BamQC report ----------------------------------- >>>>>>> Input bam file = zr3644_4.deduplicated.sorted.bam outfile = zr3644_4/genome_results.txt >>>>>>> Reference number of bases = 563,985,803 bp number of contigs = 29 >>>>>>> Globals number of windows = 428 number of reads = 49,284,630 number of mapped reads = 49,284,630 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 24,642,315 number of mapped paired reads (second in pair) = 24,642,315 number of mapped paired reads (both in pair) = 49,284,630 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 20,915,757 number of mapped bases = 5,201,705,702 bp number of sequenced bases = 5,177,973,651 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,196,375 duplication rate = 14.94% >>>>>>> Insert size mean insert size = 160.1187 std insert size = 70.0878 median insert size = 138 >>>>>>> Mapping quality mean mapping quality = 23.2676 >>>>>>> ACTG content number of A's = 2,127,870,825 bp (41.09%) number of C's = 453,469,611 bp (8.76%) number of T's = 2,149,363,579 bp (41.51%) number of G's = 447,232,847 bp (8.64%) number of N's = 36,789 bp (0%) GC percentage = 17.39% >>>>>>> Mismatches and indels general error rate = 0.1965 number of mismatches = 991,563,859 number of insertions = 11,475,610 mapped reads with insertion percentage = 17.53% number of deletions = 10,131,201 mapped reads with deletion percentage = 16.96% homopolymer indels = 48.8% >>>>>>> Coverage mean coverageData = 9.2231X std coverageData = 10.3268X paired-end adapted mean coverage = 6.5577X There is a 84.9% of reference with a coverageData >= 1X There is a 79.11% of reference with a coverageData >= 2X There is a 72.94% of reference with a coverageData >= 3X There is a 67.62% of reference with a coverageData >= 4X There is a 62.22% of reference with a coverageData >= 5X There is a 57.1% of reference with a coverageData >= 6X There is a 52.08% of reference with a coverageData >= 7X There is a 47.31% of reference with a coverageData >= 8X There is a 42.74% of reference with a coverageData >= 9X There is a 38.45% of reference with a coverageData >= 10X There is a 34.42% of reference with a coverageData >= 11X There is a 30.7% of reference with a coverageData >= 12X There is a 27.26% of reference with a coverageData >= 13X There is a 24.13% of reference with a coverageData >= 14X There is a 21.29% of reference with a coverageData >= 15X There is a 18.73% of reference with a coverageData >= 16X There is a 16.45% of reference with a coverageData >= 17X There is a 14.42% of reference with a coverageData >= 18X There is a 12.63% of reference with a coverageData >= 19X There is a 11.05% of reference with a coverageData >= 20X There is a 9.67% of reference with a coverageData >= 21X There is a 8.47% of reference with a coverageData >= 22X There is a 7.43% of reference with a coverageData >= 23X There is a 6.53% of reference with a coverageData >= 24X There is a 5.75% of reference with a coverageData >= 25X There is a 5.08% of reference with a coverageData >= 26X There is a 4.5% of reference with a coverageData >= 27X There is a 4% of reference with a coverageData >= 28X There is a 3.58% of reference with a coverageData >= 29X There is a 3.2% of reference with a coverageData >= 30X There is a 2.88% of reference with a coverageData >= 31X There is a 2.61% of reference with a coverageData >= 32X There is a 2.36% of reference with a coverageData >= 33X There is a 2.15% of reference with a coverageData >= 34X There is a 1.97% of reference with a coverageData >= 35X There is a 1.81% of reference with a coverageData >= 36X There is a 1.66% of reference with a coverageData >= 37X There is a 1.53% of reference with a coverageData >= 38X There is a 1.42% of reference with a coverageData >= 39X There is a 1.32% of reference with a coverageData >= 40X There is a 1.22% of reference with a coverageData >= 41X There is a 1.14% of reference with a coverageData >= 42X There is a 1.06% of reference with a coverageData >= 43X There is a 0.99% of reference with a coverageData >= 44X There is a 0.93% of reference with a coverageData >= 45X There is a 0.87% of reference with a coverageData >= 46X There is a 0.82% of reference with a coverageData >= 47X There is a 0.77% of reference with a coverageData >= 48X There is a 0.73% of reference with a coverageData >= 49X There is a 0.68% of reference with a coverageData >= 50X There is a 0.65% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_088853.1 76070991 596328908 7.839110548724151 11.956665010284963 NC_088854.1 61469542 621155808 10.105099009847837 9.854125463205355 NC_088855.1 61039741 620242516 10.16129010114902 9.47877841972088 NC_088856.1 57946171 493855590 8.522661316137697 10.407011521903534 NC_088857.1 57274926 570715381 9.964489190261023 9.967947834258526 NC_088858.1 56905015 578466120 10.165468192917618 9.532907864710348 NC_088859.1 53672946 562264425 10.475751135404417 10.16962651198476 NC_088860.1 51133819 484171471 9.468713279561614 10.534844810783113 NC_088861.1 50364239 367231902 7.291520914274114 9.970483807151663 NC_088862.1 37310742 303938160 8.146130141287461 9.937759067125487 NW_027062568.1 15579 116846 7.500224661403171 5.794505593996131 NW_027062569.1 16498 108265 6.562310583100982 10.874371167334461 NW_027062570.1 4000 200903 50.22575 44.33770418405198 NW_027062571.1 36893 17765 0.4815276610739165 1.286701620730673 NW_027062572.1 51000 70173 1.3759411764705882 2.598727495584928 NW_027062573.1 2000 104659 52.3295 42.822978956980556 NW_027062574.1 37061 6398 0.17263430560427404 0.6004370451356971 NW_027062575.1 49428 283757 5.740814922715869 11.184911674044557 NW_027062576.1 49232 160473 3.2595263243418913 5.503135045933684 NW_027062577.1 17087 116980 6.8461403406098205 5.704276769889191 NW_027062578.1 34507 412753 11.961428116034428 8.35127447627271 NW_027062579.1 64000 440668 6.8854375 10.198523291637771 NW_027062580.1 24229 139026 5.737999917454291 6.292207285253872 NW_027062581.1 5000 19814 3.9628 10.68952962856645 NW_027062582.1 18808 242293 12.882443641003828 10.326259430453819 NW_027062583.1 1000 0 0.0 0.0 NW_027062584.1 74000 9993 0.13504054054054054 0.5073022716065932 NW_027062585.1 39334 253428 6.44297554278741 5.620658911107314 NW_027062586.1 258015 631227 2.4464740422068485 6.4903549645182395