BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068138.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 = 1,591,461 number of mapped reads = 1,080,303 (67.88%) number of supplementary alignments = 8,502 (0.53%) number of secondary alignments = 0 number of mapped bases = 72,784,461 bp number of sequenced bases = 72,755,696 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 240,781 duplication rate = 14.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7935 >>>>>>> ACTG content number of A's = 20,395,328 bp (28.03%) number of C's = 13,442,024 bp (18.48%) number of T's = 23,129,423 bp (31.79%) number of G's = 15,746,329 bp (21.64%) number of N's = 42,592 bp (0.06%) GC percentage = 40.12% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 621,698 number of insertions = 5,739 mapped reads with insertion percentage = 0.53% number of deletions = 17,023 mapped reads with deletion percentage = 1.56% homopolymer indels = 49.14% >>>>>>> Coverage mean coverageData = 0.0235X std coverageData = 0.5295X There is a 0.58% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.25% of reference with a coverageData >= 3X There is a 0.2% of reference with a coverageData >= 4X There is a 0.16% of reference with a coverageData >= 5X There is a 0.13% of reference with a coverageData >= 6X There is a 0.11% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% 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 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% 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 6559400 0.02631648408209984 0.6653145281508657 chr2 243199373 6198333 0.025486632319566053 0.5588455868296467 chr3 198022430 4260068 0.02151305788945222 0.45273054704579824 chr4 191154276 4924321 0.02576097748396693 0.5678455970678546 chr5 180915260 4624515 0.02556177405930268 0.5018138273136226 chr6 171115067 3945451 0.023057297461713294 0.48959644180481604 chr7 159138663 4348908 0.027327790230335165 0.5773552968536224 chr8 146364022 3759955 0.02568906585526872 0.6144176674528737 chr9 141213431 3118956 0.022086822605422 0.5117411768397373 chr10 135534747 3214840 0.0237196738929243 0.5100695026893552 chr11 135006516 3140966 0.0232652918767269 0.4984777053029686 chr12 133851895 3043687 0.022739214861321164 0.49704775979882904 chr13 115169878 2165878 0.01880594160219567 0.4184035822094329 chr14 107349540 2108224 0.01963887316144997 0.4543862266405185 chr15 102531392 1857293 0.018114383934239378 0.5738228831338535 chr16 90354753 1982962 0.02194640496665405 0.4600072249392378 chr17 81195210 1900681 0.02340878236536367 0.46101911654355987 chr18 78077248 1796115 0.02300433283714098 0.6234538791206424 chr19 59128983 2031758 0.03436145688485797 0.611839933758366 chr20 63025520 1555094 0.024674036802869694 0.506362895740884 chr21 48129895 976271 0.02028408746788249 0.4442665947107931 chr22 51304566 771776 0.015043027554311637 0.3622517826755897 chrMT 16571 9478 0.5719630680103795 1.9340635041692757 chrX 155270560 4265105 0.02746885823043338 0.5468503967201299 chrY 59373566 224426 0.003779897606284925 0.16927168829491673