BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818814.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 459,288 number of mapped reads = 442,360 (96.31%) number of supplementary alignments = 3,875 (0.84%) number of secondary alignments = 0 number of mapped bases = 29,993,707 bp number of sequenced bases = 29,980,709 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 73,589 duplication rate = 14.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6787 >>>>>>> ACTG content number of A's = 8,519,951 bp (28.42%) number of C's = 6,596,607 bp (22%) number of T's = 8,432,129 bp (28.13%) number of G's = 6,430,237 bp (21.45%) number of N's = 1,785 bp (0.01%) GC percentage = 43.45% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 158,165 number of insertions = 3,830 mapped reads with insertion percentage = 0.85% number of deletions = 7,863 mapped reads with deletion percentage = 1.76% homopolymer indels = 40.14% >>>>>>> Coverage mean coverageData = 0.0097X std coverageData = 0.1543X There is a 0.76% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.03% 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 2524131 0.010126879483281207 0.19709028177643598 chr2 243199373 2653975 0.010912754285760433 0.2496839484100285 chr3 198022430 2023645 0.01021927162493663 0.12402510167473461 chr4 191154276 1929838 0.010095709289809452 0.13587863403497716 chr5 180915260 1831223 0.010121993025906162 0.1254611003901439 chr6 171115067 1802868 0.010535997978483098 0.13368741973302636 chr7 159138663 1628902 0.010235740135632533 0.13860609005183727 chr8 146364022 1548488 0.010579703801799052 0.13367478325181545 chr9 141213431 1282515 0.00908210352880669 0.1268017663974159 chr10 135534747 1428359 0.010538692339906017 0.16622041526808393 chr11 135006516 1398613 0.010359596273116181 0.1323098404983073 chr12 133851895 1370852 0.010241558403039419 0.1282961376089817 chr13 115169878 888444 0.007714204576998857 0.10747420048674756 chr14 107349540 958400 0.008927844497517176 0.12674471377503777 chr15 102531392 859249 0.00838035047841738 0.11195410544516228 chr16 90354753 910703 0.010079193066910382 0.1763381509432851 chr17 81195210 852802 0.010503107264578785 0.12978186030777478 chr18 78077248 788306 0.010096488031955224 0.1585007560018236 chr19 59128983 623325 0.010541784559358986 0.17659824186454098 chr20 63025520 654607 0.010386379993374113 0.1343972489240785 chr21 48129895 422912 0.00878688806613852 0.11815559633310548 chr22 51304566 364732 0.00710915281887386 0.10658623975949458 chrMT 16571 27057 1.632792227385191 1.8689338235012887 chrX 155270560 929603 0.005986988132199691 0.10347367258159756 chrY 59373566 290158 0.004886989607462688 0.24665765721718982