BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716720.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 = 1,243,499 number of mapped reads = 1,066,650 (85.78%) number of supplementary alignments = 5,250 (0.42%) number of secondary alignments = 0 number of mapped bases = 61,155,380 bp number of sequenced bases = 61,137,244 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 30,547 duplication rate = 1.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7625 >>>>>>> ACTG content number of A's = 15,815,576 bp (25.87%) number of C's = 10,860,970 bp (17.76%) number of T's = 19,240,656 bp (31.47%) number of G's = 15,219,278 bp (24.89%) number of N's = 764 bp (0%) GC percentage = 42.66% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 315,336 number of insertions = 4,278 mapped reads with insertion percentage = 0.4% number of deletions = 11,692 mapped reads with deletion percentage = 1.09% homopolymer indels = 41.49% >>>>>>> Coverage mean coverageData = 0.0198X std coverageData = 0.2244X There is a 1.81% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 3658599 0.014678394723036618 0.23625310511365236 chr2 243199373 6681678 0.02747407576581211 0.25593776873990814 chr3 198022430 5722809 0.028899801906279003 0.19804445864846057 chr4 191154276 3733839 0.01953311784665492 0.15710140827231636 chr5 180915260 1978731 0.01093733607656977 0.11270137808180389 chr6 171115067 4000943 0.023381593860463498 0.17285518976849035 chr7 159138663 4041570 0.025396531074287083 0.5443782357409569 chr8 146364022 4174371 0.02852047205972517 0.22929913695539766 chr9 141213431 2370085 0.016783708059610845 0.15130816787899184 chr10 135534747 3080764 0.02273043679345194 0.3306534227220477 chr11 135006516 2511372 0.018601857705890283 0.16755178715956864 chr12 133851895 2496788 0.018653363107037073 0.16859216361492402 chr13 115169878 1766857 0.015341311727359822 0.13049396671175567 chr14 107349540 1560874 0.014540108881696186 0.13075575035924858 chr15 102531392 1595591 0.015561975399690273 0.1371143437423911 chr16 90354753 2036093 0.022534431586570768 0.1680713620047677 chr17 81195210 2263852 0.027881595478353956 0.18164174235078281 chr18 78077248 1694156 0.021698459453898786 0.22319209989032968 chr19 59128983 1239823 0.020968109666286667 0.26943903606056774 chr20 63025520 1387647 0.022017224133969858 0.17175493287886592 chr21 48129895 702545 0.014596852953865784 0.1347738125452809 chr22 51304566 628706 0.012254386870751427 0.11656054185866728 chrMT 16571 5369 0.3239997586144469 0.6067950122012867 chrX 155270560 1695568 0.010920086847113838 0.13187196605630644 chrY 59373566 126750 0.0021347884006158568 0.0643389166257936