BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068177.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,399,613 number of mapped reads = 3,193,525 (93.94%) number of supplementary alignments = 24,913 (0.73%) number of secondary alignments = 0 number of mapped bases = 205,309,279 bp number of sequenced bases = 205,220,029 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 331,115 duplication rate = 8.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9562 >>>>>>> ACTG content number of A's = 54,282,509 bp (26.45%) number of C's = 36,257,591 bp (17.67%) number of T's = 67,466,765 bp (32.88%) number of G's = 47,190,020 bp (22.99%) number of N's = 23,144 bp (0.01%) GC percentage = 40.66% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 1,178,424 number of insertions = 13,053 mapped reads with insertion percentage = 0.4% number of deletions = 51,150 mapped reads with deletion percentage = 1.58% homopolymer indels = 45.16% >>>>>>> Coverage mean coverageData = 0.0663X std coverageData = 0.7441X There is a 5.15% of reference with a coverageData >= 1X There is a 1.02% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% 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 0.01% 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 21811621 0.0875087930071797 1.776244545853646 chr2 243199373 15888681 0.0653319159667406 0.9293368336593485 chr3 198022430 12020412 0.06070227498975747 0.3034200553002755 chr4 191154276 10908369 0.05706578596232919 0.31198474200032067 chr5 180915260 10736280 0.059344247688116525 0.3040287987354995 chr6 171115067 12353610 0.07219475301961574 0.44371117815405714 chr7 159138663 18081512 0.11362111292841513 1.0074708819806313 chr8 146364022 5498259 0.037565645743186805 0.8430360651114077 chr9 141213431 7291624 0.051635485012753495 0.485169157472897 chr10 135534747 11259647 0.08307572227216391 0.5112347742802381 chr11 135006516 8828462 0.06539285851951027 0.4110141742768819 chr12 133851895 8625051 0.06443727225527887 0.34767661525250476 chr13 115169878 5842019 0.05072523390187146 0.30539779383905113 chr14 107349540 4937537 0.04599495256337382 0.3187803936881993 chr15 102531392 3726742 0.03634732668020346 0.2677082503458982 chr16 90354753 4720756 0.05224690282756902 0.31140168503348986 chr17 81195210 6364229 0.07838182818912594 0.37497377246914776 chr18 78077248 6034308 0.07728638181509676 0.9208514028279919 chr19 59128983 4878717 0.08250973976670628 1.1433158860074384 chr20 63025520 3415259 0.05418850967036845 0.31158288589693445 chr21 48129895 3231010 0.06713104194388955 0.3334434164137858 chr22 51304566 1397617 0.02724157144219873 0.19783389204007146 chrMT 16571 380106 22.938024259248085 12.424552475942695 chrX 155270560 16478947 0.10613053111935708 0.46769031551962353 chrY 59373566 598504 0.010080310823843728 0.27226388212143715