[DAS] DAS and bacterial genomes

[Andy Jenkinson]

On 18 Aug 2010, at 20:47, Adam Witney wrote:
>> As mentioned elsewhere in this thread, the problem of distinguishing an individual from its taxon is not limited to bacteria. Does  the 1000 genomes project use the assembly as a surrogate for isolate/individual? 
> 
> No it's not unique to bacteria, indeed I notice that Plasmodium vivax is already in the DAS registry, does this not suffer the same problems? i.e which strain are the coordinates referring to?

So far a coordinate system always refers to the species or strain identified by its taxonomy ID. As you say, strains DO have their own NCBI taxonomy ID. It may be that this is not the case for a strain that someone wants to annotate, but I have yet to see an actual example. There is the wider question of how to handle individuals though. I can't comment on how 1000 genomes do this as I've only seen these data expressed as variations annotated upon the reference assembly, but my feeling is that if annotations of an individual were needed then it could/would be done using the assembly paradigm as a surrogate.