BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525103.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 = 667,296 number of mapped reads = 557,939 (83.61%) number of supplementary alignments = 15,346 (2.3%) number of secondary alignments = 0 number of mapped bases = 42,658,768 bp number of sequenced bases = 42,641,903 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,000 duplication rate = 1.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.543 >>>>>>> ACTG content number of A's = 11,140,821 bp (26.13%) number of C's = 8,111,656 bp (19.02%) number of T's = 13,368,024 bp (31.35%) number of G's = 10,019,801 bp (23.5%) number of N's = 1,601 bp (0%) GC percentage = 42.52% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 314,912 number of insertions = 3,845 mapped reads with insertion percentage = 0.68% number of deletions = 9,903 mapped reads with deletion percentage = 1.75% homopolymer indels = 43.37% >>>>>>> Coverage mean coverageData = 0.0138X std coverageData = 0.167X There is a 1.29% of reference with a coverageData >= 1X There is a 0.05% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 3363833 0.013495785833969898 0.22722817215540309 chr2 243199373 3675931 0.015114886829909713 0.2277291170931668 chr3 198022430 2880137 0.014544498822683875 0.12545414777684588 chr4 191154276 2783688 0.014562520170880196 0.12730549161108123 chr5 180915260 2650056 0.014648051247860462 0.1266835060802264 chr6 171115067 2478417 0.01448392034349611 0.13594338461113048 chr7 159138663 2311335 0.014524031787297345 0.2302326127910497 chr8 146364022 2231439 0.01524581635232735 0.2120207724528706 chr9 141213431 1803025 0.012768084361607219 0.16746691743951225 chr10 135534747 2024341 0.014935955869678202 0.16754002443386773 chr11 135006516 1918775 0.01421246215997456 0.17346536607554394 chr12 133851895 1943566 0.014520272574400235 0.12580840603955862 chr13 115169878 1384874 0.01202461984026761 0.11350010378320717 chr14 107349540 1263734 0.011772141734375387 0.11703485754945095 chr15 102531392 1212042 0.011821179605169117 0.11240841248664223 chr16 90354753 1196330 0.013240366004874143 0.12315500314825176 chr17 81195210 1122584 0.013825741690919945 0.1427562010929476 chr18 78077248 1172687 0.01501957394809817 0.24125201978114016 chr19 59128983 810222 0.013702620253082992 0.18491618330084011 chr20 63025520 851839 0.013515779005076039 0.12175004391631548 chr21 48129895 559582 0.01162649534140891 0.115342991247375 chr22 51304566 439869 0.008573681336666994 0.09574161705195401 chrMT 16571 625 0.037716492667913826 0.21826378500166604 chrX 155270560 2485509 0.01600759989530533 0.152659191848383 chrY 59373566 94328 0.0015887204753711442 0.0490184601793056