BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618567.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 = 239,882,962 number of mapped reads = 229,605,172 (95.72%) number of supplementary alignments = 1,945,332 (0.81%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 115,418,811 number of mapped paired reads (second in pair) = 114,186,361 number of mapped paired reads (both in pair) = 226,499,804 number of mapped paired reads (singletons) = 3,105,368 number of mapped bases = 21,636,110,743 bp number of sequenced bases = 21,621,580,470 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 89,557,839 duplication rate = 31.3% >>>>>>> Insert size mean insert size = 114,799.6428 std insert size = 3,386,466.8521 median insert size = 193 >>>>>>> Mapping quality mean mapping quality = 52.319 >>>>>>> ACTG content number of A's = 5,704,473,611 bp (26.38%) number of C's = 4,887,387,857 bp (22.6%) number of T's = 5,760,955,695 bp (26.64%) number of G's = 5,267,475,334 bp (24.36%) number of N's = 1,287,973 bp (0.01%) GC percentage = 46.97% >>>>>>> Mismatches and indels general error rate = 0.0132 number of mismatches = 280,591,816 number of insertions = 3,587,547 mapped reads with insertion percentage = 1.54% number of deletions = 10,491,280 mapped reads with deletion percentage = 4.46% homopolymer indels = 52.24% >>>>>>> Coverage mean coverageData = 6.9891X std coverageData = 27.5373X There is a 42.38% of reference with a coverageData >= 1X There is a 34.7% of reference with a coverageData >= 2X There is a 29.83% of reference with a coverageData >= 3X There is a 26.36% of reference with a coverageData >= 4X There is a 23.66% of reference with a coverageData >= 5X There is a 21.49% of reference with a coverageData >= 6X There is a 19.68% of reference with a coverageData >= 7X There is a 18.15% of reference with a coverageData >= 8X There is a 16.83% of reference with a coverageData >= 9X There is a 15.68% of reference with a coverageData >= 10X There is a 14.66% of reference with a coverageData >= 11X There is a 13.76% of reference with a coverageData >= 12X There is a 12.95% of reference with a coverageData >= 13X There is a 12.22% of reference with a coverageData >= 14X There is a 11.56% of reference with a coverageData >= 15X There is a 10.95% of reference with a coverageData >= 16X There is a 10.4% of reference with a coverageData >= 17X There is a 9.89% of reference with a coverageData >= 18X There is a 9.43% of reference with a coverageData >= 19X There is a 8.99% of reference with a coverageData >= 20X There is a 8.59% of reference with a coverageData >= 21X There is a 8.22% of reference with a coverageData >= 22X There is a 7.87% of reference with a coverageData >= 23X There is a 7.55% of reference with a coverageData >= 24X There is a 7.24% of reference with a coverageData >= 25X There is a 6.96% of reference with a coverageData >= 26X There is a 6.69% of reference with a coverageData >= 27X There is a 6.44% of reference with a coverageData >= 28X There is a 6.2% of reference with a coverageData >= 29X There is a 5.98% of reference with a coverageData >= 30X There is a 5.76% of reference with a coverageData >= 31X There is a 5.56% of reference with a coverageData >= 32X There is a 5.37% of reference with a coverageData >= 33X There is a 5.19% of reference with a coverageData >= 34X There is a 5.02% of reference with a coverageData >= 35X There is a 4.86% of reference with a coverageData >= 36X There is a 4.7% of reference with a coverageData >= 37X There is a 4.55% of reference with a coverageData >= 38X There is a 4.41% of reference with a coverageData >= 39X There is a 4.28% of reference with a coverageData >= 40X There is a 4.15% of reference with a coverageData >= 41X There is a 4.02% of reference with a coverageData >= 42X There is a 3.9% of reference with a coverageData >= 43X There is a 3.79% of reference with a coverageData >= 44X There is a 3.68% of reference with a coverageData >= 45X There is a 3.58% of reference with a coverageData >= 46X There is a 3.48% of reference with a coverageData >= 47X There is a 3.38% of reference with a coverageData >= 48X There is a 3.29% of reference with a coverageData >= 49X There is a 3.21% of reference with a coverageData >= 50X There is a 3.12% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2006948759 8.051930827486283 34.18595974808485 chr2 243199373 1854716349 7.626320438745539 31.20354215893778 chr3 198022430 1401129497 7.0756100558911434 22.167487781062434 chr4 191154276 1072842138 5.612441219991333 22.918345339329267 chr5 180915260 1240659635 6.857683729940747 21.440234994938333 chr6 171115067 1177145758 6.879264220490882 22.343351562361082 chr7 159138663 1129216432 7.095801929666834 23.556056744243786 chr8 146364022 1073656492 7.335521922183855 23.09324179580743 chr9 141213431 982188670 6.955348815227073 28.601361957078172 chr10 135534747 1141211073 8.420062738597949 26.16189180090519 chr11 135006516 1160422187 8.595305036980585 31.356977278003974 chr12 133851895 1007700309 7.528472488193014 24.14349738720797 chr13 115169878 588628094 5.110955262104211 18.209685305698265 chr14 107349540 697357126 6.496135204678101 23.093946504524823 chr15 102531392 743272317 7.249217069051398 24.078717767395464 chr16 90354753 813278756 9.000951571413182 49.29026673807706 chr17 81195210 788180775 9.707232421715517 30.628141922617367 chr18 78077248 550506119 7.050787945292334 29.017698023913333 chr19 59128983 540050223 9.133426546504275 31.767317279417366 chr20 63025520 671116439 10.6483284707528 31.923806251501567 chr21 48129895 302890172 6.2931816493678205 51.618296457714834 chr22 51304566 442992288 8.634558725240947 30.892177923730817 chrMT 16571 76743 4.631162874901937 12.858070031395453 chrX 155270560 41190970 0.26528512552540545 5.3658939318637655 chrY 59373566 208733422 3.515595172437512 23.907838172052166