BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089749.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 21,549,449 number of mapped reads = 19,834,347 (92.04%) number of supplementary alignments = 117,934 (0.55%) number of secondary alignments = 0 number of mapped bases = 1,291,934,663 bp number of sequenced bases = 1,291,483,286 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,389,588 duplication rate = 14.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3273 >>>>>>> ACTG content number of A's = 331,147,633 bp (25.64%) number of C's = 244,585,499 bp (18.94%) number of T's = 399,731,309 bp (30.95%) number of G's = 314,821,090 bp (24.38%) number of N's = 1,197,755 bp (0.09%) GC percentage = 43.32% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 12,199,437 number of insertions = 83,386 mapped reads with insertion percentage = 0.42% number of deletions = 255,247 mapped reads with deletion percentage = 1.27% homopolymer indels = 45.98% >>>>>>> Coverage mean coverageData = 0.4173X std coverageData = 2.2993X There is a 15.52% of reference with a coverageData >= 1X There is a 8.68% of reference with a coverageData >= 2X There is a 5.31% of reference with a coverageData >= 3X There is a 3.41% of reference with a coverageData >= 4X There is a 2.26% of reference with a coverageData >= 5X There is a 1.55% of reference with a coverageData >= 6X There is a 1.09% of reference with a coverageData >= 7X There is a 0.78% of reference with a coverageData >= 8X There is a 0.57% of reference with a coverageData >= 9X There is a 0.42% of reference with a coverageData >= 10X There is a 0.32% of reference with a coverageData >= 11X There is a 0.24% of reference with a coverageData >= 12X There is a 0.19% of reference with a coverageData >= 13X There is a 0.15% of reference with a coverageData >= 14X There is a 0.12% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 102481063 0.4111567007891226 3.8204866212810327 chr2 243199373 105008527 0.43177959591203385 2.6890874738350736 chr3 198022430 85739639 0.43297943066348593 1.4750833090693292 chr4 191154276 80072629 0.418890074946584 1.7210792302841713 chr5 180915260 76110798 0.42069860773491413 1.4323640434560978 chr6 171115067 68060604 0.3977475811641999 1.7461466094300055 chr7 159138663 71323431 0.4481841788503652 2.680198666395642 chr8 146364022 63389403 0.43309415889104225 2.2054516696091158 chr9 141213431 54962880 0.3892185014610969 2.459253024623711 chr10 135534747 65656771 0.4844275911032615 2.9121408013438 chr11 135006516 57731338 0.42761890100178573 2.052403550234158 chr12 133851895 66510819 0.4968985982604131 1.7458358664417106 chr13 115169878 41998347 0.3646643352352948 1.3417060312289586 chr14 107349540 43172849 0.4021707871314586 1.4863870422316767 chr15 102531392 40622204 0.3961928459919865 1.531432495273152 chr16 90354753 41793552 0.4625495683663703 1.8527363176389655 chr17 81195210 34061432 0.4195005099438748 1.7628026492457625 chr18 78077248 34094902 0.43668165660756897 4.575800063892286 chr19 59128983 25089379 0.42431609216075983 2.6291774178379588 chr20 63025520 28072992 0.4454226161085224 1.6987274812027522 chr21 48129895 18529108 0.3849812678793502 1.810331267512966 chr22 51304566 15441566 0.30097839634780266 1.287563880813422 chrMT 16571 62475 3.770140607084666 4.099895629617435 chrX 155270560 68555257 0.4415212838802153 1.6732348437218194 chrY 59373566 3392698 0.05714155690092793 1.176825455515449