BamQC report ----------------------------------- >>>>>>> Input bam file = zr3644_15.deduplicated.sorted.bam outfile = zr3644_15/genome_results.txt >>>>>>> Reference number of bases = 563,985,803 bp number of contigs = 29 >>>>>>> Globals number of windows = 428 number of reads = 65,563,762 number of mapped reads = 65,563,762 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 32,781,881 number of mapped paired reads (second in pair) = 32,781,881 number of mapped paired reads (both in pair) = 65,563,762 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 27,603,644 number of mapped bases = 6,926,456,739 bp number of sequenced bases = 6,895,455,874 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,495,363 duplication rate = 18.55% >>>>>>> Insert size mean insert size = 161.6312 std insert size = 71.1545 median insert size = 140 >>>>>>> Mapping quality mean mapping quality = 24.6522 >>>>>>> ACTG content number of A's = 2,828,264,846 bp (41.02%) number of C's = 609,626,441 bp (8.84%) number of T's = 2,856,716,037 bp (41.43%) number of G's = 600,796,931 bp (8.71%) number of N's = 51,619 bp (0%) GC percentage = 17.55% >>>>>>> Mismatches and indels general error rate = 0.1943 number of mismatches = 1,306,209,051 number of insertions = 14,707,122 mapped reads with insertion percentage = 16.96% number of deletions = 13,111,769 mapped reads with deletion percentage = 16.53% homopolymer indels = 49.02% >>>>>>> Coverage mean coverageData = 12.2813X std coverageData = 13.2218X paired-end adapted mean coverage = 8.7815X There is a 85.05% of reference with a coverageData >= 1X There is a 80.23% of reference with a coverageData >= 2X There is a 75.51% of reference with a coverageData >= 3X There is a 71.64% of reference with a coverageData >= 4X There is a 67.75% of reference with a coverageData >= 5X There is a 64.09% of reference with a coverageData >= 6X There is a 60.43% of reference with a coverageData >= 7X There is a 56.87% of reference with a coverageData >= 8X There is a 53.35% of reference with a coverageData >= 9X There is a 49.93% of reference with a coverageData >= 10X There is a 46.58% of reference with a coverageData >= 11X There is a 43.34% of reference with a coverageData >= 12X There is a 40.2% of reference with a coverageData >= 13X There is a 37.18% of reference with a coverageData >= 14X There is a 34.29% of reference with a coverageData >= 15X There is a 31.53% of reference with a coverageData >= 16X There is a 28.91% of reference with a coverageData >= 17X There is a 26.44% of reference with a coverageData >= 18X There is a 24.11% of reference with a coverageData >= 19X There is a 21.94% of reference with a coverageData >= 20X There is a 19.91% of reference with a coverageData >= 21X There is a 18.03% of reference with a coverageData >= 22X There is a 16.3% of reference with a coverageData >= 23X There is a 14.71% of reference with a coverageData >= 24X There is a 13.25% of reference with a coverageData >= 25X There is a 11.92% of reference with a coverageData >= 26X There is a 10.71% of reference with a coverageData >= 27X There is a 9.62% of reference with a coverageData >= 28X There is a 8.63% of reference with a coverageData >= 29X There is a 7.74% of reference with a coverageData >= 30X There is a 6.94% of reference with a coverageData >= 31X There is a 6.23% of reference with a coverageData >= 32X There is a 5.6% of reference with a coverageData >= 33X There is a 5.04% of reference with a coverageData >= 34X There is a 4.54% of reference with a coverageData >= 35X There is a 4.09% of reference with a coverageData >= 36X There is a 3.7% of reference with a coverageData >= 37X There is a 3.35% of reference with a coverageData >= 38X There is a 3.04% of reference with a coverageData >= 39X There is a 2.77% of reference with a coverageData >= 40X There is a 2.53% of reference with a coverageData >= 41X There is a 2.32% of reference with a coverageData >= 42X There is a 2.13% of reference with a coverageData >= 43X There is a 1.96% of reference with a coverageData >= 44X There is a 1.81% of reference with a coverageData >= 45X There is a 1.67% of reference with a coverageData >= 46X There is a 1.56% of reference with a coverageData >= 47X There is a 1.45% of reference with a coverageData >= 48X There is a 1.35% of reference with a coverageData >= 49X There is a 1.27% of reference with a coverageData >= 50X There is a 1.19% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_088853.1 76070991 709994315 9.333312287202883 14.762036293488771 NC_088854.1 61469542 842963832 13.713520624572086 12.437494828691923 NC_088855.1 61039741 844712562 13.838731098154561 12.230005246911889 NC_088856.1 57946171 654372450 11.292764279455152 13.768406251619755 NC_088857.1 57274926 772631882 13.489880056763408 12.948830215538733 NC_088858.1 56905015 796819207 14.002618345676563 12.133670299072367 NC_088859.1 53672946 765485993 14.262045407382706 13.138253681501286 NC_088860.1 51133819 648701843 12.686356225417077 13.029621047327947 NC_088861.1 50364239 477591467 9.482749595402405 12.75172336764741 NC_088862.1 37310742 408782273 10.956155012945066 12.907974782763597 NW_027062568.1 15579 142162 9.125232685024713 8.454489565082572 NW_027062569.1 16498 130849 7.93120378227664 13.88347885828768 NW_027062570.1 4000 264933 66.23325 57.07330283449083 NW_027062571.1 36893 7994 0.21668067113002468 0.8634107483485475 NW_027062572.1 51000 43367 0.8503333333333334 1.9446657306389623 NW_027062573.1 2000 136256 68.128 60.86767841802411 NW_027062574.1 37061 8753 0.23617819270931706 0.8550793422511385 NW_027062575.1 49428 375125 7.589321841871004 14.781589648222795 NW_027062576.1 49232 225140 4.573041923951902 9.80077700058388 NW_027062577.1 17087 180755 10.57850997834611 7.81849500677507 NW_027062578.1 34507 641154 18.58040397600487 10.445212323366528 NW_027062579.1 64000 632607 9.884484375 11.455096748833965 NW_027062580.1 24229 222557 9.18556275537579 10.628900611713531 NW_027062581.1 5000 52150 10.43 12.639695724185769 NW_027062582.1 18808 203342 10.811463207145895 11.40828413068502 NW_027062583.1 1000 0 0.0 0.0 NW_027062584.1 74000 20620 0.27864864864864863 1.449661976670203 NW_027062585.1 39334 331078 8.417094625514821 7.664613555431576 NW_027062586.1 258015 782073 3.0311144700889483 6.775322427930325