BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504702.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 496,966,050 number of mapped reads = 449,651,148 (90.48%) number of supplementary alignments = 2,305,963 (0.46%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 226,318,458 number of mapped paired reads (second in pair) = 223,332,690 number of mapped paired reads (both in pair) = 443,064,648 number of mapped paired reads (singletons) = 6,586,500 number of mapped bases = 43,672,354,149 bp number of sequenced bases = 43,663,096,935 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 108,002,187 duplication rate = 21.82% >>>>>>> Insert size mean insert size = 29,700.6681 std insert size = 1,631,956.2167 median insert size = 435 >>>>>>> Mapping quality mean mapping quality = 53.9521 >>>>>>> ACTG content number of A's = 11,586,231,772 bp (26.54%) number of C's = 10,110,225,845 bp (23.16%) number of T's = 11,549,815,265 bp (26.45%) number of G's = 10,379,589,884 bp (23.77%) number of N's = 37,234,169 bp (0.09%) GC percentage = 46.93% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 356,245,960 number of insertions = 3,019,886 mapped reads with insertion percentage = 0.66% number of deletions = 3,758,743 mapped reads with deletion percentage = 0.81% homopolymer indels = 40.22% >>>>>>> Coverage mean coverageData = 14.1075X std coverageData = 28.5332X There is a 85.44% of reference with a coverageData >= 1X There is a 79.85% of reference with a coverageData >= 2X There is a 73.59% of reference with a coverageData >= 3X There is a 67.8% of reference with a coverageData >= 4X There is a 62.27% of reference with a coverageData >= 5X There is a 57.22% of reference with a coverageData >= 6X There is a 52.6% of reference with a coverageData >= 7X There is a 48.42% of reference with a coverageData >= 8X There is a 44.64% of reference with a coverageData >= 9X There is a 41.23% of reference with a coverageData >= 10X There is a 38.16% of reference with a coverageData >= 11X There is a 35.38% of reference with a coverageData >= 12X There is a 32.87% of reference with a coverageData >= 13X There is a 30.59% of reference with a coverageData >= 14X There is a 28.52% of reference with a coverageData >= 15X There is a 26.65% of reference with a coverageData >= 16X There is a 24.94% of reference with a coverageData >= 17X There is a 23.37% of reference with a coverageData >= 18X There is a 21.94% of reference with a coverageData >= 19X There is a 20.63% of reference with a coverageData >= 20X There is a 19.43% of reference with a coverageData >= 21X There is a 18.32% of reference with a coverageData >= 22X There is a 17.3% of reference with a coverageData >= 23X There is a 16.35% of reference with a coverageData >= 24X There is a 15.48% of reference with a coverageData >= 25X There is a 14.67% of reference with a coverageData >= 26X There is a 13.92% of reference with a coverageData >= 27X There is a 13.22% of reference with a coverageData >= 28X There is a 12.57% of reference with a coverageData >= 29X There is a 11.96% of reference with a coverageData >= 30X There is a 11.39% of reference with a coverageData >= 31X There is a 10.86% of reference with a coverageData >= 32X There is a 10.36% of reference with a coverageData >= 33X There is a 9.89% of reference with a coverageData >= 34X There is a 9.45% of reference with a coverageData >= 35X There is a 9.04% of reference with a coverageData >= 36X There is a 8.65% of reference with a coverageData >= 37X There is a 8.29% of reference with a coverageData >= 38X There is a 7.94% of reference with a coverageData >= 39X There is a 7.62% of reference with a coverageData >= 40X There is a 7.31% of reference with a coverageData >= 41X There is a 7.02% of reference with a coverageData >= 42X There is a 6.75% of reference with a coverageData >= 43X There is a 6.49% of reference with a coverageData >= 44X There is a 6.24% of reference with a coverageData >= 45X There is a 6% of reference with a coverageData >= 46X There is a 5.78% of reference with a coverageData >= 47X There is a 5.57% of reference with a coverageData >= 48X There is a 5.37% of reference with a coverageData >= 49X There is a 5.18% of reference with a coverageData >= 50X There is a 5% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3829517971 15.364126097804185 30.658619171834573 chr2 243199373 2901575277 11.930850154782267 18.835071413076303 chr3 198022430 2470632683 12.47652946688918 18.628994370458912 chr4 191154276 2023045206 10.583311283081107 18.00914429158729 chr5 180915260 3000987398 16.58780689920795 24.999833190209216 chr6 171115067 1251921584 7.316255698278165 12.81278713017542 chr7 159138663 2064827515 12.975021129843224 19.30260964132007 chr8 146364022 2557722902 17.475079374356085 30.828139525146945 chr9 141213431 1189384928 8.422604844152536 17.601825564435135 chr10 135534747 2594281581 19.141081076426843 28.267337474056212 chr11 135006516 2498375156 18.50558943392036 30.911349403698154 chr12 133851895 1971304738 14.727507130175482 24.7721813426227 chr13 115169878 673269634 5.8458830181273616 9.671195365506982 chr14 107349540 1230114609 11.458964882383288 17.52520830661781 chr15 102531392 1767021655 17.233957527856443 27.49179370541618 chr16 90354753 2094773352 23.183875584276127 35.2347893685794 chr17 81195210 1499474825 18.467528133740895 29.429118671161195 chr18 78077248 805934496 10.322270784953895 82.92583719483596 chr19 59128983 1821058374 30.798066897243945 45.40728644139511 chr20 63025520 1410249330 22.37584600650657 30.672008425796644 chr21 48129895 549003469 11.406704066152647 26.51227238011483 chr22 51304566 955276865 18.619724119681667 34.24942611945025 chrMT 16571 330948 19.971516504737192 7.566002032166105 chrX 155270560 2443616887 15.737799148789057 22.36684264449661 chrY 59373566 68652766 1.1562850376883207 39.906366092635245