From 21880e0c5ad6b2761781200528286bd7b0c50451 Mon Sep 17 00:00:00 2001 From: Erik Danielsson Date: Thu, 17 Jun 2021 12:32:59 +0200 Subject: [PATCH] Files to reproduce ewels/MultiQC#1374 --- .../6405-JL-0001_111.mapping_metrics.csv | 95 +++++++++++++++++++ 1 file changed, 95 insertions(+) create mode 100644 data/modules/dragen/issue_1374/6405-JL-0001_111.mapping_metrics.csv diff --git a/data/modules/dragen/issue_1374/6405-JL-0001_111.mapping_metrics.csv b/data/modules/dragen/issue_1374/6405-JL-0001_111.mapping_metrics.csv new file mode 100644 index 00000000..ecabfb6e --- /dev/null +++ b/data/modules/dragen/issue_1374/6405-JL-0001_111.mapping_metrics.csv @@ -0,0 +1,95 @@ +MAPPING/ALIGNING SUMMARY,,Total input reads,35869200,100.00 +MAPPING/ALIGNING SUMMARY,,Number of duplicate marked reads,4540614,12.66 +MAPPING/ALIGNING SUMMARY,,Number of duplicate marked and mate reads removed,NA +MAPPING/ALIGNING SUMMARY,,Number of unique reads (excl. duplicate marked reads),31328586,87.34 +MAPPING/ALIGNING SUMMARY,,Reads with mate sequenced,0,0.00 +MAPPING/ALIGNING SUMMARY,,Reads without mate sequenced,35869200,100.00 +MAPPING/ALIGNING SUMMARY,,QC-failed reads,0,0.00 +MAPPING/ALIGNING SUMMARY,,Mapped reads,32036836,89.32 +MAPPING/ALIGNING SUMMARY,,Mapped reads R1,32036836,89.32 +MAPPING/ALIGNING SUMMARY,,Mapped reads R2,0,0.00 +MAPPING/ALIGNING SUMMARY,,Number of unique & mapped reads (excl. duplicate marked reads),27496222,76.66 +MAPPING/ALIGNING SUMMARY,,Unmapped reads,3832364,10.68 +MAPPING/ALIGNING SUMMARY,,Singleton reads (itself mapped; mate unmapped),0,0.00 +MAPPING/ALIGNING SUMMARY,,Paired reads (itself & mate mapped),0,0.00 +MAPPING/ALIGNING SUMMARY,,Properly paired reads,0,0.00 +MAPPING/ALIGNING SUMMARY,,Not properly paired reads (discordant),0,0.00 +MAPPING/ALIGNING SUMMARY,,Paired reads mapped to different chromosomes,0,0.00 +MAPPING/ALIGNING SUMMARY,,Paired reads mapped to different chromosomes (MAPQ>=10),0,0.00 +MAPPING/ALIGNING SUMMARY,,Reads with MAPQ [40:inf),27513057,76.70 +MAPPING/ALIGNING SUMMARY,,Reads with MAPQ [30:40),475461,1.33 +MAPPING/ALIGNING SUMMARY,,Reads with MAPQ [20:30),235959,0.66 +MAPPING/ALIGNING SUMMARY,,Reads with MAPQ [10:20),743452,2.07 +MAPPING/ALIGNING SUMMARY,,Reads with MAPQ [ 0:10),3068907,8.56 +MAPPING/ALIGNING SUMMARY,,Reads with MAPQ NA (Unmapped reads),3832364,10.68 +MAPPING/ALIGNING SUMMARY,,Reads with indel R1,547694,1.71 +MAPPING/ALIGNING SUMMARY,,Total bases,3622789200 +MAPPING/ALIGNING SUMMARY,,Total bases R1,3622789200 +MAPPING/ALIGNING SUMMARY,,Mapped bases R1,3235720436 +MAPPING/ALIGNING SUMMARY,,Soft-clipped bases R1,160311456,4.95 +MAPPING/ALIGNING SUMMARY,,Soft-clipped bases R2,NA +MAPPING/ALIGNING SUMMARY,,Mismatched bases R1,10002874,0.31 +MAPPING/ALIGNING SUMMARY,,Mismatched bases R2,NA +MAPPING/ALIGNING SUMMARY,,Mismatched bases R1 (excl. indels),8625741,0.27 +MAPPING/ALIGNING SUMMARY,,Mismatched bases R2 (excl. indels),NA +MAPPING/ALIGNING SUMMARY,,Q30 bases,3500376842,96.62 +MAPPING/ALIGNING SUMMARY,,Q30 bases R1,3500376842,96.62 +MAPPING/ALIGNING SUMMARY,,Q30 bases (excl. dups & clipped bases),2999198295 +MAPPING/ALIGNING SUMMARY,,Total alignments,32820705 +MAPPING/ALIGNING SUMMARY,,Secondary alignments,0 +MAPPING/ALIGNING SUMMARY,,Supplementary (chimeric) alignments,783869 +MAPPING/ALIGNING SUMMARY,,Estimated read length,101.00 +MAPPING/ALIGNING SUMMARY,,Bases in reference genome,3217346917 +MAPPING/ALIGNING SUMMARY,,Bases in target bed [% of genome],NA +MAPPING/ALIGNING SUMMARY,,Average sequenced coverage over genome,1.13 +MAPPING/ALIGNING SUMMARY,,Insert length: mean,NA +MAPPING/ALIGNING SUMMARY,,Insert length: median,NA +MAPPING/ALIGNING SUMMARY,,Insert length: standard deviation,NA +MAPPING/ALIGNING SUMMARY,,Provided sex chromosome ploidy,NA +MAPPING/ALIGNING SUMMARY,,Estimated sample contamination,NA +MAPPING/ALIGNING SUMMARY,,DRAGEN mapping rate [mil. reads/second],2.18 +MAPPING/ALIGNING PER RG,6405-JL-0001_111,Total reads in RG,35869200,100.00 +MAPPING/ALIGNING PER RG,6405-JL-0001_111,Number of duplicate marked reads,4540614,12.66 +MAPPING/ALIGNING PER RG,6405-JL-0001_111,Number of duplicate marked and mate reads removed,NA +MAPPING/ALIGNING PER RG,6405-JL-0001_111,Number of unique reads (excl. duplicate marked reads),31328586,87.34 +MAPPING/ALIGNING PER RG,6405-JL-0001_111,Reads with mate sequenced,0,0.00 +MAPPING/ALIGNING PER RG,6405-JL-0001_111,Reads without mate sequenced,35869200,100.00 +MAPPING/ALIGNING PER RG,6405-JL-0001_111,QC-failed reads,0,0.00 +MAPPING/ALIGNING PER RG,6405-JL-0001_111,Mapped reads,32036836,89.32 +MAPPING/ALIGNING PER RG,6405-JL-0001_111,Mapped reads R1,32036836,89.32 +MAPPING/ALIGNING PER RG,6405-JL-0001_111,Mapped reads R2,0,0.00 +MAPPING/ALIGNING PER RG,6405-JL-0001_111,Number of unique & mapped reads (excl. duplicate marked reads),27496222,76.66 +MAPPING/ALIGNING PER RG,6405-JL-0001_111,Unmapped reads,3832364,10.68 +MAPPING/ALIGNING PER RG,6405-JL-0001_111,Singleton reads (itself mapped; mate unmapped),0,0.00 +MAPPING/ALIGNING PER RG,6405-JL-0001_111,Paired reads (itself & mate mapped),0,0.00 +MAPPING/ALIGNING PER RG,6405-JL-0001_111,Properly paired reads,0,0.00 +MAPPING/ALIGNING PER RG,6405-JL-0001_111,Not properly paired reads (discordant),0,0.00 +MAPPING/ALIGNING PER RG,6405-JL-0001_111,Paired reads mapped to different chromosomes,0,0.00 +MAPPING/ALIGNING PER RG,6405-JL-0001_111,Paired reads mapped to different chromosomes (MAPQ>=10),0,0.00 +MAPPING/ALIGNING PER RG,6405-JL-0001_111,Reads with MAPQ [40:inf),27513057,76.70 +MAPPING/ALIGNING PER RG,6405-JL-0001_111,Reads with MAPQ [30:40),475461,1.33 +MAPPING/ALIGNING PER RG,6405-JL-0001_111,Reads with MAPQ [20:30),235959,0.66 +MAPPING/ALIGNING PER RG,6405-JL-0001_111,Reads with MAPQ [10:20),743452,2.07 +MAPPING/ALIGNING PER RG,6405-JL-0001_111,Reads with MAPQ [ 0:10),3068907,8.56 +MAPPING/ALIGNING PER RG,6405-JL-0001_111,Reads with MAPQ NA (Unmapped reads),3832364,10.68 +MAPPING/ALIGNING PER RG,6405-JL-0001_111,Reads with indel R1,547694,1.71 +MAPPING/ALIGNING PER RG,6405-JL-0001_111,Total bases,3622789200 +MAPPING/ALIGNING PER RG,6405-JL-0001_111,Total bases R1,3622789200 +MAPPING/ALIGNING PER RG,6405-JL-0001_111,Mapped bases R1,3235720436 +MAPPING/ALIGNING PER RG,6405-JL-0001_111,Soft-clipped bases R1,160311456,4.95 +MAPPING/ALIGNING PER RG,6405-JL-0001_111,Soft-clipped bases R2,NA +MAPPING/ALIGNING PER RG,6405-JL-0001_111,Mismatched bases R1,10002874,0.31 +MAPPING/ALIGNING PER RG,6405-JL-0001_111,Mismatched bases R2,NA +MAPPING/ALIGNING PER RG,6405-JL-0001_111,Mismatched bases R1 (excl. indels),8625741,0.27 +MAPPING/ALIGNING PER RG,6405-JL-0001_111,Mismatched bases R2 (excl. indels),NA +MAPPING/ALIGNING PER RG,6405-JL-0001_111,Q30 bases,3500376842,96.62 +MAPPING/ALIGNING PER RG,6405-JL-0001_111,Q30 bases R1,3500376842,96.62 +MAPPING/ALIGNING PER RG,6405-JL-0001_111,Q30 bases (excl. dups & clipped bases),2999198295 +MAPPING/ALIGNING PER RG,6405-JL-0001_111,Total alignments,32820705 +MAPPING/ALIGNING PER RG,6405-JL-0001_111,Secondary alignments,0 +MAPPING/ALIGNING PER RG,6405-JL-0001_111,Supplementary (chimeric) alignments,783869 +MAPPING/ALIGNING PER RG,6405-JL-0001_111,Estimated read length,101.00 +MAPPING/ALIGNING PER RG,6405-JL-0001_111,Average sequenced coverage over genome,1.13 +MAPPING/ALIGNING PER RG,6405-JL-0001_111,Insert length: mean,NA +MAPPING/ALIGNING PER RG,6405-JL-0001_111,Insert length: median,NA +MAPPING/ALIGNING PER RG,6405-JL-0001_111,Insert length: standard deviation,NA