BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525180.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 = 2,081,958 number of mapped reads = 1,916,851 (92.07%) number of supplementary alignments = 6,333 (0.3%) number of secondary alignments = 0 number of mapped bases = 112,222,680 bp number of sequenced bases = 112,187,147 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 76,670 duplication rate = 2.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9062 >>>>>>> ACTG content number of A's = 27,710,799 bp (24.7%) number of C's = 20,934,828 bp (18.66%) number of T's = 36,026,363 bp (32.11%) number of G's = 27,512,605 bp (24.52%) number of N's = 2,552 bp (0%) GC percentage = 43.18% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 562,080 number of insertions = 7,519 mapped reads with insertion percentage = 0.39% number of deletions = 22,321 mapped reads with deletion percentage = 1.16% homopolymer indels = 43.83% >>>>>>> Coverage mean coverageData = 0.0363X std coverageData = 0.3332X There is a 3.22% of reference with a coverageData >= 1X There is a 0.29% 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 12275455 0.04924944600238328 0.5727574750736774 chr2 243199373 9700119 0.03988546055996616 0.45099847569757795 chr3 198022430 8714433 0.04400730260708345 0.23214242623554102 chr4 191154276 4827311 0.025253481643277495 0.18697203830400577 chr5 180915260 5253823 0.02904024237645846 0.18731310504756582 chr6 171115067 6635137 0.03877587822234263 0.24615837821538958 chr7 159138663 8372518 0.052611463752212116 0.5950854307944397 chr8 146364022 5574633 0.03808745430622288 0.273364506489765 chr9 141213431 3647283 0.025828159362546753 0.23465170201195978 chr10 135534747 6336009 0.04674822612093709 0.3733208084075025 chr11 135006516 5310075 0.03933199046481579 0.27715301125567676 chr12 133851895 5336357 0.03986762383901998 0.2230369171272965 chr13 115169878 2369493 0.020573895198534465 0.16479338767890767 chr14 107349540 4373737 0.0407429505520005 0.2276132602058487 chr15 102531392 2269618 0.022135835237660675 0.16574687946151287 chr16 90354753 3130448 0.03464619066580814 0.23156094371144323 chr17 81195210 2103947 0.02591220590475719 0.18647068888120377 chr18 78077248 2492112 0.03191854303061501 0.5091777433289087 chr19 59128983 1934102 0.032709881040910174 0.4066231145955939 chr20 63025520 2040591 0.032377217990426733 0.20279927137817624 chr21 48129895 1482815 0.030808606584327682 0.20491085595030722 chr22 51304566 1353746 0.026386462366721902 0.17836163901055993 chrMT 16571 126388 7.627059320499668 4.88986509815431 chrX 155270560 6253046 0.04027193564575281 0.24200289990611637 chrY 59373566 309484 0.005212487995078483 0.13990197392325185