BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777251.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 12,336,476 number of mapped reads = 12,102,847 (98.11%) number of supplementary alignments = 629,074 (5.1%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,057,387 number of mapped paired reads (second in pair) = 6,045,460 number of mapped paired reads (both in pair) = 12,042,166 number of mapped paired reads (singletons) = 60,681 number of mapped bases = 1,162,866,347 bp number of sequenced bases = 1,162,212,814 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,558,381 duplication rate = 6.41% >>>>>>> Insert size mean insert size = 253,338.4571 std insert size = 3,732,915.9186 median insert size = 162 >>>>>>> Mapping quality mean mapping quality = 53.2243 >>>>>>> ACTG content number of A's = 347,507,409 bp (29.9%) number of C's = 234,100,872 bp (20.14%) number of T's = 339,458,499 bp (29.21%) number of G's = 241,120,337 bp (20.75%) number of N's = 25,697 bp (0%) GC percentage = 40.89% >>>>>>> Mismatches and indels general error rate = 0.0045 number of mismatches = 4,598,472 number of insertions = 339,006 mapped reads with insertion percentage = 2.69% number of deletions = 223,301 mapped reads with deletion percentage = 1.7% homopolymer indels = 38.83% >>>>>>> Coverage mean coverageData = 0.3756X std coverageData = 18.1042X There is a 21.48% of reference with a coverageData >= 1X There is a 9.29% of reference with a coverageData >= 2X There is a 3.07% of reference with a coverageData >= 3X There is a 1.18% of reference with a coverageData >= 4X There is a 0.44% of reference with a coverageData >= 5X There is a 0.18% of reference with a coverageData >= 6X There is a 0.08% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% 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 92668117 0.37178690519691826 1.8717512990581495 chr2 243199373 107342897 0.44137818151365055 1.1634944201509314 chr3 198022430 77617797 0.39196467289084375 0.8645757782869631 chr4 191154276 74596139 0.39024049349542145 12.908353179734009 chr5 180915260 78503877 0.4339262315406672 0.9014967542935077 chr6 171115067 54546060 0.31876830577403215 1.045343140002473 chr7 159138663 75582743 0.47494896321957913 1.2412673838874477 chr8 146364022 57235183 0.39104680383817275 0.9378891272449172 chr9 141213431 78980076 0.5592957797335864 83.19930715676527 chr10 135534747 52053642 0.3840612326520224 1.6988630379343932 chr11 135006516 66071526 0.48939508964145106 1.2451463110522591 chr12 133851895 51827544 0.3872006742975137 0.8527015423604037 chr13 115169878 50449446 0.43804375654543976 0.9180264022791228 chr14 107349540 22922684 0.21353313670463794 0.6448882151574187 chr15 102531392 40509906 0.39509759118456134 0.8777707619816965 chr16 90354753 28842951 0.3192189679274537 1.1371220604033427 chr17 81195210 24488263 0.30159738487036364 1.020160433987583 chr18 78077248 25240639 0.3232777748519005 1.6182888108618823 chr19 59128983 12461357 0.2107487118457627 1.3143490178989652 chr20 63025520 28281643 0.4487331956959657 0.9393616027765277 chr21 48129895 9955769 0.20685208226612586 0.7956476475480077 chr22 51304566 7298702 0.1422622306170566 0.5171306077068556 chrMT 16571 5000840 301.7826323094563 66.9931330574932 chrX 155270560 38910224 0.2505962753016412 0.7251794661802378 chrY 59373566 1478322 0.024898656078700072 0.6324609719807078