BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472673.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 = 15,555,610 number of mapped reads = 15,434,651 (99.22%) number of supplementary alignments = 91,846 (0.59%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,735,089 number of mapped paired reads (second in pair) = 7,699,562 number of mapped paired reads (both in pair) = 15,355,786 number of mapped paired reads (singletons) = 78,865 number of mapped bases = 1,517,905,277 bp number of sequenced bases = 1,517,705,857 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,395,514 duplication rate = 49.46% >>>>>>> Insert size mean insert size = 21,513.3743 std insert size = 1,429,630.6744 median insert size = 210 >>>>>>> Mapping quality mean mapping quality = 54.9345 >>>>>>> ACTG content number of A's = 405,634,441 bp (26.73%) number of C's = 354,971,442 bp (23.39%) number of T's = 406,696,956 bp (26.8%) number of G's = 350,118,503 bp (23.07%) number of N's = 284,515 bp (0.02%) GC percentage = 46.46% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 9,238,268 number of insertions = 97,399 mapped reads with insertion percentage = 0.62% number of deletions = 85,091 mapped reads with deletion percentage = 0.54% homopolymer indels = 45.78% >>>>>>> Coverage mean coverageData = 0.4903X std coverageData = 19.9238X There is a 3.25% of reference with a coverageData >= 1X There is a 1.52% of reference with a coverageData >= 2X There is a 0.74% of reference with a coverageData >= 3X There is a 0.57% of reference with a coverageData >= 4X There is a 0.44% of reference with a coverageData >= 5X There is a 0.4% of reference with a coverageData >= 6X There is a 0.36% of reference with a coverageData >= 7X There is a 0.34% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.31% of reference with a coverageData >= 10X There is a 0.3% of reference with a coverageData >= 11X There is a 0.29% of reference with a coverageData >= 12X There is a 0.28% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.26% of reference with a coverageData >= 15X There is a 0.25% of reference with a coverageData >= 16X There is a 0.25% of reference with a coverageData >= 17X There is a 0.24% of reference with a coverageData >= 18X There is a 0.24% of reference with a coverageData >= 19X There is a 0.23% of reference with a coverageData >= 20X There is a 0.23% of reference with a coverageData >= 21X There is a 0.22% of reference with a coverageData >= 22X There is a 0.22% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.21% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.2% of reference with a coverageData >= 28X There is a 0.19% of reference with a coverageData >= 29X There is a 0.19% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.18% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.17% 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 0.16% of reference with a coverageData >= 40X There is a 0.16% 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 0.15% 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 0.14% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 146086607 0.5861032819653437 20.730728294827816 chr2 243199373 129373456 0.5319645951554324 25.603801277225486 chr3 198022430 165918838 0.8378790119886924 28.960816406862175 chr4 191154276 32751331 0.17133454550606025 9.549101334618989 chr5 180915260 62080472 0.3431466864652545 17.669518160735905 chr6 171115067 118578678 0.6929762532249717 20.631720225377222 chr7 159138663 77456579 0.48672382650343116 18.18274125338701 chr8 146364022 84930172 0.5802667270239403 21.916340008377 chr9 141213431 112675400 0.7979085218884031 26.852072704374066 chr10 135534747 33840485 0.24968124963556393 13.341767064179304 chr11 135006516 34379843 0.2546532124419832 9.995843820868028 chr12 133851895 77920382 0.5821388034887366 24.859471542021424 chr13 115169878 40441038 0.35114249231035916 14.953744067160995 chr14 107349540 27354466 0.25481679753821024 15.630290560323324 chr15 102531392 19928828 0.19436806241741067 10.061085319213262 chr16 90354753 81737470 0.9046283375928215 27.080472411851765 chr17 81195210 56179911 0.6919116410931138 21.24443675138632 chr18 78077248 9178982 0.11756282700947657 5.42495679049012 chr19 59128983 44834468 0.7582485902049085 18.79836768580728 chr20 63025520 75890748 1.204127280504786 35.54179986165359 chr21 48129895 9371948 0.1947219706172224 13.116757499141103 chr22 51304566 16658556 0.32469928699913375 10.520955659096204 chrMT 16571 12473 0.7527005008750226 1.1294007070161078 chrX 155270560 59628142 0.3840273519977 11.93911725405085 chrY 59373566 696004 0.011722455747394387 0.875064582041106