BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618573.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 = 66,790,613 number of mapped reads = 62,641,026 (93.79%) number of supplementary alignments = 126,425 (0.19%) number of secondary alignments = 0 number of mapped bases = 6,119,514,888 bp number of sequenced bases = 6,115,741,561 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,106,426 duplication rate = 35.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.6845 >>>>>>> ACTG content number of A's = 1,593,174,272 bp (26.05%) number of C's = 1,458,275,654 bp (23.84%) number of T's = 1,587,114,718 bp (25.95%) number of G's = 1,476,810,358 bp (24.15%) number of N's = 366,559 bp (0.01%) GC percentage = 47.99% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 54,653,177 number of insertions = 947,297 mapped reads with insertion percentage = 1.49% number of deletions = 2,682,577 mapped reads with deletion percentage = 4.19% homopolymer indels = 53.7% >>>>>>> Coverage mean coverageData = 1.9768X std coverageData = 12.3557X There is a 24.36% of reference with a coverageData >= 1X There is a 17.69% of reference with a coverageData >= 2X There is a 13.99% of reference with a coverageData >= 3X There is a 11.52% of reference with a coverageData >= 4X There is a 9.73% of reference with a coverageData >= 5X There is a 8.37% of reference with a coverageData >= 6X There is a 7.3% of reference with a coverageData >= 7X There is a 6.44% of reference with a coverageData >= 8X There is a 5.73% of reference with a coverageData >= 9X There is a 5.14% of reference with a coverageData >= 10X There is a 4.65% of reference with a coverageData >= 11X There is a 4.22% of reference with a coverageData >= 12X There is a 3.86% of reference with a coverageData >= 13X There is a 3.54% of reference with a coverageData >= 14X There is a 3.26% of reference with a coverageData >= 15X There is a 3.02% of reference with a coverageData >= 16X There is a 2.8% of reference with a coverageData >= 17X There is a 2.6% of reference with a coverageData >= 18X There is a 2.42% of reference with a coverageData >= 19X There is a 2.27% of reference with a coverageData >= 20X There is a 2.12% of reference with a coverageData >= 21X There is a 1.99% of reference with a coverageData >= 22X There is a 1.87% of reference with a coverageData >= 23X There is a 1.76% of reference with a coverageData >= 24X There is a 1.66% of reference with a coverageData >= 25X There is a 1.57% of reference with a coverageData >= 26X There is a 1.49% of reference with a coverageData >= 27X There is a 1.41% of reference with a coverageData >= 28X There is a 1.33% of reference with a coverageData >= 29X There is a 1.27% of reference with a coverageData >= 30X There is a 1.2% of reference with a coverageData >= 31X There is a 1.15% of reference with a coverageData >= 32X There is a 1.09% of reference with a coverageData >= 33X There is a 1.04% of reference with a coverageData >= 34X There is a 0.99% of reference with a coverageData >= 35X There is a 0.95% of reference with a coverageData >= 36X There is a 0.91% of reference with a coverageData >= 37X There is a 0.87% of reference with a coverageData >= 38X There is a 0.83% of reference with a coverageData >= 39X There is a 0.79% of reference with a coverageData >= 40X There is a 0.76% of reference with a coverageData >= 41X There is a 0.73% of reference with a coverageData >= 42X There is a 0.7% of reference with a coverageData >= 43X There is a 0.67% of reference with a coverageData >= 44X There is a 0.65% of reference with a coverageData >= 45X There is a 0.62% of reference with a coverageData >= 46X There is a 0.6% of reference with a coverageData >= 47X There is a 0.57% of reference with a coverageData >= 48X There is a 0.55% of reference with a coverageData >= 49X There is a 0.53% of reference with a coverageData >= 50X There is a 0.51% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 548975600 2.202504442305883 12.390962265533755 chr2 243199373 486312060 1.999643559936316 12.115056717505585 chr3 198022430 356293188 1.799256720564433 9.420165158261144 chr4 191154276 256342103 1.3410220705708933 9.955725709048885 chr5 180915260 306393269 1.6935733834724611 9.632432577162994 chr6 171115067 304173665 1.7775972059783607 8.591634294587536 chr7 159138663 291179539 1.8297221650027309 8.5794452851401 chr8 146364022 269258167 1.8396472256002914 14.222895234819136 chr9 141213431 283011015 2.0041366674250694 10.319562529802235 chr10 135534747 314984021 2.3240093627060814 17.526938113470745 chr11 135006516 321040377 2.377962090363105 12.479470049160904 chr12 133851895 278039942 2.0772208118532802 14.735722715990505 chr13 115169878 141078082 1.224956424804062 8.186638729746324 chr14 107349540 198560887 1.8496668639660683 10.100310551682435 chr15 102531392 223474451 2.1795710234773757 15.831614111361771 chr16 90354753 246480982 2.727924916135845 20.11083166120482 chr17 81195210 265255664 3.266888083668975 21.538598076483137 chr18 78077248 140796733 1.8033004057724986 8.934275221214467 chr19 59128983 179115078 3.029226428602704 12.755403151470302 chr20 63025520 201434171 3.1960731303763934 12.382768590100419 chr21 48129895 84636771 1.7585072853368993 15.551511974399787 chr22 51304566 149188643 2.9079018619902173 12.631776005217269 chrMT 16571 9471 0.571540643292499 3.0474698843788377 chrX 155270560 263514440 1.6971307374688416 10.529192169764361 chrY 59373566 9966569 0.1678620583442807 6.671120505524626