BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524874.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 = 2,103,373 number of mapped reads = 1,919,824 (91.27%) number of supplementary alignments = 8,822 (0.42%) number of secondary alignments = 0 number of mapped bases = 111,766,325 bp number of sequenced bases = 111,732,221 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 67,256 duplication rate = 2.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1259 >>>>>>> ACTG content number of A's = 28,471,750 bp (25.48%) number of C's = 22,059,673 bp (19.74%) number of T's = 36,393,431 bp (32.57%) number of G's = 24,793,752 bp (22.19%) number of N's = 13,615 bp (0.01%) GC percentage = 41.93% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 552,483 number of insertions = 7,323 mapped reads with insertion percentage = 0.38% number of deletions = 21,884 mapped reads with deletion percentage = 1.13% homopolymer indels = 44.26% >>>>>>> Coverage mean coverageData = 0.0361X std coverageData = 0.3498X There is a 3.23% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 9532131 0.03824315847943263 0.7011884931438366 chr2 243199373 7186688 0.029550602500936548 0.35698684617850407 chr3 198022430 8256686 0.04169571093537232 0.2205006339739434 chr4 191154276 4450613 0.02328283255353388 0.18690132986647912 chr5 180915260 6963097 0.038488168438638067 0.21395395458534502 chr6 171115067 7392110 0.04319964413186362 0.25440296343461694 chr7 159138663 5160010 0.032424615757894105 0.477684959875375 chr8 146364022 12350864 0.0843845627581893 0.47299163786218645 chr9 141213431 4722853 0.03344478614077438 0.29302025304384804 chr10 135534747 5693006 0.04200403310599016 0.3178333662246265 chr11 135006516 5459691 0.04044020364172645 0.31159723642545056 chr12 133851895 4478943 0.033461931936040204 0.20519099015135242 chr13 115169878 3041407 0.026408007482650975 0.17809035830446743 chr14 107349540 2381801 0.022187342395691683 0.17729111743847772 chr15 102531392 3400929 0.03316963647582196 0.19812382847973772 chr16 90354753 3211895 0.03554760423062636 0.22609542526142115 chr17 81195210 2865972 0.03529730386804837 0.2364128289702305 chr18 78077248 2769362 0.035469513474655254 0.5684716599858185 chr19 59128983 1652255 0.027943233862148448 0.4829524462599684 chr20 63025520 2405905 0.038173504954818305 0.21257123077384857 chr21 48129895 1643776 0.034152910576680046 0.21874296890610725 chr22 51304566 664779 0.012957501677336088 0.12192420001843753 chrMT 16571 21701 1.3095769718182366 1.3960708599579605 chrX 155270560 5774601 0.03719057237894936 0.24574931100600778 chrY 59373566 285250 0.004804326558387953 0.1184497708253847