BamQC report ----------------------------------- >>>>>>> Input bam file = zr3644_3.deduplicated.sorted.bam outfile = zr3644_3/genome_results.txt >>>>>>> Reference number of bases = 563,985,803 bp number of contigs = 29 >>>>>>> Globals number of windows = 428 number of reads = 41,394,998 number of mapped reads = 41,394,998 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 20,697,499 number of mapped paired reads (second in pair) = 20,697,499 number of mapped paired reads (both in pair) = 41,394,998 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 17,406,575 number of mapped bases = 4,374,917,446 bp number of sequenced bases = 4,355,117,706 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,950,460 duplication rate = 13.1% >>>>>>> Insert size mean insert size = 161.847 std insert size = 71.1106 median insert size = 140 >>>>>>> Mapping quality mean mapping quality = 23.9263 >>>>>>> ACTG content number of A's = 1,786,741,220 bp (41.03%) number of C's = 384,454,251 bp (8.83%) number of T's = 1,804,968,934 bp (41.44%) number of G's = 378,920,994 bp (8.7%) number of N's = 32,307 bp (0%) GC percentage = 17.53% >>>>>>> Mismatches and indels general error rate = 0.1952 number of mismatches = 828,210,297 number of insertions = 9,454,545 mapped reads with insertion percentage = 17.21% number of deletions = 8,418,166 mapped reads with deletion percentage = 16.8% homopolymer indels = 48.8% >>>>>>> Coverage mean coverageData = 7.7571X std coverageData = 8.5893X paired-end adapted mean coverage = 5.5512X There is a 83.35% of reference with a coverageData >= 1X There is a 76.73% of reference with a coverageData >= 2X There is a 69.7% of reference with a coverageData >= 3X There is a 63.66% of reference with a coverageData >= 4X There is a 57.6% of reference with a coverageData >= 5X There is a 51.93% of reference with a coverageData >= 6X There is a 46.45% of reference with a coverageData >= 7X There is a 41.31% of reference with a coverageData >= 8X There is a 36.48% of reference with a coverageData >= 9X There is a 32.04% of reference with a coverageData >= 10X There is a 27.97% of reference with a coverageData >= 11X There is a 24.29% of reference with a coverageData >= 12X There is a 20.99% of reference with a coverageData >= 13X There is a 18.06% of reference with a coverageData >= 14X There is a 15.49% of reference with a coverageData >= 15X There is a 13.24% of reference with a coverageData >= 16X There is a 11.3% of reference with a coverageData >= 17X There is a 9.63% of reference with a coverageData >= 18X There is a 8.2% of reference with a coverageData >= 19X There is a 6.99% of reference with a coverageData >= 20X There is a 5.96% of reference with a coverageData >= 21X There is a 5.1% of reference with a coverageData >= 22X There is a 4.38% of reference with a coverageData >= 23X There is a 3.78% of reference with a coverageData >= 24X There is a 3.27% of reference with a coverageData >= 25X There is a 2.85% of reference with a coverageData >= 26X There is a 2.49% of reference with a coverageData >= 27X There is a 2.19% of reference with a coverageData >= 28X There is a 1.94% of reference with a coverageData >= 29X There is a 1.73% of reference with a coverageData >= 30X There is a 1.55% of reference with a coverageData >= 31X There is a 1.4% of reference with a coverageData >= 32X There is a 1.26% of reference with a coverageData >= 33X There is a 1.15% of reference with a coverageData >= 34X There is a 1.05% of reference with a coverageData >= 35X There is a 0.96% of reference with a coverageData >= 36X There is a 0.88% of reference with a coverageData >= 37X There is a 0.81% of reference with a coverageData >= 38X There is a 0.75% of reference with a coverageData >= 39X There is a 0.7% of reference with a coverageData >= 40X There is a 0.65% of reference with a coverageData >= 41X There is a 0.6% of reference with a coverageData >= 42X There is a 0.56% of reference with a coverageData >= 43X There is a 0.52% of reference with a coverageData >= 44X There is a 0.49% of reference with a coverageData >= 45X There is a 0.46% of reference with a coverageData >= 46X There is a 0.43% of reference with a coverageData >= 47X There is a 0.4% of reference with a coverageData >= 48X There is a 0.37% of reference with a coverageData >= 49X There is a 0.35% of reference with a coverageData >= 50X There is a 0.33% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_088853.1 76070991 475684170 6.253161208324472 10.234082596418768 NC_088854.1 61469542 525760873 8.553193270904801 7.893248326020121 NC_088855.1 61039741 528477216 8.65792035388879 7.7949934504407326 NC_088856.1 57946171 410290646 7.080548014121589 8.656156752937289 NC_088857.1 57274926 481901357 8.41382766692706 8.165607699673687 NC_088858.1 56905015 495519399 8.707833553861642 8.053779833509827 NC_088859.1 53672946 477427780 8.895129028319035 8.124398673443787 NC_088860.1 51133819 399281042 7.808551166499025 8.483680953623468 NC_088861.1 50364239 307021496 6.096021742729002 8.139081043065298 NC_088862.1 37310742 270898811 7.260611729458503 9.051495637426802 NW_027062568.1 15579 103484 6.642531613068875 5.3051071266519285 NW_027062569.1 16498 105840 6.415323069462965 11.830793332550817 NW_027062570.1 4000 153647 38.41175 35.26300975792481 NW_027062571.1 36893 9956 0.26986149133982057 1.2912964570107568 NW_027062572.1 51000 52949 1.0382156862745098 1.8133424478407545 NW_027062573.1 2000 73499 36.7495 32.73316191952742 NW_027062574.1 37061 3244 0.0875313672054181 0.4264729382183629 NW_027062575.1 49428 222926 4.510115723881201 8.518523633995743 NW_027062576.1 49232 148066 3.007515437114072 4.940509580636208 NW_027062577.1 17087 109408 6.402996430034529 4.873973487874921 NW_027062578.1 34507 394952 11.445561770075637 6.6736305579090605 NW_027062579.1 64000 328116 5.1268125 7.0929025253682285 NW_027062580.1 24229 177913 7.3429774237484 7.41045529828344 NW_027062581.1 5000 20194 4.0388 6.737871616467621 NW_027062582.1 18808 53430 2.8408124202467033 3.466650431442664 NW_027062583.1 1000 0 0.0 0.0 NW_027062584.1 74000 9400 0.12702702702702703 0.7383448411520238 NW_027062585.1 39334 247058 6.281029135099405 5.848736812872598 NW_027062586.1 258015 440574 1.7075518865182258 4.526077076062791