BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1163035.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 = 84,034,230 number of mapped reads = 81,913,366 (97.48%) number of supplementary alignments = 372,748 (0.44%) number of secondary alignments = 0 number of mapped bases = 7,769,460,356 bp number of sequenced bases = 7,768,538,690 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 45,501,109 duplication rate = 45.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.994 >>>>>>> ACTG content number of A's = 1,836,365,660 bp (23.64%) number of C's = 2,049,745,319 bp (26.39%) number of T's = 1,813,469,209 bp (23.34%) number of G's = 2,065,130,975 bp (26.58%) number of N's = 3,827,527 bp (0.05%) GC percentage = 52.97% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 41,407,653 number of insertions = 471,507 mapped reads with insertion percentage = 0.57% number of deletions = 410,116 mapped reads with deletion percentage = 0.49% homopolymer indels = 44.88% >>>>>>> Coverage mean coverageData = 2.5098X std coverageData = 30.1828X There is a 9.43% of reference with a coverageData >= 1X There is a 6.55% of reference with a coverageData >= 2X There is a 4.8% of reference with a coverageData >= 3X There is a 4.3% of reference with a coverageData >= 4X There is a 3.88% of reference with a coverageData >= 5X There is a 3.63% of reference with a coverageData >= 6X There is a 3.42% of reference with a coverageData >= 7X There is a 3.25% of reference with a coverageData >= 8X There is a 3.1% of reference with a coverageData >= 9X There is a 2.98% of reference with a coverageData >= 10X There is a 2.86% of reference with a coverageData >= 11X There is a 2.76% of reference with a coverageData >= 12X There is a 2.67% of reference with a coverageData >= 13X There is a 2.58% of reference with a coverageData >= 14X There is a 2.5% of reference with a coverageData >= 15X There is a 2.43% of reference with a coverageData >= 16X There is a 2.36% of reference with a coverageData >= 17X There is a 2.29% of reference with a coverageData >= 18X There is a 2.23% of reference with a coverageData >= 19X There is a 2.17% of reference with a coverageData >= 20X There is a 2.12% of reference with a coverageData >= 21X There is a 2.06% of reference with a coverageData >= 22X There is a 2.01% of reference with a coverageData >= 23X There is a 1.97% of reference with a coverageData >= 24X There is a 1.92% of reference with a coverageData >= 25X There is a 1.88% of reference with a coverageData >= 26X There is a 1.83% of reference with a coverageData >= 27X There is a 1.79% of reference with a coverageData >= 28X There is a 1.76% of reference with a coverageData >= 29X There is a 1.72% of reference with a coverageData >= 30X There is a 1.68% of reference with a coverageData >= 31X There is a 1.65% of reference with a coverageData >= 32X There is a 1.61% of reference with a coverageData >= 33X There is a 1.58% of reference with a coverageData >= 34X There is a 1.55% of reference with a coverageData >= 35X There is a 1.52% of reference with a coverageData >= 36X There is a 1.49% of reference with a coverageData >= 37X There is a 1.46% of reference with a coverageData >= 38X There is a 1.44% of reference with a coverageData >= 39X There is a 1.41% of reference with a coverageData >= 40X There is a 1.38% of reference with a coverageData >= 41X There is a 1.36% of reference with a coverageData >= 42X There is a 1.33% of reference with a coverageData >= 43X There is a 1.31% of reference with a coverageData >= 44X There is a 1.29% of reference with a coverageData >= 45X There is a 1.27% of reference with a coverageData >= 46X There is a 1.24% of reference with a coverageData >= 47X There is a 1.22% of reference with a coverageData >= 48X There is a 1.2% of reference with a coverageData >= 49X There is a 1.18% of reference with a coverageData >= 50X There is a 1.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1186895394 4.761855313491877 44.6262116017629 chr2 243199373 333547659 1.3714988442836158 15.37756302260711 chr3 198022430 324405060 1.6382238113126881 17.364513128294234 chr4 191154276 152813506 0.7994249942909988 12.866603854987554 chr5 180915260 428723308 2.369746521106069 37.18690184674085 chr6 171115067 435186214 2.5432372591713386 25.91139734124077 chr7 159138663 500944775 3.147850846277375 36.14933103289034 chr8 146364022 373298228 2.5504780676223833 43.40325723960186 chr9 141213431 191384316 1.3552840876729353 15.138319452043191 chr10 135534747 175105088 1.2919571687399098 13.451717457171087 chr11 135006516 437178552 3.238203347162888 29.048980713921853 chr12 133851895 219237124 1.6379082567340566 16.67416715015261 chr13 115169878 98759836 0.8575144622450672 10.340871481667799 chr14 107349540 210135617 1.957489682769018 18.568208186019103 chr15 102531392 359343232 3.5047142635106328 28.4817555508598 chr16 90354753 368907772 4.082881749452627 31.20311714656349 chr17 81195210 268642306 3.3085979579337255 25.198569412188597 chr18 78077248 135114085 1.7305180249180914 19.2816196205181 chr19 59128983 703506402 11.897826857600442 88.5743910486199 chr20 63025520 219317249 3.4798165727153063 30.68930416932963 chr21 48129895 111300420 2.3125007856343753 48.59619673694907 chr22 51304566 96463585 1.880214423800018 16.992729197744485 chrMT 16571 452 0.02727656749743528 0.2037117096625065 chrX 155270560 430011162 2.769431384803404 31.3052160566364 chrY 59373566 9239014 0.1556082044996253 8.07365043227252