BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548970.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 5,266,879 number of mapped reads = 2,334,703 (44.33%) number of secondary alignments = 0 number of mapped bases = 92,070,721 bp number of sequenced bases = 92,057,889 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 53,546 duplication rate = 1.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.385 >>>>>>> ACTG content number of A's = 28,670,487 bp (31.14%) number of C's = 17,360,003 bp (18.86%) number of T's = 28,486,248 bp (30.94%) number of G's = 17,537,069 bp (19.05%) number of N's = 4,082 bp (0%) GC percentage = 37.91% >>>>>>> Mismatches and indels general error rate = 0.0034 number of mismatches = 309,608 number of insertions = 4,508 mapped reads with insertion percentage = 0.19% number of deletions = 10,298 mapped reads with deletion percentage = 0.44% homopolymer indels = 45.28% >>>>>>> Coverage mean coverageData = 0.0297X std coverageData = 0.258X There is a 2.56% of reference with a coverageData >= 1X There is a 0.32% of reference with a coverageData >= 2X There is a 0.05% 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 7220509 0.028968870653285152 0.36064056561279434 chr2 243199373 8037593 0.033049398527849 0.24546195582750677 chr3 198022430 6453868 0.03259160086056918 0.20524294556895342 chr4 191154276 6628541 0.03467639405565796 0.21514111871442027 chr5 180915260 5989491 0.0331066102439341 0.20835216391956246 chr6 171115067 5649751 0.03301726200416939 0.22377103891700403 chr7 159138663 5208039 0.032726421736998 0.3387925917791045 chr8 146364022 4948994 0.03381291339479589 0.48605714069472433 chr9 141213431 3960868 0.02804880507435585 0.21701680541095944 chr10 135534747 4243465 0.031309056119756505 0.2231451766135769 chr11 135006516 4203224 0.03113348988281425 0.2404012299789431 chr12 133851895 4233685 0.031629623174180686 0.2053314210837397 chr13 115169878 3156767 0.0274096582788774 0.18809055488665163 chr14 107349540 2860980 0.02665106902181416 0.2009830213737393 chr15 102531392 2607691 0.02543309857726305 0.17969991260379875 chr16 90354753 2428424 0.026876549593356756 0.19004826401485433 chr17 81195210 2225069 0.027403944148922086 0.1929662716835075 chr18 78077248 2522044 0.03230190695245816 0.3416360111584483 chr19 59128983 1588571 0.026866198595027417 0.33307310465714907 chr20 63025520 1833367 0.029089280024980357 0.19431405112912123 chr21 48129895 1185258 0.02462623282265627 0.1861640123708747 chr22 51304566 921367 0.01795877193464613 0.16321815725608652 chrMT 16571 3027 0.18266851728924025 0.43875818406150885 chrX 155270560 3177924 0.020467009328748478 0.17895728707905798 chrY 59373566 782204 0.013174280284933533 0.16505201471892225