BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708607.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 6,104,164 number of mapped reads = 5,968,203 (97.77%) number of supplementary alignments = 186 (0%) number of secondary alignments = 0 number of mapped bases = 297,704,395 bp number of sequenced bases = 297,679,169 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 61,808 duplication rate = 1.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6878 >>>>>>> ACTG content number of A's = 92,163,117 bp (30.96%) number of C's = 56,560,981 bp (19%) number of T's = 91,619,761 bp (30.78%) number of G's = 57,325,069 bp (19.26%) number of N's = 10,241 bp (0%) GC percentage = 38.26% >>>>>>> Mismatches and indels general error rate = 0.0015 number of mismatches = 425,827 number of insertions = 18,860 mapped reads with insertion percentage = 0.32% number of deletions = 14,893 mapped reads with deletion percentage = 0.25% homopolymer indels = 48.26% >>>>>>> Coverage mean coverageData = 0.0962X std coverageData = 0.3268X There is a 8.73% of reference with a coverageData >= 1X There is a 0.8% of reference with a coverageData >= 2X There is a 0.08% 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 23002699 0.09228742904516174 0.3221475443055063 chr2 243199373 26173229 0.1076204624918996 0.34381185088132016 chr3 198022430 22365113 0.11294232173597708 0.35178348925238684 chr4 191154276 23877478 0.12491207886973975 0.3698368358833259 chr5 180915260 20205367 0.11168414980582622 0.34962285428386686 chr6 171115067 19998774 0.11687324997511762 0.35895350479157734 chr7 159138663 16057722 0.10090396448787559 0.3345018551066381 chr8 146364022 16171266 0.1104866194507828 0.3484930660208999 chr9 141213431 11783099 0.08344177261722364 0.304213564646681 chr10 135534747 12790800 0.09437284742930166 0.321371529854188 chr11 135006516 13967863 0.10346065815075177 0.34070739197528416 chr12 133851895 13735495 0.10261711274240831 0.33741853004313144 chr13 115169878 11666956 0.10130214777165954 0.3356229041640665 chr14 107349540 9638910 0.0897899515917814 0.31787964033036603 chr15 102531392 8062756 0.07863695052535716 0.2969021201275653 chr16 90354753 5517002 0.06105934460359822 0.25907034191681316 chr17 81195210 4648961 0.057256591860529706 0.25158336745353993 chr18 78077248 8329996 0.10668915994580137 0.3417885213775895 chr19 59128983 2507142 0.042401236632126756 0.21460183463289997 chr20 63025520 4722561 0.07493093273962674 0.28804747222931115 chr21 48129895 3661556 0.07607654244830578 0.29266158558557603 chr22 51304566 1708500 0.03330112957197611 0.19126941466313402 chrMT 16571 150 0.009051958240299317 0.09471019106894038 chrX 155270560 16718707 0.10767467445213053 0.34472857625149644 chrY 59373566 392293 0.00660719957430214 0.08644801422264058