BamQC report ----------------------------------- >>>>>>> Input bam file = CF08-CM05-Larvae.deduplicated.sorted.bam outfile = CF08-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 = 97,200 number of mapped reads = 97,200 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 48,600 number of mapped paired reads (second in pair) = 48,600 number of mapped paired reads (both in pair) = 97,200 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 43,539 number of mapped bases = 11,787,919 bp number of sequenced bases = 11,771,445 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,396 duplication rate = 22.44% >>>>>>> Insert size mean insert size = 166.1429 std insert size = 93.7268 median insert size = 147 >>>>>>> Mapping quality mean mapping quality = 18.1712 >>>>>>> ACTG content number of A's = 4,703,030 bp (39.95%) number of C's = 1,209,125 bp (10.27%) number of T's = 4,643,936 bp (39.45%) number of G's = 1,215,246 bp (10.32%) number of N's = 108 bp (0%) GC percentage = 20.6% >>>>>>> Mismatches and indels general error rate = 0.1895 number of mismatches = 2,214,398 number of insertions = 11,770 mapped reads with insertion percentage = 11.27% number of deletions = 11,642 mapped reads with deletion percentage = 11.38% homopolymer indels = 47.68% >>>>>>> Coverage mean coverageData = 0.0172X std coverageData = 0.1887X paired-end adapted mean coverage = 0.0113X There is a 1.06% of reference with a coverageData >= 1X There is a 0.59% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_035780.1 65668440 1323943 0.020161024077928455 0.19585153265303368 NC_035781.1 61752955 1272053 0.020599062830272657 0.19362095844908023 NC_035782.1 77061148 1451604 0.018837040943122208 0.18631115847719598 NC_035783.1 59691872 1289183 0.021597295524590016 0.20161692045549107 NC_035784.1 98698416 2145869 0.021741676178470788 0.1992790516644815 NC_035785.1 51258098 679859 0.013263445709593048 0.15982693174732845 NC_035786.1 57830854 781630 0.013515795564768939 0.21296322636030734 NC_035787.1 75944018 1008148 0.01327488361229452 0.15846004972047323 NC_035788.1 104168038 1302849 0.012507185745401099 0.15393211307438945 NC_035789.1 32650045 484848 0.014849841707721995 0.24497396042949096 NC_007175.2 17244 47933 2.779691486893992 2.58664398657469