BamQC report ----------------------------------- >>>>>>> Input bam file = zr3644_14.deduplicated.sorted.bam outfile = zr3644_14/genome_results.txt >>>>>>> Reference number of bases = 563,985,803 bp number of contigs = 29 >>>>>>> Globals number of windows = 428 number of reads = 23,667,126 number of mapped reads = 23,667,126 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 11,833,563 number of mapped paired reads (second in pair) = 11,833,563 number of mapped paired reads (both in pair) = 23,667,126 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 10,273,369 number of mapped bases = 2,468,414,378 bp number of sequenced bases = 2,466,448,296 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,081,576 duplication rate = 11.9% >>>>>>> Insert size mean insert size = 154.1074 std insert size = 67.3873 median insert size = 131 >>>>>>> Mapping quality mean mapping quality = 24.924 >>>>>>> ACTG content number of A's = 1,005,675,942 bp (40.77%) number of C's = 223,711,609 bp (9.07%) number of T's = 1,016,869,208 bp (41.23%) number of G's = 220,178,327 bp (8.93%) number of N's = 13,210 bp (0%) GC percentage = 18% >>>>>>> Mismatches and indels general error rate = 0.1769 number of mismatches = 435,138,341 number of insertions = 1,073,462 mapped reads with insertion percentage = 4.43% number of deletions = 1,477,032 mapped reads with deletion percentage = 6.08% homopolymer indels = 51.78% >>>>>>> Coverage mean coverageData = 4.3767X std coverageData = 6.5695X paired-end adapted mean coverage = 3.0589X There is a 60.7% of reference with a coverageData >= 1X There is a 53.3% of reference with a coverageData >= 2X There is a 45.38% of reference with a coverageData >= 3X There is a 39.82% of reference with a coverageData >= 4X There is a 34.36% of reference with a coverageData >= 5X There is a 29.84% of reference with a coverageData >= 6X There is a 25.67% of reference with a coverageData >= 7X There is a 22.09% of reference with a coverageData >= 8X There is a 18.89% of reference with a coverageData >= 9X There is a 16.13% of reference with a coverageData >= 10X There is a 13.7% of reference with a coverageData >= 11X There is a 11.62% of reference with a coverageData >= 12X There is a 9.81% of reference with a coverageData >= 13X There is a 8.27% of reference with a coverageData >= 14X There is a 6.96% of reference with a coverageData >= 15X There is a 5.84% of reference with a coverageData >= 16X There is a 4.89% of reference with a coverageData >= 17X There is a 4.1% of reference with a coverageData >= 18X There is a 3.43% of reference with a coverageData >= 19X There is a 2.86% of reference with a coverageData >= 20X There is a 2.4% of reference with a coverageData >= 21X There is a 2.01% of reference with a coverageData >= 22X There is a 1.69% of reference with a coverageData >= 23X There is a 1.42% of reference with a coverageData >= 24X There is a 1.2% of reference with a coverageData >= 25X There is a 1.02% of reference with a coverageData >= 26X There is a 0.88% of reference with a coverageData >= 27X There is a 0.75% of reference with a coverageData >= 28X There is a 0.65% of reference with a coverageData >= 29X There is a 0.57% of reference with a coverageData >= 30X There is a 0.5% of reference with a coverageData >= 31X There is a 0.44% of reference with a coverageData >= 32X There is a 0.39% of reference with a coverageData >= 33X There is a 0.35% of reference with a coverageData >= 34X There is a 0.32% of reference with a coverageData >= 35X There is a 0.29% of reference with a coverageData >= 36X There is a 0.26% of reference with a coverageData >= 37X There is a 0.24% of reference with a coverageData >= 38X There is a 0.22% of reference with a coverageData >= 39X There is a 0.2% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.14% of reference with a coverageData >= 45X There is a 0.13% of reference with a coverageData >= 46X There is a 0.12% of reference with a coverageData >= 47X There is a 0.11% of reference with a coverageData >= 48X There is a 0.1% of reference with a coverageData >= 49X There is a 0.1% of reference with a coverageData >= 50X There is a 0.09% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_088853.1 76070991 238273199 3.132247863052027 6.8116918663685455 NC_088854.1 61469542 324014708 5.271142381376455 7.440611284343609 NC_088855.1 61039741 315200670 5.163859885971665 6.397287440876708 NC_088856.1 57946171 219985476 3.796376399054909 6.010985349532148 NC_088857.1 57274926 285265338 4.980632153064676 6.6912505524942425 NC_088858.1 56905015 293137327 5.151344341091906 6.508052420067968 NC_088859.1 53672946 291140975 5.424352428875434 6.39994301282677 NC_088860.1 51133819 225374232 4.407537641575334 6.476433024331885 NC_088861.1 50364239 149715192 2.9726487478546035 5.6049392232346555 NC_088862.1 37310742 125185550 3.355214699294911 6.1603374851445905 NW_027062568.1 15579 40503 2.599845946466397 4.012614283998418 NW_027062569.1 16498 11564 0.700933446478361 2.364484675765536 NW_027062570.1 4000 17786 4.4465 5.07240739195897 NW_027062571.1 36893 0 0.0 0.0 NW_027062572.1 51000 1495 0.029313725490196077 0.21923634105928042 NW_027062573.1 2000 19937 9.9685 8.092023866128917 NW_027062574.1 37061 1032 0.02784598364857937 0.2010906816721151 NW_027062575.1 49428 80973 1.6382010196649672 4.095686239820121 NW_027062576.1 49232 79885 1.6226234969125772 4.5753688243078505 NW_027062577.1 17087 31746 1.8579036694563118 2.855765320631778 NW_027062578.1 34507 270241 7.831483467122613 6.809251129784163 NW_027062579.1 64000 87934 1.37396875 3.6115473841294814 NW_027062580.1 24229 93364 3.8533988195963516 5.7060789565844985 NW_027062581.1 5000 5441 1.0882 2.7633776506297507 NW_027062582.1 18808 73741 3.9207252233092302 4.181410802416457 NW_027062583.1 1000 0 0.0 0.0 NW_027062584.1 74000 1949 0.026337837837837837 0.31797018612164757 NW_027062585.1 39334 109751 2.7902323689428994 4.071315880411016 NW_027062586.1 258015 194369 0.7533244191229193 5.6389542975318605