BamQC report ----------------------------------- >>>>>>> Input bam file = zr3644_2.deduplicated.sorted.bam outfile = zr3644_2/genome_results.txt >>>>>>> Reference number of bases = 563,985,803 bp number of contigs = 29 >>>>>>> Globals number of windows = 428 number of reads = 60,713,774 number of mapped reads = 60,713,774 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 30,356,887 number of mapped paired reads (second in pair) = 30,356,887 number of mapped paired reads (both in pair) = 60,713,774 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 24,850,983 number of mapped bases = 6,469,852,872 bp number of sequenced bases = 6,440,715,015 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,314,805 duplication rate = 18.22% >>>>>>> Insert size mean insert size = 167.7229 std insert size = 74.526 median insert size = 146 >>>>>>> Mapping quality mean mapping quality = 24.6315 >>>>>>> ACTG content number of A's = 2,646,634,386 bp (41.09%) number of C's = 564,576,296 bp (8.77%) number of T's = 2,672,882,590 bp (41.5%) number of G's = 556,573,471 bp (8.64%) number of N's = 48,272 bp (0%) GC percentage = 17.41% >>>>>>> Mismatches and indels general error rate = 0.1946 number of mismatches = 1,221,495,920 number of insertions = 13,738,289 mapped reads with insertion percentage = 17.12% number of deletions = 12,276,221 mapped reads with deletion percentage = 16.69% homopolymer indels = 49.05% >>>>>>> Coverage mean coverageData = 11.4717X std coverageData = 12.6955X paired-end adapted mean coverage = 8.347X There is a 83.21% of reference with a coverageData >= 1X There is a 78.18% of reference with a coverageData >= 2X There is a 73.39% of reference with a coverageData >= 3X There is a 69.46% of reference with a coverageData >= 4X There is a 65.55% of reference with a coverageData >= 5X There is a 61.82% of reference with a coverageData >= 6X There is a 58.1% of reference with a coverageData >= 7X There is a 54.45% of reference with a coverageData >= 8X There is a 50.85% of reference with a coverageData >= 9X There is a 47.34% of reference with a coverageData >= 10X There is a 43.91% of reference with a coverageData >= 11X There is a 40.59% of reference with a coverageData >= 12X There is a 37.4% of reference with a coverageData >= 13X There is a 34.35% of reference with a coverageData >= 14X There is a 31.45% of reference with a coverageData >= 15X There is a 28.71% of reference with a coverageData >= 16X There is a 26.12% of reference with a coverageData >= 17X There is a 23.7% of reference with a coverageData >= 18X There is a 21.45% of reference with a coverageData >= 19X There is a 19.37% of reference with a coverageData >= 20X There is a 17.46% of reference with a coverageData >= 21X There is a 15.7% of reference with a coverageData >= 22X There is a 14.1% of reference with a coverageData >= 23X There is a 12.64% of reference with a coverageData >= 24X There is a 11.32% of reference with a coverageData >= 25X There is a 10.13% of reference with a coverageData >= 26X There is a 9.06% of reference with a coverageData >= 27X There is a 8.1% of reference with a coverageData >= 28X There is a 7.25% of reference with a coverageData >= 29X There is a 6.49% of reference with a coverageData >= 30X There is a 5.82% of reference with a coverageData >= 31X There is a 5.22% of reference with a coverageData >= 32X There is a 4.69% of reference with a coverageData >= 33X There is a 4.22% of reference with a coverageData >= 34X There is a 3.81% of reference with a coverageData >= 35X There is a 3.45% of reference with a coverageData >= 36X There is a 3.13% of reference with a coverageData >= 37X There is a 2.85% of reference with a coverageData >= 38X There is a 2.6% of reference with a coverageData >= 39X There is a 2.38% of reference with a coverageData >= 40X There is a 2.18% of reference with a coverageData >= 41X There is a 2.01% of reference with a coverageData >= 42X There is a 1.85% of reference with a coverageData >= 43X There is a 1.71% of reference with a coverageData >= 44X There is a 1.59% of reference with a coverageData >= 45X There is a 1.48% of reference with a coverageData >= 46X There is a 1.38% of reference with a coverageData >= 47X There is a 1.29% of reference with a coverageData >= 48X There is a 1.21% of reference with a coverageData >= 49X There is a 1.13% of reference with a coverageData >= 50X There is a 1.06% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_088853.1 76070991 674340280 8.864618051314725 14.093017413687589 NC_088854.1 61469542 780461795 12.69672376931001 11.951968697750553 NC_088855.1 61039741 772954190 12.66313023838027 11.411053169970558 NC_088856.1 57946171 597315709 10.308113524878115 12.312745759601604 NC_088857.1 57274926 702775197 12.27020698376808 11.859383093639833 NC_088858.1 56905015 723186841 12.708666204551568 11.404969085727426 NC_088859.1 53672946 701108246 13.06260040207221 11.381697647487197 NC_088860.1 51133819 574978068 11.244575102047433 12.726228352170438 NC_088861.1 50364239 438051373 8.697666870336311 11.915456694829027 NC_088862.1 37310742 500473150 13.413647737158376 16.96834494524148 NW_027062568.1 15579 119271 7.655882919314462 6.972402842973603 NW_027062569.1 16498 265653 16.10213359195054 14.872296906725317 NW_027062570.1 4000 280018 70.0045 55.340120102869314 NW_027062571.1 36893 4605 0.12482042663919984 0.6034955409239264 NW_027062572.1 51000 39781 0.7800196078431373 2.299512020095822 NW_027062573.1 2000 143158 71.579 56.87184842257195 NW_027062574.1 37061 5278 0.14241385823372277 1.0728139199608604 NW_027062575.1 49428 497052 10.056081573197378 16.085789696557804 NW_027062576.1 49232 218767 4.443593597660058 8.9268000254086 NW_027062577.1 17087 221674 12.973254520980863 9.124000702243242 NW_027062578.1 34507 576888 16.71799924652969 9.39352423721334 NW_027062579.1 64000 308266 4.81665625 10.457263226321231 NW_027062580.1 24229 191855 7.918403565974659 8.472282096277809 NW_027062581.1 5000 30323 6.0646 10.98433119493399 NW_027062582.1 18808 209666 11.147703105061677 9.207240824975733 NW_027062583.1 1000 222 0.222 0.4155911452377204 NW_027062584.1 74000 17774 0.2401891891891892 1.4136014276831002 NW_027062585.1 39334 201715 5.128260537956984 6.59336979329978 NW_027062586.1 258015 876057 3.3953723620719725 6.783294709476712