BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082469.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,005,763 number of mapped reads = 1,817,169 (90.6%) number of supplementary alignments = 15,594 (0.78%) number of secondary alignments = 0 number of mapped bases = 124,457,657 bp number of sequenced bases = 124,412,767 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 58,502 duplication rate = 2.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7595 >>>>>>> ACTG content number of A's = 36,080,437 bp (29%) number of C's = 23,070,382 bp (18.54%) number of T's = 38,348,245 bp (30.82%) number of G's = 26,911,103 bp (21.63%) number of N's = 2,600 bp (0%) GC percentage = 40.17% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,038,616 number of insertions = 10,178 mapped reads with insertion percentage = 0.56% number of deletions = 27,555 mapped reads with deletion percentage = 1.5% homopolymer indels = 47.52% >>>>>>> Coverage mean coverageData = 0.0402X std coverageData = 0.3486X There is a 3.6% of reference with a coverageData >= 1X There is a 0.31% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 9723334 0.03901026990821419 0.5806089732332319 chr2 243199373 10695984 0.04398031075515972 0.3907796811747092 chr3 198022430 8549263 0.0431732051768075 0.22553672800799004 chr4 191154276 8530703 0.04462731976762058 0.23513154373559148 chr5 180915260 7934231 0.04385606277767835 0.22728083375060226 chr6 171115067 7407968 0.04329231861271456 0.25757183123786775 chr7 159138663 6905196 0.043391064558585615 0.4029783060252499 chr8 146364022 6545113 0.044718045531708606 0.6845716950282666 chr9 141213431 5234920 0.03707097804315795 0.30743570223538647 chr10 135534747 5779500 0.042642201560312794 0.3137785264546404 chr11 135006516 5618657 0.041617672735144134 0.2797597368989768 chr12 133851895 5575009 0.04165057954539979 0.2232080638440623 chr13 115169878 4194634 0.0364212767508532 0.20594492954314392 chr14 107349540 3815315 0.03554104656619861 0.21921930353635993 chr15 102531392 3453291 0.03368032884991945 0.20112608942342847 chr16 90354753 3265919 0.03614551411589825 0.22901155181543614 chr17 81195210 2998150 0.03692520778011412 0.22581496588340844 chr18 78077248 3398084 0.043522077007632234 0.5345045670913616 chr19 59128983 2098765 0.03549469132591034 0.4637154577999151 chr20 63025520 2338406 0.03710252608784505 0.21312024709279187 chr21 48129895 1644176 0.03416122141966028 0.21004777445493875 chr22 51304566 1209057 0.023566265037696644 0.16509601002232613 chrMT 16571 4189 0.25279102045742563 0.5536545323749136 chrX 155270560 7255630 0.04672894848836766 0.253543011101295 chrY 59373566 282163 0.004752333723731534 0.10872312959630252