BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063575.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 = 2,835,619 number of mapped reads = 2,591,440 (91.39%) number of supplementary alignments = 14,663 (0.52%) number of secondary alignments = 0 number of mapped bases = 173,795,480 bp number of sequenced bases = 173,715,263 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 107,662 duplication rate = 2.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.9073 >>>>>>> ACTG content number of A's = 48,279,498 bp (27.79%) number of C's = 32,629,769 bp (18.78%) number of T's = 53,453,131 bp (30.77%) number of G's = 39,347,955 bp (22.65%) number of N's = 4,910 bp (0%) GC percentage = 41.43% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,397,881 number of insertions = 12,843 mapped reads with insertion percentage = 0.49% number of deletions = 45,412 mapped reads with deletion percentage = 1.73% homopolymer indels = 46.91% >>>>>>> Coverage mean coverageData = 0.0561X std coverageData = 0.6275X There is a 4.78% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.09% 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 0.01% 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 15791586 0.0633562553892293 1.4549107019694614 chr2 243199373 13249138 0.054478503939235076 0.5437055778382615 chr3 198022430 16267730 0.08215094623371706 0.3335451926729158 chr4 191154276 7242383 0.0378876327098223 0.25444349203908667 chr5 180915260 7217554 0.03989466670749609 0.23519048044438468 chr6 171115067 11656263 0.06811944269057266 0.41254966296269663 chr7 159138663 11218954 0.07049797823172613 0.8254046937114559 chr8 146364022 8292477 0.05665652587765045 0.6799950752331563 chr9 141213431 7120009 0.050420196928718485 0.5819905413622571 chr10 135534747 11760023 0.08676758735529273 0.7319751275170153 chr11 135006516 6036700 0.04471413809389763 0.3671316155905402 chr12 133851895 7859755 0.058719788763543466 0.2978719546990896 chr13 115169878 2719986 0.023617164897925827 0.17095629903275306 chr14 107349540 5414122 0.050434515136254895 0.3398066220539631 chr15 102531392 3424470 0.033399234451045 0.20489749695130635 chr16 90354753 3369205 0.03728863051620539 0.29739882758277625 chr17 81195210 4997964 0.06155491192152838 0.30356092665618306 chr18 78077248 1961480 0.025122299392519573 1.0787678850636024 chr19 59128983 4778233 0.08081033627789606 0.8495427175314668 chr20 63025520 2419365 0.038387069237984864 0.24612952747264494 chr21 48129895 2104737 0.04373034680420558 0.2899912334941161 chr22 51304566 2610567 0.050883716665686245 0.25438549228530016 chrMT 16571 51716 3.1208738157021303 2.309490563640808 chrX 155270560 15762776 0.10151812423423989 0.47717667977212114 chrY 59373566 468287 0.007887129433997614 0.18761343737416344