BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524790.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 = 1,186,248 number of mapped reads = 1,089,121 (91.81%) number of supplementary alignments = 4,119 (0.35%) number of secondary alignments = 0 number of mapped bases = 62,541,009 bp number of sequenced bases = 62,521,369 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 36,006 duplication rate = 2.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6899 >>>>>>> ACTG content number of A's = 14,605,276 bp (23.36%) number of C's = 12,068,132 bp (19.3%) number of T's = 20,832,735 bp (33.32%) number of G's = 15,007,260 bp (24%) number of N's = 7,966 bp (0.01%) GC percentage = 43.31% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 312,748 number of insertions = 4,680 mapped reads with insertion percentage = 0.43% number of deletions = 12,357 mapped reads with deletion percentage = 1.13% homopolymer indels = 42.14% >>>>>>> Coverage mean coverageData = 0.0202X std coverageData = 0.1921X There is a 1.84% of reference with a coverageData >= 1X There is a 0.14% 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 5048092 0.020253076922123296 0.24624839350482577 chr2 243199373 5159012 0.021213097453174765 0.2844204805077942 chr3 198022430 4191775 0.021168182816461753 0.15828680077040694 chr4 191154276 3901056 0.02040789294192927 0.1690063810328138 chr5 180915260 3693075 0.020413286308739242 0.15436567715124455 chr6 171115067 3519548 0.02056831149766607 0.1649745963843328 chr7 159138663 3341375 0.020996626068173013 0.22458498274199348 chr8 146364022 3166990 0.02163776286497511 0.18526027452203994 chr9 141213431 2702373 0.01913679868028984 0.17380881594242345 chr10 135534747 2948985 0.021758147377513457 0.22403150110271652 chr11 135006516 2868098 0.021244144986305696 0.17817368413454285 chr12 133851895 2901958 0.021680365451680755 0.16104556826355415 chr13 115169878 2039959 0.017712608847254313 0.1435276792957155 chr14 107349540 1853982 0.017270516482883858 0.14603549070345292 chr15 102531392 1812262 0.017675191613510916 0.1439482546329302 chr16 90354753 1857348 0.020556173730008426 0.1679557553954494 chr17 81195210 1775289 0.021864454812051105 0.16420540044981005 chr18 78077248 1654123 0.02118572365665347 0.2525923358162542 chr19 59128983 1398087 0.023644698911868652 0.2132494152230842 chr20 63025520 1304157 0.02069252264796863 0.15972314321447645 chr21 48129895 811794 0.016866731165733895 0.151421421508733 chr22 51304566 787743 0.01535424741727666 0.135330856455842 chrMT 16571 12390 0.7476917506487236 1.0341637077537935 chrX 155270560 3589221 0.023115914568737305 0.17473955667642932 chrY 59373566 202317 0.003407526507671781 0.09909556039676726