BamQC report ----------------------------------- >>>>>>> Input bam file = CF06-CM02-Larvae.deduplicated.sorted.bam outfile = CF06-CM02-Larvae/genome_results.txt >>>>>>> Reference number of bases = 684,741,128 bp number of contigs = 11 >>>>>>> Globals number of windows = 410 number of reads = 5,873,698 number of mapped reads = 5,873,698 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,936,849 number of mapped paired reads (second in pair) = 2,936,849 number of mapped paired reads (both in pair) = 5,873,698 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 2,915,310 number of mapped bases = 614,149,593 bp number of sequenced bases = 613,125,269 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,635,416 duplication rate = 33.05% >>>>>>> Insert size mean insert size = 114.2239 std insert size = 51.8395 median insert size = 104 >>>>>>> Mapping quality mean mapping quality = 13.7499 >>>>>>> ACTG content number of A's = 233,058,633 bp (38.01%) number of C's = 72,944,587 bp (11.9%) number of T's = 235,273,410 bp (38.37%) number of G's = 71,845,139 bp (11.72%) number of N's = 3,500 bp (0%) GC percentage = 23.62% >>>>>>> Mismatches and indels general error rate = 0.1711 number of mismatches = 104,318,945 number of insertions = 508,807 mapped reads with insertion percentage = 8.34% number of deletions = 734,218 mapped reads with deletion percentage = 11.93% homopolymer indels = 42.75% >>>>>>> Coverage mean coverageData = 0.8969X std coverageData = 2.4092X paired-end adapted mean coverage = 0.4882X There is a 25.62% of reference with a coverageData >= 1X There is a 22.76% of reference with a coverageData >= 2X There is a 10.42% of reference with a coverageData >= 3X There is a 9% of reference with a coverageData >= 4X There is a 4.86% of reference with a coverageData >= 5X There is a 4.15% of reference with a coverageData >= 6X There is a 2.49% of reference with a coverageData >= 7X There is a 2.12% of reference with a coverageData >= 8X There is a 1.38% of reference with a coverageData >= 9X There is a 1.18% of reference with a coverageData >= 10X There is a 0.81% of reference with a coverageData >= 11X There is a 0.7% of reference with a coverageData >= 12X There is a 0.51% of reference with a coverageData >= 13X There is a 0.45% of reference with a coverageData >= 14X There is a 0.34% of reference with a coverageData >= 15X There is a 0.3% of reference with a coverageData >= 16X There is a 0.24% of reference with a coverageData >= 17X There is a 0.21% of reference with a coverageData >= 18X There is a 0.17% of reference with a coverageData >= 19X There is a 0.16% of reference with a coverageData >= 20X There is a 0.13% of reference with a coverageData >= 21X There is a 0.12% of reference with a coverageData >= 22X There is a 0.1% of reference with a coverageData >= 23X There is a 0.09% of reference with a coverageData >= 24X There is a 0.08% of reference with a coverageData >= 25X There is a 0.07% of reference with a coverageData >= 26X There is a 0.07% of reference with a coverageData >= 27X There is a 0.06% of reference with a coverageData >= 28X There is a 0.05% of reference with a coverageData >= 29X There is a 0.05% of reference with a coverageData >= 30X There is a 0.05% of reference with a coverageData >= 31X There is a 0.04% of reference with a coverageData >= 32X There is a 0.04% of reference with a coverageData >= 33X There is a 0.04% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.03% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.03% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_035780.1 65668440 67915266 1.034214700394893 2.4673431436460342 NC_035781.1 61752955 69542081 1.1261336562760438 2.719920237361825 NC_035782.1 77061148 80079383 1.0391667536538647 2.6027544359796826 NC_035783.1 59691872 69081504 1.1573016842226023 2.793134138429266 NC_035784.1 98698416 116392594 1.1792751972838145 2.692618832152348 NC_035785.1 51258098 32595637 0.6359119489763354 2.01021074188797 NC_035786.1 57830854 38435173 0.6646136161157157 2.15395017709138 NC_035787.1 75944018 50442077 0.6642007932738033 1.913319652865308 NC_035788.1 104168038 67051026 0.6436813756634256 2.0098235795067017 NC_035789.1 32650045 21707776 0.6648620545545956 1.9467794633697881 NC_007175.2 17244 907076 52.602412433310135 44.16184860833543