BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013327.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 = 4,280,569 number of mapped reads = 3,420,499 (79.91%) number of supplementary alignments = 23,200 (0.54%) number of secondary alignments = 0 number of mapped bases = 224,220,350 bp number of sequenced bases = 224,129,102 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 129,778 duplication rate = 2.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5743 >>>>>>> ACTG content number of A's = 64,189,760 bp (28.64%) number of C's = 42,316,977 bp (18.88%) number of T's = 68,247,195 bp (30.45%) number of G's = 49,348,059 bp (22.02%) number of N's = 27,111 bp (0.01%) GC percentage = 40.9% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 1,651,200 number of insertions = 16,380 mapped reads with insertion percentage = 0.47% number of deletions = 54,387 mapped reads with deletion percentage = 1.57% homopolymer indels = 46.32% >>>>>>> Coverage mean coverageData = 0.0724X std coverageData = 0.6178X There is a 6.14% of reference with a coverageData >= 1X There is a 0.8% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% 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 18521397 0.07430832840332222 1.3939388728423996 chr2 243199373 18877892 0.07762311130629436 0.6452231428237256 chr3 198022430 15408450 0.07781163982282209 0.31442098614221314 chr4 191154276 14997298 0.07845651331388474 0.36779892986084933 chr5 180915260 13780535 0.07617121408111178 0.3144774575948905 chr6 171115067 11653244 0.06810179959196697 0.37213166878493553 chr7 159138663 13101599 0.08232819575718064 0.8073329267322025 chr8 146364022 12306546 0.08408176976716314 0.8179294623546306 chr9 141213431 9217011 0.06527007335442477 0.461628145791195 chr10 135534747 10898021 0.08040757991011707 0.5184812236281623 chr11 135006516 9855486 0.0730000765296395 0.458063803507386 chr12 133851895 10220052 0.07635343526514884 0.3206220744974017 chr13 115169878 7175279 0.06230169836595642 0.2835189599319495 chr14 107349540 5629783 0.052443475770832367 0.28487430465549923 chr15 102531392 6827997 0.06659420950804998 0.2993151554716189 chr16 90354753 5910326 0.06541245262437938 0.3292795717650663 chr17 81195210 5798920 0.07141948398187528 0.3550767577163853 chr18 78077248 6032437 0.07726241836802444 0.8873226181802897 chr19 59128983 4217654 0.07132972336087702 0.9026815209722286 chr20 63025520 4579788 0.07266561227896255 0.31778841392624735 chr21 48129895 3163126 0.06572060878171457 0.3327928050041159 chr22 51304566 2312895 0.04508165998324593 0.23867435707687798 chrMT 16571 84860 5.120994508478668 3.583841123260449 chrX 155270560 13056209 0.08408682882318451 0.38086310405059326 chrY 59373566 593545 0.009996788806655136 0.247093676545316