BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514756.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 59,632,023 number of mapped reads = 58,278,797 (97.73%) number of supplementary alignments = 5,114,580 (8.58%) number of secondary alignments = 0 number of mapped bases = 5,403,256,959 bp number of sequenced bases = 5,393,115,175 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 56,140,077 duplication rate = 50.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.9762 >>>>>>> ACTG content number of A's = 1,543,516,799 bp (28.62%) number of C's = 1,133,268,523 bp (21.01%) number of T's = 1,551,855,879 bp (28.77%) number of G's = 1,160,432,796 bp (21.52%) number of N's = 4,041,178 bp (0.07%) GC percentage = 42.53% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 51,758,900 number of insertions = 3,299,615 mapped reads with insertion percentage = 5.23% number of deletions = 3,512,458 mapped reads with deletion percentage = 5.43% homopolymer indels = 27.84% >>>>>>> Coverage mean coverageData = 1.7454X std coverageData = 433.0035X There is a 2.66% of reference with a coverageData >= 1X There is a 1.22% of reference with a coverageData >= 2X There is a 0.85% of reference with a coverageData >= 3X There is a 0.71% of reference with a coverageData >= 4X There is a 0.63% of reference with a coverageData >= 5X There is a 0.58% of reference with a coverageData >= 6X There is a 0.54% of reference with a coverageData >= 7X There is a 0.51% of reference with a coverageData >= 8X There is a 0.49% of reference with a coverageData >= 9X There is a 0.47% of reference with a coverageData >= 10X There is a 0.45% of reference with a coverageData >= 11X There is a 0.43% of reference with a coverageData >= 12X There is a 0.42% of reference with a coverageData >= 13X There is a 0.41% of reference with a coverageData >= 14X There is a 0.4% of reference with a coverageData >= 15X There is a 0.39% of reference with a coverageData >= 16X There is a 0.38% of reference with a coverageData >= 17X There is a 0.37% of reference with a coverageData >= 18X There is a 0.36% of reference with a coverageData >= 19X There is a 0.35% of reference with a coverageData >= 20X There is a 0.34% of reference with a coverageData >= 21X There is a 0.34% of reference with a coverageData >= 22X There is a 0.33% of reference with a coverageData >= 23X There is a 0.33% of reference with a coverageData >= 24X There is a 0.32% of reference with a coverageData >= 25X There is a 0.31% of reference with a coverageData >= 26X There is a 0.31% of reference with a coverageData >= 27X There is a 0.3% of reference with a coverageData >= 28X There is a 0.3% of reference with a coverageData >= 29X There is a 0.3% of reference with a coverageData >= 30X There is a 0.29% of reference with a coverageData >= 31X There is a 0.29% of reference with a coverageData >= 32X There is a 0.28% of reference with a coverageData >= 33X There is a 0.28% of reference with a coverageData >= 34X There is a 0.28% of reference with a coverageData >= 35X There is a 0.27% of reference with a coverageData >= 36X There is a 0.27% of reference with a coverageData >= 37X There is a 0.27% of reference with a coverageData >= 38X There is a 0.26% of reference with a coverageData >= 39X There is a 0.26% of reference with a coverageData >= 40X There is a 0.26% of reference with a coverageData >= 41X There is a 0.25% of reference with a coverageData >= 42X There is a 0.25% of reference with a coverageData >= 43X There is a 0.25% of reference with a coverageData >= 44X There is a 0.24% of reference with a coverageData >= 45X There is a 0.24% of reference with a coverageData >= 46X There is a 0.24% of reference with a coverageData >= 47X There is a 0.24% of reference with a coverageData >= 48X There is a 0.23% of reference with a coverageData >= 49X There is a 0.23% of reference with a coverageData >= 50X There is a 0.23% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 266666590 1.0698733224018728 61.81753539930983 chr2 243199373 358475060 1.4739966455423386 126.31803038036247 chr3 198022430 418695757 2.11438551178268 155.66673297867646 chr4 191154276 895256297 4.683422812890672 1597.5153723011692 chr5 180915260 246198086 1.3608475371287088 70.08510187427663 chr6 171115067 573352110 3.3506816205728978 481.0450576759924 chr7 159138663 380314460 2.3898306849542905 139.726610551181 chr8 146364022 339151483 2.317177940081477 465.01171626824635 chr9 141213431 95046456 0.6730695184369537 32.24856957996311 chr10 135534747 165417750 1.2204822280739565 53.78505643831685 chr11 135006516 206946777 1.5328651025999367 58.25641333338653 chr12 133851895 164530103 1.2291951712749378 59.006269579253406 chr13 115169878 97365888 0.8454110544425514 45.47738917494582 chr14 107349540 106198838 0.9892807924468051 50.8438126317406 chr15 102531392 135341846 1.3200039847308422 67.53773903164762 chr16 90354753 166628564 1.8441593659162567 120.41236501360243 chr17 81195210 142031920 1.7492647657417228 70.29963012786861 chr18 78077248 204426917 2.6182648881272046 166.052754162191 chr19 59128983 66897838 1.1313882736660632 82.48573897959129 chr20 63025520 111778124 1.7735375130582025 72.86772980876597 chr21 48129895 47528882 0.9875126883198062 46.15504821549495 chr22 51304566 39621185 0.772274050617639 46.474676221153686 chrMT 16571 1114660 67.26570514754692 181.94850128708944 chrX 155270560 133822794 0.8618684314656945 45.84917621011095 chrY 59373566 40448574 0.6812555944509043 44.46955474566354