BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240215.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 = 2,716,126 number of mapped reads = 2,129,303 (78.39%) number of supplementary alignments = 20,903 (0.77%) number of secondary alignments = 0 number of mapped bases = 140,029,371 bp number of sequenced bases = 139,969,273 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 337,251 duplication rate = 11.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2286 >>>>>>> ACTG content number of A's = 39,408,661 bp (28.16%) number of C's = 26,026,006 bp (18.59%) number of T's = 44,301,957 bp (31.65%) number of G's = 30,219,723 bp (21.59%) number of N's = 12,926 bp (0.01%) GC percentage = 40.18% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,133,026 number of insertions = 10,302 mapped reads with insertion percentage = 0.48% number of deletions = 34,998 mapped reads with deletion percentage = 1.62% homopolymer indels = 47.42% >>>>>>> Coverage mean coverageData = 0.0452X std coverageData = 0.5338X There is a 1.84% of reference with a coverageData >= 1X There is a 1.01% of reference with a coverageData >= 2X There is a 0.61% of reference with a coverageData >= 3X There is a 0.37% of reference with a coverageData >= 4X There is a 0.23% of reference with a coverageData >= 5X There is a 0.14% of reference with a coverageData >= 6X There is a 0.09% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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% 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 9502465 0.03812413771278026 0.6981888443948606 chr2 243199373 12123519 0.049850124408009885 0.5768527849967466 chr3 198022430 10402577 0.05253231666735935 0.47576132287977224 chr4 191154276 8205114 0.042924041102800126 0.4315772244388313 chr5 180915260 7147555 0.03950775075579584 0.396748155375384 chr6 171115067 11613576 0.06786997897736265 0.5844426134990726 chr7 159138663 5699277 0.0358132768779137 0.45107502482664974 chr8 146364022 6495205 0.044377060094727375 0.8357753853166946 chr9 141213431 7212686 0.051076487193346364 0.5477733500884008 chr10 135534747 6909543 0.05097986422625631 0.5009847681368615 chr11 135006516 8213690 0.060839211642199555 0.5944782630785611 chr12 133851895 5016949 0.03748134458611886 0.3963526580921678 chr13 115169878 2688559 0.023344289728256896 0.31105262521235455 chr14 107349540 2998528 0.027932378657607664 0.37510322486552516 chr15 102531392 4552846 0.044404410309771276 0.42345357349124185 chr16 90354753 4095314 0.045324831998600004 0.4499072700422226 chr17 81195210 3540488 0.04360464120974624 0.42378707224239753 chr18 78077248 4963313 0.06356926156003859 0.9187641347305512 chr19 59128983 2626788 0.04442471131289371 0.5343398572138306 chr20 63025520 4908563 0.07788214996084127 0.584045236827209 chr21 48129895 2898160 0.06021538172896492 0.5075924170729054 chr22 51304566 1266655 0.02468893314485888 0.32023520779268966 chrMT 16571 119561 7.215074527789512 7.01012328311245 chrX 155270560 6492430 0.041813657399058776 0.43606671456994134 chrY 59373566 336010 0.005659252469356481 0.1575394408994087