BamQC report ----------------------------------- >>>>>>> Input bam file = zr3644_8.deduplicated.sorted.bam outfile = zr3644_8/genome_results.txt >>>>>>> Reference number of bases = 563,985,803 bp number of contigs = 29 >>>>>>> Globals number of windows = 428 number of reads = 47,687,228 number of mapped reads = 47,687,228 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 23,843,614 number of mapped paired reads (second in pair) = 23,843,614 number of mapped paired reads (both in pair) = 47,687,228 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 20,262,065 number of mapped bases = 5,021,749,370 bp number of sequenced bases = 4,999,675,078 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,802,103 duplication rate = 14.86% >>>>>>> Insert size mean insert size = 159.561 std insert size = 69.8255 median insert size = 138 >>>>>>> Mapping quality mean mapping quality = 24.4578 >>>>>>> ACTG content number of A's = 2,049,153,486 bp (40.99%) number of C's = 444,177,632 bp (8.88%) number of T's = 2,068,685,298 bp (41.38%) number of G's = 437,620,458 bp (8.75%) number of N's = 38,204 bp (0%) GC percentage = 17.64% >>>>>>> Mismatches and indels general error rate = 0.195 number of mismatches = 950,354,570 number of insertions = 10,572,542 mapped reads with insertion percentage = 16.75% number of deletions = 9,315,821 mapped reads with deletion percentage = 16.16% homopolymer indels = 48.88% >>>>>>> Coverage mean coverageData = 8.904X std coverageData = 9.8652X paired-end adapted mean coverage = 6.3291X There is a 82.86% of reference with a coverageData >= 1X There is a 76.95% of reference with a coverageData >= 2X There is a 70.83% of reference with a coverageData >= 3X There is a 65.69% of reference with a coverageData >= 4X There is a 60.5% of reference with a coverageData >= 5X There is a 55.62% of reference with a coverageData >= 6X There is a 50.82% of reference with a coverageData >= 7X There is a 46.25% of reference with a coverageData >= 8X There is a 41.88% of reference with a coverageData >= 9X There is a 37.75% of reference with a coverageData >= 10X There is a 33.87% of reference with a coverageData >= 11X There is a 30.26% of reference with a coverageData >= 12X There is a 26.92% of reference with a coverageData >= 13X There is a 23.85% of reference with a coverageData >= 14X There is a 21.05% of reference with a coverageData >= 15X There is a 18.52% of reference with a coverageData >= 16X There is a 16.25% of reference with a coverageData >= 17X There is a 14.21% of reference with a coverageData >= 18X There is a 12.4% of reference with a coverageData >= 19X There is a 10.81% of reference with a coverageData >= 20X There is a 9.41% of reference with a coverageData >= 21X There is a 8.18% of reference with a coverageData >= 22X There is a 7.12% of reference with a coverageData >= 23X There is a 6.19% of reference with a coverageData >= 24X There is a 5.39% of reference with a coverageData >= 25X There is a 4.7% of reference with a coverageData >= 26X There is a 4.11% of reference with a coverageData >= 27X There is a 3.6% of reference with a coverageData >= 28X There is a 3.17% of reference with a coverageData >= 29X There is a 2.8% of reference with a coverageData >= 30X There is a 2.48% of reference with a coverageData >= 31X There is a 2.21% of reference with a coverageData >= 32X There is a 1.97% of reference with a coverageData >= 33X There is a 1.77% of reference with a coverageData >= 34X There is a 1.6% of reference with a coverageData >= 35X There is a 1.45% of reference with a coverageData >= 36X There is a 1.32% of reference with a coverageData >= 37X There is a 1.2% of reference with a coverageData >= 38X There is a 1.1% of reference with a coverageData >= 39X There is a 1.01% of reference with a coverageData >= 40X There is a 0.94% of reference with a coverageData >= 41X There is a 0.87% of reference with a coverageData >= 42X There is a 0.81% of reference with a coverageData >= 43X There is a 0.75% of reference with a coverageData >= 44X There is a 0.7% of reference with a coverageData >= 45X There is a 0.65% of reference with a coverageData >= 46X There is a 0.61% of reference with a coverageData >= 47X There is a 0.57% of reference with a coverageData >= 48X There is a 0.54% of reference with a coverageData >= 49X There is a 0.51% of reference with a coverageData >= 50X There is a 0.48% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_088853.1 76070991 528703598 6.95013422396456 11.089789297419536 NC_088854.1 61469542 616415594 10.027984168159248 9.23121676431541 NC_088855.1 61039741 613842652 10.056442605154567 9.111568078979527 NC_088856.1 57946171 469588741 8.103878701493494 10.124092900542733 NC_088857.1 57274926 554025945 9.673097526132116 9.327818592910392 NC_088858.1 56905015 573458449 10.077467671346717 9.111927272149435 NC_088859.1 53672946 564216776 10.512126090488866 10.46690306898803 NC_088860.1 51133819 459654761 8.989251536248446 9.85117380067342 NC_088861.1 50364239 345211210 6.854292189344904 9.294863642621245 NC_088862.1 37310742 293522387 7.86696729322617 9.437522874290213 NW_027062568.1 15579 95453 6.12702997625008 5.892118019396369 NW_027062569.1 16498 108565 6.580494605406716 13.204590917727845 NW_027062570.1 4000 179790 44.9475 35.899703463259975 NW_027062571.1 36893 6321 0.17133331526305803 0.734213014957534 NW_027062572.1 51000 38698 0.7587843137254902 2.027261801391285 NW_027062573.1 2000 113907 56.9535 43.699165338138904 NW_027062574.1 37061 5819 0.15701141361539084 0.525619533991958 NW_027062575.1 49428 297463 6.01810714574735 11.151087154388685 NW_027062576.1 49232 159420 3.238137796555086 7.723817752501683 NW_027062577.1 17087 127479 7.460584069760637 5.946897686886241 NW_027062578.1 34507 466427 13.516880632915061 7.5257886001603405 NW_027062579.1 64000 387035 6.047421875 7.632389670910615 NW_027062580.1 24229 99851 4.12113582896529 5.715798812882211 NW_027062581.1 5000 47535 9.507 10.983259197524204 NW_027062582.1 18808 149817 7.9655997447894515 9.27284859065927 NW_027062583.1 1000 0 0.0 0.0 NW_027062584.1 74000 13456 0.18183783783783783 1.191711814551166 NW_027062585.1 39334 219997 5.59304927035135 5.729762002099622 NW_027062586.1 258015 592224 2.2953084123016105 5.518101309251777