BamQC report ----------------------------------- >>>>>>> Input bam file = zr3644_6.deduplicated.sorted.bam outfile = zr3644_6/genome_results.txt >>>>>>> Reference number of bases = 563,985,803 bp number of contigs = 29 >>>>>>> Globals number of windows = 428 number of reads = 59,679,730 number of mapped reads = 59,679,730 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 29,839,865 number of mapped paired reads (second in pair) = 29,839,865 number of mapped paired reads (both in pair) = 59,679,730 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 25,239,763 number of mapped bases = 6,300,248,520 bp number of sequenced bases = 6,272,160,599 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,536,760 duplication rate = 17.46% >>>>>>> Insert size mean insert size = 160.7512 std insert size = 70.5296 median insert size = 139 >>>>>>> Mapping quality mean mapping quality = 24.781 >>>>>>> ACTG content number of A's = 2,574,241,018 bp (41.04%) number of C's = 552,991,194 bp (8.82%) number of T's = 2,600,057,371 bp (41.45%) number of G's = 544,823,431 bp (8.69%) number of N's = 47,585 bp (0%) GC percentage = 17.5% >>>>>>> Mismatches and indels general error rate = 0.1948 number of mismatches = 1,191,326,340 number of insertions = 13,308,121 mapped reads with insertion percentage = 16.87% number of deletions = 11,882,080 mapped reads with deletion percentage = 16.46% homopolymer indels = 49.06% >>>>>>> Coverage mean coverageData = 11.1709X std coverageData = 12.1346X paired-end adapted mean coverage = 7.9635X There is a 84.4% of reference with a coverageData >= 1X There is a 79.24% of reference with a coverageData >= 2X There is a 74.09% of reference with a coverageData >= 3X There is a 69.82% of reference with a coverageData >= 4X There is a 65.54% of reference with a coverageData >= 5X There is a 61.51% of reference with a coverageData >= 6X There is a 57.52% of reference with a coverageData >= 7X There is a 53.67% of reference with a coverageData >= 8X There is a 49.9% of reference with a coverageData >= 9X There is a 46.27% of reference with a coverageData >= 10X There is a 42.76% of reference with a coverageData >= 11X There is a 39.4% of reference with a coverageData >= 12X There is a 36.19% of reference with a coverageData >= 13X There is a 33.14% of reference with a coverageData >= 14X There is a 30.24% of reference with a coverageData >= 15X There is a 27.53% of reference with a coverageData >= 16X There is a 24.98% of reference with a coverageData >= 17X There is a 22.6% of reference with a coverageData >= 18X There is a 20.4% of reference with a coverageData >= 19X There is a 18.37% of reference with a coverageData >= 20X There is a 16.5% of reference with a coverageData >= 21X There is a 14.8% of reference with a coverageData >= 22X There is a 13.24% of reference with a coverageData >= 23X There is a 11.83% of reference with a coverageData >= 24X There is a 10.56% of reference with a coverageData >= 25X There is a 9.41% of reference with a coverageData >= 26X There is a 8.39% of reference with a coverageData >= 27X There is a 7.47% of reference with a coverageData >= 28X There is a 6.65% of reference with a coverageData >= 29X There is a 5.93% of reference with a coverageData >= 30X There is a 5.29% of reference with a coverageData >= 31X There is a 4.73% of reference with a coverageData >= 32X There is a 4.23% of reference with a coverageData >= 33X There is a 3.79% of reference with a coverageData >= 34X There is a 3.4% of reference with a coverageData >= 35X There is a 3.06% of reference with a coverageData >= 36X There is a 2.76% of reference with a coverageData >= 37X There is a 2.5% of reference with a coverageData >= 38X There is a 2.27% of reference with a coverageData >= 39X There is a 2.07% of reference with a coverageData >= 40X There is a 1.89% of reference with a coverageData >= 41X There is a 1.74% of reference with a coverageData >= 42X There is a 1.6% of reference with a coverageData >= 43X There is a 1.48% of reference with a coverageData >= 44X There is a 1.37% of reference with a coverageData >= 45X There is a 1.27% of reference with a coverageData >= 46X There is a 1.18% of reference with a coverageData >= 47X There is a 1.1% of reference with a coverageData >= 48X There is a 1.03% of reference with a coverageData >= 49X There is a 0.97% of reference with a coverageData >= 50X There is a 0.91% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_088853.1 76070991 650788837 8.555019836668093 13.498526456021336 NC_088854.1 61469542 774970289 12.60738674447908 11.561198174024009 NC_088855.1 61039741 771237393 12.635004349051874 11.2515271500584 NC_088856.1 57946171 595056242 10.269121008875635 12.63270184946506 NC_088857.1 57274926 702347776 12.262744363912404 11.832689708287617 NC_088858.1 56905015 726927895 12.77440828369872 11.150551156296816 NC_088859.1 53672946 705737333 13.14884659023561 12.545758148765788 NC_088860.1 51133819 572794896 11.201879836121766 11.623940858027218 NC_088861.1 50364239 432559625 8.588626247286294 11.551980172652543 NC_088862.1 37310742 363709500 9.748117579650385 11.61928655784816 NW_027062568.1 15579 127549 8.187239232299891 7.581968389978455 NW_027062569.1 16498 222632 13.494484179900594 15.374072795991541 NW_027062570.1 4000 262164 65.541 58.74141271709423 NW_027062571.1 36893 5530 0.14989293361884368 0.7913258995597947 NW_027062572.1 51000 75724 1.4847843137254901 3.232745918887861 NW_027062573.1 2000 133832 66.916 53.528458972774466 NW_027062574.1 37061 3340 0.09012169126575106 0.4949630797876476 NW_027062575.1 49428 389358 7.87727603787327 14.100805165160068 NW_027062576.1 49232 210714 4.280021124471888 9.792606198899453 NW_027062577.1 17087 167793 9.81992157780769 7.5641458497754614 NW_027062578.1 34507 546268 15.830643057930274 8.763699951546517 NW_027062579.1 64000 540635 8.447421875 10.865570850106389 NW_027062580.1 24229 197857 8.166123240744563 8.222331927646119 NW_027062581.1 5000 52638 10.5276 13.011118679037557 NW_027062582.1 18808 170301 9.054710761378137 12.010426707400402 NW_027062583.1 1000 229 0.229 0.42018924307982947 NW_027062584.1 74000 18203 0.2459864864864865 1.43826363735601 NW_027062585.1 39334 211273 5.371256419382722 6.441570065657717 NW_027062586.1 258015 782694 3.0335213069007616 7.1616505637581485