BamQC report ----------------------------------- >>>>>>> Input bam file = SRR090206.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 24,496,175 number of mapped reads = 22,726,894 (92.78%) number of supplementary alignments = 167,909 (0.69%) number of secondary alignments = 0 number of mapped bases = 1,502,772,413 bp number of sequenced bases = 1,502,221,152 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,154,263 duplication rate = 12.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4081 >>>>>>> ACTG content number of A's = 396,994,477 bp (26.43%) number of C's = 278,666,814 bp (18.55%) number of T's = 470,321,829 bp (31.31%) number of G's = 355,705,000 bp (23.68%) number of N's = 533,032 bp (0.04%) GC percentage = 42.23% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 8,688,070 number of insertions = 96,452 mapped reads with insertion percentage = 0.42% number of deletions = 312,566 mapped reads with deletion percentage = 1.36% homopolymer indels = 47.55% >>>>>>> Coverage mean coverageData = 0.4854X std coverageData = 3.5046X There is a 20.21% of reference with a coverageData >= 1X There is a 10.79% of reference with a coverageData >= 2X There is a 6.14% of reference with a coverageData >= 3X There is a 3.63% of reference with a coverageData >= 4X There is a 2.22% of reference with a coverageData >= 5X There is a 1.4% of reference with a coverageData >= 6X There is a 0.91% of reference with a coverageData >= 7X There is a 0.61% of reference with a coverageData >= 8X There is a 0.42% of reference with a coverageData >= 9X There is a 0.29% of reference with a coverageData >= 10X There is a 0.21% of reference with a coverageData >= 11X There is a 0.16% of reference with a coverageData >= 12X There is a 0.12% of reference with a coverageData >= 13X There is a 0.09% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% 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 124051405 0.497697476147913 6.4775718239853415 chr2 243199373 156833390 0.6448757990835774 3.7950664620245442 chr3 198022430 138108935 0.6974408656635513 1.7244669729488427 chr4 191154276 70422879 0.3684085989266596 1.4510364198604495 chr5 180915260 68380227 0.3779682653635741 1.2352697256007703 chr6 171115067 85379687 0.49896066136595674 1.8650680028818087 chr7 159138663 112385093 0.7062086037508056 6.678351280338917 chr8 146364022 137805825 0.941528000644858 6.186339935240548 chr9 141213431 47047018 0.3331624879222714 3.061856962318535 chr10 135534747 46906113 0.3460818280053306 2.9173520200685292 chr11 135006516 63610354 0.47116506584022955 3.044176991509559 chr12 133851895 52770342 0.39424426527543743 1.3497532381091235 chr13 115169878 34375178 0.29847368597542495 1.0273469174598349 chr14 107349540 54049948 0.503494919493833 1.4660164722967552 chr15 102531392 39412034 0.3843899242097484 1.2424824403577417 chr16 90354753 30856058 0.34149900227163477 1.3275878449739824 chr17 81195210 31841183 0.3921559289027025 1.6812071625184875 chr18 78077248 56544296 0.7242096442743474 5.34522936566951 chr19 59128983 26973482 0.4561803811169896 3.572371997951874 chr20 63025520 37638867 0.5972004197664692 1.7986706548672544 chr21 48129895 22305237 0.463438305859591 1.68645624686577 chr22 51304566 12304099 0.23982463861013853 0.921380624607181 chrMT 16571 2366984 142.83893548971093 66.50830112922633 chrX 155270560 46857112 0.3017771817142928 1.470850764321895 chrY 59373566 3546667 0.05973478163666302 2.6466362592861388