BamQC report ----------------------------------- >>>>>>> Input bam file = CF03-CM04-Larvae.deduplicated.sorted.bam outfile = CF03-CM04-Larvae/genome_results.txt >>>>>>> Reference number of bases = 684,741,128 bp number of contigs = 11 >>>>>>> Globals number of windows = 410 number of reads = 12,497,048 number of mapped reads = 12,497,048 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,248,524 number of mapped paired reads (second in pair) = 6,248,524 number of mapped paired reads (both in pair) = 12,497,048 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 6,057,711 number of mapped bases = 1,364,700,291 bp number of sequenced bases = 1,362,818,250 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,482,034 duplication rate = 36.87% >>>>>>> Insert size mean insert size = 128.5759 std insert size = 69.336 median insert size = 112 >>>>>>> Mapping quality mean mapping quality = 19.2399 >>>>>>> ACTG content number of A's = 524,212,645 bp (38.47%) number of C's = 157,660,373 bp (11.57%) number of T's = 524,587,153 bp (38.49%) number of G's = 156,349,667 bp (11.47%) number of N's = 8,412 bp (0%) GC percentage = 23.04% >>>>>>> Mismatches and indels general error rate = 0.1958 number of mismatches = 265,604,614 number of insertions = 1,055,405 mapped reads with insertion percentage = 7.97% number of deletions = 1,374,899 mapped reads with deletion percentage = 10.49% homopolymer indels = 47.04% >>>>>>> Coverage mean coverageData = 1.993X std coverageData = 4.8055X paired-end adapted mean coverage = 1.1562X There is a 38.07% of reference with a coverageData >= 1X There is a 32.5% of reference with a coverageData >= 2X There is a 21.29% of reference with a coverageData >= 3X There is a 18.24% of reference with a coverageData >= 4X There is a 13.39% of reference with a coverageData >= 5X There is a 11.54% of reference with a coverageData >= 6X There is a 8.97% of reference with a coverageData >= 7X There is a 7.77% of reference with a coverageData >= 8X There is a 6.25% of reference with a coverageData >= 9X There is a 5.45% of reference with a coverageData >= 10X There is a 4.48% of reference with a coverageData >= 11X There is a 3.92% of reference with a coverageData >= 12X There is a 3.27% of reference with a coverageData >= 13X There is a 2.87% of reference with a coverageData >= 14X There is a 2.42% of reference with a coverageData >= 15X There is a 2.13% of reference with a coverageData >= 16X There is a 1.81% of reference with a coverageData >= 17X There is a 1.6% of reference with a coverageData >= 18X There is a 1.37% of reference with a coverageData >= 19X There is a 1.21% of reference with a coverageData >= 20X There is a 1.04% of reference with a coverageData >= 21X There is a 0.93% of reference with a coverageData >= 22X There is a 0.8% of reference with a coverageData >= 23X There is a 0.71% of reference with a coverageData >= 24X There is a 0.61% of reference with a coverageData >= 25X There is a 0.55% of reference with a coverageData >= 26X There is a 0.48% of reference with a coverageData >= 27X There is a 0.42% of reference with a coverageData >= 28X There is a 0.37% of reference with a coverageData >= 29X There is a 0.33% of reference with a coverageData >= 30X There is a 0.29% of reference with a coverageData >= 31X There is a 0.26% of reference with a coverageData >= 32X There is a 0.23% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.16% of reference with a coverageData >= 36X There is a 0.15% of reference with a coverageData >= 37X There is a 0.13% of reference with a coverageData >= 38X There is a 0.12% of reference with a coverageData >= 39X There is a 0.11% of reference with a coverageData >= 40X There is a 0.1% of reference with a coverageData >= 41X There is a 0.09% of reference with a coverageData >= 42X There is a 0.08% of reference with a coverageData >= 43X There is a 0.07% of reference with a coverageData >= 44X There is a 0.07% of reference with a coverageData >= 45X There is a 0.06% of reference with a coverageData >= 46X There is a 0.06% of reference with a coverageData >= 47X There is a 0.05% of reference with a coverageData >= 48X There is a 0.05% of reference with a coverageData >= 49X There is a 0.04% of reference with a coverageData >= 50X There is a 0.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_035780.1 65668440 156703835 2.3862883753596096 5.240210395089721 NC_035781.1 61752955 156347147 2.531816445059188 5.645397885522061 NC_035782.1 77061148 180819035 2.3464357811020413 5.41564504009954 NC_035783.1 59691872 155287635 2.601487100287289 5.085121823350083 NC_035784.1 98698416 259079766 2.624963768415493 5.448847403527244 NC_035785.1 51258098 72210392 1.4087606606082028 3.766582768421926 NC_035786.1 57830854 81622464 1.4113999423214467 3.637501605734701 NC_035787.1 75944018 113182133 1.4903363817279196 3.8312438373307036 NC_035788.1 104168038 140163229 1.3455492845127792 3.780168769597287 NC_035789.1 32650045 46643719 1.4285958564528778 3.851135012776738 NC_007175.2 17244 2640936 153.15100904662492 85.29188029819926