BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618667.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 = 104,860,252 number of mapped reads = 102,827,690 (98.06%) number of supplementary alignments = 359,246 (0.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 51,637,571 number of mapped paired reads (second in pair) = 51,190,119 number of mapped paired reads (both in pair) = 101,709,374 number of mapped paired reads (singletons) = 1,118,316 number of mapped bases = 10,169,235,482 bp number of sequenced bases = 10,165,931,800 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,534,163 duplication rate = 9.65% >>>>>>> Insert size mean insert size = 41,167.9191 std insert size = 1,944,802.0635 median insert size = 170 >>>>>>> Mapping quality mean mapping quality = 53.754 >>>>>>> ACTG content number of A's = 3,028,111,578 bp (29.79%) number of C's = 2,055,156,558 bp (20.22%) number of T's = 3,017,476,168 bp (29.68%) number of G's = 2,059,901,145 bp (20.26%) number of N's = 5,286,351 bp (0.05%) GC percentage = 40.48% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 50,023,514 number of insertions = 1,066,796 mapped reads with insertion percentage = 1% number of deletions = 1,314,282 mapped reads with deletion percentage = 1.24% homopolymer indels = 41.5% >>>>>>> Coverage mean coverageData = 3.285X std coverageData = 35.938X There is a 84.6% of reference with a coverageData >= 1X There is a 70.94% of reference with a coverageData >= 2X There is a 54.19% of reference with a coverageData >= 3X There is a 38.31% of reference with a coverageData >= 4X There is a 25.31% of reference with a coverageData >= 5X There is a 15.84% of reference with a coverageData >= 6X There is a 9.5% of reference with a coverageData >= 7X There is a 5.53% of reference with a coverageData >= 8X There is a 3.16% of reference with a coverageData >= 9X There is a 1.8% of reference with a coverageData >= 10X There is a 1.04% of reference with a coverageData >= 11X There is a 0.63% of reference with a coverageData >= 12X There is a 0.4% of reference with a coverageData >= 13X There is a 0.28% of reference with a coverageData >= 14X There is a 0.21% of reference with a coverageData >= 15X There is a 0.16% of reference with a coverageData >= 16X There is a 0.14% of reference with a coverageData >= 17X There is a 0.12% of reference with a coverageData >= 18X There is a 0.11% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.09% of reference with a coverageData >= 21X There is a 0.09% of reference with a coverageData >= 22X There is a 0.08% of reference with a coverageData >= 23X There is a 0.07% of reference with a coverageData >= 24X There is a 0.07% of reference with a coverageData >= 25X There is a 0.07% of reference with a coverageData >= 26X There is a 0.06% of reference with a coverageData >= 27X There is a 0.06% of reference with a coverageData >= 28X There is a 0.06% of reference with a coverageData >= 29X There is a 0.05% of reference with a coverageData >= 30X There is a 0.05% of reference with a coverageData >= 31X There is a 0.05% of reference with a coverageData >= 32X There is a 0.05% of reference with a coverageData >= 33X There is a 0.05% of reference with a coverageData >= 34X There is a 0.04% of reference with a coverageData >= 35X There is a 0.04% of reference with a coverageData >= 36X There is a 0.04% of reference with a coverageData >= 37X There is a 0.04% of reference with a coverageData >= 38X There is a 0.04% of reference with a coverageData >= 39X There is a 0.04% of reference with a coverageData >= 40X There is a 0.04% of reference with a coverageData >= 41X There is a 0.04% of reference with a coverageData >= 42X There is a 0.04% of reference with a coverageData >= 43X There is a 0.03% of reference with a coverageData >= 44X There is a 0.03% of reference with a coverageData >= 45X There is a 0.03% of reference with a coverageData >= 46X There is a 0.03% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 829168806 3.3266469013130364 79.36404294984621 chr2 243199373 880781854 3.621645249883107 23.90351484737206 chr3 198022430 682620251 3.4471865182141235 4.597403440350577 chr4 191154276 699418309 3.6589205516909282 21.89851498721102 chr5 180915260 622619024 3.4414953387569405 3.7213123911615376 chr6 171115067 594171730 3.4723519115940853 14.786246943620945 chr7 159138663 553379513 3.477341725561688 24.483046693938523 chr8 146364022 523542683 3.5769902729237653 47.623696245274694 chr9 141213431 436941265 3.0941905589702725 37.97578900048705 chr10 135534747 536547880 3.9587477888603724 85.73414063568573 chr11 135006516 468133236 3.4674862359976757 18.56503169453847 chr12 133851895 453501297 3.3880827537032627 3.6614975517408777 chr13 115169878 333511798 2.8958248787933942 2.756428245649752 chr14 107349540 310294600 2.8905070296528517 3.859952594813609 chr15 102531392 288663235 2.8153644398000566 2.8261327399692746 chr16 90354753 314865983 3.4847749846651674 26.362156456182987 chr17 81195210 273332363 3.3663606880258086 15.581218823268488 chr18 78077248 289468030 3.7074568765538456 46.23701108120212 chr19 59128983 193786524 3.2773525632937064 34.20222765459892 chr20 63025520 210021758 3.332328840761647 12.358941754374928 chr21 48129895 144396330 3.000138063879009 18.19515648805294 chr22 51304566 123175469 2.4008675758021227 16.248463431855363 chrMT 16571 4844511 292.3487417778046 46.77932590450524 chrX 155270560 276833848 1.7829126654788905 8.286878627454032 chrY 59373566 125215185 2.1089382605046834 41.89171047268047