BamQC report ----------------------------------- >>>>>>> Input bam file = zr3644_19.deduplicated.sorted.bam outfile = zr3644_19/genome_results.txt >>>>>>> Reference number of bases = 563,985,803 bp number of contigs = 29 >>>>>>> Globals number of windows = 428 number of reads = 55,358,426 number of mapped reads = 55,358,426 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 27,679,213 number of mapped paired reads (second in pair) = 27,679,213 number of mapped paired reads (both in pair) = 55,358,426 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 23,200,551 number of mapped bases = 5,823,950,715 bp number of sequenced bases = 5,798,327,740 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,287,806 duplication rate = 16.77% >>>>>>> Insert size mean insert size = 161.8817 std insert size = 72.3254 median insert size = 140 >>>>>>> Mapping quality mean mapping quality = 24.7292 >>>>>>> ACTG content number of A's = 2,376,875,109 bp (40.99%) number of C's = 514,388,753 bp (8.87%) number of T's = 2,400,452,584 bp (41.4%) number of G's = 506,568,393 bp (8.74%) number of N's = 42,901 bp (0%) GC percentage = 17.61% >>>>>>> Mismatches and indels general error rate = 0.1946 number of mismatches = 1,100,155,523 number of insertions = 12,193,902 mapped reads with insertion percentage = 16.72% number of deletions = 10,779,011 mapped reads with deletion percentage = 16.11% homopolymer indels = 49.04% >>>>>>> Coverage mean coverageData = 10.3264X std coverageData = 11.4538X paired-end adapted mean coverage = 7.4089X There is a 83.89% of reference with a coverageData >= 1X There is a 78.28% of reference with a coverageData >= 2X There is a 72.66% of reference with a coverageData >= 3X There is a 67.99% of reference with a coverageData >= 4X There is a 63.33% of reference with a coverageData >= 5X There is a 58.96% of reference with a coverageData >= 6X There is a 54.68% of reference with a coverageData >= 7X There is a 50.59% of reference with a coverageData >= 8X There is a 46.65% of reference with a coverageData >= 9X There is a 42.89% of reference with a coverageData >= 10X There is a 39.3% of reference with a coverageData >= 11X There is a 35.91% of reference with a coverageData >= 12X There is a 32.7% of reference with a coverageData >= 13X There is a 29.7% of reference with a coverageData >= 14X There is a 26.89% of reference with a coverageData >= 15X There is a 24.28% of reference with a coverageData >= 16X There is a 21.86% of reference with a coverageData >= 17X There is a 19.64% of reference with a coverageData >= 18X There is a 17.6% of reference with a coverageData >= 19X There is a 15.73% of reference with a coverageData >= 20X There is a 14.03% of reference with a coverageData >= 21X There is a 12.5% of reference with a coverageData >= 22X There is a 11.11% of reference with a coverageData >= 23X There is a 9.87% of reference with a coverageData >= 24X There is a 8.76% of reference with a coverageData >= 25X There is a 7.77% of reference with a coverageData >= 26X There is a 6.89% of reference with a coverageData >= 27X There is a 6.11% of reference with a coverageData >= 28X There is a 5.43% of reference with a coverageData >= 29X There is a 4.82% of reference with a coverageData >= 30X There is a 4.29% of reference with a coverageData >= 31X There is a 3.83% of reference with a coverageData >= 32X There is a 3.42% of reference with a coverageData >= 33X There is a 3.06% of reference with a coverageData >= 34X There is a 2.75% of reference with a coverageData >= 35X There is a 2.47% of reference with a coverageData >= 36X There is a 2.24% of reference with a coverageData >= 37X There is a 2.03% of reference with a coverageData >= 38X There is a 1.84% of reference with a coverageData >= 39X There is a 1.68% of reference with a coverageData >= 40X There is a 1.54% of reference with a coverageData >= 41X There is a 1.42% of reference with a coverageData >= 42X There is a 1.31% of reference with a coverageData >= 43X There is a 1.21% of reference with a coverageData >= 44X There is a 1.12% of reference with a coverageData >= 45X There is a 1.04% of reference with a coverageData >= 46X There is a 0.97% of reference with a coverageData >= 47X There is a 0.91% of reference with a coverageData >= 48X There is a 0.85% of reference with a coverageData >= 49X There is a 0.8% of reference with a coverageData >= 50X There is a 0.75% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_088853.1 76070991 605335515 7.9575079414963845 13.254455050539653 NC_088854.1 61469542 714164004 11.618176754920347 10.928059644110077 NC_088855.1 61039741 714312873 11.702423065654882 10.725349380686081 NC_088856.1 57946171 541895257 9.351700856990188 11.690634369022565 NC_088857.1 57274926 649550655 11.340925259335997 11.013792445967505 NC_088858.1 56905015 668700223 11.751165042307782 10.59629870258825 NC_088859.1 53672946 649469867 12.1005071530823 10.878638394692128 NC_088860.1 51133819 539238938 10.545641779660542 11.443529422724833 NC_088861.1 50364239 398909594 7.920492832225659 10.882549083679999 NC_088862.1 37310742 338446615 9.071023433412286 10.982029832462374 NW_027062568.1 15579 122886 7.887926054303871 6.971387314763478 NW_027062569.1 16498 206583 12.521699599951509 14.4302133857355 NW_027062570.1 4000 227858 56.9645 50.3285421008795 NW_027062571.1 36893 7513 0.20364296750060987 0.6982633726795234 NW_027062572.1 51000 69337 1.3595490196078432 2.5064577694772776 NW_027062573.1 2000 113588 56.794 51.90033602974069 NW_027062574.1 37061 3171 0.08556164161787323 0.6382946587821812 NW_027062575.1 49428 283496 5.735534514849883 11.610109953614245 NW_027062576.1 49232 146535 2.9764177770555738 5.3306945575841445 NW_027062577.1 17087 145426 8.51091473049687 6.009480358724452 NW_027062578.1 34507 533410 15.458023009824094 8.510014702299056 NW_027062579.1 64000 504587 7.884171875 8.934316736308253 NW_027062580.1 24229 222544 9.185026208262826 9.60445862542454 NW_027062581.1 5000 20786 4.1572 8.835412501971824 NW_027062582.1 18808 162048 8.615908124202466 10.871508624311177 NW_027062583.1 1000 0 0.0 0.0 NW_027062584.1 74000 12399 0.16755405405405405 1.1467598023890864 NW_027062585.1 39334 268992 6.83866375146184 7.243503642281703 NW_027062586.1 258015 876015 3.395209580838323 6.714342969560469