Truncated rmpD allele?

[schorlton-bugseq]

Hi,

Thanks for your hard work this tool! I noticed that at least one of the rmpD alleles appears to be truncated at the first amino acid. Specifically, rmpD_4 starts with TGA AGG ..., which is a stop codon, while many of the other alleles start with GTG AAG G ... (note the leading G). Is this intentional? I think what this means in practice is that if an isolate has rmpD which matches closest to rmpD_4, it is identified as truncated with -0%, even if the isolate has an A or other base preceding the TGA AGG ..., which would lead to a valid start codon and protein translation. I have skimmed rmpA, rmpC and rmpA2 and didn't see similar cases, but it may be worth double checking.

Thanks for your help!