BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063533.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 = 2,971,613 number of mapped reads = 2,544,827 (85.64%) number of supplementary alignments = 21,246 (0.71%) number of secondary alignments = 0 number of mapped bases = 160,006,800 bp number of sequenced bases = 159,932,731 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 189,530 duplication rate = 6.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9297 >>>>>>> ACTG content number of A's = 42,074,908 bp (26.31%) number of C's = 28,683,992 bp (17.94%) number of T's = 51,437,480 bp (32.16%) number of G's = 37,733,585 bp (23.59%) number of N's = 2,766 bp (0%) GC percentage = 41.53% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,330,306 number of insertions = 11,738 mapped reads with insertion percentage = 0.46% number of deletions = 45,924 mapped reads with deletion percentage = 1.78% homopolymer indels = 45.38% >>>>>>> Coverage mean coverageData = 0.0517X std coverageData = 0.4624X There is a 4.02% of reference with a coverageData >= 1X There is a 0.8% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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 15052999 0.06039302505890246 0.6520905335803706 chr2 243199373 15559842 0.06397977843470838 0.8759477151519897 chr3 198022430 8827676 0.04457917216751658 0.261199655728008 chr4 191154276 6479666 0.03389757286936129 0.24939486432606328 chr5 180915260 5757013 0.03182159979207945 0.22182169391689882 chr6 171115067 12200196 0.07129819842223478 0.4120612449231786 chr7 159138663 11381190 0.07151744136495604 0.6325533172213834 chr8 146364022 3919945 0.026782162354079063 0.4674587159476754 chr9 141213431 7769085 0.055016615239665126 0.45375228947449703 chr10 135534747 10626747 0.07840607102767529 0.4443740032993011 chr11 135006516 7295119 0.05403531041420253 0.3701250352712127 chr12 133851895 9341187 0.06978748414432236 0.33803014288279026 chr13 115169878 3096459 0.02688601441428982 0.20650933800192314 chr14 107349540 3289363 0.030641612437277328 0.2523673651424732 chr15 102531392 2352383 0.022943051431506947 0.2117796775482763 chr16 90354753 3528673 0.03905354043743554 0.25953535880997297 chr17 81195210 4827551 0.059456105846638 0.3226783492731126 chr18 78077248 4808013 0.06158020579823715 0.6380740691588818 chr19 59128983 3053448 0.05164046200490206 0.5233529099992639 chr20 63025520 2364870 0.0375224194897559 0.2524273283827596 chr21 48129895 3099014 0.06438854686884316 0.32983284286069775 chr22 51304566 1986468 0.03871912687069607 0.2393610336502118 chrMT 16571 32013 1.9318689276446805 2.125970827626807 chrX 155270560 12914678 0.08317531668591908 0.41687552592947924 chrY 59373566 443202 0.007464635019564093 0.15043791003668533