BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230362.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,555,510 number of mapped reads = 3,140,526 (88.33%) number of supplementary alignments = 28,955 (0.81%) number of secondary alignments = 0 number of mapped bases = 204,131,897 bp number of sequenced bases = 204,043,810 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 179,010 duplication rate = 4.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.376 >>>>>>> ACTG content number of A's = 55,139,621 bp (27.02%) number of C's = 37,507,583 bp (18.38%) number of T's = 64,441,361 bp (31.58%) number of G's = 46,852,507 bp (22.96%) number of N's = 102,738 bp (0.05%) GC percentage = 41.34% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,758,324 number of insertions = 16,037 mapped reads with insertion percentage = 0.51% number of deletions = 54,003 mapped reads with deletion percentage = 1.7% homopolymer indels = 45.86% >>>>>>> Coverage mean coverageData = 0.0659X std coverageData = 0.5145X There is a 5.3% of reference with a coverageData >= 1X There is a 0.92% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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% 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 15472688 0.062076828286016586 0.9256994224460844 chr2 243199373 16420706 0.06751952440272121 0.668439661811857 chr3 198022430 14626681 0.07386375876712552 0.3247263984057899 chr4 191154276 13389313 0.07004453826604433 0.34201772646225637 chr5 180915260 13159020 0.07273582117948481 0.3224773879080311 chr6 171115067 12233486 0.07149274587257708 0.4164733437314446 chr7 159138663 11677815 0.07338138187072742 0.6790515913918633 chr8 146364022 9814315 0.06705414941384981 0.586482355292466 chr9 141213431 8205314 0.058105761908723824 0.4604345096363892 chr10 135534747 9782390 0.07217625159989416 0.5048197584189458 chr11 135006516 8671295 0.06422871470885154 0.44646971907362887 chr12 133851895 8891747 0.06642974311271424 0.3123577294148574 chr13 115169878 6966492 0.060488837194044784 0.29577423468237724 chr14 107349540 6307910 0.0587604753592796 0.31757266360520053 chr15 102531392 6084398 0.05934180626358803 0.29484469507484246 chr16 90354753 5699107 0.06307478921446445 0.3541453528950169 chr17 81195210 5200983 0.06405529340954966 0.33365540167757846 chr18 78077248 5079307 0.06505489281589433 0.9010167270923143 chr19 59128983 3732473 0.06312425498676343 0.6197725890304472 chr20 63025520 4194612 0.06655418313089682 0.3241990450893277 chr21 48129895 2828536 0.05876879639982593 0.31820933342267077 chr22 51304566 2301723 0.044863901587238846 0.2507843532611349 chrMT 16571 26294 1.5867479331362018 1.6716999882255295 chrX 155270560 12810529 0.08250455849454011 0.39268668715046007 chrY 59373566 554763 0.009343602504858812 0.1844697761764509