BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080641.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 = 5,487,891 number of mapped reads = 4,531,079 (82.57%) number of supplementary alignments = 32,700 (0.6%) number of secondary alignments = 0 number of mapped bases = 300,702,566 bp number of sequenced bases = 300,586,073 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 251,976 duplication rate = 4.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0413 >>>>>>> ACTG content number of A's = 81,654,759 bp (27.17%) number of C's = 54,077,008 bp (17.99%) number of T's = 96,959,734 bp (32.26%) number of G's = 67,651,609 bp (22.51%) number of N's = 242,963 bp (0.08%) GC percentage = 40.5% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 2,743,384 number of insertions = 26,335 mapped reads with insertion percentage = 0.58% number of deletions = 71,226 mapped reads with deletion percentage = 1.56% homopolymer indels = 47.84% >>>>>>> Coverage mean coverageData = 0.0971X std coverageData = 0.779X There is a 7.69% of reference with a coverageData >= 1X There is a 1.37% of reference with a coverageData >= 2X There is a 0.32% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% 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 0.01% 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 30287113 0.12151268822716393 1.0508802639772665 chr2 243199373 23154521 0.09520797983307301 0.8530261528151251 chr3 198022430 17335349 0.08754235063169359 0.35591737238528476 chr4 191154276 15027383 0.07861389927787961 0.37386903964292567 chr5 180915260 16969870 0.09380010287689386 0.372166634823537 chr6 171115067 15153665 0.0885583325049921 0.6276896617993378 chr7 159138663 17086879 0.10737101014855202 2.1396928638636297 chr8 146364022 27578661 0.18842513770221483 0.8586465635898611 chr9 141213431 10856977 0.07688345876958404 0.6564076395760092 chr10 135534747 14754384 0.10886052710896343 0.6418454296290712 chr11 135006516 13239739 0.09806740735387913 0.5687795693825689 chr12 133851895 11597475 0.08664408524063107 0.3684960295547136 chr13 115169878 7358514 0.06389269597038212 0.3021811359014243 chr14 107349540 7398250 0.06891738893338528 0.3866798270182963 chr15 102531392 6986795 0.06814298395558699 0.316939463204316 chr16 90354753 8845734 0.09790004074273768 0.4323271282478876 chr17 81195210 6573518 0.08095943098121182 0.4198540710675444 chr18 78077248 9491309 0.1215630576528517 1.0799194034191397 chr19 59128983 5643703 0.09544732064814983 0.7539662475436192 chr20 63025520 6760736 0.10726981705188629 0.4219541701325262 chr21 48129895 4577382 0.09510475765633812 0.4196585048009402 chr22 51304566 3064385 0.05972928413428154 0.28942039403193187 chrMT 16571 112678 6.79971033733631 7.833336612548728 chrX 155270560 20132954 0.12966369155878615 0.525421627262127 chrY 59373566 714592 0.012035524361127307 0.2229604104000056