BamQC report ----------------------------------- >>>>>>> Input bam file = CF05-CM02-Larvae.deduplicated.sorted.bam outfile = CF05-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 = 19,933,186 number of mapped reads = 19,933,186 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,966,593 number of mapped paired reads (second in pair) = 9,966,593 number of mapped paired reads (both in pair) = 19,933,186 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 9,881,118 number of mapped bases = 2,083,902,347 bp number of sequenced bases = 2,081,262,041 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,682,227 duplication rate = 39.87% >>>>>>> Insert size mean insert size = 114.4094 std insert size = 52.4953 median insert size = 104 >>>>>>> Mapping quality mean mapping quality = 19.0647 >>>>>>> ACTG content number of A's = 789,007,520 bp (37.91%) number of C's = 250,447,684 bp (12.03%) number of T's = 793,737,965 bp (38.14%) number of G's = 248,057,816 bp (11.92%) number of N's = 11,056 bp (0%) GC percentage = 23.95% >>>>>>> Mismatches and indels general error rate = 0.1959 number of mismatches = 406,066,835 number of insertions = 1,485,954 mapped reads with insertion percentage = 7.1% number of deletions = 1,957,758 mapped reads with deletion percentage = 9.43% homopolymer indels = 46.16% >>>>>>> Coverage mean coverageData = 3.0433X std coverageData = 7.3929X paired-end adapted mean coverage = 1.6585X There is a 41.75% of reference with a coverageData >= 1X There is a 38.32% of reference with a coverageData >= 2X There is a 26.49% of reference with a coverageData >= 3X There is a 24.27% of reference with a coverageData >= 4X There is a 18.64% of reference with a coverageData >= 5X There is a 17.08% of reference with a coverageData >= 6X There is a 13.81% of reference with a coverageData >= 7X There is a 12.68% of reference with a coverageData >= 8X There is a 10.58% of reference with a coverageData >= 9X There is a 9.72% of reference with a coverageData >= 10X There is a 8.28% of reference with a coverageData >= 11X There is a 7.62% of reference with a coverageData >= 12X There is a 6.58% of reference with a coverageData >= 13X There is a 6.07% of reference with a coverageData >= 14X There is a 5.3% of reference with a coverageData >= 15X There is a 4.9% of reference with a coverageData >= 16X There is a 4.31% of reference with a coverageData >= 17X There is a 3.98% of reference with a coverageData >= 18X There is a 3.53% of reference with a coverageData >= 19X There is a 3.26% of reference with a coverageData >= 20X There is a 2.91% of reference with a coverageData >= 21X There is a 2.69% of reference with a coverageData >= 22X There is a 2.41% of reference with a coverageData >= 23X There is a 2.23% of reference with a coverageData >= 24X There is a 2% of reference with a coverageData >= 25X There is a 1.85% of reference with a coverageData >= 26X There is a 1.67% of reference with a coverageData >= 27X There is a 1.54% of reference with a coverageData >= 28X There is a 1.39% of reference with a coverageData >= 29X There is a 1.29% of reference with a coverageData >= 30X There is a 1.16% of reference with a coverageData >= 31X There is a 1.08% of reference with a coverageData >= 32X There is a 0.98% of reference with a coverageData >= 33X There is a 0.9% of reference with a coverageData >= 34X There is a 0.82% of reference with a coverageData >= 35X There is a 0.76% of reference with a coverageData >= 36X There is a 0.69% of reference with a coverageData >= 37X There is a 0.64% of reference with a coverageData >= 38X There is a 0.58% of reference with a coverageData >= 39X There is a 0.54% of reference with a coverageData >= 40X There is a 0.49% of reference with a coverageData >= 41X There is a 0.45% of reference with a coverageData >= 42X There is a 0.41% of reference with a coverageData >= 43X There is a 0.38% of reference with a coverageData >= 44X There is a 0.35% of reference with a coverageData >= 45X There is a 0.32% of reference with a coverageData >= 46X There is a 0.3% of reference with a coverageData >= 47X There is a 0.27% of reference with a coverageData >= 48X There is a 0.25% of reference with a coverageData >= 49X There is a 0.23% of reference with a coverageData >= 50X There is a 0.22% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_035780.1 65668440 236177968 3.596521677688704 8.271987461393428 NC_035781.1 61752955 234394457 3.795680012397787 8.746889761859245 NC_035782.1 77061148 264512428 3.4325004864967754 8.35415287914923 NC_035783.1 59691872 229196485 3.839659861898786 7.736782535384993 NC_035784.1 98698416 390946472 3.9610207320855078 8.432260880404217 NC_035785.1 51258098 112984813 2.204233426687038 5.848006268859458 NC_035786.1 57830854 130471559 2.2560890938944116 5.780982685516675 NC_035787.1 75944018 178533545 2.350857245925545 6.081594074910541 NC_035788.1 104168038 231317631 2.2206200235815134 6.1103929192623045 NC_035789.1 32650045 73524740 2.2519031750185947 6.088790873747501 NC_007175.2 17244 1842249 106.83420320111343 64.58813377014796