BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472778.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 = 18,006,458 number of mapped reads = 17,816,615 (98.95%) number of supplementary alignments = 62,933 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,947,349 number of mapped paired reads (second in pair) = 8,869,266 number of mapped paired reads (both in pair) = 17,698,180 number of mapped paired reads (singletons) = 118,435 number of mapped bases = 1,756,554,188 bp number of sequenced bases = 1,756,295,197 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,139,390 duplication rate = 46.86% >>>>>>> Insert size mean insert size = 24,831.0087 std insert size = 1,560,821.7182 median insert size = 265 >>>>>>> Mapping quality mean mapping quality = 55.0994 >>>>>>> ACTG content number of A's = 491,348,085 bp (27.98%) number of C's = 388,919,287 bp (22.14%) number of T's = 488,447,941 bp (27.81%) number of G's = 387,243,385 bp (22.05%) number of N's = 336,499 bp (0.02%) GC percentage = 44.19% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 11,757,146 number of insertions = 120,585 mapped reads with insertion percentage = 0.67% number of deletions = 102,503 mapped reads with deletion percentage = 0.57% homopolymer indels = 44.45% >>>>>>> Coverage mean coverageData = 0.5674X std coverageData = 18.2253X There is a 5.13% of reference with a coverageData >= 1X There is a 2.15% of reference with a coverageData >= 2X There is a 0.99% of reference with a coverageData >= 3X There is a 0.71% of reference with a coverageData >= 4X There is a 0.55% of reference with a coverageData >= 5X There is a 0.49% of reference with a coverageData >= 6X There is a 0.45% 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 0.38% of reference with a coverageData >= 10X There is a 0.37% of reference with a coverageData >= 11X There is a 0.36% of reference with a coverageData >= 12X There is a 0.35% of reference with a coverageData >= 13X There is a 0.34% of reference with a coverageData >= 14X There is a 0.33% of reference with a coverageData >= 15X There is a 0.32% of reference with a coverageData >= 16X There is a 0.31% of reference with a coverageData >= 17X There is a 0.3% of reference with a coverageData >= 18X There is a 0.3% of reference with a coverageData >= 19X There is a 0.29% of reference with a coverageData >= 20X There is a 0.28% of reference with a coverageData >= 21X There is a 0.28% of reference with a coverageData >= 22X There is a 0.27% of reference with a coverageData >= 23X There is a 0.27% of reference with a coverageData >= 24X There is a 0.26% of reference with a coverageData >= 25X There is a 0.26% of reference with a coverageData >= 26X There is a 0.25% of reference with a coverageData >= 27X There is a 0.25% of reference with a coverageData >= 28X There is a 0.24% of reference with a coverageData >= 29X There is a 0.24% of reference with a coverageData >= 30X There is a 0.23% of reference with a coverageData >= 31X There is a 0.23% of reference with a coverageData >= 32X There is a 0.23% of reference with a coverageData >= 33X There is a 0.22% of reference with a coverageData >= 34X There is a 0.22% of reference with a coverageData >= 35X There is a 0.22% of reference with a coverageData >= 36X There is a 0.21% of reference with a coverageData >= 37X There is a 0.21% of reference with a coverageData >= 38X There is a 0.21% of reference with a coverageData >= 39X There is a 0.2% of reference with a coverageData >= 40X There is a 0.2% of reference with a coverageData >= 41X There is a 0.2% of reference with a coverageData >= 42X There is a 0.2% of reference with a coverageData >= 43X There is a 0.19% of reference with a coverageData >= 44X There is a 0.19% of reference with a coverageData >= 45X There is a 0.19% of reference with a coverageData >= 46X There is a 0.19% of reference with a coverageData >= 47X There is a 0.18% of reference with a coverageData >= 48X There is a 0.18% of reference with a coverageData >= 49X There is a 0.18% of reference with a coverageData >= 50X There is a 0.18% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 169865556 0.681505046280306 20.719457221525985 chr2 243199373 147494208 0.606474458303805 22.856683303133035 chr3 198022430 204720408 1.0338243400002718 21.22718652088966 chr4 191154276 86567632 0.45286788143834145 19.29367550013273 chr5 180915260 81096516 0.4482569132089797 12.474357066752125 chr6 171115067 98770886 0.5772191060182912 13.974861115355495 chr7 159138663 75431079 0.4739959327168659 14.314785033005275 chr8 146364022 83705391 0.5718986801278254 16.682695076683938 chr9 141213431 107685464 0.7625723929900124 21.578414206698685 chr10 135534747 42473486 0.3133771002649232 10.851249678320501 chr11 135006516 70570635 0.5227202144820922 16.902600613841887 chr12 133851895 72420076 0.5410463258663615 14.293400892013114 chr13 115169878 45470747 0.3948145799025679 17.15318132646305 chr14 107349540 50355741 0.46908203798544457 14.668546114427567 chr15 102531392 42326146 0.4128115806718005 14.593542643897026 chr16 90354753 49243642 0.5450033381199105 14.380803743123968 chr17 81195210 99459963 1.2249486515275962 35.395518781819646 chr18 78077248 35094573 0.44948527130464433 21.43404982413424 chr19 59128983 31813235 0.5380311547046226 13.609428426376457 chr20 63025520 32374719 0.5136763488821671 17.338969913781494 chr21 48129895 7326509 0.15222366473062116 6.291896816226266 chr22 51304566 13737749 0.2677685452012205 6.94731316448245 chrMT 16571 7123 0.4298473236376803 1.4991639194997826 chrX 155270560 105825148 0.681553206222738 22.923783511892832 chrY 59373566 2717556 0.045770469639637275 1.673380456809093