Hi @iskander , thanks for reaching out!
* in the codon notation is a stop codon, not a “nonsense mutation”. Every possible combination of nucleotides in a codon codes either for an amino-acid or or a stop codon.
X is the character used to designate that the codon cannot be translated, but this is because there’s a gap which isn’t ‘in-frame’ (doesn’t line up with the 3-bases that make an amino-acid).
If the nucleotide gaps do line up, the AA will show
- just like for nucleotides.
X here means there’s some kind of deletion in the nucleotides. NextClade doesn’t currently use amino-acid aware alignment, so it’s very possible the deletion is ‘in-frame’ but we haven’t aligned it right. You’d need to look back to the sequence at this position to figure out if that’s the case, or if it’s a deletion that can’t be aligned ‘in-frame’. However, we’re working hard on a better algorithm for this!
I hope this helps!