BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716445.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 = 980,146 number of mapped reads = 903,213 (92.15%) number of supplementary alignments = 13,711 (1.4%) number of secondary alignments = 0 number of mapped bases = 71,771,805 bp number of sequenced bases = 71,738,768 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 28,722 duplication rate = 1.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6025 >>>>>>> ACTG content number of A's = 17,639,381 bp (24.59%) number of C's = 13,946,581 bp (19.44%) number of T's = 22,243,418 bp (31.01%) number of G's = 17,904,868 bp (24.96%) number of N's = 4,520 bp (0.01%) GC percentage = 44.4% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 581,986 number of insertions = 6,917 mapped reads with insertion percentage = 0.75% number of deletions = 18,442 mapped reads with deletion percentage = 2.01% homopolymer indels = 43.62% >>>>>>> Coverage mean coverageData = 0.0232X std coverageData = 0.277X There is a 2.09% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 5774005 0.02316545883350076 0.41572266714621997 chr2 243199373 6134003 0.02522211683498049 0.3986892394573962 chr3 198022430 4692732 0.023697982092230663 0.16593540247961888 chr4 191154276 4539254 0.02374654700374058 0.18210939945197832 chr5 180915260 4268758 0.023595345135617635 0.16787547284515622 chr6 171115067 4026104 0.023528635266232868 0.19049252035537229 chr7 159138663 3999740 0.025133678545483318 0.3433155319085978 chr8 146364022 3599480 0.02459265570059287 0.3652651598175051 chr9 141213431 3098011 0.02193850101977906 0.3061380361836691 chr10 135534747 3420888 0.0252399334910036 0.27993589314585615 chr11 135006516 3234138 0.023955421529431958 0.26263242123904923 chr12 133851895 3291634 0.024591612991358845 0.1723297043784062 chr13 115169878 2188276 0.019000419536782005 0.146942941493954 chr14 107349540 2146997 0.02000005775525447 0.19256791092207487 chr15 102531392 2053542 0.020028422124611357 0.15372768660193606 chr16 90354753 2139301 0.023676684722938705 0.18567959540853352 chr17 81195210 2074691 0.025551889083112168 0.18285951086338 chr18 78077248 1951345 0.024992492050949337 0.5620914784699945 chr19 59128983 1637066 0.027686354761082225 0.31045506948185286 chr20 63025520 1493294 0.023693481624586357 0.17592270253289577 chr21 48129895 913695 0.018983939192055165 0.15951751664378416 chr22 51304566 865129 0.016862612189332233 0.1396057105133338 chrMT 16571 6331 0.3820529841288999 0.6957714580797879 chrX 155270560 4024556 0.025919633445000777 0.21632697786140445 chrY 59373566 198835 0.003348880880760977 0.10896037070662132