BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472627.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 17,922,114 number of mapped reads = 17,806,749 (99.36%) number of supplementary alignments = 81,164 (0.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,922,263 number of mapped paired reads (second in pair) = 8,884,486 number of mapped paired reads (both in pair) = 17,730,896 number of mapped paired reads (singletons) = 75,853 number of mapped bases = 1,753,091,777 bp number of sequenced bases = 1,752,877,268 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,984,110 duplication rate = 50.49% >>>>>>> Insert size mean insert size = 18,919.5342 std insert size = 1,325,291.4867 median insert size = 211 >>>>>>> Mapping quality mean mapping quality = 54.8318 >>>>>>> ACTG content number of A's = 470,310,373 bp (26.83%) number of C's = 408,004,865 bp (23.28%) number of T's = 470,327,617 bp (26.83%) number of G's = 403,913,915 bp (23.04%) number of N's = 320,498 bp (0.02%) GC percentage = 46.32% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 10,320,692 number of insertions = 103,230 mapped reads with insertion percentage = 0.57% number of deletions = 90,005 mapped reads with deletion percentage = 0.5% homopolymer indels = 46.22% >>>>>>> Coverage mean coverageData = 0.5663X std coverageData = 20.7517X There is a 3.61% of reference with a coverageData >= 1X There is a 1.64% of reference with a coverageData >= 2X There is a 0.77% of reference with a coverageData >= 3X There is a 0.6% of reference with a coverageData >= 4X There is a 0.47% of reference with a coverageData >= 5X There is a 0.43% of reference with a coverageData >= 6X There is a 0.39% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.34% of reference with a coverageData >= 10X There is a 0.33% of reference with a coverageData >= 11X There is a 0.32% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.3% of reference with a coverageData >= 15X There is a 0.29% of reference with a coverageData >= 16X There is a 0.28% of reference with a coverageData >= 17X There is a 0.28% of reference with a coverageData >= 18X There is a 0.27% of reference with a coverageData >= 19X There is a 0.26% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.25% of reference with a coverageData >= 22X There is a 0.25% of reference with a coverageData >= 23X There is a 0.25% of reference with a coverageData >= 24X There is a 0.24% of reference with a coverageData >= 25X There is a 0.24% of reference with a coverageData >= 26X There is a 0.23% of reference with a coverageData >= 27X There is a 0.23% of reference with a coverageData >= 28X There is a 0.23% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.22% of reference with a coverageData >= 31X There is a 0.22% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.21% of reference with a coverageData >= 34X There is a 0.21% of reference with a coverageData >= 35X There is a 0.2% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.2% of reference with a coverageData >= 38X There is a 0.2% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.19% of reference with a coverageData >= 41X There is a 0.19% of reference with a coverageData >= 42X There is a 0.19% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.18% of reference with a coverageData >= 47X There is a 0.18% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 233991382 0.9387795346756629 29.960225599220678 chr2 243199373 107157741 0.4406168473139937 15.672799823346628 chr3 198022430 166900807 0.8428378896269478 22.40796029608472 chr4 191154276 54901445 0.2872101328248603 23.948013746095572 chr5 180915260 93171751 0.5150021673130282 20.621024102236554 chr6 171115067 84626319 0.49455796315119344 13.483522917685242 chr7 159138663 91085359 0.5723647370343937 21.527227326672453 chr8 146364022 82331458 0.5625115849850041 18.583301414689608 chr9 141213431 96968829 0.6866827631997696 16.836842458313992 chr10 135534747 39510092 0.29151264066623445 10.894048760463427 chr11 135006516 49006279 0.36299195366244397 13.80503787881584 chr12 133851895 46978598 0.35097447070136734 9.633061934978551 chr13 115169878 53884837 0.46787265850885074 23.78684294902934 chr14 107349540 24891591 0.23187422135204305 10.129760572587614 chr15 102531392 22489543 0.21934299887394487 9.14458550133349 chr16 90354753 92460531 1.0233056693763525 31.143682882003063 chr17 81195210 89827568 1.1063160991886098 34.458404071058474 chr18 78077248 26870861 0.3441573786002294 17.59769802841193 chr19 59128983 70865729 1.198493960229284 30.810517049844847 chr20 63025520 60523697 0.960304603595496 26.759410030798016 chr21 48129895 11975304 0.24881217796132737 11.530621722633706 chr22 51304566 20745718 0.4043639702555909 14.232803730147866 chrMT 16571 581 0.03506125158409269 0.23235243468313993 chrX 155270560 131015954 0.8437913407409621 25.716615413923297 chrY 59373566 909803 0.01532336797826831 0.615263385302863