BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236117.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 = 5,953,122 number of mapped reads = 5,131,822 (86.2%) number of supplementary alignments = 49,761 (0.84%) number of secondary alignments = 0 number of mapped bases = 331,159,368 bp number of sequenced bases = 330,993,122 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 650,723 duplication rate = 9.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1968 >>>>>>> ACTG content number of A's = 92,341,117 bp (27.9%) number of C's = 60,314,654 bp (18.22%) number of T's = 105,275,911 bp (31.81%) number of G's = 73,007,335 bp (22.06%) number of N's = 54,105 bp (0.02%) GC percentage = 40.28% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 2,598,491 number of insertions = 24,721 mapped reads with insertion percentage = 0.48% number of deletions = 95,931 mapped reads with deletion percentage = 1.85% homopolymer indels = 45.37% >>>>>>> Coverage mean coverageData = 0.107X std coverageData = 0.9283X There is a 6.05% of reference with a coverageData >= 1X There is a 2.47% of reference with a coverageData >= 2X There is a 1.06% of reference with a coverageData >= 3X There is a 0.46% of reference with a coverageData >= 4X There is a 0.21% of reference with a coverageData >= 5X There is a 0.1% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 17920871 0.07189900241010834 1.446001927241338 chr2 243199373 27951894 0.11493407098545438 1.159561326640007 chr3 198022430 39970920 0.20185046714152532 0.7074048327905639 chr4 191154276 15353448 0.08031966807794559 0.6013327415308888 chr5 180915260 23342403 0.12902395850963594 0.5767744846543623 chr6 171115067 29795196 0.17412374329374514 0.8961791251882354 chr7 159138663 22832979 0.14347851470889886 0.9808548534227934 chr8 146364022 25540810 0.174501968796676 1.794752197238422 chr9 141213431 16259823 0.1151436013193391 0.9257863024992954 chr10 135534747 6720097 0.049582097201981715 0.8362356585702987 chr11 135006516 12447985 0.09220284597226404 0.6574596347618041 chr12 133851895 11028397 0.08239253542133267 0.4937939497632844 chr13 115169878 8177881 0.0710071169824457 0.4179494345701003 chr14 107349540 12980576 0.12091878549269983 0.6168724401159299 chr15 102531392 3589913 0.03501281831812056 0.31556884388611955 chr16 90354753 6339493 0.0701622525601946 0.5019192760860816 chr17 81195210 7878799 0.097035268459802 0.5158138413901067 chr18 78077248 8617256 0.11036833675285276 1.6299001432285378 chr19 59128983 6637695 0.11225789220829319 1.1025868745952445 chr20 63025520 5679385 0.09011246555363606 0.5005011447390109 chr21 48129895 7000923 0.14545892942421754 0.710689229997618 chr22 51304566 1735083 0.03381927058889846 0.2719643940142336 chrMT 16571 521439 31.46696035242291 20.186127677110793 chrX 155270560 11951011 0.07696894375855926 0.5192241069075911 chrY 59373566 885091 0.014907155820824372 0.4512211414960809