BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008760.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,172,535 number of mapped reads = 1,041,192 (88.8%) number of supplementary alignments = 7,215 (0.62%) number of secondary alignments = 0 number of mapped bases = 68,908,814 bp number of sequenced bases = 68,874,146 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 55,573 duplication rate = 4.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6789 >>>>>>> ACTG content number of A's = 18,433,187 bp (26.76%) number of C's = 13,466,265 bp (19.55%) number of T's = 21,077,126 bp (30.6%) number of G's = 15,793,759 bp (22.93%) number of N's = 103,809 bp (0.15%) GC percentage = 42.48% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 576,178 number of insertions = 5,059 mapped reads with insertion percentage = 0.48% number of deletions = 19,276 mapped reads with deletion percentage = 1.83% homopolymer indels = 44.57% >>>>>>> Coverage mean coverageData = 0.0223X std coverageData = 0.2456X There is a 1.73% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% 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 6859820 0.027521776966806435 0.3186748328896497 chr2 243199373 4788592 0.019689984973768827 0.31207015791778603 chr3 198022430 5064376 0.025574759384580828 0.20726386529530413 chr4 191154276 4127984 0.021595038763349454 0.1856390446667576 chr5 180915260 3655316 0.02020457533543605 0.1750531172320817 chr6 171115067 4163585 0.024332077081207583 0.2078287217365969 chr7 159138663 2621747 0.01647460743087932 0.29440238519609824 chr8 146364022 4061254 0.02774762502768611 0.2747365660603695 chr9 141213431 2152872 0.015245518678743809 0.17068219328787623 chr10 135534747 6288585 0.04639832322850759 0.4266050676673681 chr11 135006516 2944405 0.021809354742551832 0.20260170749178638 chr12 133851895 2785733 0.02081205499556058 0.17880655269331194 chr13 115169878 1147582 0.009964254715977037 0.1257924487728986 chr14 107349540 2800210 0.026084974374366205 0.2014052051565152 chr15 102531392 1536827 0.014988843611915461 0.1497893475915623 chr16 90354753 2373870 0.02627277394029288 0.28046483594334154 chr17 81195210 1867883 0.023004842280720746 0.20270917658070203 chr18 78077248 844535 0.010816659419143462 0.22756497875948198 chr19 59128983 1924750 0.032551718334137426 0.2876505678281659 chr20 63025520 1875032 0.029750361440889342 0.21704911122856987 chr21 48129895 613220 0.012740937830842972 0.14585990457709544 chr22 51304566 1054099 0.020545910085273893 0.17996835805680023 chrMT 16571 300272 18.120330698207713 10.608499826736827 chrX 155270560 2867688 0.01846897441472485 0.16956692691430855 chrY 59373566 188577 0.0031761103922914114 0.11444506862942389