BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716604.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 = 2,713,518 number of mapped reads = 2,515,113 (92.69%) number of supplementary alignments = 65,879 (2.43%) number of secondary alignments = 0 number of mapped bases = 189,128,713 bp number of sequenced bases = 189,058,719 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 98,579 duplication rate = 2.72% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8197 >>>>>>> ACTG content number of A's = 49,957,941 bp (26.42%) number of C's = 38,550,369 bp (20.39%) number of T's = 57,137,178 bp (30.22%) number of G's = 43,390,269 bp (22.95%) number of N's = 22,962 bp (0.01%) GC percentage = 43.34% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 1,416,958 number of insertions = 17,313 mapped reads with insertion percentage = 0.68% number of deletions = 40,693 mapped reads with deletion percentage = 1.6% homopolymer indels = 39.72% >>>>>>> Coverage mean coverageData = 0.0611X std coverageData = 0.4787X There is a 5.1% of reference with a coverageData >= 1X There is a 0.71% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% 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 0.01% 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 20945506 0.0840339170107825 0.809812826320224 chr2 243199373 15191182 0.06246390281606524 0.6677779601218496 chr3 198022430 13444126 0.06789193527218104 0.3066787456240082 chr4 191154276 7753152 0.0405596576871762 0.26191049444239056 chr5 180915260 10356519 0.05724513786178126 0.2759069327319302 chr6 171115067 12883721 0.07529273269664792 0.3578133559552424 chr7 159138663 10276842 0.06457790838672561 0.7041607517889317 chr8 146364022 12542641 0.08569483694565322 0.5683586297451193 chr9 141213431 9880320 0.06996728236140655 0.4528580809167733 chr10 135534747 11343730 0.08369610193023048 0.5776035559808225 chr11 135006516 7799577 0.057771855989528685 0.4172681473539043 chr12 133851895 7570250 0.056556913146429494 0.2772048574367201 chr13 115169878 6379963 0.05539610799969763 0.27201421247064295 chr14 107349540 4711952 0.04389354626018891 0.27133362527404936 chr15 102531392 3547488 0.03459904260345944 0.21686917376038414 chr16 90354753 4820141 0.05334684496342987 0.3083028295363556 chr17 81195210 5401379 0.06652337003623736 0.35355929490518967 chr18 78077248 3407358 0.043640856808887525 0.7068840272597356 chr19 59128983 3106667 0.052540511308980235 0.6210795526224574 chr20 63025520 3308283 0.052491165483442265 0.2821428366827709 chr21 48129895 3277148 0.06808965612744429 0.32328607249202007 chr22 51304566 2362573 0.04604995586552667 0.25281066214290016 chrMT 16571 83429 5.034638826866212 4.278835782392009 chrX 155270560 8247151 0.053114711507448675 0.3234462727934957 chrY 59373566 487615 0.008212661506637483 0.22563201834321364