BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717016.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,882,242 number of mapped reads = 1,757,708 (93.38%) number of supplementary alignments = 34,088 (1.81%) number of secondary alignments = 0 number of mapped bases = 136,386,690 bp number of sequenced bases = 136,333,103 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 91,703 duplication rate = 4.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3724 >>>>>>> ACTG content number of A's = 34,088,901 bp (25%) number of C's = 28,304,814 bp (20.76%) number of T's = 40,544,378 bp (29.74%) number of G's = 33,389,973 bp (24.49%) number of N's = 5,037 bp (0%) GC percentage = 45.25% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 908,583 number of insertions = 10,931 mapped reads with insertion percentage = 0.61% number of deletions = 26,263 mapped reads with deletion percentage = 1.47% homopolymer indels = 39.36% >>>>>>> Coverage mean coverageData = 0.0441X std coverageData = 0.3681X There is a 3.61% of reference with a coverageData >= 1X There is a 0.55% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.04% 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 0.01% 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 15297500 0.06137396945542615 0.731175032548208 chr2 243199373 12664595 0.052074949222833726 0.37572370359711943 chr3 198022430 8747699 0.04417529367758996 0.24839262426738845 chr4 191154276 6522928 0.03412389268236929 0.2992222674135136 chr5 180915260 8136254 0.04497273474885424 0.2554318068936621 chr6 171115067 8360934 0.0488614716785869 0.27774167029595753 chr7 159138663 8502942 0.05343102574639577 0.47431803816963336 chr8 146364022 8240075 0.05629850073401235 0.3793998347502718 chr9 141213431 4156766 0.02943605272220884 0.2501457341154543 chr10 135534747 7340193 0.05415727820704162 0.48066699051977496 chr11 135006516 4091749 0.030307788995902984 0.29488584283829455 chr12 133851895 4831917 0.0360989808922765 0.22305676909066494 chr13 115169878 2568384 0.022300831125305176 0.17335915982079037 chr14 107349540 2665771 0.024832626204080614 0.1997829926905154 chr15 102531392 2815325 0.027458175931133366 0.1935946027331171 chr16 90354753 4105469 0.04543722232299169 0.2641289035446067 chr17 81195210 2537819 0.03125577235405882 0.23045308789663047 chr18 78077248 4066335 0.05208092119230432 0.37050458507111667 chr19 59128983 3442544 0.05822092356974921 0.5539371384569207 chr20 63025520 3658053 0.05804082219393033 0.29969693909348966 chr21 48129895 2338393 0.048585042622677654 0.308064073811248 chr22 51304566 2156272 0.0420288517790015 0.2526713590866173 chrMT 16571 45889 2.769235411260636 2.4757329733454556 chrX 155270560 8669072 0.055832039248135644 0.29450148986066416 chrY 59373566 423812 0.007138058711177967 0.2354082443706963