BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013303.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 = 1,535,079 number of mapped reads = 1,023,293 (66.66%) number of supplementary alignments = 4,424 (0.29%) number of secondary alignments = 0 number of mapped bases = 57,004,358 bp number of sequenced bases = 56,981,990 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 80,660 duplication rate = 6.67% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2327 >>>>>>> ACTG content number of A's = 16,804,226 bp (29.49%) number of C's = 11,013,738 bp (19.33%) number of T's = 16,928,812 bp (29.71%) number of G's = 12,234,528 bp (21.47%) number of N's = 686 bp (0%) GC percentage = 40.8% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 457,451 number of insertions = 3,658 mapped reads with insertion percentage = 0.36% number of deletions = 13,761 mapped reads with deletion percentage = 1.33% homopolymer indels = 46.72% >>>>>>> Coverage mean coverageData = 0.0184X std coverageData = 0.2061X There is a 1.38% of reference with a coverageData >= 1X There is a 0.32% 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 3948464 0.01584134067212615 0.24205362220529586 chr2 243199373 6341311 0.026074536795783598 0.25646945641575136 chr3 198022430 4425442 0.022348185506056058 0.1941218689399689 chr4 191154276 4524701 0.023670414780572316 0.20514414372450648 chr5 180915260 2861776 0.015818322898798035 0.16027137595863422 chr6 171115067 3210601 0.018762818822961977 0.1871637132977574 chr7 159138663 3457871 0.02172866690478605 0.32152619938376226 chr8 146364022 3586383 0.024503173327663816 0.2759172688641385 chr9 141213431 1980821 0.014027143069698518 0.17260926035462426 chr10 135534747 2041281 0.015060942268922375 0.17209369634374092 chr11 135006516 2442114 0.01808886024434554 0.18597347565352096 chr12 133851895 2276842 0.01701015887746677 0.16585734419104145 chr13 115169878 1433895 0.012450260648882515 0.14403771233403545 chr14 107349540 1933294 0.01800933660265335 0.1754278240464087 chr15 102531392 1501024 0.01463965299525047 0.15989361509450944 chr16 90354753 1317834 0.014585109872415899 0.1540248438822731 chr17 81195210 1660422 0.020449753131988945 0.18638884834055586 chr18 78077248 1214196 0.015551214100169105 0.22612653758183582 chr19 59128983 925366 0.01564995629977265 0.19975605730686466 chr20 63025520 1091714 0.017321776956382113 0.17024074023325042 chr21 48129895 853956 0.017742735570065133 0.1710810792837148 chr22 51304566 539346 0.010512631565775256 0.12906232544467433 chrMT 16571 90942 5.488021241928671 5.129719737518311 chrX 155270560 3224555 0.02076733026531237 0.1917510378647552 chrY 59373566 120207 0.0020245878443615802 0.05552145755177664