Ambiguity codes/indels

[Wilding, Craig]

I hope that this is a suitable forum for this question. If submitting sequences of individuals derived from PCR products where there are heterozygous positions then ambiguity codes can be used for most such positions. However, what about where there is a heterozygous indel? It does not seem that there is a system to include such data and yet it would be incorrect to discount such a variable site by either labelling it as homozygous presence of the base or deleting the base altogether solely to get it into a format that is recognisable by Genbank.

Given that there is, as far as I am aware, no suitable ambiguity code for this can anyone suggest a way of submitting such data? These data are from multiple individuals and therefore could be submitted as individual sequences or as an alignment. I have emailed the helpdesk at EBI (data...@ebi.ac.uk) but received no reply. If there is a more suitable address to approach for advice then that would be welcome too.

With thanks for any suggestions,

Craig