BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472503.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 15,140,534 number of mapped reads = 14,941,439 (98.69%) number of supplementary alignments = 61,147 (0.4%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,501,819 number of mapped paired reads (second in pair) = 7,439,620 number of mapped paired reads (both in pair) = 14,832,980 number of mapped paired reads (singletons) = 108,459 number of mapped bases = 1,471,515,230 bp number of sequenced bases = 1,471,319,469 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,007,826 duplication rate = 44.31% >>>>>>> Insert size mean insert size = 32,943.8003 std insert size = 1,779,536.7574 median insert size = 251 >>>>>>> Mapping quality mean mapping quality = 55.1554 >>>>>>> ACTG content number of A's = 413,233,380 bp (28.09%) number of C's = 324,625,326 bp (22.06%) number of T's = 411,029,625 bp (27.94%) number of G's = 322,205,474 bp (21.9%) number of N's = 225,664 bp (0.02%) GC percentage = 43.96% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 9,519,090 number of insertions = 85,807 mapped reads with insertion percentage = 0.57% number of deletions = 80,597 mapped reads with deletion percentage = 0.53% homopolymer indels = 45.31% >>>>>>> Coverage mean coverageData = 0.4753X std coverageData = 16.9571X There is a 5.08% of reference with a coverageData >= 1X There is a 2.22% of reference with a coverageData >= 2X There is a 0.99% of reference with a coverageData >= 3X There is a 0.69% of reference with a coverageData >= 4X There is a 0.51% of reference with a coverageData >= 5X There is a 0.44% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.35% of reference with a coverageData >= 9X There is a 0.33% of reference with a coverageData >= 10X There is a 0.32% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.3% of reference with a coverageData >= 13X There is a 0.29% of reference with a coverageData >= 14X There is a 0.28% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.26% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.21% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.19% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 158602504 0.6363173875502601 19.83162903818902 chr2 243199373 111223691 0.45733543482449684 14.560316715818585 chr3 198022430 155051885 0.7830016276438987 18.117020382886164 chr4 191154276 51849172 0.27124254337894066 10.819815915333107 chr5 180915260 74868408 0.41383135949946953 11.99340771003017 chr6 171115067 89711809 0.5242776721701544 18.670131809025165 chr7 159138663 71368395 0.448466724896388 13.414113993128309 chr8 146364022 68685888 0.4692812281422548 15.387129092842239 chr9 141213431 80544257 0.570372495233828 15.457677875190393 chr10 135534747 53889053 0.3976032286392212 23.03679341779311 chr11 135006516 53295360 0.39476139062799015 13.115585792335086 chr12 133851895 90693106 0.6775631080904757 22.549239396230266 chr13 115169878 23606147 0.20496806465315523 6.430276383666074 chr14 107349540 50752486 0.4727778619265625 34.63439889503697 chr15 102531392 38011333 0.37072873252320615 14.32938029456564 chr16 90354753 44873302 0.4966346596066728 12.733591469188843 chr17 81195210 56195968 0.6921093990643044 18.018709582208093 chr18 78077248 36282527 0.46470038237003436 18.154096366095384 chr19 59128983 27914864 0.47210120289063656 14.103501201821569 chr20 63025520 38485844 0.6106390554175515 18.864869690119793 chr21 48129895 5439734 0.1130219378205583 3.3248809795930425 chr22 51304566 17089281 0.33309473858525573 13.678296590684344 chrMT 16571 2370 0.14302094019672923 0.4853188536425391 chrX 155270560 69125804 0.4451958181898745 16.246751970629454 chrY 59373566 3952042 0.06656231495342557 3.0690716545614376