BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082978.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,701,438 number of mapped reads = 3,044,426 (82.25%) number of supplementary alignments = 20,332 (0.55%) number of secondary alignments = 0 number of mapped bases = 208,592,831 bp number of sequenced bases = 208,509,381 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 116,573 duplication rate = 3.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4957 >>>>>>> ACTG content number of A's = 60,361,402 bp (28.95%) number of C's = 38,099,935 bp (18.27%) number of T's = 66,597,627 bp (31.94%) number of G's = 43,429,194 bp (20.83%) number of N's = 21,223 bp (0.01%) GC percentage = 39.1% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 1,919,868 number of insertions = 17,738 mapped reads with insertion percentage = 0.58% number of deletions = 48,129 mapped reads with deletion percentage = 1.56% homopolymer indels = 47.99% >>>>>>> Coverage mean coverageData = 0.0674X std coverageData = 0.4555X There is a 5.46% of reference with a coverageData >= 1X There is a 0.91% 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 19060887 0.0764727763707357 0.703445147436137 chr2 243199373 21255712 0.08740035690799253 0.5887371139028468 chr3 198022430 14906569 0.07527717440897982 0.3227745621520322 chr4 191154276 12035369 0.06296154735246415 0.3032388224063815 chr5 180915260 11667776 0.06449304497586329 0.30115138682494536 chr6 171115067 14990015 0.08760195851134488 0.514102920910228 chr7 159138663 10297620 0.06470847376667982 0.4210111605351849 chr8 146364022 18363242 0.12546281353213976 0.6858245379608359 chr9 141213431 6326996 0.04480449172005459 0.4320052499506364 chr10 135534747 7397947 0.054583397717192034 0.36723300540058895 chr11 135006516 8057027 0.05967880098468729 0.3462359203521502 chr12 133851895 6417887 0.047947673807681244 0.26454108598733034 chr13 115169878 6969130 0.060511742488778185 0.29036807522589847 chr14 107349540 4255511 0.03964163237215548 0.27695643471112286 chr15 102531392 3940371 0.03843087393176131 0.23079253885561907 chr16 90354753 7826143 0.08661573121670754 0.3979842589034992 chr17 81195210 4951136 0.06097817839254311 0.33254407975405675 chr18 78077248 6929193 0.08874791539783779 0.9371297197666916 chr19 59128983 2673106 0.045208049663225225 0.5039333738270995 chr20 63025520 3854831 0.06116301777438726 0.30737077028819876 chr21 48129895 4830377 0.10036126195579691 0.3889812730082002 chr22 51304566 2369402 0.046183062926601896 0.2518964331860505 chrMT 16571 207452 12.518978939110495 8.389479378083578 chrX 155270560 8656888 0.055753569768795835 0.3095917090926801 chrY 59373566 352244 0.005932673809755675 0.11405631745332022