BamQC report ----------------------------------- >>>>>>> Input bam file = EF06-EM01-Larvae.deduplicated.sorted.bam outfile = EF06-EM01-Larvae/genome_results.txt >>>>>>> Reference number of bases = 684,741,128 bp number of contigs = 11 >>>>>>> Globals number of windows = 410 number of reads = 16,759,160 number of mapped reads = 16,759,160 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,379,580 number of mapped paired reads (second in pair) = 8,379,580 number of mapped paired reads (both in pair) = 16,759,160 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 8,163,622 number of mapped bases = 1,851,881,581 bp number of sequenced bases = 1,849,378,426 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,630,883 duplication rate = 34.62% >>>>>>> Insert size mean insert size = 128.0221 std insert size = 65.0106 median insert size = 113 >>>>>>> Mapping quality mean mapping quality = 19.543 >>>>>>> ACTG content number of A's = 710,186,209 bp (38.4%) number of C's = 214,332,868 bp (11.59%) number of T's = 712,663,027 bp (38.54%) number of G's = 212,186,233 bp (11.47%) number of N's = 10,089 bp (0%) GC percentage = 23.06% >>>>>>> Mismatches and indels general error rate = 0.1928 number of mismatches = 354,910,716 number of insertions = 1,357,995 mapped reads with insertion percentage = 7.67% number of deletions = 1,838,987 mapped reads with deletion percentage = 10.48% homopolymer indels = 46.41% >>>>>>> Coverage mean coverageData = 2.7045X std coverageData = 6.0894X paired-end adapted mean coverage = 1.5482X There is a 44.33% of reference with a coverageData >= 1X There is a 38.88% of reference with a coverageData >= 2X There is a 27.11% of reference with a coverageData >= 3X There is a 23.72% of reference with a coverageData >= 4X There is a 18.17% of reference with a coverageData >= 5X There is a 15.94% of reference with a coverageData >= 6X There is a 12.8% of reference with a coverageData >= 7X There is a 11.27% of reference with a coverageData >= 8X There is a 9.3% of reference with a coverageData >= 9X There is a 8.23% of reference with a coverageData >= 10X There is a 6.92% of reference with a coverageData >= 11X There is a 6.15% of reference with a coverageData >= 12X There is a 5.23% of reference with a coverageData >= 13X There is a 4.66% of reference with a coverageData >= 14X There is a 4% of reference with a coverageData >= 15X There is a 3.57% of reference with a coverageData >= 16X There is a 3.08% of reference with a coverageData >= 17X There is a 2.76% of reference with a coverageData >= 18X There is a 2.4% of reference with a coverageData >= 19X There is a 2.14% of reference with a coverageData >= 20X There is a 1.87% of reference with a coverageData >= 21X There is a 1.68% of reference with a coverageData >= 22X There is a 1.47% of reference with a coverageData >= 23X There is a 1.31% of reference with a coverageData >= 24X There is a 1.16% of reference with a coverageData >= 25X There is a 1.04% of reference with a coverageData >= 26X There is a 0.91% of reference with a coverageData >= 27X There is a 0.82% of reference with a coverageData >= 28X There is a 0.72% of reference with a coverageData >= 29X There is a 0.65% of reference with a coverageData >= 30X There is a 0.57% of reference with a coverageData >= 31X There is a 0.52% of reference with a coverageData >= 32X There is a 0.46% of reference with a coverageData >= 33X There is a 0.41% of reference with a coverageData >= 34X There is a 0.37% of reference with a coverageData >= 35X There is a 0.33% of reference with a coverageData >= 36X There is a 0.29% of reference with a coverageData >= 37X There is a 0.26% of reference with a coverageData >= 38X There is a 0.24% of reference with a coverageData >= 39X There is a 0.21% of reference with a coverageData >= 40X There is a 0.19% 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 0.14% of reference with a coverageData >= 44X There is a 0.13% of reference with a coverageData >= 45X There is a 0.12% of reference with a coverageData >= 46X There is a 0.11% of reference with a coverageData >= 47X There is a 0.1% of reference with a coverageData >= 48X There is a 0.09% of reference with a coverageData >= 49X There is a 0.08% of reference with a coverageData >= 50X There is a 0.08% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_035780.1 65668440 201051366 3.0616132498350805 6.228237219973574 NC_035781.1 61752955 205757054 3.3319385930600407 7.050303149573522 NC_035782.1 77061148 238418213 3.0938834832826525 6.834986574698584 NC_035783.1 59691872 201252434 3.3715215699718715 6.343436700616221 NC_035784.1 98698416 349364604 3.5397184489769318 7.164675031098217 NC_035785.1 51258098 103261503 2.014540278103959 4.764660567816696 NC_035786.1 57830854 120224246 2.0788945292075405 4.658661032323908 NC_035787.1 75944018 149473656 1.9682084242632514 4.897524400527068 NC_035788.1 104168038 208147211 1.9981869198688373 5.434180933034532 NC_035789.1 32650045 73003276 2.2359318647187165 5.086482398760807 NC_007175.2 17244 1928018 111.80804917652517 55.388553192225196