BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525201.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 2,630,143 number of mapped reads = 2,406,077 (91.48%) number of supplementary alignments = 7,812 (0.3%) number of secondary alignments = 0 number of mapped bases = 139,149,955 bp number of sequenced bases = 139,104,722 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 113,164 duplication rate = 3.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7056 >>>>>>> ACTG content number of A's = 35,504,167 bp (25.52%) number of C's = 26,577,386 bp (19.11%) number of T's = 43,967,816 bp (31.61%) number of G's = 33,052,149 bp (23.76%) number of N's = 3,204 bp (0%) GC percentage = 42.87% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 721,144 number of insertions = 9,188 mapped reads with insertion percentage = 0.38% number of deletions = 28,348 mapped reads with deletion percentage = 1.17% homopolymer indels = 43.63% >>>>>>> Coverage mean coverageData = 0.0449X std coverageData = 0.4101X There is a 3.92% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.06% 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 15072216 0.060470124164705694 0.7900552769738489 chr2 243199373 11916868 0.04900040593443471 0.5896735542829462 chr3 198022430 11183763 0.056477253612128686 0.2721187743665654 chr4 191154276 7991776 0.041807989688914936 0.25276257027922155 chr5 180915260 6351472 0.035107442014565275 0.21174582823444144 chr6 171115067 7196175 0.042054595928715036 0.2728972995742502 chr7 159138663 8334403 0.05237195564474486 0.6050237280327682 chr8 146364022 6565105 0.04485463647616899 0.3655244819337336 chr9 141213431 4683105 0.03316331149832341 0.2816228916347551 chr10 135534747 7696735 0.056787909892951655 0.4377390261969307 chr11 135006516 6525851 0.048337303956499406 0.3432282919703056 chr12 133851895 6446736 0.04816320306858562 0.2513755532258052 chr13 115169878 4380149 0.03803207119833886 0.2207683249350195 chr14 107349540 5356541 0.04989812718340479 0.2628669275945713 chr15 102531392 3912889 0.03816283894789998 0.2286629885029203 chr16 90354753 3815699 0.042230196788872854 0.26726005831167365 chr17 81195210 2864429 0.03527830028396995 0.22128317538312892 chr18 78077248 3068439 0.03930004039076787 0.5788688636881123 chr19 59128983 2563531 0.04335489754660587 0.526228745146145 chr20 63025520 2628436 0.04170431279265923 0.2351912867281349 chr21 48129895 1794202 0.037278327742040575 0.2401980213870926 chr22 51304566 1152875 0.02247119681316474 0.16772469233557682 chrMT 16571 4563 0.27536056966990524 0.5848720333812777 chrX 155270560 7222515 0.04651567560521454 0.27531945029065 chrY 59373566 421482 0.007098815658133116 0.1955509680147496