BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081031.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 = 3,196,294 number of mapped reads = 2,231,976 (69.83%) number of supplementary alignments = 10,567 (0.33%) number of secondary alignments = 0 number of mapped bases = 138,078,856 bp number of sequenced bases = 138,033,124 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 90,291 duplication rate = 3.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1683 >>>>>>> ACTG content number of A's = 38,762,436 bp (28.08%) number of C's = 28,085,378 bp (20.35%) number of T's = 40,215,969 bp (29.14%) number of G's = 30,967,625 bp (22.43%) number of N's = 1,716 bp (0%) GC percentage = 42.78% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 989,329 number of insertions = 8,662 mapped reads with insertion percentage = 0.39% number of deletions = 25,530 mapped reads with deletion percentage = 1.13% homopolymer indels = 46.56% >>>>>>> Coverage mean coverageData = 0.0446X std coverageData = 0.318X There is a 3.68% of reference with a coverageData >= 1X There is a 0.58% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% 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 11368488 0.045610670715239665 0.4708374812392417 chr2 243199373 11962948 0.049189880107133335 0.32137866663657455 chr3 198022430 8887424 0.04488089556319453 0.24823396090941183 chr4 191154276 8943431 0.04678645535504526 0.2698160718899048 chr5 180915260 8264415 0.0456811382301305 0.2513784531857769 chr6 171115067 8138752 0.047563035463148315 0.291443264952182 chr7 159138663 8363992 0.052557887833957734 0.5185835397315345 chr8 146364022 6694215 0.04573675216440827 0.2930088662955956 chr9 141213431 5464040 0.03869348659901904 0.280094970398688 chr10 135534747 6000799 0.04427498580862072 0.3063617455129048 chr11 135006516 6273430 0.04646760901525671 0.30824290204527344 chr12 133851895 6343745 0.047393763084190924 0.25599568328396727 chr13 115169878 3976813 0.03452997492972946 0.2185551518173306 chr14 107349540 4594261 0.042797211799882884 0.24855506839870473 chr15 102531392 3903274 0.038069062790057506 0.24226835956095183 chr16 90354753 4478836 0.04956945651768867 0.2724755899222321 chr17 81195210 3987491 0.04910992902167505 0.2899178932419507 chr18 78077248 3338208 0.04275519547000427 0.46152235187850066 chr19 59128983 2899764 0.04904133054343248 0.3813398106001928 chr20 63025520 2657101 0.04215912855617851 0.24877221154518234 chr21 48129895 1513712 0.03145055687322817 0.23460313725527632 chr22 51304566 1774223 0.034582165649739635 0.2181322598072435 chrMT 16571 27025 1.6308611429605937 1.5907475662076809 chrX 155270560 7875311 0.050719923983013906 0.28501287082189214 chrY 59373566 347158 0.0058470127935384576 0.13556958180356343