BamQC report ----------------------------------- >>>>>>> Input bam file = EF05-EM06-Larvae.deduplicated.sorted.bam outfile = EF05-EM06-Larvae/genome_results.txt >>>>>>> Reference number of bases = 684,741,128 bp number of contigs = 11 >>>>>>> Globals number of windows = 410 number of reads = 14,255,328 number of mapped reads = 14,255,328 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,127,664 number of mapped paired reads (second in pair) = 7,127,664 number of mapped paired reads (both in pair) = 14,255,328 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 6,592,371 number of mapped bases = 1,801,547,263 bp number of sequenced bases = 1,798,719,120 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,022,413 duplication rate = 27.84% >>>>>>> Insert size mean insert size = 165.3215 std insert size = 80.733 median insert size = 149 >>>>>>> Mapping quality mean mapping quality = 18.2568 >>>>>>> ACTG content number of A's = 693,190,989 bp (38.54%) number of C's = 207,059,578 bp (11.51%) number of T's = 692,585,596 bp (38.5%) number of G's = 205,873,392 bp (11.45%) number of N's = 9,565 bp (0%) GC percentage = 22.96% >>>>>>> Mismatches and indels general error rate = 0.1785 number of mismatches = 319,282,452 number of insertions = 1,482,620 mapped reads with insertion percentage = 9.76% number of deletions = 2,020,603 mapped reads with deletion percentage = 13.38% homopolymer indels = 46.16% >>>>>>> Coverage mean coverageData = 2.631X std coverageData = 5.2689X paired-end adapted mean coverage = 1.6736X There is a 48.43% of reference with a coverageData >= 1X There is a 40.33% of reference with a coverageData >= 2X There is a 29.35% of reference with a coverageData >= 3X There is a 24.44% of reference with a coverageData >= 4X There is a 19.05% of reference with a coverageData >= 5X There is a 15.95% of reference with a coverageData >= 6X There is a 12.85% of reference with a coverageData >= 7X There is a 10.83% of reference with a coverageData >= 8X There is a 8.89% of reference with a coverageData >= 9X There is a 7.53% of reference with a coverageData >= 10X There is a 6.26% of reference with a coverageData >= 11X There is a 5.33% of reference with a coverageData >= 12X There is a 4.46% of reference with a coverageData >= 13X There is a 3.81% of reference with a coverageData >= 14X There is a 3.21% of reference with a coverageData >= 15X There is a 2.75% of reference with a coverageData >= 16X There is a 2.33% of reference with a coverageData >= 17X There is a 2% of reference with a coverageData >= 18X There is a 1.7% of reference with a coverageData >= 19X There is a 1.46% of reference with a coverageData >= 20X There is a 1.25% of reference with a coverageData >= 21X There is a 1.08% of reference with a coverageData >= 22X There is a 0.93% of reference with a coverageData >= 23X There is a 0.8% of reference with a coverageData >= 24X There is a 0.69% of reference with a coverageData >= 25X There is a 0.6% of reference with a coverageData >= 26X There is a 0.52% of reference with a coverageData >= 27X There is a 0.46% of reference with a coverageData >= 28X There is a 0.4% of reference with a coverageData >= 29X There is a 0.35% of reference with a coverageData >= 30X There is a 0.31% of reference with a coverageData >= 31X There is a 0.27% of reference with a coverageData >= 32X There is a 0.24% of reference with a coverageData >= 33X There is a 0.21% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.15% of reference with a coverageData >= 37X There is a 0.14% 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 0.09% of reference with a coverageData >= 43X There is a 0.08% of reference with a coverageData >= 44X There is a 0.07% of reference with a coverageData >= 45X There is a 0.07% of reference with a coverageData >= 46X There is a 0.06% of reference with a coverageData >= 47X There is a 0.06% of reference with a coverageData >= 48X There is a 0.05% of reference with a coverageData >= 49X There is a 0.05% of reference with a coverageData >= 50X There is a 0.05% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_035780.1 65668440 191242414 2.912242380053493 5.265509826681816 NC_035781.1 61752955 193458017 3.1327734357003645 5.7429331098255405 NC_035782.1 77061148 221341982 2.872290223343156 5.642552468271032 NC_035783.1 59691872 201923454 3.3827629664554664 5.525442271285886 NC_035784.1 98698416 369627870 3.7450233243864828 6.278498178115162 NC_035785.1 51258098 98684583 1.9252486309577854 4.735618583022022 NC_035786.1 57830854 110016886 1.9023908241092202 4.351156805224683 NC_035787.1 75944018 157791923 2.0777399873680635 4.362071078941517 NC_035788.1 104168038 191546164 1.838818966716067 4.3553583681978765 NC_035789.1 32650045 63656864 1.9496715548171526 4.36658078384662 NC_007175.2 17244 2257106 130.8922523776386 65.37325726768975