BamQC report ----------------------------------- >>>>>>> Input bam file = SRR090131.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 20,904,838 number of mapped reads = 16,847,308 (80.59%) number of supplementary alignments = 916 (0%) number of secondary alignments = 0 number of mapped bases = 784,148,409 bp number of sequenced bases = 783,990,119 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,539,945 duplication rate = 10.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.003 >>>>>>> ACTG content number of A's = 254,584,342 bp (32.47%) number of C's = 155,222,423 bp (19.8%) number of T's = 206,156,583 bp (26.3%) number of G's = 167,970,092 bp (21.43%) number of N's = 56,679 bp (0.01%) GC percentage = 41.22% >>>>>>> Mismatches and indels general error rate = 0.0046 number of mismatches = 3,518,080 number of insertions = 35,343 mapped reads with insertion percentage = 0.21% number of deletions = 105,159 mapped reads with deletion percentage = 0.62% homopolymer indels = 44.46% >>>>>>> Coverage mean coverageData = 0.2533X std coverageData = 1.6862X There is a 12.92% of reference with a coverageData >= 1X There is a 4.76% of reference with a coverageData >= 2X There is a 2.28% of reference with a coverageData >= 3X There is a 1.29% of reference with a coverageData >= 4X There is a 0.82% of reference with a coverageData >= 5X There is a 0.56% of reference with a coverageData >= 6X There is a 0.41% of reference with a coverageData >= 7X There is a 0.31% of reference with a coverageData >= 8X There is a 0.25% of reference with a coverageData >= 9X There is a 0.2% of reference with a coverageData >= 10X There is a 0.16% of reference with a coverageData >= 11X There is a 0.14% of reference with a coverageData >= 12X There is a 0.12% of reference with a coverageData >= 13X There is a 0.1% of reference with a coverageData >= 14X There is a 0.09% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% 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 63535971 0.25490797473278914 1.8683150750009117 chr2 243199373 82334691 0.3385481219970086 1.694752431475637 chr3 198022430 69427642 0.35060493904655143 1.44507069123625 chr4 191154276 41084129 0.2149265496943422 0.9924862493468903 chr5 180915260 36092776 0.1995010039506894 0.9465634775327066 chr6 171115067 44191404 0.25825548138317944 1.19223723694891 chr7 159138663 56681656 0.3561777818882392 2.61473672461124 chr8 146364022 69542731 0.47513541955003125 4.606860483233315 chr9 141213431 24729242 0.1751196173400815 1.1381145076931776 chr10 135534747 23227820 0.17137907816362397 1.0102486793543755 chr11 135006516 32588858 0.24138729718793722 1.2358602463570643 chr12 133851895 28748705 0.2147799625847658 0.9900828062936825 chr13 115169878 24374611 0.21164050377825355 0.9995734262205231 chr14 107349540 28265978 0.26330786326611183 1.1796208888234734 chr15 102531392 20868463 0.20353242643969957 0.9815261672958985 chr16 90354753 15529737 0.17187515304258538 0.9160401726023546 chr17 81195210 15672816 0.19302636202307993 0.9708192328974287 chr18 78077248 29461309 0.3773353922515302 1.9187830144487619 chr19 59128983 13241500 0.22394263063851444 1.5038409263854866 chr20 63025520 18465816 0.2929895064729335 1.2336622365585852 chr21 48129895 11297631 0.23473209322397234 1.1872285609346525 chr22 51304566 6327692 0.12333584500061846 0.7134296536714575 chrMT 16571 558530 33.705268239695855 30.325765562586447 chrX 155270560 26019367 0.16757437469150624 0.9200170754566075 chrY 59373566 1879334 0.031652705515447736 0.9902680031640949