BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080668.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 = 1,730,724 number of mapped reads = 1,570,873 (90.76%) number of supplementary alignments = 13,791 (0.8%) number of secondary alignments = 0 number of mapped bases = 103,325,621 bp number of sequenced bases = 103,287,643 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 61,444 duplication rate = 3.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7086 >>>>>>> ACTG content number of A's = 27,661,876 bp (26.78%) number of C's = 19,200,263 bp (18.59%) number of T's = 32,475,068 bp (31.44%) number of G's = 23,946,245 bp (23.18%) number of N's = 4,191 bp (0%) GC percentage = 41.77% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 722,610 number of insertions = 7,806 mapped reads with insertion percentage = 0.49% number of deletions = 23,822 mapped reads with deletion percentage = 1.5% homopolymer indels = 47.35% >>>>>>> Coverage mean coverageData = 0.0334X std coverageData = 0.2981X There is a 2.91% 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 12716572 0.051019218925035296 0.3819702703653127 chr2 243199373 7034096 0.028923166672802238 0.44820494871370314 chr3 198022430 5004938 0.025274601468126615 0.17586638273135827 chr4 191154276 4458787 0.0233255938255862 0.1751082612461357 chr5 180915260 4793462 0.02649562010413052 0.1805393123238405 chr6 171115067 6269349 0.03663820556491381 0.2917190811986335 chr7 159138663 6704672 0.0421310062156297 0.6408480494435641 chr8 146364022 12417507 0.08483988640323098 0.38399800629359354 chr9 141213431 3359509 0.023790293715050377 0.22626133458214123 chr10 135534747 4956727 0.03657163280793227 0.23664276854131405 chr11 135006516 4370877 0.032375304018659366 0.2286860706170253 chr12 133851895 3399301 0.025395987109483955 0.18037215124620018 chr13 115169878 2124654 0.018448000787150264 0.15038261180144344 chr14 107349540 2072065 0.019302038928159355 0.15817834232326816 chr15 102531392 1862021 0.01816049664087268 0.15991170834074014 chr16 90354753 2635396 0.029167209388531005 0.1946243149453895 chr17 81195210 1783784 0.021969079210460814 0.17434486636006943 chr18 78077248 3255115 0.04169095457872696 0.34095105280950666 chr19 59128983 1802929 0.03049145966200704 0.25772703893803434 chr20 63025520 2622860 0.04161584069437269 0.23045232867231316 chr21 48129895 1497410 0.031111848467568856 0.20020675988193093 chr22 51304566 1026348 0.020005003063470025 0.15582810517154716 chrMT 16571 8986 0.5422726449821978 0.8671067892608454 chrX 155270560 6930999 0.044638204434890943 0.25314144450108916 chrY 59373566 217257 0.0036591536374958513 0.0734667720126436