BamQC report ----------------------------------- >>>>>>> Input bam file = zr3644_21.deduplicated.sorted.bam outfile = zr3644_21/genome_results.txt >>>>>>> Reference number of bases = 563,985,803 bp number of contigs = 29 >>>>>>> Globals number of windows = 428 number of reads = 56,662,836 number of mapped reads = 56,662,836 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 28,331,418 number of mapped paired reads (second in pair) = 28,331,418 number of mapped paired reads (both in pair) = 56,662,836 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 23,494,387 number of mapped bases = 5,992,016,631 bp number of sequenced bases = 5,965,346,526 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,522,200 duplication rate = 16.77% >>>>>>> Insert size mean insert size = 164.4246 std insert size = 73.3555 median insert size = 142 >>>>>>> Mapping quality mean mapping quality = 24.6254 >>>>>>> ACTG content number of A's = 2,446,360,345 bp (41.01%) number of C's = 527,998,571 bp (8.85%) number of T's = 2,470,107,138 bp (41.41%) number of G's = 520,836,856 bp (8.73%) number of N's = 43,616 bp (0%) GC percentage = 17.58% >>>>>>> Mismatches and indels general error rate = 0.1946 number of mismatches = 1,132,041,251 number of insertions = 12,640,888 mapped reads with insertion percentage = 16.89% number of deletions = 11,279,032 mapped reads with deletion percentage = 16.47% homopolymer indels = 48.99% >>>>>>> Coverage mean coverageData = 10.6244X std coverageData = 11.9693X paired-end adapted mean coverage = 7.6727X There is a 84.37% of reference with a coverageData >= 1X There is a 78.99% of reference with a coverageData >= 2X There is a 73.71% of reference with a coverageData >= 3X There is a 69.25% of reference with a coverageData >= 4X There is a 64.8% of reference with a coverageData >= 5X There is a 60.6% of reference with a coverageData >= 6X There is a 56.44% of reference with a coverageData >= 7X There is a 52.42% of reference with a coverageData >= 8X There is a 48.49% of reference with a coverageData >= 9X There is a 44.71% of reference with a coverageData >= 10X There is a 41.07% of reference with a coverageData >= 11X There is a 37.6% of reference with a coverageData >= 12X There is a 34.28% of reference with a coverageData >= 13X There is a 31.15% of reference with a coverageData >= 14X There is a 28.2% of reference with a coverageData >= 15X There is a 25.45% of reference with a coverageData >= 16X There is a 22.89% of reference with a coverageData >= 17X There is a 20.53% of reference with a coverageData >= 18X There is a 18.36% of reference with a coverageData >= 19X There is a 16.37% of reference with a coverageData >= 20X There is a 14.56% of reference with a coverageData >= 21X There is a 12.93% of reference with a coverageData >= 22X There is a 11.46% of reference with a coverageData >= 23X There is a 10.15% of reference with a coverageData >= 24X There is a 8.98% of reference with a coverageData >= 25X There is a 7.94% of reference with a coverageData >= 26X There is a 7.02% of reference with a coverageData >= 27X There is a 6.21% of reference with a coverageData >= 28X There is a 5.5% of reference with a coverageData >= 29X There is a 4.88% of reference with a coverageData >= 30X There is a 4.33% of reference with a coverageData >= 31X There is a 3.86% of reference with a coverageData >= 32X There is a 3.44% of reference with a coverageData >= 33X There is a 3.08% of reference with a coverageData >= 34X There is a 2.77% of reference with a coverageData >= 35X There is a 2.5% of reference with a coverageData >= 36X There is a 2.26% of reference with a coverageData >= 37X There is a 2.05% of reference with a coverageData >= 38X There is a 1.86% of reference with a coverageData >= 39X There is a 1.7% of reference with a coverageData >= 40X There is a 1.56% of reference with a coverageData >= 41X There is a 1.44% of reference with a coverageData >= 42X There is a 1.33% of reference with a coverageData >= 43X There is a 1.23% of reference with a coverageData >= 44X There is a 1.14% of reference with a coverageData >= 45X There is a 1.06% of reference with a coverageData >= 46X There is a 0.99% of reference with a coverageData >= 47X There is a 0.93% of reference with a coverageData >= 48X There is a 0.87% of reference with a coverageData >= 49X There is a 0.82% of reference with a coverageData >= 50X There is a 0.77% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_088853.1 76070991 634716668 8.343741282402908 16.76964040905666 NC_088854.1 61469542 733177830 11.927497849260044 10.9235761390852 NC_088855.1 61039741 732100253 11.993829610122363 10.591611808882373 NC_088856.1 57946171 555838055 9.592317238700725 11.429289032135367 NC_088857.1 57274926 665219809 11.614503159724729 10.653380898097232 NC_088858.1 56905015 685301604 12.04290349453383 10.44768165500195 NC_088859.1 53672946 665778069 12.404351141821058 10.635569826224332 NC_088860.1 51133819 545895218 10.67581551067015 11.37935439776614 NC_088861.1 50364239 411732189 8.1750900475236 10.786866378647334 NC_088862.1 37310742 357783232 9.589282142928168 11.486365734603602 NW_027062568.1 15579 149080 9.56929199563515 8.350123631808561 NW_027062569.1 16498 225817 13.687537883379804 16.521947289062037 NW_027062570.1 4000 229099 57.27475 48.33984747273723 NW_027062571.1 36893 5724 0.15515138373133114 0.9030174845695211 NW_027062572.1 51000 37164 0.7287058823529412 1.5853637483343916 NW_027062573.1 2000 112479 56.2395 53.98477195700654 NW_027062574.1 37061 4272 0.11526942068481692 0.536083471434188 NW_027062575.1 49428 411265 8.320486364004209 14.962791696129806 NW_027062576.1 49232 226760 4.6059473513162175 10.869668462176126 NW_027062577.1 17087 158185 9.257622754140575 6.732262191398164 NW_027062578.1 34507 535453 15.517228388442925 8.595923951218595 NW_027062579.1 64000 668251 10.441421875 9.813350622254498 NW_027062580.1 24229 286492 11.82434272978662 11.468198866893461 NW_027062581.1 5000 36891 7.3782 8.639131324386728 NW_027062582.1 18808 201776 10.728200765631646 12.092539595239762 NW_027062583.1 1000 0 0.0 0.0 NW_027062584.1 74000 13134 0.1774864864864865 0.9986577540454591 NW_027062585.1 39334 315606 8.023745360248132 7.246962470918382 NW_027062586.1 258015 856256 3.3186287618936885 6.051026843297695