BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038414.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 14,019,392 number of mapped reads = 13,678,119 (97.57%) number of supplementary alignments = 150,672 (1.07%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,902,139 number of mapped paired reads (second in pair) = 6,775,980 number of mapped paired reads (both in pair) = 13,534,984 number of mapped paired reads (singletons) = 143,135 number of mapped bases = 2,008,705,533 bp number of sequenced bases = 2,007,926,705 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,486,915 duplication rate = 7.87% >>>>>>> Insert size mean insert size = 91,234.1153 std insert size = 2,996,924.4776 median insert size = 263 >>>>>>> Mapping quality mean mapping quality = 54.3675 >>>>>>> ACTG content number of A's = 580,016,337 bp (28.89%) number of C's = 427,637,406 bp (21.3%) number of T's = 573,921,752 bp (28.58%) number of G's = 426,305,597 bp (21.23%) number of N's = 45,613 bp (0%) GC percentage = 42.53% >>>>>>> Mismatches and indels general error rate = 0.011 number of mismatches = 21,280,113 number of insertions = 265,894 mapped reads with insertion percentage = 1.82% number of deletions = 272,344 mapped reads with deletion percentage = 1.9% homopolymer indels = 44.04% >>>>>>> Coverage mean coverageData = 0.6489X std coverageData = 6.9843X There is a 37.33% of reference with a coverageData >= 1X There is a 15.61% of reference with a coverageData >= 2X There is a 5.46% of reference with a coverageData >= 3X There is a 2.23% of reference with a coverageData >= 4X There is a 0.81% of reference with a coverageData >= 5X There is a 0.35% of reference with a coverageData >= 6X There is a 0.15% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% 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 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 144556655 0.5799650745905263 17.202041601093498 chr2 243199373 190063861 0.7815146011910155 5.405817568963875 chr3 198022430 125097718 0.6317350918277288 1.0482809238685795 chr4 191154276 114920481 0.6011923112826417 6.382482716685158 chr5 180915260 120909310 0.6683201295457332 1.1675318041415603 chr6 171115067 130614393 0.7633132212723267 5.8505252374852015 chr7 159138663 131319669 0.8251902242008907 4.9292551879979465 chr8 146364022 89845924 0.6138525217624862 3.836657122557315 chr9 141213431 82183985 0.5819841952568945 7.39432343857105 chr10 135534747 86465035 0.6379547452875682 13.088638980879502 chr11 135006516 89248556 0.661068507241532 3.183608279195196 chr12 133851895 77111145 0.5760930392505836 1.0291569397907845 chr13 115169878 112601631 0.9777003584218436 1.3363334863849465 chr14 107349540 44041226 0.41026003464942656 0.939223974620368 chr15 102531392 49357461 0.48138877310863 0.9041176893149678 chr16 90354753 71216058 0.7881827533743576 5.582715234954656 chr17 81195210 61397781 0.7561749147517446 3.2333613777474413 chr18 78077248 35560952 0.45545857353988706 7.358926648801446 chr19 59128983 45664185 0.7722809134058674 7.893347807040827 chr20 63025520 65183828 1.0342449852059927 2.389244673595764 chr21 48129895 21566196 0.44808317159220895 3.3266043919097146 chr22 51304566 20520009 0.3999645762523359 1.7628828969252863 chrMT 16571 3327752 200.81781425381692 24.533596102337256 chrX 155270560 76652421 0.49367002347386396 1.2498727004916779 chrY 59373566 19279301 0.3247118591462066 7.753960356092279