BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085056.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 = 2,659,055 number of mapped reads = 2,216,645 (83.36%) number of supplementary alignments = 11,463 (0.43%) number of secondary alignments = 0 number of mapped bases = 132,491,122 bp number of sequenced bases = 132,448,661 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 79,352 duplication rate = 2.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6352 >>>>>>> ACTG content number of A's = 39,886,161 bp (30.11%) number of C's = 26,335,746 bp (19.88%) number of T's = 38,348,808 bp (28.95%) number of G's = 27,875,006 bp (21.05%) number of N's = 2,940 bp (0%) GC percentage = 40.93% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,108,508 number of insertions = 10,404 mapped reads with insertion percentage = 0.47% number of deletions = 26,442 mapped reads with deletion percentage = 1.18% homopolymer indels = 45.63% >>>>>>> Coverage mean coverageData = 0.0428X std coverageData = 0.3288X There is a 3.62% of reference with a coverageData >= 1X There is a 0.49% 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 10356851 0.04155195665490438 0.4715181840684339 chr2 243199373 11583774 0.047630772469137904 0.40144703499037854 chr3 198022430 9356980 0.04725212189346429 0.24937403266674332 chr4 191154276 8660773 0.045307764917589394 0.2735239960923472 chr5 180915260 8138746 0.04498650915351198 0.24479775536278167 chr6 171115067 8565901 0.05005930307703412 0.2873428417244602 chr7 159138663 6633678 0.04168489212454927 0.2650874570107898 chr8 146364022 6472099 0.044219193429926376 0.5219211790453243 chr9 141213431 6294544 0.04457468355117014 0.3450051966561611 chr10 135534747 5889635 0.04345479760994426 0.3503638353326328 chr11 135006516 6098457 0.04517157527418899 0.2899800928506383 chr12 133851895 5978152 0.04466243828673475 0.24914231197577535 chr13 115169878 4295100 0.03729360553807307 0.22020431678364927 chr14 107349540 4046702 0.03769650060913163 0.24362382422578066 chr15 102531392 3539254 0.03451873549127276 0.21246068059254683 chr16 90354753 3765277 0.04167215198961365 0.25606257790040743 chr17 81195210 3363651 0.041426717167182645 0.2911934357344216 chr18 78077248 3469897 0.04444184559373814 0.5589930274678817 chr19 59128983 2117267 0.035807600479108526 0.3687132054561792 chr20 63025520 2931002 0.046505003052731655 0.25577407950249087 chr21 48129895 1803358 0.03746856293785806 0.25575894007758315 chr22 51304566 1289830 0.025140647325620102 0.18004649799978126 chrMT 16571 28149 1.69869048337457 1.5957397401104152 chrX 155270560 7428333 0.04784121986808059 0.27714296755452983 chrY 59373566 383712 0.006462673978517646 0.15454375204392648