BamQC report ----------------------------------- >>>>>>> Input bam file = CF03-CM05-Larvae.deduplicated.sorted.bam outfile = CF03-CM05-Larvae/genome_results.txt >>>>>>> Reference number of bases = 684,741,128 bp number of contigs = 11 >>>>>>> Globals number of windows = 410 number of reads = 10,789,144 number of mapped reads = 10,789,144 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,394,572 number of mapped paired reads (second in pair) = 5,394,572 number of mapped paired reads (both in pair) = 10,789,144 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 5,336,229 number of mapped bases = 1,167,302,003 bp number of sequenced bases = 1,165,252,280 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,376,034 duplication rate = 34.54% >>>>>>> Insert size mean insert size = 119.9378 std insert size = 54.5839 median insert size = 109 >>>>>>> Mapping quality mean mapping quality = 15.0862 >>>>>>> ACTG content number of A's = 438,175,012 bp (37.6%) number of C's = 143,928,265 bp (12.35%) number of T's = 440,858,970 bp (37.83%) number of G's = 142,283,263 bp (12.21%) number of N's = 6,770 bp (0%) GC percentage = 24.56% >>>>>>> Mismatches and indels general error rate = 0.1943 number of mismatches = 225,468,810 number of insertions = 897,983 mapped reads with insertion percentage = 7.97% number of deletions = 1,526,180 mapped reads with deletion percentage = 13.39% homopolymer indels = 44.63% >>>>>>> Coverage mean coverageData = 1.7047X std coverageData = 4.6205X paired-end adapted mean coverage = 0.9404X There is a 32.79% of reference with a coverageData >= 1X There is a 29.26% of reference with a coverageData >= 2X There is a 17.69% of reference with a coverageData >= 3X There is a 15.67% of reference with a coverageData >= 4X There is a 10.99% of reference with a coverageData >= 5X There is a 9.74% of reference with a coverageData >= 6X There is a 7.34% of reference with a coverageData >= 7X There is a 6.52% of reference with a coverageData >= 8X There is a 5.13% of reference with a coverageData >= 9X There is a 4.57% of reference with a coverageData >= 10X There is a 3.7% of reference with a coverageData >= 11X There is a 3.3% of reference with a coverageData >= 12X There is a 2.72% of reference with a coverageData >= 13X There is a 2.43% of reference with a coverageData >= 14X There is a 2.03% of reference with a coverageData >= 15X There is a 1.82% of reference with a coverageData >= 16X There is a 1.53% of reference with a coverageData >= 17X There is a 1.37% of reference with a coverageData >= 18X There is a 1.17% of reference with a coverageData >= 19X There is a 1.05% of reference with a coverageData >= 20X There is a 0.89% of reference with a coverageData >= 21X There is a 0.8% of reference with a coverageData >= 22X There is a 0.69% of reference with a coverageData >= 23X There is a 0.62% of reference with a coverageData >= 24X There is a 0.53% of reference with a coverageData >= 25X There is a 0.48% of reference with a coverageData >= 26X There is a 0.42% of reference with a coverageData >= 27X There is a 0.37% of reference with a coverageData >= 28X There is a 0.33% of reference with a coverageData >= 29X There is a 0.29% of reference with a coverageData >= 30X There is a 0.26% of reference with a coverageData >= 31X There is a 0.23% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.16% of reference with a coverageData >= 35X There is a 0.15% of reference with a coverageData >= 36X There is a 0.13% of reference with a coverageData >= 37X There is a 0.12% of reference with a coverageData >= 38X There is a 0.11% of reference with a coverageData >= 39X There is a 0.1% of reference with a coverageData >= 40X There is a 0.09% of reference with a coverageData >= 41X There is a 0.08% of reference with a coverageData >= 42X There is a 0.07% of reference with a coverageData >= 43X There is a 0.07% of reference with a coverageData >= 44X There is a 0.06% of reference with a coverageData >= 45X There is a 0.06% of reference with a coverageData >= 46X There is a 0.05% of reference with a coverageData >= 47X There is a 0.05% of reference with a coverageData >= 48X There is a 0.04% 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 134034741 2.0410830682135894 4.954550854438541 NC_035781.1 61752955 133120575 2.155695626225498 5.41614396245594 NC_035782.1 77061148 156102237 2.025693115809798 5.174592494416778 NC_035783.1 59691872 133981040 2.244544114816838 4.949359711187162 NC_035784.1 98698416 222319952 2.2525179330132308 5.484373981531923 NC_035785.1 51258098 61684153 1.20340307984116 3.4564567471697436 NC_035786.1 57830854 69306637 1.198437031554125 3.3294898942091673 NC_035787.1 75944018 95486353 1.2573255341849308 3.719806738232796 NC_035788.1 104168038 117974947 1.1325445814770938 3.665962734574747 NC_035789.1 32650045 41052568 1.2573510388729938 3.7066987647804264 NC_007175.2 17244 2238800 129.8306657388077 79.15869664972645