BamQC report ----------------------------------- >>>>>>> Input bam file = SRR22354863.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP408873/SRP408873.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 = 177,280,132 number of mapped reads = 174,249,832 (98.29%) number of supplementary alignments = 7,210,071 (4.07%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 87,256,215 number of mapped paired reads (second in pair) = 86,993,617 number of mapped paired reads (both in pair) = 173,837,182 number of mapped paired reads (singletons) = 412,650 number of mapped bases = 20,962,467,096 bp number of sequenced bases = 20,953,785,257 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 160,699,846 duplication rate = 86.29% >>>>>>> Insert size mean insert size = 469,745.0619 std insert size = 7,968,018.1932 median insert size = 140 >>>>>>> Mapping quality mean mapping quality = 53.6914 >>>>>>> ACTG content number of A's = 5,763,295,653 bp (27.5%) number of C's = 4,521,870,740 bp (21.58%) number of T's = 5,876,661,908 bp (28.05%) number of G's = 4,791,505,896 bp (22.87%) number of N's = 451,060 bp (0%) GC percentage = 44.45% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 121,501,744 number of insertions = 3,149,715 mapped reads with insertion percentage = 1.71% number of deletions = 3,437,799 mapped reads with deletion percentage = 1.9% homopolymer indels = 43.69% >>>>>>> Coverage mean coverageData = 6.7715X std coverageData = 368.5341X There is a 45.4% of reference with a coverageData >= 1X There is a 44.17% of reference with a coverageData >= 2X There is a 41.62% of reference with a coverageData >= 3X There is a 40.26% of reference with a coverageData >= 4X There is a 37.38% of reference with a coverageData >= 5X There is a 35.87% of reference with a coverageData >= 6X There is a 32.74% of reference with a coverageData >= 7X There is a 31.3% of reference with a coverageData >= 8X There is a 28.17% of reference with a coverageData >= 9X There is a 26.92% of reference with a coverageData >= 10X There is a 23.98% of reference with a coverageData >= 11X There is a 22.93% of reference with a coverageData >= 12X There is a 20.23% of reference with a coverageData >= 13X There is a 19.37% of reference with a coverageData >= 14X There is a 16.97% of reference with a coverageData >= 15X There is a 16.25% of reference with a coverageData >= 16X There is a 14.16% of reference with a coverageData >= 17X There is a 13.58% of reference with a coverageData >= 18X There is a 11.77% of reference with a coverageData >= 19X There is a 11.3% of reference with a coverageData >= 20X There is a 9.73% of reference with a coverageData >= 21X There is a 9.34% of reference with a coverageData >= 22X There is a 8.01% of reference with a coverageData >= 23X There is a 7.69% of reference with a coverageData >= 24X There is a 6.56% of reference with a coverageData >= 25X There is a 6.29% of reference with a coverageData >= 26X There is a 5.34% of reference with a coverageData >= 27X There is a 5.11% of reference with a coverageData >= 28X There is a 4.33% of reference with a coverageData >= 29X There is a 4.13% of reference with a coverageData >= 30X There is a 3.5% of reference with a coverageData >= 31X There is a 3.33% of reference with a coverageData >= 32X There is a 2.82% of reference with a coverageData >= 33X There is a 2.68% of reference with a coverageData >= 34X There is a 2.26% of reference with a coverageData >= 35X There is a 2.15% of reference with a coverageData >= 36X There is a 1.82% of reference with a coverageData >= 37X There is a 1.72% of reference with a coverageData >= 38X There is a 1.46% of reference with a coverageData >= 39X There is a 1.38% of reference with a coverageData >= 40X There is a 1.17% of reference with a coverageData >= 41X There is a 1.11% of reference with a coverageData >= 42X There is a 0.94% of reference with a coverageData >= 43X There is a 0.89% of reference with a coverageData >= 44X There is a 0.75% of reference with a coverageData >= 45X There is a 0.71% of reference with a coverageData >= 46X There is a 0.61% of reference with a coverageData >= 47X There is a 0.58% of reference with a coverageData >= 48X There is a 0.49% of reference with a coverageData >= 49X There is a 0.47% of reference with a coverageData >= 50X There is a 0.4% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1671190297 6.704859110461354 177.44470441134064 chr2 243199373 2051184210 8.434167344666633 1282.6124317870338 chr3 198022430 1376732831 6.952408527660225 18.331213127940693 chr4 191154276 1362550305 7.128013735878971 62.4116679805967 chr5 180915260 1246701174 6.891078032886778 11.372391243695635 chr6 171115067 1170050032 6.8377966506012005 29.016317099542157 chr7 159138663 1162500590 7.304953856499347 132.43054266236138 chr8 146364022 1057386166 7.224358497062892 24.481556228075856 chr9 141213431 894260399 6.332686577100446 81.47484392010445 chr10 135534747 1146276435 8.457435900182851 195.57737257192892 chr11 135006516 951063935 7.044578018737999 35.6613366609868 chr12 133851895 910091406 6.799241848611856 11.360759624528358 chr13 115169878 639903616 5.556171692740701 9.573412128037713 chr14 107349540 650774362 6.06219981939373 50.99340180420943 chr15 102531392 602858405 5.879744663956187 9.895317429736586 chr16 90354753 657059778 7.272000156981227 38.08640774304612 chr17 81195210 574859841 7.079972340732907 39.15251762312112 chr18 78077248 580985537 7.441163102982318 81.45970050657698 chr19 59128983 417447388 7.059945340172686 87.60079913014137 chr20 63025520 444794510 7.057371521885103 23.657440899442275 chr21 48129895 288887704 6.002250867158551 40.4253686422962 chr22 51304566 245960619 4.794127271245214 23.306039040136362 chrMT 16571 57315263 3458.769114718484 672.8556979776615 chrX 155270560 579827047 3.734301254532733 16.56066795795089 chrY 59373566 221805246 3.735757525495437 84.79438004087127