BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365371.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP102259/SRP102259.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 = 597,850,476 number of mapped reads = 570,889,125 (95.49%) number of supplementary alignments = 13,075,796 (2.19%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 285,778,771 number of mapped paired reads (second in pair) = 285,110,354 number of mapped paired reads (both in pair) = 568,200,476 number of mapped paired reads (singletons) = 2,688,649 number of mapped bases = 82,135,858,178 bp number of sequenced bases = 82,118,426,041 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 214,667,014 duplication rate = 35.57% >>>>>>> Insert size mean insert size = 87,953.4831 std insert size = 2,977,367.4723 median insert size = 183 >>>>>>> Mapping quality mean mapping quality = 54.6788 >>>>>>> ACTG content number of A's = 22,189,311,995 bp (27.02%) number of C's = 18,936,290,933 bp (23.06%) number of T's = 21,702,580,841 bp (26.43%) number of G's = 19,289,378,490 bp (23.49%) number of N's = 863,782 bp (0%) GC percentage = 46.55% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 378,852,439 number of insertions = 7,570,057 mapped reads with insertion percentage = 1.29% number of deletions = 6,009,015 mapped reads with deletion percentage = 1.02% homopolymer indels = 43.19% >>>>>>> Coverage mean coverageData = 26.5323X std coverageData = 53.2045X There is a 83.72% of reference with a coverageData >= 1X There is a 80.81% of reference with a coverageData >= 2X There is a 75.89% of reference with a coverageData >= 3X There is a 73.02% of reference with a coverageData >= 4X There is a 69.22% of reference with a coverageData >= 5X There is a 66.49% of reference with a coverageData >= 6X There is a 63.38% of reference with a coverageData >= 7X There is a 60.89% of reference with a coverageData >= 8X There is a 58.26% of reference with a coverageData >= 9X There is a 56% of reference with a coverageData >= 10X There is a 53.72% of reference with a coverageData >= 11X There is a 51.68% of reference with a coverageData >= 12X There is a 49.68% of reference with a coverageData >= 13X There is a 47.84% of reference with a coverageData >= 14X There is a 46.06% of reference with a coverageData >= 15X There is a 44.4% of reference with a coverageData >= 16X There is a 42.8% of reference with a coverageData >= 17X There is a 41.3% of reference with a coverageData >= 18X There is a 39.85% of reference with a coverageData >= 19X There is a 38.49% of reference with a coverageData >= 20X There is a 37.19% of reference with a coverageData >= 21X There is a 35.95% of reference with a coverageData >= 22X There is a 34.76% of reference with a coverageData >= 23X There is a 33.62% of reference with a coverageData >= 24X There is a 32.54% of reference with a coverageData >= 25X There is a 31.5% of reference with a coverageData >= 26X There is a 30.5% of reference with a coverageData >= 27X There is a 29.55% of reference with a coverageData >= 28X There is a 28.63% of reference with a coverageData >= 29X There is a 27.75% of reference with a coverageData >= 30X There is a 26.91% of reference with a coverageData >= 31X There is a 26.1% of reference with a coverageData >= 32X There is a 25.33% of reference with a coverageData >= 33X There is a 24.58% of reference with a coverageData >= 34X There is a 23.86% of reference with a coverageData >= 35X There is a 23.17% of reference with a coverageData >= 36X There is a 22.5% of reference with a coverageData >= 37X There is a 21.86% of reference with a coverageData >= 38X There is a 21.24% of reference with a coverageData >= 39X There is a 20.65% of reference with a coverageData >= 40X There is a 20.08% of reference with a coverageData >= 41X There is a 19.52% of reference with a coverageData >= 42X There is a 18.99% of reference with a coverageData >= 43X There is a 18.47% of reference with a coverageData >= 44X There is a 17.98% of reference with a coverageData >= 45X There is a 17.5% of reference with a coverageData >= 46X There is a 17.03% of reference with a coverageData >= 47X There is a 16.58% of reference with a coverageData >= 48X There is a 16.15% of reference with a coverageData >= 49X There is a 15.73% of reference with a coverageData >= 50X There is a 15.32% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 7321049643 29.372242338365126 57.7072091246672 chr2 243199373 7091811226 29.160483181015437 108.47709929418487 chr3 198022430 5620614196 28.383724995193727 42.08145214239815 chr4 191154276 4603346477 24.08183888598966 38.6331085303366 chr5 180915260 4860950132 26.86865735925206 39.491477867622265 chr6 171115067 4777152148 27.917776217800856 45.9893343768711 chr7 159138663 4314815173 27.113556766528824 41.173075537790524 chr8 146364022 4161765844 28.434350102786873 45.209596006585265 chr9 141213431 3471402784 24.582667239350624 45.18278295689074 chr10 135534747 4037368475 29.78843849540664 48.72260905352973 chr11 135006516 3994791148 29.589617348543385 45.481824649204235 chr12 133851895 3829943266 28.61329132471378 44.19170331380551 chr13 115169878 2364314310 20.528929534856328 35.692010967481124 chr14 107349540 2671222677 24.88341055769778 43.052833342221405 chr15 102531392 2630640437 25.656926973155695 42.10482268649196 chr16 90354753 2616799687 28.961394947313952 44.91656948377579 chr17 81195210 2515589818 30.981997805042933 54.44387060153518 chr18 78077248 2184749800 27.981900694040856 60.45375501001396 chr19 59128983 1891388652 31.987505213813673 55.16783925623396 chr20 63025520 2036223908 32.307927138086285 51.493764123645946 chr21 48129895 1008474628 20.953185707136907 49.009943613158725 chr22 51304566 1248118929 24.327638382127624 48.34843327346728 chrMT 16571 2119245 127.88878160642085 55.06707475657304 chrX 155270560 2513431300 16.187429864360634 29.958932341345736 chrY 59373566 367774275 6.194242653372041 28.94352402922901