BamQC report ----------------------------------- >>>>>>> Input bam file = SRR961010.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 = 369,392,790 number of mapped reads = 349,640,451 (94.65%) number of supplementary alignments = 5,985,123 (1.62%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 182,486,325 number of mapped paired reads (second in pair) = 167,154,126 number of mapped paired reads (both in pair) = 333,456,374 number of mapped paired reads (singletons) = 16,184,077 number of mapped bases = 34,265,337,226 bp number of sequenced bases = 34,255,370,365 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,777,515 duplication rate = 10.65% >>>>>>> Insert size mean insert size = 86,906.5123 std insert size = 2,840,282.095 median insert size = 142 >>>>>>> Mapping quality mean mapping quality = 53.1009 >>>>>>> ACTG content number of A's = 9,986,409,907 bp (29.15%) number of C's = 7,105,123,285 bp (20.74%) number of T's = 9,936,963,786 bp (29.01%) number of G's = 7,158,343,326 bp (20.9%) number of N's = 68,530,061 bp (0.2%) GC percentage = 41.64% >>>>>>> Mismatches and indels general error rate = 0.0111 number of mismatches = 371,977,684 number of insertions = 3,462,074 mapped reads with insertion percentage = 0.96% number of deletions = 4,072,076 mapped reads with deletion percentage = 1.13% homopolymer indels = 40.62% >>>>>>> Coverage mean coverageData = 11.0687X std coverageData = 137.4503X There is a 91.2% of reference with a coverageData >= 1X There is a 90.17% of reference with a coverageData >= 2X There is a 88.31% of reference with a coverageData >= 3X There is a 85.55% of reference with a coverageData >= 4X There is a 81.78% of reference with a coverageData >= 5X There is a 77.08% of reference with a coverageData >= 6X There is a 71.59% of reference with a coverageData >= 7X There is a 65.53% of reference with a coverageData >= 8X There is a 59.12% of reference with a coverageData >= 9X There is a 52.61% of reference with a coverageData >= 10X There is a 46.21% of reference with a coverageData >= 11X There is a 40.09% of reference with a coverageData >= 12X There is a 34.39% of reference with a coverageData >= 13X There is a 29.18% of reference with a coverageData >= 14X There is a 24.53% of reference with a coverageData >= 15X There is a 20.43% of reference with a coverageData >= 16X There is a 16.89% of reference with a coverageData >= 17X There is a 13.86% of reference with a coverageData >= 18X There is a 11.31% of reference with a coverageData >= 19X There is a 9.18% of reference with a coverageData >= 20X There is a 7.43% of reference with a coverageData >= 21X There is a 6% of reference with a coverageData >= 22X There is a 4.83% of reference with a coverageData >= 23X There is a 3.89% of reference with a coverageData >= 24X There is a 3.13% of reference with a coverageData >= 25X There is a 2.53% of reference with a coverageData >= 26X There is a 2.05% of reference with a coverageData >= 27X There is a 1.67% of reference with a coverageData >= 28X There is a 1.36% of reference with a coverageData >= 29X There is a 1.12% of reference with a coverageData >= 30X There is a 0.93% of reference with a coverageData >= 31X There is a 0.78% of reference with a coverageData >= 32X There is a 0.66% of reference with a coverageData >= 33X There is a 0.56% of reference with a coverageData >= 34X There is a 0.48% of reference with a coverageData >= 35X There is a 0.42% of reference with a coverageData >= 36X There is a 0.37% of reference with a coverageData >= 37X There is a 0.33% of reference with a coverageData >= 38X There is a 0.3% of reference with a coverageData >= 39X There is a 0.27% of reference with a coverageData >= 40X There is a 0.25% of reference with a coverageData >= 41X There is a 0.23% of reference with a coverageData >= 42X There is a 0.22% of reference with a coverageData >= 43X There is a 0.21% of reference with a coverageData >= 44X There is a 0.19% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.18% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3169650987 12.716722527242972 348.68556575053015 chr2 243199373 2892921035 11.895265186395033 81.88264554920664 chr3 198022430 2316559666 11.698471057041367 30.73261650878022 chr4 191154276 2048738775 10.717724017850378 95.1501917247773 chr5 180915260 1644983090 9.09256129084965 13.655966609980547 chr6 171115067 1680124163 9.818680449688278 42.43208863745577 chr7 159138663 1932816528 12.14548678217813 86.64740528148312 chr8 146364022 1761335896 12.033940253431954 118.05387601371744 chr9 141213431 1629741544 11.540981140809475 107.06685082286474 chr10 135534747 1703689557 12.570131237268624 304.98754011744364 chr11 135006516 1554281118 11.512637790016003 58.37516020959357 chr12 133851895 1286362713 9.610343678735367 11.691665939929164 chr13 115169878 1046629570 9.087702341752937 6.860140484530315 chr14 107349540 753300751 7.017270414013884 11.335025312622362 chr15 102531392 905928591 8.835621689404158 6.9133741653122005 chr16 90354753 1280288284 14.169573171208825 143.0942763463807 chr17 81195210 733629986 9.035385043033942 34.95906937852447 chr18 78077248 1303700366 16.697570667449753 134.21314808974816 chr19 59128983 761056137 12.87111833125897 171.70027338373978 chr20 63025520 669984995 10.630376314229537 33.912131849305716 chr21 48129895 479510078 9.96283241424067 51.551740457516765 chr22 51304566 396533877 7.729017276941783 9.161256332986932 chrMT 16571 7784684 469.7775632128417 87.06446914058283 chrX 155270560 2185769045 14.077163404318243 45.115608538274024 chrY 59373566 120015790 2.0213673876350966 107.7018911781962