BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472379.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 = 19,931,070 number of mapped reads = 19,780,116 (99.24%) number of supplementary alignments = 73,272 (0.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,915,468 number of mapped paired reads (second in pair) = 9,864,648 number of mapped paired reads (both in pair) = 19,694,640 number of mapped paired reads (singletons) = 85,476 number of mapped bases = 1,943,769,958 bp number of sequenced bases = 1,943,542,020 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,598,597 duplication rate = 48.11% >>>>>>> Insert size mean insert size = 18,375.8653 std insert size = 1,333,264.0599 median insert size = 214 >>>>>>> Mapping quality mean mapping quality = 54.93 >>>>>>> ACTG content number of A's = 515,652,370 bp (26.53%) number of C's = 457,739,527 bp (23.55%) number of T's = 516,099,550 bp (26.55%) number of G's = 453,808,301 bp (23.35%) number of N's = 242,272 bp (0.01%) GC percentage = 46.9% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 10,247,288 number of insertions = 113,998 mapped reads with insertion percentage = 0.57% number of deletions = 95,799 mapped reads with deletion percentage = 0.47% homopolymer indels = 44.83% >>>>>>> Coverage mean coverageData = 0.6279X std coverageData = 19.4074X There is a 5.19% of reference with a coverageData >= 1X There is a 2.24% of reference with a coverageData >= 2X There is a 0.95% of reference with a coverageData >= 3X There is a 0.7% of reference with a coverageData >= 4X There is a 0.53% of reference with a coverageData >= 5X There is a 0.48% of reference with a coverageData >= 6X There is a 0.44% of reference with a coverageData >= 7X There is a 0.42% of reference with a coverageData >= 8X There is a 0.4% of reference with a coverageData >= 9X There is a 0.39% of reference with a coverageData >= 10X There is a 0.38% of reference with a coverageData >= 11X There is a 0.37% of reference with a coverageData >= 12X There is a 0.36% of reference with a coverageData >= 13X There is a 0.35% of reference with a coverageData >= 14X There is a 0.34% of reference with a coverageData >= 15X There is a 0.33% of reference with a coverageData >= 16X There is a 0.32% of reference with a coverageData >= 17X There is a 0.32% of reference with a coverageData >= 18X There is a 0.31% of reference with a coverageData >= 19X There is a 0.31% of reference with a coverageData >= 20X There is a 0.3% of reference with a coverageData >= 21X There is a 0.29% of reference with a coverageData >= 22X There is a 0.29% of reference with a coverageData >= 23X There is a 0.28% of reference with a coverageData >= 24X There is a 0.28% of reference with a coverageData >= 25X There is a 0.27% of reference with a coverageData >= 26X There is a 0.27% of reference with a coverageData >= 27X There is a 0.27% of reference with a coverageData >= 28X There is a 0.26% of reference with a coverageData >= 29X There is a 0.26% of reference with a coverageData >= 30X There is a 0.25% of reference with a coverageData >= 31X There is a 0.25% of reference with a coverageData >= 32X There is a 0.25% of reference with a coverageData >= 33X There is a 0.24% of reference with a coverageData >= 34X There is a 0.24% of reference with a coverageData >= 35X There is a 0.24% of reference with a coverageData >= 36X There is a 0.23% of reference with a coverageData >= 37X There is a 0.23% of reference with a coverageData >= 38X There is a 0.23% of reference with a coverageData >= 39X There is a 0.23% of reference with a coverageData >= 40X There is a 0.22% of reference with a coverageData >= 41X There is a 0.22% of reference with a coverageData >= 42X There is a 0.22% of reference with a coverageData >= 43X There is a 0.22% of reference with a coverageData >= 44X There is a 0.21% of reference with a coverageData >= 45X There is a 0.21% of reference with a coverageData >= 46X There is a 0.21% of reference with a coverageData >= 47X There is a 0.21% of reference with a coverageData >= 48X There is a 0.2% of reference with a coverageData >= 49X There is a 0.2% of reference with a coverageData >= 50X There is a 0.2% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 172629737 0.6925950126318843 21.1851445604453 chr2 243199373 183866148 0.7560305182201271 28.746371912390074 chr3 198022430 125474316 0.6336368864880609 14.423843177556499 chr4 191154276 60903467 0.31860897006562383 11.99071391182103 chr5 180915260 80778806 0.44650078716411207 18.70836342657366 chr6 171115067 141362347 0.8261244873310893 17.11893611525728 chr7 159138663 134755657 0.8467813820956884 20.94094346883076 chr8 146364022 89166044 0.6092073911442526 17.366941091756136 chr9 141213431 71531911 0.5065517528569927 15.711235507643366 chr10 135534747 48886258 0.36069169775334436 10.386773674965415 chr11 135006516 56714389 0.4200863090193365 14.19635715597126 chr12 133851895 99309770 0.7419377215391684 20.2013582293118 chr13 115169878 61865141 0.5371642487977629 15.893658117372636 chr14 107349540 34847870 0.32462058058190096 9.367262022202445 chr15 102531392 64135436 0.6255199968415527 27.152647956691627 chr16 90354753 105265281 1.1650220658563473 29.075058063622674 chr17 81195210 90436669 1.1138177855565619 25.491622988251905 chr18 78077248 19711742 0.2524646104329907 9.676635923112824 chr19 59128983 51668741 0.8738310449208978 18.137339032265217 chr20 63025520 82534112 1.309534804314189 31.424869215578916 chr21 48129895 15786332 0.3279943162144858 17.45578911628133 chr22 51304566 20653270 0.40256202537606495 9.674231279633815 chrMT 16571 24707 1.490978214953835 1.5115543794668105 chrX 155270560 131028746 0.8438737259658238 21.804568142036626 chrY 59373566 433061 0.007293835105002789 0.5135030852996432