BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514739.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 53,261,248 number of mapped reads = 50,409,660 (94.65%) number of supplementary alignments = 1,577,910 (2.96%) number of secondary alignments = 0 number of mapped bases = 4,749,061,164 bp number of sequenced bases = 4,745,619,740 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 33,142,740 duplication rate = 42.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.153 >>>>>>> ACTG content number of A's = 1,253,853,740 bp (26.42%) number of C's = 1,098,019,705 bp (23.14%) number of T's = 1,265,309,237 bp (26.66%) number of G's = 1,100,388,703 bp (23.19%) number of N's = 28,048,355 bp (0.59%) GC percentage = 46.33% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 44,185,692 number of insertions = 1,803,448 mapped reads with insertion percentage = 3.42% number of deletions = 1,434,018 mapped reads with deletion percentage = 2.74% homopolymer indels = 42.37% >>>>>>> Coverage mean coverageData = 1.5341X std coverageData = 34.7347X There is a 6.04% of reference with a coverageData >= 1X There is a 3.81% of reference with a coverageData >= 2X There is a 3% of reference with a coverageData >= 3X There is a 2.62% of reference with a coverageData >= 4X There is a 2.38% of reference with a coverageData >= 5X There is a 2.2% of reference with a coverageData >= 6X There is a 2.06% of reference with a coverageData >= 7X There is a 1.95% of reference with a coverageData >= 8X There is a 1.85% of reference with a coverageData >= 9X There is a 1.77% of reference with a coverageData >= 10X There is a 1.69% of reference with a coverageData >= 11X There is a 1.62% of reference with a coverageData >= 12X There is a 1.56% of reference with a coverageData >= 13X There is a 1.51% of reference with a coverageData >= 14X There is a 1.46% of reference with a coverageData >= 15X There is a 1.41% of reference with a coverageData >= 16X There is a 1.37% of reference with a coverageData >= 17X There is a 1.32% of reference with a coverageData >= 18X There is a 1.29% of reference with a coverageData >= 19X There is a 1.25% of reference with a coverageData >= 20X There is a 1.22% of reference with a coverageData >= 21X There is a 1.19% of reference with a coverageData >= 22X There is a 1.16% of reference with a coverageData >= 23X There is a 1.13% of reference with a coverageData >= 24X There is a 1.1% of reference with a coverageData >= 25X There is a 1.07% of reference with a coverageData >= 26X There is a 1.05% of reference with a coverageData >= 27X There is a 1.03% of reference with a coverageData >= 28X There is a 1% of reference with a coverageData >= 29X There is a 0.98% of reference with a coverageData >= 30X There is a 0.96% of reference with a coverageData >= 31X There is a 0.94% of reference with a coverageData >= 32X There is a 0.92% of reference with a coverageData >= 33X There is a 0.9% of reference with a coverageData >= 34X There is a 0.89% of reference with a coverageData >= 35X There is a 0.87% of reference with a coverageData >= 36X There is a 0.85% of reference with a coverageData >= 37X There is a 0.84% of reference with a coverageData >= 38X There is a 0.82% of reference with a coverageData >= 39X There is a 0.81% of reference with a coverageData >= 40X There is a 0.79% of reference with a coverageData >= 41X There is a 0.78% of reference with a coverageData >= 42X There is a 0.77% of reference with a coverageData >= 43X There is a 0.75% of reference with a coverageData >= 44X There is a 0.74% of reference with a coverageData >= 45X There is a 0.73% of reference with a coverageData >= 46X There is a 0.72% of reference with a coverageData >= 47X There is a 0.7% of reference with a coverageData >= 48X There is a 0.69% of reference with a coverageData >= 49X There is a 0.68% of reference with a coverageData >= 50X There is a 0.67% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 165438861 0.6637450303483898 13.346967484596837 chr2 243199373 250995123 1.0320549757338395 62.42844404248001 chr3 198022430 1042576512 5.264941511928725 49.04257462528785 chr4 191154276 244616782 1.279682501060034 19.22601157582679 chr5 180915260 151226475 0.8358967341947827 15.297359929253476 chr6 171115067 152670612 0.8922102224931484 16.3488915169421 chr7 159138663 126178246 0.7928824059556162 12.257053702112183 chr8 146364022 252786979 1.7271114550268372 26.19044318013494 chr9 141213431 72223933 0.5114522923814521 34.59211122766458 chr10 135534747 314421599 2.31985971095663 44.917858788736 chr11 135006516 198378368 1.4693984696264586 21.436210661589794 chr12 133851895 430634139 3.2172434988686565 25.869089920976247 chr13 115169878 12543549 0.10891345217887614 6.434837852755639 chr14 107349540 83233152 0.7753470764755955 14.116898476226652 chr15 102531392 108172830 1.0550215684187727 17.168632162311482 chr16 90354753 154371151 1.7085006142399615 48.98031797734733 chr17 81195210 250137156 3.080688577565105 41.11515697840655 chr18 78077248 41360858 0.5297427747453394 32.70628240608321 chr19 59128983 145488157 2.46052188991649 27.08802636531061 chr20 63025520 85806477 1.361456073666667 23.365802728541748 chr21 48129895 73005198 1.5168368432966663 38.503588897693305 chr22 51304566 270382929 5.270153323195444 107.08568098763155 chrMT 16571 5097645 307.6244644258041 149.68025802408138 chrX 155270560 85405728 0.5500445673667951 14.313982933007559 chrY 59373566 31908705 0.5374227480289797 44.72489295116163