BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472781.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 = 12,734,862 number of mapped reads = 12,585,527 (98.83%) number of supplementary alignments = 47,575 (0.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,327,197 number of mapped paired reads (second in pair) = 6,258,330 number of mapped paired reads (both in pair) = 12,487,628 number of mapped paired reads (singletons) = 97,899 number of mapped bases = 1,238,066,314 bp number of sequenced bases = 1,237,893,543 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,620,749 duplication rate = 46% >>>>>>> Insert size mean insert size = 27,311.072 std insert size = 1,622,164.914 median insert size = 242 >>>>>>> Mapping quality mean mapping quality = 55.0283 >>>>>>> ACTG content number of A's = 340,539,189 bp (27.51%) number of C's = 280,239,739 bp (22.64%) number of T's = 338,393,034 bp (27.34%) number of G's = 278,482,495 bp (22.5%) number of N's = 239,086 bp (0.02%) GC percentage = 45.13% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 7,781,824 number of insertions = 77,332 mapped reads with insertion percentage = 0.61% number of deletions = 68,116 mapped reads with deletion percentage = 0.53% homopolymer indels = 43.83% >>>>>>> Coverage mean coverageData = 0.3999X std coverageData = 14.1455X There is a 3.67% of reference with a coverageData >= 1X There is a 1.61% of reference with a coverageData >= 2X There is a 0.75% of reference with a coverageData >= 3X There is a 0.55% of reference with a coverageData >= 4X There is a 0.43% of reference with a coverageData >= 5X There is a 0.38% of reference with a coverageData >= 6X There is a 0.35% of reference with a coverageData >= 7X There is a 0.33% of reference with a coverageData >= 8X There is a 0.31% of reference with a coverageData >= 9X There is a 0.3% of reference with a coverageData >= 10X There is a 0.28% of reference with a coverageData >= 11X There is a 0.27% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.26% of reference with a coverageData >= 14X There is a 0.25% of reference with a coverageData >= 15X There is a 0.24% of reference with a coverageData >= 16X There is a 0.24% of reference with a coverageData >= 17X There is a 0.23% of reference with a coverageData >= 18X There is a 0.22% of reference with a coverageData >= 19X There is a 0.22% of reference with a coverageData >= 20X There is a 0.21% of reference with a coverageData >= 21X There is a 0.21% of reference with a coverageData >= 22X There is a 0.2% of reference with a coverageData >= 23X There is a 0.2% of reference with a coverageData >= 24X There is a 0.2% of reference with a coverageData >= 25X There is a 0.19% of reference with a coverageData >= 26X There is a 0.19% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.18% of reference with a coverageData >= 29X There is a 0.18% of reference with a coverageData >= 30X There is a 0.18% of reference with a coverageData >= 31X There is a 0.17% of reference with a coverageData >= 32X There is a 0.17% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.16% of reference with a coverageData >= 35X There is a 0.16% of reference with a coverageData >= 36X There is a 0.16% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.15% of reference with a coverageData >= 39X There is a 0.15% of reference with a coverageData >= 40X There is a 0.15% of reference with a coverageData >= 41X There is a 0.15% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.14% of reference with a coverageData >= 44X There is a 0.14% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.13% of reference with a coverageData >= 49X There is a 0.13% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 150071490 0.6020907366164596 22.648369624080317 chr2 243199373 92420266 0.3800185208536701 13.99444310013422 chr3 198022430 130855975 0.6608139037582763 17.435283044402546 chr4 191154276 48864216 0.2556271145093296 10.888226825804573 chr5 180915260 60768050 0.33589233987226946 11.321093606997955 chr6 171115067 94273930 0.5509388018998935 16.684031554929273 chr7 159138663 43150461 0.2711500787209705 9.630135992756335 chr8 146364022 55547001 0.3795126714951848 13.64734659321936 chr9 141213431 85055297 0.6023173319823948 17.784186092293925 chr10 135534747 40598035 0.29953968187951097 14.240192270681398 chr11 135006516 41070498 0.30421122784918025 10.46339525296188 chr12 133851895 72265147 0.5398888599970886 15.721868442340774 chr13 115169878 26975072 0.23421985391006492 9.937962680195762 chr14 107349540 29925214 0.2787642499446202 10.240920381151037 chr15 102531392 27521756 0.2684227285239627 9.572055638084352 chr16 90354753 44054988 0.4875779805407691 15.121331216117943 chr17 81195210 45201575 0.5567024828188757 14.484538605223685 chr18 78077248 26923622 0.34483313243827446 16.005232675400787 chr19 59128983 19754105 0.3340849782584625 6.81146549644636 chr20 63025520 20370883 0.3232164209037863 10.50792299346933 chr21 48129895 4841463 0.10059159696899402 3.552595278840774 chr22 51304566 9585607 0.18683730800880374 5.123433260928463 chrMT 16571 1789 0.10795968861263654 0.3791261734917118 chrX 155270560 65198310 0.41990130002751325 13.0296369316998 chrY 59373566 2771564 0.046680100029700085 2.7110517281755446