BamQC report ----------------------------------- >>>>>>> Input bam file = zr3644_1.deduplicated.sorted.bam outfile = zr3644_1/genome_results.txt >>>>>>> Reference number of bases = 563,985,803 bp number of contigs = 29 >>>>>>> Globals number of windows = 428 number of reads = 56,970,170 number of mapped reads = 56,970,170 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 28,485,085 number of mapped paired reads (second in pair) = 28,485,085 number of mapped paired reads (both in pair) = 56,970,170 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 24,674,126 number of mapped bases = 5,964,350,879 bp number of sequenced bases = 5,938,640,543 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,428,255 duplication rate = 17.9% >>>>>>> Insert size mean insert size = 155.3509 std insert size = 67.4495 median insert size = 133 >>>>>>> Mapping quality mean mapping quality = 24.6238 >>>>>>> ACTG content number of A's = 2,435,573,174 bp (41.01%) number of C's = 526,471,850 bp (8.87%) number of T's = 2,458,720,826 bp (41.4%) number of G's = 517,829,811 bp (8.72%) number of N's = 44,882 bp (0%) GC percentage = 17.58% >>>>>>> Mismatches and indels general error rate = 0.1959 number of mismatches = 1,134,611,174 number of insertions = 12,421,519 mapped reads with insertion percentage = 16.56% number of deletions = 10,760,610 mapped reads with deletion percentage = 15.63% homopolymer indels = 49.05% >>>>>>> Coverage mean coverageData = 10.5754X std coverageData = 12.6075X paired-end adapted mean coverage = 7.411X There is a 81.2% of reference with a coverageData >= 1X There is a 75.87% of reference with a coverageData >= 2X There is a 70.53% of reference with a coverageData >= 3X There is a 66.25% of reference with a coverageData >= 4X There is a 61.92% of reference with a coverageData >= 5X There is a 57.89% of reference with a coverageData >= 6X There is a 53.89% of reference with a coverageData >= 7X There is a 50.07% of reference with a coverageData >= 8X There is a 46.36% of reference with a coverageData >= 9X There is a 42.82% of reference with a coverageData >= 10X There is a 39.44% of reference with a coverageData >= 11X There is a 36.23% of reference with a coverageData >= 12X There is a 33.21% of reference with a coverageData >= 13X There is a 30.37% of reference with a coverageData >= 14X There is a 27.71% of reference with a coverageData >= 15X There is a 25.23% of reference with a coverageData >= 16X There is a 22.93% of reference with a coverageData >= 17X There is a 20.8% of reference with a coverageData >= 18X There is a 18.83% of reference with a coverageData >= 19X There is a 17.02% of reference with a coverageData >= 20X There is a 15.36% of reference with a coverageData >= 21X There is a 13.85% of reference with a coverageData >= 22X There is a 12.47% of reference with a coverageData >= 23X There is a 11.22% of reference with a coverageData >= 24X There is a 10.09% of reference with a coverageData >= 25X There is a 9.06% of reference with a coverageData >= 26X There is a 8.14% of reference with a coverageData >= 27X There is a 7.31% of reference with a coverageData >= 28X There is a 6.57% of reference with a coverageData >= 29X There is a 5.9% of reference with a coverageData >= 30X There is a 5.3% of reference with a coverageData >= 31X There is a 4.77% of reference with a coverageData >= 32X There is a 4.3% of reference with a coverageData >= 33X There is a 3.88% of reference with a coverageData >= 34X There is a 3.5% of reference with a coverageData >= 35X There is a 3.17% of reference with a coverageData >= 36X There is a 2.87% of reference with a coverageData >= 37X There is a 2.61% of reference with a coverageData >= 38X There is a 2.38% of reference with a coverageData >= 39X There is a 2.17% of reference with a coverageData >= 40X There is a 1.99% of reference with a coverageData >= 41X There is a 1.83% of reference with a coverageData >= 42X There is a 1.68% of reference with a coverageData >= 43X There is a 1.55% of reference with a coverageData >= 44X There is a 1.44% of reference with a coverageData >= 45X There is a 1.33% of reference with a coverageData >= 46X There is a 1.24% of reference with a coverageData >= 47X There is a 1.16% of reference with a coverageData >= 48X There is a 1.08% of reference with a coverageData >= 49X There is a 1.01% of reference with a coverageData >= 50X There is a 0.95% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_088853.1 76070991 631115793 8.296405564113131 15.147835222106952 NC_088854.1 61469542 735079694 11.958437790214868 11.817426750613002 NC_088855.1 61039741 725899562 11.892245119454225 11.50204953903858 NC_088856.1 57946171 570746153 9.849592184443042 12.847215646066237 NC_088857.1 57274926 673882727 11.765754651520632 12.326917603006004 NC_088858.1 56905015 680423713 11.957183615538982 11.389889335547918 NC_088859.1 53672946 657532810 12.25073074990145 11.167414833931542 NC_088860.1 51133819 532712800 10.418013174412026 12.534298968065036 NC_088861.1 50364239 411898178 8.178385818556695 11.557383363917019 NC_088862.1 37310742 342031326 9.167100616760717 13.677316747624994 NW_027062568.1 15579 118471 7.604531741446819 9.254954144643715 NW_027062569.1 16498 117782 7.139168384046551 14.783881989781381 NW_027062570.1 4000 74041 18.51025 18.284742609960357 NW_027062571.1 36893 7155 0.19393922966416394 1.0820917216647612 NW_027062572.1 51000 12400 0.24313725490196078 0.7999698667912017 NW_027062573.1 2000 63673 31.8365 17.650159992192705 NW_027062574.1 37061 9886 0.26674941312970507 1.0571968440107178 NW_027062575.1 49428 355357 7.189386582503844 17.197609415622047 NW_027062576.1 49232 206992 4.204419889502763 8.510768607998667 NW_027062577.1 17087 146715 8.586352197577105 6.744123529052292 NW_027062578.1 34507 560029 16.229431709508216 9.754665136493626 NW_027062579.1 64000 278308 4.3485625 10.48919442100119 NW_027062580.1 24229 202402 8.353708366007677 9.717218092857756 NW_027062581.1 5000 19704 3.9408 7.348272352056639 NW_027062582.1 18808 199757 10.620852828583581 11.214667425417996 NW_027062583.1 1000 0 0.0 0.0 NW_027062584.1 74000 9701 0.1310945945945946 0.8251594481461537 NW_027062585.1 39334 263581 6.701098286469721 7.305709803455967 NW_027062586.1 258015 382169 1.4811890781543708 4.76570681033491