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08-Results.Rmd
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# Results{-}
## Assembly{-}
### Stats{-}
Scaffolds = 694
Contigs = 694
Scaffold Length = 1,216,826,970
Contig Length = 1,216,826,970
Contig N50 = 28,813,006
Contig L50 = 17
Scaffold N50 = 28,813,006
Scaffold L50 = 17
Max scaffold size = 50,275,871
Min scaffold size = 14,196
#### C. variegatus{-}
Scaffolds = 1,139
Contigs = 1,139
Contig Length = 1,272,562,944
Scaffold Length = 1,272,562,944
Contig N50 = 26,363,765
Contig L50 = 17
Scaffold N50 = 26,363,765
Scaffold L50 = 17
Max scaffold size = 79,807,540
Min scaffold size = 10,992
#### C. desquamator{-}
Scaffolds = 694
Contigs = 694
Scaffold Length = 1,216,826,970
Contig Length = 1,216,826,970
Contig N50 = 28,813,006
Contig L50 = 17
Scaffold N50 = 28,813,006
Scaffold L50 = 17
Max scaffold size = 50,275,871
Min scaffold size = 14,196
#### C. brontotheroides{-}
Scaffolds = 1,121
Contigs = 1,121
Scaffold Length = 1,263,524,688
Contig Length = 1,263,524,688
Contig N50 = 27,861,740
Contig L50 = 17
Scaffold N50 = 27,861,740
Scaffold L50 = 17
Max scaffold size = 47,301,365
Min scaffold size = 12,425
### Busco (Benchmarking Universal Single-Copy Orthologue)
C:99.3%[S:97.7%,D:1.6%],F:0.5%,M:0.2%,n:954
947 Complete BUSCOs (C)
932 Complete and single-copy BUSCOs (S)
15 Complete and duplicated BUSCOs (D)
5 Fragmented BUSCOs (F)
2 Missing BUSCOs (M)
954 Total BUSCO groups searched
#### C. variegatus
C:99.1% [S:96.6%,D:2.5%],F:0.6%,M:0.3%,n:954
946 Complete BUSCOs (C)
922 Complete and single-copy BUSCOs (S)
24 Complete and duplicated BUSCOs (D)
6 Fragmented BUSCOs (F)
2 Missing BUSCOs (M)
954 Total BUSCO groups searched
#### C. desquamator
C:99.3% [S:97.7%,D:1.6%],F:0.5%,M:0.2%,n:954
947 Complete BUSCOs (C)
932 Complete and single-copy BUSCOs (S)
15 Complete and duplicated BUSCOs (D)
5 Fragmented BUSCOs (F).
2 Missing BUSCOs (M)
954 Total BUSCO groups searched
#### C. brontotheroides
C:99.3%[S:95.7%,D:3.6%],F:0.5%,M:0.2%,n:954
947 Complete BUSCOs (C)
913 Complete and single-copy BUSCOs (S)
34 Complete and duplicated BUSCOs (D)
5 Fragmented BUSCOs (F)
2 Missing BUSCOs (M)
954 Total BUSCO groups searched
Kat
Dotplots
## Annotation{-}
What we found:
How many genes
Quality
##dn/ds{-}
-We are not doing phased haplotypes
-Get this stuff into genbank at some point
-We should not do the reproductive genes