BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084272.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 = 1,334,734 number of mapped reads = 1,114,010 (83.46%) number of supplementary alignments = 8,628 (0.65%) number of secondary alignments = 0 number of mapped bases = 75,346,411 bp number of sequenced bases = 75,323,656 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,500 duplication rate = 1.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3363 >>>>>>> ACTG content number of A's = 22,757,598 bp (30.21%) number of C's = 14,109,685 bp (18.73%) number of T's = 22,062,133 bp (29.29%) number of G's = 16,393,441 bp (21.76%) number of N's = 799 bp (0%) GC percentage = 40.5% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 620,005 number of insertions = 5,779 mapped reads with insertion percentage = 0.51% number of deletions = 13,947 mapped reads with deletion percentage = 1.24% homopolymer indels = 43.32% >>>>>>> Coverage mean coverageData = 0.0243X std coverageData = 0.2316X There is a 2.3% of reference with a coverageData >= 1X There is a 0.09% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 6190995 0.024838433602137343 0.39366640513616985 chr2 243199373 6606231 0.027163848814692464 0.258463198490548 chr3 198022430 5131551 0.025913988632499864 0.16628456676418776 chr4 191154276 4790758 0.025062259135652295 0.16629616021512886 chr5 180915260 4572393 0.02527367232592762 0.16431732646059422 chr6 171115067 4303249 0.025148276393451664 0.1949492584422785 chr7 159138663 4203073 0.02641138816153055 0.3042761757201697 chr8 146364022 3887934 0.02656345423467524 0.21830877400934703 chr9 141213431 3125610 0.022133942769225683 0.2113136312984149 chr10 135534747 3823964 0.028213901487564662 0.2523165502874718 chr11 135006516 3557439 0.026350128167147133 0.21349570831608533 chr12 133851895 3437108 0.025678441085948016 0.1662302852063508 chr13 115169878 2398532 0.020826035779945865 0.14854000554922878 chr14 107349540 2194609 0.02044358084813405 0.16254135134698144 chr15 102531392 2022560 0.01972625125385989 0.15021355685793097 chr16 90354753 1951307 0.021596063684663054 0.17187083300522102 chr17 81195210 1853352 0.02282587852165171 0.177348414146801 chr18 78077248 2116299 0.02710519458882567 0.4358937799756379 chr19 59128983 1355293 0.022920959083635853 0.2856370361880243 chr20 63025520 1481595 0.023507858404024275 0.16277611032264655 chr21 48129895 919662 0.019107916192212762 0.1488608546622158 chr22 51304566 725117 0.014133576337045713 0.1224677627849368 chrMT 16571 33738 2.0359664474081227 1.8440635503429537 chrX 155270560 4499761 0.028980129910009984 0.19699450821829506 chrY 59373566 164281 0.0027669047198546235 0.06684408951176986