BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524332.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 2,934,700 number of mapped reads = 2,696,915 (91.9%) number of supplementary alignments = 12,262 (0.42%) number of secondary alignments = 0 number of mapped bases = 157,441,596 bp number of sequenced bases = 157,400,881 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 117,882 duplication rate = 3.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1884 >>>>>>> ACTG content number of A's = 37,000,689 bp (23.51%) number of C's = 31,470,405 bp (19.99%) number of T's = 48,436,345 bp (30.77%) number of G's = 40,471,348 bp (25.71%) number of N's = 22,094 bp (0.01%) GC percentage = 45.71% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 785,537 number of insertions = 8,604 mapped reads with insertion percentage = 0.32% number of deletions = 25,250 mapped reads with deletion percentage = 0.93% homopolymer indels = 42.85% >>>>>>> Coverage mean coverageData = 0.0509X std coverageData = 0.4186X There is a 4.37% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 13637557 0.054714234794223444 0.7968620395741062 chr2 243199373 10242529 0.04211577058629999 0.5534406788028486 chr3 198022430 11043523 0.05576905101103951 0.2683683255529284 chr4 191154276 8171123 0.042746221381937594 0.2825388705991344 chr5 180915260 7040113 0.03891387050489826 0.2247320258696889 chr6 171115067 10063649 0.0588121734481745 0.30802815889313273 chr7 159138663 7172146 0.04506853246592878 0.508260701729938 chr8 146364022 16492964 0.11268455030567553 0.526660484440717 chr9 141213431 6691729 0.047387340939262355 0.33244137016774133 chr10 135534747 8177677 0.060336387391493045 0.43078147469799605 chr11 135006516 7804608 0.05780912085754439 0.35976230779546975 chr12 133851895 6236683 0.0465939088871323 0.2518010855495512 chr13 115169878 3994900 0.03468702120184585 0.20962727375785506 chr14 107349540 3330819 0.031027790151685792 0.21933839615838516 chr15 102531392 5019242 0.04895322205320298 0.2532775669605488 chr16 90354753 5086706 0.056297049475637434 0.29002313480208447 chr17 81195210 5124375 0.06311178947625112 0.31898968613998807 chr18 78077248 3723522 0.047690231090112195 0.6236586610809456 chr19 59128983 2962731 0.05010623977753854 0.5257576172161539 chr20 63025520 3798895 0.06027550427192033 0.28613234215394734 chr21 48129895 2288238 0.04754296679849395 0.2799598766910871 chr22 51304566 1254116 0.0244445299469057 0.1755548245546209 chrMT 16571 11304 0.6821555729889566 0.9061733080450523 chrX 155270560 7600114 0.048947553225801466 0.28595508967577127 chrY 59373566 472333 0.007955274237696958 0.2195048021700014