BamQC report ----------------------------------- >>>>>>> Input bam file = EF08-EM04-Larvae.deduplicated.sorted.bam outfile = EF08-EM04-Larvae/genome_results.txt >>>>>>> Reference number of bases = 684,741,128 bp number of contigs = 11 >>>>>>> Globals number of windows = 410 number of reads = 13,350,292 number of mapped reads = 13,350,292 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,675,146 number of mapped paired reads (second in pair) = 6,675,146 number of mapped paired reads (both in pair) = 13,350,292 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 6,651,158 number of mapped bases = 1,260,560,196 bp number of sequenced bases = 1,258,647,265 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,847,849 duplication rate = 40.79% >>>>>>> Insert size mean insert size = 100.1468 std insert size = 46.0439 median insert size = 91 >>>>>>> Mapping quality mean mapping quality = 17.4543 >>>>>>> ACTG content number of A's = 472,556,927 bp (37.54%) number of C's = 155,468,940 bp (12.35%) number of T's = 476,787,232 bp (37.88%) number of G's = 153,826,303 bp (12.22%) number of N's = 7,863 bp (0%) GC percentage = 24.57% >>>>>>> Mismatches and indels general error rate = 0.1927 number of mismatches = 241,598,250 number of insertions = 877,602 mapped reads with insertion percentage = 6.33% number of deletions = 1,443,244 mapped reads with deletion percentage = 10.34% homopolymer indels = 45.14% >>>>>>> Coverage mean coverageData = 1.8409X std coverageData = 4.7035X paired-end adapted mean coverage = 0.9741X There is a 33.77% of reference with a coverageData >= 1X There is a 31.49% of reference with a coverageData >= 2X There is a 18.69% of reference with a coverageData >= 3X There is a 17.3% of reference with a coverageData >= 4X There is a 11.8% of reference with a coverageData >= 5X There is a 10.88% of reference with a coverageData >= 6X There is a 7.97% of reference with a coverageData >= 7X There is a 7.33% of reference with a coverageData >= 8X There is a 5.62% of reference with a coverageData >= 9X There is a 5.17% of reference with a coverageData >= 10X There is a 4.07% of reference with a coverageData >= 11X There is a 3.75% of reference with a coverageData >= 12X There is a 3.01% of reference with a coverageData >= 13X There is a 2.77% of reference with a coverageData >= 14X There is a 2.26% of reference with a coverageData >= 15X There is a 2.07% of reference with a coverageData >= 16X There is a 1.71% of reference with a coverageData >= 17X There is a 1.57% of reference with a coverageData >= 18X There is a 1.31% of reference with a coverageData >= 19X There is a 1.2% of reference with a coverageData >= 20X There is a 1% of reference with a coverageData >= 21X There is a 0.92% of reference with a coverageData >= 22X There is a 0.77% of reference with a coverageData >= 23X There is a 0.71% of reference with a coverageData >= 24X There is a 0.6% of reference with a coverageData >= 25X There is a 0.55% of reference with a coverageData >= 26X There is a 0.47% of reference with a coverageData >= 27X There is a 0.43% of reference with a coverageData >= 28X There is a 0.37% of reference with a coverageData >= 29X There is a 0.34% 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 0.21% of reference with a coverageData >= 34X There is a 0.18% 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 0.13% 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 142812184 2.1747461033032 5.3104897772196225 NC_035781.1 61752955 147696152 2.3917260639592066 5.509149858119872 NC_035782.1 77061148 163989394 2.1280424475378954 5.127316340295258 NC_035783.1 59691872 140526977 2.354206230958882 4.943839968284182 NC_035784.1 98698416 243068215 2.462736737335278 5.738001522875152 NC_035785.1 51258098 67303289 1.3130274361721341 3.6764485478289277 NC_035786.1 57830854 76267216 1.3187980243210657 3.5224236044892394 NC_035787.1 75944018 103247724 1.3595241168303736 3.749200224247113 NC_035788.1 104168038 129660709 1.2447264198256283 3.5805771111527203 NC_035789.1 32650045 44413024 1.3602745111071057 3.855231666660096 NC_007175.2 17244 1575312 91.35421016005567 65.22607667036205