BamQC report ----------------------------------- >>>>>>> Input bam file = EF05-EM01-Larvae.deduplicated.sorted.bam outfile = EF05-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 = 8,495,260 number of mapped reads = 8,495,260 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,247,630 number of mapped paired reads (second in pair) = 4,247,630 number of mapped paired reads (both in pair) = 8,495,260 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 4,201,373 number of mapped bases = 932,576,887 bp number of sequenced bases = 931,183,388 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,774,639 duplication rate = 37.21% >>>>>>> Insert size mean insert size = 122.1592 std insert size = 55.0197 median insert size = 111 >>>>>>> Mapping quality mean mapping quality = 16.2567 >>>>>>> ACTG content number of A's = 350,270,349 bp (37.62%) number of C's = 115,312,274 bp (12.38%) number of T's = 351,313,896 bp (37.73%) number of G's = 114,281,740 bp (12.27%) number of N's = 5,129 bp (0%) GC percentage = 24.66% >>>>>>> Mismatches and indels general error rate = 0.1948 number of mismatches = 180,429,668 number of insertions = 769,294 mapped reads with insertion percentage = 8.66% number of deletions = 1,012,312 mapped reads with deletion percentage = 11.38% homopolymer indels = 44.16% >>>>>>> Coverage mean coverageData = 1.3619X std coverageData = 3.8018X paired-end adapted mean coverage = 0.7542X There is a 29.9% of reference with a coverageData >= 1X There is a 26.47% of reference with a coverageData >= 2X There is a 15.19% of reference with a coverageData >= 3X There is a 13.32% of reference with a coverageData >= 4X There is a 8.89% of reference with a coverageData >= 5X There is a 7.77% of reference with a coverageData >= 6X There is a 5.58% of reference with a coverageData >= 7X There is a 4.88% of reference with a coverageData >= 8X There is a 3.66% of reference with a coverageData >= 9X There is a 3.19% of reference with a coverageData >= 10X There is a 2.46% of reference with a coverageData >= 11X There is a 2.15% of reference with a coverageData >= 12X There is a 1.68% of reference with a coverageData >= 13X There is a 1.47% of reference with a coverageData >= 14X There is a 1.17% of reference with a coverageData >= 15X There is a 1.02% of reference with a coverageData >= 16X There is a 0.82% of reference with a coverageData >= 17X There is a 0.72% of reference with a coverageData >= 18X There is a 0.58% of reference with a coverageData >= 19X There is a 0.51% of reference with a coverageData >= 20X There is a 0.42% of reference with a coverageData >= 21X There is a 0.37% of reference with a coverageData >= 22X There is a 0.3% of reference with a coverageData >= 23X There is a 0.27% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.17% of reference with a coverageData >= 27X There is a 0.15% of reference with a coverageData >= 28X There is a 0.13% of reference with a coverageData >= 29X There is a 0.11% of reference with a coverageData >= 30X There is a 0.1% of reference with a coverageData >= 31X There is a 0.09% of reference with a coverageData >= 32X There is a 0.08% of reference with a coverageData >= 33X There is a 0.07% of reference with a coverageData >= 34X There is a 0.06% of reference with a coverageData >= 35X There is a 0.06% of reference with a coverageData >= 36X There is a 0.05% of reference with a coverageData >= 37X There is a 0.05% of reference with a coverageData >= 38X There is a 0.04% of reference with a coverageData >= 39X There is a 0.04% of reference with a coverageData >= 40X There is a 0.04% of reference with a coverageData >= 41X There is a 0.03% of reference with a coverageData >= 42X There is a 0.03% of reference with a coverageData >= 43X There is a 0.03% of reference with a coverageData >= 44X There is a 0.03% of reference with a coverageData >= 45X There is a 0.03% of reference with a coverageData >= 46X There is a 0.03% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_035780.1 65668440 105580198 1.6077768559752599 3.8494244876087644 NC_035781.1 61752955 107567017 1.741892626838667 4.059605827537944 NC_035782.1 77061148 121456105 1.5761003845932844 3.8916937728123524 NC_035783.1 59691872 105260994 1.7634058117661313 3.8448320798403133 NC_035784.1 98698416 177858192 1.8020369445442772 4.824343313464299 NC_035785.1 51258098 49063759 0.957190393603758 2.8022137694128677 NC_035786.1 57830854 56611069 0.9789077124816452 2.801476601474017 NC_035787.1 75944018 76313408 1.0048639775683188 2.9114394739772744 NC_035788.1 104168038 95996620 0.921555419907208 2.7982013585827894 NC_035789.1 32650045 33497397 1.0259525522859156 3.006637854329744 NC_007175.2 17244 3372128 195.5536998376247 109.00128616417354