offers options for setting ploidy and genetic code (see figure 26.11
Figure 26.10: Ploidy and genetic code.
- Maximum expected alleles. This is not a filtering option but a reporting option that is related to the minimum variant frequency setting. If the frequency or count threshold is set low enough the algorithm can call more allelic variants than the ploidy number of the organism sequenced. For this reason, you can use the maximum expected variants setting to mark reported variants as "complex" when they involve more allelic variants then expected from the ploidy number. Note, that with this interpretation the "complex" flag holds true regardless of whether the sequencing data are generated from a population sample or from an individual sample (however, see below for an exception). For example, using a minimum variant frequency of 30% with a diploid organism, you are allowing variants with up to 3 different alleles within the sequencing reads, and by then setting the maximum expected variants count to 2 (the default), any variant with 3 different alleles will be marked as "complex" (see Reporting the SNVs).
- 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).