BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975242.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 50,026,366 number of mapped reads = 49,962,959 (99.87%) number of supplementary alignments = 128,500 (0.26%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 24,985,054 number of mapped paired reads (second in pair) = 24,977,905 number of mapped paired reads (both in pair) = 49,925,910 number of mapped paired reads (singletons) = 37,049 number of mapped bases = 4,893,412,928 bp number of sequenced bases = 4,892,797,406 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,351,556 duplication rate = 40.94% >>>>>>> Insert size mean insert size = 151,995.1864 std insert size = 3,857,291.1868 median insert size = 232 >>>>>>> Mapping quality mean mapping quality = 56.3731 >>>>>>> ACTG content number of A's = 1,282,679,713 bp (26.22%) number of C's = 1,168,382,613 bp (23.88%) number of T's = 1,296,929,062 bp (26.51%) number of G's = 1,144,667,913 bp (23.39%) number of N's = 138,105 bp (0%) GC percentage = 47.27% >>>>>>> Mismatches and indels general error rate = 0.0037 number of mismatches = 17,542,650 number of insertions = 375,683 mapped reads with insertion percentage = 0.74% number of deletions = 274,750 mapped reads with deletion percentage = 0.54% homopolymer indels = 33.88% >>>>>>> Coverage mean coverageData = 1.5807X std coverageData = 12.2417X There is a 11.56% of reference with a coverageData >= 1X There is a 6.24% of reference with a coverageData >= 2X There is a 4.44% of reference with a coverageData >= 3X There is a 3.81% of reference with a coverageData >= 4X There is a 3.47% of reference with a coverageData >= 5X There is a 3.27% of reference with a coverageData >= 6X There is a 3.1% of reference with a coverageData >= 7X There is a 2.97% of reference with a coverageData >= 8X There is a 2.85% of reference with a coverageData >= 9X There is a 2.75% of reference with a coverageData >= 10X There is a 2.65% of reference with a coverageData >= 11X There is a 2.56% of reference with a coverageData >= 12X There is a 2.48% of reference with a coverageData >= 13X There is a 2.4% of reference with a coverageData >= 14X There is a 2.33% of reference with a coverageData >= 15X There is a 2.26% of reference with a coverageData >= 16X There is a 2.2% of reference with a coverageData >= 17X There is a 2.13% of reference with a coverageData >= 18X There is a 2.07% of reference with a coverageData >= 19X There is a 2.02% of reference with a coverageData >= 20X There is a 1.96% of reference with a coverageData >= 21X There is a 1.91% of reference with a coverageData >= 22X There is a 1.86% of reference with a coverageData >= 23X There is a 1.81% of reference with a coverageData >= 24X There is a 1.76% of reference with a coverageData >= 25X There is a 1.71% of reference with a coverageData >= 26X There is a 1.67% of reference with a coverageData >= 27X There is a 1.63% of reference with a coverageData >= 28X There is a 1.58% of reference with a coverageData >= 29X There is a 1.54% of reference with a coverageData >= 30X There is a 1.51% of reference with a coverageData >= 31X There is a 1.47% of reference with a coverageData >= 32X There is a 1.43% of reference with a coverageData >= 33X There is a 1.4% of reference with a coverageData >= 34X There is a 1.36% of reference with a coverageData >= 35X There is a 1.33% of reference with a coverageData >= 36X There is a 1.3% of reference with a coverageData >= 37X There is a 1.26% of reference with a coverageData >= 38X There is a 1.23% of reference with a coverageData >= 39X There is a 1.21% of reference with a coverageData >= 40X There is a 1.18% of reference with a coverageData >= 41X There is a 1.15% of reference with a coverageData >= 42X There is a 1.12% of reference with a coverageData >= 43X There is a 1.1% of reference with a coverageData >= 44X There is a 1.07% of reference with a coverageData >= 45X There is a 1.04% of reference with a coverageData >= 46X There is a 1.02% of reference with a coverageData >= 47X There is a 1% of reference with a coverageData >= 48X There is a 0.97% of reference with a coverageData >= 49X There is a 0.95% of reference with a coverageData >= 50X There is a 0.93% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 500197074 2.006803722266353 14.25237534683876 chr2 243199373 394270203 1.6211810011533212 12.393431243922823 chr3 198022430 314193805 1.5866576579228928 12.159839163025694 chr4 191154276 231668268 1.2119439483530046 11.118213376145011 chr5 180915260 248985394 1.3762542419030876 11.301573885950887 chr6 171115067 288472588 1.6858397863935617 13.43506131309458 chr7 159138663 244777164 1.5381376177579171 12.64153659471368 chr8 146364022 179941040 1.2294075930763915 10.300918777864876 chr9 141213431 194763681 1.3792149912425824 11.197120135022043 chr10 135534747 204134798 1.5061436459537567 11.771974737718129 chr11 135006516 293553161 2.1743629100094695 15.159311232307228 chr12 133851895 270954102 2.0242828986470456 13.948875605974171 chr13 115169878 106493957 0.9246684884045809 9.558292657914649 chr14 107349540 160878752 1.4986440743015759 11.949850064775164 chr15 102531392 170991276 1.6676968162102004 12.640390321280986 chr16 90354753 168944606 1.8697921292530122 12.586190973243005 chr17 81195210 241568328 2.975154913695032 16.357749516813243 chr18 78077248 84744759 1.0853963372274598 9.913015485899628 chr19 59128983 228909813 3.8713639468481977 18.041508099518296 chr20 63025520 112089668 1.7784806535511328 12.590934830746818 chr21 48129895 51731953 1.0748403461092113 10.555235912213089 chr22 51304566 83771007 1.6328177690851142 11.041098720368621 chrMT 16571 221611 13.37342345060648 23.56591376781491 chrX 155270560 109717202 0.7066194776395474 6.458616908286693 chrY 59373566 7438718 0.1252866974505119 2.0074375787349497