:99:76:0,120,1800 20 10008146 . TA T, 2166.03 . DP=77;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=282400,77 GT:AD:DP:GQ:PL:SB 1/1:0,70,0:70:99:2180,211,0,2180,211,2180:0,0,38,32 20 10008148 . A . . END=10008220 GT:DP:GQ:MIN_DP:PL 0/0:80:99:72:0,120,1800 @@ -259,22 +259,22 @@ 20 10008459 . A . . END=10008732 GT:DP:GQ:MIN_DP:PL 0/0:70:99:40:0,105,1575 20 10008733 . T . . END=10008733 GT:DP:GQ:MIN_DP:PL 0/0:47:94:47:0,94,1689 20 10008734 . G . . END=10008741 GT:DP:GQ:MIN_DP:PL 0/0:48:99:47:0,120,1800 -20 10008742 . G T, 736.64 . BaseQRankSum=3.893;DP=50;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.502;RAW_MQandDP=68715,50;ReadPosRankSum=0.190 GT:AD:DP:GQ:PL:SB 0/1:23,26,0:49:99:744,0,580,813,658,1471:10,13,11,15 +20 10008742 . G T, 736.64 . BaseQRankSum=3.893;DP=50;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.502;RAW_MQandDP=68715,50;ReadPosRankSum=0.200 GT:AD:DP:GQ:PL:SB 0/1:23,26,0:49:99:744,0,580,813,658,1471:10,13,11,15 20 10008743 . T . . END=10008757 GT:DP:GQ:MIN_DP:PL 0/0:46:99:42:0,99,1485 -20 10008758 . C CA, 706.49 . BaseQRankSum=0.119;DP=51;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.875;RAW_MQandDP=72567,51;ReadPosRankSum=-0.052 GT:AD:DP:GQ:PL:SB 1/1:4,34,0:38:10:720,10,0,733,102,825:3,1,16,18 +20 10008758 . C CA, 706.49 . BaseQRankSum=0.130;DP=51;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.875;RAW_MQandDP=72567,51;ReadPosRankSum=-0.262 GT:AD:DP:GQ:PL:SB 1/1:4,34,0:38:10:720,10,0,733,102,825:3,1,16,18 20 10008759 . A . . END=10008772 GT:DP:GQ:MIN_DP:PL 0/0:55:99:53:0,120,1800 20 10008773 . T . . END=10008773 GT:DP:GQ:MIN_DP:PL 0/0:54:0:54:0,0,1660 20 10008774 . T . . END=10008774 GT:DP:GQ:MIN_DP:PL 0/0:55:99:55:0,117,1755 20 10008775 . A . . END=10008775 GT:DP:GQ:MIN_DP:PL 0/0:55:60:55:0,60,1923 20 10008776 . G . . END=10008920 GT:DP:GQ:MIN_DP:PL 0/0:54:99:45:0,99,1480 -20 10008921 . C CA, 283.60 . BaseQRankSum=0.516;DP=60;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.306;RAW_MQandDP=188135,60;ReadPosRankSum=0.173 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:18,17,0:35:99:0|1:10008921_C_CA:291,0,366,345,416,761:10008921:10,8,8,9 +20 10008921 . C CA, 283.60 . BaseQRankSum=0.610;DP=60;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.306;RAW_MQandDP=188135,60;ReadPosRankSum=-0.017 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:18,17,0:35:99:0|1:10008921_C_CA:291,0,366,345,416,761:10008921:10,8,8,9 20 10008922 . A . . END=10008942 GT:DP:GQ:MIN_DP:PL 0/0:53:99:47:0,114,1710 20 10008943 . A . . END=10008944 GT:DP:GQ:MIN_DP:PL 0/0:47:78:47:0,78,1170 20 10008945 . A . . END=10008947 GT:DP:GQ:MIN_DP:PL 0/0:47:81:46:0,81,1215 -20 10008948 . TA T, 2094.03 . BaseQRankSum=0.956;DP=56;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=1.946;RAW_MQandDP=147147,56;ReadPosRankSum=0.884 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 1|1:1,53,0:54:99:0|1:10008921_C_CA:2108,117,0,2111,159,2153:10008921:1,0,36,17 +20 10008948 . TA T, 2094.03 . BaseQRankSum=0.994;DP=56;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=1.946;RAW_MQandDP=147147,56;ReadPosRankSum=0.884 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 1|1:1,53,0:54:99:0|1:10008921_C_CA:2108,117,0,2111,159,2153:10008921:1,0,36,17 20 10008950 . A . . END=10008950 GT:DP:GQ:MIN_DP:PL 0/0:52:96:52:0,96,1440 20 10008951 . A . . END=10008951 GT:DP:GQ:MIN_DP:PL 0/0:51:87:51:0,87,1305 -20 10008952 . CACACACACACACA C,CCA,CCACACACACA,CCACACACACACA, 1702.02 . BaseQRankSum=1.046;DP=63;ExcessHet=3.0103;MLEAC=0,1,0,1,0;MLEAF=0.00,0.500,0.00,0.500,0.00;MQRankSum=1.844;RAW_MQandDP=165341,63;ReadPosRankSum=0.716 GT:AD:DP:GQ:PL:SB 2/4:1,3,14,5,11,0:34:99:1719,888,1213,538,767,801,740,494,153,687,597,341,0,444,535,1150,1059,712,761,609,1293:1,0,25,8 +20 10008952 . CACACACACACACA C,CCA,CCACACACACA,CCACACACACACA, 1702.02 . BaseQRankSum=1.026;DP=63;ExcessHet=3.0103;MLEAC=0,1,0,1,0;MLEAF=0.00,0.500,0.00,0.500,0.00;MQRankSum=1.844;RAW_MQandDP=165341,63;ReadPosRankSum=0.666 GT:AD:DP:GQ:PL:SB 2/4:1,3,14,5,11,0:34:99:1719,888,1213,538,767,801,740,494,153,687,597,341,0,444,535,1150,1059,712,761,609,1293:1,0,25,8 20 10008966 . C . . END=10008986 GT:DP:GQ:MIN_DP:PL 0/0:58:99:56:0,120,1800 20 10008987 . A . . END=10008989 GT:DP:GQ:MIN_DP:PL 0/0:59:94:59:0,94,2181 20 10008990 . C . . END=10009226 GT:DP:GQ:MIN_DP:PL 0/0:61:99:38:0,102,1530 @@ -292,9 +292,9 @@ 20 10009796 . C . . END=10009832 GT:DP:GQ:MIN_DP:PL 0/0:49:99:44:0,99,1485 20 10009833 . A . . END=10009840 GT:DP:GQ:MIN_DP:PL 0/0:53:63:51:0,63,945 20 10009841 . A . . END=10009841 GT:DP:GQ:MIN_DP:PL 0/0:51:39:51:0,39,585 -20 10009842 . G GAA, 562.60 . BaseQRankSum=0.183;DP=52;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.936;RAW_MQandDP=150768,52;ReadPosRankSum=1.754 GT:AD:DP:GQ:PL:SB 0/1:19,16,0:35:99:570,0,691,628,739,1367:9,10,8,8 +20 10009842 . G GAA, 562.60 . BaseQRankSum=0.383;DP=52;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.936;RAW_MQandDP=150768,52;ReadPosRankSum=1.757 GT:AD:DP:GQ:PL:SB 0/1:19,16,0:35:99:570,0,691,628,739,1367:9,10,8,8 20 10009843 . A . . END=10009843 GT:DP:GQ:MIN_DP:PL 0/0:51:36:51:0,36,540 -20 10009844 . G A, 683.64 . BaseQRankSum=0.998;DP=54;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.975;RAW_MQandDP=155209,54;ReadPosRankSum=-1.575 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:16,19,0:35:99:0|1:10009844_G_A:691,0,585,739,644,1383:10009844:8,8,9,10 +20 10009844 . G A, 683.64 . BaseQRankSum=1.116;DP=54;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.975;RAW_MQandDP=155209,54;ReadPosRankSum=-2.354 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:16,19,0:35:99:0|1:10009844_G_A:691,0,585,739,644,1383:10009844:8,8,9,10 20 10009845 . A . . END=10009847 GT:DP:GQ:MIN_DP:PL 0/0:51:42:51:0,42,630 20 10009848 . G . . END=10009848 GT:DP:GQ:MIN_DP:PL 0/0:54:51:54:0,51,765 20 10009849 . A . . END=10009850 GT:DP:GQ:MIN_DP:PL 0/0:55:57:54:0,57,855 @@ -303,9 +303,9 @@ 20 10009861 . A . . END=10009864 GT:DP:GQ:MIN_DP:PL 0/0:58:84:56:0,84,1260 20 10009865 . A . . END=10009869 GT:DP:GQ:MIN_DP:PL 0/0:57:90:56:0,90,1350 20 10009870 . G . . END=10009870 GT:DP:GQ:MIN_DP:PL 0/0:57:99:57:0,99,1485 -20 10009871 . A G, 679.64 . BaseQRankSum=-0.803;DP=62;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.336;RAW_MQandDP=161937,62;ReadPosRankSum=1.491 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:18,19,0:37:99:0|1:10009844_G_A:687,0,593,740,652,1392:10009844:10,8,9,10 +20 10009871 . A G, 679.64 . BaseQRankSum=-0.803;DP=62;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.336;RAW_MQandDP=161937,62;ReadPosRankSum=0.840 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:18,19,0:37:99:0|1:10009844_G_A:687,0,593,740,652,1392:10009844:10,8,9,10 20 10009872 . G . . END=10009874 GT:DP:GQ:MIN_DP:PL 0/0:57:99:55:0,108,1620 -20 10009875 . A G,AGGGAGG, 2389.06 . BaseQRankSum=0.378;DP=58;ExcessHet=3.0103;MLEAC=1,1,0;MLEAF=0.500,0.500,0.00;MQRankSum=1.413;RAW_MQandDP=147537,58;ReadPosRankSum=1.040 GT:AD:DP:GQ:PL:SB 1/2:2,15,14,0:31:99:2406,645,532,697,0,574,1881,654,701,1805:2,0,13,16 +20 10009875 . A G,AGGGAGG, 2389.06 . BaseQRankSum=0.378;DP=58;ExcessHet=3.0103;MLEAC=1,1,0;MLEAF=0.500,0.500,0.00;MQRankSum=1.413;RAW_MQandDP=147537,58;ReadPosRankSum=1.373 GT:AD:DP:GQ:PL:SB 1/2:2,15,14,0:31:99:2406,645,532,697,0,574,1881,654,701,1805:2,0,13,16 20 10009876 . G . . END=10009878 GT:DP:GQ:MIN_DP:PL 0/0:52:99:51:0,114,1710 20 10009879 . A G, 2259.06 . BaseQRankSum=1.534;DP=53;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=1.681;RAW_MQandDP=135061,53;ReadPosRankSum=1.113 GT:AD:DP:GQ:PL:SB 1/1:2,51,0:53:99:2273,150,0,2276,154,2279:2,0,18,33 20 10009880 . G . . END=10009882 GT:DP:GQ:MIN_DP:PL 0/0:49:99:48:0,120,1800 @@ -332,7 +332,7 @@ 20 10011076 . G . . END=10011308 GT:DP:GQ:MIN_DP:PL 0/0:74:99:52:0,120,1800 20 10011309 . T C, 2707.06 . DP=80;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=288000,80 GT:AD:DP:GQ:PL:SB 1/1:0,77,0:77:99:2721,231,0,2721,231,2721:0,0,30,47 20 10011310 . G . . END=10011516 GT:DP:GQ:MIN_DP:PL 0/0:80:99:70:0,120,1800 -20 10011517 . GAA G,GA,GAAA, 520.60 . BaseQRankSum=0.690;DP=99;ExcessHet=3.0103;MLEAC=0,1,0,0;MLEAF=0.00,0.500,0.00,0.00;MQRankSum=1.797;RAW_MQandDP=355310,99;ReadPosRankSum=0.315 GT:AD:DP:GQ:PL:SB 0/2:37,2,28,6,0:73:99:528,611,2117,0,1040,874,605,1499,722,1650,667,1699,965,1470,1638:23,14,19,17 +20 10011517 . GAA G,GA,GAAA, 520.60 . BaseQRankSum=0.690;DP=99;ExcessHet=3.0103;MLEAC=0,1,0,0;MLEAF=0.00,0.500,0.00,0.00;MQRankSum=1.797;RAW_MQandDP=355310,99;ReadPosRankSum=0.337 GT:AD:DP:GQ:PL:SB 0/2:37,2,28,6,0:73:99:528,611,2117,0,1040,874,605,1499,722,1650,667,1699,965,1470,1638:23,14,19,17 20 10011520 . A . . END=10011665 GT:DP:GQ:MIN_DP:PL 0/0:68:99:62:0,120,1800 20 10011666 . C T, 2976.06 . DP=74;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=258123,74 GT:AD:DP:GQ:PL:SB 1/1:0,73,0:73:99:2990,220,0,2990,220,2990:0,0,43,30 20 10011667 . A . . END=10011938 GT:DP:GQ:MIN_DP:PL 0/0:87:99:64:0,111,1665 @@ -490,11 +490,11 @@ 20 10012622 . G . . END=10012624 GT:DP:GQ:MIN_DP:PL 0/0:19:54:19:0,54,810 20 10012625 . C . . END=10012625 GT:DP:GQ:MIN_DP:PL 0/0:20:57:20:0,57,855 20 10012626 . C . . END=10012630 GT:DP:GQ:MIN_DP:PL 0/0:21:60:21:0,60,900 -20 10012631 . C CG, 514.60 . BaseQRankSum=-1.030;DP=21;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.670;RAW_MQandDP=49065,21;ReadPosRankSum=-1.813 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:8,13,0:21:99:0|1:10012631_C_CG:522,0,297,546,336,882:10012631:8,0,9,4 +20 10012631 . C CG, 514.60 . BaseQRankSum=-1.030;DP=21;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.670;RAW_MQandDP=49065,21;ReadPosRankSum=-1.777 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:8,13,0:21:99:0|1:10012631_C_CG:522,0,297,546,336,882:10012631:8,0,9,4 20 10012632 . G . . END=10012632 GT:DP:GQ:MIN_DP:PL 0/0:21:54:21:0,54,810 20 10012633 . C . . END=10012633 GT:DP:GQ:MIN_DP:PL 0/0:20:51:20:0,51,765 20 10012634 . C . . END=10012635 GT:DP:GQ:MIN_DP:PL 0/0:22:54:22:0,54,810 -20 10012636 . G C, 548.64 . BaseQRankSum=2.711;DP=22;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.513;RAW_MQandDP=52665,22;ReadPosRankSum=-1.915 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:8,14,0:22:99:0|1:10012631_C_CG:556,0,294,580,336,916:10012631:8,0,10,4 +20 10012636 . G C, 548.64 . BaseQRankSum=2.711;DP=22;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.513;RAW_MQandDP=52665,22;ReadPosRankSum=-1.777 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:8,14,0:22:99:0|1:10012631_C_CG:556,0,294,580,336,916:10012631:8,0,10,4 20 10012637 . A . . END=10012639 GT:DP:GQ:MIN_DP:PL 0/0:20:54:20:0,54,810 20 10012640 . C . . END=10012640 GT:DP:GQ:MIN_DP:PL 0/0:22:57:22:0,57,855 20 10012641 . T . . END=10012662 GT:DP:GQ:MIN_DP:PL 0/0:24:60:23:0,60,895 @@ -569,7 +569,7 @@ 20 10013575 . T . . END=10014589 GT:DP:GQ:MIN_DP:PL 0/0:72:99:43:0,101,1658 20 10014590 . A . . END=10014590 GT:DP:GQ:MIN_DP:PL 0/0:44:93:44:0,93,1625 20 10014591 . T . . END=10014989 GT:DP:GQ:MIN_DP:PL 0/0:72:99:42:0,116,1732 -20 10014990 . C CAT, 1265.60 . BaseQRankSum=1.756;DP=89;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=3.260;RAW_MQandDP=329869,89;ReadPosRankSum=-0.437 GT:AD:DP:GQ:PL:SB 0/1:38,39,0:77:99:1273,0,1250,1388,1367,2755:28,10,26,13 +20 10014990 . C CAT, 1265.60 . BaseQRankSum=1.930;DP=89;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=3.260;RAW_MQandDP=329869,89;ReadPosRankSum=-0.311 GT:AD:DP:GQ:PL:SB 0/1:38,39,0:77:99:1273,0,1250,1388,1367,2755:28,10,26,13 20 10014991 . A . . END=10015385 GT:DP:GQ:MIN_DP:PL 0/0:73:99:41:0,102,1530 20 10015386 . G . . END=10015388 GT:DP:GQ:MIN_DP:PL 0/0:39:90:39:0,90,1350 20 10015389 . A . . END=10015390 GT:DP:GQ:MIN_DP:PL 0/0:38:81:38:0,81,1215 @@ -704,7 +704,7 @@ 20 10024297 . T . . END=10024297 GT:DP:GQ:MIN_DP:PL 0/0:68:65:68:0,65,2188 20 10024298 . T . . END=10024298 GT:DP:GQ:MIN_DP:PL 0/0:66:59:66:0,59,2080 20 10024299 . C . . END=10024299 GT:DP:GQ:MIN_DP:PL 0/0:62:0:62:0,0,1480 -20 10024300 . CTT C,CT,CTTTT, 126.96 . BaseQRankSum=2.384;DP=56;ExcessHet=3.0103;MLEAC=0,1,1,0;MLEAF=0.00,0.500,0.500,0.00;MQRankSum=-0.597;RAW_MQandDP=153536,56;ReadPosRankSum=-1.290 GT:AD:DP:GQ:PL:SB 2/3:3,5,4,8,0:20:9:144,72,401,88,202,222,47,9,0,215,183,284,255,136,369:1,2,11,6 +20 10024300 . CTT C,CT,CTTTT, 126.96 . BaseQRankSum=2.355;DP=56;ExcessHet=3.0103;MLEAC=0,1,1,0;MLEAF=0.00,0.500,0.500,0.00;MQRankSum=-0.597;RAW_MQandDP=153536,56;ReadPosRankSum=-1.290 GT:AD:DP:GQ:PL:SB 2/3:3,5,4,8,0:20:9:144,72,401,88,202,222,47,9,0,215,183,284,255,136,369:1,2,11,6 20 10024303 . T . . END=10024303 GT:DP:GQ:MIN_DP:PL 0/0:67:57:67:0,57,855 20 10024304 . T . . END=10024307 GT:DP:GQ:MIN_DP:PL 0/0:69:63:68:0,63,945 20 10024308 . T . . END=10024310 GT:DP:GQ:MIN_DP:PL 0/0:70:78:70:0,78,1170 @@ -723,19 +723,19 @@ 20 10026358 . A . . END=10026793 GT:DP:GQ:MIN_DP:PL 0/0:72:99:41:0,102,1530 20 10026794 . C T, 1105.64 . BaseQRankSum=2.828;DP=56;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.719;RAW_MQandDP=198841,56;ReadPosRankSum=-0.533 GT:AD:DP:GQ:PL:SB 0/1:19,33,0:52:99:1113,0,529,1170,627,1798:7,12,15,18 20 10026795 . G . . END=10027233 GT:DP:GQ:MIN_DP:PL 0/0:70:99:52:0,115,1800 -20 10027234 . A ATTAG, 1350.60 . BaseQRankSum=-0.406;DP=75;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.845;RAW_MQandDP=247451,75;ReadPosRankSum=-0.979 GT:AD:DP:GQ:PL:SB 0/1:34,35,0:69:99:1358,0,1321,1461,1426,2887:18,16,15,20 +20 10027234 . A ATTAG, 1350.60 . BaseQRankSum=-0.406;DP=75;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.845;RAW_MQandDP=247451,75;ReadPosRankSum=-0.510 GT:AD:DP:GQ:PL:SB 0/1:34,35,0:69:99:1358,0,1321,1461,1426,2887:18,16,15,20 20 10027235 . T . . END=10027867 GT:DP:GQ:MIN_DP:PL 0/0:78:99:56:0,120,1800 -20 10027868 . A G, 1760.64 . BaseQRankSum=-5.798;DP=91;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.047;RAW_MQandDP=322082,91;ReadPosRankSum=1.872 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:44,46,0:90:99:0|1:10027868_A_G:1768,0,1671,1901,1810,3710:10027868:19,25,27,19 +20 10027868 . A G, 1760.64 . BaseQRankSum=-5.793;DP=91;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.047;RAW_MQandDP=322082,91;ReadPosRankSum=1.872 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:44,46,0:90:99:0|1:10027868_A_G:1768,0,1671,1901,1810,3710:10027868:19,25,27,19 20 10027869 . A . . END=10027871 GT:DP:GQ:MIN_DP:PL 0/0:86:99:85:0,120,1800 20 10027872 . A G, 1745.64 . BaseQRankSum=-5.491;DP=88;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.065;RAW_MQandDP=311282,88;ReadPosRankSum=1.053 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:42,45,0:87:99:0|1:10027868_A_G:1753,0,1606,1879,1742,3621:10027868:17,25,26,19 20 10027873 . G . . END=10028866 GT:DP:GQ:MIN_DP:PL 0/0:80:99:55:0,120,1800 -20 10028867 . A ATG, 1134.60 . BaseQRankSum=-0.874;DP=93;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=2.711;RAW_MQandDP=342441,93;ReadPosRankSum=0.364 GT:AD:DP:GQ:PL:SB 0/1:32,39,0:71:99:1142,0,918,1240,1035,2275:11,21,18,21 +20 10028867 . A ATG, 1134.60 . BaseQRankSum=-0.874;DP=93;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=2.711;RAW_MQandDP=342441,93;ReadPosRankSum=0.630 GT:AD:DP:GQ:PL:SB 0/1:32,39,0:71:99:1142,0,918,1240,1035,2275:11,21,18,21 20 10028868 . T . . END=10030187 GT:DP:GQ:MIN_DP:PL 0/0:80:99:60:0,120,1800 20 10030188 . T A, 1393.64 . BaseQRankSum=0.711;DP=82;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.013;RAW_MQandDP=290210,82;ReadPosRankSum=-0.553 GT:AD:DP:GQ:PL:SB 0/1:42,39,0:81:99:1401,0,1524,1527,1641,3168:24,18,15,24 20 10030189 . G . . END=10030566 GT:DP:GQ:MIN_DP:PL 0/0:71:99:41:0,103,1575 20 10030567 . G . . END=10030567 GT:DP:GQ:MIN_DP:PL 0/0:41:90:41:0,90,1511 20 10030568 . C . . END=10031253 GT:DP:GQ:MIN_DP:PL 0/0:70:99:42:0,114,1710 -20 10031254 . A AT, 1493.60 . BaseQRankSum=-0.091;DP=90;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.017;RAW_MQandDP=323069,90;ReadPosRankSum=0.495 GT:AD:DP:GQ:PL:SB 0/1:38,47,0:85:99:1501,0,1159,1615,1300,2916:27,11,25,22 +20 10031254 . A AT, 1493.60 . BaseQRankSum=-0.091;DP=90;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.017;RAW_MQandDP=323069,90;ReadPosRankSum=0.663 GT:AD:DP:GQ:PL:SB 0/1:38,47,0:85:99:1501,0,1159,1615,1300,2916:27,11,25,22 20 10031255 . T . . END=10031341 GT:DP:GQ:MIN_DP:PL 0/0:95:99:86:0,120,1800 20 10031342 . G A, 1855.64 . BaseQRankSum=1.833;DP=93;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.866;RAW_MQandDP=332041,93;ReadPosRankSum=-0.012 GT:AD:DP:GQ:PL:SB 0/1:41,52,0:93:99:1863,0,1375,1986,1531,3517:22,19,31,21 20 10031343 . A . . END=10031797 GT:DP:GQ:MIN_DP:PL 0/0:91:99:66:0,120,1800 @@ -749,7 +749,7 @@ 20 10032414 . T . . END=10032881 GT:DP:GQ:MIN_DP:PL 0/0:70:99:55:0,120,1800 20 10032882 . A T, 1223.64 . BaseQRankSum=-3.697;DP=76;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.014;RAW_MQandDP=270841,76;ReadPosRankSum=0.626 GT:AD:DP:GQ:PL:SB 0/1:39,36,0:75:99:1231,0,1406,1348,1514,2862:28,11,22,14 20 10032883 . A . . END=10032971 GT:DP:GQ:MIN_DP:PL 0/0:67:99:61:0,120,1800 -20 10032972 . C CAT, 1152.60 . BaseQRankSum=-0.354;DP=67;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.017;RAW_MQandDP=238441,67;ReadPosRankSum=-1.232 GT:AD:DP:GQ:PL:SB 0/1:33,30,0:63:99:1160,0,1296,1260,1386,2646:17,16,11,19 +20 10032972 . C CAT, 1152.60 . BaseQRankSum=-0.354;DP=67;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.017;RAW_MQandDP=238441,67;ReadPosRankSum=-0.723 GT:AD:DP:GQ:PL:SB 0/1:33,30,0:63:99:1160,0,1296,1260,1386,2646:17,16,11,19 20 10032973 . T . . END=10033636 GT:DP:GQ:MIN_DP:PL 0/0:78:99:50:0,120,1800 20 10033637 . C . . END=10033637 GT:DP:GQ:MIN_DP:PL 0/0:58:97:58:0,97,2210 20 10033638 . C . . END=10034305 GT:DP:GQ:MIN_DP:PL 0/0:85:99:53:0,120,1800 @@ -767,7 +767,7 @@ 20 10036158 . T . . END=10036160 GT:DP:GQ:MIN_DP:PL 0/0:42:99:40:0,117,1755 20 10036161 . T . . END=10036161 GT:DP:GQ:MIN_DP:PL 0/0:42:82:42:0,82,1514 20 10036162 . G . . END=10036929 GT:DP:GQ:MIN_DP:PL 0/0:76:99:43:0,113,1513 -20 10036930 . CGATAGCCCTAGCCCTAGATA C, 1070.60 . BaseQRankSum=0.200;DP=98;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.048;RAW_MQandDP=290616,98;ReadPosRankSum=0.460 GT:AD:DP:GQ:PL:SB 0/1:39,29,0:68:99:1078,0,1500,1196,1598,2794:11,28,15,14 +20 10036930 . CGATAGCCCTAGCCCTAGATA C, 1070.60 . BaseQRankSum=0.720;DP=98;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.048;RAW_MQandDP=290616,98;ReadPosRankSum=0.460 GT:AD:DP:GQ:PL:SB 0/1:39,29,0:68:99:1078,0,1500,1196,1598,2794:11,28,15,14 20 10036951 . G . . END=10036956 GT:DP:GQ:MIN_DP:PL 0/0:74:99:70:0,120,1800 20 10036957 . C . . END=10036957 GT:DP:GQ:MIN_DP:PL 0/0:70:37:70:0,37,2472 20 10036958 . C . . END=10036958 GT:DP:GQ:MIN_DP:PL 0/0:70:40:70:0,40,2490 @@ -808,13 +808,13 @@ 20 10040773 . T . . END=10040811 GT:DP:GQ:MIN_DP:PL 0/0:77:99:75:0,120,1800 20 10040812 . AT A, 2631.03 . DP=83;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=217699,83 GT:AD:DP:GQ:PL:SB 1/1:0,71,0:71:99:2645,214,0,2645,214,2645:0,0,36,35 20 10040814 . T . . END=10040820 GT:DP:GQ:MIN_DP:PL 0/0:77:99:75:0,120,1800 -20 10040821 . T A, 1166.64 . BaseQRankSum=0.152;DP=83;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.175;RAW_MQandDP=217699,83;ReadPosRankSum=-1.350 GT:AD:DP:GQ:PL:SB 0/1:38,39,0:77:99:1174,0,1102,1288,1219,2507:20,18,21,18 +20 10040821 . T A, 1166.64 . BaseQRankSum=0.152;DP=83;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.175;RAW_MQandDP=217699,83;ReadPosRankSum=-1.315 GT:AD:DP:GQ:PL:SB 0/1:38,39,0:77:99:1174,0,1102,1288,1219,2507:20,18,21,18 20 10040822 . A . . END=10041303 GT:DP:GQ:MIN_DP:PL 0/0:71:99:54:0,119,1800 20 10041304 . C T, 2780.06 . DP=68;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=239810,68 GT:AD:DP:GQ:PL:SB 1/1:0,68,0:68:99:2794,204,0,2794,204,2794:0,0,34,34 20 10041305 . G . . END=10041697 GT:DP:GQ:MIN_DP:PL 0/0:62:99:48:0,120,1800 -20 10041698 . C CAT, 9.61 . BaseQRankSum=1.595;DP=80;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.194;RAW_MQandDP=275031,80;ReadPosRankSum=0.579 GT:AD:DP:GQ:PL:SB 0/1:50,7,0:57:17:17,0,1423,167,1444,1611:21,29,2,5 +20 10041698 . C CAT, 9.61 . BaseQRankSum=1.887;DP=80;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.194;RAW_MQandDP=275031,80;ReadPosRankSum=-0.164 GT:AD:DP:GQ:PL:SB 0/1:50,7,0:57:17:17,0,1423,167,1444,1611:21,29,2,5 20 10041699 . A . . END=10041700 GT:DP:GQ:MIN_DP:PL 0/0:79:99:78:0,120,1800 -20 10041701 . A ATG,ATATG, 1431.60 . BaseQRankSum=0.848;DP=80;ExcessHet=3.0103;MLEAC=0,1,0;MLEAF=0.00,0.500,0.00;MQRankSum=0.340;RAW_MQandDP=277790,80;ReadPosRankSum=-0.223 GT:AD:DP:GQ:PL:SB 0/2:8,0,48,0:56:58:1439,1580,2725,0,261,58,1573,2315,265,2200:2,6,21,27 +20 10041701 . A ATG,ATATG, 1431.60 . BaseQRankSum=0.848;DP=80;ExcessHet=3.0103;MLEAC=0,1,0;MLEAF=0.00,0.500,0.00;MQRankSum=0.340;RAW_MQandDP=277790,80;ReadPosRankSum=-0.023 GT:AD:DP:GQ:PL:SB 0/2:8,0,48,0:56:58:1439,1580,2725,0,261,58,1573,2315,265,2200:2,6,21,27 20 10041702 . T . . END=10042318 GT:DP:GQ:MIN_DP:PL 0/0:64:99:49:0,117,1800 20 10042319 . C T, 2673.06 . DP=69;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=240651,69 GT:AD:DP:GQ:PL:SB 1/1:0,66,0:66:99:2687,199,0,2687,199,2687:0,0,38,28 20 10042320 . C . . END=10042760 GT:DP:GQ:MIN_DP:PL 0/0:74:99:60:0,120,1800 @@ -868,7 +868,7 @@ 20 10052689 . A . . END=10058021 GT:DP:GQ:MIN_DP:PL 0/0:74:99:36:0,99,1485 20 10058022 . T C, 996.64 . BaseQRankSum=-2.346;DP=72;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.466;RAW_MQandDP=251979,72;ReadPosRankSum=0.018 GT:AD:DP:GQ:PL:SB 0/1:36,32,0:68:99:1004,0,1261,1112,1357,2469:16,20,13,19 20 10058023 . A . . END=10062934 GT:DP:GQ:MIN_DP:PL 0/0:76:99:46:0,105,1575 -20 10062935 . CAAA C,CA,CAA,CAAAA, 119.60 . BaseQRankSum=1.234;DP=90;ExcessHet=3.0103;MLEAC=0,0,0,1,0;MLEAF=0.00,0.00,0.00,0.500,0.00;MQRankSum=-1.515;RAW_MQandDP=266450,90;ReadPosRankSum=-0.973 GT:AD:DP:GQ:PL:SB 0/4:5,2,3,4,10,0:24:6:127,208,1805,130,1135,1006,104,613,541,490,0,148,50,6,109,237,973,853,595,166,879:2,3,9,10 +20 10062935 . CAAA C,CA,CAA,CAAAA, 119.60 . BaseQRankSum=1.237;DP=90;ExcessHet=3.0103;MLEAC=0,0,0,1,0;MLEAF=0.00,0.00,0.00,0.500,0.00;MQRankSum=-1.515;RAW_MQandDP=266450,90;ReadPosRankSum=-0.974 GT:AD:DP:GQ:PL:SB 0/4:5,2,3,4,10,0:24:6:127,208,1805,130,1135,1006,104,613,541,490,0,148,50,6,109,237,973,853,595,166,879:2,3,9,10 20 10062939 . A . . END=10062955 GT:DP:GQ:MIN_DP:PL 0/0:82:99:74:0,120,1800 20 10062956 . T . . END=10062956 GT:DP:GQ:MIN_DP:PL 0/0:69:80:69:0,80,2241 20 10062957 . C . . END=10065775 GT:DP:GQ:MIN_DP:PL 0/0:70:99:42:0,105,1575 @@ -882,7 +882,7 @@ 20 10065803 . G . . END=10065803 GT:DP:GQ:MIN_DP:PL 0/0:59:81:59:0,81,2051 20 10065804 . C . . END=10067046 GT:DP:GQ:MIN_DP:PL 0/0:72:99:48:0,102,1530 20 10067047 . A . . END=10067048 GT:DP:GQ:MIN_DP:PL 0/0:51:96:50:0,96,1440 -20 10067049 . TAAAAAAAAA T,TA,TAA, 639.02 . BaseQRankSum=0.177;DP=73;ExcessHet=3.0103;MLEAC=0,1,1,0;MLEAF=0.00,0.500,0.500,0.00;MQRankSum=-0.342;RAW_MQandDP=218656,73;ReadPosRankSum=-1.322 GT:AD:DP:GQ:PL:SB 2/3:2,4,7,9,0:22:99:656,367,923,167,381,339,137,101,0,106,446,592,395,171,628:1,1,12,8 +20 10067049 . TAAAAAAAAA T,TA,TAA, 639.02 . BaseQRankSum=-0.086;DP=73;ExcessHet=3.0103;MLEAC=0,1,1,0;MLEAF=0.00,0.500,0.500,0.00;MQRankSum=-0.342;RAW_MQandDP=218656,73;ReadPosRankSum=-1.322 GT:AD:DP:GQ:PL:SB 2/3:2,4,7,9,0:22:99:656,367,923,167,381,339,137,101,0,106,446,592,395,171,628:1,1,12,8 20 10067059 . A . . END=10067067 GT:DP:GQ:MIN_DP:PL 0/0:57:99:50:0,99,1485 20 10067068 . A . . END=10067070 GT:DP:GQ:MIN_DP:PL 0/0:44:96:44:0,96,1440 20 10067071 . A . . END=10067089 GT:DP:GQ:MIN_DP:PL 0/0:48:99:46:0,102,1530 @@ -996,11 +996,11 @@ 20 10076340 . A . . END=10076398 GT:DP:GQ:MIN_DP:PL 0/0:88:99:71:0,120,1800 20 10076399 . G A, 1828.64 . BaseQRankSum=4.154;DP=95;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=342000,95;ReadPosRankSum=-1.058 GT:AD:DP:GQ:PL:SB 0/1:44,50,0:94:99:1836,0,1544,1969,1694,3663:22,22,22,28 20 10076400 . G . . END=10076988 GT:DP:GQ:MIN_DP:PL 0/0:73:99:51:0,120,1800 -20 10076989 . CAA C,CA,CAAA, 242.02 . BaseQRankSum=-0.673;DP=83;ExcessHet=3.0103;MLEAC=0,1,1,0;MLEAF=0.00,0.500,0.500,0.00;MQRankSum=-0.706;RAW_MQandDP=279487,83;ReadPosRankSum=-1.056 GT:AD:DP:GQ:PL:SB 2/3:7,5,13,7,0:32:40:259,260,1130,40,436,371,157,266,0,379,329,700,422,328,711:4,3,13,12 +20 10076989 . CAA C,CA,CAAA, 242.02 . BaseQRankSum=-0.600;DP=83;ExcessHet=3.0103;MLEAC=0,1,1,0;MLEAF=0.00,0.500,0.500,0.00;MQRankSum=-0.706;RAW_MQandDP=279487,83;ReadPosRankSum=-0.957 GT:AD:DP:GQ:PL:SB 2/3:7,5,13,7,0:32:40:259,260,1130,40,436,371,157,266,0,379,329,700,422,328,711:4,3,13,12 20 10076992 . A . . END=10077007 GT:DP:GQ:MIN_DP:PL 0/0:70:99:60:0,120,1800 -20 10077008 . T A, 0 . BaseQRankSum=-1.801;DP=69;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=-1.347;RAW_MQandDP=226328,69;ReadPosRankSum=0.806 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|0:50,4,0:54:45:0|1:10077008_T_A:0,45,2017,151,2029,2135:10077008:19,31,4,0 +20 10077008 . T A, 0 . BaseQRankSum=-1.698;DP=69;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=-1.347;RAW_MQandDP=226328,69;ReadPosRankSum=0.789 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|0:50,4,0:54:45:0|1:10077008_T_A:0,45,2017,151,2029,2135:10077008:19,31,4,0 20 10077009 . A . . END=10077009 GT:DP:GQ:MIN_DP:PL 0/0:53:99:53:0,120,1800 -20 10077010 . G A, 0 . BaseQRankSum=-1.733;DP=58;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=-1.347;RAW_MQandDP=197764,58;ReadPosRankSum=0.859 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|0:50,4,0:54:45:0|1:10077008_T_A:0,45,2017,151,2029,2134:10077008:19,31,4,0 +20 10077010 . G A, 0 . BaseQRankSum=-1.733;DP=58;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=-1.347;RAW_MQandDP=197764,58;ReadPosRankSum=0.943 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|0:50,4,0:54:45:0|1:10077008_T_A:0,45,2017,151,2029,2134:10077008:19,31,4,0 20 10077011 . A . . END=10077751 GT:DP:GQ:MIN_DP:PL 0/0:69:99:44:0,102,1654 20 10077752 . T C, 1366.64 . BaseQRankSum=-6.503;DP=83;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=298800,83;ReadPosRankSum=-0.352 GT:AD:DP:GQ:PL:SB 0/1:34,45,0:79:99:1374,0,1187,1477,1322,2799:16,18,16,29 20 10077753 . G . . END=10079475 GT:DP:GQ:MIN_DP:PL 0/0:70:99:46:0,108,1620 @@ -1047,7 +1047,7 @@ 20 10087755 . G . . END=10087803 GT:DP:GQ:MIN_DP:PL 0/0:101:99:82:0,120,1800 20 10087804 . C T, 1640.64 . BaseQRankSum=1.940;DP=104;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=2.618;RAW_MQandDP=376641,104;ReadPosRankSum=0.341 GT:AD:DP:GQ:PL:SB 0/1:50,50,0:100:99:1648,0,1511,1797,1661,3458:33,17,28,22 20 10087805 . G . . END=10087819 GT:DP:GQ:MIN_DP:PL 0/0:101:99:96:0,120,1800 -20 10087820 . CAG C,CAGAG, 456.60 . BaseQRankSum=-1.974;DP=102;ExcessHet=3.0103;MLEAC=0,1,0;MLEAF=0.00,0.500,0.00;MQRankSum=0.422;RAW_MQandDP=373500,102;ReadPosRankSum=-0.357 GT:AD:DP:GQ:PL:SB 0/2:35,0,18,0:53:99:464,665,2541,0,1195,1170,657,2217,1237,2172:17,18,8,10 +20 10087820 . CAG C,CAGAG, 456.60 . BaseQRankSum=-1.974;DP=102;ExcessHet=3.0103;MLEAC=0,1,0;MLEAF=0.00,0.500,0.00;MQRankSum=0.422;RAW_MQandDP=373500,102;ReadPosRankSum=-0.019 GT:AD:DP:GQ:PL:SB 0/2:35,0,18,0:53:99:464,665,2541,0,1195,1170,657,2217,1237,2172:17,18,8,10 20 10087823 . A . . END=10087841 GT:DP:GQ:MIN_DP:PL 0/0:85:99:82:0,120,1800 20 10087842 . A . . END=10087842 GT:DP:GQ:MIN_DP:PL 0/0:81:0:81:0,0,2313 20 10087843 . A . . END=10087843 GT:DP:GQ:MIN_DP:PL 0/0:81:99:81:0,120,1800 @@ -1057,9 +1057,9 @@ 20 10088064 . G . . END=10088698 GT:DP:GQ:MIN_DP:PL 0/0:87:99:60:0,120,1800 20 10088699 . C T, 797.64 . BaseQRankSum=3.803;DP=67;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.140;RAW_MQandDP=216897,67;ReadPosRankSum=-1.456 GT:AD:DP:GQ:PL:SB 0/1:36,26,0:62:99:805,0,1088,913,1166,2079:15,21,19,7 20 10088700 . G . . END=10088729 GT:DP:GQ:MIN_DP:PL 0/0:53:99:51:0,120,1800 -20 10088730 . G A, 993.64 . BaseQRankSum=-0.058;DP=57;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.213;RAW_MQandDP=159641,57;ReadPosRankSum=0.581 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:30,26,0:56:99:0|1:10088730_G_A:1001,0,1152,1092,1231,2322:10088730:11,19,16,10 +20 10088730 . G A, 993.64 . BaseQRankSum=0.224;DP=57;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.213;RAW_MQandDP=159641,57;ReadPosRankSum=0.581 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:30,26,0:56:99:0|1:10088730_G_A:1001,0,1152,1092,1231,2322:10088730:11,19,16,10 20 10088731 . G . . END=10088735 GT:DP:GQ:MIN_DP:PL 0/0:55:99:55:0,120,1800 -20 10088736 . A C, 1102.64 . BaseQRankSum=0.016;DP=60;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.157;RAW_MQandDP=167682,60;ReadPosRankSum=0.573 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:31,29,0:60:99:0|1:10088730_G_A:1110,0,1194,1203,1281,2484:10088730:12,19,17,12 +20 10088736 . A C, 1102.64 . BaseQRankSum=0.282;DP=60;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.157;RAW_MQandDP=167682,60;ReadPosRankSum=0.573 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:31,29,0:60:99:0|1:10088730_G_A:1110,0,1194,1203,1281,2484:10088730:12,19,17,12 20 10088737 . C . . END=10088746 GT:DP:GQ:MIN_DP:PL 0/0:56:99:53:0,120,1800 20 10088747 . A G, 1132.64 . BaseQRankSum=-3.877;DP=56;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.881;RAW_MQandDP=152598,56;ReadPosRankSum=0.009 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:26,30,0:56:99:0|1:10088730_G_A:1140,0,995,1219,1085,2304:10088730:10,16,19,11 20 10088748 . G . . END=10088798 GT:DP:GQ:MIN_DP:PL 0/0:49:99:46:0,114,1710 @@ -1084,11 +1084,11 @@ 20 10088871 . T . . END=10088894 GT:DP:GQ:MIN_DP:PL 0/0:39:99:33:0,99,1294 20 10088895 . C T, 556.64 . BaseQRankSum=2.330;DP=43;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.260;RAW_MQandDP=143650,43;ReadPosRankSum=1.238 GT:AD:DP:GQ:PL:SB 0/1:22,18,0:40:99:564,0,651,630,704,1334:10,12,8,10 20 10088896 . G . . END=10088967 GT:DP:GQ:MIN_DP:PL 0/0:49:99:41:0,107,1668 -20 10088968 . C CAAA, 1289.60 . BaseQRankSum=0.117;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.320;RAW_MQandDP=216408,79;ReadPosRankSum=1.802 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:32,34,0:66:99:0|1:10088968_C_CAAA:1297,0,1230,1394,1333,2726:10088968:17,15,19,15 +20 10088968 . C CAAA, 1289.60 . BaseQRankSum=0.337;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.320;RAW_MQandDP=216408,79;ReadPosRankSum=0.205 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:32,34,0:66:99:0|1:10088968_C_CAAA:1297,0,1230,1394,1333,2726:10088968:17,15,19,15 20 10088969 . A . . END=10088979 GT:DP:GQ:MIN_DP:PL 0/0:73:99:72:0,120,1800 -20 10088980 . T C, 1352.64 . BaseQRankSum=-1.772;DP=76;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.207;RAW_MQandDP=197331,76;ReadPosRankSum=1.124 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:39,36,0:75:99:0|1:10088968_C_CAAA:1360,0,1491,1478,1599,3077:10088968:20,19,20,16 +20 10088980 . T C, 1352.64 . BaseQRankSum=-1.845;DP=76;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.207;RAW_MQandDP=197331,76;ReadPosRankSum=1.483 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:39,36,0:75:99:0|1:10088968_C_CAAA:1360,0,1491,1478,1599,3077:10088968:20,19,20,16 20 10088981 . A . . END=10088984 GT:DP:GQ:MIN_DP:PL 0/0:73:99:71:0,120,1800 -20 10088985 . T C, 1283.64 . BaseQRankSum=-0.525;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.440;RAW_MQandDP=204246,79;ReadPosRankSum=1.155 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:42,34,0:76:99:0|1:10088968_C_CAAA:1291,0,1593,1417,1696,3113:10088968:22,20,17,17 +20 10088985 . T C, 1283.64 . BaseQRankSum=-0.525;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.440;RAW_MQandDP=204246,79;ReadPosRankSum=1.432 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:42,34,0:76:99:0|1:10088968_C_CAAA:1291,0,1593,1417,1696,3113:10088968:22,20,17,17 20 10088986 . A . . END=10088989 GT:DP:GQ:MIN_DP:PL 0/0:82:99:81:0,120,1800 20 10088990 . A . . END=10088990 GT:DP:GQ:MIN_DP:PL 0/0:84:7:84:0,7,2771 20 10088991 . C . . END=10088991 GT:DP:GQ:MIN_DP:PL 0/0:81:95:81:0,95,2703 @@ -1106,7 +1106,7 @@ 20 10089442 . G . . END=10089524 GT:DP:GQ:MIN_DP:PL 0/0:81:99:74:0,120,1800 20 10089525 . C T, 1569.64 . BaseQRankSum=5.859;DP=83;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.531;RAW_MQandDP=293810,83;ReadPosRankSum=0.862 GT:AD:DP:GQ:PL:SB 0/1:38,43,0:81:99:1577,0,1088,1691,1217,2908:22,16,20,23 20 10089526 . G . . END=10090288 GT:DP:GQ:MIN_DP:PL 0/0:72:99:55:0,111,1800 -20 10090289 . CAA C,CA, 405.60 . BaseQRankSum=0.285;DP=88;ExcessHet=3.0103;MLEAC=0,1,0;MLEAF=0.00,0.500,0.00;MQRankSum=1.470;RAW_MQandDP=316482,88;ReadPosRankSum=0.455 GT:AD:DP:GQ:PL:SB 0/2:15,3,20,0:38:99:413,386,1030,0,295,240,474,906,358,938:8,7,10,13 +20 10090289 . CAA C,CA, 405.60 . BaseQRankSum=0.252;DP=88;ExcessHet=3.0103;MLEAC=0,1,0;MLEAF=0.00,0.500,0.00;MQRankSum=1.470;RAW_MQandDP=316482,88;ReadPosRankSum=0.455 GT:AD:DP:GQ:PL:SB 0/2:15,3,20,0:38:99:413,386,1030,0,295,240,474,906,358,938:8,7,10,13 20 10090292 . A . . END=10090763 GT:DP:GQ:MIN_DP:PL 0/0:75:99:61:0,120,1800 20 10090764 . A G, 861.64 . BaseQRankSum=-2.659;DP=67;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=241200,67;ReadPosRankSum=1.207 GT:AD:DP:GQ:PL:SB 0/1:34,29,0:63:99:869,0,1207,972,1294,2265:12,22,14,15 20 10090765 . A . . END=10090969 GT:DP:GQ:MIN_DP:PL 0/0:75:99:65:0,120,1800 @@ -1128,7 +1128,7 @@ 20 10094583 . T . . END=10094773 GT:DP:GQ:MIN_DP:PL 0/0:78:99:67:0,120,1800 20 10094774 . C T, 1057.64 . BaseQRankSum=-0.784;DP=81;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.962;RAW_MQandDP=286082,81;ReadPosRankSum=0.197 GT:AD:DP:GQ:PL:SB 0/1:40,35,0:75:99:1065,0,1282,1185,1385,2570:24,16,21,14 20 10094775 . A . . END=10095431 GT:DP:GQ:MIN_DP:PL 0/0:77:99:63:0,120,1800 -20 10095432 . GTGATGATGA G, 875.60 . BaseQRankSum=1.109;DP=78;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.378;RAW_MQandDP=231348,78;ReadPosRankSum=0.396 GT:AD:DP:GQ:PL:SB 0/1:26,23,0:49:99:883,0,978,961,1053,2014:16,10,12,11 +20 10095432 . GTGATGATGA G, 875.60 . BaseQRankSum=1.063;DP=78;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.378;RAW_MQandDP=231348,78;ReadPosRankSum=0.396 GT:AD:DP:GQ:PL:SB 0/1:26,23,0:49:99:883,0,978,961,1053,2014:16,10,12,11 20 10095442 . T . . END=10095740 GT:DP:GQ:MIN_DP:PL 0/0:80:99:64:0,120,1800 20 10095741 . A G, 1096.64 . BaseQRankSum=-0.534;DP=72;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.313;RAW_MQandDP=237128,72;ReadPosRankSum=-0.500 GT:AD:DP:GQ:PL:SB 0/1:36,34,0:70:99:1104,0,1233,1213,1335,2547:14,22,18,16 20 10095742 . G . . END=10096292 GT:DP:GQ:MIN_DP:PL 0/0:73:99:63:0,120,1800 @@ -1138,19 +1138,19 @@ 20 10096597 . T . . END=10096767 GT:DP:GQ:MIN_DP:PL 0/0:90:99:75:0,120,1800 20 10096768 . A C, 1703.64 . BaseQRankSum=-2.764;DP=96;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.609;RAW_MQandDP=337323,96;ReadPosRankSum=0.613 GT:AD:DP:GQ:PL:SB 0/1:42,49,0:91:99:1711,0,1452,1838,1600,3437:25,17,24,25 20 10096769 . A . . END=10096898 GT:DP:GQ:MIN_DP:PL 0/0:78:99:65:0,120,1800 -20 10096899 . G T, 1636.64 . BaseQRankSum=2.494;DP=84;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.677;RAW_MQandDP=295179,84;ReadPosRankSum=0.422 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:40,43,0:83:99:0|1:10096899_G_T:1644,0,1519,1764,1649,3413:10096899:20,20,12,31 +20 10096899 . G T, 1636.64 . BaseQRankSum=2.755;DP=84;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.677;RAW_MQandDP=295179,84;ReadPosRankSum=0.422 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:40,43,0:83:99:0|1:10096899_G_T:1644,0,1519,1764,1649,3413:10096899:20,20,12,31 20 10096900 . G . . END=10096904 GT:DP:GQ:MIN_DP:PL 0/0:82:99:78:0,120,1800 20 10096905 . TA T, 1630.60 . BaseQRankSum=-0.755;DP=86;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.739;RAW_MQandDP=302379,86;ReadPosRankSum=0.461 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:43,43,0:86:99:0|1:10096899_G_T:1638,0,1623,1768,1752,3520:10096899:22,21,13,30 20 10096907 . A . . END=10096932 GT:DP:GQ:MIN_DP:PL 0/0:84:99:82:0,120,1800 -20 10096933 . G C, 1534.64 . BaseQRankSum=-1.724;DP=89;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.840;RAW_MQandDP=313179,89;ReadPosRankSum=0.334 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:47,42,0:89:99:0|1:10096933_G_C:1542,0,1763,1684,1889,3573:10096933:29,18,14,28 +20 10096933 . G C, 1534.64 . BaseQRankSum=-1.914;DP=89;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.840;RAW_MQandDP=313179,89;ReadPosRankSum=0.383 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:47,42,0:89:99:0|1:10096933_G_C:1542,0,1763,1684,1889,3573:10096933:29,18,14,28 20 10096934 . T . . END=10096957 GT:DP:GQ:MIN_DP:PL 0/0:89:99:85:0,120,1800 -20 10096958 . G A, 1789.64 . BaseQRankSum=2.697;DP=93;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.664;RAW_MQandDP=327579,93;ReadPosRankSum=-1.824 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:44,48,0:92:99:0|1:10096933_G_C:1797,0,1622,1929,1766,3695:10096933:27,17,16,32 +20 10096958 . G A, 1789.64 . BaseQRankSum=2.697;DP=93;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.664;RAW_MQandDP=327579,93;ReadPosRankSum=-1.593 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:44,48,0:92:99:0|1:10096933_G_C:1797,0,1622,1929,1766,3695:10096933:27,17,16,32 20 10096959 . G . . END=10097074 GT:DP:GQ:MIN_DP:PL 0/0:92:99:84:0,120,1800 -20 10097075 . T G, 1466.64 . BaseQRankSum=-2.533;DP=96;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.389;RAW_MQandDP=324510,96;ReadPosRankSum=0.082 GT:AD:DP:GQ:PL:SB 0/1:44,48,0:92:99:1474,0,1482,1606,1626,3232:18,26,26,22 +20 10097075 . T G, 1466.64 . BaseQRankSum=-2.533;DP=96;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.389;RAW_MQandDP=324510,96;ReadPosRankSum=0.235 GT:AD:DP:GQ:PL:SB 0/1:44,48,0:92:99:1474,0,1482,1606,1626,3232:18,26,26,22 20 10097076 . A . . END=10097100 GT:DP:GQ:MIN_DP:PL 0/0:91:99:77:0,120,1800 -20 10097101 . C CTTT,CTTTT, 1105.60 . BaseQRankSum=-0.953;DP=81;ExcessHet=3.0103;MLEAC=1,0,0;MLEAF=0.500,0.00,0.00;MQRankSum=-2.210;RAW_MQandDP=274973,81;ReadPosRankSum=2.373 GT:AD:DP:GQ:PL:SB 0/1:34,26,3,0:63:99:1113,0,1263,585,1269,1857,973,1359,1937,2255:22,12,14,15 +20 10097101 . C CTTT,CTTTT, 1105.60 . BaseQRankSum=-0.953;DP=81;ExcessHet=3.0103;MLEAC=1,0,0;MLEAF=0.500,0.00,0.00;MQRankSum=-2.210;RAW_MQandDP=274973,81;ReadPosRankSum=2.829 GT:AD:DP:GQ:PL:SB 0/1:34,26,3,0:63:99:1113,0,1263,585,1269,1857,973,1359,1937,2255:22,12,14,15 20 10097102 . T . . END=10097435 GT:DP:GQ:MIN_DP:PL 0/0:70:99:60:0,120,1800 -20 10097436 . CTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT C, 1089.60 . BaseQRankSum=1.820;DP=90;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-6.464;RAW_MQandDP=265743,90;ReadPosRankSum=-3.097 GT:AD:DP:GQ:PL:SB 0/1:57,32,0:89:99:1097,0,2238,1269,2335,3603:23,34,11,21 +20 10097436 . CTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT C, 1089.60 . BaseQRankSum=1.650;DP=90;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-6.464;RAW_MQandDP=265743,90;ReadPosRankSum=-3.097 GT:AD:DP:GQ:PL:SB 0/1:57,32,0:89:99:1097,0,2238,1269,2335,3603:23,34,11,21 20 10097437 . TTTTC *,T, 931.01 . DP=78;ExcessHet=3.0103;MLEAC=1,1,0;MLEAF=0.500,0.500,0.00;RAW_MQandDP=224774,78 GT:AD:DP:GQ:PL:SB 1/2:0,32,23,0:55:99:2133,941,1797,1201,0,1129,2207,1453,1267,2647:0,0,16,39 20 10097442 . T . . END=10097475 GT:DP:GQ:MIN_DP:PL 0/0:78:0:63:0,0,557 20 10097476 . T . . END=10097476 GT:DP:GQ:MIN_DP:PL 0/0:66:11:66:0,11,2255 @@ -1212,13 +1212,13 @@ 20 10098219 . TATATATA T, 325.60 . BaseQRankSum=3.147;DP=21;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.205;RAW_MQandDP=65705,21;ReadPosRankSum=0.427 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:12,9,0:21:99:0|1:10098219_TATATATA_T:333,0,461,369,488,857:10098219:0,12,0,9 20 10098227 . T . . END=10098228 GT:DP:GQ:MIN_DP:PL 0/0:18:30:18:0,30,450 20 10098229 . A . . END=10098236 GT:DP:GQ:MIN_DP:PL 0/0:17:21:13:0,21,315 -20 10098237 . A T, 265.64 . BaseQRankSum=0.006;DP=14;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.885;RAW_MQandDP=40664,14;ReadPosRankSum=0.277 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:7,7,0:14:99:0|1:10098219_TATATATA_T:273,0,273,294,294,588:10098219:0,7,0,7 +20 10098237 . A T, 265.64 . BaseQRankSum=0.006;DP=14;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.885;RAW_MQandDP=40664,14;ReadPosRankSum=1.118 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:7,7,0:14:99:0|1:10098219_TATATATA_T:273,0,273,294,294,588:10098219:0,7,0,7 20 10098238 . A . . END=10098244 GT:DP:GQ:MIN_DP:PL 0/0:10:21:9:0,21,315 20 10098245 . T . . END=10098248 GT:DP:GQ:MIN_DP:PL 0/0:10:24:10:0,24,360 20 10098249 . A . . END=10098250 GT:DP:GQ:MIN_DP:PL 0/0:10:18:9:0,18,270 20 10098251 . A . . END=10098255 GT:DP:GQ:MIN_DP:PL 0/0:8:15:8:0,15,225 20 10098256 . T . . END=10098264 GT:DP:GQ:MIN_DP:PL 0/0:8:9:6:0,9,135 -20 10098265 . T C, 154.64 . BaseQRankSum=1.834;DP=6;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.834;RAW_MQandDP=10564,6;ReadPosRankSum=0.000 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:2,4,0:6:59:0|1:10098219_TATATATA_T:162,0,59,168,71,239:10098219:0,2,0,4 +20 10098265 . T C, 154.64 . BaseQRankSum=1.834;DP=6;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.834;RAW_MQandDP=10564,6;ReadPosRankSum=0.842 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:2,4,0:6:59:0|1:10098219_TATATATA_T:162,0,59,168,71,239:10098219:0,2,0,4 20 10098266 . A . . END=10098272 GT:DP:GQ:MIN_DP:PL 0/0:4:9:4:0,9,135 20 10098273 . A . . END=10098279 GT:DP:GQ:MIN_DP:PL 0/0:3:6:3:0,6,90 20 10098280 . A . . END=10098290 GT:DP:GQ:MIN_DP:PL 0/0:4:9:3:0,9,126 @@ -1293,7 +1293,7 @@ 20 10098882 . C . . END=10098882 GT:DP:GQ:MIN_DP:PL 0/0:32:60:32:0,60,1207 20 10098883 . T . . END=10098883 GT:DP:GQ:MIN_DP:PL 0/0:32:56:32:0,56,1237 20 10098884 . C . . END=10098884 GT:DP:GQ:MIN_DP:PL 0/0:32:84:32:0,84,1260 -20 10098885 . C CA, 463.60 . BaseQRankSum=0.165;DP=33;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.449;RAW_MQandDP=81598,33;ReadPosRankSum=-1.073 GT:AD:DP:GQ:PL:SB 0/1:17,14,0:31:99:471,0,572,522,615,1137:16,1,13,1 +20 10098885 . C CA, 463.60 . BaseQRankSum=0.165;DP=33;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.449;RAW_MQandDP=81598,33;ReadPosRankSum=-0.954 GT:AD:DP:GQ:PL:SB 0/1:17,14,0:31:99:471,0,572,522,615,1137:16,1,13,1 20 10098886 . C . . END=10098890 GT:DP:GQ:MIN_DP:PL 0/0:31:84:29:0,84,1260 20 10098891 . C . . END=10098891 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 20 10098892 . G . . END=10098900 GT:DP:GQ:MIN_DP:PL 0/0:31:81:30:0,81,1215 @@ -1326,10 +1326,10 @@ 20 10099022 . C . . END=10099022 GT:DP:GQ:MIN_DP:PL 0/0:25:69:25:0,69,1035 20 10099023 . T . . END=10099027 GT:DP:GQ:MIN_DP:PL 0/0:27:72:26:0,72,1080 20 10099028 . A . . END=10099028 GT:DP:GQ:MIN_DP:PL 0/0:28:69:28:0,69,1035 -20 10099029 . T C, 355.64 . BaseQRankSum=-1.518;DP=30;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.731;RAW_MQandDP=84058,30;ReadPosRankSum=-1.224 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:19,10,0:29:99:0|1:10099029_T_C:363,0,768,420,798,1218:10099029:14,5,9,1 +20 10099029 . T C, 355.64 . BaseQRankSum=-1.809;DP=30;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.731;RAW_MQandDP=84058,30;ReadPosRankSum=-1.224 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:19,10,0:29:99:0|1:10099029_T_C:363,0,768,420,798,1218:10099029:14,5,9,1 20 10099030 . C . . END=10099031 GT:DP:GQ:MIN_DP:PL 0/0:29:72:28:0,72,1080 20 10099032 . T . . END=10099033 GT:DP:GQ:MIN_DP:PL 0/0:28:63:28:0,63,945 -20 10099034 . C A, 355.64 . BaseQRankSum=2.752;DP=29;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.731;RAW_MQandDP=83217,29;ReadPosRankSum=-1.850 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:19,10,0:29:99:0|1:10099029_T_C:363,0,768,420,798,1218:10099029:14,5,9,1 +20 10099034 . C A, 355.64 . BaseQRankSum=2.757;DP=29;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.731;RAW_MQandDP=83217,29;ReadPosRankSum=-1.850 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:19,10,0:29:99:0|1:10099029_T_C:363,0,768,420,798,1218:10099029:14,5,9,1 20 10099035 . G . . END=10099039 GT:DP:GQ:MIN_DP:PL 0/0:29:60:26:0,60,900 20 10099040 . T . . END=10099040 GT:DP:GQ:MIN_DP:PL 0/0:26:51:26:0,51,765 20 10099041 . C . . END=10099041 GT:DP:GQ:MIN_DP:PL 0/0:27:54:27:0,54,810 @@ -1339,13 +1339,13 @@ 20 10099046 . T C, 325.64 . BaseQRankSum=-2.165;DP=24;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.418;RAW_MQandDP=59851,24;ReadPosRankSum=-2.297 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:15,9,0:24:99:0|1:10099029_T_C:333,0,603,378,630,1008:10099029:12,3,7,2 20 10099047 . G . . END=10099052 GT:DP:GQ:MIN_DP:PL 0/0:24:57:23:0,57,855 20 10099053 . G . . END=10099054 GT:DP:GQ:MIN_DP:PL 0/0:23:54:23:0,54,810 -20 10099055 . T C, 277.64 . BaseQRankSum=-0.996;DP=25;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.179;RAW_MQandDP=62996,25;ReadPosRankSum=-1.970 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:17,8,0:25:99:0|1:10099029_T_C:285,0,673,336,697,1033:10099029:12,5,6,2 +20 10099055 . T C, 277.64 . BaseQRankSum=-1.554;DP=25;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.179;RAW_MQandDP=62996,25;ReadPosRankSum=-1.970 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:17,8,0:25:99:0|1:10099029_T_C:285,0,673,336,697,1033:10099029:12,5,6,2 20 10099056 . T . . END=10099061 GT:DP:GQ:MIN_DP:PL 0/0:24:60:23:0,60,900 20 10099062 . A . . END=10099067 GT:DP:GQ:MIN_DP:PL 0/0:25:72:24:0,72,921 20 10099068 . G . . END=10099072 GT:DP:GQ:MIN_DP:PL 0/0:27:81:27:0,81,1042 20 10099073 . T . . END=10099077 GT:DP:GQ:MIN_DP:PL 0/0:27:78:27:0,78,1170 20 10099078 . G . . END=10099078 GT:DP:GQ:MIN_DP:PL 0/0:28:81:28:0,81,1215 -20 10099079 . C T, 137.64 . BaseQRankSum=1.432;DP=30;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.614;RAW_MQandDP=79539,30;ReadPosRankSum=0.969 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:24,6,0:30:99:0|1:10099029_T_C:145,0,886,217,904,1120:10099029:12,12,4,2 +20 10099079 . C T, 137.64 . BaseQRankSum=1.434;DP=30;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.614;RAW_MQandDP=79539,30;ReadPosRankSum=0.969 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:24,6,0:30:99:0|1:10099029_T_C:145,0,886,217,904,1120:10099029:12,12,4,2 20 10099080 . G . . END=10099089 GT:DP:GQ:MIN_DP:PL 0/0:30:81:29:0,81,1215 20 10099090 . A . . END=10099095 GT:DP:GQ:MIN_DP:PL 0/0:34:90:31:0,90,1350 20 10099096 . A . . END=10099096 GT:DP:GQ:MIN_DP:PL 0/0:35:74:35:0,74,1310 @@ -1353,9 +1353,9 @@ 20 10099101 . G . . END=10099105 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,99,1485 20 10099106 . T . . END=10099106 GT:DP:GQ:MIN_DP:PL 0/0:36:96:36:0,96,1440 20 10099107 . T . . END=10099110 GT:DP:GQ:MIN_DP:PL 0/0:41:99:39:0,99,1485 -20 10099111 . T TTTTGTTTG, 685.60 . BaseQRankSum=-0.622;DP=52;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.973;RAW_MQandDP=150778,52;ReadPosRankSum=-0.273 GT:AD:DP:GQ:PL:SB 0/1:23,19,0:42:99:693,0,802,763,860,1623:13,10,12,7 +20 10099111 . T TTTTGTTTG, 685.60 . BaseQRankSum=-1.207;DP=52;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.973;RAW_MQandDP=150778,52;ReadPosRankSum=-1.860 GT:AD:DP:GQ:PL:SB 0/1:23,19,0:42:99:693,0,802,763,860,1623:13,10,12,7 20 10099112 . T . . END=10099139 GT:DP:GQ:MIN_DP:PL 0/0:57:99:49:0,114,1710 -20 10099140 . G T, 1027.64 . BaseQRankSum=-0.286;DP=63;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.435;RAW_MQandDP=196112,63;ReadPosRankSum=0.116 GT:AD:DP:GQ:PL:SB 0/1:29,32,0:61:99:1035,0,930,1122,1026,2148:17,12,22,10 +20 10099140 . G T, 1027.64 . BaseQRankSum=-0.286;DP=63;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.435;RAW_MQandDP=196112,63;ReadPosRankSum=0.636 GT:AD:DP:GQ:PL:SB 0/1:29,32,0:61:99:1035,0,930,1122,1026,2148:17,12,22,10 20 10099141 . G . . END=10099189 GT:DP:GQ:MIN_DP:PL 0/0:67:99:64:0,120,1800 20 10099190 . G T, 1030.64 . BaseQRankSum=-0.264;DP=62;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.445;RAW_MQandDP=207310,62;ReadPosRankSum=-1.577 GT:AD:DP:GQ:PL:SB 0/1:31,31,0:62:99:1038,0,1088,1131,1182,2313:20,11,20,11 20 10099191 . C . . END=10099219 GT:DP:GQ:MIN_DP:PL 0/0:58:99:46:0,111,1665 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.g.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.g.vcf.idx index 428b1fb14b02606b52445b6a9db38f6e101b1b08..1ab781ac88e3424c0fb88d4deca8d9ed49b994de 100644 GIT binary patch delta 396 zcmcb(kLlt*rU}z|*g}~YK;XkngVh@s+s&DnIginSDOq&Ct|1O2lFPB5; pid7K$@_Gm@yAeXC?}yMPx# diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testVCFMode.gatk4.nonstrict.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testVCFMode.gatk4.nonstrict.vcf index c012a87f9b7..ff9922c1bd7 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testVCFMode.gatk4.nonstrict.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testVCFMode.gatk4.nonstrict.vcf @@ -52,13 +52,13 @@ 20 10004094 . A C 1840.06 . AC=2;AF=1.00;AN=2;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.62;QD=34.72;SOR=1.524 GT:AD:DP:GQ:PL 1/1:0,53:53:99:1854,157,0 20 10004147 . A G 1852.06 . AC=2;AF=1.00;AN=2;DP=54;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=55.19;QD=26.61;SOR=1.136 GT:AD:DP:GQ:PL 1/1:0,52:52:99:1866,156,0 20 10004193 . G T 937.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.392;DP=54;ExcessHet=3.0103;FS=2.369;MLEAC=1;MLEAF=0.500;MQ=59.14;MQRankSum=3.385;QD=18.39;ReadPosRankSum=1.724;SOR=0.941 GT:AD:DP:GQ:PL 0/1:23,28:51:99:945,0,776 -20 10004222 . C CA 41.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.124;DP=68;ExcessHet=3.0103;FS=3.221;MLEAC=1;MLEAF=0.500;MQ=58.19;MQRankSum=-2.220;QD=0.92;ReadPosRankSum=1.271;SOR=0.932 GT:AD:DP:GQ:PL 0/1:35,10:45:49:49,0,924 -20 10004223 . A AG 80.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.749;DP=68;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.27;MQRankSum=2.272;QD=1.71;ReadPosRankSum=0.490;SOR=0.544 GT:AD:DP:GQ:PL 0/1:35,12:47:88:88,0,953 +20 10004222 . C CA 41.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.335;DP=68;ExcessHet=3.0103;FS=3.221;MLEAC=1;MLEAF=0.500;MQ=58.19;MQRankSum=-2.220;QD=0.92;ReadPosRankSum=0.198;SOR=0.932 GT:AD:DP:GQ:PL 0/1:35,10:45:49:49,0,924 +20 10004223 . A AG 80.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.765;DP=68;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.27;MQRankSum=2.272;QD=1.71;ReadPosRankSum=0.183;SOR=0.544 GT:AD:DP:GQ:PL 0/1:35,12:47:88:88,0,953 20 10004351 . C G 2770.06 . AC=2;AF=1.00;AN=2;DP=71;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.05;QD=29.20;SOR=0.874 GT:AD:DP:GQ:PL 1/1:0,70:70:99:2784,211,0 20 10004389 . T G 2509.06 . AC=2;AF=1.00;AN=2;DP=67;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.62;QD=28.55;SOR=1.143 GT:AD:DP:GQ:PL 1/1:0,62:62:99:2523,187,0 20 10004610 . A C 3640.06 . AC=2;AF=1.00;AN=2;DP=93;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.75;QD=34.42;SOR=0.761 GT:AD:DP:GQ:PL 1/1:0,89:89:99:3654,267,0 20 10004725 . A G 975.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.393;DP=66;ExcessHet=3.0103;FS=13.744;MLEAC=1;MLEAF=0.500;MQ=55.34;MQRankSum=2.856;QD=15.24;ReadPosRankSum=1.932;SOR=0.613 GT:AD:DP:GQ:PL 0/1:34,30:64:99:983,0,1139 -20 10004769 . TAAAACTATGC T 970.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.796;DP=79;ExcessHet=3.0103;FS=3.721;MLEAC=1;MLEAF=0.500;MQ=53.03;MQRankSum=-6.531;QD=15.41;ReadPosRankSum=1.721;SOR=1.236 GT:AD:DP:GQ:PL 0/1:37,26:63:99:978,0,1473 +20 10004769 . TAAAACTATGC T 970.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.807;DP=79;ExcessHet=3.0103;FS=3.721;MLEAC=1;MLEAF=0.500;MQ=53.03;MQRankSum=-6.531;QD=15.41;ReadPosRankSum=1.721;SOR=1.236 GT:AD:DP:GQ:PL 0/1:37,26:63:99:978,0,1473 20 10004874 . A C 3617.06 . AC=2;AF=1.00;AN=2;DP=90;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.35;QD=28.53;SOR=1.286 GT:AD:DP:GQ:PL 1/1:0,87:87:99:3631,261,0 20 10004887 . A G 1344.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.356;DP=90;ExcessHet=3.0103;FS=1.793;MLEAC=1;MLEAF=0.500;MQ=59.49;MQRankSum=-0.067;QD=15.82;ReadPosRankSum=-1.114;SOR=0.984 GT:AD:DP:GQ:PL 0/1:45,40:85:99:1352,0,1542 20 10005010 . C T 2981.06 . AC=2;AF=1.00;AN=2;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.68;QD=27.23;SOR=1.257 GT:AD:DP:GQ:PL 1/1:0,73:73:99:2995,220,0 @@ -75,25 +75,25 @@ 20 10007352 . C T 2779.06 . AC=2;AF=1.00;AN=2;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.67;QD=31.26;SOR=1.054 GT:AD:DP:GQ:PL 1/1:0,69:69:99:2793,208,0 20 10007531 . A G 2935.06 . AC=2;AF=1.00;AN=2;DP=75;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.75;QD=27.76;SOR=1.577 GT:AD:DP:GQ:PL 1/1:0,72:72:99:2949,217,0 20 10007980 . A C 3539.06 . AC=2;AF=1.00;AN=2;DP=92;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.70;QD=29.09;SOR=0.990 GT:AD:DP:GQ:PL 1/1:0,90:90:99:3553,270,0 -20 10008029 . T TA 2009.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.438;DP=97;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=61.11;MQRankSum=0.651;QD=26.09;ReadPosRankSum=-1.326;SOR=0.774 GT:AD:DP:GQ:PL 1/1:3,74:77:99:2023,145,0 +20 10008029 . T TA 2009.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.409;DP=97;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=61.11;MQRankSum=0.651;QD=26.09;ReadPosRankSum=-1.357;SOR=0.774 GT:AD:DP:GQ:PL 1/1:3,74:77:99:2023,145,0 20 10008146 . TA T 2166.03 . AC=2;AF=1.00;AN=2;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.56;QD=30.94;SOR=0.874 GT:AD:DP:GQ:PL 1/1:0,70:70:99:2180,211,0 20 10008221 . T C 3239.06 . AC=2;AF=1.00;AN=2;DP=83;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.17;QD=26.08;SOR=0.850 GT:AD:DP:GQ:PL 1/1:0,80:80:99:3253,240,0 20 10008458 . T G 2669.06 . AC=2;AF=1.00;AN=2;DP=72;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.76;QD=33.85;SOR=0.980 GT:AD:DP:GQ:PL 1/1:0,69:69:99:2683,207,0 -20 10008742 . G T 736.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.893;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=37.07;MQRankSum=-1.502;QD=15.03;ReadPosRankSum=0.190;SOR=0.741 GT:AD:DP:GQ:PL 0/1:23,26:49:99:744,0,580 -20 10008758 . C CA 706.49 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.119;DP=51;ExcessHet=3.0103;FS=2.191;MLEAC=1;MLEAF=0.500;MQ=37.72;MQRankSum=-0.875;QD=18.59;ReadPosRankSum=-0.052;SOR=0.405 GT:AD:DP:GQ:PL 1/1:4,34:38:10:720,10,0 -20 10008921 . C CA 283.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.516;DP=60;ExcessHet=3.0103;FS=1.311;MLEAC=1;MLEAF=0.500;MQ=56.00;MQRankSum=-1.306;QD=8.10;ReadPosRankSum=0.173;SOR=0.644 GT:AD:DP:GQ:PL 0/1:18,17:35:99:291,0,366 -20 10008948 . TA T 2094.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.956;DP=56;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.26;MQRankSum=1.946;QD=27.08;ReadPosRankSum=0.884;SOR=0.721 GT:AD:DP:GQ:PL 1/1:1,53:54:99:2108,117,0 -20 10008952 . CACACACACACA C,CCACACACACA 1702.02 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=0.963;DP=63;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=51.23;MQRankSum=1.976;QD=25.42;ReadPosRankSum=0.934;SOR=1.112 GT:AD:DP:GQ:PL 1/2:1,17,18:36:99:1719,538,801,597,0,535 +20 10008742 . G T 736.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.893;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=37.07;MQRankSum=-1.502;QD=15.03;ReadPosRankSum=0.200;SOR=0.741 GT:AD:DP:GQ:PL 0/1:23,26:49:99:744,0,580 +20 10008758 . C CA 706.49 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.130;DP=51;ExcessHet=3.0103;FS=2.191;MLEAC=1;MLEAF=0.500;MQ=37.72;MQRankSum=-0.875;QD=18.59;ReadPosRankSum=-0.262;SOR=0.405 GT:AD:DP:GQ:PL 1/1:4,34:38:10:720,10,0 +20 10008921 . C CA 283.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.610;DP=60;ExcessHet=3.0103;FS=1.311;MLEAC=1;MLEAF=0.500;MQ=56.00;MQRankSum=-1.306;QD=8.10;ReadPosRankSum=-0.017;SOR=0.644 GT:AD:DP:GQ:PL 0/1:18,17:35:99:291,0,366 +20 10008948 . TA T 2094.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.994;DP=56;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.26;MQRankSum=1.946;QD=27.08;ReadPosRankSum=0.884;SOR=0.721 GT:AD:DP:GQ:PL 1/1:1,53:54:99:2108,117,0 +20 10008952 . CACACACACACA C,CCACACACACA 1702.02 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=0.963;DP=63;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=51.23;MQRankSum=1.976;QD=25.42;ReadPosRankSum=0.868;SOR=1.112 GT:AD:DP:GQ:PL 1/2:1,17,18:36:99:1719,538,801,597,0,535 20 10009227 . A G 1390.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.220;DP=63;ExcessHet=3.0103;FS=9.110;MLEAC=1;MLEAF=0.500;MQ=56.82;MQRankSum=1.428;QD=22.43;ReadPosRankSum=-1.159;SOR=0.281 GT:AD:DP:GQ:PL 0/1:23,39:62:99:1398,0,740 20 10009246 . A G 3017.06 . AC=2;AF=1.00;AN=2;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=55.68;QD=27.65;SOR=0.887 GT:AD:DP:GQ:PL 1/1:0,77:77:99:3031,231,0 20 10009400 . T A 3013.06 . AC=2;AF=1.00;AN=2;DP=75;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.48;SOR=0.804 GT:AD:DP:GQ:PL 1/1:0,74:74:99:3027,223,0 20 10009512 . C G 3054.06 . AC=2;AF=1.00;AN=2;DP=80;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.53;QD=30.56;SOR=1.223 GT:AD:DP:GQ:PL 1/1:0,77:77:99:3068,231,0 20 10009719 . A G 1901.06 . AC=2;AF=1.00;AN=2;DP=65;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.71;QD=33.35;SOR=1.047 GT:AD:DP:GQ:PL 1/1:0,57:57:99:1915,170,0 20 10009795 . A G 1895.06 . AC=2;AF=1.00;AN=2;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.62;QD=33.63;SOR=1.514 GT:AD:DP:GQ:PL 1/1:0,47:47:99:1909,141,0 -20 10009842 . G GAA 562.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.183;DP=52;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.85;MQRankSum=-0.936;QD=16.07;ReadPosRankSum=1.754;SOR=0.602 GT:AD:DP:GQ:PL 0/1:19,16:35:99:570,0,691 -20 10009844 . G A 683.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.998;DP=54;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.61;MQRankSum=0.975;QD=19.53;ReadPosRankSum=-1.575;SOR=0.793 GT:AD:DP:GQ:PL 0/1:16,19:35:99:691,0,585 -20 10009871 . A G 679.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.803;DP=62;ExcessHet=3.0103;FS=1.273;MLEAC=1;MLEAF=0.500;MQ=51.11;MQRankSum=1.336;QD=18.37;ReadPosRankSum=1.491;SOR=0.631 GT:AD:DP:GQ:PL 0/1:18,19:37:99:687,0,593 -20 10009875 . A G,AGGGAGG 2389.06 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=0.378;DP=58;ExcessHet=3.0103;FS=6.463;MLEAC=1,1;MLEAF=0.500,0.500;MQ=50.44;MQRankSum=1.413;QD=30.55;ReadPosRankSum=1.040;SOR=0.461 GT:AD:DP:GQ:PL 1/2:2,15,14:31:99:2406,645,532,697,0,574 +20 10009842 . G GAA 562.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.383;DP=52;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.85;MQRankSum=-0.936;QD=16.07;ReadPosRankSum=1.757;SOR=0.602 GT:AD:DP:GQ:PL 0/1:19,16:35:99:570,0,691 +20 10009844 . G A 683.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.116;DP=54;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.61;MQRankSum=0.975;QD=19.53;ReadPosRankSum=-2.354;SOR=0.793 GT:AD:DP:GQ:PL 0/1:16,19:35:99:691,0,585 +20 10009871 . A G 679.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.803;DP=62;ExcessHet=3.0103;FS=1.273;MLEAC=1;MLEAF=0.500;MQ=51.11;MQRankSum=1.336;QD=18.37;ReadPosRankSum=0.840;SOR=0.631 GT:AD:DP:GQ:PL 0/1:18,19:37:99:687,0,593 +20 10009875 . A G,AGGGAGG 2389.06 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=0.378;DP=58;ExcessHet=3.0103;FS=6.463;MLEAC=1,1;MLEAF=0.500,0.500;MQ=50.44;MQRankSum=1.413;QD=30.55;ReadPosRankSum=1.373;SOR=0.461 GT:AD:DP:GQ:PL 1/2:2,15,14:31:99:2406,645,532,697,0,574 20 10009879 . A G 2259.06 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.534;DP=53;ExcessHet=3.0103;FS=8.605;MLEAC=2;MLEAF=1.00;MQ=50.48;MQRankSum=1.681;QD=32.62;ReadPosRankSum=1.113;SOR=1.198 GT:AD:DP:GQ:PL 1/1:2,51:53:99:2273,150,0 20 10009883 . A G 2166.06 . AC=2;AF=1.00;AN=2;DP=52;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=50.81;QD=29.33;SOR=1.755 GT:AD:DP:GQ:PL 1/1:0,49:49:99:2180,147,0 20 10010393 . T G 1485.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.351;DP=79;ExcessHet=3.0103;FS=11.600;MLEAC=1;MLEAF=0.500;MQ=59.42;MQRankSum=-1.284;QD=18.81;ReadPosRankSum=-1.738;SOR=0.606 GT:AD:DP:GQ:PL 0/1:36,43:79:99:1493,0,1230 @@ -115,8 +115,8 @@ 20 10012521 . C T 92.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.517;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=40.86;MQRankSum=-0.376;QD=7.72;ReadPosRankSum=2.405;SOR=0.693 GT:AD:DP:GQ:PL 0/1:8,4:12:99:100,0,221 20 10012570 . G GCA 481.02 . AC=2;AF=1.00;AN=2;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=39.52;QD=29.94;SOR=3.442 GT:AD:DP:GQ:PL 1/1:0,11:11:33:495,33,0 20 10012572 . GT G 481.02 . AC=2;AF=1.00;AN=2;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=40.60;QD=31.54;SOR=3.442 GT:AD:DP:GQ:PL 1/1:0,11:11:33:495,33,0 -20 10012631 . C CG 514.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.030;DP=21;ExcessHet=3.0103;FS=8.822;MLEAC=1;MLEAF=0.500;MQ=48.34;MQRankSum=-1.670;QD=24.50;ReadPosRankSum=-1.813;SOR=0.048 GT:AD:DP:GQ:PL 0/1:8,13:21:99:522,0,297 -20 10012636 . G C 548.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.711;DP=22;ExcessHet=3.0103;FS=5.959;MLEAC=1;MLEAF=0.500;MQ=48.93;MQRankSum=-1.513;QD=24.94;ReadPosRankSum=-1.915;SOR=0.058 GT:AD:DP:GQ:PL 0/1:8,14:22:99:556,0,294 +20 10012631 . C CG 514.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.030;DP=21;ExcessHet=3.0103;FS=8.822;MLEAC=1;MLEAF=0.500;MQ=48.34;MQRankSum=-1.670;QD=24.50;ReadPosRankSum=-1.777;SOR=0.048 GT:AD:DP:GQ:PL 0/1:8,13:21:99:522,0,297 +20 10012636 . G C 548.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.711;DP=22;ExcessHet=3.0103;FS=5.959;MLEAC=1;MLEAF=0.500;MQ=48.93;MQRankSum=-1.513;QD=24.94;ReadPosRankSum=-1.777;SOR=0.058 GT:AD:DP:GQ:PL 0/1:8,14:22:99:556,0,294 20 10012714 . G C 1315.06 . AC=2;AF=1.00;AN=2;DP=36;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.52;QD=28.86;SOR=2.964 GT:AD:DP:GQ:PL 1/1:0,35:35:99:1329,105,0 20 10012751 . T C 952.06 . AC=2;AF=1.00;AN=2;DP=31;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=50.73;QD=31.74;SOR=0.976 GT:AD:DP:GQ:PL 1/1:0,30:30:89:966,89,0 20 10013119 . C T 1032.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.724;DP=61;ExcessHet=3.0103;FS=2.248;MLEAC=1;MLEAF=0.500;MQ=51.43;MQRankSum=-1.089;QD=17.50;ReadPosRankSum=0.159;SOR=0.405 GT:AD:DP:GQ:PL 0/1:29,30:59:99:1040,0,936 @@ -130,24 +130,24 @@ 20 10020229 . G A 1559.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=5.792;DP=84;ExcessHet=3.0103;FS=0.833;MLEAC=1;MLEAF=0.500;MQ=59.50;MQRankSum=0.104;QD=19.02;ReadPosRankSum=-0.549;SOR=0.573 GT:AD:DP:GQ:PL 0/1:38,44:82:99:1567,0,1130 20 10023689 . G A 1873.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.144;DP=82;ExcessHet=3.0103;FS=0.877;MLEAC=1;MLEAF=0.500;MQ=59.77;MQRankSum=1.352;QD=23.42;ReadPosRankSum=1.162;SOR=0.549 GT:AD:DP:GQ:PL 0/1:29,51:80:99:1881,0,946 20 10024107 . C T 1715.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=5.770;DP=89;ExcessHet=3.0103;FS=0.817;MLEAC=1;MLEAF=0.500;MQ=59.43;MQRankSum=-1.546;QD=19.95;ReadPosRankSum=0.148;SOR=0.823 GT:AD:DP:GQ:PL 0/1:38,48:86:99:1723,0,1086 -20 10024300 . C CTT 126.96 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.362;DP=56;ExcessHet=3.0103;FS=3.090;MLEAC=1;MLEAF=0.500;MQ=52.36;MQRankSum=-0.084;QD=6.68;ReadPosRankSum=-0.431;SOR=1.773 GT:AD:DP:GQ:PL 0/1:11,8:19:97:97,0,168 +20 10024300 . C CTT 126.96 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.241;DP=56;ExcessHet=3.0103;FS=3.090;MLEAC=1;MLEAF=0.500;MQ=52.36;MQRankSum=-0.084;QD=6.68;ReadPosRankSum=-0.431;SOR=1.773 GT:AD:DP:GQ:PL 0/1:11,8:19:97:97,0,168 20 10026357 . T C 1187.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.700;DP=63;ExcessHet=3.0103;FS=8.911;MLEAC=1;MLEAF=0.500;MQ=58.43;MQRankSum=-0.148;QD=18.85;ReadPosRankSum=-0.076;SOR=0.722 GT:AD:DP:GQ:PL 0/1:28,35:63:99:1195,0,932 20 10026794 . C T 1105.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.828;DP=56;ExcessHet=3.0103;FS=2.399;MLEAC=1;MLEAF=0.500;MQ=59.59;MQRankSum=-0.719;QD=21.26;ReadPosRankSum=-0.533;SOR=0.428 GT:AD:DP:GQ:PL 0/1:19,33:52:99:1113,0,529 -20 10027234 . A ATTAG 1350.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.406;DP=75;ExcessHet=3.0103;FS=3.248;MLEAC=1;MLEAF=0.500;MQ=57.44;MQRankSum=-0.845;QD=19.57;ReadPosRankSum=-0.979;SOR=0.926 GT:AD:DP:GQ:PL 0/1:34,35:69:99:1358,0,1321 -20 10027868 . A G 1760.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-5.798;DP=91;ExcessHet=3.0103;FS=6.873;MLEAC=1;MLEAF=0.500;MQ=59.49;MQRankSum=0.047;QD=19.56;ReadPosRankSum=1.872;SOR=0.937 GT:AD:DP:GQ:PL 0/1:44,46:90:99:1768,0,1671 +20 10027234 . A ATTAG 1350.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.406;DP=75;ExcessHet=3.0103;FS=3.248;MLEAC=1;MLEAF=0.500;MQ=57.44;MQRankSum=-0.845;QD=19.57;ReadPosRankSum=-0.510;SOR=0.926 GT:AD:DP:GQ:PL 0/1:34,35:69:99:1358,0,1321 +20 10027868 . A G 1760.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-5.793;DP=91;ExcessHet=3.0103;FS=6.873;MLEAC=1;MLEAF=0.500;MQ=59.49;MQRankSum=0.047;QD=19.56;ReadPosRankSum=1.872;SOR=0.937 GT:AD:DP:GQ:PL 0/1:44,46:90:99:1768,0,1671 20 10027872 . A G 1745.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-5.491;DP=88;ExcessHet=3.0103;FS=8.704;MLEAC=1;MLEAF=0.500;MQ=59.48;MQRankSum=0.065;QD=20.06;ReadPosRankSum=1.053;SOR=0.834 GT:AD:DP:GQ:PL 0/1:42,45:87:99:1753,0,1606 -20 10028867 . A ATG 1134.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.874;DP=93;ExcessHet=3.0103;FS=4.652;MLEAC=1;MLEAF=0.500;MQ=60.68;MQRankSum=2.711;QD=15.98;ReadPosRankSum=0.364;SOR=0.336 GT:AD:DP:GQ:PL 0/1:32,39:71:99:1142,0,918 +20 10028867 . A ATG 1134.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.874;DP=93;ExcessHet=3.0103;FS=4.652;MLEAC=1;MLEAF=0.500;MQ=60.68;MQRankSum=2.711;QD=15.98;ReadPosRankSum=0.630;SOR=0.336 GT:AD:DP:GQ:PL 0/1:32,39:71:99:1142,0,918 20 10030188 . T A 1393.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.711;DP=82;ExcessHet=3.0103;FS=9.186;MLEAC=1;MLEAF=0.500;MQ=59.49;MQRankSum=-1.013;QD=17.21;ReadPosRankSum=-0.553;SOR=1.105 GT:AD:DP:GQ:PL 0/1:42,39:81:99:1401,0,1524 -20 10031254 . A AT 1493.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.091;DP=90;ExcessHet=3.0103;FS=9.250;MLEAC=1;MLEAF=0.500;MQ=59.91;MQRankSum=0.017;QD=17.57;ReadPosRankSum=0.495;SOR=0.211 GT:AD:DP:GQ:PL 0/1:38,47:85:99:1501,0,1159 +20 10031254 . A AT 1493.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.091;DP=90;ExcessHet=3.0103;FS=9.250;MLEAC=1;MLEAF=0.500;MQ=59.91;MQRankSum=0.017;QD=17.57;ReadPosRankSum=0.663;SOR=0.211 GT:AD:DP:GQ:PL 0/1:38,47:85:99:1501,0,1159 20 10031342 . G A 1855.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.833;DP=93;ExcessHet=3.0103;FS=1.714;MLEAC=1;MLEAF=0.500;MQ=59.75;MQRankSum=-0.866;QD=19.95;ReadPosRankSum=-0.012;SOR=0.955 GT:AD:DP:GQ:PL 0/1:41,52:93:99:1863,0,1375 20 10031798 . G A 4311.06 . AC=2;AF=1.00;AN=2;DP=107;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.61;QD=31.11;SOR=0.900 GT:AD:DP:GQ:PL 1/1:0,104:104:99:4325,313,0 20 10031827 . C T 2025.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.552;DP=115;ExcessHet=3.0103;FS=4.729;MLEAC=1;MLEAF=0.500;MQ=59.84;MQRankSum=-0.945;QD=18.76;ReadPosRankSum=-1.396;SOR=0.382 GT:AD:DP:GQ:PL 0/1:52,56:108:99:2033,0,1798 20 10032094 . G A 1241.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=5.488;DP=86;ExcessHet=3.0103;FS=6.039;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=14.96;ReadPosRankSum=-0.579;SOR=0.260 GT:AD:DP:GQ:PL 0/1:47,36:83:99:1249,0,1497 20 10032413 . T G 890.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-6.142;DP=66;ExcessHet=3.0103;FS=10.444;MLEAC=1;MLEAF=0.500;MQ=59.43;MQRankSum=-0.065;QD=13.49;ReadPosRankSum=-1.003;SOR=1.293 GT:AD:DP:GQ:PL 0/1:35,31:66:99:898,0,1277 20 10032882 . A T 1223.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.697;DP=76;ExcessHet=3.0103;FS=4.673;MLEAC=1;MLEAF=0.500;MQ=59.70;MQRankSum=-1.014;QD=16.32;ReadPosRankSum=0.626;SOR=0.338 GT:AD:DP:GQ:PL 0/1:39,36:75:99:1231,0,1406 -20 10032972 . C CAT 1152.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.354;DP=67;ExcessHet=3.0103;FS=5.062;MLEAC=1;MLEAF=0.500;MQ=59.66;MQRankSum=-1.017;QD=18.30;ReadPosRankSum=-1.232;SOR=1.300 GT:AD:DP:GQ:PL 0/1:33,30:63:99:1160,0,1296 +20 10032972 . C CAT 1152.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.354;DP=67;ExcessHet=3.0103;FS=5.062;MLEAC=1;MLEAF=0.500;MQ=59.66;MQRankSum=-1.017;QD=18.30;ReadPosRankSum=-0.723;SOR=1.300 GT:AD:DP:GQ:PL 0/1:33,30:63:99:1160,0,1296 20 10034306 . T C 803.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.661;DP=80;ExcessHet=3.0103;FS=0.890;MLEAC=1;MLEAF=0.500;MQ=59.48;MQRankSum=1.150;QD=10.72;ReadPosRankSum=0.539;SOR=0.685 GT:AD:DP:GQ:PL 0/1:46,29:75:99:811,0,1593 -20 10036930 . CGATAGCCCTAGCCCTAGATA C 1070.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.200;DP=98;ExcessHet=3.0103;FS=11.152;MLEAC=1;MLEAF=0.500;MQ=54.46;MQRankSum=-4.048;QD=15.74;ReadPosRankSum=0.460;SOR=0.269 GT:AD:DP:GQ:PL 0/1:39,29:68:99:1078,0,1500 +20 10036930 . CGATAGCCCTAGCCCTAGATA C 1070.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.720;DP=98;ExcessHet=3.0103;FS=11.152;MLEAC=1;MLEAF=0.500;MQ=54.46;MQRankSum=-4.048;QD=15.74;ReadPosRankSum=0.460;SOR=0.269 GT:AD:DP:GQ:PL 0/1:39,29:68:99:1078,0,1500 20 10037037 . C T 1457.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.504;DP=88;ExcessHet=3.0103;FS=1.943;MLEAC=1;MLEAF=0.500;MQ=60.08;MQRankSum=-1.193;QD=18.00;ReadPosRankSum=-1.609;SOR=0.495 GT:AD:DP:GQ:PL 0/1:39,42:81:99:1465,0,1124 20 10037110 . T TGATA 2803.03 . AC=2;AF=1.00;AN=2;DP=84;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=55.01;QD=34.66;SOR=0.933 GT:AD:DP:GQ:PL 1/1:0,63:63:99:2817,189,0 20 10037144 . T TGATAGATA 1845.03 . AC=2;AF=1.00;AN=2;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.21;QD=29.40;SOR=1.179 GT:AD:DP:GQ:PL 1/1:0,43:43:99:1859,126,0 @@ -155,9 +155,9 @@ 20 10039371 . T G 1345.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.260;DP=76;ExcessHet=3.0103;FS=6.144;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=18.18;ReadPosRankSum=0.391;SOR=1.031 GT:AD:DP:GQ:PL 0/1:34,40:74:99:1353,0,1194 20 10040772 . C CT 2019.03 . AC=2;AF=1.00;AN=2;DP=85;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.32;QD=28.84;SOR=0.811 GT:AD:DP:GQ:PL 1/1:0,70:70:99:2033,210,0 20 10040812 . AT A 2631.03 . AC=2;AF=1.00;AN=2;DP=83;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.21;QD=36.76;SOR=0.721 GT:AD:DP:GQ:PL 1/1:0,71:71:99:2645,214,0 -20 10040821 . T A 1166.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.152;DP=83;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.21;MQRankSum=-0.175;QD=15.15;ReadPosRankSum=-1.350;SOR=0.741 GT:AD:DP:GQ:PL 0/1:38,39:77:99:1174,0,1102 +20 10040821 . T A 1166.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.152;DP=83;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.21;MQRankSum=-0.175;QD=15.15;ReadPosRankSum=-1.315;SOR=0.741 GT:AD:DP:GQ:PL 0/1:38,39:77:99:1174,0,1102 20 10041304 . C T 2780.06 . AC=2;AF=1.00;AN=2;DP=68;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.39;QD=30.54;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,68:68:99:2794,204,0 -20 10041701 . A ATATG 1431.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.848;DP=80;ExcessHet=3.0103;FS=3.477;MLEAC=1;MLEAF=0.500;MQ=58.93;MQRankSum=0.340;QD=24.26;ReadPosRankSum=-0.223;SOR=0.260 GT:AD:DP:GQ:PL 0/1:9,50:59:58:1439,0,58 +20 10041701 . A ATATG 1431.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.848;DP=80;ExcessHet=3.0103;FS=3.477;MLEAC=1;MLEAF=0.500;MQ=58.93;MQRankSum=0.340;QD=24.26;ReadPosRankSum=-0.023;SOR=0.260 GT:AD:DP:GQ:PL 0/1:9,50:59:58:1439,0,58 20 10042319 . C T 2673.06 . AC=2;AF=1.00;AN=2;DP=69;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.06;QD=21.53;SOR=1.033 GT:AD:DP:GQ:PL 1/1:0,66:66:99:2687,199,0 20 10042761 . A G 3568.06 . AC=2;AF=1.00;AN=2;DP=94;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=34.87;SOR=1.389 GT:AD:DP:GQ:PL 1/1:0,91:91:99:3582,272,0 20 10042829 . A G 3070.06 . AC=2;AF=1.00;AN=2;DP=82;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.77;QD=31.04;SOR=0.855 GT:AD:DP:GQ:PL 1/1:0,78:78:99:3084,235,0 @@ -171,8 +171,8 @@ 20 10051448 . T C 1155.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.501;DP=71;ExcessHet=3.0103;FS=3.687;MLEAC=1;MLEAF=0.500;MQ=59.41;MQRankSum=-1.404;QD=16.51;ReadPosRankSum=-0.705;SOR=0.302 GT:AD:DP:GQ:PL 0/1:35,35:70:99:1163,0,1150 20 10052688 . C A 1083.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.180;DP=83;ExcessHet=3.0103;FS=3.135;MLEAC=1;MLEAF=0.500;MQ=59.78;MQRankSum=0.870;QD=14.07;ReadPosRankSum=1.443;SOR=0.379 GT:AD:DP:GQ:PL 0/1:45,32:77:99:1091,0,1645 20 10058022 . T C 996.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.346;DP=72;ExcessHet=3.0103;FS=0.920;MLEAC=1;MLEAF=0.500;MQ=59.16;MQRankSum=0.466;QD=14.66;ReadPosRankSum=0.018;SOR=0.849 GT:AD:DP:GQ:PL 0/1:36,32:68:99:1004,0,1261 -20 10062935 . C CA 119.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.304;DP=90;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.41;MQRankSum=-1.502;QD=5.44;ReadPosRankSum=-1.113;SOR=0.743 GT:AD:DP:GQ:PL 0/1:12,10:22:99:127,0,109 -20 10067049 . TAAAAAAAA T,TA 639.02 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=0.217;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=54.73;MQRankSum=-0.429;QD=29.05;ReadPosRankSum=-1.226;SOR=0.941 GT:AD:DP:GQ:PL 1/2:2,11,9:22:99:656,167,339,137,0,106 +20 10062935 . C CA 119.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.242;DP=90;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.41;MQRankSum=-1.502;QD=5.44;ReadPosRankSum=-1.113;SOR=0.743 GT:AD:DP:GQ:PL 0/1:12,10:22:99:127,0,109 +20 10067049 . TAAAAAAAA T,TA 639.02 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=-0.106;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=54.73;MQRankSum=-0.429;QD=29.05;ReadPosRankSum=-1.226;SOR=0.941 GT:AD:DP:GQ:PL 1/2:2,11,9:22:99:656,167,339,137,0,106 20 10067090 . C A 2019.06 . AC=2;AF=1.00;AN=2;DP=56;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=54.57;QD=33.11;SOR=0.729 GT:AD:DP:GQ:PL 1/1:0,55:55:99:2033,164,0 20 10067264 . G A 2937.06 . AC=2;AF=1.00;AN=2;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.37;QD=30.20;SOR=0.776 GT:AD:DP:GQ:PL 1/1:0,73:73:99:2951,219,0 20 10067722 . A C 2161.06 . AC=2;AF=1.00;AN=2;DP=59;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.49;SOR=0.846 GT:AD:DP:GQ:PL 1/1:0,54:54:99:2175,163,0 @@ -196,7 +196,7 @@ 20 10076250 . A G 1128.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.386;DP=82;ExcessHet=3.0103;FS=7.546;MLEAC=1;MLEAF=0.500;MQ=59.41;MQRankSum=-1.423;QD=14.29;ReadPosRankSum=0.270;SOR=0.344 GT:AD:DP:GQ:PL 0/1:40,39:79:99:1136,0,1339 20 10076339 . A G 1330.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.069;DP=76;ExcessHet=3.0103;FS=1.992;MLEAC=1;MLEAF=0.500;MQ=59.70;MQRankSum=-0.866;QD=18.48;ReadPosRankSum=1.015;SOR=0.446 GT:AD:DP:GQ:PL 0/1:32,40:72:99:1338,0,1035 20 10076399 . G A 1828.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=4.154;DP=95;ExcessHet=3.0103;FS=1.680;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=19.45;ReadPosRankSum=-1.058;SOR=0.952 GT:AD:DP:GQ:PL 0/1:44,50:94:99:1836,0,1544 -20 10076989 . CA C,CAA 242.02 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=-0.625;DP=83;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=58.03;MQRankSum=-0.507;QD=7.56;ReadPosRankSum=-0.724;SOR=0.653 GT:AD:DP:GQ:PL 1/2:7,18,7:32:40:259,40,371,157,0,379 +20 10076989 . CA C,CAA 242.02 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=-0.566;DP=83;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=58.03;MQRankSum=-0.507;QD=7.56;ReadPosRankSum=-0.608;SOR=0.653 GT:AD:DP:GQ:PL 1/2:7,18,7:32:40:259,40,371,157,0,379 20 10077752 . T C 1366.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-6.503;DP=83;ExcessHet=3.0103;FS=4.458;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=17.30;ReadPosRankSum=-0.352;SOR=1.251 GT:AD:DP:GQ:PL 0/1:34,45:79:99:1374,0,1187 20 10079476 . T G 31.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-4.570;DP=55;ExcessHet=3.0103;FS=57.922;MLEAC=1;MLEAF=0.500;MQ=58.81;MQRankSum=-0.826;QD=0.72;ReadPosRankSum=1.533;SOR=4.970 GT:AD:DP:GQ:PL 0/1:33,11:44:39:39,0,1137 20 10081750 . C A 1374.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.670;DP=92;ExcessHet=3.0103;FS=0.824;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=16.56;ReadPosRankSum=-0.406;SOR=0.664 GT:AD:DP:GQ:PL 0/1:44,39:83:99:1382,0,1525 @@ -212,20 +212,20 @@ 20 10087394 . T G 1709.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.340;DP=85;ExcessHet=3.0103;FS=4.225;MLEAC=1;MLEAF=0.500;MQ=59.46;MQRankSum=1.207;QD=20.35;ReadPosRankSum=0.885;SOR=0.436 GT:AD:DP:GQ:PL 0/1:35,49:84:99:1717,0,1186 20 10087754 . T G 1403.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.239;DP=87;ExcessHet=3.0103;FS=0.851;MLEAC=1;MLEAF=0.500;MQ=60.60;MQRankSum=2.166;QD=17.77;ReadPosRankSum=-0.378;SOR=0.596 GT:AD:DP:GQ:PL 0/1:37,42:79:99:1411,0,1236 20 10087804 . C T 1640.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.940;DP=104;ExcessHet=3.0103;FS=3.847;MLEAC=1;MLEAF=0.500;MQ=60.18;MQRankSum=2.618;QD=16.41;ReadPosRankSum=0.341;SOR=0.369 GT:AD:DP:GQ:PL 0/1:50,50:100:99:1648,0,1511 -20 10087820 . C CAG 456.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.974;DP=102;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.51;MQRankSum=0.422;QD=8.30;ReadPosRankSum=-0.357;SOR=0.850 GT:AD:DP:GQ:PL 0/1:37,18:55:99:464,0,1170 +20 10087820 . C CAG 456.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.974;DP=102;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.51;MQRankSum=0.422;QD=8.30;ReadPosRankSum=-0.019;SOR=0.850 GT:AD:DP:GQ:PL 0/1:37,18:55:99:464,0,1170 20 10088063 . C T 1438.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.405;DP=94;ExcessHet=3.0103;FS=2.739;MLEAC=1;MLEAF=0.500;MQ=59.36;MQRankSum=0.515;QD=15.47;ReadPosRankSum=0.285;SOR=1.053 GT:AD:DP:GQ:PL 0/1:49,44:93:99:1446,0,1403 20 10088699 . C T 797.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.803;DP=67;ExcessHet=3.0103;FS=16.952;MLEAC=1;MLEAF=0.500;MQ=56.90;MQRankSum=-3.140;QD=12.87;ReadPosRankSum=-1.456;SOR=1.914 GT:AD:DP:GQ:PL 0/1:36,26:62:99:805,0,1088 -20 10088730 . G A 993.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.058;DP=57;ExcessHet=3.0103;FS=9.708;MLEAC=1;MLEAF=0.500;MQ=52.92;MQRankSum=-5.213;QD=17.74;ReadPosRankSum=0.581;SOR=1.011 GT:AD:DP:GQ:PL 0/1:30,26:56:99:1001,0,1152 -20 10088736 . A C 1102.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.016;DP=60;ExcessHet=3.0103;FS=7.080;MLEAC=1;MLEAF=0.500;MQ=52.86;MQRankSum=-5.157;QD=18.38;ReadPosRankSum=0.573;SOR=0.850 GT:AD:DP:GQ:PL 0/1:31,29:60:99:1110,0,1194 +20 10088730 . G A 993.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.224;DP=57;ExcessHet=3.0103;FS=9.708;MLEAC=1;MLEAF=0.500;MQ=52.92;MQRankSum=-5.213;QD=17.74;ReadPosRankSum=0.581;SOR=1.011 GT:AD:DP:GQ:PL 0/1:30,26:56:99:1001,0,1152 +20 10088736 . A C 1102.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.282;DP=60;ExcessHet=3.0103;FS=7.080;MLEAC=1;MLEAF=0.500;MQ=52.86;MQRankSum=-5.157;QD=18.38;ReadPosRankSum=0.573;SOR=0.850 GT:AD:DP:GQ:PL 0/1:31,29:60:99:1110,0,1194 20 10088747 . A G 1132.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.877;DP=56;ExcessHet=3.0103;FS=9.708;MLEAC=1;MLEAF=0.500;MQ=52.20;MQRankSum=-4.881;QD=20.23;ReadPosRankSum=0.009;SOR=1.162 GT:AD:DP:GQ:PL 0/1:26,30:56:99:1140,0,995 20 10088799 . G A 1039.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=5.503;DP=54;ExcessHet=3.0103;FS=10.098;MLEAC=1;MLEAF=0.500;MQ=53.34;MQRankSum=-2.498;QD=19.62;ReadPosRankSum=1.075;SOR=1.003 GT:AD:DP:GQ:PL 0/1:22,31:53:99:1047,0,617 20 10088895 . C T 556.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.330;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.80;MQRankSum=0.260;QD=13.92;ReadPosRankSum=1.238;SOR=0.727 GT:AD:DP:GQ:PL 0/1:22,18:40:99:564,0,651 -20 10088968 . C CAAA 1289.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.117;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=52.34;MQRankSum=-5.320;QD=19.54;ReadPosRankSum=1.802;SOR=0.804 GT:AD:DP:GQ:PL 0/1:32,34:66:99:1297,0,1230 -20 10088980 . T C 1352.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.772;DP=76;ExcessHet=3.0103;FS=0.874;MLEAC=1;MLEAF=0.500;MQ=50.96;MQRankSum=-5.207;QD=18.04;ReadPosRankSum=1.124;SOR=0.869 GT:AD:DP:GQ:PL 0/1:39,36:75:99:1360,0,1491 -20 10088985 . T C 1283.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.525;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.85;MQRankSum=-5.440;QD=16.89;ReadPosRankSum=1.155;SOR=0.606 GT:AD:DP:GQ:PL 0/1:42,34:76:99:1291,0,1593 +20 10088968 . C CAAA 1289.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.337;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=52.34;MQRankSum=-5.320;QD=19.54;ReadPosRankSum=0.205;SOR=0.804 GT:AD:DP:GQ:PL 0/1:32,34:66:99:1297,0,1230 +20 10088980 . T C 1352.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.845;DP=76;ExcessHet=3.0103;FS=0.874;MLEAC=1;MLEAF=0.500;MQ=50.96;MQRankSum=-5.207;QD=18.04;ReadPosRankSum=1.483;SOR=0.869 GT:AD:DP:GQ:PL 0/1:39,36:75:99:1360,0,1491 +20 10088985 . T C 1283.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.525;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.85;MQRankSum=-5.440;QD=16.89;ReadPosRankSum=1.432;SOR=0.606 GT:AD:DP:GQ:PL 0/1:42,34:76:99:1291,0,1593 20 10089441 . A G 1200.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-4.885;DP=79;ExcessHet=3.0103;FS=6.071;MLEAC=1;MLEAF=0.500;MQ=59.71;MQRankSum=-0.948;QD=15.80;ReadPosRankSum=-0.156;SOR=1.363 GT:AD:DP:GQ:PL 0/1:37,39:76:99:1208,0,1313 20 10089525 . C T 1569.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=5.859;DP=83;ExcessHet=3.0103;FS=4.260;MLEAC=1;MLEAF=0.500;MQ=59.50;MQRankSum=1.531;QD=19.38;ReadPosRankSum=0.862;SOR=0.617 GT:AD:DP:GQ:PL 0/1:38,43:81:99:1577,0,1088 -20 10090289 . CA C 405.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.134;DP=88;ExcessHet=3.0103;FS=2.958;MLEAC=1;MLEAF=0.500;MQ=59.97;MQRankSum=1.581;QD=10.67;ReadPosRankSum=0.788;SOR=1.057 GT:AD:DP:GQ:PL 0/1:15,23:38:99:413,0,240 +20 10090289 . CA C 405.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.105;DP=88;ExcessHet=3.0103;FS=2.958;MLEAC=1;MLEAF=0.500;MQ=59.97;MQRankSum=1.581;QD=10.67;ReadPosRankSum=0.788;SOR=1.057 GT:AD:DP:GQ:PL 0/1:15,23:38:99:413,0,240 20 10090764 . A G 861.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.659;DP=67;ExcessHet=3.0103;FS=4.975;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=13.68;ReadPosRankSum=1.207;SOR=0.310 GT:AD:DP:GQ:PL 0/1:34,29:63:99:869,0,1207 20 10090970 . T C 1278.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.484;DP=70;ExcessHet=3.0103;FS=0.927;MLEAC=1;MLEAF=0.500;MQ=59.47;MQRankSum=1.509;QD=18.53;ReadPosRankSum=-0.072;SOR=0.518 GT:AD:DP:GQ:PL 0/1:33,36:69:99:1286,0,1092 20 10091214 . C T 1270.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.361;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.74;MQRankSum=-0.916;QD=18.15;ReadPosRankSum=-0.035;SOR=0.625 GT:AD:DP:GQ:PL 0/1:33,37:70:99:1278,0,1110 @@ -236,18 +236,18 @@ 20 10094251 . T A 1291.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.251;DP=67;ExcessHet=3.0103;FS=11.483;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=20.83;ReadPosRankSum=1.806;SOR=1.211 GT:AD:DP:GQ:PL 0/1:26,36:62:99:1299,0,781 20 10094582 . A G 944.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.388;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.43;MQRankSum=1.270;QD=13.69;ReadPosRankSum=-0.018;SOR=0.772 GT:AD:DP:GQ:PL 0/1:39,30:69:99:952,0,1350 20 10094774 . C T 1057.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.784;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.43;MQRankSum=0.962;QD=14.10;ReadPosRankSum=0.197;SOR=0.690 GT:AD:DP:GQ:PL 0/1:40,35:75:99:1065,0,1282 -20 10095432 . GTGATGATGA G 875.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.109;DP=78;ExcessHet=3.0103;FS=2.430;MLEAC=1;MLEAF=0.500;MQ=54.46;MQRankSum=-4.378;QD=17.87;ReadPosRankSum=0.396;SOR=0.400 GT:AD:DP:GQ:PL 0/1:26,23:49:99:883,0,978 +20 10095432 . GTGATGATGA G 875.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.063;DP=78;ExcessHet=3.0103;FS=2.430;MLEAC=1;MLEAF=0.500;MQ=54.46;MQRankSum=-4.378;QD=17.87;ReadPosRankSum=0.396;SOR=0.400 GT:AD:DP:GQ:PL 0/1:26,23:49:99:883,0,978 20 10095741 . A G 1096.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.534;DP=72;ExcessHet=3.0103;FS=4.721;MLEAC=1;MLEAF=0.500;MQ=57.39;MQRankSum=-2.313;QD=15.67;ReadPosRankSum=-0.500;SOR=0.515 GT:AD:DP:GQ:PL 0/1:36,34:70:99:1104,0,1233 20 10096293 . C T 1376.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=4.664;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.64;MQRankSum=1.397;QD=18.36;ReadPosRankSum=-1.135;SOR=0.638 GT:AD:DP:GQ:PL 0/1:37,38:75:99:1384,0,1258 20 10096596 . C T 1583.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.728;DP=91;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.82;MQRankSum=0.612;QD=18.20;ReadPosRankSum=-0.170;SOR=0.640 GT:AD:DP:GQ:PL 0/1:40,47:87:99:1591,0,1273 20 10096768 . A C 1703.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.764;DP=96;ExcessHet=3.0103;FS=3.983;MLEAC=1;MLEAF=0.500;MQ=59.28;MQRankSum=-1.609;QD=18.72;ReadPosRankSum=0.613;SOR=0.445 GT:AD:DP:GQ:PL 0/1:42,49:91:99:1711,0,1452 -20 10096899 . G T 1636.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.494;DP=84;ExcessHet=3.0103;FS=13.441;MLEAC=1;MLEAF=0.500;MQ=59.28;MQRankSum=-1.677;QD=19.72;ReadPosRankSum=0.422;SOR=1.954 GT:AD:DP:GQ:PL 0/1:40,43:83:99:1644,0,1519 +20 10096899 . G T 1636.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.755;DP=84;ExcessHet=3.0103;FS=13.441;MLEAC=1;MLEAF=0.500;MQ=59.28;MQRankSum=-1.677;QD=19.72;ReadPosRankSum=0.422;SOR=1.954 GT:AD:DP:GQ:PL 0/1:40,43:83:99:1644,0,1519 20 10096905 . TA T 1630.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.755;DP=86;ExcessHet=3.0103;FS=11.056;MLEAC=1;MLEAF=0.500;MQ=59.30;MQRankSum=-1.739;QD=18.96;ReadPosRankSum=0.461;SOR=1.761 GT:AD:DP:GQ:PL 0/1:43,43:86:99:1638,0,1623 -20 10096933 . G C 1534.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.724;DP=89;ExcessHet=3.0103;FS=19.713;MLEAC=1;MLEAF=0.500;MQ=59.32;MQRankSum=-1.840;QD=17.24;ReadPosRankSum=0.334;SOR=1.420 GT:AD:DP:GQ:PL 0/1:47,42:89:99:1542,0,1763 -20 10096958 . G A 1789.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.697;DP=93;ExcessHet=3.0103;FS=19.322;MLEAC=1;MLEAF=0.500;MQ=59.35;MQRankSum=-1.664;QD=19.45;ReadPosRankSum=-1.824;SOR=1.431 GT:AD:DP:GQ:PL 0/1:44,48:92:99:1797,0,1622 -20 10097075 . T G 1466.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.533;DP=96;ExcessHet=3.0103;FS=6.613;MLEAC=1;MLEAF=0.500;MQ=58.14;MQRankSum=-1.389;QD=15.94;ReadPosRankSum=0.082;SOR=0.628 GT:AD:DP:GQ:PL 0/1:44,48:92:99:1474,0,1482 -20 10097101 . C CTTT 1105.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.894;DP=81;ExcessHet=3.0103;FS=7.156;MLEAC=1;MLEAF=0.500;MQ=58.26;MQRankSum=-1.750;QD=16.50;ReadPosRankSum=2.739;SOR=0.501 GT:AD:DP:GQ:PL 0/1:34,33:67:99:1113,0,1263 -20 10097436 . CTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT C 1089.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.820;DP=90;ExcessHet=3.0103;FS=1.851;MLEAC=1;MLEAF=0.500;MQ=54.34;MQRankSum=-6.464;QD=12.24;ReadPosRankSum=-3.097;SOR=0.948 GT:AD:DP:GQ:PL 0/1:57,32:89:99:1097,0,2238 +20 10096933 . G C 1534.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.914;DP=89;ExcessHet=3.0103;FS=19.713;MLEAC=1;MLEAF=0.500;MQ=59.32;MQRankSum=-1.840;QD=17.24;ReadPosRankSum=0.383;SOR=1.420 GT:AD:DP:GQ:PL 0/1:47,42:89:99:1542,0,1763 +20 10096958 . G A 1789.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.697;DP=93;ExcessHet=3.0103;FS=19.322;MLEAC=1;MLEAF=0.500;MQ=59.35;MQRankSum=-1.664;QD=19.45;ReadPosRankSum=-1.593;SOR=1.431 GT:AD:DP:GQ:PL 0/1:44,48:92:99:1797,0,1622 +20 10097075 . T G 1466.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.533;DP=96;ExcessHet=3.0103;FS=6.613;MLEAC=1;MLEAF=0.500;MQ=58.14;MQRankSum=-1.389;QD=15.94;ReadPosRankSum=0.235;SOR=0.628 GT:AD:DP:GQ:PL 0/1:44,48:92:99:1474,0,1482 +20 10097101 . C CTTT 1105.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.894;DP=81;ExcessHet=3.0103;FS=7.156;MLEAC=1;MLEAF=0.500;MQ=58.26;MQRankSum=-1.750;QD=16.50;ReadPosRankSum=3.135;SOR=0.501 GT:AD:DP:GQ:PL 0/1:34,33:67:99:1113,0,1263 +20 10097436 . CTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT C 1089.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.650;DP=90;ExcessHet=3.0103;FS=1.851;MLEAC=1;MLEAF=0.500;MQ=54.34;MQRankSum=-6.464;QD=12.24;ReadPosRankSum=-3.097;SOR=0.948 GT:AD:DP:GQ:PL 0/1:57,32:89:99:1097,0,2238 20 10097437 . TTTTC *,T 931.01 . AC=1,1;AF=0.500,0.500;AN=2;DP=78;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=53.68;QD=16.93;SOR=1.877 GT:AD:DP:GQ:PL 1/2:0,32,23:55:99:2133,941,1797,1201,0,1129 20 10097626 . C A 647.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.085;DP=54;ExcessHet=3.0103;FS=2.701;MLEAC=1;MLEAF=0.500;MQ=58.00;MQRankSum=-1.331;QD=13.49;ReadPosRankSum=1.015;SOR=0.324 GT:AD:DP:GQ:PL 0/1:28,20:48:99:655,0,957 20 10097789 . T C 709.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.157;DP=60;ExcessHet=3.0103;FS=5.374;MLEAC=1;MLEAF=0.500;MQ=58.05;MQRankSum=-2.805;QD=12.45;ReadPosRankSum=0.220;SOR=0.756 GT:AD:DP:GQ:PL 0/1:34,23:57:99:717,0,1190 @@ -255,19 +255,19 @@ 20 10098110 . G C 607.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.510;DP=36;ExcessHet=3.0103;FS=6.658;MLEAC=1;MLEAF=0.500;MQ=58.71;MQRankSum=-1.477;QD=16.88;ReadPosRankSum=-0.730;SOR=0.069 GT:AD:DP:GQ:PL 0/1:19,17:36:99:615,0,727 20 10098135 . C A 492.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.155;DP=39;ExcessHet=3.0103;FS=4.449;MLEAC=1;MLEAF=0.500;MQ=59.65;MQRankSum=1.563;QD=12.63;ReadPosRankSum=-0.591;SOR=0.070 GT:AD:DP:GQ:PL 0/1:25,14:39:99:500,0,964 20 10098219 . TATATATA T 325.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.147;DP=21;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.94;MQRankSum=-0.205;QD=15.50;ReadPosRankSum=0.427;SOR=0.465 GT:AD:DP:GQ:PL 0/1:12,9:21:99:333,0,461 -20 10098237 . A T 265.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.006;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.89;MQRankSum=-1.885;QD=18.97;ReadPosRankSum=0.277;SOR=0.693 GT:AD:DP:GQ:PL 0/1:7,7:14:99:273,0,273 -20 10098265 . T C 154.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.834;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=41.96;MQRankSum=-1.834;QD=25.77;ReadPosRankSum=0.000;SOR=1.329 GT:AD:DP:GQ:PL 0/1:2,4:6:59:162,0,59 -20 10098885 . C CA 463.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.165;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.73;MQRankSum=-4.449;QD=14.95;ReadPosRankSum=-1.073;SOR=0.518 GT:AD:DP:GQ:PL 0/1:17,14:31:99:471,0,572 +20 10098237 . A T 265.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.006;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.89;MQRankSum=-1.885;QD=18.97;ReadPosRankSum=1.118;SOR=0.693 GT:AD:DP:GQ:PL 0/1:7,7:14:99:273,0,273 +20 10098265 . T C 154.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.834;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=41.96;MQRankSum=-1.834;QD=25.77;ReadPosRankSum=0.842;SOR=1.329 GT:AD:DP:GQ:PL 0/1:2,4:6:59:162,0,59 +20 10098885 . C CA 463.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.165;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.73;MQRankSum=-4.449;QD=14.95;ReadPosRankSum=-0.954;SOR=0.518 GT:AD:DP:GQ:PL 0/1:17,14:31:99:471,0,572 20 10098945 . T C 428.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.475;DP=22;ExcessHet=3.0103;FS=3.882;MLEAC=1;MLEAF=0.500;MQ=51.15;MQRankSum=-2.504;QD=19.48;ReadPosRankSum=1.038;SOR=2.368 GT:AD:DP:GQ:PL 0/1:9,13:22:99:436,0,248 20 10098987 . C T 400.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.127;DP=25;ExcessHet=3.0103;FS=7.005;MLEAC=1;MLEAF=0.500;MQ=51.36;MQRankSum=-2.734;QD=16.69;ReadPosRankSum=0.436;SOR=2.925 GT:AD:DP:GQ:PL 0/1:11,13:24:99:408,0,350 -20 10099029 . T C 355.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.518;DP=30;ExcessHet=3.0103;FS=1.987;MLEAC=1;MLEAF=0.500;MQ=52.93;MQRankSum=-3.731;QD=12.26;ReadPosRankSum=-1.224;SOR=1.609 GT:AD:DP:GQ:PL 0/1:19,10:29:99:363,0,768 -20 10099034 . C A 355.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.752;DP=29;ExcessHet=3.0103;FS=1.987;MLEAC=1;MLEAF=0.500;MQ=53.57;MQRankSum=-3.731;QD=12.26;ReadPosRankSum=-1.850;SOR=1.609 GT:AD:DP:GQ:PL 0/1:19,10:29:99:363,0,768 +20 10099029 . T C 355.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.809;DP=30;ExcessHet=3.0103;FS=1.987;MLEAC=1;MLEAF=0.500;MQ=52.93;MQRankSum=-3.731;QD=12.26;ReadPosRankSum=-1.224;SOR=1.609 GT:AD:DP:GQ:PL 0/1:19,10:29:99:363,0,768 +20 10099034 . C A 355.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.757;DP=29;ExcessHet=3.0103;FS=1.987;MLEAC=1;MLEAF=0.500;MQ=53.57;MQRankSum=-3.731;QD=12.26;ReadPosRankSum=-1.850;SOR=1.609 GT:AD:DP:GQ:PL 0/1:19,10:29:99:363,0,768 20 10099044 . A C 355.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.148;DP=29;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.81;MQRankSum=-4.533;QD=12.26;ReadPosRankSum=-2.207;SOR=0.892 GT:AD:DP:GQ:PL 0/1:19,10:29:99:363,0,768 20 10099046 . T C 325.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.165;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.94;MQRankSum=-4.418;QD=13.57;ReadPosRankSum=-2.297;SOR=0.515 GT:AD:DP:GQ:PL 0/1:15,9:24:99:333,0,603 -20 10099055 . T C 277.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.996;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.20;MQRankSum=-4.179;QD=11.11;ReadPosRankSum=-1.970;SOR=0.770 GT:AD:DP:GQ:PL 0/1:17,8:25:99:285,0,673 -20 10099079 . C T 137.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.432;DP=30;ExcessHet=3.0103;FS=1.826;MLEAC=1;MLEAF=0.500;MQ=51.49;MQRankSum=-2.614;QD=4.59;ReadPosRankSum=0.969;SOR=1.329 GT:AD:DP:GQ:PL 0/1:24,6:30:99:145,0,886 -20 10099111 . T TTTTGTTTG 685.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.622;DP=52;ExcessHet=3.0103;FS=1.206;MLEAC=1;MLEAF=0.500;MQ=53.85;MQRankSum=-0.973;QD=16.32;ReadPosRankSum=-0.273;SOR=0.967 GT:AD:DP:GQ:PL 0/1:23,19:42:99:693,0,802 -20 10099140 . G T 1027.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.286;DP=63;ExcessHet=3.0103;FS=3.596;MLEAC=1;MLEAF=0.500;MQ=55.79;MQRankSum=-2.435;QD=16.85;ReadPosRankSum=0.116;SOR=1.188 GT:AD:DP:GQ:PL 0/1:29,32:61:99:1035,0,930 +20 10099055 . T C 277.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.554;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.20;MQRankSum=-4.179;QD=11.11;ReadPosRankSum=-1.970;SOR=0.770 GT:AD:DP:GQ:PL 0/1:17,8:25:99:285,0,673 +20 10099079 . C T 137.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.434;DP=30;ExcessHet=3.0103;FS=1.826;MLEAC=1;MLEAF=0.500;MQ=51.49;MQRankSum=-2.614;QD=4.59;ReadPosRankSum=0.969;SOR=1.329 GT:AD:DP:GQ:PL 0/1:24,6:30:99:145,0,886 +20 10099111 . T TTTTGTTTG 685.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.207;DP=52;ExcessHet=3.0103;FS=1.206;MLEAC=1;MLEAF=0.500;MQ=53.85;MQRankSum=-0.973;QD=16.32;ReadPosRankSum=-1.860;SOR=0.967 GT:AD:DP:GQ:PL 0/1:23,19:42:99:693,0,802 +20 10099140 . G T 1027.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.286;DP=63;ExcessHet=3.0103;FS=3.596;MLEAC=1;MLEAF=0.500;MQ=55.79;MQRankSum=-2.435;QD=16.85;ReadPosRankSum=0.636;SOR=1.188 GT:AD:DP:GQ:PL 0/1:29,32:61:99:1035,0,930 20 10099190 . G T 1030.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.264;DP=62;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.82;MQRankSum=-1.445;QD=16.62;ReadPosRankSum=-1.577;SOR=0.693 GT:AD:DP:GQ:PL 0/1:31,31:62:99:1038,0,1088 20 10099220 . A G 598.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.664;DP=47;ExcessHet=3.0103;FS=1.137;MLEAC=1;MLEAF=0.500;MQ=57.74;MQRankSum=-2.596;QD=13.30;ReadPosRankSum=0.629;SOR=0.519 GT:AD:DP:GQ:PL 0/1:25,20:45:99:606,0,873 20 10099250 . G A 720.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.170;DP=39;ExcessHet=3.0103;FS=7.195;MLEAC=1;MLEAF=0.500;MQ=56.89;MQRankSum=-2.272;QD=19.48;ReadPosRankSum=0.583;SOR=0.162 GT:AD:DP:GQ:PL 0/1:16,21:37:99:728,0,424 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testVCFMode.gatk4.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testVCFMode.gatk4.vcf index 97e99ff3440..aae4d993cd7 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testVCFMode.gatk4.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testVCFMode.gatk4.vcf @@ -52,13 +52,13 @@ 20 10004094 . A C 1840.06 . AC=2;AF=1.00;AN=2;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.62;QD=34.72;SOR=1.524 GT:AD:DP:GQ:PL 1/1:0,53:53:99:1854,157,0 20 10004147 . A G 1852.06 . AC=2;AF=1.00;AN=2;DP=54;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=55.19;QD=26.61;SOR=1.136 GT:AD:DP:GQ:PL 1/1:0,52:52:99:1866,156,0 20 10004193 . G T 937.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.392;DP=54;ExcessHet=3.0103;FS=2.369;MLEAC=1;MLEAF=0.500;MQ=59.14;MQRankSum=3.385;QD=18.39;ReadPosRankSum=1.724;SOR=0.941 GT:AD:DP:GQ:PL 0/1:23,28:51:99:945,0,776 -20 10004222 . C CA 41.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.124;DP=68;ExcessHet=3.0103;FS=3.221;MLEAC=1;MLEAF=0.500;MQ=58.19;MQRankSum=-2.220;QD=0.92;ReadPosRankSum=1.271;SOR=0.932 GT:AD:DP:GQ:PL 0/1:35,10:45:49:49,0,924 -20 10004223 . A AG 80.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.749;DP=68;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.27;MQRankSum=2.272;QD=1.71;ReadPosRankSum=0.490;SOR=0.544 GT:AD:DP:GQ:PL 0/1:35,12:47:88:88,0,953 +20 10004222 . C CA 41.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.335;DP=68;ExcessHet=3.0103;FS=3.221;MLEAC=1;MLEAF=0.500;MQ=58.19;MQRankSum=-2.220;QD=0.92;ReadPosRankSum=0.198;SOR=0.932 GT:AD:DP:GQ:PL 0/1:35,10:45:49:49,0,924 +20 10004223 . A AG 80.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.765;DP=68;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.27;MQRankSum=2.272;QD=1.71;ReadPosRankSum=0.183;SOR=0.544 GT:AD:DP:GQ:PL 0/1:35,12:47:88:88,0,953 20 10004351 . C G 2770.06 . AC=2;AF=1.00;AN=2;DP=71;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.05;QD=29.20;SOR=0.874 GT:AD:DP:GQ:PL 1/1:0,70:70:99:2784,211,0 20 10004389 . T G 2509.06 . AC=2;AF=1.00;AN=2;DP=67;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.62;QD=28.55;SOR=1.143 GT:AD:DP:GQ:PL 1/1:0,62:62:99:2523,187,0 20 10004610 . A C 3640.06 . AC=2;AF=1.00;AN=2;DP=93;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.75;QD=34.42;SOR=0.761 GT:AD:DP:GQ:PL 1/1:0,89:89:99:3654,267,0 20 10004725 . A G 975.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.393;DP=66;ExcessHet=3.0103;FS=13.744;MLEAC=1;MLEAF=0.500;MQ=55.34;MQRankSum=2.856;QD=15.24;ReadPosRankSum=1.932;SOR=0.613 GT:AD:DP:GQ:PL 0/1:34,30:64:99:983,0,1139 -20 10004769 . TAAAACTATGC T 970.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.796;DP=79;ExcessHet=3.0103;FS=3.721;MLEAC=1;MLEAF=0.500;MQ=53.03;MQRankSum=-6.531;QD=15.41;ReadPosRankSum=1.721;SOR=1.236 GT:AD:DP:GQ:PL 0/1:37,26:63:99:978,0,1473 +20 10004769 . TAAAACTATGC T 970.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.807;DP=79;ExcessHet=3.0103;FS=3.721;MLEAC=1;MLEAF=0.500;MQ=53.03;MQRankSum=-6.531;QD=15.41;ReadPosRankSum=1.721;SOR=1.236 GT:AD:DP:GQ:PL 0/1:37,26:63:99:978,0,1473 20 10004874 . A C 3617.06 . AC=2;AF=1.00;AN=2;DP=90;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.35;QD=28.53;SOR=1.286 GT:AD:DP:GQ:PL 1/1:0,87:87:99:3631,261,0 20 10004887 . A G 1344.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.356;DP=90;ExcessHet=3.0103;FS=1.793;MLEAC=1;MLEAF=0.500;MQ=59.49;MQRankSum=-0.067;QD=15.82;ReadPosRankSum=-1.114;SOR=0.984 GT:AD:DP:GQ:PL 0/1:45,40:85:99:1352,0,1542 20 10005010 . C T 2949.06 . AC=2;AF=1.00;AN=2;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.68;QD=27.23;SOR=1.226 GT:AD:DP:GQ:PL 1/1:0,72:72:99:2963,217,0 @@ -75,25 +75,25 @@ 20 10007352 . C T 2779.06 . AC=2;AF=1.00;AN=2;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.67;QD=31.26;SOR=1.054 GT:AD:DP:GQ:PL 1/1:0,69:69:99:2793,208,0 20 10007531 . A G 2935.06 . AC=2;AF=1.00;AN=2;DP=75;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.75;QD=27.76;SOR=1.577 GT:AD:DP:GQ:PL 1/1:0,72:72:99:2949,217,0 20 10007980 . A C 3539.06 . AC=2;AF=1.00;AN=2;DP=92;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.70;QD=29.09;SOR=0.990 GT:AD:DP:GQ:PL 1/1:0,90:90:99:3553,270,0 -20 10008029 . T TA 2009.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.438;DP=97;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=61.11;MQRankSum=0.651;QD=26.09;ReadPosRankSum=-1.326;SOR=0.774 GT:AD:DP:GQ:PL 1/1:3,74:77:99:2023,145,0 +20 10008029 . T TA 2009.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.409;DP=97;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=61.11;MQRankSum=0.651;QD=26.09;ReadPosRankSum=-1.357;SOR=0.774 GT:AD:DP:GQ:PL 1/1:3,74:77:99:2023,145,0 20 10008146 . TA T 2166.03 . AC=2;AF=1.00;AN=2;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.56;QD=30.94;SOR=0.874 GT:AD:DP:GQ:PL 1/1:0,70:70:99:2180,211,0 20 10008221 . T C 3239.06 . AC=2;AF=1.00;AN=2;DP=83;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.17;QD=26.08;SOR=0.850 GT:AD:DP:GQ:PL 1/1:0,80:80:99:3253,240,0 20 10008458 . T G 2669.06 . AC=2;AF=1.00;AN=2;DP=72;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.76;QD=33.85;SOR=0.980 GT:AD:DP:GQ:PL 1/1:0,69:69:99:2683,207,0 -20 10008742 . G T 736.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.893;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=37.07;MQRankSum=-1.502;QD=15.03;ReadPosRankSum=0.190;SOR=0.741 GT:AD:DP:GQ:PL 0/1:23,26:49:99:744,0,580 -20 10008758 . C CA 706.49 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.119;DP=51;ExcessHet=3.0103;FS=2.191;MLEAC=1;MLEAF=0.500;MQ=37.72;MQRankSum=-0.875;QD=18.59;ReadPosRankSum=-0.052;SOR=0.405 GT:AD:DP:GQ:PL 1/1:4,34:38:10:720,10,0 -20 10008921 . C CA 283.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.516;DP=60;ExcessHet=3.0103;FS=1.311;MLEAC=1;MLEAF=0.500;MQ=56.00;MQRankSum=-1.306;QD=8.10;ReadPosRankSum=0.173;SOR=0.644 GT:AD:DP:GQ:PL 0/1:18,17:35:99:291,0,366 -20 10008948 . TA T 2094.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.956;DP=56;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.26;MQRankSum=1.946;QD=27.08;ReadPosRankSum=0.884;SOR=0.721 GT:AD:DP:GQ:PL 1/1:1,53:54:99:2108,117,0 -20 10008952 . CACACACACACA C,CCACACACACA 1702.02 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=0.963;DP=63;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=51.23;MQRankSum=1.976;QD=25.42;ReadPosRankSum=0.934;SOR=1.112 GT:AD:DP:GQ:PL 1/2:1,17,18:36:99:1719,538,801,597,0,535 +20 10008742 . G T 736.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.893;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=37.07;MQRankSum=-1.502;QD=15.03;ReadPosRankSum=0.200;SOR=0.741 GT:AD:DP:GQ:PL 0/1:23,26:49:99:744,0,580 +20 10008758 . C CA 706.49 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.130;DP=51;ExcessHet=3.0103;FS=2.191;MLEAC=1;MLEAF=0.500;MQ=37.72;MQRankSum=-0.875;QD=18.59;ReadPosRankSum=-0.262;SOR=0.405 GT:AD:DP:GQ:PL 1/1:4,34:38:10:720,10,0 +20 10008921 . C CA 283.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.610;DP=60;ExcessHet=3.0103;FS=1.311;MLEAC=1;MLEAF=0.500;MQ=56.00;MQRankSum=-1.306;QD=8.10;ReadPosRankSum=-0.017;SOR=0.644 GT:AD:DP:GQ:PL 0/1:18,17:35:99:291,0,366 +20 10008948 . TA T 2094.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.994;DP=56;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.26;MQRankSum=1.946;QD=27.08;ReadPosRankSum=0.884;SOR=0.721 GT:AD:DP:GQ:PL 1/1:1,53:54:99:2108,117,0 +20 10008952 . CACACACACACA C,CCACACACACA 1702.02 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=0.963;DP=63;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=51.23;MQRankSum=1.976;QD=25.42;ReadPosRankSum=0.868;SOR=1.112 GT:AD:DP:GQ:PL 1/2:1,17,18:36:99:1719,538,801,597,0,535 20 10009227 . A G 1390.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.220;DP=63;ExcessHet=3.0103;FS=9.110;MLEAC=1;MLEAF=0.500;MQ=56.82;MQRankSum=1.428;QD=22.43;ReadPosRankSum=-1.159;SOR=0.281 GT:AD:DP:GQ:PL 0/1:23,39:62:99:1398,0,740 20 10009246 . A G 3017.06 . AC=2;AF=1.00;AN=2;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=55.68;QD=27.65;SOR=0.887 GT:AD:DP:GQ:PL 1/1:0,77:77:99:3031,231,0 20 10009400 . T A 3013.06 . AC=2;AF=1.00;AN=2;DP=75;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.48;SOR=0.804 GT:AD:DP:GQ:PL 1/1:0,74:74:99:3027,223,0 20 10009512 . C G 3054.06 . AC=2;AF=1.00;AN=2;DP=80;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.53;QD=30.56;SOR=1.223 GT:AD:DP:GQ:PL 1/1:0,77:77:99:3068,231,0 20 10009719 . A G 1901.06 . AC=2;AF=1.00;AN=2;DP=65;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.71;QD=33.35;SOR=1.047 GT:AD:DP:GQ:PL 1/1:0,57:57:99:1915,170,0 20 10009795 . A G 1895.06 . AC=2;AF=1.00;AN=2;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.62;QD=33.63;SOR=1.514 GT:AD:DP:GQ:PL 1/1:0,47:47:99:1909,141,0 -20 10009842 . G GAA 562.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.183;DP=52;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.85;MQRankSum=-0.936;QD=16.07;ReadPosRankSum=1.754;SOR=0.602 GT:AD:DP:GQ:PL 0/1:19,16:35:99:570,0,691 -20 10009844 . G A 683.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.998;DP=54;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.61;MQRankSum=0.975;QD=19.53;ReadPosRankSum=-1.575;SOR=0.793 GT:AD:DP:GQ:PL 0/1:16,19:35:99:691,0,585 -20 10009871 . A G 679.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.803;DP=62;ExcessHet=3.0103;FS=1.273;MLEAC=1;MLEAF=0.500;MQ=51.11;MQRankSum=1.336;QD=18.37;ReadPosRankSum=1.491;SOR=0.631 GT:AD:DP:GQ:PL 0/1:18,19:37:99:687,0,593 -20 10009875 . A G,AGGGAGG 2389.06 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=0.378;DP=58;ExcessHet=3.0103;FS=6.463;MLEAC=1,1;MLEAF=0.500,0.500;MQ=50.44;MQRankSum=1.413;QD=30.55;ReadPosRankSum=1.040;SOR=0.461 GT:AD:DP:GQ:PL 1/2:2,15,14:31:99:2406,645,532,697,0,574 +20 10009842 . G GAA 562.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.383;DP=52;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.85;MQRankSum=-0.936;QD=16.07;ReadPosRankSum=1.757;SOR=0.602 GT:AD:DP:GQ:PL 0/1:19,16:35:99:570,0,691 +20 10009844 . G A 683.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.116;DP=54;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.61;MQRankSum=0.975;QD=19.53;ReadPosRankSum=-2.354;SOR=0.793 GT:AD:DP:GQ:PL 0/1:16,19:35:99:691,0,585 +20 10009871 . A G 679.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.803;DP=62;ExcessHet=3.0103;FS=1.273;MLEAC=1;MLEAF=0.500;MQ=51.11;MQRankSum=1.336;QD=18.37;ReadPosRankSum=0.840;SOR=0.631 GT:AD:DP:GQ:PL 0/1:18,19:37:99:687,0,593 +20 10009875 . A G,AGGGAGG 2389.06 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=0.378;DP=58;ExcessHet=3.0103;FS=6.463;MLEAC=1,1;MLEAF=0.500,0.500;MQ=50.44;MQRankSum=1.413;QD=30.55;ReadPosRankSum=1.373;SOR=0.461 GT:AD:DP:GQ:PL 1/2:2,15,14:31:99:2406,645,532,697,0,574 20 10009879 . A G 2259.06 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.534;DP=53;ExcessHet=3.0103;FS=8.605;MLEAC=2;MLEAF=1.00;MQ=50.48;MQRankSum=1.681;QD=32.62;ReadPosRankSum=1.113;SOR=1.198 GT:AD:DP:GQ:PL 1/1:2,51:53:99:2273,150,0 20 10009883 . A G 2166.06 . AC=2;AF=1.00;AN=2;DP=52;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=50.81;QD=29.33;SOR=1.755 GT:AD:DP:GQ:PL 1/1:0,49:49:99:2180,147,0 20 10010393 . T G 1485.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.351;DP=79;ExcessHet=3.0103;FS=11.600;MLEAC=1;MLEAF=0.500;MQ=59.42;MQRankSum=-1.284;QD=18.81;ReadPosRankSum=-1.738;SOR=0.606 GT:AD:DP:GQ:PL 0/1:36,43:79:99:1493,0,1230 @@ -115,13 +115,13 @@ 20 10012521 . C T 92.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.517;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=40.86;MQRankSum=-0.376;QD=7.72;ReadPosRankSum=2.405;SOR=0.693 GT:AD:DP:GQ:PL 0/1:8,4:12:99:100,0,221 20 10012570 . G GCA 481.02 . AC=2;AF=1.00;AN=2;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=39.52;QD=29.94;SOR=3.442 GT:AD:DP:GQ:PL 1/1:0,11:11:33:495,33,0 20 10012572 . GT G 481.02 . AC=2;AF=1.00;AN=2;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=40.60;QD=31.54;SOR=3.442 GT:AD:DP:GQ:PL 1/1:0,11:11:33:495,33,0 -20 10012631 . C CG 514.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.030;DP=21;ExcessHet=3.0103;FS=8.822;MLEAC=1;MLEAF=0.500;MQ=48.34;MQRankSum=-1.670;QD=24.50;ReadPosRankSum=-1.813;SOR=0.048 GT:AD:DP:GQ:PL 0/1:8,13:21:99:522,0,297 -20 10012636 . G C 548.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.711;DP=22;ExcessHet=3.0103;FS=5.959;MLEAC=1;MLEAF=0.500;MQ=48.93;MQRankSum=-1.513;QD=24.94;ReadPosRankSum=-1.915;SOR=0.058 GT:AD:DP:GQ:PL 0/1:8,14:22:99:556,0,294 +20 10012631 . C CG 514.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.030;DP=21;ExcessHet=3.0103;FS=8.822;MLEAC=1;MLEAF=0.500;MQ=48.34;MQRankSum=-1.670;QD=24.50;ReadPosRankSum=-1.777;SOR=0.048 GT:AD:DP:GQ:PL 0/1:8,13:21:99:522,0,297 +20 10012636 . G C 548.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.711;DP=22;ExcessHet=3.0103;FS=5.959;MLEAC=1;MLEAF=0.500;MQ=48.93;MQRankSum=-1.513;QD=24.94;ReadPosRankSum=-1.777;SOR=0.058 GT:AD:DP:GQ:PL 0/1:8,14:22:99:556,0,294 20 10012714 . G C 1315.06 . AC=2;AF=1.00;AN=2;DP=36;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.52;QD=28.86;SOR=2.964 GT:AD:DP:GQ:PL 1/1:0,35:35:99:1329,105,0 20 10012751 . T C 952.06 . AC=2;AF=1.00;AN=2;DP=31;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=50.73;QD=31.74;SOR=0.976 GT:AD:DP:GQ:PL 1/1:0,30:30:89:966,89,0 20 10013119 . C T 1032.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.724;DP=61;ExcessHet=3.0103;FS=2.248;MLEAC=1;MLEAF=0.500;MQ=51.43;MQRankSum=-1.089;QD=17.50;ReadPosRankSum=0.159;SOR=0.405 GT:AD:DP:GQ:PL 0/1:29,30:59:99:1040,0,936 20 10013574 . G A 1071.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.469;DP=73;ExcessHet=3.0103;FS=7.109;MLEAC=1;MLEAF=0.500;MQ=58.17;MQRankSum=-0.271;QD=15.53;ReadPosRankSum=0.706;SOR=1.675 GT:AD:DP:GQ:PL 0/1:38,31:69:99:1079,0,1301 -20 10014990 . C CAT 1265.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.756;DP=89;ExcessHet=3.0103;FS=2.076;MLEAC=1;MLEAF=0.500;MQ=60.88;MQRankSum=3.260;QD=16.44;ReadPosRankSum=-0.437;SOR=0.429 GT:AD:DP:GQ:PL 0/1:38,39:77:99:1273,0,1250 +20 10014990 . C CAT 1265.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.930;DP=89;ExcessHet=3.0103;FS=2.076;MLEAC=1;MLEAF=0.500;MQ=60.88;MQRankSum=3.260;QD=16.44;ReadPosRankSum=-0.311;SOR=0.429 GT:AD:DP:GQ:PL 0/1:38,39:77:99:1273,0,1250 20 10015679 . C T 161.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.200;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=16.16;ReadPosRankSum=0.497;SOR=0.693 GT:AD:DP:GQ:PL 0/1:5,5:10:99:169,0,166 20 10015761 . T C 365.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.982;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.99;MQRankSum=1.294;QD=16.62;ReadPosRankSum=1.805;SOR=0.352 GT:AD:DP:GQ:PL 0/1:9,13:22:99:373,0,284 20 10018158 . G C 1660.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=5.213;DP=94;ExcessHet=3.0103;FS=0.808;MLEAC=1;MLEAF=0.500;MQ=59.80;MQRankSum=1.118;QD=18.87;ReadPosRankSum=1.179;SOR=0.834 GT:AD:DP:GQ:PL 0/1:40,48:88:99:1668,0,1165 @@ -130,24 +130,24 @@ 20 10020229 . G A 1559.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=5.792;DP=84;ExcessHet=3.0103;FS=0.833;MLEAC=1;MLEAF=0.500;MQ=59.50;MQRankSum=0.104;QD=19.02;ReadPosRankSum=-0.549;SOR=0.573 GT:AD:DP:GQ:PL 0/1:38,44:82:99:1567,0,1130 20 10023689 . G A 1873.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.144;DP=82;ExcessHet=3.0103;FS=0.877;MLEAC=1;MLEAF=0.500;MQ=59.77;MQRankSum=1.352;QD=23.42;ReadPosRankSum=1.162;SOR=0.549 GT:AD:DP:GQ:PL 0/1:29,51:80:99:1881,0,946 20 10024107 . C T 1715.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=5.770;DP=89;ExcessHet=3.0103;FS=0.817;MLEAC=1;MLEAF=0.500;MQ=59.43;MQRankSum=-1.546;QD=19.95;ReadPosRankSum=0.148;SOR=0.823 GT:AD:DP:GQ:PL 0/1:38,48:86:99:1723,0,1086 -20 10024300 . C CTT 126.96 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.362;DP=56;ExcessHet=3.0103;FS=3.090;MLEAC=1;MLEAF=0.500;MQ=52.36;MQRankSum=-0.084;QD=6.68;ReadPosRankSum=-0.431;SOR=1.773 GT:AD:DP:GQ:PL 0/1:11,8:19:97:97,0,168 +20 10024300 . C CTT 126.96 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.241;DP=56;ExcessHet=3.0103;FS=3.090;MLEAC=1;MLEAF=0.500;MQ=52.36;MQRankSum=-0.084;QD=6.68;ReadPosRankSum=-0.431;SOR=1.773 GT:AD:DP:GQ:PL 0/1:11,8:19:97:97,0,168 20 10026357 . T C 1187.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.700;DP=63;ExcessHet=3.0103;FS=8.911;MLEAC=1;MLEAF=0.500;MQ=58.43;MQRankSum=-0.148;QD=18.85;ReadPosRankSum=-0.076;SOR=0.722 GT:AD:DP:GQ:PL 0/1:28,35:63:99:1195,0,932 20 10026794 . C T 1105.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.828;DP=56;ExcessHet=3.0103;FS=2.399;MLEAC=1;MLEAF=0.500;MQ=59.59;MQRankSum=-0.719;QD=21.26;ReadPosRankSum=-0.533;SOR=0.428 GT:AD:DP:GQ:PL 0/1:19,33:52:99:1113,0,529 -20 10027234 . A ATTAG 1350.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.406;DP=75;ExcessHet=3.0103;FS=3.248;MLEAC=1;MLEAF=0.500;MQ=57.44;MQRankSum=-0.845;QD=19.57;ReadPosRankSum=-0.979;SOR=0.926 GT:AD:DP:GQ:PL 0/1:34,35:69:99:1358,0,1321 -20 10027868 . A G 1760.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-5.798;DP=91;ExcessHet=3.0103;FS=6.873;MLEAC=1;MLEAF=0.500;MQ=59.49;MQRankSum=0.047;QD=19.56;ReadPosRankSum=1.872;SOR=0.937 GT:AD:DP:GQ:PL 0/1:44,46:90:99:1768,0,1671 +20 10027234 . A ATTAG 1350.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.406;DP=75;ExcessHet=3.0103;FS=3.248;MLEAC=1;MLEAF=0.500;MQ=57.44;MQRankSum=-0.845;QD=19.57;ReadPosRankSum=-0.510;SOR=0.926 GT:AD:DP:GQ:PL 0/1:34,35:69:99:1358,0,1321 +20 10027868 . A G 1760.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-5.793;DP=91;ExcessHet=3.0103;FS=6.873;MLEAC=1;MLEAF=0.500;MQ=59.49;MQRankSum=0.047;QD=19.56;ReadPosRankSum=1.872;SOR=0.937 GT:AD:DP:GQ:PL 0/1:44,46:90:99:1768,0,1671 20 10027872 . A G 1745.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-5.491;DP=88;ExcessHet=3.0103;FS=8.704;MLEAC=1;MLEAF=0.500;MQ=59.48;MQRankSum=0.065;QD=20.06;ReadPosRankSum=1.053;SOR=0.834 GT:AD:DP:GQ:PL 0/1:42,45:87:99:1753,0,1606 -20 10028867 . A ATG 1134.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.874;DP=93;ExcessHet=3.0103;FS=4.652;MLEAC=1;MLEAF=0.500;MQ=60.68;MQRankSum=2.711;QD=15.98;ReadPosRankSum=0.364;SOR=0.336 GT:AD:DP:GQ:PL 0/1:32,39:71:99:1142,0,918 +20 10028867 . A ATG 1134.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.874;DP=93;ExcessHet=3.0103;FS=4.652;MLEAC=1;MLEAF=0.500;MQ=60.68;MQRankSum=2.711;QD=15.98;ReadPosRankSum=0.630;SOR=0.336 GT:AD:DP:GQ:PL 0/1:32,39:71:99:1142,0,918 20 10030188 . T A 1393.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.711;DP=82;ExcessHet=3.0103;FS=9.186;MLEAC=1;MLEAF=0.500;MQ=59.49;MQRankSum=-1.013;QD=17.21;ReadPosRankSum=-0.553;SOR=1.105 GT:AD:DP:GQ:PL 0/1:42,39:81:99:1401,0,1524 -20 10031254 . A AT 1493.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.091;DP=90;ExcessHet=3.0103;FS=9.250;MLEAC=1;MLEAF=0.500;MQ=59.91;MQRankSum=0.017;QD=17.57;ReadPosRankSum=0.495;SOR=0.211 GT:AD:DP:GQ:PL 0/1:38,47:85:99:1501,0,1159 +20 10031254 . A AT 1493.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.091;DP=90;ExcessHet=3.0103;FS=9.250;MLEAC=1;MLEAF=0.500;MQ=59.91;MQRankSum=0.017;QD=17.57;ReadPosRankSum=0.663;SOR=0.211 GT:AD:DP:GQ:PL 0/1:38,47:85:99:1501,0,1159 20 10031342 . G A 1855.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.833;DP=93;ExcessHet=3.0103;FS=1.714;MLEAC=1;MLEAF=0.500;MQ=59.75;MQRankSum=-0.866;QD=19.95;ReadPosRankSum=-0.012;SOR=0.955 GT:AD:DP:GQ:PL 0/1:41,52:93:99:1863,0,1375 20 10031798 . G A 4311.06 . AC=2;AF=1.00;AN=2;DP=107;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.61;QD=29.41;SOR=0.900 GT:AD:DP:GQ:PL 1/1:0,104:104:99:4325,313,0 20 10031827 . C T 2025.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.552;DP=115;ExcessHet=3.0103;FS=4.729;MLEAC=1;MLEAF=0.500;MQ=59.84;MQRankSum=-0.945;QD=18.76;ReadPosRankSum=-1.396;SOR=0.382 GT:AD:DP:GQ:PL 0/1:52,56:108:99:2033,0,1798 20 10032094 . G A 1241.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=5.488;DP=86;ExcessHet=3.0103;FS=6.039;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=14.96;ReadPosRankSum=-0.579;SOR=0.260 GT:AD:DP:GQ:PL 0/1:47,36:83:99:1249,0,1497 20 10032413 . T G 890.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-6.142;DP=66;ExcessHet=3.0103;FS=10.444;MLEAC=1;MLEAF=0.500;MQ=59.43;MQRankSum=-0.065;QD=13.49;ReadPosRankSum=-1.003;SOR=1.293 GT:AD:DP:GQ:PL 0/1:35,31:66:99:898,0,1277 20 10032882 . A T 1223.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.697;DP=76;ExcessHet=3.0103;FS=4.673;MLEAC=1;MLEAF=0.500;MQ=59.70;MQRankSum=-1.014;QD=16.32;ReadPosRankSum=0.626;SOR=0.338 GT:AD:DP:GQ:PL 0/1:39,36:75:99:1231,0,1406 -20 10032972 . C CAT 1152.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.354;DP=67;ExcessHet=3.0103;FS=5.062;MLEAC=1;MLEAF=0.500;MQ=59.66;MQRankSum=-1.017;QD=18.30;ReadPosRankSum=-1.232;SOR=1.300 GT:AD:DP:GQ:PL 0/1:33,30:63:99:1160,0,1296 +20 10032972 . C CAT 1152.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.354;DP=67;ExcessHet=3.0103;FS=5.062;MLEAC=1;MLEAF=0.500;MQ=59.66;MQRankSum=-1.017;QD=18.30;ReadPosRankSum=-0.723;SOR=1.300 GT:AD:DP:GQ:PL 0/1:33,30:63:99:1160,0,1296 20 10034306 . T C 803.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.661;DP=80;ExcessHet=3.0103;FS=0.890;MLEAC=1;MLEAF=0.500;MQ=59.48;MQRankSum=1.150;QD=10.72;ReadPosRankSum=0.539;SOR=0.685 GT:AD:DP:GQ:PL 0/1:46,29:75:99:811,0,1593 -20 10036930 . CGATAGCCCTAGCCCTAGATA C 1070.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.200;DP=98;ExcessHet=3.0103;FS=11.152;MLEAC=1;MLEAF=0.500;MQ=54.46;MQRankSum=-4.048;QD=15.74;ReadPosRankSum=0.460;SOR=0.269 GT:AD:DP:GQ:PL 0/1:39,29:68:99:1078,0,1500 +20 10036930 . CGATAGCCCTAGCCCTAGATA C 1070.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.720;DP=98;ExcessHet=3.0103;FS=11.152;MLEAC=1;MLEAF=0.500;MQ=54.46;MQRankSum=-4.048;QD=15.74;ReadPosRankSum=0.460;SOR=0.269 GT:AD:DP:GQ:PL 0/1:39,29:68:99:1078,0,1500 20 10037037 . C T 1457.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.504;DP=88;ExcessHet=3.0103;FS=1.943;MLEAC=1;MLEAF=0.500;MQ=60.08;MQRankSum=-1.193;QD=18.00;ReadPosRankSum=-1.609;SOR=0.495 GT:AD:DP:GQ:PL 0/1:39,42:81:99:1465,0,1124 20 10037110 . T TGATA 2803.03 . AC=2;AF=1.00;AN=2;DP=84;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=55.01;QD=31.11;SOR=0.933 GT:AD:DP:GQ:PL 1/1:0,63:63:99:2817,189,0 20 10037144 . T TGATAGATA 1845.03 . AC=2;AF=1.00;AN=2;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.21;QD=34.66;SOR=1.179 GT:AD:DP:GQ:PL 1/1:0,43:43:99:1859,126,0 @@ -155,9 +155,9 @@ 20 10039371 . T G 1345.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.260;DP=76;ExcessHet=3.0103;FS=6.144;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=18.18;ReadPosRankSum=0.391;SOR=1.031 GT:AD:DP:GQ:PL 0/1:34,40:74:99:1353,0,1194 20 10040772 . C CT 2019.03 . AC=2;AF=1.00;AN=2;DP=85;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.32;QD=28.84;SOR=0.811 GT:AD:DP:GQ:PL 1/1:0,70:70:99:2033,210,0 20 10040812 . AT A 2631.03 . AC=2;AF=1.00;AN=2;DP=83;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.21;QD=29.40;SOR=0.721 GT:AD:DP:GQ:PL 1/1:0,71:71:99:2645,214,0 -20 10040821 . T A 1166.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.152;DP=83;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.21;MQRankSum=-0.175;QD=15.15;ReadPosRankSum=-1.350;SOR=0.741 GT:AD:DP:GQ:PL 0/1:38,39:77:99:1174,0,1102 +20 10040821 . T A 1166.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.152;DP=83;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.21;MQRankSum=-0.175;QD=15.15;ReadPosRankSum=-1.315;SOR=0.741 GT:AD:DP:GQ:PL 0/1:38,39:77:99:1174,0,1102 20 10041304 . C T 2780.06 . AC=2;AF=1.00;AN=2;DP=68;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.39;QD=36.76;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,68:68:99:2794,204,0 -20 10041701 . A ATATG 1431.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.848;DP=80;ExcessHet=3.0103;FS=3.477;MLEAC=1;MLEAF=0.500;MQ=58.93;MQRankSum=0.340;QD=24.26;ReadPosRankSum=-0.223;SOR=0.260 GT:AD:DP:GQ:PL 0/1:9,50:59:58:1439,0,58 +20 10041701 . A ATATG 1431.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.848;DP=80;ExcessHet=3.0103;FS=3.477;MLEAC=1;MLEAF=0.500;MQ=58.93;MQRankSum=0.340;QD=24.26;ReadPosRankSum=-0.023;SOR=0.260 GT:AD:DP:GQ:PL 0/1:9,50:59:58:1439,0,58 20 10042319 . C T 2673.06 . AC=2;AF=1.00;AN=2;DP=69;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.06;QD=30.54;SOR=1.033 GT:AD:DP:GQ:PL 1/1:0,66:66:99:2687,199,0 20 10042761 . A G 3568.06 . AC=2;AF=1.00;AN=2;DP=94;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=21.53;SOR=1.389 GT:AD:DP:GQ:PL 1/1:0,91:91:99:3582,272,0 20 10042829 . A G 3070.06 . AC=2;AF=1.00;AN=2;DP=82;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.77;QD=34.87;SOR=0.855 GT:AD:DP:GQ:PL 1/1:0,78:78:99:3084,235,0 @@ -171,8 +171,8 @@ 20 10051448 . T C 1155.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.501;DP=71;ExcessHet=3.0103;FS=3.687;MLEAC=1;MLEAF=0.500;MQ=59.41;MQRankSum=-1.404;QD=16.51;ReadPosRankSum=-0.705;SOR=0.302 GT:AD:DP:GQ:PL 0/1:35,35:70:99:1163,0,1150 20 10052688 . C A 1083.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.180;DP=83;ExcessHet=3.0103;FS=3.135;MLEAC=1;MLEAF=0.500;MQ=59.78;MQRankSum=0.870;QD=14.07;ReadPosRankSum=1.443;SOR=0.379 GT:AD:DP:GQ:PL 0/1:45,32:77:99:1091,0,1645 20 10058022 . T C 996.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.346;DP=72;ExcessHet=3.0103;FS=0.920;MLEAC=1;MLEAF=0.500;MQ=59.16;MQRankSum=0.466;QD=14.66;ReadPosRankSum=0.018;SOR=0.849 GT:AD:DP:GQ:PL 0/1:36,32:68:99:1004,0,1261 -20 10062935 . C CA 119.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.304;DP=90;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.41;MQRankSum=-1.502;QD=5.44;ReadPosRankSum=-1.113;SOR=0.743 GT:AD:DP:GQ:PL 0/1:12,10:22:99:127,0,109 -20 10067049 . TAAAAAAAA T,TA 639.02 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=0.217;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=54.73;MQRankSum=-0.429;QD=29.05;ReadPosRankSum=-1.226;SOR=0.941 GT:AD:DP:GQ:PL 1/2:2,11,9:22:99:656,167,339,137,0,106 +20 10062935 . C CA 119.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.242;DP=90;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.41;MQRankSum=-1.502;QD=5.44;ReadPosRankSum=-1.113;SOR=0.743 GT:AD:DP:GQ:PL 0/1:12,10:22:99:127,0,109 +20 10067049 . TAAAAAAAA T,TA 639.02 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=-0.106;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=54.73;MQRankSum=-0.429;QD=29.05;ReadPosRankSum=-1.226;SOR=0.941 GT:AD:DP:GQ:PL 1/2:2,11,9:22:99:656,167,339,137,0,106 20 10067090 . C A 2019.06 . AC=2;AF=1.00;AN=2;DP=56;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=54.57;QD=25.57;SOR=0.729 GT:AD:DP:GQ:PL 1/1:0,55:55:99:2033,164,0 20 10067264 . G A 2937.06 . AC=2;AF=1.00;AN=2;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.37;QD=33.11;SOR=0.776 GT:AD:DP:GQ:PL 1/1:0,73:73:99:2951,219,0 20 10067722 . A C 2161.06 . AC=2;AF=1.00;AN=2;DP=59;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.20;SOR=0.846 GT:AD:DP:GQ:PL 1/1:0,54:54:99:2175,163,0 @@ -196,7 +196,7 @@ 20 10076250 . A G 1128.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.386;DP=82;ExcessHet=3.0103;FS=7.546;MLEAC=1;MLEAF=0.500;MQ=59.41;MQRankSum=-1.423;QD=14.29;ReadPosRankSum=0.270;SOR=0.344 GT:AD:DP:GQ:PL 0/1:40,39:79:99:1136,0,1339 20 10076339 . A G 1330.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.069;DP=76;ExcessHet=3.0103;FS=1.992;MLEAC=1;MLEAF=0.500;MQ=59.70;MQRankSum=-0.866;QD=18.48;ReadPosRankSum=1.015;SOR=0.446 GT:AD:DP:GQ:PL 0/1:32,40:72:99:1338,0,1035 20 10076399 . G A 1828.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=4.154;DP=95;ExcessHet=3.0103;FS=1.680;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=19.45;ReadPosRankSum=-1.058;SOR=0.952 GT:AD:DP:GQ:PL 0/1:44,50:94:99:1836,0,1544 -20 10076989 . CA C,CAA 242.02 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=-0.625;DP=83;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=58.03;MQRankSum=-0.507;QD=7.56;ReadPosRankSum=-0.724;SOR=0.653 GT:AD:DP:GQ:PL 1/2:7,18,7:32:40:259,40,371,157,0,379 +20 10076989 . CA C,CAA 242.02 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=-0.566;DP=83;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=58.03;MQRankSum=-0.507;QD=7.56;ReadPosRankSum=-0.608;SOR=0.653 GT:AD:DP:GQ:PL 1/2:7,18,7:32:40:259,40,371,157,0,379 20 10077752 . T C 1366.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-6.503;DP=83;ExcessHet=3.0103;FS=4.458;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=17.30;ReadPosRankSum=-0.352;SOR=1.251 GT:AD:DP:GQ:PL 0/1:34,45:79:99:1374,0,1187 20 10079476 . T G 31.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-4.570;DP=55;ExcessHet=3.0103;FS=57.922;MLEAC=1;MLEAF=0.500;MQ=58.81;MQRankSum=-0.826;QD=0.72;ReadPosRankSum=1.533;SOR=4.970 GT:AD:DP:GQ:PL 0/1:33,11:44:39:39,0,1137 20 10081750 . C A 1374.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.670;DP=92;ExcessHet=3.0103;FS=0.824;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=16.56;ReadPosRankSum=-0.406;SOR=0.664 GT:AD:DP:GQ:PL 0/1:44,39:83:99:1382,0,1525 @@ -212,20 +212,20 @@ 20 10087394 . T G 1709.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.340;DP=85;ExcessHet=3.0103;FS=4.225;MLEAC=1;MLEAF=0.500;MQ=59.46;MQRankSum=1.207;QD=20.35;ReadPosRankSum=0.885;SOR=0.436 GT:AD:DP:GQ:PL 0/1:35,49:84:99:1717,0,1186 20 10087754 . T G 1403.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.239;DP=87;ExcessHet=3.0103;FS=0.851;MLEAC=1;MLEAF=0.500;MQ=60.60;MQRankSum=2.166;QD=17.77;ReadPosRankSum=-0.378;SOR=0.596 GT:AD:DP:GQ:PL 0/1:37,42:79:99:1411,0,1236 20 10087804 . C T 1640.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.940;DP=104;ExcessHet=3.0103;FS=3.847;MLEAC=1;MLEAF=0.500;MQ=60.18;MQRankSum=2.618;QD=16.41;ReadPosRankSum=0.341;SOR=0.369 GT:AD:DP:GQ:PL 0/1:50,50:100:99:1648,0,1511 -20 10087820 . C CAG 456.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.974;DP=102;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.51;MQRankSum=0.422;QD=8.30;ReadPosRankSum=-0.357;SOR=0.850 GT:AD:DP:GQ:PL 0/1:37,18:55:99:464,0,1170 +20 10087820 . C CAG 456.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.974;DP=102;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.51;MQRankSum=0.422;QD=8.30;ReadPosRankSum=-0.019;SOR=0.850 GT:AD:DP:GQ:PL 0/1:37,18:55:99:464,0,1170 20 10088063 . C T 1438.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.405;DP=94;ExcessHet=3.0103;FS=2.739;MLEAC=1;MLEAF=0.500;MQ=59.36;MQRankSum=0.515;QD=15.47;ReadPosRankSum=0.285;SOR=1.053 GT:AD:DP:GQ:PL 0/1:49,44:93:99:1446,0,1403 20 10088699 . C T 797.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.803;DP=67;ExcessHet=3.0103;FS=16.952;MLEAC=1;MLEAF=0.500;MQ=56.90;MQRankSum=-3.140;QD=12.87;ReadPosRankSum=-1.456;SOR=1.914 GT:AD:DP:GQ:PL 0/1:36,26:62:99:805,0,1088 -20 10088730 . G A 993.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.058;DP=57;ExcessHet=3.0103;FS=9.708;MLEAC=1;MLEAF=0.500;MQ=52.92;MQRankSum=-5.213;QD=17.74;ReadPosRankSum=0.581;SOR=1.011 GT:AD:DP:GQ:PL 0/1:30,26:56:99:1001,0,1152 -20 10088736 . A C 1102.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.016;DP=60;ExcessHet=3.0103;FS=7.080;MLEAC=1;MLEAF=0.500;MQ=52.86;MQRankSum=-5.157;QD=18.38;ReadPosRankSum=0.573;SOR=0.850 GT:AD:DP:GQ:PL 0/1:31,29:60:99:1110,0,1194 +20 10088730 . G A 993.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.224;DP=57;ExcessHet=3.0103;FS=9.708;MLEAC=1;MLEAF=0.500;MQ=52.92;MQRankSum=-5.213;QD=17.74;ReadPosRankSum=0.581;SOR=1.011 GT:AD:DP:GQ:PL 0/1:30,26:56:99:1001,0,1152 +20 10088736 . A C 1102.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.282;DP=60;ExcessHet=3.0103;FS=7.080;MLEAC=1;MLEAF=0.500;MQ=52.86;MQRankSum=-5.157;QD=18.38;ReadPosRankSum=0.573;SOR=0.850 GT:AD:DP:GQ:PL 0/1:31,29:60:99:1110,0,1194 20 10088747 . A G 1132.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.877;DP=56;ExcessHet=3.0103;FS=9.708;MLEAC=1;MLEAF=0.500;MQ=52.20;MQRankSum=-4.881;QD=20.23;ReadPosRankSum=0.009;SOR=1.162 GT:AD:DP:GQ:PL 0/1:26,30:56:99:1140,0,995 20 10088799 . G A 1039.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=5.503;DP=54;ExcessHet=3.0103;FS=10.098;MLEAC=1;MLEAF=0.500;MQ=53.34;MQRankSum=-2.498;QD=19.62;ReadPosRankSum=1.075;SOR=1.003 GT:AD:DP:GQ:PL 0/1:22,31:53:99:1047,0,617 20 10088895 . C T 556.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.330;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.80;MQRankSum=0.260;QD=13.92;ReadPosRankSum=1.238;SOR=0.727 GT:AD:DP:GQ:PL 0/1:22,18:40:99:564,0,651 -20 10088968 . C CAAA 1289.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.117;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=52.34;MQRankSum=-5.320;QD=19.54;ReadPosRankSum=1.802;SOR=0.804 GT:AD:DP:GQ:PL 0/1:32,34:66:99:1297,0,1230 -20 10088980 . T C 1352.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.772;DP=76;ExcessHet=3.0103;FS=0.874;MLEAC=1;MLEAF=0.500;MQ=50.96;MQRankSum=-5.207;QD=18.04;ReadPosRankSum=1.124;SOR=0.869 GT:AD:DP:GQ:PL 0/1:39,36:75:99:1360,0,1491 -20 10088985 . T C 1283.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.525;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.85;MQRankSum=-5.440;QD=16.89;ReadPosRankSum=1.155;SOR=0.606 GT:AD:DP:GQ:PL 0/1:42,34:76:99:1291,0,1593 +20 10088968 . C CAAA 1289.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.337;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=52.34;MQRankSum=-5.320;QD=19.54;ReadPosRankSum=0.205;SOR=0.804 GT:AD:DP:GQ:PL 0/1:32,34:66:99:1297,0,1230 +20 10088980 . T C 1352.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.845;DP=76;ExcessHet=3.0103;FS=0.874;MLEAC=1;MLEAF=0.500;MQ=50.96;MQRankSum=-5.207;QD=18.04;ReadPosRankSum=1.483;SOR=0.869 GT:AD:DP:GQ:PL 0/1:39,36:75:99:1360,0,1491 +20 10088985 . T C 1283.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.525;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.85;MQRankSum=-5.440;QD=16.89;ReadPosRankSum=1.432;SOR=0.606 GT:AD:DP:GQ:PL 0/1:42,34:76:99:1291,0,1593 20 10089441 . A G 1200.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-4.885;DP=79;ExcessHet=3.0103;FS=6.071;MLEAC=1;MLEAF=0.500;MQ=59.71;MQRankSum=-0.948;QD=15.80;ReadPosRankSum=-0.156;SOR=1.363 GT:AD:DP:GQ:PL 0/1:37,39:76:99:1208,0,1313 20 10089525 . C T 1569.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=5.859;DP=83;ExcessHet=3.0103;FS=4.260;MLEAC=1;MLEAF=0.500;MQ=59.50;MQRankSum=1.531;QD=19.38;ReadPosRankSum=0.862;SOR=0.617 GT:AD:DP:GQ:PL 0/1:38,43:81:99:1577,0,1088 -20 10090289 . CA C 405.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.134;DP=88;ExcessHet=3.0103;FS=2.958;MLEAC=1;MLEAF=0.500;MQ=59.97;MQRankSum=1.581;QD=10.67;ReadPosRankSum=0.788;SOR=1.057 GT:AD:DP:GQ:PL 0/1:15,23:38:99:413,0,240 +20 10090289 . CA C 405.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.105;DP=88;ExcessHet=3.0103;FS=2.958;MLEAC=1;MLEAF=0.500;MQ=59.97;MQRankSum=1.581;QD=10.67;ReadPosRankSum=0.788;SOR=1.057 GT:AD:DP:GQ:PL 0/1:15,23:38:99:413,0,240 20 10090764 . A G 861.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.659;DP=67;ExcessHet=3.0103;FS=4.975;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=13.68;ReadPosRankSum=1.207;SOR=0.310 GT:AD:DP:GQ:PL 0/1:34,29:63:99:869,0,1207 20 10090970 . T C 1278.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.484;DP=70;ExcessHet=3.0103;FS=0.927;MLEAC=1;MLEAF=0.500;MQ=59.47;MQRankSum=1.509;QD=18.53;ReadPosRankSum=-0.072;SOR=0.518 GT:AD:DP:GQ:PL 0/1:33,36:69:99:1286,0,1092 20 10091214 . C T 1270.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.361;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.74;MQRankSum=-0.916;QD=18.15;ReadPosRankSum=-0.035;SOR=0.625 GT:AD:DP:GQ:PL 0/1:33,37:70:99:1278,0,1110 @@ -236,18 +236,18 @@ 20 10094251 . T A 1291.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.251;DP=67;ExcessHet=3.0103;FS=11.483;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=20.83;ReadPosRankSum=1.806;SOR=1.211 GT:AD:DP:GQ:PL 0/1:26,36:62:99:1299,0,781 20 10094582 . A G 944.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.388;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.43;MQRankSum=1.270;QD=13.69;ReadPosRankSum=-0.018;SOR=0.772 GT:AD:DP:GQ:PL 0/1:39,30:69:99:952,0,1350 20 10094774 . C T 1057.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.784;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.43;MQRankSum=0.962;QD=14.10;ReadPosRankSum=0.197;SOR=0.690 GT:AD:DP:GQ:PL 0/1:40,35:75:99:1065,0,1282 -20 10095432 . GTGATGATGA G 875.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.109;DP=78;ExcessHet=3.0103;FS=2.430;MLEAC=1;MLEAF=0.500;MQ=54.46;MQRankSum=-4.378;QD=17.87;ReadPosRankSum=0.396;SOR=0.400 GT:AD:DP:GQ:PL 0/1:26,23:49:99:883,0,978 +20 10095432 . GTGATGATGA G 875.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.063;DP=78;ExcessHet=3.0103;FS=2.430;MLEAC=1;MLEAF=0.500;MQ=54.46;MQRankSum=-4.378;QD=17.87;ReadPosRankSum=0.396;SOR=0.400 GT:AD:DP:GQ:PL 0/1:26,23:49:99:883,0,978 20 10095741 . A G 1096.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.534;DP=72;ExcessHet=3.0103;FS=4.721;MLEAC=1;MLEAF=0.500;MQ=57.39;MQRankSum=-2.313;QD=15.67;ReadPosRankSum=-0.500;SOR=0.515 GT:AD:DP:GQ:PL 0/1:36,34:70:99:1104,0,1233 20 10096293 . C T 1376.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=4.664;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.64;MQRankSum=1.397;QD=18.36;ReadPosRankSum=-1.135;SOR=0.638 GT:AD:DP:GQ:PL 0/1:37,38:75:99:1384,0,1258 20 10096596 . C T 1583.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.728;DP=91;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.82;MQRankSum=0.612;QD=18.20;ReadPosRankSum=-0.170;SOR=0.640 GT:AD:DP:GQ:PL 0/1:40,47:87:99:1591,0,1273 20 10096768 . A C 1703.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.764;DP=96;ExcessHet=3.0103;FS=3.983;MLEAC=1;MLEAF=0.500;MQ=59.28;MQRankSum=-1.609;QD=18.72;ReadPosRankSum=0.613;SOR=0.445 GT:AD:DP:GQ:PL 0/1:42,49:91:99:1711,0,1452 -20 10096899 . G T 1636.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.494;DP=84;ExcessHet=3.0103;FS=13.441;MLEAC=1;MLEAF=0.500;MQ=59.28;MQRankSum=-1.677;QD=19.72;ReadPosRankSum=0.422;SOR=1.954 GT:AD:DP:GQ:PL 0/1:40,43:83:99:1644,0,1519 +20 10096899 . G T 1636.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.755;DP=84;ExcessHet=3.0103;FS=13.441;MLEAC=1;MLEAF=0.500;MQ=59.28;MQRankSum=-1.677;QD=19.72;ReadPosRankSum=0.422;SOR=1.954 GT:AD:DP:GQ:PL 0/1:40,43:83:99:1644,0,1519 20 10096905 . TA T 1630.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.755;DP=86;ExcessHet=3.0103;FS=11.056;MLEAC=1;MLEAF=0.500;MQ=59.30;MQRankSum=-1.739;QD=18.96;ReadPosRankSum=0.461;SOR=1.761 GT:AD:DP:GQ:PL 0/1:43,43:86:99:1638,0,1623 -20 10096933 . G C 1534.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.724;DP=89;ExcessHet=3.0103;FS=19.713;MLEAC=1;MLEAF=0.500;MQ=59.32;MQRankSum=-1.840;QD=17.24;ReadPosRankSum=0.334;SOR=1.420 GT:AD:DP:GQ:PL 0/1:47,42:89:99:1542,0,1763 -20 10096958 . G A 1789.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.697;DP=93;ExcessHet=3.0103;FS=19.322;MLEAC=1;MLEAF=0.500;MQ=59.35;MQRankSum=-1.664;QD=19.45;ReadPosRankSum=-1.824;SOR=1.431 GT:AD:DP:GQ:PL 0/1:44,48:92:99:1797,0,1622 -20 10097075 . T G 1466.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.533;DP=96;ExcessHet=3.0103;FS=6.613;MLEAC=1;MLEAF=0.500;MQ=58.14;MQRankSum=-1.389;QD=15.94;ReadPosRankSum=0.082;SOR=0.628 GT:AD:DP:GQ:PL 0/1:44,48:92:99:1474,0,1482 -20 10097101 . C CTTT 1105.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.894;DP=81;ExcessHet=3.0103;FS=7.156;MLEAC=1;MLEAF=0.500;MQ=58.26;MQRankSum=-1.750;QD=16.50;ReadPosRankSum=2.739;SOR=0.501 GT:AD:DP:GQ:PL 0/1:34,33:67:99:1113,0,1263 -20 10097436 . CTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT C 1089.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.820;DP=90;ExcessHet=3.0103;FS=1.851;MLEAC=1;MLEAF=0.500;MQ=54.34;MQRankSum=-6.464;QD=12.24;ReadPosRankSum=-3.097;SOR=0.948 GT:AD:DP:GQ:PL 0/1:57,32:89:99:1097,0,2238 +20 10096933 . G C 1534.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.914;DP=89;ExcessHet=3.0103;FS=19.713;MLEAC=1;MLEAF=0.500;MQ=59.32;MQRankSum=-1.840;QD=17.24;ReadPosRankSum=0.383;SOR=1.420 GT:AD:DP:GQ:PL 0/1:47,42:89:99:1542,0,1763 +20 10096958 . G A 1789.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.697;DP=93;ExcessHet=3.0103;FS=19.322;MLEAC=1;MLEAF=0.500;MQ=59.35;MQRankSum=-1.664;QD=19.45;ReadPosRankSum=-1.593;SOR=1.431 GT:AD:DP:GQ:PL 0/1:44,48:92:99:1797,0,1622 +20 10097075 . T G 1466.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.533;DP=96;ExcessHet=3.0103;FS=6.613;MLEAC=1;MLEAF=0.500;MQ=58.14;MQRankSum=-1.389;QD=15.94;ReadPosRankSum=0.235;SOR=0.628 GT:AD:DP:GQ:PL 0/1:44,48:92:99:1474,0,1482 +20 10097101 . C CTTT 1105.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.894;DP=81;ExcessHet=3.0103;FS=7.156;MLEAC=1;MLEAF=0.500;MQ=58.26;MQRankSum=-1.750;QD=16.50;ReadPosRankSum=3.135;SOR=0.501 GT:AD:DP:GQ:PL 0/1:34,33:67:99:1113,0,1263 +20 10097436 . CTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT C 1089.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.650;DP=90;ExcessHet=3.0103;FS=1.851;MLEAC=1;MLEAF=0.500;MQ=54.34;MQRankSum=-6.464;QD=12.24;ReadPosRankSum=-3.097;SOR=0.948 GT:AD:DP:GQ:PL 0/1:57,32:89:99:1097,0,2238 20 10097437 . TTTTC *,T 931.01 . AC=1,1;AF=0.500,0.500;AN=2;DP=78;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=53.68;QD=16.93;SOR=1.877 GT:AD:DP:GQ:PL 1/2:0,32,23:55:99:2133,941,1797,1201,0,1129 20 10097626 . C A 647.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.085;DP=54;ExcessHet=3.0103;FS=2.701;MLEAC=1;MLEAF=0.500;MQ=58.00;MQRankSum=-1.331;QD=13.49;ReadPosRankSum=1.015;SOR=0.324 GT:AD:DP:GQ:PL 0/1:28,20:48:99:655,0,957 20 10097789 . T C 709.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.157;DP=60;ExcessHet=3.0103;FS=5.374;MLEAC=1;MLEAF=0.500;MQ=58.05;MQRankSum=-2.805;QD=12.45;ReadPosRankSum=0.220;SOR=0.756 GT:AD:DP:GQ:PL 0/1:34,23:57:99:717,0,1190 @@ -255,19 +255,19 @@ 20 10098110 . G C 607.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.510;DP=36;ExcessHet=3.0103;FS=6.658;MLEAC=1;MLEAF=0.500;MQ=58.71;MQRankSum=-1.477;QD=16.88;ReadPosRankSum=-0.730;SOR=0.069 GT:AD:DP:GQ:PL 0/1:19,17:36:99:615,0,727 20 10098135 . C A 492.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.155;DP=39;ExcessHet=3.0103;FS=4.449;MLEAC=1;MLEAF=0.500;MQ=59.65;MQRankSum=1.563;QD=12.63;ReadPosRankSum=-0.591;SOR=0.070 GT:AD:DP:GQ:PL 0/1:25,14:39:99:500,0,964 20 10098219 . TATATATA T 325.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.147;DP=21;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.94;MQRankSum=-0.205;QD=15.50;ReadPosRankSum=0.427;SOR=0.465 GT:AD:DP:GQ:PL 0/1:12,9:21:99:333,0,461 -20 10098237 . A T 265.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.006;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.89;MQRankSum=-1.885;QD=18.97;ReadPosRankSum=0.277;SOR=0.693 GT:AD:DP:GQ:PL 0/1:7,7:14:99:273,0,273 -20 10098265 . T C 154.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.834;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=41.96;MQRankSum=-1.834;QD=25.77;ReadPosRankSum=0.000;SOR=1.329 GT:AD:DP:GQ:PL 0/1:2,4:6:59:162,0,59 -20 10098885 . C CA 463.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.165;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.73;MQRankSum=-4.449;QD=14.95;ReadPosRankSum=-1.073;SOR=0.518 GT:AD:DP:GQ:PL 0/1:17,14:31:99:471,0,572 +20 10098237 . A T 265.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.006;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.89;MQRankSum=-1.885;QD=18.97;ReadPosRankSum=1.118;SOR=0.693 GT:AD:DP:GQ:PL 0/1:7,7:14:99:273,0,273 +20 10098265 . T C 154.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.834;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=41.96;MQRankSum=-1.834;QD=25.77;ReadPosRankSum=0.842;SOR=1.329 GT:AD:DP:GQ:PL 0/1:2,4:6:59:162,0,59 +20 10098885 . C CA 463.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.165;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.73;MQRankSum=-4.449;QD=14.95;ReadPosRankSum=-0.954;SOR=0.518 GT:AD:DP:GQ:PL 0/1:17,14:31:99:471,0,572 20 10098945 . T C 428.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.475;DP=22;ExcessHet=3.0103;FS=3.882;MLEAC=1;MLEAF=0.500;MQ=51.15;MQRankSum=-2.504;QD=19.48;ReadPosRankSum=1.038;SOR=2.368 GT:AD:DP:GQ:PL 0/1:9,13:22:99:436,0,248 20 10098987 . C T 400.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.127;DP=25;ExcessHet=3.0103;FS=7.005;MLEAC=1;MLEAF=0.500;MQ=51.36;MQRankSum=-2.734;QD=16.69;ReadPosRankSum=0.436;SOR=2.925 GT:AD:DP:GQ:PL 0/1:11,13:24:99:408,0,350 -20 10099029 . T C 355.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.518;DP=30;ExcessHet=3.0103;FS=1.987;MLEAC=1;MLEAF=0.500;MQ=52.93;MQRankSum=-3.731;QD=12.26;ReadPosRankSum=-1.224;SOR=1.609 GT:AD:DP:GQ:PL 0/1:19,10:29:99:363,0,768 -20 10099034 . C A 355.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.752;DP=29;ExcessHet=3.0103;FS=1.987;MLEAC=1;MLEAF=0.500;MQ=53.57;MQRankSum=-3.731;QD=12.26;ReadPosRankSum=-1.850;SOR=1.609 GT:AD:DP:GQ:PL 0/1:19,10:29:99:363,0,768 +20 10099029 . T C 355.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.809;DP=30;ExcessHet=3.0103;FS=1.987;MLEAC=1;MLEAF=0.500;MQ=52.93;MQRankSum=-3.731;QD=12.26;ReadPosRankSum=-1.224;SOR=1.609 GT:AD:DP:GQ:PL 0/1:19,10:29:99:363,0,768 +20 10099034 . C A 355.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.757;DP=29;ExcessHet=3.0103;FS=1.987;MLEAC=1;MLEAF=0.500;MQ=53.57;MQRankSum=-3.731;QD=12.26;ReadPosRankSum=-1.850;SOR=1.609 GT:AD:DP:GQ:PL 0/1:19,10:29:99:363,0,768 20 10099044 . A C 355.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.148;DP=29;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.81;MQRankSum=-4.533;QD=12.26;ReadPosRankSum=-2.207;SOR=0.892 GT:AD:DP:GQ:PL 0/1:19,10:29:99:363,0,768 20 10099046 . T C 325.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.165;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.94;MQRankSum=-4.418;QD=13.57;ReadPosRankSum=-2.297;SOR=0.515 GT:AD:DP:GQ:PL 0/1:15,9:24:99:333,0,603 -20 10099055 . T C 277.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.996;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.20;MQRankSum=-4.179;QD=11.11;ReadPosRankSum=-1.970;SOR=0.770 GT:AD:DP:GQ:PL 0/1:17,8:25:99:285,0,673 -20 10099079 . C T 137.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.432;DP=30;ExcessHet=3.0103;FS=1.826;MLEAC=1;MLEAF=0.500;MQ=51.49;MQRankSum=-2.614;QD=4.59;ReadPosRankSum=0.969;SOR=1.329 GT:AD:DP:GQ:PL 0/1:24,6:30:99:145,0,886 -20 10099111 . T TTTTGTTTG 685.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.622;DP=52;ExcessHet=3.0103;FS=1.206;MLEAC=1;MLEAF=0.500;MQ=53.85;MQRankSum=-0.973;QD=16.32;ReadPosRankSum=-0.273;SOR=0.967 GT:AD:DP:GQ:PL 0/1:23,19:42:99:693,0,802 -20 10099140 . G T 1027.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.286;DP=63;ExcessHet=3.0103;FS=3.596;MLEAC=1;MLEAF=0.500;MQ=55.79;MQRankSum=-2.435;QD=16.85;ReadPosRankSum=0.116;SOR=1.188 GT:AD:DP:GQ:PL 0/1:29,32:61:99:1035,0,930 +20 10099055 . T C 277.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.554;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.20;MQRankSum=-4.179;QD=11.11;ReadPosRankSum=-1.970;SOR=0.770 GT:AD:DP:GQ:PL 0/1:17,8:25:99:285,0,673 +20 10099079 . C T 137.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.434;DP=30;ExcessHet=3.0103;FS=1.826;MLEAC=1;MLEAF=0.500;MQ=51.49;MQRankSum=-2.614;QD=4.59;ReadPosRankSum=0.969;SOR=1.329 GT:AD:DP:GQ:PL 0/1:24,6:30:99:145,0,886 +20 10099111 . T TTTTGTTTG 685.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.207;DP=52;ExcessHet=3.0103;FS=1.206;MLEAC=1;MLEAF=0.500;MQ=53.85;MQRankSum=-0.973;QD=16.32;ReadPosRankSum=-1.860;SOR=0.967 GT:AD:DP:GQ:PL 0/1:23,19:42:99:693,0,802 +20 10099140 . G T 1027.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.286;DP=63;ExcessHet=3.0103;FS=3.596;MLEAC=1;MLEAF=0.500;MQ=55.79;MQRankSum=-2.435;QD=16.85;ReadPosRankSum=0.636;SOR=1.188 GT:AD:DP:GQ:PL 0/1:29,32:61:99:1035,0,930 20 10099190 . G T 1030.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.264;DP=62;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.82;MQRankSum=-1.445;QD=16.62;ReadPosRankSum=-1.577;SOR=0.693 GT:AD:DP:GQ:PL 0/1:31,31:62:99:1038,0,1088 20 10099220 . A G 598.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.664;DP=47;ExcessHet=3.0103;FS=1.137;MLEAC=1;MLEAF=0.500;MQ=57.74;MQRankSum=-2.596;QD=13.30;ReadPosRankSum=0.629;SOR=0.519 GT:AD:DP:GQ:PL 0/1:25,20:45:99:606,0,873 20 10099250 . G A 720.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.170;DP=39;ExcessHet=3.0103;FS=7.195;MLEAC=1;MLEAF=0.500;MQ=56.89;MQRankSum=-2.272;QD=19.48;ReadPosRankSum=0.583;SOR=0.162 GT:AD:DP:GQ:PL 0/1:16,21:37:99:728,0,424 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/IntervalTest.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/IntervalTest.vcf index 4e7564bb6e2..8362c4a8b62 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/IntervalTest.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/IntervalTest.vcf @@ -8,7 +8,7 @@ ##FORMAT= ##FORMAT= ##FORMAT= -##GATKCommandLine= +##GATKCommandLine= ##GVCFBlock=minGQ=0(inclusive),maxGQ=5(exclusive) ##INFO= ##INFO= diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/IntervalTest.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/IntervalTest.vcf.idx index c1dfbedce571edcbb6e455851f5b000f753a8f87..2f6fda06c550c1c1c643225b18ebec72e62f09b7 100644 GIT binary patch delta 49 lcmaDL@IYWfH?Ob;0~oAmEnHEsamEIAiM8?&5f}|q0RTy}3FQC) delta 49 lcmaDL@IYWfH?Nom0~l!hI&d<7 ##FORMAT= ##FORMAT= -##GATKCommandLine= +##GATKCommandLine= ##GVCFBlock=minGQ=0(inclusive),maxGQ=5(exclusive) ##INFO= ##INFO= diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/convertToBasePairResolution.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/convertToBasePairResolution.vcf.idx index 3922f7d0c59552c7d6cd9807758a81d71a257a0b..ff7d2d796efe79aa99ad8530fc42ac456ebaa5f0 100644 GIT binary patch delta 315 xcmew*^h;>MEZ%*^3}7&!vv5Vh#^syY>vzjTLMEZ&2~3}7Je@4(6YjmtN)*YA^uhzt;2&oDq1L+w>!!07;3SOEZOdMYOX diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/gvcfWithTrailingReferenceBlocksBandedExpected.g.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/gvcfWithTrailingReferenceBlocksBandedExpected.g.vcf index 8b756ddfc99..2e05815251e 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/gvcfWithTrailingReferenceBlocksBandedExpected.g.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/gvcfWithTrailingReferenceBlocksBandedExpected.g.vcf @@ -8,7 +8,7 @@ ##FORMAT= ##FORMAT= ##FORMAT= -##GATKCommandLine= +##GATKCommandLine= ##GVCFBlock=minGQ=0(inclusive),maxGQ=5(exclusive) ##INFO= ##INFO= diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/gvcfWithTrailingReferenceBlocksExpected.g.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/gvcfWithTrailingReferenceBlocksExpected.g.vcf index 237da3cb975..dba61fc2d7a 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/gvcfWithTrailingReferenceBlocksExpected.g.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/gvcfWithTrailingReferenceBlocksExpected.g.vcf @@ -8,7 +8,7 @@ ##FORMAT= ##FORMAT= ##FORMAT= -##GATKCommandLine= +##GATKCommandLine= ##GVCFBlock=minGQ=0(inclusive),maxGQ=5(exclusive) ##INFO= ##INFO= diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/newMQcalc.combined.g.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/newMQcalc.combined.g.vcf index fdd622100f9..9fb68abe597 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/newMQcalc.combined.g.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/newMQcalc.combined.g.vcf @@ -11,7 +11,7 @@ ##FORMAT= ##FORMAT= ##FORMAT= -##GATKCommandLine= +##GATKCommandLine= ##GATKCommandLine= ##GVCFBlock0-1=minGQ=0(inclusive),maxGQ=1(exclusive) ##GVCFBlock1-2=minGQ=1(inclusive),maxGQ=2(exclusive) @@ -1061,7 +1061,7 @@ 20 10004219 . C . . . GT:DP:GQ:MIN_DP:PL ./.:50:99:46:0,105,1575 ./.:34:48:34:0,48,720 20 10004220 . T . . . GT:DP:GQ:MIN_DP:PL ./.:50:99:46:0,105,1575 ./.:36:45:36:0,45,675 20 10004221 . C . . . GT:DP:GQ:MIN_DP:PL ./.:50:99:46:0,105,1575 ./.:36:51:36:0,51,765 -20 10004222 . C CA, . . BaseQRankSum=0.124;DP=106;ExcessHet=3.01;MQRankSum=-2.220e+00;RAW_MQandDP=230226,68;ReadPosRankSum=1.27 GT:AD:DP:GQ:MIN_DP:PL:SB ./.:35,10,0:45:49:.:49,0,924,153,952,1105:20,15,4,6 ./.:.:38:0:38:0,0,689,0,689,689 +20 10004222 . C CA, . . BaseQRankSum=0.335;DP=106;ExcessHet=3.01;MQRankSum=-2.220e+00;RAW_MQandDP=230226,68;ReadPosRankSum=0.198 GT:AD:DP:GQ:MIN_DP:PL:SB ./.:35,10,0:45:49:.:49,0,924,153,952,1105:20,15,4,6 ./.:.:38:0:38:0,0,689,0,689,689 20 10004223 . A AG, . . BaseQRankSum=0.803;ClippingRankSum=0.00;DP=96;ExcessHet=3.01;MQRankSum=2.27;RAW_MQandDP=328226,96;ReadPosRankSum=1.09 GT:AD:DP:GQ:PL:SB ./.:35,12,0:47:88:88,0,953,193,987,1180:16,19,6,6 ./.:13,8,0:21:99:125,0,211,162,235,398:5,8,5,3 20 10004224 . A G, . . BaseQRankSum=-5.440e-01;ClippingRankSum=0.00;DP=93;ExcessHet=3.01;MQRankSum=0.069;RAW_MQandDP=97316,28;ReadPosRankSum=0.459 GT:AD:DP:GQ:MIN_DP:PL:SB ./.:.:65:0:65:0,0,1201,0,1201,1201 ./.:11,10,0:21:99:.:151,0,199,184,228,412:5,6,5,5 20 10004225 . A . . . GT:DP:GQ:MIN_DP:PL ./.:70:99:65:0,117,1755 ./.:40:96:40:0,96,1440 @@ -1121,7 +1121,7 @@ 20 10004748 . C . . END=10004755 GT:DP:GQ:MIN_DP:PL ./.:65:99:61:0,120,1800 ./.:40:81:39:0,81,1215 20 10004756 . C . . END=10004767 GT:DP:GQ:MIN_DP:PL ./.:65:99:61:0,120,1800 ./.:41:72:40:0,72,1080 20 10004768 . C . . . GT:DP:GQ:MIN_DP:PL ./.:65:99:61:0,120,1800 ./.:40:66:40:0,66,990 -20 10004769 . TAAAACTATGC T, . . BaseQRankSum=1.80;ClippingRankSum=0.00;DP=117;ExcessHet=3.01;MQRankSum=0.00;RAW_MQandDP=358944,117;ReadPosRankSum=1.72 GT:AD:DP:GQ:PL:SB ./.:37,26,0:63:99:978,0,1473,1089,1554,2643:14,23,7,19 ./.:18,14,0:32:99:535,0,1946,589,1990,2578:9,9,7,7 +20 10004769 . TAAAACTATGC T, . . BaseQRankSum=0.822;ClippingRankSum=0.00;DP=117;ExcessHet=3.01;MQRankSum=0.00;RAW_MQandDP=358944,117;ReadPosRankSum=1.72 GT:AD:DP:GQ:PL:SB ./.:37,26,0:63:99:978,0,1473,1089,1554,2643:14,23,7,19 ./.:18,14,0:32:99:535,0,1946,589,1990,2578:9,9,7,7 20 10004770 . A *, . . DP=117 GT:AD:DP:GQ:PL:SB ./.:37,26,0:63:99:978,0,1473,1089,1554,2643:14,23,7,19 ./.:18,14,0:32:99:535,0,1946,589,1990,2578:9,9,7,7 20 10004771 . A *, . . DP=117 GT:AD:DP:GQ:PL:SB ./.:37,26,0:63:99:978,0,1473,1089,1554,2643:14,23,7,19 ./.:18,14,0:32:99:535,0,1946,589,1990,2578:9,9,7,7 20 10004772 . A *, . . DP=117 GT:AD:DP:GQ:PL:SB ./.:37,26,0:63:99:978,0,1473,1089,1554,2643:14,23,7,19 ./.:18,14,0:32:99:535,0,1946,589,1990,2578:9,9,7,7 @@ -1396,7 +1396,7 @@ 20 10008025 . A . . END=10008026 GT:DP:GQ:MIN_DP:PL ./.:86:99:80:0,120,1800 ./.:48:12:47:0,12,180 20 10008027 . A . . . GT:DP:GQ:MIN_DP:PL ./.:86:99:80:0,120,1800 ./.:47:15:47:0,15,225 20 10008028 . A . . . GT:DP:GQ:MIN_DP:PL ./.:86:99:80:0,120,1800 ./.:49:18:49:0,18,270 -20 10008029 . T TA,TAA, . . BaseQRankSum=0.438;DP=139;ExcessHet=3.01;MQRankSum=0.651;RAW_MQandDP=513451,139;ReadPosRankSum=-1.326e+00 GT:AD:DP:GQ:PL:SB ./.:3,74,0,0:77:99:2023,145,0,2032,222,2109,2032,222,2109,2109:1,2,28,46 ./.:0,17,22,0:39:99:1244,629,524,416,0,337,1157,615,414,1113:0,0,17,22 +20 10008029 . T TA,TAA, . . BaseQRankSum=0.409;DP=139;ExcessHet=3.01;MQRankSum=0.651;RAW_MQandDP=513451,139;ReadPosRankSum=-1.357e+00 GT:AD:DP:GQ:PL:SB ./.:3,74,0,0:77:99:2023,145,0,2032,222,2109,2032,222,2109,2109:1,2,28,46 ./.:0,17,22,0:39:99:1244,629,524,416,0,337,1157,615,414,1113:0,0,17,22 20 10008030 . A . . . GT:DP:GQ:MIN_DP:PL ./.:82:99:76:0,120,1800 ./.:47:0:47:0,0,0 20 10008031 . A . . END=10008032 GT:DP:GQ:MIN_DP:PL ./.:82:99:76:0,120,1800 ./.:48:82:47:0,82,1361 20 10008033 . A . . END=10008038 GT:DP:GQ:MIN_DP:PL ./.:82:99:76:0,120,1800 ./.:49:99:47:0,120,1800 @@ -1472,7 +1472,7 @@ 20 10008754 . A . . END=10008755 GT:DP:GQ:MIN_DP:PL ./.:46:99:42:0,99,1485 ./.:43:24:42:0,24,360 20 10008756 . T . . . GT:DP:GQ:MIN_DP:PL ./.:46:99:42:0,99,1485 ./.:43:21:43:0,21,315 20 10008757 . A . . . GT:DP:GQ:MIN_DP:PL ./.:46:99:42:0,99,1485 ./.:44:18:44:0,18,270 -20 10008758 . C CA,CAA, . . BaseQRankSum=0.119;DP=88;ExcessHet=3.01;MQRankSum=-8.750e-01;RAW_MQandDP=200368,88;ReadPosRankSum=-5.200e-02 GT:AD:DP:GQ:PL:SB ./.:4,34,0,0:38:10:720,10,0,733,102,825,733,102,825,825:3,1,16,18 ./.:0,20,11,0:31:99:804,284,194,434,0,396,767,275,433,745:0,0,14,17 +20 10008758 . C CA,CAA, . . BaseQRankSum=0.130;DP=88;ExcessHet=3.01;MQRankSum=-8.750e-01;RAW_MQandDP=200368,88;ReadPosRankSum=-2.620e-01 GT:AD:DP:GQ:PL:SB ./.:4,34,0,0:38:10:720,10,0,733,102,825,733,102,825,825:3,1,16,18 ./.:0,20,11,0:31:99:804,284,194,434,0,396,767,275,433,745:0,0,14,17 20 10008759 . A . . . GT:DP:GQ:MIN_DP:PL ./.:55:99:53:0,120,1800 ./.:42:0:42:0,0,0 20 10008760 . A . . END=10008772 GT:DP:GQ:MIN_DP:PL ./.:55:99:53:0,120,1800 ./.:43:99:41:0,102,1530 20 10008773 . T . . . GT:DP:GQ:MIN_DP:PL ./.:54:0:54:0,0,1660 ./.:42:34:42:0,34,1130 @@ -1492,7 +1492,7 @@ 20 10008907 . G . . END=10008910 GT:DP:GQ:MIN_DP:PL ./.:54:99:45:0,99,1480 ./.:36:81:30:0,81,1215 20 10008911 . G . . END=10008913 GT:DP:GQ:MIN_DP:PL ./.:54:99:45:0,99,1480 ./.:36:75:35:0,75,1125 20 10008914 . A . . END=10008920 GT:DP:GQ:MIN_DP:PL ./.:54:99:45:0,99,1480 ./.:34:63:32:0,63,945 -20 10008921 . C CA, . . BaseQRankSum=0.516;DP=91;ExcessHet=3.01;MQRankSum=-1.306e+00;RAW_MQandDP=188135,60;ReadPosRankSum=0.173 GT:AD:DP:GQ:MIN_DP:PGT:PID:PL:PS:SB .|.:18,17,0:35:99:.:0|1:10008921_C_CA:291,0,366,345,416,761:10008921:10,8,8,9 ./.:.:31:6:31:.:.:0,6,658,6,658,658 +20 10008921 . C CA, . . BaseQRankSum=0.610;DP=91;ExcessHet=3.01;MQRankSum=-1.306e+00;RAW_MQandDP=188135,60;ReadPosRankSum=-1.700e-02 GT:AD:DP:GQ:MIN_DP:PGT:PID:PL:PS:SB .|.:18,17,0:35:99:.:0|1:10008921_C_CA:291,0,366,345,416,761:10008921:10,8,8,9 ./.:.:31:6:31:.:.:0,6,658,6,658,658 20 10008922 . A . . END=10008930 GT:DP:GQ:MIN_DP:PL ./.:53:99:47:0,114,1710 ./.:37:57:33:0,57,855 20 10008931 . A . . . GT:DP:GQ:MIN_DP:PL ./.:53:99:47:0,114,1710 ./.:40:54:40:0,54,810 20 10008932 . A . . . GT:DP:GQ:MIN_DP:PL ./.:53:99:47:0,114,1710 ./.:41:57:41:0,57,855 @@ -1508,11 +1508,11 @@ 20 10008944 . T . . . GT:DP:GQ:MIN_DP:PL ./.:47:78:47:0,78,1170 ./.:38:33:38:0,33,495 20 10008945 . A . . END=10008946 GT:DP:GQ:MIN_DP:PL ./.:47:81:46:0,81,1215 ./.:38:30:38:0,30,450 20 10008947 . T . . . GT:DP:GQ:MIN_DP:PL ./.:47:81:46:0,81,1215 ./.:38:0:38:0,0,894 -20 10008948 . TA T, . . BaseQRankSum=0.956;DP=89;ExcessHet=3.01;MQRankSum=1.95;RAW_MQandDP=264948,89;ReadPosRankSum=0.884 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:1,53,0:54:99:0|1:10008921_C_CA:2108,117,0,2111,159,2153:10008921:1,0,36,17 ./.:0,33,0:33:99:.:.:1406,99,0,1406,99,1406:.:0,0,15,18 +20 10008948 . TA T, . . BaseQRankSum=0.994;DP=89;ExcessHet=3.01;MQRankSum=1.95;RAW_MQandDP=264948,89;ReadPosRankSum=0.884 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:1,53,0:54:99:0|1:10008921_C_CA:2108,117,0,2111,159,2153:10008921:1,0,36,17 ./.:0,33,0:33:99:.:.:1406,99,0,1406,99,1406:.:0,0,15,18 20 10008949 . A *, . . DP=89 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:1,53,0:54:99:0|1:10008921_C_CA:2108,117,0,2111,159,2153:10008921:1,0,36,17 ./.:0,33,0:33:99:.:.:1406,99,0,1406,99,1406:.:0,0,15,18 20 10008950 . A . . . GT:DP:GQ:MIN_DP:PL ./.:52:96:52:0,96,1440 ./.:39:0:39:0,0,0 20 10008951 . A . . . GT:DP:GQ:MIN_DP:PL ./.:51:87:51:0,87,1305 ./.:39:0:39:0,0,0 -20 10008952 . CACACACACACACA C,CCA,CCACACACACA,CCACACACACACA,CCACA, . . BaseQRankSum=1.05;DP=99;ExcessHet=3.01;MQRankSum=1.84;RAW_MQandDP=293942,99;ReadPosRankSum=0.716 GT:AD:DP:GQ:PL:SB ./.:1,3,14,5,11,0,0:34:99:1719,888,1213,538,767,801,740,494,153,687,597,341,0,444,535,1150,1059,712,761,609,1293,1150,1059,712,761,609,1293,1293:1,0,25,8 ./.:0,0,0,15,0,12,0:27:99:1315,1243,1282,1243,1282,1282,505,512,512,439,1243,1282,1282,512,1282,648,714,714,0,714,719,1243,1282,1282,512,1282,714,1282:0,0,12,15 +20 10008952 . CACACACACACACA C,CCA,CCACACACACA,CCACACACACACA,CCACA, . . BaseQRankSum=1.03;DP=99;ExcessHet=3.01;MQRankSum=1.84;RAW_MQandDP=293942,99;ReadPosRankSum=0.666 GT:AD:DP:GQ:PL:SB ./.:1,3,14,5,11,0,0:34:99:1719,888,1213,538,767,801,740,494,153,687,597,341,0,444,535,1150,1059,712,761,609,1293,1150,1059,712,761,609,1293,1293:1,0,25,8 ./.:0,0,0,15,0,12,0:27:99:1315,1243,1282,1243,1282,1282,505,512,512,439,1243,1282,1282,512,1282,648,714,714,0,714,719,1243,1282,1282,512,1282,714,1282:0,0,12,15 20 10008953 . A *, . . DP=99 GT:AD:DP:GQ:PL:SB ./.:1,11,0:34:99:1719,597,535,1150,609,1293:1,0,25,8 ./.:0,15,0:27:99:1315,505,439,1243,512,1282:0,0,12,15 20 10008954 . C *, . . DP=99 GT:AD:DP:GQ:PL:SB ./.:1,11,0:34:99:1719,597,535,1150,609,1293:1,0,25,8 ./.:0,15,0:27:99:1315,505,439,1243,512,1282:0,0,12,15 20 10008955 . A *, . . DP=99 GT:AD:DP:GQ:PL:SB ./.:1,11,0:34:99:1719,597,535,1150,609,1293:1,0,25,8 ./.:0,15,0:27:99:1315,505,439,1243,512,1282:0,0,12,15 @@ -1589,9 +1589,9 @@ 20 10009836 . A . . END=10009838 GT:DP:GQ:MIN_DP:PL ./.:53:63:51:0,63,945 ./.:39:51:38:0,51,765 20 10009839 . A . . END=10009840 GT:DP:GQ:MIN_DP:PL ./.:53:63:51:0,63,945 ./.:37:57:36:0,57,855 20 10009841 . A . . . GT:DP:GQ:MIN_DP:PL ./.:51:39:51:0,39,585 ./.:35:54:34:0,54,810 -20 10009842 . G GAA, . . BaseQRankSum=0.183;DP=86;ExcessHet=3.01;MQRankSum=-9.360e-01;RAW_MQandDP=150768,52;ReadPosRankSum=1.75 GT:AD:DP:GQ:MIN_DP:PL:SB ./.:19,16,0:35:99:.:570,0,691,628,739,1367:9,10,8,8 ./.:.:35:54:34:0,54,810,54,810,810 +20 10009842 . G GAA, . . BaseQRankSum=0.383;DP=86;ExcessHet=3.01;MQRankSum=-9.360e-01;RAW_MQandDP=150768,52;ReadPosRankSum=1.76 GT:AD:DP:GQ:MIN_DP:PL:SB ./.:19,16,0:35:99:.:570,0,691,628,739,1367:9,10,8,8 ./.:.:35:54:34:0,54,810,54,810,810 20 10009843 . A . . . GT:DP:GQ:MIN_DP:PL ./.:51:36:51:0,36,540 ./.:35:54:34:0,54,810 -20 10009844 . G A, . . BaseQRankSum=0.998;DP=86;ExcessHet=3.01;MQRankSum=0.975;RAW_MQandDP=270409,86;ReadPosRankSum=-1.575e+00 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:16,19,0:35:99:0|1:10009844_G_A:691,0,585,739,644,1383:10009844:8,8,9,10 ./.:0,31,0:31:93:0|1:10009844_G_A:1294,93,0,1294,93,1294:10009844:0,0,17,14 +20 10009844 . G A, . . BaseQRankSum=1.12;DP=86;ExcessHet=3.01;MQRankSum=0.975;RAW_MQandDP=270409,86;ReadPosRankSum=-2.354e+00 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:16,19,0:35:99:0|1:10009844_G_A:691,0,585,739,644,1383:10009844:8,8,9,10 ./.:0,31,0:31:93:0|1:10009844_G_A:1294,93,0,1294,93,1294:10009844:0,0,17,14 20 10009845 . A . . END=10009847 GT:DP:GQ:MIN_DP:PL ./.:51:42:51:0,42,630 ./.:34:57:32:0,57,855 20 10009848 . G . . . GT:DP:GQ:MIN_DP:PL ./.:54:51:54:0,51,765 ./.:34:57:32:0,57,855 20 10009849 . A . . END=10009850 GT:DP:GQ:MIN_DP:PL ./.:55:57:54:0,57,855 ./.:34:60:32:0,60,900 @@ -1603,9 +1603,9 @@ 20 10009865 . A . . END=10009868 GT:DP:GQ:MIN_DP:PL ./.:57:90:56:0,90,1350 ./.:35:84:34:0,84,1260 20 10009869 . A . . . GT:DP:GQ:MIN_DP:PL ./.:57:90:56:0,90,1350 ./.:38:93:37:0,93,1395 20 10009870 . G . . . GT:DP:GQ:MIN_DP:PL ./.:57:99:57:0,99,1485 ./.:38:93:37:0,93,1395 -20 10009871 . A G, . . BaseQRankSum=-8.030e-01;DP=100;ExcessHet=3.01;MQRankSum=1.34;RAW_MQandDP=298737,100;ReadPosRankSum=1.49 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:18,19,0:37:99:0|1:10009844_G_A:687,0,593,740,652,1392:10009844:10,8,9,10 ./.:0,37,0:37:99:0|1:10009844_G_A:1665,111,0,1665,111,1665:10009844:0,0,15,22 +20 10009871 . A G, . . BaseQRankSum=-8.030e-01;DP=100;ExcessHet=3.01;MQRankSum=1.34;RAW_MQandDP=298737,100;ReadPosRankSum=0.840 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:18,19,0:37:99:0|1:10009844_G_A:687,0,593,740,652,1392:10009844:10,8,9,10 ./.:0,37,0:37:99:0|1:10009844_G_A:1665,111,0,1665,111,1665:10009844:0,0,15,22 20 10009872 . G . . END=10009874 GT:DP:GQ:MIN_DP:PL ./.:57:99:55:0,108,1620 ./.:38:96:38:0,96,1440 -20 10009875 . A G,AGGGAGG, . . BaseQRankSum=0.378;DP=96;ExcessHet=3.01;MQRankSum=1.41;RAW_MQandDP=284337,96;ReadPosRankSum=1.04 GT:AD:DP:GQ:PGT:PID:PL:PS:SB ./.:2,15,14,0:31:99:.:.:2406,645,532,697,0,574,1881,654,701,1805:.:2,0,13,16 ./.:0,37,0,0:37:99:0|1:10009844_G_A:1665,111,0,1665,111,1665,1665,111,1665,1665:10009844:0,0,15,22 +20 10009875 . A G,AGGGAGG, . . BaseQRankSum=0.378;DP=96;ExcessHet=3.01;MQRankSum=1.41;RAW_MQandDP=284337,96;ReadPosRankSum=1.37 GT:AD:DP:GQ:PGT:PID:PL:PS:SB ./.:2,15,14,0:31:99:.:.:2406,645,532,697,0,574,1881,654,701,1805:.:2,0,13,16 ./.:0,37,0,0:37:99:0|1:10009844_G_A:1665,111,0,1665,111,1665,1665,111,1665,1665:10009844:0,0,15,22 20 10009876 . G . . END=10009878 GT:DP:GQ:MIN_DP:PL ./.:52:99:51:0,114,1710 ./.:36:99:34:0,99,1485 20 10009879 . A G, . . BaseQRankSum=1.53;DP=89;ExcessHet=3.01;MQRankSum=1.68;RAW_MQandDP=264661,89;ReadPosRankSum=1.11 GT:AD:DP:GQ:PGT:PID:PL:PS:SB ./.:2,51,0:53:99:.:.:2273,150,0,2276,154,2279:.:2,0,18,33 ./.:0,35,0:35:99:0|1:10009844_G_A:1575,105,0,1575,105,1575:10009844:0,0,15,20 20 10009880 . G . . . GT:DP:GQ:MIN_DP:PL ./.:49:99:48:0,120,1800 ./.:37:99:37:0,102,1530 @@ -1797,7 +1797,7 @@ 20 10011509 . C . . END=10011510 GT:DP:GQ:MIN_DP:PL ./.:80:99:70:0,120,1800 ./.:45:24:44:0,24,360 20 10011511 . T . . END=10011513 GT:DP:GQ:MIN_DP:PL ./.:80:99:70:0,120,1800 ./.:46:12:46:0,12,180 20 10011514 . A . . END=10011516 GT:DP:GQ:MIN_DP:PL ./.:80:99:70:0,120,1800 ./.:47:9:46:0,9,135 -20 10011517 . GAA GA,G,GAAA, . . BaseQRankSum=0.690;ClippingRankSum=0.00;DP=143;ExcessHet=3.01;MQRankSum=1.80;RAW_MQandDP=515010,143;ReadPosRankSum=0.315 GT:AD:DP:GQ:PL:SB ./.:37,28,2,6,0:73:99:528,0,874,611,1040,2117,605,722,1499,1650,667,965,1699,1470,1638:23,14,19,17 ./.:1,37,0,0,0:38:88:942,88,0,945,111,968,945,111,968,968,945,111,968,968,968:1,0,20,17 +20 10011517 . GAA GA,G,GAAA, . . BaseQRankSum=0.690;ClippingRankSum=0.00;DP=143;ExcessHet=3.01;MQRankSum=1.80;RAW_MQandDP=515010,143;ReadPosRankSum=0.337 GT:AD:DP:GQ:PL:SB ./.:37,28,2,6,0:73:99:528,0,874,611,1040,2117,605,722,1499,1650,667,965,1699,1470,1638:23,14,19,17 ./.:1,37,0,0,0:38:88:942,88,0,945,111,968,945,111,968,968,945,111,968,968,968:1,0,20,17 20 10011518 . A *, . . DP=143 GT:AD:DP:GQ:PL:SB ./.:37,28,0:73:99:528,0,874,667,965,1638:23,14,19,17 ./.:1,37,0:38:88:942,88,0,945,111,968:1,0,20,17 20 10011519 . A *, . . DP=147 GT:AD:DP:GQ:MIN_DP:PL:SB ./.:37,28,0:73:99:.:528,0,874,667,965,1638:23,14,19,17 ./.:.:48:0:48:0,0,0,0,0,0 20 10011520 . A . . END=10011556 GT:DP:GQ:MIN_DP:PL ./.:68:99:62:0,120,1800 ./.:48:99:44:0,100,1332 @@ -2019,11 +2019,11 @@ 20 10012624 . T . . . GT:DP:GQ:MIN_DP:PL ./.:19:54:19:0,54,810 ./.:48:0:44:0,0,0 20 10012625 . C . . . GT:DP:GQ:MIN_DP:PL ./.:20:57:20:0,57,855 ./.:48:0:44:0,0,0 20 10012626 . C . . END=10012630 GT:DP:GQ:MIN_DP:PL ./.:21:60:21:0,60,900 ./.:48:0:44:0,0,0 -20 10012631 . C CG, . . BaseQRankSum=-1.030e+00;DP=65;ExcessHet=3.01;MQRankSum=-1.670e+00;RAW_MQandDP=189832,65;ReadPosRankSum=-1.813e+00 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:8,13,0:21:99:0|1:10012631_C_CG:522,0,297,546,336,882:10012631:8,0,9,4 ./.:0,43,0:43:99:0|1:10012631_C_CG:1933,132,0,1933,132,1933:10012631:0,0,20,23 +20 10012631 . C CG, . . BaseQRankSum=-1.030e+00;DP=65;ExcessHet=3.01;MQRankSum=-1.670e+00;RAW_MQandDP=189832,65;ReadPosRankSum=-1.777e+00 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:8,13,0:21:99:0|1:10012631_C_CG:522,0,297,546,336,882:10012631:8,0,9,4 ./.:0,43,0:43:99:0|1:10012631_C_CG:1933,132,0,1933,132,1933:10012631:0,0,20,23 20 10012632 . G . . . GT:DP:GQ:MIN_DP:PL ./.:21:54:21:0,54,810 ./.:48:0:48:0,0,0 20 10012633 . C . . . GT:DP:GQ:MIN_DP:PL ./.:20:51:20:0,51,765 ./.:45:52:45:0,52,1226 20 10012634 . C . . END=10012635 GT:DP:GQ:MIN_DP:PL ./.:22:54:22:0,54,810 ./.:46:99:45:0,114,1710 -20 10012636 . G C, . . BaseQRankSum=2.71;DP=64;ExcessHet=3.01;MQRankSum=-1.513e+00;RAW_MQandDP=187532,64;ReadPosRankSum=-1.915e+00 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:8,14,0:22:99:0|1:10012631_C_CG:556,0,294,580,336,916:10012631:8,0,10,4 ./.:0,41,0:41:99:0|1:10012631_C_CG:1932,132,0,1932,132,1932:10012631:0,0,19,22 +20 10012636 . G C, . . BaseQRankSum=2.71;DP=64;ExcessHet=3.01;MQRankSum=-1.513e+00;RAW_MQandDP=187532,64;ReadPosRankSum=-1.777e+00 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:8,14,0:22:99:0|1:10012631_C_CG:556,0,294,580,336,916:10012631:8,0,10,4 ./.:0,41,0:41:99:0|1:10012631_C_CG:1932,132,0,1932,132,1932:10012631:0,0,19,22 20 10012637 . A . . . GT:DP:GQ:MIN_DP:PL ./.:20:54:20:0,54,810 ./.:45:53:45:0,53,1153 20 10012638 . G . . . GT:DP:GQ:MIN_DP:PL ./.:20:54:20:0,54,810 ./.:44:51:44:0,51,1203 20 10012639 . C . . . GT:DP:GQ:MIN_DP:PL ./.:20:54:20:0,54,810 ./.:44:99:41:0,100,1128 @@ -2341,7 +2341,7 @@ 20 10014985 . A . . END=10014987 GT:DP:GQ:MIN_DP:PL ./.:72:99:42:0,116,1732 ./.:38:54:37:0,54,810 20 10014988 . A . . . GT:DP:GQ:MIN_DP:PL ./.:72:99:42:0,116,1732 ./.:38:42:38:0,42,630 20 10014989 . G . . . GT:DP:GQ:MIN_DP:PL ./.:72:99:42:0,116,1732 ./.:38:39:38:0,39,585 -20 10014990 . C CAT, . . BaseQRankSum=1.76;ClippingRankSum=0.00;DP=125;ExcessHet=3.01;MQRankSum=3.26;RAW_MQandDP=460769,125;ReadPosRankSum=0.144 GT:AD:DP:GQ:PL:SB ./.:38,39,0:77:99:1273,0,1250,1388,1367,2755:28,10,26,13 ./.:12,22,0:34:99:735,0,363,772,429,1201:3,9,10,12 +20 10014990 . C CAT, . . BaseQRankSum=1.93;ClippingRankSum=0.00;DP=125;ExcessHet=3.01;MQRankSum=3.26;RAW_MQandDP=460769,125;ReadPosRankSum=0.144 GT:AD:DP:GQ:PL:SB ./.:38,39,0:77:99:1273,0,1250,1388,1367,2755:28,10,26,13 ./.:12,22,0:34:99:735,0,363,772,429,1201:3,9,10,12 20 10014991 . A . . . GT:DP:GQ:MIN_DP:PL ./.:73:99:41:0,102,1530 ./.:38:0:38:0,0,0 20 10014992 . T . . END=10014993 GT:DP:GQ:MIN_DP:PL ./.:73:99:41:0,102,1530 ./.:36:99:35:0,99,1485 20 10014994 . T . . . GT:DP:GQ:MIN_DP:PL ./.:73:99:41:0,102,1530 ./.:35:83:35:0,83,1046 @@ -3426,7 +3426,7 @@ 20 10024297 . T . . . GT:DP:GQ:MIN_DP:PL ./.:68:65:68:0,65,2188 ./.:36:75:36:0,75,1125 20 10024298 . T . . . GT:DP:GQ:MIN_DP:PL ./.:66:59:66:0,59,2080 ./.:36:75:36:0,75,1125 20 10024299 . C . . . GT:DP:GQ:MIN_DP:PL ./.:62:0:62:0,0,1480 ./.:34:69:34:0,69,1035 -20 10024300 . CTT C,CT,CTTTT, . . BaseQRankSum=2.38;ClippingRankSum=0.00;DP=83;ExcessHet=3.01;MQRankSum=0.00;RAW_MQandDP=250036,83;ReadPosRankSum=-1.290e+00 GT:AD:DP:GQ:PL:SB ./.:3,5,4,8,0:20:9:144,72,401,88,202,222,47,9,0,215,183,284,255,136,369:1,2,11,6 ./.:7,0,5,0,0:12:65:65,85,180,0,95,80,85,180,95,180,85,180,95,180,180:7,0,1,4 +20 10024300 . CTT C,CT,CTTTT, . . BaseQRankSum=2.36;ClippingRankSum=0.00;DP=83;ExcessHet=3.01;MQRankSum=0.00;RAW_MQandDP=250036,83;ReadPosRankSum=-1.290e+00 GT:AD:DP:GQ:PL:SB ./.:3,5,4,8,0:20:9:144,72,401,88,202,222,47,9,0,215,183,284,255,136,369:1,2,11,6 ./.:7,0,5,0,0:12:65:65,85,180,0,95,80,85,180,95,180,85,180,95,180,180:7,0,1,4 20 10024301 . T *, . . DP=83 GT:AD:DP:GQ:PL:SB ./.:3,4,0:20:9:144,88,222,183,255,369:1,2,11,6 ./.:7,5,0:12:65:65,0,80,85,95,180:7,0,1,4 20 10024302 . T *, . . DP=92 GT:AD:DP:GQ:MIN_DP:PL:SB ./.:3,4,0:20:9:.:144,88,222,183,255,369:1,2,11,6 ./.:.:36:0:36:0,0,684,0,684,684 20 10024303 . T . . . GT:DP:GQ:MIN_DP:PL ./.:67:57:67:0,57,855 ./.:33:33:30:0,33,495 @@ -3707,7 +3707,7 @@ 20 10028853 . G . . . GT:DP:GQ:MIN_DP:PL ./.:80:99:55:0,120,1800 ./.:44:78:44:0,78,1170 20 10028854 . C . . END=10028865 GT:DP:GQ:MIN_DP:PL ./.:80:99:55:0,120,1800 ./.:42:63:39:0,63,945 20 10028866 . A . . . GT:DP:GQ:MIN_DP:PL ./.:80:99:55:0,120,1800 ./.:39:32:39:0,32,952 -20 10028867 . A ATG, . . BaseQRankSum=-6.100e-02;ClippingRankSum=0.00;DP=129;ExcessHet=3.01;MQRankSum=2.71;RAW_MQandDP=474641,129;ReadPosRankSum=0.364 GT:AD:DP:GQ:PL:SB ./.:32,39,0:71:99:1142,0,918,1240,1035,2275:11,21,18,21 ./.:13,19,0:32:99:584,0,361,623,421,1045:6,7,9,10 +20 10028867 . A ATG, . . BaseQRankSum=-6.100e-02;ClippingRankSum=0.00;DP=129;ExcessHet=3.01;MQRankSum=2.71;RAW_MQandDP=474641,129;ReadPosRankSum=0.630 GT:AD:DP:GQ:PL:SB ./.:32,39,0:71:99:1142,0,918,1240,1035,2275:11,21,18,21 ./.:13,19,0:32:99:584,0,361,623,421,1045:6,7,9,10 20 10028868 . T . . . GT:DP:GQ:MIN_DP:PL ./.:80:99:60:0,120,1800 ./.:40:0:40:0,0,31 20 10028869 . G . . . GT:DP:GQ:MIN_DP:PL ./.:80:99:60:0,120,1800 ./.:41:95:41:0,95,1143 20 10028870 . T . . END=10028871 GT:DP:GQ:MIN_DP:PL ./.:80:99:60:0,120,1800 ./.:41:80:41:0,80,1120 @@ -4003,7 +4003,7 @@ 20 10031226 . T . . END=10031234 GT:DP:GQ:MIN_DP:PL ./.:70:99:42:0,114,1710 ./.:49:90:46:0,90,1350 20 10031235 . T . . END=10031239 GT:DP:GQ:MIN_DP:PL ./.:70:99:42:0,114,1710 ./.:48:84:47:0,84,1260 20 10031240 . G . . END=10031253 GT:DP:GQ:MIN_DP:PL ./.:70:99:42:0,114,1710 ./.:47:75:43:0,75,1125 -20 10031254 . A AT, . . BaseQRankSum=0.497;ClippingRankSum=0.00;DP=134;ExcessHet=3.01;MQRankSum=0.017;RAW_MQandDP=482769,134;ReadPosRankSum=0.495 GT:AD:DP:GQ:PL:SB ./.:38,47,0:85:99:1501,0,1159,1615,1300,2916:27,11,25,22 ./.:23,19,0:42:99:583,0,725,653,782,1435:12,11,8,11 +20 10031254 . A AT, . . BaseQRankSum=0.497;ClippingRankSum=0.00;DP=134;ExcessHet=3.01;MQRankSum=0.017;RAW_MQandDP=482769,134;ReadPosRankSum=0.663 GT:AD:DP:GQ:PL:SB ./.:38,47,0:85:99:1501,0,1159,1615,1300,2916:27,11,25,22 ./.:23,19,0:42:99:583,0,725,653,782,1435:12,11,8,11 20 10031255 . T . . . GT:DP:GQ:MIN_DP:PL ./.:95:99:86:0,120,1800 ./.:48:0:48:0,0,216 20 10031256 . G . . END=10031341 GT:DP:GQ:MIN_DP:PL ./.:95:99:86:0,120,1800 ./.:48:99:45:0,105,1321 20 10031342 . G A, . . BaseQRankSum=3.43;ClippingRankSum=0.00;DP=138;ExcessHet=3.01;MQRankSum=0.00;RAW_MQandDP=494041,138;ReadPosRankSum=0.857 GT:AD:DP:GQ:PL:SB ./.:41,52,0:93:99:1863,0,1375,1986,1531,3517:22,19,31,21 ./.:22,23,0:45:99:620,0,534,685,603,1288:12,10,10,13 @@ -4106,7 +4106,7 @@ 20 10032959 . T . . END=10032961 GT:DP:GQ:MIN_DP:PL ./.:67:99:61:0,120,1800 ./.:45:12:45:0,12,180 20 10032962 . G . . . GT:DP:GQ:MIN_DP:PL ./.:67:99:61:0,120,1800 ./.:46:6:46:0,6,90 20 10032963 . C . . END=10032971 GT:DP:GQ:MIN_DP:PL ./.:67:99:61:0,120,1800 ./.:45:0:44:0,0,0 -20 10032972 . C CAT, . . BaseQRankSum=-3.540e-01;DP=111;ExcessHet=3.01;MQRankSum=-1.017e+00;RAW_MQandDP=398141,111;ReadPosRankSum=-1.232e+00 GT:AD:DP:GQ:PL:SB ./.:33,30,0:63:99:1160,0,1296,1260,1386,2646:17,16,11,19 ./.:0,43,0:43:99:1944,132,0,1944,132,1944:0,0,21,22 +20 10032972 . C CAT, . . BaseQRankSum=-3.540e-01;DP=111;ExcessHet=3.01;MQRankSum=-1.017e+00;RAW_MQandDP=398141,111;ReadPosRankSum=-7.230e-01 GT:AD:DP:GQ:PL:SB ./.:33,30,0:63:99:1160,0,1296,1260,1386,2646:17,16,11,19 ./.:0,43,0:43:99:1944,132,0,1944,132,1944:0,0,21,22 20 10032973 . T . . . GT:DP:GQ:MIN_DP:PL ./.:78:99:50:0,120,1800 ./.:43:0:43:0,0,0 20 10032974 . G . . . GT:DP:GQ:MIN_DP:PL ./.:78:99:50:0,120,1800 ./.:44:96:44:0,96,1179 20 10032975 . A . . END=10033031 GT:DP:GQ:MIN_DP:PL ./.:78:99:50:0,120,1800 ./.:42:99:36:0,99,1093 @@ -4425,7 +4425,7 @@ 20 10036915 . T . . END=10036925 GT:DP:GQ:MIN_DP:PL ./.:76:99:43:0,113,1513 ./.:29:75:28:0,75,1125 20 10036926 . A . . . GT:DP:GQ:MIN_DP:PL ./.:76:99:43:0,113,1513 ./.:29:81:29:0,81,1215 20 10036927 . G . . END=10036929 GT:DP:GQ:MIN_DP:PL ./.:76:99:43:0,113,1513 ./.:29:78:27:0,78,1170 -20 10036930 . CGATAGCCCTAGCCCTAGATA C, . . BaseQRankSum=0.200;ClippingRankSum=0.00;DP=134;ExcessHet=3.01;MQRankSum=0.00;RAW_MQandDP=420216,134;ReadPosRankSum=0.460 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1078,0,1500,1196,1598,2794:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 +20 10036930 . CGATAGCCCTAGCCCTAGATA C, . . BaseQRankSum=0.720;ClippingRankSum=0.00;DP=134;ExcessHet=3.01;MQRankSum=0.00;RAW_MQandDP=420216,134;ReadPosRankSum=0.460 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1078,0,1500,1196,1598,2794:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 20 10036931 . G *, . . DP=134 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1078,0,1500,1196,1598,2794:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 20 10036932 . A *, . . DP=134 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1078,0,1500,1196,1598,2794:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 20 10036933 . T *, . . DP=134 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1078,0,1500,1196,1598,2794:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 @@ -4899,7 +4899,7 @@ 20 10041694 . T . . END=10041695 GT:DP:GQ:MIN_DP:PL ./.:62:99:48:0,120,1800 ./.:30:48:29:0,48,720 20 10041696 . A . . . GT:DP:GQ:MIN_DP:PL ./.:62:99:48:0,120,1800 ./.:29:41:29:0,41,825 20 10041697 . A . . . GT:DP:GQ:MIN_DP:PL ./.:62:99:48:0,120,1800 ./.:29:42:29:0,42,630 -20 10041698 . C CAT, . . BaseQRankSum=1.60;DP=106;ExcessHet=3.01;MQRankSum=0.194;RAW_MQandDP=371231,106;ReadPosRankSum=0.579 GT:AD:DP:GQ:PL:SB ./.:50,7,0:57:17:17,0,1423,167,1444,1611:21,29,2,5 ./.:23,0,0:23:69:0,69,825,69,825,825:12,11,0,0 +20 10041698 . C CAT, . . BaseQRankSum=1.89;DP=106;ExcessHet=3.01;MQRankSum=0.194;RAW_MQandDP=371231,106;ReadPosRankSum=-1.640e-01 GT:AD:DP:GQ:PL:SB ./.:50,7,0:57:17:17,0,1423,167,1444,1611:21,29,2,5 ./.:23,0,0:23:69:0,69,825,69,825,825:12,11,0,0 20 10041699 . A . . . GT:DP:GQ:MIN_DP:PL ./.:79:99:78:0,120,1800 ./.:29:39:29:0,39,585 20 10041700 . T . . . GT:DP:GQ:MIN_DP:PL ./.:79:99:78:0,120,1800 ./.:28:36:28:0,36,540 20 10041701 . A ATG,ATATG, . . BaseQRankSum=0.848;ClippingRankSum=0.00;DP=105;ExcessHet=3.01;MQRankSum=0.959;RAW_MQandDP=370390,105;ReadPosRankSum=1.12 GT:AD:DP:GQ:PL:SB ./.:8,0,48,0:56:58:1439,1580,2725,0,261,58,1573,2315,265,2200:2,6,21,27 ./.:8,0,11,0:19:99:291,346,691,0,266,568,349,679,452,810:3,5,6,5 @@ -6990,7 +6990,7 @@ 20 10062930 . T . . END=10062931 GT:DP:GQ:MIN_DP:PL ./.:76:99:46:0,105,1575 ./.:31:45:30:0,45,675 20 10062932 . T . . . GT:DP:GQ:MIN_DP:PL ./.:76:99:46:0,105,1575 ./.:30:36:30:0,36,540 20 10062933 . C . . END=10062934 GT:DP:GQ:MIN_DP:PL ./.:76:99:46:0,105,1575 ./.:31:33:30:0,33,495 -20 10062935 . CAAA CAA,C,CA,CAAAA, . . BaseQRankSum=1.23;ClippingRankSum=0.00;DP=122;ExcessHet=3.01;MQRankSum=1.71;RAW_MQandDP=384250,122;ReadPosRankSum=-8.900e-02 GT:AD:DP:GQ:PL:SB ./.:5,4,2,3,10,0:24:6:127,104,490,208,613,1805,130,541,1135,1006,0,6,148,50,109,237,595,973,853,166,879:2,3,9,10 ./.:13,10,0,0,0,0:23:99:138,0,197,177,227,404,177,227,404,404,177,227,404,404,404,177,227,404,404,404,404:7,6,8,2 +20 10062935 . CAAA CAA,C,CA,CAAAA, . . BaseQRankSum=1.24;ClippingRankSum=0.00;DP=122;ExcessHet=3.01;MQRankSum=1.71;RAW_MQandDP=384250,122;ReadPosRankSum=-8.900e-02 GT:AD:DP:GQ:PL:SB ./.:5,4,2,3,10,0:24:6:127,104,490,208,613,1805,130,541,1135,1006,0,6,148,50,109,237,595,973,853,166,879:2,3,9,10 ./.:13,10,0,0,0,0:23:99:138,0,197,177,227,404,177,227,404,404,177,227,404,404,404,177,227,404,404,404,404:7,6,8,2 20 10062936 . A *, . . DP=122 GT:AD:DP:GQ:PL:SB ./.:5,4,0:24:6:127,104,490,237,595,879:2,3,9,10 ./.:13,10,0:23:99:138,0,197,177,227,404:7,6,8,2 20 10062937 . A *, . . DP=131 GT:AD:DP:GQ:MIN_DP:PL:SB ./.:5,4,0:24:6:.:127,104,490,237,595,879:2,3,9,10 ./.:.:41:0:41:0,0,653,0,653,653 20 10062938 . A *, . . DP=130 GT:AD:DP:GQ:MIN_DP:PL:SB ./.:5,4,0:24:6:.:127,104,490,237,595,879:2,3,9,10 ./.:.:41:99:40:0,99,1272,99,1272,1272 @@ -7570,7 +7570,7 @@ 20 10067045 . T . . . GT:DP:GQ:MIN_DP:PL ./.:72:99:48:0,102,1530 ./.:33:33:33:0,33,495 20 10067046 . T . . . GT:DP:GQ:MIN_DP:PL ./.:72:99:48:0,102,1530 ./.:33:30:33:0,30,450 20 10067047 . A . . END=10067048 GT:DP:GQ:MIN_DP:PL ./.:51:96:50:0,96,1440 ./.:32:24:30:0,24,360 -20 10067049 . TAAAAAAAAA TAA,TAAAAAA,T,TA, . . BaseQRankSum=0.177;ClippingRankSum=0.00;DP=103;ExcessHet=3.01;MQRankSum=0.00;RAW_MQandDP=324656,103;ReadPosRankSum=-1.322e+00 GT:AD:DP:GQ:PL:SB ./.:2,9,0,4,7,0:22:99:656,137,106,446,171,628,367,101,592,923,167,0,395,381,339,446,171,628,592,395,628:1,1,12,8 ./.:1,8,9,0,0,0:18:99:571,324,502,248,0,237,593,443,276,696,593,443,276,696,696,593,443,276,696,696,696:0,1,9,8 +20 10067049 . TAAAAAAAAA TAA,TAAAAAA,T,TA, . . BaseQRankSum=-8.600e-02;ClippingRankSum=0.00;DP=103;ExcessHet=3.01;MQRankSum=0.00;RAW_MQandDP=324656,103;ReadPosRankSum=-1.322e+00 GT:AD:DP:GQ:PL:SB ./.:2,9,0,4,7,0:22:99:656,137,106,446,171,628,367,101,592,923,167,0,395,381,339,446,171,628,592,395,628:1,1,12,8 ./.:1,8,9,0,0,0:18:99:571,324,502,248,0,237,593,443,276,696,593,443,276,696,696,593,443,276,696,696,696:0,1,9,8 20 10067050 . A *, . . DP=103 GT:AD:DP:GQ:PL:SB ./.:2,9,0:22:99:656,137,106,446,171,628:1,1,12,8 ./.:1,9,0:18:99:571,248,237,593,276,696:0,1,9,8 20 10067051 . A *, . . DP=103 GT:AD:DP:GQ:PL:SB ./.:2,9,0:22:99:656,137,106,446,171,628:1,1,12,8 ./.:1,9,0:18:99:571,248,237,593,276,696:0,1,9,8 20 10067052 . A *, . . DP=103 GT:AD:DP:GQ:PL:SB ./.:2,9,0:22:99:656,137,106,446,171,628:1,1,12,8 ./.:1,9,0:18:99:571,248,237,593,276,696:0,1,9,8 @@ -8871,9 +8871,9 @@ 20 10076996 . A . . END=10076998 GT:DP:GQ:MIN_DP:PL ./.:70:99:60:0,120,1800 ./.:36:81:36:0,81,1215 20 10076999 . A . . END=10077000 GT:DP:GQ:MIN_DP:PL ./.:70:99:60:0,120,1800 ./.:36:75:36:0,75,1125 20 10077001 . A . . END=10077007 GT:DP:GQ:MIN_DP:PL ./.:70:99:60:0,120,1800 ./.:38:81:38:0,81,1215 -20 10077008 . T A, . . BaseQRankSum=-1.748e+00;ClippingRankSum=0.00;DP=97;ExcessHet=3.01;MQRankSum=0.725;RAW_MQandDP=321128,97;ReadPosRankSum=0.806 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:50,4,0:54:45:0|1:10077008_T_A:0,45,2017,151,2029,2135:10077008:19,31,4,0 ./.:23,3,0:26:7:0|1:10076989_C_CAAAA:0,7,855,69,864,926:10076989:11,12,3,0 +20 10077008 . T A, . . BaseQRankSum=-1.698e+00;ClippingRankSum=0.00;DP=97;ExcessHet=3.01;MQRankSum=0.725;RAW_MQandDP=321128,97;ReadPosRankSum=0.789 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:50,4,0:54:45:0|1:10077008_T_A:0,45,2017,151,2029,2135:10077008:19,31,4,0 ./.:23,3,0:26:7:0|1:10076989_C_CAAAA:0,7,855,69,864,926:10076989:11,12,3,0 20 10077009 . A . . . GT:DP:GQ:MIN_DP:PL ./.:53:99:53:0,120,1800 ./.:36:78:36:0,78,1170 -20 10077010 . G A, . . BaseQRankSum=-1.733e+00;ClippingRankSum=0.00;DP=83;ExcessHet=3.01;MQRankSum=0.558;RAW_MQandDP=283764,83;ReadPosRankSum=0.859 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:50,4,0:54:45:0|1:10077008_T_A:0,45,2017,151,2029,2134:10077008:19,31,4,0 ./.:21,2,0:23:7:0|1:10076989_C_CAAAA:0,7,855,69,864,925:10076989:10,11,2,0 +20 10077010 . G A, . . BaseQRankSum=-1.733e+00;ClippingRankSum=0.00;DP=83;ExcessHet=3.01;MQRankSum=0.558;RAW_MQandDP=283764,83;ReadPosRankSum=0.943 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:50,4,0:54:45:0|1:10077008_T_A:0,45,2017,151,2029,2134:10077008:19,31,4,0 ./.:21,2,0:23:7:0|1:10076989_C_CAAAA:0,7,855,69,864,925:10076989:10,11,2,0 20 10077011 . A . . END=10077012 GT:DP:GQ:MIN_DP:PL ./.:69:99:44:0,102,1654 ./.:33:78:33:0,78,1170 20 10077013 . A . . . GT:DP:GQ:MIN_DP:PL ./.:69:99:44:0,102,1654 ./.:33:81:33:0,81,1215 20 10077014 . A . . . GT:DP:GQ:MIN_DP:PL ./.:69:99:44:0,102,1654 ./.:32:71:32:0,71,971 @@ -9976,7 +9976,7 @@ 20 10087806 . G . . END=10087810 GT:DP:GQ:MIN_DP:PL ./.:101:99:96:0,120,1800 ./.:36:24:36:0,24,360 20 10087811 . A . . END=10087814 GT:DP:GQ:MIN_DP:PL ./.:101:99:96:0,120,1800 ./.:36:12:36:0,12,180 20 10087815 . A . . END=10087819 GT:DP:GQ:MIN_DP:PL ./.:101:99:96:0,120,1800 ./.:37:3:37:0,3,45 -20 10087820 . CAG CAGAGAG,C,CAGAG, . . BaseQRankSum=-1.974e+00;DP=136;ExcessHet=3.01;MQRankSum=0.422;RAW_MQandDP=503700,136;ReadPosRankSum=-3.570e-01 GT:AD:DP:GQ:PL:SB ./.:35,0,0,18,0:53:99:464,657,2172,665,2217,2541,0,1237,1195,1170,657,2172,2217,1237,2172:17,18,8,10 ./.:0,32,0,0,0:32:96:1428,96,0,1428,96,1428,1428,96,1428,1428,1428,96,1428,1428,1428:0,0,21,11 +20 10087820 . CAG CAGAGAG,C,CAGAG, . . BaseQRankSum=-1.974e+00;DP=136;ExcessHet=3.01;MQRankSum=0.422;RAW_MQandDP=503700,136;ReadPosRankSum=-1.900e-02 GT:AD:DP:GQ:PL:SB ./.:35,0,0,18,0:53:99:464,657,2172,665,2217,2541,0,1237,1195,1170,657,2172,2217,1237,2172:17,18,8,10 ./.:0,32,0,0,0:32:96:1428,96,0,1428,96,1428,1428,96,1428,1428,1428,96,1428,1428,1428:0,0,21,11 20 10087821 . A *, . . DP=137 GT:AD:DP:GQ:MIN_DP:PL:SB ./.:35,0,0:53:99:.:464,665,2541,657,2217,2172:17,18,8,10 ./.:.:35:0:35:0,0,0,0,0,0 20 10087822 . G *, . . DP=137 GT:AD:DP:GQ:MIN_DP:PL:SB ./.:35,0,0:53:99:.:464,665,2541,657,2217,2172:17,18,8,10 ./.:.:35:72:35:0,72,995,72,995,995 20 10087823 . A . . . GT:DP:GQ:MIN_DP:PL ./.:85:99:82:0,120,1800 ./.:35:72:35:0,72,995 @@ -10094,9 +10094,9 @@ 20 10088700 . G . . END=10088718 GT:DP:GQ:MIN_DP:PL ./.:53:99:51:0,120,1800 ./.:46:99:44:0,99,1303 20 10088719 . C . . . GT:DP:GQ:MIN_DP:PL ./.:53:99:51:0,120,1800 ./.:44:78:44:0,78,1193 20 10088720 . C . . END=10088729 GT:DP:GQ:MIN_DP:PL ./.:53:99:51:0,120,1800 ./.:44:99:43:0,100,1277 -20 10088730 . G A, . . BaseQRankSum=-5.800e-02;DP=99;ExcessHet=3.01;MQRankSum=-5.213e+00;RAW_MQandDP=309545,99;ReadPosRankSum=0.581 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:30,26,0:56:99:0|1:10088730_G_A:1001,0,1152,1092,1231,2322:10088730:11,19,16,10 ./.:0,41,0:41:99:0|1:10088730_G_A:1825,123,0,1825,123,1825:10088730:0,0,23,18 +20 10088730 . G A, . . BaseQRankSum=0.224;DP=99;ExcessHet=3.01;MQRankSum=-5.213e+00;RAW_MQandDP=309545,99;ReadPosRankSum=0.581 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:30,26,0:56:99:0|1:10088730_G_A:1001,0,1152,1092,1231,2322:10088730:11,19,16,10 ./.:0,41,0:41:99:0|1:10088730_G_A:1825,123,0,1825,123,1825:10088730:0,0,23,18 20 10088731 . G . . END=10088735 GT:DP:GQ:MIN_DP:PL ./.:55:99:55:0,120,1800 ./.:43:99:42:0,108,1292 -20 10088736 . A C, . . BaseQRankSum=0.016;DP=104;ExcessHet=3.01;MQRankSum=-5.157e+00;RAW_MQandDP=324786,104;ReadPosRankSum=0.573 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:31,29,0:60:99:0|1:10088730_G_A:1110,0,1194,1203,1281,2484:10088730:12,19,17,12 ./.:0,43,0:43:99:0|1:10088730_G_A:1999,138,0,1999,138,1999:10088730:0,0,23,20 +20 10088736 . A C, . . BaseQRankSum=0.282;DP=104;ExcessHet=3.01;MQRankSum=-5.157e+00;RAW_MQandDP=324786,104;ReadPosRankSum=0.573 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:31,29,0:60:99:0|1:10088730_G_A:1110,0,1194,1203,1281,2484:10088730:12,19,17,12 ./.:0,43,0:43:99:0|1:10088730_G_A:1999,138,0,1999,138,1999:10088730:0,0,23,20 20 10088737 . C . . END=10088746 GT:DP:GQ:MIN_DP:PL ./.:56:99:53:0,120,1800 ./.:46:99:45:0,120,1800 20 10088747 . A G, . . BaseQRankSum=-3.877e+00;DP=104;ExcessHet=3.01;MQRankSum=-4.881e+00;RAW_MQandDP=324102,104;ReadPosRankSum=9.000e-03 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:26,30,0:56:99:0|1:10088730_G_A:1140,0,995,1219,1085,2304:10088730:10,16,19,11 ./.:0,47,0:47:99:0|1:10088730_G_A:2038,144,0,2038,144,2038:10088730:0,0,25,22 20 10088748 . G . . END=10088780 GT:DP:GQ:MIN_DP:PL ./.:49:99:46:0,114,1710 ./.:45:99:42:0,112,1329 @@ -10167,14 +10167,14 @@ 20 10088964 . G . . . GT:DP:GQ:MIN_DP:PL ./.:49:99:41:0,107,1668 ./.:37:30:37:0,30,450 20 10088965 . T . . . GT:DP:GQ:MIN_DP:PL ./.:49:99:41:0,107,1668 ./.:41:27:41:0,27,405 20 10088966 . C . . END=10088967 GT:DP:GQ:MIN_DP:PL ./.:49:99:41:0,107,1668 ./.:42:0:41:0,0,683 -20 10088968 . C CAAA, . . BaseQRankSum=0.117;DP=112;ExcessHet=3.01;MQRankSum=-5.320e+00;RAW_MQandDP=331050,112;ReadPosRankSum=1.80 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:32,34,0:66:99:0|1:10088968_C_CAAA:1297,0,1230,1394,1333,2726:10088968:17,15,19,15 ./.:0,30,0:30:99:0|1:10088968_C_CAAA:1781,128,0,1781,128,1781:10088968:0,0,18,12 +20 10088968 . C CAAA, . . BaseQRankSum=0.337;DP=112;ExcessHet=3.01;MQRankSum=-5.320e+00;RAW_MQandDP=331050,112;ReadPosRankSum=0.205 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:32,34,0:66:99:0|1:10088968_C_CAAA:1297,0,1230,1394,1333,2726:10088968:17,15,19,15 ./.:0,30,0:30:99:0|1:10088968_C_CAAA:1781,128,0,1781,128,1781:10088968:0,0,18,12 20 10088969 . A . . . GT:DP:GQ:MIN_DP:PL ./.:73:99:72:0,120,1800 ./.:53:0:53:0,0,0 20 10088970 . A . . END=10088979 GT:DP:GQ:MIN_DP:PL ./.:73:99:72:0,120,1800 ./.:54:99:53:0,120,1800 -20 10088980 . T C, . . BaseQRankSum=-1.772e+00;DP=121;ExcessHet=3.01;MQRankSum=-5.207e+00;RAW_MQandDP=353173,121;ReadPosRankSum=1.12 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:39,36,0:75:99:0|1:10088968_C_CAAA:1360,0,1491,1478,1599,3077:10088968:20,19,20,16 ./.:0,44,0:44:99:0|1:10088968_C_CAAA:1859,135,0,1859,135,1859:10088968:0,0,18,26 +20 10088980 . T C, . . BaseQRankSum=-1.845e+00;DP=121;ExcessHet=3.01;MQRankSum=-5.207e+00;RAW_MQandDP=353173,121;ReadPosRankSum=1.48 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:39,36,0:75:99:0|1:10088968_C_CAAA:1360,0,1491,1478,1599,3077:10088968:20,19,20,16 ./.:0,44,0:44:99:0|1:10088968_C_CAAA:1859,135,0,1859,135,1859:10088968:0,0,18,26 20 10088981 . A . . END=10088982 GT:DP:GQ:MIN_DP:PL ./.:73:99:71:0,120,1800 ./.:54:99:54:0,120,1800 20 10088983 . A . . . GT:DP:GQ:MIN_DP:PL ./.:73:99:71:0,120,1800 ./.:51:43:51:0,43,1358 20 10088984 . A . . . GT:DP:GQ:MIN_DP:PL ./.:73:99:71:0,120,1800 ./.:53:99:53:0,120,1800 -20 10088985 . T C, . . BaseQRankSum=-5.250e-01;DP=123;ExcessHet=3.01;MQRankSum=-5.440e+00;RAW_MQandDP=358567,123;ReadPosRankSum=1.16 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:42,34,0:76:99:0|1:10088968_C_CAAA:1291,0,1593,1417,1696,3113:10088968:22,20,17,17 ./.:0,43,0:43:99:.:.:1926,132,0,1926,132,1926:.:0,0,18,25 +20 10088985 . T C, . . BaseQRankSum=-5.250e-01;DP=123;ExcessHet=3.01;MQRankSum=-5.440e+00;RAW_MQandDP=358567,123;ReadPosRankSum=1.43 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:42,34,0:76:99:0|1:10088968_C_CAAA:1291,0,1593,1417,1696,3113:10088968:22,20,17,17 ./.:0,43,0:43:99:.:.:1926,132,0,1926,132,1926:.:0,0,18,25 20 10088986 . A . . END=10088989 GT:DP:GQ:MIN_DP:PL ./.:82:99:81:0,120,1800 ./.:52:99:49:0,110,1473 20 10088990 . A . . . GT:DP:GQ:MIN_DP:PL ./.:84:7:84:0,7,2771 ./.:52:99:49:0,110,1473 20 10088991 . C . . . GT:DP:GQ:MIN_DP:PL ./.:81:95:81:0,95,2703 ./.:52:99:49:0,110,1473 @@ -10255,7 +10255,7 @@ 20 10090284 . A . . END=10090285 GT:DP:GQ:MIN_DP:PL ./.:72:99:55:0,111,1800 ./.:43:15:42:0,15,225 20 10090286 . T . . . GT:DP:GQ:MIN_DP:PL ./.:72:99:55:0,111,1800 ./.:39:12:39:0,12,180 20 10090287 . G . . END=10090288 GT:DP:GQ:MIN_DP:PL ./.:72:99:55:0,111,1800 ./.:39:9:38:0,9,135 -20 10090289 . CAA C,CA, . . BaseQRankSum=0.285;ClippingRankSum=0.00;DP=126;ExcessHet=3.01;MQRankSum=1.47;RAW_MQandDP=453282,126;ReadPosRankSum=0.455 GT:AD:DP:GQ:PL:SB ./.:15,3,20,0:38:99:413,386,1030,0,295,240,474,906,358,938:8,7,10,13 ./.:1,29,0,0:30:66:1009,66,0,1012,88,1033,1012,88,1033,1033:0,1,12,17 +20 10090289 . CAA C,CA, . . BaseQRankSum=0.252;ClippingRankSum=0.00;DP=126;ExcessHet=3.01;MQRankSum=1.47;RAW_MQandDP=453282,126;ReadPosRankSum=0.455 GT:AD:DP:GQ:PL:SB ./.:15,3,20,0:38:99:413,386,1030,0,295,240,474,906,358,938:8,7,10,13 ./.:1,29,0,0:30:66:1009,66,0,1012,88,1033,1012,88,1033,1033:0,1,12,17 20 10090290 . A *, . . DP=126 GT:AD:DP:GQ:PL:SB ./.:15,20,0:38:99:413,0,240,474,358,938:8,7,10,13 ./.:1,29,0:30:66:1009,66,0,1012,88,1033:0,1,12,17 20 10090291 . A *, . . DP=126 GT:AD:DP:GQ:PL:SB ./.:15,20,0:38:99:413,0,240,474,358,938:8,7,10,13 ./.:1,29,0:30:66:1009,66,0,1012,88,1033:0,1,12,17 20 10090292 . A . . . GT:DP:GQ:MIN_DP:PL ./.:75:99:61:0,120,1800 ./.:41:0:41:0,0,0 @@ -10670,7 +10670,7 @@ 20 10095429 . C . . . GT:DP:GQ:MIN_DP:PL ./.:77:99:63:0,120,1800 ./.:41:21:41:0,21,315 20 10095430 . A . . . GT:DP:GQ:MIN_DP:PL ./.:77:99:63:0,120,1800 ./.:40:18:40:0,18,270 20 10095431 . A . . . GT:DP:GQ:MIN_DP:PL ./.:77:99:63:0,120,1800 ./.:39:15:39:0,15,225 -20 10095432 . GTGATGATGA GTGA,G, . . BaseQRankSum=1.11;DP=113;ExcessHet=3.01;MQRankSum=-4.378e+00;RAW_MQandDP=357348,113;ReadPosRankSum=0.396 GT:AD:DP:GQ:PL:SB ./.:26,0,23,0:49:99:883,961,2014,0,1053,978,961,2014,1053,2014:16,10,12,11 ./.:0,27,0,0:27:82:1217,82,0,1217,82,1217,1217,82,1217,1217:0,0,13,14 +20 10095432 . GTGATGATGA GTGA,G, . . BaseQRankSum=1.06;DP=113;ExcessHet=3.01;MQRankSum=-4.378e+00;RAW_MQandDP=357348,113;ReadPosRankSum=0.396 GT:AD:DP:GQ:PL:SB ./.:26,0,23,0:49:99:883,961,2014,0,1053,978,961,2014,1053,2014:16,10,12,11 ./.:0,27,0,0:27:82:1217,82,0,1217,82,1217,1217,82,1217,1217:0,0,13,14 20 10095433 . T *, . . DP=113 GT:AD:DP:GQ:PL:SB ./.:26,23,0:49:99:883,0,978,961,1053,2014:16,10,12,11 ./.:0,27,0:27:82:1217,82,0,1217,82,1217:0,0,13,14 20 10095434 . G *, . . DP=113 GT:AD:DP:GQ:PL:SB ./.:26,23,0:49:99:883,0,978,961,1053,2014:16,10,12,11 ./.:0,27,0:27:82:1217,82,0,1217,82,1217:0,0,13,14 20 10095435 . A *, . . DP=113 GT:AD:DP:GQ:PL:SB ./.:26,23,0:49:99:883,0,978,961,1053,2014:16,10,12,11 ./.:0,27,0:27:82:1217,82,0,1217,82,1217:0,0,13,14 @@ -10801,7 +10801,7 @@ 20 10096895 . A . . . GT:DP:GQ:MIN_DP:PL ./.:78:99:65:0,120,1800 ./.:50:9:50:0,9,135 20 10096896 . T . . . GT:DP:GQ:MIN_DP:PL ./.:78:99:65:0,120,1800 ./.:48:6:48:0,6,90 20 10096897 . T . . END=10096898 GT:DP:GQ:MIN_DP:PL ./.:78:99:65:0,120,1800 ./.:47:0:47:0,0,0 -20 10096899 . G T, . . BaseQRankSum=2.49;DP=125;ExcessHet=3.01;MQRankSum=-1.677e+00;RAW_MQandDP=444079,125;ReadPosRankSum=0.422 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:40,43,0:83:99:0|1:10096899_G_T:1644,0,1519,1764,1649,3413:10096899:20,20,12,31 ./.:0,41,0:41:99:0|1:10096899_G_T:1835,123,0,1835,123,1835:10096899:0,0,14,27 +20 10096899 . G T, . . BaseQRankSum=2.76;DP=125;ExcessHet=3.01;MQRankSum=-1.677e+00;RAW_MQandDP=444079,125;ReadPosRankSum=0.422 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:40,43,0:83:99:0|1:10096899_G_T:1644,0,1519,1764,1649,3413:10096899:20,20,12,31 ./.:0,41,0:41:99:0|1:10096899_G_T:1835,123,0,1835,123,1835:10096899:0,0,14,27 20 10096900 . G . . END=10096904 GT:DP:GQ:MIN_DP:PL ./.:82:99:78:0,120,1800 ./.:47:0:46:0,0,0 20 10096905 . TA T, . . BaseQRankSum=-7.550e-01;DP=126;ExcessHet=3.01;MQRankSum=-1.739e+00;RAW_MQandDP=447679,126;ReadPosRankSum=0.461 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:43,43,0:86:99:0|1:10096899_G_T:1638,0,1623,1768,1752,3520:10096899:22,21,13,30 ./.:0,40,0:40:99:0|1:10096899_G_T:1835,123,0,1835,123,1835:10096899:0,0,13,27 20 10096906 . A *, . . DP=126 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:43,43,0:86:99:0|1:10096899_G_T:1638,0,1623,1768,1752,3520:10096899:22,21,13,30 ./.:0,40,0:40:99:0|1:10096899_G_T:1835,123,0,1835,123,1835:10096899:0,0,13,27 @@ -10809,9 +10809,9 @@ 20 10096908 . T . . END=10096924 GT:DP:GQ:MIN_DP:PL ./.:84:99:82:0,120,1800 ./.:47:99:45:0,112,1358 20 10096925 . T C, . . BaseQRankSum=-4.687e+00;ClippingRankSum=0.00;DP=120;ExcessHet=3.01;MQRankSum=0.00;RAW_MQandDP=136800,38;ReadPosRankSum=-6.140e-01 GT:AD:DP:GQ:MIN_DP:PL:SB ./.:.:84:99:82:0,120,1800,120,1800,1800 ./.:20,18,0:38:99:.:364,0,556,424,609,1033:6,14,7,11 20 10096926 . G . . END=10096932 GT:DP:GQ:MIN_DP:PL ./.:84:99:82:0,120,1800 ./.:46:99:43:0,118,1289 -20 10096933 . G C, . . BaseQRankSum=-1.724e+00;DP=127;ExcessHet=3.01;MQRankSum=-1.840e+00;RAW_MQandDP=449979,127;ReadPosRankSum=0.334 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:47,42,0:89:99:0|1:10096933_G_C:1542,0,1763,1684,1889,3573:10096933:29,18,14,28 ./.:0,38,0:38:99:0|1:10096933_G_C:1730,117,0,1730,117,1730:10096933:0,0,13,25 +20 10096933 . G C, . . BaseQRankSum=-1.914e+00;DP=127;ExcessHet=3.01;MQRankSum=-1.840e+00;RAW_MQandDP=449979,127;ReadPosRankSum=0.383 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:47,42,0:89:99:0|1:10096933_G_C:1542,0,1763,1684,1889,3573:10096933:29,18,14,28 ./.:0,38,0:38:99:0|1:10096933_G_C:1730,117,0,1730,117,1730:10096933:0,0,13,25 20 10096934 . T . . END=10096957 GT:DP:GQ:MIN_DP:PL ./.:89:99:85:0,120,1800 ./.:48:99:43:0,116,1435 -20 10096958 . G A, . . BaseQRankSum=2.70;DP=140;ExcessHet=3.01;MQRankSum=-1.664e+00;RAW_MQandDP=496779,140;ReadPosRankSum=-1.824e+00 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:44,48,0:92:99:0|1:10096933_G_C:1797,0,1622,1929,1766,3695:10096933:27,17,16,32 ./.:0,47,0:47:99:0|1:10096933_G_C:1897,141,0,1897,141,1897:10096933:0,0,16,31 +20 10096958 . G A, . . BaseQRankSum=2.70;DP=140;ExcessHet=3.01;MQRankSum=-1.664e+00;RAW_MQandDP=496779,140;ReadPosRankSum=-1.593e+00 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:44,48,0:92:99:0|1:10096933_G_C:1797,0,1622,1929,1766,3695:10096933:27,17,16,32 ./.:0,47,0:47:99:0|1:10096933_G_C:1897,141,0,1897,141,1897:10096933:0,0,16,31 20 10096959 . G . . END=10097023 GT:DP:GQ:MIN_DP:PL ./.:92:99:84:0,120,1800 ./.:54:99:40:0,99,1197 20 10097024 . A . . . GT:DP:GQ:MIN_DP:PL ./.:92:99:84:0,120,1800 ./.:41:96:41:0,96,1215 20 10097025 . G . . END=10097039 GT:DP:GQ:MIN_DP:PL ./.:92:99:84:0,120,1800 ./.:42:99:40:0,104,1197 @@ -10835,7 +10835,7 @@ 20 10097098 . A . . . GT:DP:GQ:MIN_DP:PL ./.:91:99:77:0,120,1800 ./.:36:24:36:0,24,360 20 10097099 . T . . . GT:DP:GQ:MIN_DP:PL ./.:91:99:77:0,120,1800 ./.:39:18:39:0,18,270 20 10097100 . T . . . GT:DP:GQ:MIN_DP:PL ./.:91:99:77:0,120,1800 ./.:39:21:39:0,21,315 -20 10097101 . C CTTTT,CTTT, . . BaseQRankSum=-9.530e-01;DP=109;ExcessHet=3.01;MQRankSum=-2.210e+00;RAW_MQandDP=375773,109;ReadPosRankSum=2.37 GT:AD:DP:GQ:PL:SB ./.:34,3,26,0:63:99:1113,585,1857,0,1269,1263,973,1937,1359,2255:22,12,14,15 ./.:0,22,0,0:22:71:1008,71,0,1008,71,1009,1008,71,1009,1009:0,0,13,9 +20 10097101 . C CTTTT,CTTT, . . BaseQRankSum=-9.530e-01;DP=109;ExcessHet=3.01;MQRankSum=-2.210e+00;RAW_MQandDP=375773,109;ReadPosRankSum=2.83 GT:AD:DP:GQ:PL:SB ./.:34,3,26,0:63:99:1113,585,1857,0,1269,1263,973,1937,1359,2255:22,12,14,15 ./.:0,22,0,0:22:71:1008,71,0,1008,71,1009,1008,71,1009,1009:0,0,13,9 20 10097102 . T . . . GT:DP:GQ:MIN_DP:PL ./.:70:99:60:0,120,1800 ./.:36:0:36:0,0,0 20 10097103 . T . . END=10097107 GT:DP:GQ:MIN_DP:PL ./.:70:99:60:0,120,1800 ./.:36:60:35:0,60,900 20 10097108 . T . . . GT:DP:GQ:MIN_DP:PL ./.:70:99:60:0,120,1800 ./.:36:72:36:0,72,1080 @@ -10870,7 +10870,7 @@ 20 10097433 . A . . . GT:DP:GQ:MIN_DP:PL ./.:70:99:60:0,120,1800 ./.:30:64:30:0,64,876 20 10097434 . C . . . GT:DP:GQ:MIN_DP:PL ./.:70:99:60:0,120,1800 ./.:30:78:30:0,78,1170 20 10097435 . T . . . GT:DP:GQ:MIN_DP:PL ./.:70:99:60:0,120,1800 ./.:30:66:30:0,66,990 -20 10097436 . CTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT C, . . BaseQRankSum=1.82;DP=120;ExcessHet=3.01;MQRankSum=-6.464e+00;RAW_MQandDP=265743,90;ReadPosRankSum=-3.097e+00 GT:AD:DP:GQ:MIN_DP:PL:SB ./.:57,32,0:89:99:.:1097,0,2238,1269,2335,3603:23,34,11,21 ./.:.:30:66:30:0,66,990,66,990,990 +20 10097436 . CTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT C, . . BaseQRankSum=1.65;DP=120;ExcessHet=3.01;MQRankSum=-6.464e+00;RAW_MQandDP=265743,90;ReadPosRankSum=-3.097e+00 GT:AD:DP:GQ:MIN_DP:PL:SB ./.:57,32,0:89:99:.:1097,0,2238,1269,2335,3603:23,34,11,21 ./.:.:30:66:30:0,66,990,66,990,990 20 10097437 . TTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC *,TTTTCTTTCTTTCTTTCTTTCTTTCTTTC,T, . . DP=108;ExcessHet=3.01;RAW_MQandDP=332774,108 GT:AD:DP:GQ:PL:SB ./.:0,32,23,0,0:55:99:2133,941,1797,1201,0,1129,2207,1453,1267,2647,2207,1453,1267,2647,2647:0,0,16,39 ./.:0,0,0,21,0:21:67:928,928,928,928,928,928,67,67,67,0,928,928,928,67,928:0,0,6,15 20 10097438 . T *, . . DP=108 GT:AD:DP:GQ:PL:SB ./.:0,23,0:55:99:2133,1201,1129,2207,1267,2647:0,0,16,39 ./.:0,21,0:21:67:928,67,0,928,67,928:0,0,6,15 20 10097439 . T *, . . DP=108 GT:AD:DP:GQ:PL:SB ./.:0,23,0:55:99:2133,1201,1129,2207,1267,2647:0,0,16,39 ./.:0,21,0:21:67:928,67,0,928,67,928:0,0,6,15 @@ -11169,7 +11169,7 @@ 20 10098230 . T . . . GT:DP:GQ:MIN_DP:PL ./.:17:21:13:0,21,315 ./.:34:78:34:0,78,1170 20 10098231 . A . . END=10098233 GT:DP:GQ:MIN_DP:PL ./.:17:21:13:0,21,315 ./.:37:84:36:0,84,1260 20 10098234 . T . . END=10098236 GT:DP:GQ:MIN_DP:PL ./.:17:21:13:0,21,315 ./.:41:93:40:0,93,1395 -20 10098237 . A T, . . BaseQRankSum=6.000e-03;DP=48;ExcessHet=3.01;MQRankSum=-1.885e+00;RAW_MQandDP=162600,48;ReadPosRankSum=0.277 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:7,7,0:14:99:0|1:10098219_TATATATA_T:273,0,273,294,294,588:10098219:0,7,0,7 ./.:0,33,0:33:98:0|1:10098219_TATATATA_T:1345,98,0,1345,98,1345:10098219:0,0,16,17 +20 10098237 . A T, . . BaseQRankSum=6.000e-03;DP=48;ExcessHet=3.01;MQRankSum=-1.885e+00;RAW_MQandDP=162600,48;ReadPosRankSum=1.12 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:7,7,0:14:99:0|1:10098219_TATATATA_T:273,0,273,294,294,588:10098219:0,7,0,7 ./.:0,33,0:33:98:0|1:10098219_TATATATA_T:1345,98,0,1345,98,1345:10098219:0,0,16,17 20 10098238 . A . . END=10098241 GT:DP:GQ:MIN_DP:PL ./.:10:21:9:0,21,315 ./.:42:84:41:0,84,1260 20 10098242 . A . . . GT:DP:GQ:MIN_DP:PL ./.:10:21:9:0,21,315 ./.:35:44:35:0,44,916 20 10098243 . T . . END=10098244 GT:DP:GQ:MIN_DP:PL ./.:10:21:9:0,21,315 ./.:42:81:39:0,81,1215 @@ -11182,7 +11182,7 @@ 20 10098257 . A . . END=10098260 GT:DP:GQ:MIN_DP:PL ./.:8:9:6:0,9,135 ./.:48:0:47:0,0,405 20 10098261 . T . . END=10098262 GT:DP:GQ:MIN_DP:PL ./.:8:9:6:0,9,135 ./.:48:87:48:0,87,1305 20 10098263 . T . . END=10098264 GT:DP:GQ:MIN_DP:PL ./.:8:9:6:0,9,135 ./.:49:90:44:0,90,1350 -20 10098265 . T C, . . BaseQRankSum=1.83;DP=50;ExcessHet=3.01;MQRankSum=-1.834e+00;RAW_MQandDP=10564,6;ReadPosRankSum=0.00 GT:AD:DP:GQ:MIN_DP:PGT:PID:PL:PS:SB .|.:2,4,0:6:59:.:0|1:10098219_TATATATA_T:162,0,59,168,71,239:10098219:0,2,0,4 ./.:.:49:90:44:.:.:0,90,1350,90,1350,1350 +20 10098265 . T C, . . BaseQRankSum=1.83;DP=50;ExcessHet=3.01;MQRankSum=-1.834e+00;RAW_MQandDP=10564,6;ReadPosRankSum=0.842 GT:AD:DP:GQ:MIN_DP:PGT:PID:PL:PS:SB .|.:2,4,0:6:59:.:0|1:10098219_TATATATA_T:162,0,59,168,71,239:10098219:0,2,0,4 ./.:.:49:90:44:.:.:0,90,1350,90,1350,1350 20 10098266 . A . . END=10098270 GT:DP:GQ:MIN_DP:PL ./.:4:9:4:0,9,135 ./.:44:81:43:0,81,1215 20 10098271 . A . . END=10098272 GT:DP:GQ:MIN_DP:PL ./.:4:9:4:0,9,135 ./.:49:72:43:0,72,1080 20 10098273 . A . . END=10098275 GT:DP:GQ:MIN_DP:PL ./.:3:6:3:0,6,90 ./.:49:72:43:0,72,1080 @@ -11373,7 +11373,7 @@ 20 10098882 . C . . . GT:DP:GQ:MIN_DP:PL ./.:32:60:32:0,60,1207 ./.:33:6:32:0,6,90 20 10098883 . T . . . GT:DP:GQ:MIN_DP:PL ./.:32:56:32:0,56,1237 ./.:33:6:32:0,6,90 20 10098884 . C . . . GT:DP:GQ:MIN_DP:PL ./.:32:84:32:0,84,1260 ./.:33:6:32:0,6,90 -20 10098885 . C CA, . . BaseQRankSum=0.165;DP=63;ExcessHet=3.01;MQRankSum=-4.449e+00;RAW_MQandDP=187457,63;ReadPosRankSum=-1.073e+00 GT:AD:DP:GQ:PL:SB ./.:17,14,0:31:99:471,0,572,522,615,1137:16,1,13,1 ./.:0,29,0:29:87:1163,87,0,1163,87,1163:0,0,16,13 +20 10098885 . C CA, . . BaseQRankSum=0.165;DP=63;ExcessHet=3.01;MQRankSum=-4.449e+00;RAW_MQandDP=187457,63;ReadPosRankSum=-9.540e-01 GT:AD:DP:GQ:PL:SB ./.:17,14,0:31:99:471,0,572,522,615,1137:16,1,13,1 ./.:0,29,0:29:87:1163,87,0,1163,87,1163:0,0,16,13 20 10098886 . C . . . GT:DP:GQ:MIN_DP:PL ./.:31:84:29:0,84,1260 ./.:33:0:33:0,0,0 20 10098887 . C . . END=10098888 GT:DP:GQ:MIN_DP:PL ./.:31:84:29:0,84,1260 ./.:35:99:34:0,102,1027 20 10098889 . A . . . GT:DP:GQ:MIN_DP:PL ./.:31:84:29:0,84,1260 ./.:32:96:32:0,96,972 @@ -11437,10 +11437,10 @@ 20 10099026 . T . . . GT:DP:GQ:MIN_DP:PL ./.:27:72:26:0,72,1080 ./.:33:83:33:0,83,1048 20 10099027 . G . . . GT:DP:GQ:MIN_DP:PL ./.:27:72:26:0,72,1080 ./.:32:90:32:0,90,1350 20 10099028 . A . . . GT:DP:GQ:MIN_DP:PL ./.:28:69:28:0,69,1035 ./.:33:88:33:0,88,999 -20 10099029 . T C, . . BaseQRankSum=-1.518e+00;DP=59;ExcessHet=3.01;MQRankSum=-3.731e+00;RAW_MQandDP=185752,59;ReadPosRankSum=-1.224e+00 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:19,10,0:29:99:0|1:10099029_T_C:363,0,768,420,798,1218:10099029:14,5,9,1 ./.:0,29,0:29:87:0|1:10099029_T_C:1277,87,0,1277,87,1277:10099029:0,0,17,12 +20 10099029 . T C, . . BaseQRankSum=-1.809e+00;DP=59;ExcessHet=3.01;MQRankSum=-3.731e+00;RAW_MQandDP=185752,59;ReadPosRankSum=-1.224e+00 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:19,10,0:29:99:0|1:10099029_T_C:363,0,768,420,798,1218:10099029:14,5,9,1 ./.:0,29,0:29:87:0|1:10099029_T_C:1277,87,0,1277,87,1277:10099029:0,0,17,12 20 10099030 . C . . END=10099031 GT:DP:GQ:MIN_DP:PL ./.:29:72:28:0,72,1080 ./.:32:90:31:0,90,1350 20 10099032 . T . . END=10099033 GT:DP:GQ:MIN_DP:PL ./.:28:63:28:0,63,945 ./.:31:87:31:0,87,1305 -20 10099034 . C A, . . BaseQRankSum=2.75;DP=56;ExcessHet=3.01;MQRankSum=-3.731e+00;RAW_MQandDP=177711,56;ReadPosRankSum=-1.850e+00 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:19,10,0:29:99:0|1:10099029_T_C:363,0,768,420,798,1218:10099029:14,5,9,1 ./.:0,27,0:27:81:0|1:10099029_T_C:1215,81,0,1215,81,1215:10099029:0,0,17,10 +20 10099034 . C A, . . BaseQRankSum=2.76;DP=56;ExcessHet=3.01;MQRankSum=-3.731e+00;RAW_MQandDP=177711,56;ReadPosRankSum=-1.850e+00 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:19,10,0:29:99:0|1:10099029_T_C:363,0,768,420,798,1218:10099029:14,5,9,1 ./.:0,27,0:27:81:0|1:10099029_T_C:1215,81,0,1215,81,1215:10099029:0,0,17,10 20 10099035 . G . . . GT:DP:GQ:MIN_DP:PL ./.:29:60:26:0,60,900 ./.:31:87:31:0,87,1305 20 10099036 . G . . . GT:DP:GQ:MIN_DP:PL ./.:29:60:26:0,60,900 ./.:32:90:32:0,90,1350 20 10099037 . T . . . GT:DP:GQ:MIN_DP:PL ./.:29:60:26:0,60,900 ./.:31:82:31:0,82,961 @@ -11456,7 +11456,7 @@ 20 10099051 . C . . . GT:DP:GQ:MIN_DP:PL ./.:24:57:23:0,57,855 ./.:31:67:31:0,67,886 20 10099052 . G . . . GT:DP:GQ:MIN_DP:PL ./.:24:57:23:0,57,855 ./.:32:84:31:0,84,1260 20 10099053 . G . . END=10099054 GT:DP:GQ:MIN_DP:PL ./.:23:54:23:0,54,810 ./.:32:84:31:0,84,1260 -20 10099055 . T C, . . BaseQRankSum=-9.960e-01;DP=56;ExcessHet=3.01;MQRankSum=-4.179e+00;RAW_MQandDP=169190,56;ReadPosRankSum=-1.970e+00 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:17,8,0:25:99:0|1:10099029_T_C:285,0,673,336,697,1033:10099029:12,5,6,2 ./.:0,30,0:30:90:0|1:10099029_T_C:1350,90,0,1350,90,1350:10099029:0,0,20,10 +20 10099055 . T C, . . BaseQRankSum=-1.554e+00;DP=56;ExcessHet=3.01;MQRankSum=-4.179e+00;RAW_MQandDP=169190,56;ReadPosRankSum=-1.970e+00 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:17,8,0:25:99:0|1:10099029_T_C:285,0,673,336,697,1033:10099029:12,5,6,2 ./.:0,30,0:30:90:0|1:10099029_T_C:1350,90,0,1350,90,1350:10099029:0,0,20,10 20 10099056 . T . . . GT:DP:GQ:MIN_DP:PL ./.:24:60:23:0,60,900 ./.:35:87:35:0,87,1305 20 10099057 . C . . . GT:DP:GQ:MIN_DP:PL ./.:24:60:23:0,60,900 ./.:34:76:34:0,76,995 20 10099058 . C . . END=10099061 GT:DP:GQ:MIN_DP:PL ./.:24:60:23:0,60,900 ./.:34:87:32:0,87,1305 @@ -11488,7 +11488,7 @@ 20 10099107 . T . . . GT:DP:GQ:MIN_DP:PL ./.:41:99:39:0,99,1485 ./.:36:0:36:0,0,787 20 10099108 . T . . END=10099109 GT:DP:GQ:MIN_DP:PL ./.:41:99:39:0,99,1485 ./.:38:30:38:0,30,450 20 10099110 . G . . . GT:DP:GQ:MIN_DP:PL ./.:41:99:39:0,99,1485 ./.:36:0:36:0,0,675 -20 10099111 . T TTTTGTTTG, . . BaseQRankSum=-6.220e-01;DP=80;ExcessHet=3.01;MQRankSum=-9.730e-01;RAW_MQandDP=250187,80;ReadPosRankSum=-2.730e-01 GT:AD:DP:GQ:PL:SB ./.:23,19,0:42:99:693,0,802,763,860,1623:13,10,12,7 ./.:0,23,0:23:72:1041,72,0,1042,72,1042:0,0,12,11 +20 10099111 . T TTTTGTTTG, . . BaseQRankSum=-1.207e+00;DP=80;ExcessHet=3.01;MQRankSum=-9.730e-01;RAW_MQandDP=250187,80;ReadPosRankSum=-1.860e+00 GT:AD:DP:GQ:PL:SB ./.:23,19,0:42:99:693,0,802,763,860,1623:13,10,12,7 ./.:0,23,0:23:72:1041,72,0,1042,72,1042:0,0,12,11 20 10099112 . T . . . GT:DP:GQ:MIN_DP:PL ./.:57:99:49:0,114,1710 ./.:38:0:38:0,0,97 20 10099113 . T . . END=10099114 GT:DP:GQ:MIN_DP:PL ./.:57:99:49:0,114,1710 ./.:39:75:38:0,75,1125 20 10099115 . G . . . GT:DP:GQ:MIN_DP:PL ./.:57:99:49:0,114,1710 ./.:36:60:36:0,60,948 @@ -11501,7 +11501,7 @@ 20 10099133 . T . . END=10099134 GT:DP:GQ:MIN_DP:PL ./.:57:99:49:0,114,1710 ./.:39:93:37:0,93,1099 20 10099135 . T . . . GT:DP:GQ:MIN_DP:PL ./.:57:99:49:0,114,1710 ./.:42:87:42:0,87,1228 20 10099136 . T . . END=10099139 GT:DP:GQ:MIN_DP:PL ./.:57:99:49:0,114,1710 ./.:41:99:40:0,117,1755 -20 10099140 . G T, . . BaseQRankSum=-2.860e-01;DP=96;ExcessHet=3.01;MQRankSum=-2.435e+00;RAW_MQandDP=310730,96;ReadPosRankSum=0.116 GT:AD:DP:GQ:PL:SB ./.:29,32,0:61:99:1035,0,930,1122,1026,2148:17,12,22,10 ./.:0,31,0:31:93:1030,93,0,1030,93,1030:0,0,15,16 +20 10099140 . G T, . . BaseQRankSum=-2.860e-01;DP=96;ExcessHet=3.01;MQRankSum=-2.435e+00;RAW_MQandDP=310730,96;ReadPosRankSum=0.636 GT:AD:DP:GQ:PL:SB ./.:29,32,0:61:99:1035,0,930,1122,1026,2148:17,12,22,10 ./.:0,31,0:31:93:1030,93,0,1030,93,1030:0,0,15,16 20 10099141 . G . . . GT:DP:GQ:MIN_DP:PL ./.:67:99:64:0,120,1800 ./.:40:90:40:0,90,1214 20 10099142 . G . . . GT:DP:GQ:MIN_DP:PL ./.:67:99:64:0,120,1800 ./.:41:22:41:0,22,1104 20 10099143 . G . . . 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a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testBasepairResolutionInput.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testBasepairResolutionInput.vcf @@ -7,7 +7,7 @@ ##FORMAT= ##FORMAT= ##FORMAT= -##GATKCommandLine= +##GATKCommandLine= ##INFO= ##INFO= ##INFO= diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testBasepairResolutionInput.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testBasepairResolutionInput.vcf.idx index e803a69a3dc4be00a4c06f6eb5651ec4b3b2bf49..4d73ee665d0697c623439cf8ff0eff2a82712100 100644 GIT binary patch literal 42144 zcmeIz&2Ah;5C`z)Lm&tj#DyaVByOIr{_fn&dSfglwq(}U!o^zKld#INYj)P*2{`fy z9Fg)W+;{?>h3b!qrg;VaR;;xuwKdh%-M?9!oh;uILVUo#FV~y?Y1egEL%$!o`_-HE z{cXSPZuh&@efMg0c-;;AyYA2rhi=~wyT|=qKXkkOtCF$a4u|#O@z8fa^_vZU@xI@8 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a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testBreakBandsArgumet.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testBreakBandsArgumet.vcf.idx index 649a65ae5ccb82899cef5ce36a3162419715caaf..1de19f9e280188351bf491fad1ba88306703f625 100644 GIT binary patch delta 49 lcmaDS@J?XD6kZQY1~91TEnHEsap6{WiBtuM2#kiQ002)K3GM&@ delta 49 lcmaDS@J?XD6kcyj1~3r#ci?3H#)VtiB{CEsA}|`J0svmB3UUAd diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSample.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSample.vcf index 4fc6f911cf0..fa993a46045 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSample.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSample.vcf @@ -8,7 +8,7 @@ ##FORMAT= ##FORMAT= ##FORMAT= -##GATKCommandLine= +##GATKCommandLine= ##GVCFBlock=minGQ=0(inclusive),maxGQ=5(exclusive) ##INFO= ##INFO= diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSample.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSample.vcf.idx index a13302fb9862c7a300863f9b40d4b52efc3b2b76..af0690684b0bbbe5f010a30d15c051d97b0f70a6 100644 GIT binary patch delta 64 kcmZ3>yq0;w3f}9&3}En~vT#Mg#H|-Jd;}o^xM-LL0P!6Q9smFU delta 64 kcmZ3>yq0;w3f^173}E2!?ZC ##FORMAT= ##FORMAT= -##GATKCommandLine= +##GATKCommandLine= ##GVCFBlock=minGQ=0(inclusive),maxGQ=5(exclusive) ##INFO= ##INFO= diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSampleHaploid.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSampleHaploid.vcf.idx index a25fa0d639be7cb874f7519812b003fe6eae2c63..91b01a309969dc4135bdabc2c0f635dd870de4b5 100644 GIT binary patch delta 64 kcmdnOyoGtfdfqZ&1~9l$TezZN;+_i{(Si^GTr^Ar0O4>7pa1{> delta 64 kcmdnOyoGtfdfrN51~72=cHm_G#61@@;shZAxM-LL0P$T50ssI2 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSampleTetraploid.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSampleTetraploid.vcf index 8f0403ad131..80566353516 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSampleTetraploid.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSampleTetraploid.vcf @@ -8,7 +8,7 @@ ##FORMAT= ##FORMAT= ##FORMAT= -##GATKCommandLine= +##GATKCommandLine= ##GVCFBlock=minGQ=0(inclusive),maxGQ=5(exclusive) ##INFO= ##INFO= diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSampleTetraploid.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSampleTetraploid.vcf.idx index ae9c5be01a0ab95755fb7d855c65ff0e397c62eb..b8f715cd3b38ec59c46b970839cab78f291ca374 100644 GIT binary patch delta 64 kcmdnayq$T%Cf)-g3}A4hws1wk#QhgE5(OawxM-LL0QtoWS^xk5 delta 64 kcmdnayq$T%Cf>s$3}E2!?ZC ##FORMAT= ##FORMAT= -##GATKCommandLine= +##GATKCommandLine= ##GVCFBlock=minGQ=0(inclusive),maxGQ=1(exclusive) ##INFO= ##INFO= diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testWrongReferenceBaseBugFix.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testWrongReferenceBaseBugFix.vcf.idx index 902df91a3920a082e4def76abc00fe80d7ed42d8..67c9c480744e5dec0269cc3df477e1a125db8ad1 100644 GIT binary patch delta 49 lcmX>qa8zKzY~F{)3}8^vTezZNx2~Bl~2#kiQ002=A3N`=$ delta 49 lcmX>qa8zKzY~Clv3}7Je@4(6YjVoH&C3MswA}|`J0svs13c3IQ diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/newMQcalc.combined.genotyped.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/newMQcalc.combined.genotyped.vcf index fff5e62a517..0cfbad7c60a 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/newMQcalc.combined.genotyped.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/newMQcalc.combined.genotyped.vcf @@ -12,8 +12,8 @@ ##FORMAT= ##FORMAT= ##FORMAT= -##GATKCommandLine= -##GATKCommandLine= +##GATKCommandLine= +##GATKCommandLine= ##GATKCommandLine= ##INFO= ##INFO= @@ -152,14 +152,14 @@ 20 10004094 . A C 3293.13 . AC=4;AF=1.00;AN=4;DP=102;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=56.14;QD=32.93;SOR=1.167 GT:AD:DP:GQ:PL 1/1:0,53:53:99:1854,157,0 1/1:0,47:47:99:1455,140,0 20 10004147 . A G 2825.13 . AC=4;AF=1.00;AN=4;DP=89;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=57.13;QD=32.47;SOR=1.030 GT:AD:DP:GQ:PL 1/1:0,52:52:99:1866,156,0 1/1:0,35:35:99:975,103,0 20 10004193 . G T 936.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=-3.920e-01;DP=90;ExcessHet=3.0103;FS=2.369;MLEAC=1;MLEAF=0.250;MQ=59.14;MQRankSum=3.39;QD=18.37;ReadPosRankSum=1.72;SOR=0.941 GT:AD:DP:GQ:PL 0/1:23,28:51:99:945,0,776 0/0:36,0:36:99:0,102,1152 -20 10004222 . C CA 42.29 . AC=1;AF=0.250;AN=4;BaseQRankSum=0.124;DP=106;ExcessHet=3.0103;FS=3.221;MLEAC=1;MLEAF=0.250;MQ=58.19;MQRankSum=-2.220e+00;QD=0.94;ReadPosRankSum=1.27;SOR=0.932 GT:AD:DP:GQ:PL 0/1:35,10:45:49:49,0,924 0/0:38,0:38:0:0,0,689 +20 10004222 . C CA 42.29 . AC=1;AF=0.250;AN=4;BaseQRankSum=0.335;DP=106;ExcessHet=3.0103;FS=3.221;MLEAC=1;MLEAF=0.250;MQ=58.19;MQRankSum=-2.220e+00;QD=0.94;ReadPosRankSum=0.198;SOR=0.932 GT:AD:DP:GQ:PL 0/1:35,10:45:49:49,0,924 0/0:38,0:38:0:0,0,689 20 10004223 . A AG 203.46 . AC=2;AF=0.500;AN=4;BaseQRankSum=0.803;ClippingRankSum=0.00;DP=96;ExcessHet=4.7712;FS=3.618;MLEAC=2;MLEAF=0.500;MQ=58.47;MQRankSum=2.27;QD=2.99;ReadPosRankSum=1.09;SOR=0.721 GT:AD:DP:GQ:PL 0/1:35,12:47:88:88,0,953 0/1:13,8:21:99:125,0,211 20 10004224 . A G 144.34 . AC=1;AF=0.250;AN=4;BaseQRankSum=-5.440e-01;ClippingRankSum=0.00;DP=93;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=58.95;MQRankSum=0.069;QD=6.87;ReadPosRankSum=0.459;SOR=0.551 GT:AD:DP:GQ:PL 0/0:65,0:65:0:0,0,1201 0/1:11,10:21:99:151,0,199 20 10004351 . C G 4289.13 . AC=4;AF=1.00;AN=4;DP=126;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=59.47;QD=34.87;SOR=0.924 GT:AD:DP:GQ:PL 1/1:0,70:70:99:2784,211,0 1/1:0,53:53:99:1521,157,0 20 10004389 . T G 3864.13 . AC=4;AF=1.00;AN=4;BaseQRankSum=1.77;ClippingRankSum=0.00;DP=118;ExcessHet=3.0103;FS=3.502;MLEAC=4;MLEAF=1.00;MQ=58.11;MQRankSum=0.00;QD=34.50;ReadPosRankSum=1.41;SOR=0.608 GT:AD:DP:GQ:PL 1/1:0,62:62:99:2523,187,0 1/1:1,49:50:99:1357,138,0 20 10004610 . A C 4975.13 . AC=4;AF=1.00;AN=4;DP=138;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=59.16;QD=29.03;SOR=0.818 GT:AD:DP:GQ:PL 1/1:0,89:89:99:3654,267,0 1/1:0,45:45:99:1337,134,0 20 10004725 . A G 974.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=-2.393e+00;DP=108;ExcessHet=3.0103;FS=13.744;MLEAC=1;MLEAF=0.250;MQ=55.34;MQRankSum=2.86;QD=15.23;ReadPosRankSum=1.93;SOR=0.613 GT:AD:DP:GQ:PL 0/1:34,30:64:99:983,0,1139 0/0:42,0:42:93:0,93,1395 -20 10004769 . TAAAACTATGC T 1503.46 . AC=2;AF=0.500;AN=4;BaseQRankSum=1.80;ClippingRankSum=0.00;DP=117;ExcessHet=4.7712;FS=2.757;MLEAC=2;MLEAF=0.500;MQ=55.39;MQRankSum=0.00;QD=15.83;ReadPosRankSum=1.72;SOR=0.998 GT:AD:DP:GQ:PL 0/1:37,26:63:99:978,0,1473 0/1:18,14:32:99:535,0,1946 +20 10004769 . TAAAACTATGC T 1503.46 . AC=2;AF=0.500;AN=4;BaseQRankSum=0.822;ClippingRankSum=0.00;DP=117;ExcessHet=4.7712;FS=2.757;MLEAC=2;MLEAF=0.500;MQ=55.39;MQRankSum=0.00;QD=15.83;ReadPosRankSum=1.72;SOR=0.998 GT:AD:DP:GQ:PL 0/1:37,26:63:99:978,0,1473 0/1:18,14:32:99:535,0,1946 20 10004874 . A C 5359.13 . AC=4;AF=1.00;AN=4;DP=137;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=59.57;QD=30.67;SOR=0.994 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,87:87:99:1|1:10004874_A_C:3631,261,0:10004874 1/1:0,47:47:99:1|1:10004874_A_C:1744,141,0:10004874 20 10004887 . A G 1853.50 . AC=2;AF=0.500;AN=4;BaseQRankSum=0.356;ClippingRankSum=0.00;DP=138;ExcessHet=4.7712;FS=2.181;MLEAC=2;MLEAF=0.500;MQ=59.67;MQRankSum=0.00;QD=13.94;ReadPosRankSum=2.05;SOR=0.889 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:45,40:85:99:0|1:10004874_A_C:1352,0,1542:10004874 0/1:27,21:48:99:0|1:10004874_A_C:511,0,709:10004874 20 10005010 . C T 4313.13 . AC=4;AF=1.00;AN=4;DP=118;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=59.80;QD=26.61;SOR=0.984 GT:AD:DP:GQ:PL 1/1:0,72:72:99:2963,217,0 1/1:0,43:43:99:1366,129,0 @@ -180,26 +180,26 @@ 20 10007575 . C T 491.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=-2.490e-01;ClippingRankSum=0.00;DP=102;ExcessHet=3.0103;FS=1.317;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=13.29;ReadPosRankSum=-8.910e-01;SOR=0.399 GT:AD:DP:GQ:PL 0/0:65,0:65:99:0,120,1800 0/1:17,20:37:99:500,0,413 20 10007835 . T C 530.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=-4.583e+00;ClippingRankSum=0.00;DP=105;ExcessHet=3.0103;FS=13.142;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=13.61;ReadPosRankSum=0.073;SOR=0.376 GT:AD:DP:GQ:PL 0/0:65,0:65:99:0,120,1800 0/1:15,24:39:99:539,0,382 20 10007980 . A C 4844.13 . AC=4;AF=1.00;AN=4;DP=135;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=60.48;QD=32.91;SOR=0.978 GT:AD:DP:GQ:PL 1/1:0,90:90:99:3553,270,0 1/1:0,43:43:99:1307,128,0 -20 10008029 . T TA,TAA 3244.33 . AC=3,1;AF=0.750,0.250;AN=4;BaseQRankSum=0.438;DP=139;ExcessHet=3.0103;FS=0.000;MLEAC=3,1;MLEAF=0.750,0.250;MQ=60.78;MQRankSum=0.651;QD=27.97;ReadPosRankSum=-1.326e+00;SOR=0.693 GT:AD:DP:GQ:PL 1/1:3,74,0:77:99:2023,145,0,2032,222,2109 1/2:0,17,22:39:99:1244,629,524,416,0,337 +20 10008029 . T TA,TAA 3244.33 . AC=3,1;AF=0.750,0.250;AN=4;BaseQRankSum=0.409;DP=139;ExcessHet=3.0103;FS=0.000;MLEAC=3,1;MLEAF=0.750,0.250;MQ=60.78;MQRankSum=0.651;QD=27.97;ReadPosRankSum=-1.357e+00;SOR=0.693 GT:AD:DP:GQ:PL 1/1:3,74,0:77:99:2023,145,0,2032,222,2109 1/2:0,17,22:39:99:1244,629,524,416,0,337 20 10008146 . TA T 3532.09 . AC=4;AF=1.00;AN=4;DP=125;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=60.43;QD=30.98;SOR=0.841 GT:AD:DP:GQ:PL 1/1:0,70:70:99:2180,211,0 1/1:0,44:44:99:1368,132,0 20 10008221 . T C 4276.13 . AC=4;AF=1.00;AN=4;DP=119;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=60.21;QD=31.31;SOR=0.877 GT:AD:DP:GQ:PL 1/1:0,80:80:99:3253,240,0 1/1:0,36:36:99:1039,106,0 20 10008389 . A G 665.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=-3.469e+00;ClippingRankSum=0.00;DP=102;ExcessHet=3.0103;FS=5.563;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=12.11;ReadPosRankSum=0.498;SOR=0.369 GT:AD:DP:GQ:PL 0/0:45,0:45:99:0,108,1620 0/1:26,29:55:99:674,0,697 20 10008458 . T G 4065.13 . AC=4;AF=1.00;AN=4;DP=120;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=55.77;QD=31.45;SOR=0.820 GT:AD:DP:GQ:PL 1/1:0,69:69:99:2683,207,0 1/1:0,46:46:99:1398,138,0 20 10008742 . G T 1276.50 . AC=2;AF=0.500;AN=4;BaseQRankSum=3.89;ClippingRankSum=0.00;DP=85;ExcessHet=4.7712;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=47.19;MQRankSum=-1.113e+00;QD=15.57;ReadPosRankSum=0.221;SOR=0.757 GT:AD:DP:GQ:PL 0/1:23,26:49:99:744,0,580 0/1:13,20:33:99:542,0,265 -20 10008758 . C CA,CAA 1501.07 . AC=3,1;AF=0.750,0.250;AN=4;BaseQRankSum=0.119;DP=88;ExcessHet=3.0103;FS=4.651;MLEAC=3,1;MLEAF=0.750,0.250;MQ=47.72;MQRankSum=-8.750e-01;QD=21.75;ReadPosRankSum=-5.200e-02;SOR=0.469 GT:AD:DP:GQ:PL 1/1:4,34,0:38:10:720,10,0,733,102,825 1/2:0,20,11:31:99:804,284,194,434,0,396 -20 10008921 . C CA 283.23 . AC=1;AF=0.250;AN=4;BaseQRankSum=0.516;DP=91;ExcessHet=3.0103;FS=1.311;MLEAC=1;MLEAF=0.250;MQ=56.00;MQRankSum=-1.306e+00;QD=8.09;ReadPosRankSum=0.173;SOR=0.644 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:18,17:35:99:0|1:10008921_C_CA:291,0,366:10008921 0/0:31,0:31:6:.:.:0,6,658 -20 10008948 . TA T 3498.09 . AC=4;AF=1.00;AN=4;BaseQRankSum=0.956;DP=89;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=54.56;MQRankSum=1.95;QD=33.27;ReadPosRankSum=0.884;SOR=0.420 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:1,53:54:99:1|1:10008921_C_CA:2108,117,0:10008921 1/1:0,33:33:99:.:.:1406,99,0 -20 10008952 . CACACACACACA C,CCACACACA,CCACACACACA,CCA 3000.04 . AC=1,1,1,1;AF=0.250,0.250,0.250,0.250;AN=4;BaseQRankSum=1.05;DP=99;ExcessHet=3.0103;FS=0.000;MLEAC=1,1,1,1;MLEAF=0.250,0.250,0.250,0.250;MQ=54.49;MQRankSum=1.84;QD=31.26;ReadPosRankSum=0.716;SOR=0.487 GT:AD:DP:GQ:PL 1/3:1,14,5,11,0:34:99:1719,538,801,740,153,687,597,0,444,535,1150,712,761,609,1293 2/4:0,0,15,0,12:27:99:1315,1243,1282,505,512,439,1243,1282,512,1282,648,714,0,714,719 +20 10008758 . C CA,CAA 1501.07 . AC=3,1;AF=0.750,0.250;AN=4;BaseQRankSum=0.130;DP=88;ExcessHet=3.0103;FS=4.651;MLEAC=3,1;MLEAF=0.750,0.250;MQ=47.72;MQRankSum=-8.750e-01;QD=21.75;ReadPosRankSum=-2.620e-01;SOR=0.469 GT:AD:DP:GQ:PL 1/1:4,34,0:38:10:720,10,0,733,102,825 1/2:0,20,11:31:99:804,284,194,434,0,396 +20 10008921 . C CA 283.23 . AC=1;AF=0.250;AN=4;BaseQRankSum=0.610;DP=91;ExcessHet=3.0103;FS=1.311;MLEAC=1;MLEAF=0.250;MQ=56.00;MQRankSum=-1.306e+00;QD=8.09;ReadPosRankSum=-1.700e-02;SOR=0.644 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:18,17:35:99:0|1:10008921_C_CA:291,0,366:10008921 0/0:31,0:31:6:.:.:0,6,658 +20 10008948 . TA T 3498.09 . AC=4;AF=1.00;AN=4;BaseQRankSum=0.994;DP=89;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=54.56;MQRankSum=1.95;QD=33.27;ReadPosRankSum=0.884;SOR=0.420 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:1,53:54:99:1|1:10008921_C_CA:2108,117,0:10008921 1/1:0,33:33:99:.:.:1406,99,0 +20 10008952 . CACACACACACA C,CCACACACA,CCACACACACA,CCA 3000.04 . AC=1,1,1,1;AF=0.250,0.250,0.250,0.250;AN=4;BaseQRankSum=1.03;DP=99;ExcessHet=3.0103;FS=0.000;MLEAC=1,1,1,1;MLEAF=0.250,0.250,0.250,0.250;MQ=54.49;MQRankSum=1.84;QD=31.26;ReadPosRankSum=0.666;SOR=0.487 GT:AD:DP:GQ:PL 1/3:1,14,5,11,0:34:99:1719,538,801,740,153,687,597,0,444,535,1150,712,761,609,1293 2/4:0,0,15,0,12:27:99:1315,1243,1282,505,512,439,1243,1282,512,1282,648,714,0,714,719 20 10009227 . A G 2028.50 . AC=2;AF=0.500;AN=4;BaseQRankSum=-1.130e-01;ClippingRankSum=0.00;DP=104;ExcessHet=4.7712;FS=1.650;MLEAC=2;MLEAF=0.500;MQ=58.10;MQRankSum=1.43;QD=19.89;ReadPosRankSum=-1.119e+00;SOR=0.502 GT:AD:DP:GQ:PGT:PID:PL:PS 0/1:23,39:62:99:.:.:1398,0,740 0/1:16,24:40:99:0|1:10009227_A_G:640,0,377:10009227 20 10009246 . A G 4327.13 . AC=4;AF=1.00;AN=4;BaseQRankSum=1.56;ClippingRankSum=0.00;DP=118;ExcessHet=3.0103;FS=3.371;MLEAC=4;MLEAF=1.00;MQ=57.07;MQRankSum=0.00;QD=27.76;ReadPosRankSum=1.72;SOR=0.514 GT:AD:DP:GQ:PGT:PID:PL:PS 1/1:0,77:77:99:.:.:3031,231,0 1/1:1,35:36:99:1|1:10009227_A_G:1312,101,0:10009227 20 10009400 . T A 4867.13 . AC=4;AF=1.00;AN=4;DP=133;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=60.00;QD=29.09;SOR=0.820 GT:AD:DP:GQ:PL 1/1:0,74:74:99:3027,223,0 1/1:0,58:58:99:1856,174,0 20 10009512 . C G 4630.13 . AC=4;AF=1.00;AN=4;DP=134;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=59.13;QD=26.08;SOR=0.856 GT:AD:DP:GQ:PL 1/1:0,77:77:99:3068,231,0 1/1:0,53:53:99:1578,158,0 20 10009719 . A G 2618.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=-3.827e+00;ClippingRankSum=0.00;DP=121;ExcessHet=3.0103;FS=7.566;MLEAC=3;MLEAF=0.750;MQ=59.85;MQRankSum=0.00;QD=23.17;ReadPosRankSum=-1.459e+00;SOR=0.257 GT:AD:DP:GQ:PL 1/1:0,57:57:99:1915,170,0 0/1:24,32:56:99:717,0,596 20 10009795 . A G 3322.13 . AC=4;AF=1.00;AN=4;DP=94;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=59.80;QD=33.85;SOR=1.071 GT:AD:DP:GQ:PL 1/1:0,47:47:99:1909,141,0 1/1:0,44:44:99:1429,132,0 -20 10009842 . G GAA 561.88 . AC=1;AF=0.250;AN=4;BaseQRankSum=0.183;DP=86;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=53.85;MQRankSum=-9.360e-01;QD=16.05;ReadPosRankSum=1.75;SOR=0.602 GT:AD:DP:GQ:PL 0/1:19,16:35:99:570,0,691 0/0:34,0:34:54:0,54,810 -20 10009844 . G A 1971.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=0.998;DP=86;ExcessHet=3.0103;FS=0.000;MLEAC=3;MLEAF=0.750;MQ=56.07;MQRankSum=0.975;QD=29.87;ReadPosRankSum=-1.575e+00;SOR=0.773 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:16,19:35:99:0|1:10009844_G_A:691,0,585:10009844 1/1:0,31:31:93:1|1:10009844_G_A:1294,93,0:10009844 -20 10009871 . A G 2338.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=-8.030e-01;DP=100;ExcessHet=3.0103;FS=3.771;MLEAC=3;MLEAF=0.750;MQ=54.66;MQRankSum=1.34;QD=31.60;ReadPosRankSum=1.49;SOR=0.880 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:18,19:37:99:0|1:10009844_G_A:687,0,593:10009844 1/1:0,37:37:99:1|1:10009844_G_A:1665,111,0:10009844 -20 10009875 . A G,AGGGAGG 4048.37 . AC=3,1;AF=0.750,0.250;AN=4;BaseQRankSum=0.378;DP=96;ExcessHet=3.0103;FS=7.191;MLEAC=3,1;MLEAF=0.750,0.250;MQ=54.42;MQRankSum=1.41;QD=27.08;ReadPosRankSum=1.04;SOR=0.652 GT:AD:DP:GQ:PGT:PID:PL:PS 1/2:2,15,14:31:99:.:.:2406,645,532,697,0,574 1/1:0,37,0:37:99:1|1:10009844_G_A:1665,111,0,1665,111,1665:10009844 +20 10009842 . G GAA 561.88 . AC=1;AF=0.250;AN=4;BaseQRankSum=0.383;DP=86;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=53.85;MQRankSum=-9.360e-01;QD=16.05;ReadPosRankSum=1.76;SOR=0.602 GT:AD:DP:GQ:PL 0/1:19,16:35:99:570,0,691 0/0:34,0:34:54:0,54,810 +20 10009844 . G A 1971.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=1.12;DP=86;ExcessHet=3.0103;FS=0.000;MLEAC=3;MLEAF=0.750;MQ=56.07;MQRankSum=0.975;QD=29.87;ReadPosRankSum=-2.354e+00;SOR=0.773 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:16,19:35:99:0|1:10009844_G_A:691,0,585:10009844 1/1:0,31:31:93:1|1:10009844_G_A:1294,93,0:10009844 +20 10009871 . A G 2338.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=-8.030e-01;DP=100;ExcessHet=3.0103;FS=3.771;MLEAC=3;MLEAF=0.750;MQ=54.66;MQRankSum=1.34;QD=31.60;ReadPosRankSum=0.840;SOR=0.880 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:18,19:37:99:0|1:10009844_G_A:687,0,593:10009844 1/1:0,37:37:99:1|1:10009844_G_A:1665,111,0:10009844 +20 10009875 . A G,AGGGAGG 4048.37 . AC=3,1;AF=0.750,0.250;AN=4;BaseQRankSum=0.378;DP=96;ExcessHet=3.0103;FS=7.191;MLEAC=3,1;MLEAF=0.750,0.250;MQ=54.42;MQRankSum=1.41;QD=27.08;ReadPosRankSum=1.37;SOR=0.652 GT:AD:DP:GQ:PGT:PID:PL:PS 1/2:2,15,14:31:99:.:.:2406,645,532,697,0,574 1/1:0,37,0:37:99:1|1:10009844_G_A:1665,111,0,1665,111,1665:10009844 20 10009879 . A G 3832.13 . AC=4;AF=1.00;AN=4;BaseQRankSum=1.53;DP=89;ExcessHet=3.0103;FS=8.085;MLEAC=4;MLEAF=1.00;MQ=54.53;MQRankSum=1.68;QD=25.42;ReadPosRankSum=1.11;SOR=0.968 GT:AD:DP:GQ:PGT:PID:PL:PS 1/1:2,51:53:99:.:.:2273,150,0 1/1:0,35:35:99:1|1:10009844_G_A:1575,105,0:10009844 20 10009883 . A G 3649.13 . AC=4;AF=1.00;AN=4;DP=86;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=54.63;QD=27.65;SOR=1.525 GT:AD:DP:GQ:PGT:PID:PL:PS 1/1:0,49:49:99:.:.:2180,147,0 1/1:0,33:33:99:1|1:10009844_G_A:1485,99,0:10009844 20 10010393 . T G 2013.50 . AC=2;AF=0.500;AN=4;BaseQRankSum=-1.738e+00;ClippingRankSum=0.00;DP=118;ExcessHet=4.7712;FS=8.582;MLEAC=2;MLEAF=0.500;MQ=59.61;MQRankSum=0.00;QD=17.06;ReadPosRankSum=-3.900e-01;SOR=0.398 GT:AD:DP:GQ:PL 0/1:36,43:79:99:1493,0,1230 0/1:18,21:39:99:530,0,466 @@ -208,7 +208,7 @@ 20 10010832 . T C 4287.13 . AC=4;AF=1.00;AN=4;DP=119;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=59.69;QD=29.48;SOR=1.040 GT:AD:DP:GQ:PL 1/1:0,75:75:99:2980,226,0 1/1:0,43:43:99:1323,128,0 20 10011075 . C T 1345.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=5.36;DP=120;ExcessHet=3.0103;FS=1.800;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=16.22;ReadPosRankSum=-1.036e+00;SOR=0.968 GT:AD:DP:GQ:PL 0/1:44,39:83:99:1354,0,1333 0/0:34,0:34:99:0,99,932 20 10011309 . T C 4163.13 . AC=4;AF=1.00;AN=4;DP=132;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=60.00;QD=32.27;SOR=0.740 GT:AD:DP:GQ:PL 1/1:0,77:77:99:2721,231,0 1/1:0,52:52:99:1458,154,0 -20 10011517 . GA G 1456.09 . AC=3;AF=0.750;AN=4;BaseQRankSum=0.690;ClippingRankSum=0.00;DP=143;ExcessHet=3.0103;FS=3.769;MLEAC=3;MLEAF=0.750;MQ=60.01;MQRankSum=1.80;QD=14.14;ReadPosRankSum=0.315;SOR=0.385 GT:AD:DP:GQ:PL 0/1:37,28:73:99:528,0,874 1/1:1,37:38:88:942,88,0 +20 10011517 . GA G 1456.09 . AC=3;AF=0.750;AN=4;BaseQRankSum=0.690;ClippingRankSum=0.00;DP=143;ExcessHet=3.0103;FS=3.769;MLEAC=3;MLEAF=0.750;MQ=60.01;MQRankSum=1.80;QD=14.14;ReadPosRankSum=0.337;SOR=0.385 GT:AD:DP:GQ:PL 0/1:37,28:73:99:528,0,874 1/1:1,37:38:88:942,88,0 20 10011666 . C T 4114.13 . AC=4;AF=1.00;AN=4;DP=109;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=59.36;QD=30.56;SOR=0.892 GT:AD:DP:GQ:PL 1/1:0,73:73:99:2990,220,0 1/1:0,35:35:99:1140,105,0 20 10011939 . C T 3830.13 . AC=4;AF=1.00;AN=4;DP=108;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=57.91;QD=33.63;SOR=0.994 GT:AD:DP:GQ:PL 1/1:0,62:62:99:2542,187,0 1/1:0,42:42:99:1304,126,0 20 10012021 . CA C 3373.09 . AC=4;AF=1.00;AN=4;DP=120;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=58.31;QD=30.39;SOR=1.138 GT:AD:DP:GQ:PL 1/1:0,66:66:99:2014,198,0 1/1:0,45:45:99:1375,135,0 @@ -221,15 +221,15 @@ 20 10012521 . C T 91.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=1.52;DP=66;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=40.86;MQRankSum=-3.760e-01;QD=7.66;ReadPosRankSum=2.41;SOR=0.693 GT:AD:DP:GQ:PL 0/1:8,4:12:99:100,0,221 0/0:54,0:54:99:0,99,1485 20 10012570 . G GCA 2647.08 . AC=4;AF=1.00;AN=4;DP=60;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=51.24;QD=35.36;SOR=0.960 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,11:11:33:1|1:10012570_G_GCA:495,33,0:10012570 1/1:0,46:46:99:1|1:10012570_G_GCA:2168,147,0:10012570 20 10012572 . GT G 2647.08 . AC=4;AF=1.00;AN=4;DP=61;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=51.24;QD=34.30;SOR=1.034 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,11:11:33:1|1:10012570_G_GCA:495,33,0:10012570 1/1:0,48:48:99:1|1:10012570_G_GCA:2168,147,0:10012570 -20 10012631 . C CG 2441.09 . AC=3;AF=0.750;AN=4;BaseQRankSum=-1.030e+00;DP=65;ExcessHet=3.0103;FS=17.786;MLEAC=3;MLEAF=0.750;MQ=54.04;MQRankSum=-1.670e+00;QD=27.00;ReadPosRankSum=-1.813e+00;SOR=0.014 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:8,13:21:99:0|1:10012631_C_CG:522,0,297:10012631 1/1:0,43:43:99:1|1:10012631_C_CG:1933,132,0:10012631 -20 10012636 . G C 2474.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=2.71;DP=64;ExcessHet=3.0103;FS=17.784;MLEAC=3;MLEAF=0.750;MQ=54.13;MQRankSum=-1.513e+00;QD=30.82;ReadPosRankSum=-1.915e+00;SOR=0.015 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:8,14:22:99:0|1:10012631_C_CG:556,0,294:10012631 1/1:0,41:41:99:1|1:10012631_C_CG:1932,132,0:10012631 +20 10012631 . C CG 2441.09 . AC=3;AF=0.750;AN=4;BaseQRankSum=-1.030e+00;DP=65;ExcessHet=3.0103;FS=17.786;MLEAC=3;MLEAF=0.750;MQ=54.04;MQRankSum=-1.670e+00;QD=27.00;ReadPosRankSum=-1.777e+00;SOR=0.014 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:8,13:21:99:0|1:10012631_C_CG:522,0,297:10012631 1/1:0,43:43:99:1|1:10012631_C_CG:1933,132,0:10012631 +20 10012636 . G C 2474.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=2.71;DP=64;ExcessHet=3.0103;FS=17.784;MLEAC=3;MLEAF=0.750;MQ=54.13;MQRankSum=-1.513e+00;QD=30.82;ReadPosRankSum=-1.777e+00;SOR=0.015 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:8,14:22:99:0|1:10012631_C_CG:556,0,294:10012631 1/1:0,41:41:99:1|1:10012631_C_CG:1932,132,0:10012631 20 10012714 . G C 2654.13 . AC=4;AF=1.00;AN=4;DP=80;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=56.84;QD=33.60;SOR=1.358 GT:AD:DP:GQ:PL 1/1:0,35:35:99:1329,105,0 1/1:0,44:44:99:1341,132,0 20 10012751 . T C 2248.13 . AC=4;AF=1.00;AN=4;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=56.34;QD=31.22;SOR=0.807 GT:AD:DP:GQ:PL 1/1:0,30:30:89:966,89,0 1/1:0,42:42:99:1298,125,0 20 10012969 . G A 634.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=-3.050e-01;ClippingRankSum=0.00;DP=81;ExcessHet=3.0103;FS=1.174;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=14.77;ReadPosRankSum=0.498;SOR=0.941 GT:AD:DP:GQ:PL 0/0:38,0:38:99:0,99,1485 0/1:18,25:43:99:643,0,410 20 10012997 . C T 639.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=0.991;ClippingRankSum=0.00;DP=82;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=14.54;ReadPosRankSum=0.206;SOR=0.631 GT:AD:DP:GQ:PL 0/0:38,0:38:99:0,99,1485 0/1:19,25:44:99:648,0,454 20 10013119 . C T 1484.50 . AC=2;AF=0.500;AN=4;BaseQRankSum=2.72;ClippingRankSum=0.00;DP=94;ExcessHet=4.7712;FS=6.668;MLEAC=2;MLEAF=0.500;MQ=54.47;MQRankSum=0.131;QD=16.14;ReadPosRankSum=0.159;SOR=0.462 GT:AD:DP:GQ:PL 0/1:29,30:59:99:1040,0,936 0/1:15,18:33:99:454,0,354 20 10013574 . G A 1070.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=3.47;DP=108;ExcessHet=3.0103;FS=7.109;MLEAC=1;MLEAF=0.250;MQ=58.17;MQRankSum=-2.710e-01;QD=15.52;ReadPosRankSum=0.706;SOR=1.675 GT:AD:DP:GQ:PL 0/1:38,31:69:99:1079,0,1301 0/0:35,0:35:99:0,105,1074 -20 10014990 . C CAT 1998.46 . AC=2;AF=0.500;AN=4;BaseQRankSum=1.76;ClippingRankSum=0.00;DP=125;ExcessHet=4.7712;FS=0.727;MLEAC=2;MLEAF=0.500;MQ=60.71;MQRankSum=3.26;QD=18.00;ReadPosRankSum=0.144;SOR=0.583 GT:AD:DP:GQ:PL 0/1:38,39:77:99:1273,0,1250 0/1:12,22:34:99:735,0,363 +20 10014990 . C CAT 1998.46 . AC=2;AF=0.500;AN=4;BaseQRankSum=1.93;ClippingRankSum=0.00;DP=125;ExcessHet=4.7712;FS=0.727;MLEAC=2;MLEAF=0.500;MQ=60.71;MQRankSum=3.26;QD=18.00;ReadPosRankSum=0.144;SOR=0.583 GT:AD:DP:GQ:PL 0/1:38,39:77:99:1273,0,1250 0/1:12,22:34:99:735,0,363 20 10015547 . GGGCGGAGGCGGAGGCGGA G 184.88 . AC=1;AF=0.250;AN=4;BaseQRankSum=-6.510e-01;ClippingRankSum=0.00;DP=46;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=60.69;MQRankSum=-8.130e-01;QD=8.40;ReadPosRankSum=-4.540e-01;SOR=0.693 GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:15,0:15:24:.:.:0,24,360 0/1:16,6:22:99:0|1:10015547_GGGCGGAGGCGGAGGCGGA_G:193,0,619:10015547 20 10015558 . GA G 574.37 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.93;ClippingRankSum=0.00;DP=35;ExcessHet=3.0103;FS=1.441;MLEAC=1;MLEAF=0.500;MQ=60.74;MQRankSum=1.30;QD=20.51;ReadPosRankSum=1.42;SOR=0.446 GT:AD:DP:GQ:PGT:PID:PL:PS ./.:6,0:6:.:.:.:0,0,0 0/1:12,16:28:99:1|0:10015547_GGGCGGAGGCGGAGGCGGA_G:581,0,362:10015547 20 10015560 . GGCGGAGGCGGA G 571.37 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.91;ClippingRankSum=0.00;DP=36;ExcessHet=3.0103;FS=1.483;MLEAC=1;MLEAF=0.500;MQ=60.72;MQRankSum=1.35;QD=19.70;ReadPosRankSum=1.70;SOR=0.368 GT:AD:DP:GQ:PGT:PID:PL:PS ./.:6,0:6:.:.:.:0,0,0 0/1:13,16:29:99:1|0:10015547_GGGCGGAGGCGGAGGCGGA_G:578,0,383:10015547 @@ -247,7 +247,7 @@ 20 10023442 . G A 948.48 . AC=2;AF=0.500;AN=4;BaseQRankSum=0.223;ClippingRankSum=0.00;DP=79;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=29.64;ReadPosRankSum=-5.460e-01;SOR=0.379 GT:AD:DP:GQ:PL 0/0:46,0:46:99:0,105,1721 1/1:1,31:32:62:964,62,0 20 10023689 . G A 1872.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=2.14;DP=121;ExcessHet=3.0103;FS=0.877;MLEAC=1;MLEAF=0.250;MQ=59.77;MQRankSum=1.35;QD=23.41;ReadPosRankSum=1.16;SOR=0.549 GT:AD:DP:GQ:PL 0/1:29,51:80:99:1881,0,946 0/0:39,0:39:99:0,102,1217 20 10024107 . C T 1714.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=5.77;DP=141;ExcessHet=3.0103;FS=0.817;MLEAC=1;MLEAF=0.250;MQ=59.43;MQRankSum=-1.546e+00;QD=19.94;ReadPosRankSum=0.148;SOR=0.823 GT:AD:DP:GQ:PL 0/1:38,48:86:99:1723,0,1086 0/0:52,0:52:96:0,96,1322 -20 10024300 . CT C,CTTT 189.81 . AC=2,1;AF=0.500,0.250;AN=4;BaseQRankSum=2.38;ClippingRankSum=0.00;DP=83;ExcessHet=3.0103;FS=6.057;MLEAC=2,1;MLEAF=0.500,0.250;MQ=54.89;MQRankSum=0.00;QD=7.03;ReadPosRankSum=-1.290e+00;SOR=0.144 GT:AD:DP:GQ:PL 1/2:3,4,8:20:47:144,88,222,47,0,215 0/1:7,5,0:12:65:65,0,80,85,95,180 +20 10024300 . CT C,CTTT 189.81 . AC=2,1;AF=0.500,0.250;AN=4;BaseQRankSum=2.36;ClippingRankSum=0.00;DP=83;ExcessHet=3.0103;FS=6.057;MLEAC=2,1;MLEAF=0.500,0.250;MQ=54.89;MQRankSum=0.00;QD=7.03;ReadPosRankSum=-1.290e+00;SOR=0.144 GT:AD:DP:GQ:PL 1/2:3,4,8:20:47:144,88,222,47,0,215 0/1:7,5,0:12:65:65,0,80,85,95,180 20 10024388 . C T 342.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=-9.240e-01;ClippingRankSum=0.00;DP=67;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=12.70;ReadPosRankSum=0.267;SOR=0.527 GT:AD:DP:GQ:PL 0/0:39,0:39:99:0,105,1509 0/1:13,14:27:99:351,0,344 20 10024950 . G T 941.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=0.081;ClippingRankSum=0.00;DP=80;ExcessHet=3.0103;FS=7.110;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=22.97;ReadPosRankSum=0.132;SOR=1.770 GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:39,0:39:99:.:.:0,105,1509 0/1:17,24:41:99:0|1:10024950_G_T:950,0,913:10024950 20 10024951 . G T 941.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=1.14;ClippingRankSum=0.00;DP=80;ExcessHet=3.0103;FS=7.110;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=22.97;ReadPosRankSum=-8.000e-02;SOR=1.770 GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:39,0:39:99:.:.:0,105,1509 0/1:17,24:41:99:0|1:10024950_G_T:950,0,913:10024950 @@ -259,22 +259,22 @@ 20 10028302 . G T 625.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=1.50;ClippingRankSum=0.00;DP=104;ExcessHet=3.0103;FS=13.880;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=13.04;ReadPosRankSum=0.800;SOR=2.280 GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:55,0:55:99:.:.:0,120,1800 0/1:30,18:48:99:0|1:10028302_G_T:634,0,1476:10028302 20 10028316 . C T 612.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=0.911;ClippingRankSum=0.00;DP=98;ExcessHet=3.0103;FS=6.822;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=14.59;ReadPosRankSum=-7.190e-01;SOR=1.715 GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:55,0:55:99:.:.:0,120,1800 0/1:25,17:42:99:0|1:10028302_G_T:621,0,1379:10028302 20 10028725 . A G 458.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=-2.165e+00;ClippingRankSum=0.00;DP=91;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=12.75;ReadPosRankSum=0.184;SOR=0.892 GT:AD:DP:GQ:PL 0/0:55,0:55:99:0,120,1800 0/1:17,19:36:99:467,0,436 -20 10028867 . A ATG 1716.46 . AC=2;AF=0.500;AN=4;BaseQRankSum=-6.100e-02;ClippingRankSum=0.00;DP=129;ExcessHet=4.7712;FS=3.716;MLEAC=2;MLEAF=0.500;MQ=60.66;MQRankSum=2.71;QD=16.66;ReadPosRankSum=0.364;SOR=0.408 GT:AD:DP:GQ:PL 0/1:32,39:71:99:1142,0,918 0/1:13,19:32:99:584,0,361 +20 10028867 . A ATG 1716.46 . AC=2;AF=0.500;AN=4;BaseQRankSum=-6.100e-02;ClippingRankSum=0.00;DP=129;ExcessHet=4.7712;FS=3.716;MLEAC=2;MLEAF=0.500;MQ=60.66;MQRankSum=2.71;QD=16.66;ReadPosRankSum=0.630;SOR=0.408 GT:AD:DP:GQ:PL 0/1:32,39:71:99:1142,0,918 0/1:13,19:32:99:584,0,361 20 10029104 . G A 1331.48 . AC=2;AF=0.500;AN=4;DP=103;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;QD=30.96;SOR=0.739 GT:AD:DP:GQ:PL 0/0:60,0:60:99:0,120,1800 1/1:0,43:43:99:1347,128,0 20 10030188 . T A 1805.50 . AC=2;AF=0.500;AN=4;BaseQRankSum=1.36;ClippingRankSum=0.00;DP=114;ExcessHet=4.7712;FS=4.632;MLEAC=2;MLEAF=0.500;MQ=59.63;MQRankSum=0.00;QD=16.12;ReadPosRankSum=0.917;SOR=0.650 GT:AD:DP:GQ:PL 0/1:42,39:81:99:1401,0,1524 0/1:16,15:31:99:414,0,398 20 10030452 . G A 759.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=-1.085e+00;ClippingRankSum=0.00;DP=82;ExcessHet=3.0103;FS=2.968;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=19.00;ReadPosRankSum=-4.040e-01;SOR=0.339 GT:AD:DP:GQ:PL 0/0:41,0:41:99:0,103,1575 0/1:12,28:40:99:768,0,241 20 10030931 . C A 562.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=3.73;ClippingRankSum=0.00;DP=95;ExcessHet=3.0103;FS=6.218;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=10.62;ReadPosRankSum=-2.630e-01;SOR=1.773 GT:AD:DP:GQ:PL 0/0:42,0:42:99:0,114,1710 0/1:31,22:53:99:571,0,659 -20 10031254 . A AT 2074.46 . AC=2;AF=0.500;AN=4;BaseQRankSum=0.497;ClippingRankSum=0.00;DP=134;ExcessHet=4.7712;FS=8.195;MLEAC=2;MLEAF=0.500;MQ=60.02;MQRankSum=0.017;QD=16.33;ReadPosRankSum=0.495;SOR=0.286 GT:AD:DP:GQ:PL 0/1:38,47:85:99:1501,0,1159 0/1:23,19:42:99:583,0,725 +20 10031254 . A AT 2074.46 . AC=2;AF=0.500;AN=4;BaseQRankSum=0.497;ClippingRankSum=0.00;DP=134;ExcessHet=4.7712;FS=8.195;MLEAC=2;MLEAF=0.500;MQ=60.02;MQRankSum=0.017;QD=16.33;ReadPosRankSum=0.663;SOR=0.286 GT:AD:DP:GQ:PL 0/1:38,47:85:99:1501,0,1159 0/1:23,19:42:99:583,0,725 20 10031342 . G A 2473.50 . AC=2;AF=0.500;AN=4;BaseQRankSum=3.43;ClippingRankSum=0.00;DP=138;ExcessHet=4.7712;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=59.83;MQRankSum=0.00;QD=17.92;ReadPosRankSum=0.857;SOR=0.722 GT:AD:DP:GQ:PL 0/1:41,52:93:99:1863,0,1375 0/1:22,23:45:99:620,0,534 20 10031798 . G A 5365.13 . AC=4;AF=1.00;AN=4;DP=141;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=59.70;QD=29.27;SOR=0.783 GT:AD:DP:GQ:PL 1/1:0,104:104:99:4325,313,0 1/1:0,34:34:99:1056,102,0 20 10031827 . C T 2340.50 . AC=2;AF=0.500;AN=4;BaseQRankSum=3.55;ClippingRankSum=0.00;DP=147;ExcessHet=4.7712;FS=5.086;MLEAC=2;MLEAF=0.500;MQ=59.87;MQRankSum=0.00;QD=16.84;ReadPosRankSum=-6.750e-01;SOR=0.563 GT:AD:DP:GQ:PL 0/1:52,56:108:99:2033,0,1798 0/1:18,13:31:99:317,0,456 20 10032094 . G A 1916.50 . AC=2;AF=0.500;AN=4;BaseQRankSum=5.49;ClippingRankSum=0.00;DP=135;ExcessHet=4.7712;FS=9.336;MLEAC=2;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=14.63;ReadPosRankSum=0.092;SOR=0.468 GT:AD:DP:GQ:PL 0/1:47,36:83:99:1249,0,1497 0/1:21,27:48:99:677,0,458 20 10032413 . T G 1453.50 . AC=2;AF=0.500;AN=4;BaseQRankSum=-2.742e+00;ClippingRankSum=0.00;DP=116;ExcessHet=4.7712;FS=8.785;MLEAC=2;MLEAF=0.500;MQ=59.68;MQRankSum=0.00;QD=12.64;ReadPosRankSum=-1.110e-01;SOR=1.453 GT:AD:DP:GQ:PL 0/1:35,31:66:99:898,0,1277 0/1:23,26:49:99:565,0,554 20 10032882 . A T 2523.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=-1.280e-01;ClippingRankSum=0.00;DP=120;ExcessHet=3.0103;FS=9.634;MLEAC=3;MLEAF=0.750;MQ=59.81;MQRankSum=0.00;QD=21.57;ReadPosRankSum=0.626;SOR=0.225 GT:AD:DP:GQ:PL 0/1:39,36:75:99:1231,0,1406 1/1:1,41:42:93:1306,93,0 -20 10032972 . C CAT 3090.09 . AC=3;AF=0.750;AN=4;BaseQRankSum=-3.540e-01;DP=111;ExcessHet=3.0103;FS=2.753;MLEAC=3;MLEAF=0.750;MQ=59.89;MQRankSum=-1.017e+00;QD=29.15;ReadPosRankSum=-1.232e+00;SOR=0.921 GT:AD:DP:GQ:PL 0/1:33,30:63:99:1160,0,1296 1/1:0,43:43:99:1944,132,0 +20 10032972 . C CAT 3090.09 . AC=3;AF=0.750;AN=4;BaseQRankSum=-3.540e-01;DP=111;ExcessHet=3.0103;FS=2.753;MLEAC=3;MLEAF=0.750;MQ=59.89;MQRankSum=-1.017e+00;QD=29.15;ReadPosRankSum=-7.230e-01;SOR=0.921 GT:AD:DP:GQ:PL 0/1:33,30:63:99:1160,0,1296 1/1:0,43:43:99:1944,132,0 20 10034306 . T C 1287.50 . AC=2;AF=0.500;AN=4;BaseQRankSum=-2.200e-01;ClippingRankSum=0.00;DP=111;ExcessHet=4.7712;FS=2.552;MLEAC=2;MLEAF=0.500;MQ=59.62;MQRankSum=1.15;QD=12.26;ReadPosRankSum=0.885;SOR=1.023 GT:AD:DP:GQ:PL 0/1:46,29:75:99:811,0,1593 0/1:11,19:30:99:486,0,219 20 10034425 . C T 551.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=1.76;ClippingRankSum=0.00;DP=87;ExcessHet=3.0103;FS=5.760;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=17.25;ReadPosRankSum=-8.950e-01;SOR=0.499 GT:AD:DP:GQ:PL 0/0:55,0:55:99:0,120,1800 0/1:10,22:32:99:560,0,175 -20 10036930 . CGATAGCCCTAGCCCTAGATA C 1555.46 . AC=2;AF=0.500;AN=4;BaseQRankSum=0.200;ClippingRankSum=0.00;DP=134;ExcessHet=4.7712;FS=10.062;MLEAC=2;MLEAF=0.500;MQ=56.00;MQRankSum=0.00;QD=15.40;ReadPosRankSum=0.460;SOR=0.213 GT:AD:DP:GQ:PL 0/1:39,29:68:99:1078,0,1500 0/1:20,13:33:99:487,0,3108 +20 10036930 . CGATAGCCCTAGCCCTAGATA C 1555.46 . AC=2;AF=0.500;AN=4;BaseQRankSum=0.720;ClippingRankSum=0.00;DP=134;ExcessHet=4.7712;FS=10.062;MLEAC=2;MLEAF=0.500;MQ=56.00;MQRankSum=0.00;QD=15.40;ReadPosRankSum=0.460;SOR=0.213 GT:AD:DP:GQ:PL 0/1:39,29:68:99:1078,0,1500 0/1:20,13:33:99:487,0,3108 20 10037037 . C T 1456.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=3.50;DP=123;ExcessHet=3.0103;FS=1.943;MLEAC=1;MLEAF=0.250;MQ=60.08;MQRankSum=-1.193e+00;QD=17.99;ReadPosRankSum=-1.609e+00;SOR=0.495 GT:AD:DP:GQ:PL 0/1:39,42:81:99:1465,0,1124 0/0:35,0:35:99:0,102,1530 20 10037110 . T TGATA 4492.09 . AC=4;AF=1.00;AN=4;DP=121;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=56.43;QD=35.92;SOR=0.888 GT:AD:DP:GQ:PL 1/1:0,63:63:99:2817,189,0 1/1:0,36:36:99:1691,114,0 20 10037144 . TGATA T,TGATAGATA,TGATAGATAGATA 3046.05 . AC=1,1,2;AF=0.250,0.250,0.500;AN=4;DP=121;ExcessHet=3.0103;FS=0.000;MLEAC=1,1,2;MLEAF=0.250,0.250,0.500;MQ=55.39;QD=29.63;SOR=1.073 GT:AD:DP:GQ:PL 3/3:0,0,0,43:43:99:1859,1862,1866,1862,1866,1866,126,129,129,0 1/2:0,18,11,0:29:99:1218,461,407,756,0,724,1218,462,757,1218 @@ -328,7 +328,7 @@ 20 10062531 . A G 304.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=-2.520e-01;ClippingRankSum=0.00;DP=90;ExcessHet=3.0103;FS=2.923;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=6.93;ReadPosRankSum=0.447;SOR=1.387 GT:AD:DP:GQ:PL 0/0:46,0:46:99:0,105,1575 0/1:29,15:44:99:313,0,725 20 10062696 . T C 659.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=0.953;ClippingRankSum=0.00;DP=93;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=14.66;ReadPosRankSum=-1.579e+00;SOR=0.638 GT:AD:DP:GQ:PL 0/0:46,0:46:99:0,105,1575 0/1:18,27:45:99:668,0,404 20 10062922 . T C 901.48 . AC=2;AF=0.500;AN=4;DP=77;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;QD=29.08;SOR=1.044 GT:AD:DP:GQ:PL 0/0:46,0:46:99:0,105,1575 1/1:0,31:31:92:917,92,0 -20 10062935 . CA C,CAA 249.65 . AC=1,1;AF=0.250,0.250;AN=4;BaseQRankSum=1.23;ClippingRankSum=0.00;DP=122;ExcessHet=4.7712;FS=1.172;MLEAC=1,1;MLEAF=0.250,0.250;MQ=56.12;MQRankSum=1.71;QD=5.94;ReadPosRankSum=-8.900e-02;SOR=1.071 GT:AD:DP:GQ:PL 0/2:5,4,10:24:6:127,104,490,0,6,109 0/1:13,10,0:23:99:138,0,197,177,227,404 +20 10062935 . CA C,CAA 249.65 . AC=1,1;AF=0.250,0.250;AN=4;BaseQRankSum=1.24;ClippingRankSum=0.00;DP=122;ExcessHet=4.7712;FS=1.172;MLEAC=1,1;MLEAF=0.250,0.250;MQ=56.12;MQRankSum=1.71;QD=5.94;ReadPosRankSum=-8.900e-02;SOR=1.071 GT:AD:DP:GQ:PL 0/2:5,4,10:24:6:127,104,490,0,6,109 0/1:13,10,0:23:99:138,0,197,177,227,404 20 10064261 . T G 563.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=0.993;ClippingRankSum=0.00;DP=90;ExcessHet=3.0103;FS=1.174;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=12.53;ReadPosRankSum=-1.260e+00;SOR=0.960 GT:AD:DP:GQ:PL 0/0:42,0:42:99:0,105,1575 0/1:22,23:45:99:572,0,499 20 10064306 . T A 1495.48 . AC=2;AF=0.500;AN=4;DP=90;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;QD=31.16;SOR=0.963 GT:AD:DP:GQ:PL 0/0:42,0:42:99:0,105,1575 1/1:0,48:48:99:1511,144,0 20 10064529 . A G 1033.48 . AC=2;AF=0.500;AN=4;DP=83;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;QD=26.50;SOR=0.968 GT:AD:DP:GQ:PL 0/0:42,0:42:99:0,105,1575 1/1:0,39:39:99:1049,115,0 @@ -336,7 +336,7 @@ 20 10065517 . T C 264.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=0.690;ClippingRankSum=0.00;DP=73;ExcessHet=3.0103;FS=3.325;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=8.83;ReadPosRankSum=-1.828e+00;SOR=1.445 GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:42,0:42:99:.:.:0,105,1575 0/1:18,12:30:99:0|1:10065517_T_C:273,0,706:10065517 20 10065525 . G A 472.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=0.814;ClippingRankSum=0.00;DP=70;ExcessHet=3.0103;FS=1.583;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=17.52;ReadPosRankSum=0.551;SOR=0.557 GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:42,0:42:99:.:.:0,105,1575 0/1:10,17:27:99:1|0:10065517_T_C:481,0,391:10065517 20 10065779 . G GTT,GTTT 671.24 . AC=1,1;AF=0.250,0.250;AN=4;DP=78;ExcessHet=0.7918;FS=0.000;MLEAC=1,1;MLEAF=0.250,0.250;MQ=59.32;QD=29.41;SOR=0.836 GT:AD:DP:GQ:PL 0/0:52,0,0:52:0:0,0,1441,0,1441,1441 1/2:0,7,6:13:50:687,131,50,154,0,87 -20 10067049 . TAAAAAAAA TA,TAAAAA,T 1199.06 . AC=2,1,1;AF=0.500,0.250,0.250;AN=4;BaseQRankSum=0.177;ClippingRankSum=0.00;DP=103;ExcessHet=3.0103;FS=2.372;MLEAC=2,1,1;MLEAF=0.500,0.250,0.250;MQ=56.14;MQRankSum=0.00;QD=33.31;ReadPosRankSum=-1.322e+00;SOR=0.751 GT:AD:DP:GQ:PL 1/3:2,9,0,7:22:99:656,137,106,446,171,628,167,0,395,339 1/2:1,8,9,0:18:99:571,324,502,248,0,237,593,443,276,696 +20 10067049 . TAAAAAAAA TA,TAAAAA,T 1199.06 . AC=2,1,1;AF=0.500,0.250,0.250;AN=4;BaseQRankSum=-8.600e-02;ClippingRankSum=0.00;DP=103;ExcessHet=3.0103;FS=2.372;MLEAC=2,1,1;MLEAF=0.500,0.250,0.250;MQ=56.14;MQRankSum=0.00;QD=33.31;ReadPosRankSum=-1.322e+00;SOR=0.751 GT:AD:DP:GQ:PL 1/3:2,9,0,7:22:99:656,137,106,446,171,628,167,0,395,339 1/2:1,8,9,0:18:99:571,324,502,248,0,237,593,443,276,696 20 10067090 . C A 2986.13 . AC=4;AF=1.00;AN=4;DP=86;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=56.53;QD=31.11;SOR=0.716 GT:AD:DP:GQ:PL 1/1:0,55:55:99:2033,164,0 1/1:0,30:30:90:969,90,0 20 10067264 . G A 3256.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=0.369;ClippingRankSum=0.00;DP=106;ExcessHet=3.0103;FS=3.400;MLEAC=3;MLEAF=0.750;MQ=59.56;MQRankSum=0.00;QD=30.72;ReadPosRankSum=-4.930e-01;SOR=0.518 GT:AD:DP:GQ:PL 1/1:0,73:73:99:2951,219,0 0/1:20,13:33:99:319,0,534 20 10067722 . A C 3344.13 . AC=4;AF=1.00;AN=4;DP=97;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=60.00;QD=34.66;SOR=0.782 GT:AD:DP:GQ:PL 1/1:0,54:54:99:2175,163,0 1/1:0,38:38:99:1185,114,0 @@ -398,21 +398,21 @@ 20 10087394 . T G 1708.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=-2.340e+00;DP=123;ExcessHet=3.0103;FS=4.225;MLEAC=1;MLEAF=0.250;MQ=59.46;MQRankSum=1.21;QD=20.34;ReadPosRankSum=0.885;SOR=0.436 GT:AD:DP:GQ:PL 0/1:35,49:84:99:1717,0,1186 0/0:38,0:38:99:0,99,1150 20 10087754 . T G 1402.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=0.239;DP=118;ExcessHet=3.0103;FS=0.851;MLEAC=1;MLEAF=0.250;MQ=60.60;MQRankSum=2.17;QD=17.76;ReadPosRankSum=-3.780e-01;SOR=0.596 GT:AD:DP:GQ:PL 0/1:37,42:79:99:1411,0,1236 0/0:31,0:31:90:0,90,1350 20 10087804 . C T 2516.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=1.94;DP=136;ExcessHet=3.0103;FS=1.477;MLEAC=3;MLEAF=0.750;MQ=60.53;MQRankSum=2.62;QD=19.06;ReadPosRankSum=0.341;SOR=0.554 GT:AD:DP:GQ:PL 0/1:50,50:100:99:1648,0,1511 1/1:0,32:32:94:882,94,0 -20 10087820 . C CAGAG,CAG 1869.80 . AC=2,1;AF=0.500,0.250;AN=4;BaseQRankSum=-1.974e+00;DP=136;ExcessHet=3.0103;FS=2.946;MLEAC=2,1;MLEAF=0.500,0.250;MQ=60.86;MQRankSum=0.422;QD=22.00;ReadPosRankSum=-3.570e-01;SOR=1.014 GT:AD:DP:GQ:PL 0/2:35,0,18:53:99:464,657,2172,0,1237,1170 1/1:0,32,0:32:96:1428,96,0,1428,96,1428 +20 10087820 . C CAGAG,CAG 1869.80 . AC=2,1;AF=0.500,0.250;AN=4;BaseQRankSum=-1.974e+00;DP=136;ExcessHet=3.0103;FS=2.946;MLEAC=2,1;MLEAF=0.500,0.250;MQ=60.86;MQRankSum=0.422;QD=22.00;ReadPosRankSum=-1.900e-02;SOR=1.014 GT:AD:DP:GQ:PL 0/2:35,0,18:53:99:464,657,2172,0,1237,1170 1/1:0,32,0:32:96:1428,96,0,1428,96,1428 20 10088063 . C T 2739.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=3.41;DP=141;ExcessHet=3.0103;FS=4.363;MLEAC=3;MLEAF=0.750;MQ=59.57;MQRankSum=0.515;QD=20.29;ReadPosRankSum=0.285;SOR=1.138 GT:AD:DP:GQ:PL 0/1:49,44:93:99:1446,0,1403 1/1:0,42:42:99:1307,125,0 20 10088699 . C T 2196.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=3.80;DP=117;ExcessHet=3.0103;FS=11.595;MLEAC=3;MLEAF=0.750;MQ=58.15;MQRankSum=-3.140e+00;QD=20.52;ReadPosRankSum=-1.456e+00;SOR=1.041 GT:AD:DP:GQ:PL 0/1:36,26:62:99:805,0,1088 1/1:0,45:45:99:1405,135,0 -20 10088730 . G A 2812.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=-5.800e-02;DP=99;ExcessHet=3.0103;FS=11.087;MLEAC=3;MLEAF=0.750;MQ=55.92;MQRankSum=-5.213e+00;QD=28.99;ReadPosRankSum=0.581;SOR=0.816 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:30,26:56:99:0|1:10088730_G_A:1001,0,1152:10088730 1/1:0,41:41:99:1|1:10088730_G_A:1825,123,0:10088730 -20 10088736 . A C 3095.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=0.016;DP=104;ExcessHet=3.0103;FS=8.654;MLEAC=3;MLEAF=0.750;MQ=55.88;MQRankSum=-5.157e+00;QD=30.05;ReadPosRankSum=0.573;SOR=0.676 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:31,29:60:99:0|1:10088730_G_A:1110,0,1194:10088730 1/1:0,43:43:99:1|1:10088730_G_A:1999,138,0:10088730 +20 10088730 . G A 2812.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=0.224;DP=99;ExcessHet=3.0103;FS=11.087;MLEAC=3;MLEAF=0.750;MQ=55.92;MQRankSum=-5.213e+00;QD=28.99;ReadPosRankSum=0.581;SOR=0.816 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:30,26:56:99:0|1:10088730_G_A:1001,0,1152:10088730 1/1:0,41:41:99:1|1:10088730_G_A:1825,123,0:10088730 +20 10088736 . A C 3095.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=0.282;DP=104;ExcessHet=3.0103;FS=8.654;MLEAC=3;MLEAF=0.750;MQ=55.88;MQRankSum=-5.157e+00;QD=30.05;ReadPosRankSum=0.573;SOR=0.676 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:31,29:60:99:0|1:10088730_G_A:1110,0,1194:10088730 1/1:0,43:43:99:1|1:10088730_G_A:1999,138,0:10088730 20 10088747 . A G 3164.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=-3.877e+00;DP=104;ExcessHet=3.0103;FS=9.358;MLEAC=3;MLEAF=0.750;MQ=55.82;MQRankSum=-4.881e+00;QD=30.72;ReadPosRankSum=9.000e-03;SOR=0.775 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:26,30:56:99:0|1:10088730_G_A:1140,0,995:10088730 1/1:0,47:47:99:1|1:10088730_G_A:2038,144,0:10088730 20 10088799 . G A 2353.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=5.50;DP=95;ExcessHet=3.0103;FS=8.265;MLEAC=3;MLEAF=0.750;MQ=56.19;MQRankSum=-2.498e+00;QD=25.30;ReadPosRankSum=1.08;SOR=0.604 GT:AD:DP:GQ:PL 0/1:22,31:53:99:1047,0,617 1/1:0,40:40:99:1320,120,0 20 10088895 . C T 1482.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=2.33;DP=76;ExcessHet=3.0103;FS=2.120;MLEAC=3;MLEAF=0.750;MQ=58.53;MQRankSum=0.260;QD=20.88;ReadPosRankSum=1.24;SOR=0.684 GT:AD:DP:GQ:PL 0/1:22,18:40:99:564,0,651 1/1:0,31:31:92:932,92,0 -20 10088968 . C CAAA 3064.09 . AC=3;AF=0.750;AN=4;BaseQRankSum=0.117;DP=112;ExcessHet=3.0103;FS=1.741;MLEAC=3;MLEAF=0.750;MQ=54.37;MQRankSum=-5.320e+00;QD=31.92;ReadPosRankSum=1.80;SOR=0.898 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:32,34:66:99:0|1:10088968_C_CAAA:1297,0,1230:10088968 1/1:0,30:30:99:1|1:10088968_C_CAAA:1781,128,0:10088968 -20 10088980 . T C 3205.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=-1.772e+00;DP=121;ExcessHet=3.0103;FS=0.730;MLEAC=3;MLEAF=0.750;MQ=54.03;MQRankSum=-5.207e+00;QD=26.93;ReadPosRankSum=1.12;SOR=0.753 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:39,36:75:99:0|1:10088968_C_CAAA:1360,0,1491:10088968 1/1:0,44:44:99:1|1:10088968_C_CAAA:1859,135,0:10088968 -20 10088985 . T C 3203.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=-5.250e-01;DP=123;ExcessHet=3.0103;FS=2.478;MLEAC=3;MLEAF=0.750;MQ=53.99;MQRankSum=-5.440e+00;QD=26.92;ReadPosRankSum=1.16;SOR=0.816 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:42,34:76:99:0|1:10088968_C_CAAA:1291,0,1593:10088968 1/1:0,43:43:99:.:.:1926,132,0 +20 10088968 . C CAAA 3064.09 . AC=3;AF=0.750;AN=4;BaseQRankSum=0.337;DP=112;ExcessHet=3.0103;FS=1.741;MLEAC=3;MLEAF=0.750;MQ=54.37;MQRankSum=-5.320e+00;QD=31.92;ReadPosRankSum=0.205;SOR=0.898 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:32,34:66:99:0|1:10088968_C_CAAA:1297,0,1230:10088968 1/1:0,30:30:99:1|1:10088968_C_CAAA:1781,128,0:10088968 +20 10088980 . T C 3205.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=-1.845e+00;DP=121;ExcessHet=3.0103;FS=0.730;MLEAC=3;MLEAF=0.750;MQ=54.03;MQRankSum=-5.207e+00;QD=26.93;ReadPosRankSum=1.48;SOR=0.753 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:39,36:75:99:0|1:10088968_C_CAAA:1360,0,1491:10088968 1/1:0,44:44:99:1|1:10088968_C_CAAA:1859,135,0:10088968 +20 10088985 . T C 3203.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=-5.250e-01;DP=123;ExcessHet=3.0103;FS=2.478;MLEAC=3;MLEAF=0.750;MQ=53.99;MQRankSum=-5.440e+00;QD=26.92;ReadPosRankSum=1.43;SOR=0.816 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:42,34:76:99:0|1:10088968_C_CAAA:1291,0,1593:10088968 1/1:0,43:43:99:.:.:1926,132,0 20 10089149 . A G 1121.48 . AC=2;AF=0.500;AN=4;BaseQRankSum=1.75;ClippingRankSum=0.00;DP=114;ExcessHet=0.7918;FS=3.979;MLEAC=2;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=28.04;ReadPosRankSum=-4.740e-01;SOR=0.990 GT:AD:DP:GQ:PL 0/0:74,0:74:99:0,120,1800 1/1:1,39:40:99:1137,108,0 20 10089441 . A G 1199.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=-4.885e+00;DP=117;ExcessHet=3.0103;FS=6.071;MLEAC=1;MLEAF=0.250;MQ=59.71;MQRankSum=-9.480e-01;QD=15.79;ReadPosRankSum=-1.560e-01;SOR=1.363 GT:AD:DP:GQ:PL 0/1:37,39:76:99:1208,0,1313 0/0:38,0:38:99:0,102,1104 20 10089525 . C T 2915.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=5.86;DP=126;ExcessHet=3.0103;FS=7.522;MLEAC=3;MLEAF=0.750;MQ=59.67;MQRankSum=1.53;QD=23.51;ReadPosRankSum=0.862;SOR=0.754 GT:AD:DP:GQ:PL 0/1:38,43:81:99:1577,0,1088 1/1:0,43:43:99:1352,128,0 -20 10090289 . CAA C,CA 1399.80 . AC=2,1;AF=0.500,0.250;AN=4;BaseQRankSum=0.285;ClippingRankSum=0.00;DP=126;ExcessHet=3.0103;FS=1.112;MLEAC=2,1;MLEAF=0.500,0.250;MQ=59.98;MQRankSum=1.47;QD=20.59;ReadPosRankSum=0.455;SOR=1.036 GT:AD:DP:GQ:PL 0/2:15,3,20:38:99:413,386,1030,0,295,240 1/1:1,29,0:30:66:1009,66,0,1012,88,1033 +20 10090289 . CAA C,CA 1399.80 . AC=2,1;AF=0.500,0.250;AN=4;BaseQRankSum=0.252;ClippingRankSum=0.00;DP=126;ExcessHet=3.0103;FS=1.112;MLEAC=2,1;MLEAF=0.500,0.250;MQ=59.98;MQRankSum=1.47;QD=20.59;ReadPosRankSum=0.455;SOR=1.036 GT:AD:DP:GQ:PL 0/2:15,3,20:38:99:413,386,1030,0,295,240 1/1:1,29,0:30:66:1009,66,0,1012,88,1033 20 10090764 . A G 2042.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=-2.659e+00;DP=113;ExcessHet=3.0103;FS=9.917;MLEAC=3;MLEAF=0.750;MQ=60.00;MQRankSum=0.00;QD=18.91;ReadPosRankSum=1.21;SOR=0.441 GT:AD:DP:GQ:PL 0/1:34,29:63:99:869,0,1207 1/1:0,45:45:99:1187,133,0 20 10090886 . G A 1451.48 . AC=2;AF=0.500;AN=4;BaseQRankSum=1.03;ClippingRankSum=0.00;DP=121;ExcessHet=0.7918;FS=1.777;MLEAC=2;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=25.92;ReadPosRankSum=1.80;SOR=0.597 GT:AD:DP:GQ:PL 0/0:65,0:65:99:0,120,1800 1/1:5,51:56:48:1467,48,0 20 10090970 . T C 1277.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=-4.840e-01;DP=114;ExcessHet=3.0103;FS=0.927;MLEAC=1;MLEAF=0.250;MQ=59.47;MQRankSum=1.51;QD=18.52;ReadPosRankSum=-7.200e-02;SOR=0.518 GT:AD:DP:GQ:PL 0/1:33,36:69:99:1286,0,1092 0/0:44,0:44:99:0,113,1448 @@ -426,21 +426,21 @@ 20 10094251 . T A 1290.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=0.251;DP=104;ExcessHet=3.0103;FS=11.483;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=20.82;ReadPosRankSum=1.81;SOR=1.211 GT:AD:DP:GQ:PL 0/1:26,36:62:99:1299,0,781 0/0:37,0:37:99:0,100,1165 20 10094582 . A G 943.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=-1.388e+00;DP=110;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=59.43;MQRankSum=1.27;QD=13.68;ReadPosRankSum=-1.800e-02;SOR=0.772 GT:AD:DP:GQ:PL 0/1:39,30:69:99:952,0,1350 0/0:37,0:37:99:0,99,1130 20 10094774 . C T 1056.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=-7.840e-01;DP=130;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=59.43;MQRankSum=0.962;QD=14.09;ReadPosRankSum=0.197;SOR=0.690 GT:AD:DP:GQ:PL 0/1:40,35:75:99:1065,0,1282 0/0:49,0:49:97:0,97,1393 -20 10095432 . GTGATGATGA GTGA,G 2077.80 . AC=2,1;AF=0.500,0.250;AN=4;BaseQRankSum=1.11;DP=113;ExcessHet=3.0103;FS=3.304;MLEAC=2,1;MLEAF=0.500,0.250;MQ=56.23;MQRankSum=-4.378e+00;QD=27.34;ReadPosRankSum=0.396;SOR=0.350 GT:AD:DP:GQ:PL 0/2:26,0,23:49:99:883,961,2014,0,1053,978 1/1:0,27,0:27:82:1217,82,0,1217,82,1217 +20 10095432 . GTGATGATGA GTGA,G 2077.80 . AC=2,1;AF=0.500,0.250;AN=4;BaseQRankSum=1.06;DP=113;ExcessHet=3.0103;FS=3.304;MLEAC=2,1;MLEAF=0.500,0.250;MQ=56.23;MQRankSum=-4.378e+00;QD=27.34;ReadPosRankSum=0.396;SOR=0.350 GT:AD:DP:GQ:PL 0/2:26,0,23:49:99:883,961,2014,0,1053,978 1/1:0,27,0:27:82:1217,82,0,1217,82,1217 20 10095741 . A G 1095.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=-5.340e-01;DP=106;ExcessHet=3.0103;FS=4.721;MLEAC=1;MLEAF=0.250;MQ=57.39;MQRankSum=-2.313e+00;QD=15.66;ReadPosRankSum=-5.000e-01;SOR=0.515 GT:AD:DP:GQ:PL 0/1:36,34:70:99:1104,0,1233 0/0:34,0:34:67:0,67,972 20 10096293 . C T 1375.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=4.66;DP=119;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=58.64;MQRankSum=1.40;QD=18.35;ReadPosRankSum=-1.135e+00;SOR=0.638 GT:AD:DP:GQ:PL 0/1:37,38:75:99:1384,0,1258 0/0:40,0:40:99:0,108,1181 20 10096357 . A G 1150.48 . AC=2;AF=0.500;AN=4;BaseQRankSum=0.964;ClippingRankSum=0.00;DP=101;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=27.39;ReadPosRankSum=1.55;SOR=0.460 GT:AD:DP:GQ:PL 0/0:57,0:57:99:0,120,1800 1/1:1,41:42:94:1166,94,0 20 10096596 . C T 1582.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=2.73;DP=134;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=58.82;MQRankSum=0.612;QD=18.19;ReadPosRankSum=-1.700e-01;SOR=0.640 GT:AD:DP:GQ:PL 0/1:40,47:87:99:1591,0,1273 0/0:43,0:43:99:0,99,1273 20 10096733 . C T 1731.48 . AC=2;AF=0.500;AN=4;BaseQRankSum=1.16;ClippingRankSum=0.00;DP=134;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=30.38;ReadPosRankSum=-9.330e-01;SOR=0.252 GT:AD:DP:GQ:PL 0/0:75,0:75:99:0,120,1800 1/1:1,56:57:99:1747,143,0 20 10096768 . A C 3482.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=-2.764e+00;DP=153;ExcessHet=3.0103;FS=6.852;MLEAC=3;MLEAF=0.750;MQ=59.62;MQRankSum=-1.609e+00;QD=23.69;ReadPosRankSum=0.613;SOR=0.522 GT:AD:DP:GQ:PL 0/1:42,49:91:99:1711,0,1452 1/1:0,56:56:99:1785,168,0 -20 10096899 . G T 3465.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=2.49;DP=125;ExcessHet=3.0103;FS=13.179;MLEAC=3;MLEAF=0.750;MQ=59.60;MQRankSum=-1.677e+00;QD=27.94;ReadPosRankSum=0.422;SOR=1.754 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:40,43:83:99:0|1:10096899_G_T:1644,0,1519:10096899 1/1:0,41:41:99:1|1:10096899_G_T:1835,123,0:10096899 +20 10096899 . G T 3465.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=2.76;DP=125;ExcessHet=3.0103;FS=13.179;MLEAC=3;MLEAF=0.750;MQ=59.60;MQRankSum=-1.677e+00;QD=27.94;ReadPosRankSum=0.422;SOR=1.754 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:40,43:83:99:0|1:10096899_G_T:1644,0,1519:10096899 1/1:0,41:41:99:1|1:10096899_G_T:1835,123,0:10096899 20 10096905 . TA T 3459.09 . AC=3;AF=0.750;AN=4;BaseQRankSum=-7.550e-01;DP=126;ExcessHet=3.0103;FS=14.591;MLEAC=3;MLEAF=0.750;MQ=59.61;MQRankSum=-1.739e+00;QD=27.45;ReadPosRankSum=0.461;SOR=1.710 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:43,43:86:99:0|1:10096899_G_T:1638,0,1623:10096899 1/1:0,40:40:99:1|1:10096899_G_T:1835,123,0:10096899 20 10096925 . T C 355.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=-4.687e+00;ClippingRankSum=0.00;DP=120;ExcessHet=3.0103;FS=1.342;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=9.37;ReadPosRankSum=-6.140e-01;SOR=0.399 GT:AD:DP:GQ:PL 0/0:82,0:82:99:0,120,1800 0/1:20,18:38:99:364,0,556 -20 10096933 . G C 3258.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=-1.724e+00;DP=127;ExcessHet=3.0103;FS=25.243;MLEAC=3;MLEAF=0.750;MQ=59.52;MQRankSum=-1.840e+00;QD=25.65;ReadPosRankSum=0.334;SOR=1.416 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:47,42:89:99:0|1:10096933_G_C:1542,0,1763:10096933 1/1:0,38:38:99:1|1:10096933_G_C:1730,117,0:10096933 -20 10096958 . G A 3680.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=2.70;DP=140;ExcessHet=3.0103;FS=25.191;MLEAC=3;MLEAF=0.750;MQ=59.57;MQRankSum=-1.664e+00;QD=26.48;ReadPosRankSum=-1.824e+00;SOR=1.429 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:44,48:92:99:0|1:10096933_G_C:1797,0,1622:10096933 1/1:0,47:47:99:1|1:10096933_G_C:1897,141,0:10096933 +20 10096933 . G C 3258.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=-1.914e+00;DP=127;ExcessHet=3.0103;FS=25.243;MLEAC=3;MLEAF=0.750;MQ=59.52;MQRankSum=-1.840e+00;QD=25.65;ReadPosRankSum=0.383;SOR=1.416 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:47,42:89:99:0|1:10096933_G_C:1542,0,1763:10096933 1/1:0,38:38:99:1|1:10096933_G_C:1730,117,0:10096933 +20 10096958 . G A 3680.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=2.70;DP=140;ExcessHet=3.0103;FS=25.191;MLEAC=3;MLEAF=0.750;MQ=59.57;MQRankSum=-1.664e+00;QD=26.48;ReadPosRankSum=-1.593e+00;SOR=1.429 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:44,48:92:99:0|1:10096933_G_C:1797,0,1622:10096933 1/1:0,47:47:99:1|1:10096933_G_C:1897,141,0:10096933 20 10097075 . T G 2516.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=1.82;ClippingRankSum=0.00;DP=130;ExcessHet=3.0103;FS=5.781;MLEAC=3;MLEAF=0.750;MQ=58.63;MQRankSum=0.00;QD=19.97;ReadPosRankSum=1.53;SOR=0.480 GT:AD:DP:GQ:PL 0/1:44,48:92:99:1474,0,1482 1/1:1,33:34:92:1056,92,0 -20 10097101 . C CTTTT,CTTT 2098.80 . AC=2,1;AF=0.500,0.250;AN=4;BaseQRankSum=-9.530e-01;DP=109;ExcessHet=3.0103;FS=4.307;MLEAC=2,1;MLEAF=0.500,0.250;MQ=58.72;MQRankSum=-2.210e+00;QD=24.69;ReadPosRankSum=2.37;SOR=0.337 GT:AD:DP:GQ:PL 0/2:34,3,26:63:99:1113,585,1857,0,1269,1263 1/1:0,22,0:22:71:1008,71,0,1008,71,1009 -20 10097436 . CTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT C 1088.88 . AC=1;AF=0.250;AN=4;BaseQRankSum=1.82;DP=120;ExcessHet=3.0103;FS=1.851;MLEAC=1;MLEAF=0.250;MQ=54.34;MQRankSum=-6.464e+00;QD=12.23;ReadPosRankSum=-3.097e+00;SOR=0.948 GT:AD:DP:GQ:PL 0/1:57,32:89:99:1097,0,2238 0/0:30,0:30:66:0,66,990 +20 10097101 . C CTTTT,CTTT 2098.80 . AC=2,1;AF=0.500,0.250;AN=4;BaseQRankSum=-9.530e-01;DP=109;ExcessHet=3.0103;FS=4.307;MLEAC=2,1;MLEAF=0.500,0.250;MQ=58.72;MQRankSum=-2.210e+00;QD=24.69;ReadPosRankSum=2.83;SOR=0.337 GT:AD:DP:GQ:PL 0/2:34,3,26:63:99:1113,585,1857,0,1269,1263 1/1:0,22,0:22:71:1008,71,0,1008,71,1009 +20 10097436 . CTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT C 1088.88 . AC=1;AF=0.250;AN=4;BaseQRankSum=1.65;DP=120;ExcessHet=3.0103;FS=1.851;MLEAC=1;MLEAF=0.250;MQ=54.34;MQRankSum=-6.464e+00;QD=12.23;ReadPosRankSum=-3.097e+00;SOR=0.948 GT:AD:DP:GQ:PL 0/1:57,32:89:99:1097,0,2238 0/0:30,0:30:66:0,66,990 20 10097437 . TTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC *,TTTTCTTTCTTTCTTTCTTTCTTTCTTTC,T 1844.24 . AC=1,1,2;AF=0.250,0.250,0.500;AN=4;DP=108;ExcessHet=3.0103;FS=0.000;MLEAC=1,1,2;MLEAF=0.250,0.250,0.500;MQ=55.51;QD=24.27;SOR=1.905 GT:AD:DP:GQ:PL 1/2:0,32,23,0:55:99:2133,941,1797,1201,0,1129,2207,1453,1267,2647 3/3:0,0,0,21:21:67:928,928,928,928,928,928,67,67,67,0 20 10097626 . C A 646.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=1.09;DP=83;ExcessHet=3.0103;FS=2.701;MLEAC=1;MLEAF=0.250;MQ=58.00;MQRankSum=-1.331e+00;QD=13.48;ReadPosRankSum=1.02;SOR=0.324 GT:AD:DP:GQ:PL 0/1:28,20:48:99:655,0,957 0/0:29,0:29:81:0,81,1014 20 10097751 . T C 978.48 . AC=2;AF=0.500;AN=4;BaseQRankSum=-3.680e-01;ClippingRankSum=0.00;DP=87;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=25.75;ReadPosRankSum=1.08;SOR=0.350 GT:AD:DP:GQ:PL 0/0:49,0:49:99:0,120,1800 1/1:1,37:38:82:994,82,0 @@ -449,8 +449,8 @@ 20 10098110 . G C 2494.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=2.51;DP=80;ExcessHet=3.0103;FS=26.615;MLEAC=3;MLEAF=0.750;MQ=59.42;MQRankSum=-1.477e+00;QD=31.18;ReadPosRankSum=-7.300e-01;SOR=0.010 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:19,17:36:99:0|1:10098110_G_C:615,0,727:10098110 1/1:0,44:44:99:1|1:10098110_G_C:1893,135,0:10098110 20 10098135 . C A 2266.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=-1.155e+00;DP=81;ExcessHet=3.0103;FS=41.259;MLEAC=3;MLEAF=0.750;MQ=59.83;MQRankSum=1.56;QD=28.33;ReadPosRankSum=-5.910e-01;SOR=0.003 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:25,14:39:99:0|1:10098110_G_C:500,0,964:10098110 1/1:0,41:41:99:1|1:10098110_G_C:1780,126,0:10098110 20 10098219 . TATATATA T 1688.09 . AC=3;AF=0.750;AN=4;BaseQRankSum=3.15;DP=54;ExcessHet=3.0103;FS=19.931;MLEAC=3;MLEAF=0.750;MQ=58.45;MQRankSum=-2.050e-01;QD=32.46;ReadPosRankSum=0.427;SOR=0.013 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:12,9:21:99:0|1:10098219_TATATATA_T:333,0,461:10098219 1/1:0,31:31:96:1|1:10098219_TATATATA_T:1369,96,0:10098219 -20 10098237 . A T 1604.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=6.000e-03;DP=48;ExcessHet=3.0103;FS=11.066;MLEAC=3;MLEAF=0.750;MQ=58.20;MQRankSum=-1.885e+00;QD=34.13;ReadPosRankSum=0.277;SOR=0.033 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:7,7:14:99:0|1:10098219_TATATATA_T:273,0,273:10098219 1/1:0,33:33:98:1|1:10098219_TATATATA_T:1345,98,0:10098219 -20 10098265 . T C 153.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=1.83;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=41.96;MQRankSum=-1.834e+00;QD=25.65;ReadPosRankSum=0.00;SOR=1.329 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:2,4:6:59:0|1:10098219_TATATATA_T:162,0,59:10098219 0/0:44,0:44:90:.:.:0,90,1350 +20 10098237 . A T 1604.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=6.000e-03;DP=48;ExcessHet=3.0103;FS=11.066;MLEAC=3;MLEAF=0.750;MQ=58.20;MQRankSum=-1.885e+00;QD=34.13;ReadPosRankSum=1.12;SOR=0.033 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:7,7:14:99:0|1:10098219_TATATATA_T:273,0,273:10098219 1/1:0,33:33:98:1|1:10098219_TATATATA_T:1345,98,0:10098219 +20 10098265 . T C 153.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=1.83;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=41.96;MQRankSum=-1.834e+00;QD=25.65;ReadPosRankSum=0.842;SOR=1.329 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:2,4:6:59:0|1:10098219_TATATATA_T:162,0,59:10098219 0/0:44,0:44:90:.:.:0,90,1350 20 10098644 . ATT A 212.32 . AC=2;AF=1.00;AN=2;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=35.33;QD=31.67;SOR=0.693 GT:AD:DP:GQ:PGT:PID:PL:PS ./.:1,0:1:.:.:.:0,0,0 1/1:0,4:4:15:1|1:10098644_ATT_A:225,15,0:10098644 20 10098660 . G A 300.91 . AC=2;AF=0.500;AN=4;DP=11;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=41.04;QD=29.53;SOR=1.609 GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:1,0:1:3:.:.:0,3,33 1/1:0,7:7:21:1|1:10098644_ATT_A:315,21,0:10098644 20 10098668 . A AAT 390.92 . AC=2;AF=0.500;AN=4;DP=12;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=43.11;QD=32.63;SOR=1.863 GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:1,0:1:3:.:.:0,3,33 1/1:0,8:8:27:1|1:10098644_ATT_A:405,27,0:10098644 @@ -458,17 +458,17 @@ 20 10098704 . A G 794.53 . AC=2;AF=0.500;AN=4;DP=26;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=49.08;QD=28.13;SOR=1.609 GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:6,0:6:18:.:.:0,18,231 1/1:0,16:16:54:1|1:10098644_ATT_A:810,54,0:10098644 20 10098729 . T TATATA 839.45 . AC=2;AF=0.500;AN=4;DP=32;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=51.87;QD=27.97;SOR=1.292 GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:9,0:9:24:.:.:0,24,360 1/1:0,19:19:57:1|1:10098644_ATT_A:855,57,0:10098644 20 10098784 . TAC T 308.47 . AC=2;AF=0.500;AN=4;DP=19;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=57.51;QD=28.31;SOR=0.693 GT:AD:DP:GQ:PL 0/0:9,0:9:18:0,18,270 1/1:0,8:8:24:324,24,0 -20 10098885 . C CA 1620.09 . AC=3;AF=0.750;AN=4;BaseQRankSum=0.165;DP=63;ExcessHet=3.0103;FS=13.392;MLEAC=3;MLEAF=0.750;MQ=54.55;MQRankSum=-4.449e+00;QD=27.00;ReadPosRankSum=-1.073e+00;SOR=0.054 GT:AD:DP:GQ:PL 0/1:17,14:31:99:471,0,572 1/1:0,29:29:87:1163,87,0 +20 10098885 . C CA 1620.09 . AC=3;AF=0.750;AN=4;BaseQRankSum=0.165;DP=63;ExcessHet=3.0103;FS=13.392;MLEAC=3;MLEAF=0.750;MQ=54.55;MQRankSum=-4.449e+00;QD=27.00;ReadPosRankSum=-9.540e-01;SOR=0.054 GT:AD:DP:GQ:PL 0/1:17,14:31:99:471,0,572 1/1:0,29:29:87:1163,87,0 20 10098945 . T C 1215.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=1.48;DP=48;ExcessHet=3.0103;FS=3.874;MLEAC=3;MLEAF=0.750;MQ=55.63;MQRankSum=-2.504e+00;QD=25.85;ReadPosRankSum=1.04;SOR=0.193 GT:AD:DP:GQ:PL 0/1:9,13:22:99:436,0,248 1/1:0,25:25:75:793,75,0 20 10098987 . C T 399.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=3.13;DP=56;ExcessHet=3.0103;FS=7.005;MLEAC=1;MLEAF=0.250;MQ=51.36;MQRankSum=-2.734e+00;QD=16.66;ReadPosRankSum=0.436;SOR=2.925 GT:AD:DP:GQ:PL 0/1:11,13:24:99:408,0,350 0/0:31,0:31:90:0,90,977 -20 10099029 . T C 1626.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=-1.518e+00;DP=59;ExcessHet=3.0103;FS=1.168;MLEAC=3;MLEAF=0.750;MQ=56.11;MQRankSum=-3.731e+00;QD=28.04;ReadPosRankSum=-1.224e+00;SOR=0.467 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:19,10:29:99:0|1:10099029_T_C:363,0,768:10099029 1/1:0,29:29:87:1|1:10099029_T_C:1277,87,0:10099029 -20 10099034 . C A 1564.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=2.75;DP=56;ExcessHet=3.0103;FS=0.000;MLEAC=3;MLEAF=0.750;MQ=56.33;MQRankSum=-3.731e+00;QD=27.93;ReadPosRankSum=-1.850e+00;SOR=0.593 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:19,10:29:99:0|1:10099029_T_C:363,0,768:10099029 1/1:0,27:27:81:1|1:10099029_T_C:1215,81,0:10099029 +20 10099029 . T C 1626.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=-1.809e+00;DP=59;ExcessHet=3.0103;FS=1.168;MLEAC=3;MLEAF=0.750;MQ=56.11;MQRankSum=-3.731e+00;QD=28.04;ReadPosRankSum=-1.224e+00;SOR=0.467 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:19,10:29:99:0|1:10099029_T_C:363,0,768:10099029 1/1:0,29:29:87:1|1:10099029_T_C:1277,87,0:10099029 +20 10099034 . C A 1564.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=2.76;DP=56;ExcessHet=3.0103;FS=0.000;MLEAC=3;MLEAF=0.750;MQ=56.33;MQRankSum=-3.731e+00;QD=27.93;ReadPosRankSum=-1.850e+00;SOR=0.593 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:19,10:29:99:0|1:10099029_T_C:363,0,768:10099029 1/1:0,27:27:81:1|1:10099029_T_C:1215,81,0:10099029 20 10099044 . A C 1564.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=-1.148e+00;DP=56;ExcessHet=3.0103;FS=0.000;MLEAC=3;MLEAF=0.750;MQ=55.04;MQRankSum=-4.533e+00;QD=27.93;ReadPosRankSum=-2.207e+00;SOR=0.593 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:19,10:29:99:0|1:10099029_T_C:363,0,768:10099029 1/1:0,27:27:81:1|1:10099029_T_C:1215,81,0:10099029 20 10099046 . T C 1579.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=-2.165e+00;DP=51;ExcessHet=3.0103;FS=2.900;MLEAC=3;MLEAF=0.750;MQ=54.53;MQRankSum=-4.418e+00;QD=30.96;ReadPosRankSum=-2.297e+00;SOR=0.368 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:15,9:24:99:0|1:10099029_T_C:333,0,603:10099029 1/1:0,27:27:84:1|1:10099029_T_C:1260,84,0:10099029 -20 10099055 . T C 1621.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=-9.960e-01;DP=56;ExcessHet=3.0103;FS=0.000;MLEAC=3;MLEAF=0.750;MQ=54.97;MQRankSum=-4.179e+00;QD=29.48;ReadPosRankSum=-1.970e+00;SOR=0.652 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:17,8:25:99:0|1:10099029_T_C:285,0,673:10099029 1/1:0,30:30:90:1|1:10099029_T_C:1350,90,0:10099029 +20 10099055 . T C 1621.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=-1.554e+00;DP=56;ExcessHet=3.0103;FS=0.000;MLEAC=3;MLEAF=0.750;MQ=54.97;MQRankSum=-4.179e+00;QD=29.48;ReadPosRankSum=-1.970e+00;SOR=0.652 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:17,8:25:99:0|1:10099029_T_C:285,0,673:10099029 1/1:0,30:30:90:1|1:10099029_T_C:1350,90,0:10099029 20 10099079 . C T 1517.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=1.43;DP=62;ExcessHet=3.0103;FS=5.323;MLEAC=3;MLEAF=0.750;MQ=55.33;MQRankSum=-2.614e+00;QD=24.87;ReadPosRankSum=0.969;SOR=1.432 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:24,6:30:99:0|1:10099029_T_C:145,0,886:10099029 1/1:0,31:31:96:1|1:10099029_T_C:1386,96,0:10099029 -20 10099111 . T TTTTGTTTG 1720.09 . AC=3;AF=0.750;AN=4;BaseQRankSum=-6.220e-01;DP=80;ExcessHet=3.0103;FS=0.000;MLEAC=3;MLEAF=0.750;MQ=55.92;MQRankSum=-9.730e-01;QD=26.46;ReadPosRankSum=-2.730e-01;SOR=0.727 GT:AD:DP:GQ:PL 0/1:23,19:42:99:693,0,802 1/1:0,23:23:72:1041,72,0 -20 10099140 . G T 2051.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=-2.860e-01;DP=96;ExcessHet=3.0103;FS=0.000;MLEAC=3;MLEAF=0.750;MQ=56.89;MQRankSum=-2.435e+00;QD=22.29;ReadPosRankSum=0.116;SOR=0.710 GT:AD:DP:GQ:PL 0/1:29,32:61:99:1035,0,930 1/1:0,31:31:93:1030,93,0 +20 10099111 . T TTTTGTTTG 1720.09 . AC=3;AF=0.750;AN=4;BaseQRankSum=-1.207e+00;DP=80;ExcessHet=3.0103;FS=0.000;MLEAC=3;MLEAF=0.750;MQ=55.92;MQRankSum=-9.730e-01;QD=26.46;ReadPosRankSum=-1.860e+00;SOR=0.727 GT:AD:DP:GQ:PL 0/1:23,19:42:99:693,0,802 1/1:0,23:23:72:1041,72,0 +20 10099140 . G T 2051.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=-2.860e-01;DP=96;ExcessHet=3.0103;FS=0.000;MLEAC=3;MLEAF=0.750;MQ=56.89;MQRankSum=-2.435e+00;QD=22.29;ReadPosRankSum=0.636;SOR=0.710 GT:AD:DP:GQ:PL 0/1:29,32:61:99:1035,0,930 1/1:0,31:31:93:1030,93,0 20 10099190 . G T 2171.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=-2.640e-01;DP=100;ExcessHet=3.0103;FS=1.812;MLEAC=3;MLEAF=0.750;MQ=58.42;MQRankSum=-1.445e+00;QD=22.15;ReadPosRankSum=-1.577e+00;SOR=0.483 GT:AD:DP:GQ:PL 0/1:31,31:62:99:1038,0,1088 1/1:0,36:36:99:1147,108,0 20 10099220 . A G 1516.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=-1.664e+00;DP=78;ExcessHet=3.0103;FS=2.044;MLEAC=3;MLEAF=0.750;MQ=58.65;MQRankSum=-2.596e+00;QD=20.22;ReadPosRankSum=0.629;SOR=0.439 GT:AD:DP:GQ:PL 0/1:25,20:45:99:606,0,873 1/1:0,30:30:89:924,89,0 20 10099250 . G A 719.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=3.17;DP=71;ExcessHet=3.0103;FS=7.195;MLEAC=1;MLEAF=0.250;MQ=56.89;MQRankSum=-2.272e+00;QD=19.46;ReadPosRankSum=0.583;SOR=0.162 GT:AD:DP:GQ:PL 0/1:16,21:37:99:728,0,424 0/0:32,0:32:90:0,90,1350 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/newMQcalc.combined.genotyped.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/newMQcalc.combined.genotyped.vcf.idx index bb819d7605ddf186821e6fda11562ec4cab42e3d..458091e1b0628ecba502ffa796b64e6ae29f9850 100644 GIT binary patch literal 12142 zcmeHNyN+B%5N!km#2`Wl5CO?d*P|chh-G(duVfFB85^5qg!f^A7kgQZZ9ag6|3E?_ zA}8P@_ylq?VorD8Yu)A#kb0z5&z!9}Rdu@R++=pgNB3WI&b^Mm^RF(>uC3SW=U-l} z&!1kLo?U&n4sm^vPrlAE89z)(UVeKalJv2ho_zD{lpcrmZvE)&$)T%J98esazt zDj{c9Pn;9!3ZVPr*OJ4z%MZT)<+8nX?sEV~$A`OX>|GSkA>d5|$Z00FY@q?-$g*cv znIaSbQBY2?MFdCL8wHM2M0Au0AwH%SksJjh$uUX;vLlTW6}$~F0K|j_r~%|1NeH4z zClaE9cpn2ziHU(o4)m&6LbZhdTTXf6LAgGOTF|LFLcQo%NNh?DKJyYZg{eGBE)!W` zR8du->{9kAvCg#S&=F_L(^t?)An_XFRNQ^^960$ftMUNfkR-1HZton$5Upjnam#zp zKCPfX$EmOeas&u9{git`t)K>3mjpsUIYH_rO1`2ocf3*&?M0yC7?^Mty89 z43>HwR4Z!Si7qYHq(eO;7MtXIeG7wnOwY11X|XXZD`Q_OQ}Vux)p8d~COvP9HR-!3 zsw-o)mf5surdal#x7Hwmd)}H&qII!S$1K2Emb_AVgY~?=beu`%RjBs{O8{yZ$^JGg z$}umMgj*n%d_>91bXFOAYsJ^)z=rng zMU^`e&7Lxm6p<*x#X6m-=s}q7elVz}#CXq}J}FXD7U${Oq1t6)(xoO$<-RE~TOVCk z2XN3{*9I%hec3$Kl*w=#OPH%v$)fdo*LE^2YRL_kD=9OqthbCZPLyK~J@*X9ZlHWs zFekX^q7n>wCBYgln0nLR}3D!0^#w2O`SsyKfSx%IXtagdA?$9KYri2zu$1~!}8$8>jd~apS1Vm z96A&Q#vF_}7;`Z8VEDlBf#Czg2Zj#}9~eF`d|>#%@PXk2!v}^B3?CRiFnnP6!0>_L z1H%V~4-6j|J}`V>_`vXi;RC}5h7SxM7(Ot3;Q#IeKfi2y{L^pkeCzjiUjMV55B_TB lkN>pu>dp2e_V?ay=fjWM`R=BjRDVV{{n8KR*C=s literal 12144 zcmeHNyN+B%5N!m+mf!=BkdPpmsp_hJlu10=9n4DhAer%lXn=iK-~~T0#{2<4!50t_ z6A%(3_yR;uMnu5r?t87<`~gyrwCby~HK$HhSDl;8{^a=HOU}8M@ptjr<@we1dj0H^ zC+mxcmuKfszFLR4zRahe=a|fYnvy(!d?}Ljft;Ow@$`%zg!O)X|NP5`PrrS1e*f9& zMaU!)lsSk74a7dL0K2b$C|R8Q?)x_nkJ_VicL5xq9PO`qa#6^KfQJUK)6Cwog$9UY z%jCVv6rli+MSY4bA~?=u9DJN2qT|E}p_p1kavY2$$0!ZRjx|bD@HW5zuxC->1~566 zfLfAHB+LaNih-xZ?14xQ{6Z{4E#v=|Q=WJrmy)OjozyY(qGDmODLMFz(7O~Sd7NBk zw&0L5NEyML2 zMC2*0(0?B%VGZ;VAi7CY?g_Pm8rr%f5C-ZKTD?S>DjIXgD}@35^SX?cP*6qRmnaop zi9FZeG-#2FYn*R!LMubWJuMj6YHZ>(%~gvfDGW)it4&MAk}+fp2Cr3b4z#R-t;HJm zvAHl<>ieKtQS)8XrNx?bD0##xG4=f|3`&@ur7~%;F)WpND$10Jx>zlDp={Fgwpf$C ziqduUSgmC?Ej?2a?Rl#P3BKp8*(6#QD|O5Qyk*HNl{Z+=OQqt>GOt3tH&_Bt!$|hG zSy3PJvXgKN#4<%lUZ(R!1Xc*Q-@%0g2E?-?wL#$`gC!-bVqM7w`^pWUu&xxU%YhB; z*NZE6WS%``A}LMc2p8-6%%vZU>Fx)EYf6mwyy;U%YRcj~T{&E z28wD2bApR5lwim!3D$5~JX;lrjqPv87bPAqj#%@PXk2!v}^B3?CRiFnnP6!0>_L z1H%V~4-6j|J}`V>_`vXi;RC}5h7SxM7(Ot3VEDlQ-3LB?-uC#~kL~>Vr*{7HTRX4( m+0J+WZs*&twjZ(o{#rX