BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238505.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 = 3,004,667 number of mapped reads = 2,719,813 (90.52%) number of supplementary alignments = 16,695 (0.56%) number of secondary alignments = 0 number of mapped bases = 168,041,809 bp number of sequenced bases = 167,970,461 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 376,736 duplication rate = 11.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8238 >>>>>>> ACTG content number of A's = 41,446,165 bp (24.67%) number of C's = 29,668,290 bp (17.66%) number of T's = 55,716,081 bp (33.17%) number of G's = 41,128,480 bp (24.49%) number of N's = 11,445 bp (0.01%) GC percentage = 42.15% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 910,826 number of insertions = 10,816 mapped reads with insertion percentage = 0.39% number of deletions = 40,968 mapped reads with deletion percentage = 1.49% homopolymer indels = 43.14% >>>>>>> Coverage mean coverageData = 0.0543X std coverageData = 0.5768X There is a 4.01% of reference with a coverageData >= 1X There is a 0.94% of reference with a coverageData >= 2X There is a 0.25% 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% 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 15512091 0.062234914150926024 1.1270173148542653 chr2 243199373 16727756 0.06878206877613949 1.029413915989215 chr3 198022430 14861254 0.07504833669599954 0.35752956125313395 chr4 191154276 8642946 0.04521450516754331 0.31873556549096504 chr5 180915260 12052558 0.06661990812715302 0.3385568442717005 chr6 171115067 9164444 0.05355720078115623 0.4565368791501878 chr7 159138663 9562694 0.06009032512733879 0.675302514093907 chr8 146364022 10153062 0.0693685638127654 0.4725207449505848 chr9 141213431 6624970 0.04691458845724101 0.36971156938897703 chr10 135534747 7926139 0.05848049430453432 0.5101425381037257 chr11 135006516 6536691 0.04841759637734819 0.3587154357919657 chr12 133851895 6234463 0.046577323391648655 0.2880903472853061 chr13 115169878 3250400 0.028222657316698728 0.2767944605454807 chr14 107349540 5045326 0.046999046293072146 0.2906763391934139 chr15 102531392 4993458 0.04870174785103864 0.3401296640721293 chr16 90354753 3852285 0.0426351118463021 0.31996552858640726 chr17 81195210 3590008 0.04421452940388971 0.2885828794494037 chr18 78077248 4119357 0.05276001787358079 0.8497160353687158 chr19 59128983 2755544 0.04660225595288862 0.7028924923233235 chr20 63025520 3028210 0.04804736240176995 0.2980994934349831 chr21 48129895 1650008 0.034282393510312044 0.277542175839652 chr22 51304566 1912629 0.03727989824531407 0.24804904405703318 chrMT 16571 66640 4.0214833142236435 3.1558774563089105 chrX 155270560 9287045 0.05981201458924345 0.34030122045354894 chrY 59373566 491831 0.008283669537383017 0.23479337258538627