BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231819.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 = 4,968,866 number of mapped reads = 4,646,751 (93.52%) number of supplementary alignments = 23,765 (0.48%) number of secondary alignments = 0 number of mapped bases = 296,503,635 bp number of sequenced bases = 296,395,963 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 433,033 duplication rate = 7.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1805 >>>>>>> ACTG content number of A's = 77,136,835 bp (26.02%) number of C's = 53,090,732 bp (17.91%) number of T's = 96,266,074 bp (32.48%) number of G's = 69,790,456 bp (23.55%) number of N's = 111,866 bp (0.04%) GC percentage = 41.46% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 1,765,182 number of insertions = 17,434 mapped reads with insertion percentage = 0.37% number of deletions = 60,575 mapped reads with deletion percentage = 1.29% homopolymer indels = 44.59% >>>>>>> Coverage mean coverageData = 0.0958X std coverageData = 1.1777X There is a 7.5% of reference with a coverageData >= 1X There is a 1.39% of reference with a coverageData >= 2X There is a 0.3% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% 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 0.01% 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% 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 28471199 0.11422719384117402 2.941165647513307 chr2 243199373 23935672 0.09841995768632184 1.0527740830705152 chr3 198022430 31607053 0.15961349933944352 0.48369678719223663 chr4 191154276 9191854 0.04808604961575644 0.3116697116470148 chr5 180915260 13429271 0.07422961998893847 0.36253304234315337 chr6 171115067 22243424 0.12999103112293436 0.8170145549182984 chr7 159138663 26672226 0.16760368283350477 2.2629379112105954 chr8 146364022 25000332 0.17080927169383198 1.1229508340664631 chr9 141213431 12999802 0.09205782982498315 0.7198864192479567 chr10 135534747 16290511 0.12019435134224289 0.9528401888705291 chr11 135006516 5493034 0.040687176906335394 0.5123726478245542 chr12 133851895 9899044 0.07395520250198923 0.37095774397608755 chr13 115169878 6337807 0.05503007479091017 0.2929404120998946 chr14 107349540 11788498 0.10981414545418638 0.44330838087825997 chr15 102531392 7186609 0.07009179198503421 0.3453534669912622 chr16 90354753 5707673 0.06316959330296659 0.4171408553554192 chr17 81195210 6796403 0.08370448207474308 0.3994789772350062 chr18 78077248 6221036 0.07967796201013642 1.4541570580856804 chr19 59128983 7807856 0.1320478655957942 1.448097474123592 chr20 63025520 8067026 0.12799618313343547 0.46880273463240246 chr21 48129895 4729827 0.09827212380164137 0.40383457022522407 chr22 51304566 2484287 0.04842233730229781 0.2601367839203589 chrMT 16571 236374 14.26431718061674 8.633063965779312 chrX 155270560 3396194 0.02187274909036201 0.3269742607413662 chrY 59373566 510623 0.008600174023571366 0.189820633874235