BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365361.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 = 543,506,528 number of mapped reads = 484,600,078 (89.16%) number of supplementary alignments = 12,282,365 (2.26%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 242,079,239 number of mapped paired reads (second in pair) = 242,520,839 number of mapped paired reads (both in pair) = 475,216,138 number of mapped paired reads (singletons) = 9,383,940 number of mapped bases = 60,855,396,109 bp number of sequenced bases = 60,824,163,523 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 287,117,375 duplication rate = 46.31% >>>>>>> Insert size mean insert size = 116,567.3694 std insert size = 3,423,485.6275 median insert size = 148 >>>>>>> Mapping quality mean mapping quality = 52.9119 >>>>>>> ACTG content number of A's = 15,711,642,042 bp (25.83%) number of C's = 14,086,808,965 bp (23.16%) number of T's = 15,817,576,450 bp (26.01%) number of G's = 15,205,850,959 bp (25%) number of N's = 2,285,107 bp (0%) GC percentage = 48.16% >>>>>>> Mismatches and indels general error rate = 0.0117 number of mismatches = 692,994,888 number of insertions = 7,458,986 mapped reads with insertion percentage = 1.45% number of deletions = 16,926,072 mapped reads with deletion percentage = 3.38% homopolymer indels = 40.3% >>>>>>> Coverage mean coverageData = 19.6581X std coverageData = 150.3529X There is a 52.48% of reference with a coverageData >= 1X There is a 48.36% of reference with a coverageData >= 2X There is a 42.12% of reference with a coverageData >= 3X There is a 39.86% of reference with a coverageData >= 4X There is a 36.63% of reference with a coverageData >= 5X There is a 34.91% of reference with a coverageData >= 6X There is a 32.76% of reference with a coverageData >= 7X There is a 31.37% of reference with a coverageData >= 8X There is a 29.77% of reference with a coverageData >= 9X There is a 28.61% of reference with a coverageData >= 10X There is a 27.35% of reference with a coverageData >= 11X There is a 26.35% of reference with a coverageData >= 12X There is a 25.32% of reference with a coverageData >= 13X There is a 24.46% of reference with a coverageData >= 14X There is a 23.58% of reference with a coverageData >= 15X There is a 22.82% of reference with a coverageData >= 16X There is a 22.06% of reference with a coverageData >= 17X There is a 21.39% of reference with a coverageData >= 18X There is a 20.73% of reference with a coverageData >= 19X There is a 20.13% of reference with a coverageData >= 20X There is a 19.53% of reference with a coverageData >= 21X There is a 18.99% of reference with a coverageData >= 22X There is a 18.47% of reference with a coverageData >= 23X There is a 17.98% of reference with a coverageData >= 24X There is a 17.5% of reference with a coverageData >= 25X There is a 17.06% of reference with a coverageData >= 26X There is a 16.62% of reference with a coverageData >= 27X There is a 16.22% of reference with a coverageData >= 28X There is a 15.82% of reference with a coverageData >= 29X There is a 15.45% of reference with a coverageData >= 30X There is a 15.08% of reference with a coverageData >= 31X There is a 14.74% of reference with a coverageData >= 32X There is a 14.4% of reference with a coverageData >= 33X There is a 14.08% of reference with a coverageData >= 34X There is a 13.77% of reference with a coverageData >= 35X There is a 13.47% of reference with a coverageData >= 36X There is a 13.19% of reference with a coverageData >= 37X There is a 12.91% of reference with a coverageData >= 38X There is a 12.64% of reference with a coverageData >= 39X There is a 12.38% of reference with a coverageData >= 40X There is a 12.13% of reference with a coverageData >= 41X There is a 11.89% of reference with a coverageData >= 42X There is a 11.65% of reference with a coverageData >= 43X There is a 11.42% of reference with a coverageData >= 44X There is a 11.2% of reference with a coverageData >= 45X There is a 10.99% of reference with a coverageData >= 46X There is a 10.78% of reference with a coverageData >= 47X There is a 10.58% of reference with a coverageData >= 48X There is a 10.38% of reference with a coverageData >= 49X There is a 10.19% of reference with a coverageData >= 50X There is a 10.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 5208240926 20.895598595118447 129.064665454411 chr2 243199373 5140077932 21.135243354430852 264.85873361525415 chr3 198022430 3713715476 18.75401425989975 57.72378425552511 chr4 191154276 3302201517 17.275059632984615 114.5021214977573 chr5 180915260 3373502265 18.646864089850684 62.851327928830166 chr6 171115067 3274957121 19.138917328653474 144.919310935827 chr7 159138663 3138487363 19.721715036653286 113.08666077165506 chr8 146364022 2960225017 20.225086578995487 105.66551876416173 chr9 141213431 2690474898 19.05254251629932 196.37779240684918 chr10 135534747 2997492677 22.116045835832786 82.07659409153153 chr11 135006516 3012099106 22.310768363209966 281.55008348700227 chr12 133851895 2755490842 20.586117529378274 61.312692834141174 chr13 115169878 1626300676 14.120885636433513 50.63929962847707 chr14 107349540 1858469870 17.31232262383239 64.5744761315079 chr15 102531392 1898180255 18.513161851933113 57.27063741138702 chr16 90354753 2276836616 25.198858282529972 121.07372579781367 chr17 81195210 2308837566 28.435637594877825 271.14173346618327 chr18 78077248 1587636084 20.334170640850456 294.68083436752556 chr19 59128983 1805149841 30.529018924610966 101.0584792143788 chr20 63025520 1701659358 26.99952904791583 83.89402901355756 chr21 48129895 865065062 17.97354974491426 176.1504897265067 chr22 51304566 1172780234 22.859178537832285 100.70353154806288 chrMT 16571 20305733 1225.3776476977853 3371.381928850984 chrX 155270560 1742004903 11.219157727002466 70.16428244842649 chrY 59373566 425204771 7.16151647350944 117.59714911478093