BamQC report ----------------------------------- >>>>>>> Input bam file = EF06-EM02-Larvae.deduplicated.sorted.bam outfile = EF06-EM02-Larvae/genome_results.txt >>>>>>> Reference number of bases = 684,741,128 bp number of contigs = 11 >>>>>>> Globals number of windows = 410 number of reads = 11,759,718 number of mapped reads = 11,759,718 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,879,859 number of mapped paired reads (second in pair) = 5,879,859 number of mapped paired reads (both in pair) = 11,759,718 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 5,838,434 number of mapped bases = 1,214,420,347 bp number of sequenced bases = 1,212,396,453 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,895,189 duplication rate = 36.93% >>>>>>> Insert size mean insert size = 112.2018 std insert size = 50.9156 median insert size = 102 >>>>>>> Mapping quality mean mapping quality = 16.6311 >>>>>>> ACTG content number of A's = 456,783,875 bp (37.68%) number of C's = 148,693,155 bp (12.26%) number of T's = 459,994,916 bp (37.94%) number of G's = 146,917,523 bp (12.12%) number of N's = 6,984 bp (0%) GC percentage = 24.38% >>>>>>> Mismatches and indels general error rate = 0.1932 number of mismatches = 233,266,442 number of insertions = 893,723 mapped reads with insertion percentage = 7.29% number of deletions = 1,514,115 mapped reads with deletion percentage = 12.24% homopolymer indels = 44.84% >>>>>>> Coverage mean coverageData = 1.7735X std coverageData = 4.4935X paired-end adapted mean coverage = 0.9602X There is a 33.91% of reference with a coverageData >= 1X There is a 30.93% of reference with a coverageData >= 2X There is a 18.54% of reference with a coverageData >= 3X There is a 16.75% of reference with a coverageData >= 4X There is a 11.54% of reference with a coverageData >= 5X There is a 10.38% of reference with a coverageData >= 6X There is a 7.68% of reference with a coverageData >= 7X There is a 6.91% of reference with a coverageData >= 8X There is a 5.34% of reference with a coverageData >= 9X There is a 4.8% of reference with a coverageData >= 10X There is a 3.82% of reference with a coverageData >= 11X There is a 3.44% of reference with a coverageData >= 12X There is a 2.79% of reference with a coverageData >= 13X There is a 2.51% of reference with a coverageData >= 14X There is a 2.06% of reference with a coverageData >= 15X There is a 1.86% of reference with a coverageData >= 16X There is a 1.54% of reference with a coverageData >= 17X There is a 1.39% of reference with a coverageData >= 18X There is a 1.16% of reference with a coverageData >= 19X There is a 1.05% of reference with a coverageData >= 20X There is a 0.88% of reference with a coverageData >= 21X There is a 0.79% of reference with a coverageData >= 22X There is a 0.67% of reference with a coverageData >= 23X There is a 0.6% of reference with a coverageData >= 24X There is a 0.52% of reference with a coverageData >= 25X There is a 0.46% of reference with a coverageData >= 26X There is a 0.4% of reference with a coverageData >= 27X There is a 0.36% of reference with a coverageData >= 28X There is a 0.31% of reference with a coverageData >= 29X There is a 0.28% of reference with a coverageData >= 30X There is a 0.24% of reference with a coverageData >= 31X There is a 0.22% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.15% of reference with a coverageData >= 35X There is a 0.13% of reference with a coverageData >= 36X There is a 0.12% of reference with a coverageData >= 37X There is a 0.11% of reference with a coverageData >= 38X There is a 0.09% of reference with a coverageData >= 39X There is a 0.09% of reference with a coverageData >= 40X There is a 0.08% of reference with a coverageData >= 41X There is a 0.07% of reference with a coverageData >= 42X There is a 0.06% of reference with a coverageData >= 43X There is a 0.06% of reference with a coverageData >= 44X There is a 0.05% of reference with a coverageData >= 45X There is a 0.05% of reference with a coverageData >= 46X There is a 0.04% of reference with a coverageData >= 47X There is a 0.04% 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 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_035780.1 65668440 131182020 1.9976417895719771 4.575429908363844 NC_035781.1 61752955 137514175 2.2268436384947083 5.244615593099459 NC_035782.1 77061148 159958282 2.075731885022009 4.962740406552536 NC_035783.1 59691872 133661989 2.239199149257708 4.721067456504239 NC_035784.1 98698416 234700236 2.377953421258554 5.33713148771848 NC_035785.1 51258098 68217421 1.330861340192529 3.5649191877948447 NC_035786.1 57830854 79451099 1.3738531165387944 3.4526068085187216 NC_035787.1 75944018 96531730 1.2710906341563335 3.6282965789615513 NC_035788.1 104168038 129485289 1.2430424099952808 3.744172304789082 NC_035789.1 32650045 41624414 1.2748654404611082 3.447895660880866 NC_007175.2 17244 2093692 121.41568081651589 86.91611131244191