BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504637.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 = 421,641,610 number of mapped reads = 393,541,396 (93.34%) number of supplementary alignments = 2,348,294 (0.56%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 198,047,545 number of mapped paired reads (second in pair) = 195,493,851 number of mapped paired reads (both in pair) = 388,434,190 number of mapped paired reads (singletons) = 5,107,206 number of mapped bases = 37,106,966,147 bp number of sequenced bases = 37,098,647,162 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 107,029,805 duplication rate = 24.14% >>>>>>> Insert size mean insert size = 45,773.8414 std insert size = 2,034,781.8255 median insert size = 349 >>>>>>> Mapping quality mean mapping quality = 53.739 >>>>>>> ACTG content number of A's = 9,782,232,720 bp (26.37%) number of C's = 8,471,201,784 bp (22.83%) number of T's = 9,764,496,625 bp (26.32%) number of G's = 8,760,279,296 bp (23.61%) number of N's = 320,436,737 bp (0.86%) GC percentage = 46.45% >>>>>>> Mismatches and indels general error rate = 0.0223 number of mismatches = 363,070,794 number of insertions = 141,455,694 mapped reads with insertion percentage = 33.3% number of deletions = 3,790,175 mapped reads with deletion percentage = 0.94% homopolymer indels = 28.98% >>>>>>> Coverage mean coverageData = 11.9866X std coverageData = 27.7926X There is a 72.86% of reference with a coverageData >= 1X There is a 64.78% of reference with a coverageData >= 2X There is a 58.42% of reference with a coverageData >= 3X There is a 53.1% of reference with a coverageData >= 4X There is a 48.51% of reference with a coverageData >= 5X There is a 44.49% of reference with a coverageData >= 6X There is a 40.95% of reference with a coverageData >= 7X There is a 37.81% of reference with a coverageData >= 8X There is a 35% of reference with a coverageData >= 9X There is a 32.48% of reference with a coverageData >= 10X There is a 30.22% of reference with a coverageData >= 11X There is a 28.17% of reference with a coverageData >= 12X There is a 26.32% of reference with a coverageData >= 13X There is a 24.64% of reference with a coverageData >= 14X There is a 23.11% of reference with a coverageData >= 15X There is a 21.72% of reference with a coverageData >= 16X There is a 20.44% of reference with a coverageData >= 17X There is a 19.27% of reference with a coverageData >= 18X There is a 18.19% of reference with a coverageData >= 19X There is a 17.2% of reference with a coverageData >= 20X There is a 16.28% of reference with a coverageData >= 21X There is a 15.43% of reference with a coverageData >= 22X There is a 14.65% of reference with a coverageData >= 23X There is a 13.92% of reference with a coverageData >= 24X There is a 13.24% of reference with a coverageData >= 25X There is a 12.6% of reference with a coverageData >= 26X There is a 12.01% of reference with a coverageData >= 27X There is a 11.46% of reference with a coverageData >= 28X There is a 10.95% of reference with a coverageData >= 29X There is a 10.46% of reference with a coverageData >= 30X There is a 10.01% of reference with a coverageData >= 31X There is a 9.58% of reference with a coverageData >= 32X There is a 9.18% of reference with a coverageData >= 33X There is a 8.8% of reference with a coverageData >= 34X There is a 8.45% of reference with a coverageData >= 35X There is a 8.11% of reference with a coverageData >= 36X There is a 7.79% of reference with a coverageData >= 37X There is a 7.49% of reference with a coverageData >= 38X There is a 7.2% of reference with a coverageData >= 39X There is a 6.93% of reference with a coverageData >= 40X There is a 6.68% of reference with a coverageData >= 41X There is a 6.43% of reference with a coverageData >= 42X There is a 6.2% of reference with a coverageData >= 43X There is a 5.98% of reference with a coverageData >= 44X There is a 5.77% of reference with a coverageData >= 45X There is a 5.57% of reference with a coverageData >= 46X There is a 5.38% of reference with a coverageData >= 47X There is a 5.2% of reference with a coverageData >= 48X There is a 5.03% of reference with a coverageData >= 49X There is a 4.87% of reference with a coverageData >= 50X There is a 4.71% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3133414684 12.571341533387795 26.181815643732726 chr2 243199373 2065945259 8.49486260394265 17.730412154472248 chr3 198022430 1825933027 9.220839411979744 18.413579240510163 chr4 191154276 1420282542 7.430032807636487 13.206357888918166 chr5 180915260 2507700471 13.8611882214911 23.45147198797475 chr6 171115067 973395231 5.688541915481937 12.816093928831844 chr7 159138663 1901217317 11.946922772626285 20.129164116350832 chr8 146364022 2154573902 14.720652470181504 39.28414783730345 chr9 141213431 1022871001 7.243439903389926 16.322295079849038 chr10 135534747 2141254162 15.79856243063633 26.476651936256413 chr11 135006516 1644089254 12.177851134237105 22.75593246739487 chr12 133851895 1777936676 13.282865184687896 27.576825181275208 chr13 115169878 477847343 4.149065287713511 7.95993710548682 chr14 107349540 1118519943 10.41941999006237 19.111745068351304 chr15 102531392 1512524739 14.751820974009599 27.905415318505543 chr16 90354753 2214303861 24.50677786701492 39.51771086077093 chr17 81195210 1655203076 20.385476877268992 35.87165882188505 chr18 78077248 500345801 6.408343196215112 55.82730037456368 chr19 59128983 1956204505 33.08368258253317 68.45227518918307 chr20 63025520 1870675371 29.68123660066589 42.434935594556244 chr21 48129895 563135103 11.700318544222878 22.935843107239712 chr22 51304566 765661016 14.923837695069869 31.8762265739717 chrMT 16571 443850 26.78474443304568 21.08753672466736 chrX 155270560 1851828429 11.926461970640153 21.623047972469504 chrY 59373566 51659584 0.8700771653162958 31.406523663860746