BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013267.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,127,917 number of mapped reads = 1,886,177 (88.64%) number of supplementary alignments = 11,824 (0.56%) number of secondary alignments = 0 number of mapped bases = 125,663,003 bp number of sequenced bases = 125,607,999 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 90,039 duplication rate = 3.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2444 >>>>>>> ACTG content number of A's = 34,457,438 bp (27.43%) number of C's = 22,977,219 bp (18.29%) number of T's = 40,328,129 bp (32.11%) number of G's = 27,817,841 bp (22.15%) number of N's = 27,372 bp (0.02%) GC percentage = 40.44% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 998,013 number of insertions = 8,406 mapped reads with insertion percentage = 0.44% number of deletions = 32,329 mapped reads with deletion percentage = 1.7% homopolymer indels = 46.21% >>>>>>> Coverage mean coverageData = 0.0406X std coverageData = 0.3214X There is a 3.37% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 10825794 0.04343336821616184 0.38154477795332137 chr2 243199373 19959314 0.08206975928346658 0.5327701257005858 chr3 198022430 5213502 0.02632783569012864 0.18816630438211354 chr4 191154276 11176757 0.05846982465618504 0.2832735897232334 chr5 180915260 3682426 0.020354424496861128 0.17049608292532814 chr6 171115067 3547818 0.02073352196390748 0.21577411466384142 chr7 159138663 2998602 0.018842699463926 0.2184201604125264 chr8 146364022 6862014 0.046883201938793403 0.38982510195080017 chr9 141213431 1648626 0.011674711026601996 0.25612981757536823 chr10 135534747 6617165 0.04882264619566523 0.37351348834224035 chr11 135006516 5400630 0.04000273586794877 0.26347299743091224 chr12 133851895 7186370 0.05368896719766276 0.2723768451983109 chr13 115169878 424098 0.003682369100017628 0.07875487566916385 chr14 107349540 2373488 0.02210990377788298 0.18554942214530956 chr15 102531392 4251179 0.041462218712489535 0.23483287820046883 chr16 90354753 3054046 0.03380061256987776 0.22287128354696 chr17 81195210 5235951 0.06448595920867746 0.31744921389626596 chr18 78077248 2048178 0.026232712505440764 0.4627686203747517 chr19 59128983 1626109 0.02750104800551026 0.3445210906183614 chr20 63025520 4094830 0.06497098318268536 0.3898717024260032 chr21 48129895 739415 0.015362904905568566 0.15194616378827697 chr22 51304566 998872 0.01946945618836343 0.15989687527384475 chrMT 16571 447674 27.015509021785046 15.345032079893224 chrX 155270560 14948535 0.09627411017259163 0.4002707824021272 chrY 59373566 301610 0.005079870055303736 0.09147851310957977