BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716814.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 = 2,336,610 number of mapped reads = 1,998,693 (85.54%) number of supplementary alignments = 9,481 (0.41%) number of secondary alignments = 0 number of mapped bases = 115,649,879 bp number of sequenced bases = 115,616,050 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 82,214 duplication rate = 3.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8036 >>>>>>> ACTG content number of A's = 27,834,048 bp (24.07%) number of C's = 20,607,496 bp (17.82%) number of T's = 38,109,319 bp (32.96%) number of G's = 29,062,012 bp (25.14%) number of N's = 3,175 bp (0%) GC percentage = 42.96% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 574,977 number of insertions = 8,056 mapped reads with insertion percentage = 0.4% number of deletions = 21,571 mapped reads with deletion percentage = 1.07% homopolymer indels = 43.53% >>>>>>> Coverage mean coverageData = 0.0374X std coverageData = 0.3434X There is a 3.29% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.05% 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 10376830 0.04163211292460531 0.5875757926351494 chr2 243199373 10729774 0.044119250258099964 0.4296541746628025 chr3 198022430 8633439 0.04359828833531636 0.2328477879779208 chr4 191154276 5887915 0.030801900554921408 0.2067762663955402 chr5 180915260 5463343 0.030198353638051317 0.19433742090353961 chr6 171115067 9108463 0.05323004665626552 0.3293199491717954 chr7 159138663 7304235 0.04589855703387429 0.6668324684671738 chr8 146364022 7475823 0.05107691697622248 0.3111917282110919 chr9 141213431 4588009 0.03248989113507199 0.26630744923427757 chr10 135534747 6032197 0.044506645959947085 0.3063239454218771 chr11 135006516 4106100 0.030414087568928896 0.27281737866969974 chr12 133851895 5036956 0.03763081576095729 0.22042983420714907 chr13 115169878 2598302 0.022560603910685744 0.16812471907463525 chr14 107349540 2735255 0.02547989493015061 0.1900378611859761 chr15 102531392 3705559 0.036140726539633836 0.21592658217071284 chr16 90354753 2597454 0.028747286819543406 0.20485108742722546 chr17 81195210 3505616 0.04317515774637445 0.24710954862332693 chr18 78077248 2412859 0.030903484200672647 0.48457467177123814 chr19 59128983 2291687 0.038757422903756014 0.4025974053102755 chr20 63025520 1902384 0.030184344373517268 0.19583416604541806 chr21 48129895 1167647 0.024260327183344157 0.1870828209943121 chr22 51304566 1918596 0.03739620368292366 0.21523213650964235 chrMT 16571 32831 1.981232273248446 1.8624302164865978 chrX 155270560 5757623 0.0370812277613992 0.24695116285820048 chrY 59373566 280982 0.004732442717016526 0.10803278111730505