Setting ploidy and genetic code
Clicking Next offers options for setting ploidy and genetic code (see figure 26.15:
Figure 26.15: Ploidy and genetic code.
- Maximum expected alleles. This is the ploidy of your organism or better the expected maximum number of expected alleles. If set to 1, only homozygote 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 polypoid organism 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 is calculated separately (see Amino acid changes).