BamQC report ----------------------------------- >>>>>>> Input bam file = zr3644_7.deduplicated.sorted.bam outfile = zr3644_7/genome_results.txt >>>>>>> Reference number of bases = 563,985,803 bp number of contigs = 29 >>>>>>> Globals number of windows = 428 number of reads = 91,564,948 number of mapped reads = 91,564,948 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 45,782,474 number of mapped paired reads (second in pair) = 45,782,474 number of mapped paired reads (both in pair) = 91,564,948 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 38,199,434 number of mapped bases = 9,693,946,403 bp number of sequenced bases = 9,650,153,482 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,360,886 duplication rate = 22.81% >>>>>>> Insert size mean insert size = 163.5316 std insert size = 72.752 median insert size = 141 >>>>>>> Mapping quality mean mapping quality = 24.554 >>>>>>> ACTG content number of A's = 3,963,529,394 bp (41.07%) number of C's = 848,526,519 bp (8.79%) number of T's = 4,002,039,155 bp (41.47%) number of G's = 835,984,342 bp (8.66%) number of N's = 74,072 bp (0%) GC percentage = 17.46% >>>>>>> Mismatches and indels general error rate = 0.1946 number of mismatches = 1,830,634,671 number of insertions = 20,734,897 mapped reads with insertion percentage = 17.11% number of deletions = 18,574,455 mapped reads with deletion percentage = 16.76% homopolymer indels = 49.01% >>>>>>> Coverage mean coverageData = 17.1883X std coverageData = 17.5892X paired-end adapted mean coverage = 12.3501X There is a 87.55% of reference with a coverageData >= 1X There is a 83.62% of reference with a coverageData >= 2X There is a 79.92% of reference with a coverageData >= 3X There is a 76.97% of reference with a coverageData >= 4X There is a 74.06% of reference with a coverageData >= 5X There is a 71.36% of reference with a coverageData >= 6X There is a 68.67% of reference with a coverageData >= 7X There is a 66.06% of reference with a coverageData >= 8X There is a 63.44% of reference with a coverageData >= 9X There is a 60.86% of reference with a coverageData >= 10X There is a 58.3% of reference with a coverageData >= 11X There is a 55.76% of reference with a coverageData >= 12X There is a 53.23% of reference with a coverageData >= 13X There is a 50.73% of reference with a coverageData >= 14X There is a 48.26% of reference with a coverageData >= 15X There is a 45.83% of reference with a coverageData >= 16X There is a 43.44% of reference with a coverageData >= 17X There is a 41.09% of reference with a coverageData >= 18X There is a 38.8% of reference with a coverageData >= 19X There is a 36.56% of reference with a coverageData >= 20X There is a 34.38% of reference with a coverageData >= 21X There is a 32.28% of reference with a coverageData >= 22X There is a 30.24% of reference with a coverageData >= 23X There is a 28.28% of reference with a coverageData >= 24X There is a 26.4% of reference with a coverageData >= 25X There is a 24.6% of reference with a coverageData >= 26X There is a 22.89% of reference with a coverageData >= 27X There is a 21.26% of reference with a coverageData >= 28X There is a 19.71% of reference with a coverageData >= 29X There is a 18.25% of reference with a coverageData >= 30X There is a 16.88% of reference with a coverageData >= 31X There is a 15.59% of reference with a coverageData >= 32X There is a 14.37% of reference with a coverageData >= 33X There is a 13.24% of reference with a coverageData >= 34X There is a 12.2% of reference with a coverageData >= 35X There is a 11.22% of reference with a coverageData >= 36X There is a 10.32% of reference with a coverageData >= 37X There is a 9.49% of reference with a coverageData >= 38X There is a 8.73% of reference with a coverageData >= 39X There is a 8.02% of reference with a coverageData >= 40X There is a 7.37% of reference with a coverageData >= 41X There is a 6.78% of reference with a coverageData >= 42X There is a 6.24% of reference with a coverageData >= 43X There is a 5.74% of reference with a coverageData >= 44X There is a 5.29% of reference with a coverageData >= 45X There is a 4.88% of reference with a coverageData >= 46X There is a 4.5% of reference with a coverageData >= 47X There is a 4.16% of reference with a coverageData >= 48X There is a 3.85% of reference with a coverageData >= 49X There is a 3.57% of reference with a coverageData >= 50X There is a 3.32% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_088853.1 76070991 1018795692 13.392696461651196 20.745202831619913 NC_088854.1 61469542 1187224246 19.314024594489414 16.418657434929095 NC_088855.1 61039741 1188066853 19.46382526426513 16.352796195172136 NC_088856.1 57946171 904507513 15.609444030391586 18.06779097323044 NC_088857.1 57274926 1067922586 18.645551562999838 16.555015057993057 NC_088858.1 56905015 1108439659 19.478769296519822 15.994913626153764 NC_088859.1 53672946 1080529829 20.131740653848215 16.326012075038665 NC_088860.1 51133819 893449836 17.472777380465168 17.93005949538894 NC_088861.1 50364239 669417087 13.291515970289952 16.605951891058268 NC_088862.1 37310742 569508932 15.263940127483929 17.289805680385083 NW_027062568.1 15579 215576 13.837601899993581 10.98010537046447 NW_027062569.1 16498 361426 21.907261486240756 22.962054305802607 NW_027062570.1 4000 363318 90.8295 76.18365989173793 NW_027062571.1 36893 15987 0.4333342368470984 1.9633581297276206 NW_027062572.1 51000 32651 0.6402156862745098 1.7668608971378248 NW_027062573.1 2000 199032 99.516 89.71069523752449 NW_027062574.1 37061 6959 0.1877715118318448 1.1235299158194565 NW_027062575.1 49428 641852 12.98559520919317 21.864600648562607 NW_027062576.1 49232 313136 6.36041598960026 11.93292831829437 NW_027062577.1 17087 244526 14.310645519985954 10.09209115323705 NW_027062578.1 34507 909516 26.357434723389456 12.81910519151391 NW_027062579.1 64000 732476 11.4449375 13.344545264723921 NW_027062580.1 24229 450979 18.613190804407942 16.25262113450134 NW_027062581.1 5000 26506 5.3012 12.367778135138098 NW_027062582.1 18808 238440 12.677584006805615 9.612681499040548 NW_027062583.1 1000 228 0.228 0.4195426080864731 NW_027062584.1 74000 22342 0.3019189189189189 1.5520003506396778 NW_027062585.1 39334 428552 10.895205166014135 10.020420175674367 NW_027062586.1 258015 880668 3.4132434160804603 9.897543473880608