Setting ploidy and genetic codeClicking Next offers options for setting ploidy and genetic code (see figure 31.12):
Figure 31.12: Ploidy and genetic code.
- Maximum expected alleles. This is the ploidy of your organism (or
actually "the maximum expected number of alleles"). If set to 1, only
homozygous alleles are reported even if another allele is present as well. For
cancer samples, which often have a lot of genome duplications, we recommend a
setting of 3. For polyploid organisms like plants, a setting of 4 should be used.
Genetic code. For the table report, the variant's effect on the protein level is calculated, and the translation table specified here is used. When reporting the variant as a track, this setting has no effect, since the amino acid consequences are calculated separately (see Amino acid changes).