BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525196.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 841,876 number of mapped reads = 762,498 (90.57%) number of supplementary alignments = 2,000 (0.24%) number of secondary alignments = 0 number of mapped bases = 43,774,122 bp number of sequenced bases = 43,760,405 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,381 duplication rate = 1.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6878 >>>>>>> ACTG content number of A's = 11,116,549 bp (25.4%) number of C's = 7,909,337 bp (18.07%) number of T's = 14,259,824 bp (32.59%) number of G's = 10,473,662 bp (23.93%) number of N's = 1,033 bp (0%) GC percentage = 42.01% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 230,854 number of insertions = 2,713 mapped reads with insertion percentage = 0.35% number of deletions = 8,741 mapped reads with deletion percentage = 1.14% homopolymer indels = 42.35% >>>>>>> Coverage mean coverageData = 0.0141X std coverageData = 0.1645X There is a 1.33% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 4655251 0.018676988572076617 0.25907181252850614 chr2 243199373 3684635 0.015150676395863899 0.21598895147224734 chr3 198022430 3052266 0.015413738736566358 0.13081592898491548 chr4 191154276 2476050 0.012953149946800038 0.1221926862482772 chr5 180915260 1999035 0.01104956541532207 0.10961088159019852 chr6 171115067 2902181 0.016960405947186404 0.14783120787250062 chr7 159138663 3234256 0.02032350868751486 0.2691760760703395 chr8 146364022 2587958 0.017681654033803472 0.15888102225833295 chr9 141213431 1460309 0.010341148073939228 0.12371948246766111 chr10 135534747 2346571 0.01731342738257371 0.1904267143793424 chr11 135006516 2026869 0.015013119811194891 0.14178922958216447 chr12 133851895 1960703 0.014648302140212508 0.12812731692884896 chr13 115169878 964700 0.00837632214909527 0.09605931628385249 chr14 107349540 1646133 0.015334327468939318 0.13061085519854887 chr15 102531392 927168 0.009042771993186243 0.1023534862908558 chr16 90354753 1172426 0.0129758088099693 0.12599283100580844 chr17 81195210 788454 0.009710597460121108 0.10441658609062722 chr18 78077248 937875 0.012012142128779948 0.19160208636633394 chr19 59128983 650759 0.011005753303756298 0.18184029144782868 chr20 63025520 907904 0.014405339297478227 0.12673144981019283 chr21 48129895 521254 0.010830150367043186 0.11432263681333976 chr22 51304566 356789 0.0069543322908140375 0.08680729283688328 chrMT 16571 25636 1.5470400096554222 1.4583023534865416 chrX 155270560 2366207 0.015239250763312761 0.13529809203071144 chrY 59373566 122733 0.0020671320297655695 0.06714722394032777