BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506023.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 6,102,974 number of mapped reads = 4,524,431 (74.13%) number of supplementary alignments = 170 (0%) number of secondary alignments = 0 number of mapped bases = 209,939,188 bp number of sequenced bases = 209,898,112 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 368,563 duplication rate = 5.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0817 >>>>>>> ACTG content number of A's = 62,136,050 bp (29.6%) number of C's = 43,443,265 bp (20.7%) number of T's = 60,292,578 bp (28.72%) number of G's = 43,325,027 bp (20.64%) number of N's = 701,192 bp (0.33%) GC percentage = 41.34% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,681,540 number of insertions = 8,809 mapped reads with insertion percentage = 0.19% number of deletions = 29,448 mapped reads with deletion percentage = 0.65% homopolymer indels = 45.56% >>>>>>> Coverage mean coverageData = 0.0678X std coverageData = 0.669X There is a 4.5% of reference with a coverageData >= 1X There is a 1.36% of reference with a coverageData >= 2X There is a 0.48% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 20923617 0.08394609777120676 1.5121901328905705 chr2 243199373 12878316 0.052953738495041265 0.4939957214649587 chr3 198022430 13301693 0.06717265816806713 0.3712821725467311 chr4 191154276 8929978 0.04671607764609984 0.3214773641499114 chr5 180915260 14641568 0.08093053068049649 0.40571346666982144 chr6 171115067 13912710 0.08130616575102648 0.4742470964481436 chr7 159138663 13257404 0.08330724759199466 0.8822072009422645 chr8 146364022 12400372 0.08472281528311651 0.8135059484333802 chr9 141213431 9835673 0.0696511155514662 0.4787655731801353 chr10 135534747 6748945 0.04979494298978549 0.6717575053376854 chr11 135006516 11073710 0.08202352247946314 0.5345124733081235 chr12 133851895 6212651 0.04641436716304988 0.3223480285936889 chr13 115169878 6506043 0.05649083868960945 0.3329412947028439 chr14 107349540 7380468 0.06875174313741819 0.7211536643068256 chr15 102531392 6774883 0.06607618279482638 0.35995980132612687 chr16 90354753 6522075 0.07218297636207362 0.43464454061891805 chr17 81195210 3273536 0.04031686105621255 0.31902383090982894 chr18 78077248 6451053 0.08262398029192833 0.7434294817400439 chr19 59128983 5125069 0.08667608911859688 1.0427599423535285 chr20 63025520 4969107 0.07884277670378602 0.4046934786593303 chr21 48129895 3153496 0.06552052523696551 0.4025204136127603 chr22 51304566 1515437 0.02953805320173647 0.23796805103723356 chrMT 16571 27562 1.6632671534608654 2.091739673794412 chrX 155270560 13450454 0.0866259128581748 0.47206805613267594 chrY 59373566 673368 0.011341208644938053 0.2205436528894743