BamQC report ----------------------------------- >>>>>>> Input bam file = zr3644_20.deduplicated.sorted.bam outfile = zr3644_20/genome_results.txt >>>>>>> Reference number of bases = 563,985,803 bp number of contigs = 29 >>>>>>> Globals number of windows = 428 number of reads = 59,407,036 number of mapped reads = 59,407,036 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 29,703,518 number of mapped paired reads (second in pair) = 29,703,518 number of mapped paired reads (both in pair) = 59,407,036 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 24,563,541 number of mapped bases = 6,293,632,151 bp number of sequenced bases = 6,266,238,442 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,426,159 duplication rate = 17.32% >>>>>>> Insert size mean insert size = 165.091 std insert size = 72.8821 median insert size = 143 >>>>>>> Mapping quality mean mapping quality = 24.1428 >>>>>>> ACTG content number of A's = 2,567,118,026 bp (40.97%) number of C's = 555,983,504 bp (8.87%) number of T's = 2,591,313,626 bp (41.35%) number of G's = 551,788,788 bp (8.81%) number of N's = 34,498 bp (0%) GC percentage = 17.68% >>>>>>> Mismatches and indels general error rate = 0.1961 number of mismatches = 1,198,511,871 number of insertions = 13,178,274 mapped reads with insertion percentage = 16.81% number of deletions = 11,637,984 mapped reads with deletion percentage = 16.21% homopolymer indels = 48.56% >>>>>>> Coverage mean coverageData = 11.1592X std coverageData = 12.2163X paired-end adapted mean coverage = 8.0823X There is a 84.59% of reference with a coverageData >= 1X There is a 79.31% of reference with a coverageData >= 2X There is a 74.1% of reference with a coverageData >= 3X There is a 69.73% of reference with a coverageData >= 4X There is a 65.39% of reference with a coverageData >= 5X There is a 61.28% of reference with a coverageData >= 6X There is a 57.24% of reference with a coverageData >= 7X There is a 53.35% of reference with a coverageData >= 8X There is a 49.56% of reference with a coverageData >= 9X There is a 45.91% of reference with a coverageData >= 10X There is a 42.4% of reference with a coverageData >= 11X There is a 39.05% of reference with a coverageData >= 12X There is a 35.86% of reference with a coverageData >= 13X There is a 32.83% of reference with a coverageData >= 14X There is a 29.98% of reference with a coverageData >= 15X There is a 27.3% of reference with a coverageData >= 16X There is a 24.8% of reference with a coverageData >= 17X There is a 22.47% of reference with a coverageData >= 18X There is a 20.3% of reference with a coverageData >= 19X There is a 18.31% of reference with a coverageData >= 20X There is a 16.48% of reference with a coverageData >= 21X There is a 14.8% of reference with a coverageData >= 22X There is a 13.28% of reference with a coverageData >= 23X There is a 11.89% of reference with a coverageData >= 24X There is a 10.64% of reference with a coverageData >= 25X There is a 9.51% of reference with a coverageData >= 26X There is a 8.49% of reference with a coverageData >= 27X There is a 7.58% of reference with a coverageData >= 28X There is a 6.77% of reference with a coverageData >= 29X There is a 6.04% of reference with a coverageData >= 30X There is a 5.4% of reference with a coverageData >= 31X There is a 4.84% of reference with a coverageData >= 32X There is a 4.33% of reference with a coverageData >= 33X There is a 3.89% of reference with a coverageData >= 34X There is a 3.5% of reference with a coverageData >= 35X There is a 3.15% of reference with a coverageData >= 36X There is a 2.85% of reference with a coverageData >= 37X There is a 2.58% of reference with a coverageData >= 38X There is a 2.35% of reference with a coverageData >= 39X There is a 2.14% of reference with a coverageData >= 40X There is a 1.96% of reference with a coverageData >= 41X There is a 1.79% of reference with a coverageData >= 42X There is a 1.65% of reference with a coverageData >= 43X There is a 1.52% of reference with a coverageData >= 44X There is a 1.4% of reference with a coverageData >= 45X There is a 1.3% of reference with a coverageData >= 46X There is a 1.21% of reference with a coverageData >= 47X There is a 1.13% of reference with a coverageData >= 48X There is a 1.06% of reference with a coverageData >= 49X There is a 0.99% of reference with a coverageData >= 50X There is a 0.93% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_088853.1 76070991 661986753 8.702223335042396 14.069309220147229 NC_088854.1 61469542 770808298 12.539678561457315 11.490442080914269 NC_088855.1 61039741 775016524 12.696916980692956 11.422631664126579 NC_088856.1 57946171 584490182 10.086778330875392 12.537108478937478 NC_088857.1 57274926 697741828 12.182326136920718 11.60475486742301 NC_088858.1 56905015 723141267 12.707865326105265 11.314742545957044 NC_088859.1 53672946 702087266 13.080840876519057 12.231518855275098 NC_088860.1 51133819 578587896 11.315170807015216 12.005567965693242 NC_088861.1 50364239 431711322 8.57178288745711 11.383093831874728 NC_088862.1 37310742 364263767 9.762973006540584 11.908509421973825 NW_027062568.1 15579 132503 8.505231401245267 7.976867527937874 NW_027062569.1 16498 121465 7.362407564553279 15.370421912858115 NW_027062570.1 4000 221477 55.36925 50.22801497234885 NW_027062571.1 36893 6432 0.17434201610061528 0.7015314675822678 NW_027062572.1 51000 49978 0.9799607843137255 3.30797508320358 NW_027062573.1 2000 116401 58.2005 57.195604335036094 NW_027062574.1 37061 4485 0.12101670219368069 0.8208135893637168 NW_027062575.1 49428 394208 7.97539855952092 14.716346353838823 NW_027062576.1 49232 197633 4.014319954501137 7.621724793686764 NW_027062577.1 17087 155669 9.11037630947504 6.462248863803609 NW_027062578.1 34507 588015 17.040455559741503 10.192477748085832 NW_027062579.1 64000 450035 7.031796875 9.694335816601818 NW_027062580.1 24229 268414 11.078212059928186 10.57953941399142 NW_027062581.1 5000 21081 4.2162 8.537758869867432 NW_027062582.1 18808 42566 2.2631858783496384 4.634904660180089 NW_027062583.1 1000 0 0.0 0.0 NW_027062584.1 74000 16430 0.22202702702702704 1.2234566491660441 NW_027062585.1 39334 331416 8.42568770020847 7.963449385747526 NW_027062586.1 258015 678840 2.6310098250101737 6.049884535675741