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Files to reproduce ewels/MultiQC#1374 #198

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Jun 28, 2021
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Files to reproduce ewels/MultiQC#1374 #198

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95 changes: 95 additions & 0 deletions data/modules/dragen/issue_1374/6405-JL-0001_111.mapping_metrics.csv
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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