BamQC report ----------------------------------- >>>>>>> Input bam file = zr3644_24.deduplicated.sorted.bam outfile = zr3644_24/genome_results.txt >>>>>>> Reference number of bases = 563,985,803 bp number of contigs = 29 >>>>>>> Globals number of windows = 428 number of reads = 58,963,892 number of mapped reads = 58,963,892 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 29,481,946 number of mapped paired reads (second in pair) = 29,481,946 number of mapped paired reads (both in pair) = 58,963,892 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 24,893,548 number of mapped bases = 6,225,805,790 bp number of sequenced bases = 6,198,718,993 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,644,815 duplication rate = 17.71% >>>>>>> Insert size mean insert size = 161.0392 std insert size = 70.5866 median insert size = 139 >>>>>>> Mapping quality mean mapping quality = 24.8471 >>>>>>> ACTG content number of A's = 2,540,018,021 bp (40.98%) number of C's = 551,050,922 bp (8.89%) number of T's = 2,564,984,424 bp (41.38%) number of G's = 542,619,100 bp (8.75%) number of N's = 46,526 bp (0%) GC percentage = 17.64% >>>>>>> Mismatches and indels general error rate = 0.1949 number of mismatches = 1,178,210,732 number of insertions = 12,997,487 mapped reads with insertion percentage = 16.71% number of deletions = 11,286,578 mapped reads with deletion percentage = 15.83% homopolymer indels = 49.06% >>>>>>> Coverage mean coverageData = 11.0389X std coverageData = 13.0511X paired-end adapted mean coverage = 7.8805X There is a 83.95% of reference with a coverageData >= 1X There is a 78.62% of reference with a coverageData >= 2X There is a 73.27% of reference with a coverageData >= 3X There is a 68.83% of reference with a coverageData >= 4X There is a 64.4% of reference with a coverageData >= 5X There is a 60.25% of reference with a coverageData >= 6X There is a 56.16% of reference with a coverageData >= 7X There is a 52.26% of reference with a coverageData >= 8X There is a 48.48% of reference with a coverageData >= 9X There is a 44.87% of reference with a coverageData >= 10X There is a 41.42% of reference with a coverageData >= 11X There is a 38.14% of reference with a coverageData >= 12X There is a 35.04% of reference with a coverageData >= 13X There is a 32.11% of reference with a coverageData >= 14X There is a 29.35% of reference with a coverageData >= 15X There is a 26.78% of reference with a coverageData >= 16X There is a 24.37% of reference with a coverageData >= 17X There is a 22.14% of reference with a coverageData >= 18X There is a 20.07% of reference with a coverageData >= 19X There is a 18.16% of reference with a coverageData >= 20X There is a 16.4% of reference with a coverageData >= 21X There is a 14.79% of reference with a coverageData >= 22X There is a 13.32% of reference with a coverageData >= 23X There is a 11.97% of reference with a coverageData >= 24X There is a 10.75% of reference with a coverageData >= 25X There is a 9.64% of reference with a coverageData >= 26X There is a 8.65% of reference with a coverageData >= 27X There is a 7.75% of reference with a coverageData >= 28X There is a 6.94% of reference with a coverageData >= 29X There is a 6.22% of reference with a coverageData >= 30X There is a 5.58% of reference with a coverageData >= 31X There is a 5.01% of reference with a coverageData >= 32X There is a 4.5% of reference with a coverageData >= 33X There is a 4.04% of reference with a coverageData >= 34X There is a 3.64% of reference with a coverageData >= 35X There is a 3.28% of reference with a coverageData >= 36X There is a 2.97% of reference with a coverageData >= 37X There is a 2.69% of reference with a coverageData >= 38X There is a 2.44% of reference with a coverageData >= 39X There is a 2.22% of reference with a coverageData >= 40X There is a 2.03% of reference with a coverageData >= 41X There is a 1.85% of reference with a coverageData >= 42X There is a 1.7% of reference with a coverageData >= 43X There is a 1.56% of reference with a coverageData >= 44X There is a 1.44% of reference with a coverageData >= 45X There is a 1.34% of reference with a coverageData >= 46X There is a 1.24% of reference with a coverageData >= 47X There is a 1.15% of reference with a coverageData >= 48X There is a 1.07% of reference with a coverageData >= 49X There is a 1% of reference with a coverageData >= 50X There is a 0.94% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_088853.1 76070991 626888047 8.240829240675989 18.257429649133652 NC_088854.1 61469542 763654043 12.423291570970221 11.953654164521149 NC_088855.1 61039741 764243908 12.520431697113525 11.47121219680721 NC_088856.1 57946171 583604386 10.07149179882826 12.65598328545165 NC_088857.1 57274926 697259021 12.173896497046544 11.814728784336374 NC_088858.1 56905015 716529472 12.591675303134531 11.384600790463839 NC_088859.1 53672946 694824770 12.945530696228227 11.692845875879375 NC_088860.1 51133819 572534959 11.196796370715045 12.016218756123727 NC_088861.1 50364239 430951622 8.55669877192029 11.74826222320031 NC_088862.1 37310742 371393050 9.954051570456572 12.484028051630524 NW_027062568.1 15579 151816 9.744913023942487 8.228191118140117 NW_027062569.1 16498 130623 7.917505152139653 15.131520802851144 NW_027062570.1 4000 68658 17.1645 17.458368079519914 NW_027062571.1 36893 8411 0.22798362833057761 0.771314579983796 NW_027062572.1 51000 47159 0.9246862745098039 3.2889857895169983 NW_027062573.1 2000 50513 25.2565 13.846504567940606 NW_027062574.1 37061 5982 0.16140956800949785 1.135379529050653 NW_027062575.1 49428 405284 8.199482074937283 16.830695470523462 NW_027062576.1 49232 190325 3.8658799155021124 8.851734551591194 NW_027062577.1 17087 165555 9.688944811845262 7.287636139857691 NW_027062578.1 34507 604844 17.528153707943314 10.454613566669838 NW_027062579.1 64000 519368 8.115125 9.495870001940316 NW_027062580.1 24229 259509 10.71067728754798 10.544810690082665 NW_027062581.1 5000 58219 11.6438 13.874294076456648 NW_027062582.1 18808 185099 9.841503615482774 7.764139457677629 NW_027062583.1 1000 0 0.0 0.0 NW_027062584.1 74000 15749 0.21282432432432433 1.2679468648927605 NW_027062585.1 39334 350659 8.914908221894544 9.101262912466488 NW_027062586.1 258015 704739 2.7313877100168593 6.272334207088205