BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716222.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 = 1,530,630 number of mapped reads = 1,365,947 (89.24%) number of supplementary alignments = 4,861 (0.32%) number of secondary alignments = 0 number of mapped bases = 78,910,756 bp number of sequenced bases = 78,886,990 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 42,135 duplication rate = 2.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3972 >>>>>>> ACTG content number of A's = 19,395,881 bp (24.59%) number of C's = 14,495,146 bp (18.37%) number of T's = 24,445,150 bp (30.99%) number of G's = 20,550,127 bp (26.05%) number of N's = 686 bp (0%) GC percentage = 44.42% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 408,018 number of insertions = 5,117 mapped reads with insertion percentage = 0.37% number of deletions = 14,791 mapped reads with deletion percentage = 1.07% homopolymer indels = 42.23% >>>>>>> Coverage mean coverageData = 0.0255X std coverageData = 0.2246X There is a 2.3% of reference with a coverageData >= 1X There is a 0.18% 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 6276757 0.025182512985594527 0.2874267001876449 chr2 243199373 6646023 0.027327467657574923 0.32589209733623137 chr3 198022430 5188567 0.026201915611276966 0.178112359454514 chr4 191154276 5003286 0.026174073134518843 0.19317110542317478 chr5 180915260 4711753 0.026043977716418174 0.1749629743965084 chr6 171115067 4491208 0.02624671268720013 0.19999900551663252 chr7 159138663 4349764 0.02733316918717609 0.2793560758938114 chr8 146364022 3972313 0.02713995520019257 0.233078943915084 chr9 141213431 3286711 0.023274776179044894 0.19192137494557354 chr10 135534747 3886657 0.028676461837494706 0.280748801168745 chr11 135006516 3546914 0.026272168967014897 0.20696834584947782 chr12 133851895 3599912 0.026894740638524393 0.180867584063044 chr13 115169878 2439875 0.021185009851273785 0.15842059003114425 chr14 107349540 2383356 0.022201827786127448 0.16663005888993163 chr15 102531392 2322577 0.022652350218750564 0.16582368896790659 chr16 90354753 2366118 0.026186978785720325 0.19234275724111802 chr17 81195210 2296906 0.02828868845834625 0.18947124154688239 chr18 78077248 2055280 0.026323673703253475 0.29466230691321954 chr19 59128983 1744182 0.029497919827235992 0.2585676775562622 chr20 63025520 1736045 0.027545111884836493 0.18450489290163113 chr21 48129895 1028705 0.021373514319946055 0.17836623318268302 chr22 51304566 974714 0.01899858191958977 0.15122500498176067 chrMT 16571 5264 0.3176633878462374 0.6195714986573478 chrX 155270560 4346653 0.027994057598555708 0.19422725672558075 chrY 59373566 251216 0.004231108503740537 0.13496226696647895