BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618669.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 590,513,222 number of mapped reads = 514,933,663 (87.2%) number of supplementary alignments = 1,492,832 (0.25%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 268,422,538 number of mapped paired reads (second in pair) = 246,511,125 number of mapped paired reads (both in pair) = 487,783,156 number of mapped paired reads (singletons) = 27,150,507 number of mapped bases = 50,060,037,967 bp number of sequenced bases = 50,046,674,677 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 83,431,124 duplication rate = 11.73% >>>>>>> Insert size mean insert size = 44,951.3993 std insert size = 2,034,860.7886 median insert size = 173 >>>>>>> Mapping quality mean mapping quality = 53.3285 >>>>>>> ACTG content number of A's = 14,696,788,973 bp (29.37%) number of C's = 10,325,644,352 bp (20.63%) number of T's = 14,527,172,327 bp (29.03%) number of G's = 10,415,021,376 bp (20.81%) number of N's = 82,047,649 bp (0.16%) GC percentage = 41.44% >>>>>>> Mismatches and indels general error rate = 0.0164 number of mismatches = 796,783,430 number of insertions = 17,105,125 mapped reads with insertion percentage = 3.27% number of deletions = 5,735,846 mapped reads with deletion percentage = 1.08% homopolymer indels = 35.08% >>>>>>> Coverage mean coverageData = 16.1709X std coverageData = 168.696X There is a 92.25% of reference with a coverageData >= 1X There is a 92.09% of reference with a coverageData >= 2X There is a 91.85% of reference with a coverageData >= 3X There is a 91.45% of reference with a coverageData >= 4X There is a 90.82% of reference with a coverageData >= 5X There is a 89.89% of reference with a coverageData >= 6X There is a 88.6% of reference with a coverageData >= 7X There is a 86.87% of reference with a coverageData >= 8X There is a 84.62% of reference with a coverageData >= 9X There is a 81.77% of reference with a coverageData >= 10X There is a 78.27% of reference with a coverageData >= 11X There is a 74.08% of reference with a coverageData >= 12X There is a 69.2% of reference with a coverageData >= 13X There is a 63.72% of reference with a coverageData >= 14X There is a 57.77% of reference with a coverageData >= 15X There is a 51.51% of reference with a coverageData >= 16X There is a 45.16% of reference with a coverageData >= 17X There is a 38.9% of reference with a coverageData >= 18X There is a 32.93% of reference with a coverageData >= 19X There is a 27.4% of reference with a coverageData >= 20X There is a 22.43% of reference with a coverageData >= 21X There is a 18.07% of reference with a coverageData >= 22X There is a 14.34% of reference with a coverageData >= 23X There is a 11.23% of reference with a coverageData >= 24X There is a 8.69% of reference with a coverageData >= 25X There is a 6.66% of reference with a coverageData >= 26X There is a 5.07% of reference with a coverageData >= 27X There is a 3.84% of reference with a coverageData >= 28X There is a 2.92% of reference with a coverageData >= 29X There is a 2.22% of reference with a coverageData >= 30X There is a 1.71% of reference with a coverageData >= 31X There is a 1.34% of reference with a coverageData >= 32X There is a 1.07% of reference with a coverageData >= 33X There is a 0.87% of reference with a coverageData >= 34X There is a 0.73% of reference with a coverageData >= 35X There is a 0.63% of reference with a coverageData >= 36X There is a 0.55% of reference with a coverageData >= 37X There is a 0.49% of reference with a coverageData >= 38X There is a 0.45% of reference with a coverageData >= 39X There is a 0.41% of reference with a coverageData >= 40X There is a 0.39% of reference with a coverageData >= 41X There is a 0.36% of reference with a coverageData >= 42X There is a 0.35% of reference with a coverageData >= 43X There is a 0.33% of reference with a coverageData >= 44X There is a 0.31% of reference with a coverageData >= 45X There is a 0.3% of reference with a coverageData >= 46X There is a 0.29% of reference with a coverageData >= 47X There is a 0.28% of reference with a coverageData >= 48X There is a 0.27% of reference with a coverageData >= 49X There is a 0.26% of reference with a coverageData >= 50X There is a 0.25% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 4127023552 16.557726257380118 402.753473247759 chr2 243199373 4311571302 17.728546125815875 106.49493062749544 chr3 198022430 3338971293 16.861581251174425 16.13505158034311 chr4 191154276 3347922151 17.51424148628514 83.14789849814025 chr5 180915260 3040599835 16.80676265230473 13.946407000640178 chr6 171115067 2905887695 16.98206794963298 77.19548493049253 chr7 159138663 2730073232 17.15531084988442 125.1043146928913 chr8 146364022 2555993321 17.463262392447785 168.6373744152903 chr9 141213431 2153697990 15.251367909898033 168.2527325664942 chr10 135534747 2645940677 19.522231276972835 388.9709768020047 chr11 135006516 2325085442 17.222023876240165 89.11382061515465 chr12 133851895 2233061452 16.683076858941742 12.675539155666016 chr13 115169878 1612889904 14.004442237926135 9.351655066659132 chr14 107349540 1529040704 14.243570154096608 15.953963909196458 chr15 102531392 1442530262 14.06915710263643 9.970712372949338 chr16 90354753 1587985153 17.57500408417917 126.83899851039436 chr17 81195210 1392373296 17.14846597477856 76.59476032269457 chr18 78077248 1411418203 18.07720224718986 215.836877619197 chr19 59128983 1003801790 16.97647649376956 177.46962141294733 chr20 63025520 1059902326 16.817034210903774 43.768605469724676 chr21 48129895 705213911 14.652305204488812 77.08547636402818 chr22 51304566 638291856 12.44122903212942 70.80921996076944 chrMT 16571 23391018 1411.5634542272644 255.6901204369 chrX 155270560 1358452161 8.748935799548866 37.537113156664475 chrY 59373566 578919441 9.750457653158309 175.0843826104572