BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365370.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 = 608,316,104 number of mapped reads = 513,474,098 (84.41%) number of supplementary alignments = 4,575,720 (0.75%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 254,194,314 number of mapped paired reads (second in pair) = 259,279,784 number of mapped paired reads (both in pair) = 503,688,392 number of mapped paired reads (singletons) = 9,785,706 number of mapped bases = 68,173,252,077 bp number of sequenced bases = 68,125,130,129 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 243,069,702 duplication rate = 41.87% >>>>>>> Insert size mean insert size = 46,126.4287 std insert size = 2,187,368.8279 median insert size = 161 >>>>>>> Mapping quality mean mapping quality = 54.2344 >>>>>>> ACTG content number of A's = 17,979,883,466 bp (26.39%) number of C's = 15,981,596,722 bp (23.46%) number of T's = 17,426,123,873 bp (25.58%) number of G's = 16,735,434,733 bp (24.57%) number of N's = 2,091,335 bp (0%) GC percentage = 48.02% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 685,155,159 number of insertions = 9,759,383 mapped reads with insertion percentage = 1.84% number of deletions = 33,094,333 mapped reads with deletion percentage = 6.21% homopolymer indels = 51.34% >>>>>>> Coverage mean coverageData = 22.022X std coverageData = 82.7997X There is a 65.35% of reference with a coverageData >= 1X There is a 61.52% of reference with a coverageData >= 2X There is a 54.54% of reference with a coverageData >= 3X There is a 51.69% of reference with a coverageData >= 4X There is a 47.55% of reference with a coverageData >= 5X There is a 45.17% of reference with a coverageData >= 6X There is a 42.31% of reference with a coverageData >= 7X There is a 40.32% of reference with a coverageData >= 8X There is a 38.17% of reference with a coverageData >= 9X There is a 36.49% of reference with a coverageData >= 10X There is a 34.78% of reference with a coverageData >= 11X There is a 33.36% of reference with a coverageData >= 12X There is a 31.95% of reference with a coverageData >= 13X There is a 30.73% of reference with a coverageData >= 14X There is a 29.54% of reference with a coverageData >= 15X There is a 28.47% of reference with a coverageData >= 16X There is a 27.45% of reference with a coverageData >= 17X There is a 26.52% of reference with a coverageData >= 18X There is a 25.62% of reference with a coverageData >= 19X There is a 24.79% of reference with a coverageData >= 20X There is a 24% of reference with a coverageData >= 21X There is a 23.26% of reference with a coverageData >= 22X There is a 22.56% of reference with a coverageData >= 23X There is a 21.89% of reference with a coverageData >= 24X There is a 21.26% of reference with a coverageData >= 25X There is a 20.66% of reference with a coverageData >= 26X There is a 20.09% of reference with a coverageData >= 27X There is a 19.55% of reference with a coverageData >= 28X There is a 19.03% of reference with a coverageData >= 29X There is a 18.53% of reference with a coverageData >= 30X There is a 18.05% of reference with a coverageData >= 31X There is a 17.6% of reference with a coverageData >= 32X There is a 17.16% of reference with a coverageData >= 33X There is a 16.74% of reference with a coverageData >= 34X There is a 16.34% of reference with a coverageData >= 35X There is a 15.95% of reference with a coverageData >= 36X There is a 15.58% of reference with a coverageData >= 37X There is a 15.22% of reference with a coverageData >= 38X There is a 14.88% of reference with a coverageData >= 39X There is a 14.55% of reference with a coverageData >= 40X There is a 14.23% of reference with a coverageData >= 41X There is a 13.92% of reference with a coverageData >= 42X There is a 13.62% of reference with a coverageData >= 43X There is a 13.33% of reference with a coverageData >= 44X There is a 13.05% of reference with a coverageData >= 45X There is a 12.78% of reference with a coverageData >= 46X There is a 12.52% of reference with a coverageData >= 47X There is a 12.26% of reference with a coverageData >= 48X There is a 12.02% of reference with a coverageData >= 49X There is a 11.78% of reference with a coverageData >= 50X There is a 11.55% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 6271343170 25.160792558266085 92.8405866745525 chr2 243199373 5741684764 23.608962034618404 164.73607581777094 chr3 198022430 4255499459 21.489987063586685 51.645820342353595 chr4 191154276 3261159148 17.060351545575678 55.58068529342101 chr5 180915260 3808715681 21.052484356488225 64.08854083963803 chr6 171115067 3554718093 20.773846250488276 51.074136177058996 chr7 159138663 3444088526 21.64206020758136 69.47956178113171 chr8 146364022 3503422824 23.93636616517685 61.625725984374974 chr9 141213431 3104879759 21.987141995013207 84.33268238632633 chr10 135534747 3819186584 28.17865284390873 100.45894730686874 chr11 135006516 3492339186 25.867930596772084 72.09378740312306 chr12 133851895 3071739396 22.94879273842182 55.62919111686553 chr13 115169878 1718731401 14.923445529741727 40.38066455205491 chr14 107349540 2079840087 19.374466690774828 54.74057799974755 chr15 102531392 2215088108 21.603999173248326 57.32085283778593 chr16 90354753 2547099110 28.189984759296504 107.77431822453515 chr17 81195210 2468790682 30.405619765008304 90.3227936715055 chr18 78077248 1680263825 21.52053085938685 89.83748870314047 chr19 59128983 1704155347 28.820981869415885 80.29092047185067 chr20 63025520 2029585641 32.20260048627921 83.38417055254016 chr21 48129895 917580527 19.064669204036285 87.96425924104128 chr22 51304566 1383461992 26.965669917176573 74.70546958981402 chrMT 16571 11026070 665.3835012974473 541.1127352813792 chrX 155270560 1701845589 10.960516848783183 38.80628287960584 chrY 59373566 387007108 6.51817187466894 78.60518280254605