BamQC report ----------------------------------- >>>>>>> Input bam file = SRR4012102.sorted.bam outfile = /mainsd/zhouyj/SRP081010/SRP081010.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 = 330,389,873 number of mapped reads = 245,744,614 (74.38%) number of supplementary alignments = 19,599 (0.01%) number of secondary alignments = 0 number of mapped bases = 12,131,936,602 bp number of sequenced bases = 12,128,308,776 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 181,961,977 duplication rate = 49.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.9906 >>>>>>> ACTG content number of A's = 3,644,665,702 bp (30.05%) number of C's = 2,432,912,591 bp (20.06%) number of T's = 3,627,546,933 bp (29.91%) number of G's = 2,423,125,543 bp (19.98%) number of N's = 58,007 bp (0%) GC percentage = 40.04% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 67,999,201 number of insertions = 782,161 mapped reads with insertion percentage = 0.32% number of deletions = 2,548,015 mapped reads with deletion percentage = 1.03% homopolymer indels = 47.24% >>>>>>> Coverage mean coverageData = 3.919X std coverageData = 43.42X There is a 44.83% of reference with a coverageData >= 1X There is a 34.62% of reference with a coverageData >= 2X There is a 28.46% of reference with a coverageData >= 3X There is a 24.11% of reference with a coverageData >= 4X There is a 20.81% of reference with a coverageData >= 5X There is a 18.19% of reference with a coverageData >= 6X There is a 16.06% of reference with a coverageData >= 7X There is a 14.29% of reference with a coverageData >= 8X There is a 12.8% of reference with a coverageData >= 9X There is a 11.53% of reference with a coverageData >= 10X There is a 10.44% of reference with a coverageData >= 11X There is a 9.48% of reference with a coverageData >= 12X There is a 8.65% of reference with a coverageData >= 13X There is a 7.92% of reference with a coverageData >= 14X There is a 7.26% of reference with a coverageData >= 15X There is a 6.68% of reference with a coverageData >= 16X There is a 6.16% of reference with a coverageData >= 17X There is a 5.69% of reference with a coverageData >= 18X There is a 5.27% of reference with a coverageData >= 19X There is a 4.88% of reference with a coverageData >= 20X There is a 4.53% of reference with a coverageData >= 21X There is a 4.22% of reference with a coverageData >= 22X There is a 3.93% of reference with a coverageData >= 23X There is a 3.66% of reference with a coverageData >= 24X There is a 3.42% of reference with a coverageData >= 25X There is a 3.19% of reference with a coverageData >= 26X There is a 2.98% of reference with a coverageData >= 27X There is a 2.79% of reference with a coverageData >= 28X There is a 2.62% of reference with a coverageData >= 29X There is a 2.45% of reference with a coverageData >= 30X There is a 2.3% of reference with a coverageData >= 31X There is a 2.16% of reference with a coverageData >= 32X There is a 2.03% of reference with a coverageData >= 33X There is a 1.91% of reference with a coverageData >= 34X There is a 1.8% of reference with a coverageData >= 35X There is a 1.69% of reference with a coverageData >= 36X There is a 1.6% of reference with a coverageData >= 37X There is a 1.51% of reference with a coverageData >= 38X There is a 1.42% of reference with a coverageData >= 39X There is a 1.34% of reference with a coverageData >= 40X There is a 1.27% of reference with a coverageData >= 41X There is a 1.2% of reference with a coverageData >= 42X There is a 1.13% of reference with a coverageData >= 43X There is a 1.07% of reference with a coverageData >= 44X There is a 1.01% of reference with a coverageData >= 45X There is a 0.96% of reference with a coverageData >= 46X There is a 0.91% of reference with a coverageData >= 47X There is a 0.86% of reference with a coverageData >= 48X There is a 0.82% of reference with a coverageData >= 49X There is a 0.78% of reference with a coverageData >= 50X There is a 0.74% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 964845927 3.870987053629046 103.18164668667754 chr2 243199373 1039076143 4.272528050473222 43.93036873750649 chr3 198022430 801169595 4.045852760215093 10.968792323802369 chr4 191154276 795454208 4.161320503235826 16.5172964879581 chr5 180915260 755166652 4.174145685665211 18.576495567901535 chr6 171115067 692996973 4.04988868104759 20.88430814936091 chr7 159138663 662520435 4.163164516469514 65.80705251526638 chr8 146364022 616028716 4.208880758961379 27.705847296481824 chr9 141213431 508438387 3.6004959542410666 31.190557363726494 chr10 135534747 585370484 4.318969835831102 45.67259837242426 chr11 135006516 565571249 4.189214459841331 34.018243246812766 chr12 133851895 547505400 4.090382134672057 15.236983953254876 chr13 115169878 384739598 3.340626947612118 8.956988164872646 chr14 107349540 373516602 3.4794429673382856 19.52356981765856 chr15 102531392 331779434 3.235881494713346 9.857009980773453 chr16 90354753 343702419 3.8039218479187253 32.18442934863975 chr17 81195210 294780380 3.630514410887046 19.536549862583986 chr18 78077248 333428174 4.270490860538527 53.03020721224747 chr19 59128983 224964057 3.804632611387887 89.91173326141349 chr20 63025520 243050927 3.856389078582771 14.381383352525523 chr21 48129895 159608421 3.316201313133968 16.905210273499506 chr22 51304566 125718655 2.4504379395783213 9.813909575175117 chrMT 16571 15855479 956.8208919196186 666.2897512032193 chrX 155270560 717775666 4.622741529366546 24.513159604058682 chrY 59373566 48872621 0.8231377074437469 31.949842064641746