BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504699.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 504,585,878 number of mapped reads = 457,360,252 (90.64%) number of supplementary alignments = 2,361,568 (0.47%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 230,213,658 number of mapped paired reads (second in pair) = 227,146,594 number of mapped paired reads (both in pair) = 450,714,394 number of mapped paired reads (singletons) = 6,645,858 number of mapped bases = 44,445,767,025 bp number of sequenced bases = 44,436,322,527 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 111,131,987 duplication rate = 22.06% >>>>>>> Insert size mean insert size = 29,776.0688 std insert size = 1,635,753.1269 median insert size = 435 >>>>>>> Mapping quality mean mapping quality = 53.9675 >>>>>>> ACTG content number of A's = 11,799,856,739 bp (26.55%) number of C's = 10,297,792,924 bp (23.17%) number of T's = 11,761,551,800 bp (26.47%) number of G's = 10,562,067,819 bp (23.77%) number of N's = 15,053,245 bp (0.03%) GC percentage = 46.94% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 317,077,897 number of insertions = 3,077,413 mapped reads with insertion percentage = 0.66% number of deletions = 3,833,824 mapped reads with deletion percentage = 0.81% homopolymer indels = 40.39% >>>>>>> Coverage mean coverageData = 14.3573X std coverageData = 29.1368X There is a 85.56% of reference with a coverageData >= 1X There is a 80.07% of reference with a coverageData >= 2X There is a 73.9% of reference with a coverageData >= 3X There is a 68.19% of reference with a coverageData >= 4X There is a 62.71% of reference with a coverageData >= 5X There is a 57.7% of reference with a coverageData >= 6X There is a 53.11% of reference with a coverageData >= 7X There is a 48.95% of reference with a coverageData >= 8X There is a 45.18% of reference with a coverageData >= 9X There is a 41.77% of reference with a coverageData >= 10X There is a 38.69% of reference with a coverageData >= 11X There is a 35.9% of reference with a coverageData >= 12X There is a 33.38% of reference with a coverageData >= 13X There is a 31.09% of reference with a coverageData >= 14X There is a 29.01% of reference with a coverageData >= 15X There is a 27.12% of reference with a coverageData >= 16X There is a 25.39% of reference with a coverageData >= 17X There is a 23.82% of reference with a coverageData >= 18X There is a 22.37% of reference with a coverageData >= 19X There is a 21.05% of reference with a coverageData >= 20X There is a 19.83% of reference with a coverageData >= 21X There is a 18.71% of reference with a coverageData >= 22X There is a 17.67% of reference with a coverageData >= 23X There is a 16.71% of reference with a coverageData >= 24X There is a 15.83% of reference with a coverageData >= 25X There is a 15.01% of reference with a coverageData >= 26X There is a 14.24% of reference with a coverageData >= 27X There is a 13.53% of reference with a coverageData >= 28X There is a 12.87% of reference with a coverageData >= 29X There is a 12.25% of reference with a coverageData >= 30X There is a 11.67% of reference with a coverageData >= 31X There is a 11.13% of reference with a coverageData >= 32X There is a 10.63% of reference with a coverageData >= 33X There is a 10.15% of reference with a coverageData >= 34X There is a 9.71% of reference with a coverageData >= 35X There is a 9.29% of reference with a coverageData >= 36X There is a 8.89% of reference with a coverageData >= 37X There is a 8.52% of reference with a coverageData >= 38X There is a 8.17% of reference with a coverageData >= 39X There is a 7.84% of reference with a coverageData >= 40X There is a 7.52% of reference with a coverageData >= 41X There is a 7.22% of reference with a coverageData >= 42X There is a 6.94% of reference with a coverageData >= 43X There is a 6.68% of reference with a coverageData >= 44X There is a 6.43% of reference with a coverageData >= 45X There is a 6.19% of reference with a coverageData >= 46X There is a 5.96% of reference with a coverageData >= 47X There is a 5.74% of reference with a coverageData >= 48X There is a 5.54% of reference with a coverageData >= 49X There is a 5.34% of reference with a coverageData >= 50X There is a 5.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3895478369 15.628760936968739 31.217769655312463 chr2 243199373 2953332931 12.143670004445283 19.158623000622303 chr3 198022430 2512169436 12.686287285738286 18.96337928890164 chr4 191154276 2058413511 10.768336205045186 18.29072586390357 chr5 180915260 3052946911 16.87501049386326 25.438065397298537 chr6 171115067 1274121443 7.445992134637682 13.047772250895326 chr7 159138663 2102427752 13.211294555113863 19.650216878210042 chr8 146364022 2603458190 17.78755567403033 31.39791626477612 chr9 141213431 1210239165 8.570283693482386 17.970372755182677 chr10 135534747 2640160714 19.47958565931436 28.797202801125792 chr11 135006516 2543254841 18.838015499933352 31.465113469927132 chr12 133851895 2007017927 14.994318362097152 25.247887375046567 chr13 115169878 684586199 5.944142781847872 9.814551871005126 chr14 107349540 1251708606 11.660120816540061 17.852712722996092 chr15 102531392 1799543708 17.55114870575443 27.97252703245662 chr16 90354753 2132572982 23.602222475224963 35.839185187201124 chr17 81195210 1526561727 18.80113034993074 29.978636649013946 chr18 78077248 820790983 10.512550122155945 85.60347419609455 chr19 59128983 1854428431 31.36242730574277 46.25138905769281 chr20 63025520 1435499375 22.776478083798438 31.239185477144325 chr21 48129895 558268757 11.599209950489191 26.932934959236338 chr22 51304566 972633659 18.958033072533933 34.90901718373434 chrMT 16571 324834 19.60255868686259 7.609321318186864 chrX 155270560 2485788590 16.00940055861201 22.747582385197216 chrY 59373566 70037984 1.1796155885263822 40.68246996484457