BamQC report ----------------------------------- >>>>>>> Input bam file = zr3644_17.deduplicated.sorted.bam outfile = zr3644_17/genome_results.txt >>>>>>> Reference number of bases = 563,985,803 bp number of contigs = 29 >>>>>>> Globals number of windows = 428 number of reads = 63,717,702 number of mapped reads = 63,717,702 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 31,858,851 number of mapped paired reads (second in pair) = 31,858,851 number of mapped paired reads (both in pair) = 63,717,702 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 27,008,867 number of mapped bases = 6,690,220,649 bp number of sequenced bases = 6,661,385,289 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,887,834 duplication rate = 19.3% >>>>>>> Insert size mean insert size = 159.633 std insert size = 70.7314 median insert size = 138 >>>>>>> Mapping quality mean mapping quality = 24.8046 >>>>>>> ACTG content number of A's = 2,727,212,428 bp (40.94%) number of C's = 594,734,704 bp (8.93%) number of T's = 2,754,518,742 bp (41.35%) number of G's = 584,869,194 bp (8.78%) number of N's = 50,221 bp (0%) GC percentage = 17.71% >>>>>>> Mismatches and indels general error rate = 0.195 number of mismatches = 1,267,344,328 number of insertions = 13,813,327 mapped reads with insertion percentage = 16.46% number of deletions = 12,043,148 mapped reads with deletion percentage = 15.64% homopolymer indels = 49.07% >>>>>>> Coverage mean coverageData = 11.8624X std coverageData = 15.5617X paired-end adapted mean coverage = 8.4475X There is a 82.76% of reference with a coverageData >= 1X There is a 77.7% of reference with a coverageData >= 2X There is a 72.72% of reference with a coverageData >= 3X There is a 68.68% of reference with a coverageData >= 4X There is a 64.63% of reference with a coverageData >= 5X There is a 60.84% of reference with a coverageData >= 6X There is a 57.08% of reference with a coverageData >= 7X There is a 53.48% of reference with a coverageData >= 8X There is a 49.96% of reference with a coverageData >= 9X There is a 46.58% of reference with a coverageData >= 10X There is a 43.32% of reference with a coverageData >= 11X There is a 40.22% of reference with a coverageData >= 12X There is a 37.26% of reference with a coverageData >= 13X There is a 34.45% of reference with a coverageData >= 14X There is a 31.8% of reference with a coverageData >= 15X There is a 29.3% of reference with a coverageData >= 16X There is a 26.94% of reference with a coverageData >= 17X There is a 24.74% of reference with a coverageData >= 18X There is a 22.68% of reference with a coverageData >= 19X There is a 20.77% of reference with a coverageData >= 20X There is a 18.99% of reference with a coverageData >= 21X There is a 17.33% of reference with a coverageData >= 22X There is a 15.81% of reference with a coverageData >= 23X There is a 14.4% of reference with a coverageData >= 24X There is a 13.1% of reference with a coverageData >= 25X There is a 11.92% of reference with a coverageData >= 26X There is a 10.83% of reference with a coverageData >= 27X There is a 9.84% of reference with a coverageData >= 28X There is a 8.93% of reference with a coverageData >= 29X There is a 8.1% of reference with a coverageData >= 30X There is a 7.35% of reference with a coverageData >= 31X There is a 6.67% of reference with a coverageData >= 32X There is a 6.05% of reference with a coverageData >= 33X There is a 5.5% of reference with a coverageData >= 34X There is a 4.99% of reference with a coverageData >= 35X There is a 4.54% of reference with a coverageData >= 36X There is a 4.13% of reference with a coverageData >= 37X There is a 3.77% of reference with a coverageData >= 38X There is a 3.44% of reference with a coverageData >= 39X There is a 3.14% of reference with a coverageData >= 40X There is a 2.88% of reference with a coverageData >= 41X There is a 2.64% of reference with a coverageData >= 42X There is a 2.43% of reference with a coverageData >= 43X There is a 2.23% of reference with a coverageData >= 44X There is a 2.06% of reference with a coverageData >= 45X There is a 1.91% of reference with a coverageData >= 46X There is a 1.77% of reference with a coverageData >= 47X There is a 1.64% of reference with a coverageData >= 48X There is a 1.53% of reference with a coverageData >= 49X There is a 1.43% of reference with a coverageData >= 50X There is a 1.34% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_088853.1 76070991 694994452 9.136129855334737 24.524584600430053 NC_088854.1 61469542 826164016 13.440217530822013 13.623561454107351 NC_088855.1 61039741 817558354 13.393869970713014 13.056573884334231 NC_088856.1 57946171 622721056 10.74654364996783 13.668367394937567 NC_088857.1 57274926 745678268 13.019279466201318 13.635778382052777 NC_088858.1 56905015 766317247 13.466603022598273 12.43061695509767 NC_088859.1 53672946 742316681 13.830369605573727 12.978529815372747 NC_088860.1 51133819 614753077 12.022436208021153 14.567903391802014 NC_088861.1 50364239 461934322 9.17187137484595 12.819525019119506 NC_088862.1 37310742 394221861 10.565907828903537 15.259114737998372 NW_027062568.1 15579 122044 7.833878939598177 8.428078765373833 NW_027062569.1 16498 112409 6.813492544550854 13.663392459447696 NW_027062570.1 4000 52536 13.134 11.463285480175394 NW_027062571.1 36893 6310 0.1710351557205974 0.8655057816912928 NW_027062572.1 51000 39952 0.7833725490196078 2.2098307669263817 NW_027062573.1 2000 35899 17.9495 10.548801010067448 NW_027062574.1 37061 2451 0.066134211165376 0.5705654639779356 NW_027062575.1 49428 285828 5.782714251031804 11.237386456893507 NW_027062576.1 49232 218035 4.4287252193695155 8.917952115409246 NW_027062577.1 17087 176445 10.32627143442383 8.186517368929952 NW_027062578.1 34507 627244 18.17729735995595 10.618018009358432 NW_027062579.1 64000 334982 5.23409375 11.451720957595194 NW_027062580.1 24229 161180 6.652358743654299 7.422984313892832 NW_027062581.1 5000 28679 5.7358 9.651174616594604 NW_027062582.1 18808 113232 6.020416843896214 6.5762023223903965 NW_027062583.1 1000 0 0.0 0.0 NW_027062584.1 74000 13716 0.18535135135135136 1.0882880545611586 NW_027062585.1 39334 312227 7.937840036609549 8.027197147844554 NW_027062586.1 258015 918146 3.558498536906769 7.418787264120775