BamQC report ----------------------------------- >>>>>>> Input bam file = zr3644_11.deduplicated.sorted.bam outfile = zr3644_11/genome_results.txt >>>>>>> Reference number of bases = 563,985,803 bp number of contigs = 29 >>>>>>> Globals number of windows = 428 number of reads = 62,468,064 number of mapped reads = 62,468,064 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 31,234,032 number of mapped paired reads (second in pair) = 31,234,032 number of mapped paired reads (both in pair) = 62,468,064 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 26,538,560 number of mapped bases = 6,569,405,347 bp number of sequenced bases = 6,540,162,823 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,360,661 duplication rate = 17.82% >>>>>>> Insert size mean insert size = 159.4285 std insert size = 70.4206 median insert size = 137 >>>>>>> Mapping quality mean mapping quality = 24.6674 >>>>>>> ACTG content number of A's = 2,679,500,764 bp (40.97%) number of C's = 581,228,239 bp (8.89%) number of T's = 2,706,993,988 bp (41.39%) number of G's = 572,391,560 bp (8.75%) number of N's = 48,272 bp (0%) GC percentage = 17.64% >>>>>>> Mismatches and indels general error rate = 0.1947 number of mismatches = 1,241,100,621 number of insertions = 13,930,254 mapped reads with insertion percentage = 16.84% number of deletions = 12,405,298 mapped reads with deletion percentage = 16.43% homopolymer indels = 48.97% >>>>>>> Coverage mean coverageData = 11.6482X std coverageData = 13.167X paired-end adapted mean coverage = 8.2742X There is a 84.97% of reference with a coverageData >= 1X There is a 80.01% of reference with a coverageData >= 2X There is a 75.06% of reference with a coverageData >= 3X There is a 70.98% of reference with a coverageData >= 4X There is a 66.87% of reference with a coverageData >= 5X There is a 63% of reference with a coverageData >= 6X There is a 59.13% of reference with a coverageData >= 7X There is a 55.37% of reference with a coverageData >= 8X There is a 51.68% of reference with a coverageData >= 9X There is a 48.11% of reference with a coverageData >= 10X There is a 44.62% of reference with a coverageData >= 11X There is a 41.26% of reference with a coverageData >= 12X There is a 38.03% of reference with a coverageData >= 13X There is a 34.95% of reference with a coverageData >= 14X There is a 32.01% of reference with a coverageData >= 15X There is a 29.23% of reference with a coverageData >= 16X There is a 26.62% of reference with a coverageData >= 17X There is a 24.17% of reference with a coverageData >= 18X There is a 21.88% of reference with a coverageData >= 19X There is a 19.77% of reference with a coverageData >= 20X There is a 17.82% of reference with a coverageData >= 21X There is a 16.02% of reference with a coverageData >= 22X There is a 14.38% of reference with a coverageData >= 23X There is a 12.89% of reference with a coverageData >= 24X There is a 11.53% of reference with a coverageData >= 25X There is a 10.3% of reference with a coverageData >= 26X There is a 9.19% of reference with a coverageData >= 27X There is a 8.2% of reference with a coverageData >= 28X There is a 7.32% of reference with a coverageData >= 29X There is a 6.53% of reference with a coverageData >= 30X There is a 5.83% of reference with a coverageData >= 31X There is a 5.21% of reference with a coverageData >= 32X There is a 4.67% of reference with a coverageData >= 33X There is a 4.18% of reference with a coverageData >= 34X There is a 3.76% of reference with a coverageData >= 35X There is a 3.38% of reference with a coverageData >= 36X There is a 3.05% of reference with a coverageData >= 37X There is a 2.76% of reference with a coverageData >= 38X There is a 2.51% of reference with a coverageData >= 39X There is a 2.28% of reference with a coverageData >= 40X There is a 2.09% of reference with a coverageData >= 41X There is a 1.91% of reference with a coverageData >= 42X There is a 1.76% of reference with a coverageData >= 43X There is a 1.62% of reference with a coverageData >= 44X There is a 1.5% of reference with a coverageData >= 45X There is a 1.39% of reference with a coverageData >= 46X There is a 1.29% of reference with a coverageData >= 47X There is a 1.21% of reference with a coverageData >= 48X There is a 1.13% of reference with a coverageData >= 49X There is a 1.06% of reference with a coverageData >= 50X There is a 0.99% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_088853.1 76070991 683607240 8.98643794452474 18.208275864139242 NC_088854.1 61469542 803525139 13.07192331122298 11.64656309883794 NC_088855.1 61039741 805905084 13.202957135745383 11.569648785412259 NC_088856.1 57946171 608904690 10.508109155305533 12.829840978518806 NC_088857.1 57274926 729617799 12.738869343977852 11.983040544781648 NC_088858.1 56905015 753320405 13.238207651821197 11.441105720666354 NC_088859.1 53672946 735059170 13.695152302614432 12.360869281544861 NC_088860.1 51133819 605734028 11.846054917196778 12.366963223613817 NC_088861.1 50364239 452972393 8.993929065422789 11.930120445062004 NC_088862.1 37310742 386160157 10.349838579999293 12.478745581725496 NW_027062568.1 15579 150063 9.632389755440016 7.895194638033749 NW_027062569.1 16498 117344 7.112619711480179 14.561824489386886 NW_027062570.1 4000 79079 19.76975 19.157248081666115 NW_027062571.1 36893 9778 0.26503672783454857 1.283394085989729 NW_027062572.1 51000 67064 1.3149803921568628 2.757048049444094 NW_027062573.1 2000 50435 25.2175 14.711926072068195 NW_027062574.1 37061 5493 0.1482151048271768 1.1346225114869188 NW_027062575.1 49428 401381 8.120518734320628 14.114925556173574 NW_027062576.1 49232 236790 4.809676633084173 9.820503006324744 NW_027062577.1 17087 159890 9.35740621525136 6.945148624444909 NW_027062578.1 34507 614401 17.8051120062596 9.725321496004355 NW_027062579.1 64000 720987 11.265421875 12.071335511269446 NW_027062580.1 24229 257450 10.625696479425482 11.546127366683473 NW_027062581.1 5000 49467 9.8934 11.270953494713746 NW_027062582.1 18808 327912 17.434708634623565 14.267113337857582 NW_027062583.1 1000 0 0.0 0.0 NW_027062584.1 74000 18828 0.2544324324324324 1.2868517015103405 NW_027062585.1 39334 321205 8.166090405247369 8.536983512432165 NW_027062586.1 258015 1011675 3.92099296552526 7.423123855196023