BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524959.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 = 805,508 number of mapped reads = 730,214 (90.65%) number of supplementary alignments = 2,217 (0.28%) number of secondary alignments = 0 number of mapped bases = 42,251,220 bp number of sequenced bases = 42,237,585 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,369 duplication rate = 1.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3444 >>>>>>> ACTG content number of A's = 10,844,968 bp (25.68%) number of C's = 8,162,808 bp (19.33%) number of T's = 13,156,534 bp (31.15%) number of G's = 10,072,730 bp (23.85%) number of N's = 545 bp (0%) GC percentage = 43.17% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 206,088 number of insertions = 2,311 mapped reads with insertion percentage = 0.31% number of deletions = 8,177 mapped reads with deletion percentage = 1.11% homopolymer indels = 44.77% >>>>>>> Coverage mean coverageData = 0.0136X std coverageData = 0.1519X There is a 1.28% 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 4444825 0.017832753965335155 0.24988553107147643 chr2 243199373 4048707 0.016647686834291305 0.17282277368466548 chr3 198022430 2321157 0.011721687285627188 0.11299526488898026 chr4 191154276 2720969 0.014234413464023165 0.12976979997420798 chr5 180915260 1855310 0.010255132706881664 0.10634895750041247 chr6 171115067 2831147 0.016545281778138216 0.15952399943534348 chr7 159138663 2480999 0.015590171195544102 0.20356324270668125 chr8 146364022 2836985 0.019383076259000317 0.16483942255822803 chr9 141213431 1156949 0.008192910488804708 0.11763607701577178 chr10 135534747 2102011 0.015509019248030912 0.15140488984004272 chr11 135006516 1763358 0.01306128068662997 0.13559228560719533 chr12 133851895 2268629 0.01694880001512119 0.1358639292855186 chr13 115169878 832120 0.007225153090810776 0.08838125985710649 chr14 107349540 961955 0.008960960615201519 0.10023844562863003 chr15 102531392 1157408 0.011288328163924664 0.11465017728104383 chr16 90354753 1333547 0.0147590132862186 0.12972301546388226 chr17 81195210 1226827 0.015109598213983312 0.15897950945935185 chr18 78077248 852969 0.010924680644481731 0.16974221885473717 chr19 59128983 1021678 0.017278802173884843 0.17977722864452816 chr20 63025520 999911 0.015865176518972 0.13154909544451787 chr21 48129895 595743 0.012377816323929234 0.11832214444208831 chr22 51304566 543115 0.01058609481269172 0.10670786162586114 chrMT 16571 3768 0.22738519099631888 0.4645847154831846 chrX 155270560 1781407 0.01147292184687168 0.11950685985205074 chrY 59373566 109726 0.0018480614757078932 0.053470456008670494