BamQC report ----------------------------------- >>>>>>> Input bam file = SRR620536.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP016866/SRP016866.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 = 8,692,981 number of mapped reads = 5,106,494 (58.74%) number of supplementary alignments = 504 (0.01%) number of secondary alignments = 0 number of mapped bases = 233,121,849 bp number of sequenced bases = 233,064,240 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 310,997 duplication rate = 3.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.2941 >>>>>>> ACTG content number of A's = 63,422,425 bp (27.21%) number of C's = 44,829,156 bp (19.23%) number of T's = 71,366,083 bp (30.62%) number of G's = 53,432,014 bp (22.93%) number of N's = 14,562 bp (0.01%) GC percentage = 42.16% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 1,706,098 number of insertions = 15,441 mapped reads with insertion percentage = 0.3% number of deletions = 37,713 mapped reads with deletion percentage = 0.73% homopolymer indels = 45.22% >>>>>>> Coverage mean coverageData = 0.0753X std coverageData = 0.8429X There is a 6.35% of reference with a coverageData >= 1X There is a 0.69% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% 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 19245725 0.07721435125331143 1.5034972996899902 chr2 243199373 19461371 0.08002229101141638 0.8290965733983473 chr3 198022430 15251436 0.0770187296459295 0.4121771997076406 chr4 191154276 13793869 0.07216092304416984 0.4654900125877641 chr5 180915260 13793371 0.07624216442548848 0.3590769109369053 chr6 171115067 13165170 0.07693752648911975 0.5126608059477796 chr7 159138663 12654626 0.07951949426645617 1.067021572675466 chr8 146364022 11549617 0.0789102187968024 0.9215615744238586 chr9 141213431 9519459 0.06741185263036346 0.6210156957030812 chr10 135534747 11226313 0.08282977796092393 0.8137467476464418 chr11 135006516 10883831 0.08061707925267844 1.1826356423780027 chr12 133851895 10501380 0.07845522097389805 0.4204036082899196 chr13 115169878 7042776 0.061151197885266496 0.3184518224701101 chr14 107349540 7061113 0.06577683518718384 0.3537335392639522 chr15 102531392 6767886 0.06600794028037774 0.33735487237246653 chr16 90354753 7102004 0.07860133268252087 0.47101164075827634 chr17 81195210 6747314 0.0830999020755042 0.5407825742226295 chr18 78077248 6311941 0.08084225765744202 2.2587836594215527 chr19 59128983 5335450 0.09023409044596624 0.9968080744003335 chr20 63025520 5048352 0.08010012452098769 0.4451413846261338 chr21 48129895 3037094 0.06310202837550341 0.42111175008980495 chr22 51304566 2921179 0.05693799261453649 0.2839484039461761 chrMT 16571 498564 30.08653672077726 23.55781061253637 chrX 155270560 13303914 0.0856821409029503 0.6747078433837508 chrY 59373566 898094 0.015126159004833903 0.3002625814118408