BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716724.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 = 2,460,750 number of mapped reads = 2,255,258 (91.65%) number of supplementary alignments = 11,971 (0.49%) number of secondary alignments = 0 number of mapped bases = 131,069,661 bp number of sequenced bases = 131,032,613 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 89,500 duplication rate = 2.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2936 >>>>>>> ACTG content number of A's = 33,575,633 bp (25.62%) number of C's = 26,351,857 bp (20.11%) number of T's = 40,156,154 bp (30.65%) number of G's = 30,947,303 bp (23.62%) number of N's = 1,666 bp (0%) GC percentage = 43.73% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 645,583 number of insertions = 8,520 mapped reads with insertion percentage = 0.38% number of deletions = 23,298 mapped reads with deletion percentage = 1.03% homopolymer indels = 42.75% >>>>>>> Coverage mean coverageData = 0.0423X std coverageData = 0.3505X There is a 3.69% of reference with a coverageData >= 1X There is a 0.39% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% 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% 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 10862460 0.04358047316560146 0.5686626032494873 chr2 243199373 12883046 0.05297318755834128 0.4710920973247684 chr3 198022430 8640051 0.04363167849217889 0.2369916844311738 chr4 191154276 7281996 0.03809486322974015 0.24706235956413342 chr5 180915260 6978769 0.03857479463037004 0.21998150102737402 chr6 171115067 7222412 0.04220792550079766 0.2567444983493331 chr7 159138663 6343815 0.03986344286428999 0.5603890370297336 chr8 146364022 11643381 0.07955084071138739 0.4391664047453116 chr9 141213431 5493513 0.03890219904082636 0.2685276301602903 chr10 135534747 6129138 0.04522189427925814 0.4118848792203645 chr11 135006516 4427426 0.03279416528310382 0.26605036717401687 chr12 133851895 6054029 0.04522931109791161 0.2521165560913397 chr13 115169878 3357612 0.02915356044746353 0.19040372317145718 chr14 107349540 4256188 0.039647938873329125 0.23106791559914738 chr15 102531392 3115465 0.030385474528620462 0.20393987955176418 chr16 90354753 4022742 0.044521642375581504 0.24968243198579138 chr17 81195210 5559034 0.06846504861555257 0.31269061147005794 chr18 78077248 3001588 0.03844382424954322 0.4349291452574972 chr19 59128983 2656847 0.044933074529626194 0.4749172181419248 chr20 63025520 2925774 0.04642205252729371 0.248856048870457 chr21 48129895 1353041 0.02811227824203647 0.20277215484738575 chr22 51304566 2025713 0.03948406853300348 0.2239209558744105 chrMT 16571 5308 0.3203186289300585 0.6311140518103955 chrX 155270560 4533355 0.029196487730835774 0.22160958520164403 chrY 59373566 296958 0.005001518689310324 0.12793441674803552