BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714129.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 676,534 number of mapped reads = 500,400 (73.97%) number of supplementary alignments = 14,379 (2.13%) number of secondary alignments = 0 number of mapped bases = 64,894,832 bp number of sequenced bases = 63,390,308 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 439,384 duplication rate = 44.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.4588 >>>>>>> ACTG content number of A's = 17,202,039 bp (27.14%) number of C's = 13,015,476 bp (20.53%) number of T's = 16,377,452 bp (25.84%) number of G's = 16,794,883 bp (26.49%) number of N's = 458 bp (0%) GC percentage = 47.03% >>>>>>> Mismatches and indels general error rate = 0.047 number of mismatches = 2,745,990 number of insertions = 74,984 mapped reads with insertion percentage = 14.33% number of deletions = 247,935 mapped reads with deletion percentage = 45.28% homopolymer indels = 31.98% >>>>>>> Coverage mean coverageData = 0.021X std coverageData = 5.7836X There is a 0.06% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3957541 0.01587775783314899 2.289907097585605 chr2 243199373 8341963 0.03430092313601483 15.560458068394787 chr3 198022430 3833713 0.019359993713843428 4.204158424001498 chr4 191154276 2400096 0.012555805971089028 2.0698922776146524 chr5 180915260 4241184 0.023442931237530766 4.855638535169572 chr6 171115067 1855924 0.010846058342717419 1.6083819268421127 chr7 159138663 2785264 0.017502120147886376 7.469757869238375 chr8 146364022 2867456 0.019591262666996127 5.329412445609592 chr9 141213431 2807209 0.019879192652715875 3.8744125153952567 chr10 135534747 2564068 0.018918159783778546 2.59084211294656 chr11 135006516 3772070 0.02793991069290315 4.833413060194073 chr12 133851895 1906869 0.014246111345677997 1.860337037692641 chr13 115169878 2268760 0.019699248096798367 3.984832024488691 chr14 107349540 2634368 0.024540095840187112 4.933143690581563 chr15 102531392 1780851 0.017368836658337772 2.422122374973953 chr16 90354753 2240865 0.02480074291166509 4.284541380368442 chr17 81195210 1846319 0.022739260111526282 5.1636159605938845 chr18 78077248 1703109 0.021813127942214357 3.151940701943971 chr19 59128983 1159091 0.019602755555596145 2.9231225022178537 chr20 63025520 1466984 0.0232760316773269 3.8298942405292085 chr21 48129895 619124 0.01286360587323118 2.05265009673593 chr22 51304566 681626 0.01328587400973239 2.6880272342469875 chrMT 16571 536852 32.3970792348078 248.36040604123986 chrX 155270560 6292597 0.04052665875617374 3.483766637710657 chrY 59373566 330929 0.005573675665699446 1.1559159586663412