BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085039.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,400,610 number of mapped reads = 3,119,370 (91.73%) number of supplementary alignments = 17,585 (0.52%) number of secondary alignments = 0 number of mapped bases = 208,645,585 bp number of sequenced bases = 208,580,633 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 123,629 duplication rate = 3.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4101 >>>>>>> ACTG content number of A's = 57,699,830 bp (27.66%) number of C's = 40,900,989 bp (19.61%) number of T's = 63,229,878 bp (30.31%) number of G's = 46,727,856 bp (22.4%) number of N's = 22,080 bp (0.01%) GC percentage = 42.01% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,761,290 number of insertions = 13,838 mapped reads with insertion percentage = 0.44% number of deletions = 37,034 mapped reads with deletion percentage = 1.18% homopolymer indels = 46.41% >>>>>>> Coverage mean coverageData = 0.0674X std coverageData = 0.4418X There is a 5.42% of reference with a coverageData >= 1X There is a 0.94% of reference with a coverageData >= 2X There is a 0.21% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 18079865 0.07253689048983353 0.5771033086251963 chr2 243199373 19874570 0.08172130443773801 0.6131864592992696 chr3 198022430 12682311 0.06404482057916368 0.3028841776560704 chr4 191154276 12009023 0.06282372150545039 0.3043834068732577 chr5 180915260 10432234 0.05766364871597896 0.2861813708518683 chr6 171115067 14240693 0.08322290520448442 0.4563971690506746 chr7 159138663 18479790 0.11612382341053097 0.5725592427176285 chr8 146364022 12339221 0.08430501452057665 0.6378372105315518 chr9 141213431 7499281 0.053106003776652096 0.4503021052542958 chr10 135534747 14884584 0.10982116637588145 0.5085145281005456 chr11 135006516 8298324 0.06146609990291135 0.4469207615411646 chr12 133851895 8633280 0.06449875065272703 0.315730208402371 chr13 115169878 4046995 0.03513935301728808 0.21968773317750795 chr14 107349540 6851376 0.06382305876671665 0.33328045159451314 chr15 102531392 3745068 0.036526062183960206 0.2480530462380847 chr16 90354753 5881688 0.06509550194885708 0.32435615054515016 chr17 81195210 3431720 0.042265054798183294 0.2738361870867773 chr18 78077248 4971635 0.06367584830858793 0.7375780746186681 chr19 59128983 3491095 0.0590420268178805 0.4561288390052469 chr20 63025520 4991061 0.0791911117909063 0.34008909367747947 chr21 48129895 2474283 0.05140844375413659 0.2877885738007995 chr22 51304566 1614554 0.03146998651153193 0.20841518605283305 chrMT 16571 9330 0.5630318025466176 0.8546857883974343 chrX 155270560 9297073 0.05987659862887079 0.337907384519785 chrY 59373566 386531 0.006510153019948305 0.11697672517792837