BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237275.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,367,796 number of mapped reads = 2,174,369 (91.83%) number of supplementary alignments = 15,019 (0.63%) number of secondary alignments = 0 number of mapped bases = 150,489,318 bp number of sequenced bases = 150,405,039 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 86,971 duplication rate = 2.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0927 >>>>>>> ACTG content number of A's = 43,896,392 bp (29.19%) number of C's = 28,585,923 bp (19.01%) number of T's = 46,043,363 bp (30.61%) number of G's = 31,876,844 bp (21.19%) number of N's = 2,517 bp (0%) GC percentage = 40.2% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,284,777 number of insertions = 12,855 mapped reads with insertion percentage = 0.59% number of deletions = 47,612 mapped reads with deletion percentage = 2.16% homopolymer indels = 45.41% >>>>>>> Coverage mean coverageData = 0.0486X std coverageData = 0.5992X There is a 4.16% of reference with a coverageData >= 1X There is a 0.45% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 12508860 0.050185872957163064 1.1988040996093883 chr2 243199373 11027812 0.04534473861493056 0.647077737681392 chr3 198022430 10201453 0.051516653946727144 0.26097224223398785 chr4 191154276 7047657 0.03686894767658768 0.2798678892772735 chr5 180915260 7878734 0.04354930590155855 0.2463153226641646 chr6 171115067 17272829 0.10094277086657717 0.6899516713163252 chr7 159138663 8884949 0.05583149206173738 0.7265729617289325 chr8 146364022 8711809 0.059521519571250917 0.7822373515508663 chr9 141213431 7497529 0.053093597024775924 0.6270419608671872 chr10 135534747 5795220 0.04275818657779322 0.5691829358065363 chr11 135006516 4881209 0.0361553586050617 0.37938171631254586 chr12 133851895 4457450 0.03330135893854921 0.22442983874404096 chr13 115169878 5703176 0.04951968430495342 0.24549482668241573 chr14 107349540 4904721 0.045689259590679196 0.3000197173430431 chr15 102531392 4228819 0.04124413916081428 0.22572745791506868 chr16 90354753 3486929 0.03859153928515526 0.3524436026300907 chr17 81195210 4003741 0.0493100639803752 0.3799115745216905 chr18 78077248 3873469 0.049610726546099576 1.24666898784692 chr19 59128983 3310818 0.055993149755340796 0.7710909070210679 chr20 63025520 2864524 0.04545022397276532 0.25626201601875886 chr21 48129895 2778231 0.05772360400952464 0.34941601054803595 chr22 51304566 1530331 0.029828358746860854 0.18966994115039273 chrMT 16571 61266 3.6971818236678535 2.8079286801698515 chrX 155270560 7176285 0.04621793725739123 0.30364890458483546 chrY 59373566 401497 0.006762218055085322 0.22054951431774966