BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618630.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 = 22,985,524 number of mapped reads = 22,205,560 (96.61%) number of supplementary alignments = 29,844 (0.13%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 11,214,972 number of mapped paired reads (second in pair) = 10,990,588 number of mapped paired reads (both in pair) = 21,796,274 number of mapped paired reads (singletons) = 409,286 number of mapped bases = 2,125,387,435 bp number of sequenced bases = 2,124,051,303 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,721,601 duplication rate = 29.32% >>>>>>> Insert size mean insert size = 26,082.8628 std insert size = 1,597,077.9803 median insert size = 195 >>>>>>> Mapping quality mean mapping quality = 53.9755 >>>>>>> ACTG content number of A's = 569,650,682 bp (26.82%) number of C's = 482,483,693 bp (22.72%) number of T's = 572,806,810 bp (26.97%) number of G's = 499,013,781 bp (23.49%) number of N's = 96,337 bp (0%) GC percentage = 46.21% >>>>>>> Mismatches and indels general error rate = 0.0131 number of mismatches = 27,246,058 number of insertions = 361,922 mapped reads with insertion percentage = 1.6% number of deletions = 961,799 mapped reads with deletion percentage = 4.23% homopolymer indels = 51.69% >>>>>>> Coverage mean coverageData = 0.6866X std coverageData = 3.2254X There is a 15.99% of reference with a coverageData >= 1X There is a 10.54% of reference with a coverageData >= 2X There is a 7.47% of reference with a coverageData >= 3X There is a 5.68% of reference with a coverageData >= 4X There is a 4.39% of reference with a coverageData >= 5X There is a 3.51% of reference with a coverageData >= 6X There is a 2.83% of reference with a coverageData >= 7X There is a 2.33% of reference with a coverageData >= 8X There is a 1.93% of reference with a coverageData >= 9X There is a 1.63% of reference with a coverageData >= 10X There is a 1.38% of reference with a coverageData >= 11X There is a 1.18% of reference with a coverageData >= 12X There is a 1.01% of reference with a coverageData >= 13X There is a 0.88% of reference with a coverageData >= 14X There is a 0.76% of reference with a coverageData >= 15X There is a 0.67% of reference with a coverageData >= 16X There is a 0.58% of reference with a coverageData >= 17X There is a 0.52% of reference with a coverageData >= 18X There is a 0.46% of reference with a coverageData >= 19X There is a 0.41% of reference with a coverageData >= 20X There is a 0.36% of reference with a coverageData >= 21X There is a 0.32% of reference with a coverageData >= 22X There is a 0.29% of reference with a coverageData >= 23X There is a 0.26% of reference with a coverageData >= 24X There is a 0.24% of reference with a coverageData >= 25X There is a 0.21% of reference with a coverageData >= 26X There is a 0.19% of reference with a coverageData >= 27X There is a 0.18% of reference with a coverageData >= 28X There is a 0.16% of reference with a coverageData >= 29X There is a 0.15% of reference with a coverageData >= 30X There is a 0.13% of reference with a coverageData >= 31X There is a 0.12% of reference with a coverageData >= 32X There is a 0.11% of reference with a coverageData >= 33X There is a 0.1% of reference with a coverageData >= 34X There is a 0.09% of reference with a coverageData >= 35X There is a 0.09% of reference with a coverageData >= 36X There is a 0.08% of reference with a coverageData >= 37X There is a 0.07% of reference with a coverageData >= 38X There is a 0.07% of reference with a coverageData >= 39X There is a 0.06% of reference with a coverageData >= 40X There is a 0.06% of reference with a coverageData >= 41X There is a 0.05% of reference with a coverageData >= 42X There is a 0.05% of reference with a coverageData >= 43X There is a 0.05% of reference with a coverageData >= 44X There is a 0.04% of reference with a coverageData >= 45X There is a 0.04% of reference with a coverageData >= 46X There is a 0.04% of reference with a coverageData >= 47X There is a 0.04% 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 202075308 0.8107314123803125 3.6152686394268234 chr2 243199373 164657666 0.6770480695277121 3.718681688038943 chr3 198022430 127765409 0.6452067525885831 2.6375411266566906 chr4 191154276 95450898 0.4993395910222798 2.6177740812505386 chr5 180915260 117356515 0.6486822338812105 2.5733965301804984 chr6 171115067 110205698 0.6440443844725842 2.6261540745523706 chr7 159138663 103392911 0.6497032779520084 2.616038404476919 chr8 146364022 100999389 0.690056119119219 2.7836023063792483 chr9 141213431 91923433 0.6509538954548877 3.014492662612751 chr10 135534747 112222544 0.8279983287237774 3.285411985298705 chr11 135006516 107632078 0.7972361719192872 3.286419726594167 chr12 133851895 92688008 0.6924669090415193 2.829327057164052 chr13 115169878 56196648 0.48794571094362016 2.235612754663462 chr14 107349540 67496160 0.6287512736430916 2.688189370343892 chr15 102531392 72735844 0.7094007267549826 2.8854378443892292 chr16 90354753 78201111 0.8654897324549158 7.094565031579503 chr17 81195210 78117271 0.962092111098672 3.57868429940634 chr18 78077248 51350750 0.6576915979415668 2.887609152901309 chr19 59128983 51290644 0.8674366004231799 3.657119339986816 chr20 63025520 65951807 1.0464301920872687 3.6998658677145926 chr21 48129895 26641321 0.5535295890423197 4.095373832611728 chr22 51304566 43117730 0.840426756558081 3.5423196430428567 chrMT 16571 1878 0.11333051716854746 0.7647397095032658 chrX 155270560 104699511 0.6743036864167941 2.6605631305106985 chrY 59373566 3216903 0.054180727497486 2.270544590101625