BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238262.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 = 1,752,196 number of mapped reads = 1,371,756 (78.29%) number of supplementary alignments = 14,337 (0.82%) number of secondary alignments = 0 number of mapped bases = 86,920,136 bp number of sequenced bases = 86,867,123 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 156,939 duplication rate = 8.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.243 >>>>>>> ACTG content number of A's = 24,435,621 bp (28.13%) number of C's = 16,411,578 bp (18.89%) number of T's = 26,948,452 bp (31.02%) number of G's = 19,051,622 bp (21.93%) number of N's = 19,850 bp (0.02%) GC percentage = 40.82% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 856,464 number of insertions = 7,290 mapped reads with insertion percentage = 0.53% number of deletions = 32,204 mapped reads with deletion percentage = 2.32% homopolymer indels = 46.54% >>>>>>> Coverage mean coverageData = 0.0281X std coverageData = 0.3229X There is a 1.72% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.25% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% 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 6175005 0.024774281304599036 0.4635312745273817 chr2 243199373 7675493 0.03156049666295809 0.3835767460558022 chr3 198022430 5634010 0.028451372907604456 0.2554834630777051 chr4 191154276 5995257 0.031363446978293075 0.2777982514786966 chr5 180915260 5331587 0.029470078975095855 0.2594524919848376 chr6 171115067 5250967 0.03068676003849503 0.3076213176339381 chr7 159138663 5491815 0.034509621335702685 0.40521922340030236 chr8 146364022 4314675 0.029479068291796463 0.4018471968966766 chr9 141213431 3458864 0.024493874098987085 0.27660183288749934 chr10 135534747 3622877 0.02673024504926401 0.28776291012528427 chr11 135006516 3631024 0.026895175933582347 0.2735610859043919 chr12 133851895 3812517 0.028483100668839988 0.2566159090904206 chr13 115169878 3249046 0.028210900770425405 0.2603155582044925 chr14 107349540 3101003 0.028886970545006527 0.32095527728553497 chr15 102531392 2312234 0.022551473796434948 0.3349084732337518 chr16 90354753 2517961 0.027867499123150723 0.25692701686369934 chr17 81195210 2185106 0.02691175994248922 0.2602214405677961 chr18 78077248 2384643 0.030542098512488555 0.4363076987917542 chr19 59128983 1473418 0.024918710338718324 0.3358439121485023 chr20 63025520 1715501 0.027219148687706186 0.2490967058448414 chr21 48129895 1161638 0.02413547754467364 0.23719404679794923 chr22 51304566 941825 0.018357527866038278 0.19750957264241809 chrMT 16571 17441 1.052501357793736 1.8467217760268382 chrX 155270560 5220689 0.033623173639613334 0.2967297898938954 chrY 59373566 245540 0.0041355104054218335 0.11658022961426251