BamQC report ----------------------------------- >>>>>>> Input bam file = CF01-CM02-Larvae.deduplicated.sorted.bam outfile = CF01-CM02-Larvae/genome_results.txt >>>>>>> Reference number of bases = 684,741,128 bp number of contigs = 11 >>>>>>> Globals number of windows = 410 number of reads = 17,062,072 number of mapped reads = 17,062,072 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,531,036 number of mapped paired reads (second in pair) = 8,531,036 number of mapped paired reads (both in pair) = 17,062,072 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 8,504,529 number of mapped bases = 1,696,468,093 bp number of sequenced bases = 1,693,914,502 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,689,477 duplication rate = 41.79% >>>>>>> Insert size mean insert size = 105.2772 std insert size = 44.4523 median insert size = 97 >>>>>>> Mapping quality mean mapping quality = 18.6288 >>>>>>> ACTG content number of A's = 637,922,220 bp (37.66%) number of C's = 207,801,024 bp (12.27%) number of T's = 642,412,262 bp (37.92%) number of G's = 205,768,420 bp (12.15%) number of N's = 10,576 bp (0%) GC percentage = 24.42% >>>>>>> Mismatches and indels general error rate = 0.1929 number of mismatches = 325,488,513 number of insertions = 1,205,367 mapped reads with insertion percentage = 6.76% number of deletions = 1,932,135 mapped reads with deletion percentage = 10.83% homopolymer indels = 45.59% >>>>>>> Coverage mean coverageData = 2.4775X std coverageData = 6.0417X paired-end adapted mean coverage = 1.3091X There is a 37.59% of reference with a coverageData >= 1X There is a 35.36% of reference with a coverageData >= 2X There is a 22.95% of reference with a coverageData >= 3X There is a 21.49% of reference with a coverageData >= 4X There is a 15.66% of reference with a coverageData >= 5X There is a 14.62% of reference with a coverageData >= 6X There is a 11.29% of reference with a coverageData >= 7X There is a 10.53% of reference with a coverageData >= 8X There is a 8.42% of reference with a coverageData >= 9X There is a 7.84% of reference with a coverageData >= 10X There is a 6.43% of reference with a coverageData >= 11X There is a 5.98% of reference with a coverageData >= 12X There is a 4.98% of reference with a coverageData >= 13X There is a 4.63% of reference with a coverageData >= 14X There is a 3.91% of reference with a coverageData >= 15X There is a 3.63% of reference with a coverageData >= 16X There is a 3.09% of reference with a coverageData >= 17X There is a 2.87% of reference with a coverageData >= 18X There is a 2.46% of reference with a coverageData >= 19X There is a 2.28% of reference with a coverageData >= 20X There is a 1.96% of reference with a coverageData >= 21X There is a 1.82% of reference with a coverageData >= 22X There is a 1.57% of reference with a coverageData >= 23X There is a 1.45% of reference with a coverageData >= 24X There is a 1.26% of reference with a coverageData >= 25X There is a 1.17% of reference with a coverageData >= 26X There is a 1.01% of reference with a coverageData >= 27X There is a 0.94% of reference with a coverageData >= 28X There is a 0.82% of reference with a coverageData >= 29X There is a 0.75% of reference with a coverageData >= 30X There is a 0.66% of reference with a coverageData >= 31X There is a 0.61% of reference with a coverageData >= 32X There is a 0.53% of reference with a coverageData >= 33X There is a 0.49% of reference with a coverageData >= 34X There is a 0.43% of reference with a coverageData >= 35X There is a 0.4% of reference with a coverageData >= 36X There is a 0.35% of reference with a coverageData >= 37X There is a 0.32% of reference with a coverageData >= 38X There is a 0.28% of reference with a coverageData >= 39X There is a 0.26% of reference with a coverageData >= 40X There is a 0.23% of reference with a coverageData >= 41X There is a 0.21% of reference with a coverageData >= 42X There is a 0.19% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.13% of reference with a coverageData >= 47X There is a 0.12% of reference with a coverageData >= 48X There is a 0.11% 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_035780.1 65668440 193303626 2.943630547642064 6.713134560292448 NC_035781.1 61752955 196105445 3.1756447120627667 6.83394107705057 NC_035782.1 77061148 221999111 2.8808175943602605 6.491554866871701 NC_035783.1 59691872 190640250 3.1937388393515285 6.358140402229631 NC_035784.1 98698416 325306387 3.2959636049275605 7.148890442112241 NC_035785.1 51258098 89739682 1.7507415511203712 4.810241335549243 NC_035786.1 57830854 102143481 1.7662454197892357 4.703573106027836 NC_035787.1 75944018 140465176 1.8495884165623158 4.870307114365118 NC_035788.1 104168038 175301244 1.682869787755818 4.66624673238243 NC_035789.1 32650045 58082947 1.7789545772448399 4.8427525179758515 NC_007175.2 17244 3380744 196.05335189051263 102.35123528423645