BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716999.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 = 1,446,318 number of mapped reads = 1,291,081 (89.27%) number of supplementary alignments = 6,309 (0.44%) number of secondary alignments = 0 number of mapped bases = 74,246,229 bp number of sequenced bases = 74,226,194 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 43,332 duplication rate = 2.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0807 >>>>>>> ACTG content number of A's = 19,545,676 bp (26.33%) number of C's = 13,828,920 bp (18.63%) number of T's = 23,629,659 bp (31.83%) number of G's = 17,220,749 bp (23.2%) number of N's = 1,190 bp (0%) GC percentage = 41.83% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 397,556 number of insertions = 4,600 mapped reads with insertion percentage = 0.36% number of deletions = 11,920 mapped reads with deletion percentage = 0.92% homopolymer indels = 42.23% >>>>>>> Coverage mean coverageData = 0.024X std coverageData = 0.2417X There is a 2.18% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 5817103 0.023338369134895755 0.3797856494548159 chr2 243199373 6029895 0.024794040073450353 0.27671776278922366 chr3 198022430 4392906 0.022183880886624815 0.159350462758667 chr4 191154276 4635620 0.024250673837921365 0.1791884344100387 chr5 180915260 4180814 0.023109239099012434 0.1645092129423995 chr6 171115067 3513284 0.02053170455176808 0.16837222840944058 chr7 159138663 5123185 0.03219321378865675 0.36254490601228606 chr8 146364022 3038913 0.020762704922115353 0.22784492088586475 chr9 141213431 3313251 0.02346271864182664 0.25023016716752067 chr10 135534747 2887018 0.02130094358755102 0.23508130475044897 chr11 135006516 2920931 0.02163548165334479 0.2088812111036901 chr12 133851895 5493317 0.04104026319537725 0.23908709378137963 chr13 115169878 2574833 0.022356826669556774 0.1591294806000384 chr14 107349540 2589570 0.02412278618054628 0.19364886827175268 chr15 102531392 1988144 0.01939058820151393 0.14993959184133013 chr16 90354753 2159634 0.02390171992390926 0.1806486951423548 chr17 81195210 2279071 0.028069032643674423 0.186062846459691 chr18 78077248 2125493 0.02722294976380315 0.4411567593059119 chr19 59128983 1260324 0.02131482626717933 0.30105306195972886 chr20 63025520 2338390 0.03710227222242672 0.21420603496190047 chr21 48129895 924792 0.019214502753434223 0.1642775099913601 chr22 51304566 749820 0.014615073442001244 0.1277121360040418 chrMT 16571 12019 0.72530324060105 1.0063878643599171 chrX 155270560 3698295 0.0238183915869177 0.1932648160093213 chrY 59373566 199607 0.003361883300053091 0.0830952423692726