Hi
I will post this question to the ensembl mailing list but i thought i would try this forum too.
ensembl variation database has the concept of variation synonyms where, as the name suggests, database entries from different (or the same) source represent the same sequence variations and so the ids from the different sources are synonyms for the variation. However when i look at some snps and their synonyms i don't understand the why they are considered to be the same snp. I am only looking at snps and not other variants.
Example 1
Variationid in ensembl (e!6037e) = 2092683
dbSNP id (v132) = rs43654637
This variation maps to 11[1955348] in dbSNP and ensembl (i.e. there is a variation feature for this variation at 11[1955348])
There is one synonym for this snp. This synonym is in dbSNP with the id rs43654640 and genome mapping in dbSNP = 11[1955248])
The synonym maps to a different genome location (but i appreciate a variation in ensembl is defined by its location). Also The flanking sequence of rs4365460 is also different to rs43654637. I don't see how these 2 snps could be classed as synonyms
Example 2
rs41569419 and rs41603348 are synonyms for the same snp in cow variation database.
both snps are unmapped in dbsnp and have the same flanking sequence (but different alleles). I could see why these could be synonyms in ensembl as i think ensembl defines variations based on flanking sequence? I also wasn't sure why they hadn't been merged in dbSNP.
I have more examples but perhaps the answers to these 2 will answer those as well
Many thanks
Hi - the second link you provide is to a different question about variation sets, not this question. Thanks for posting a link to the answers though
Sorry Andrea, they appeared as part of the same thread - it would be great if you could repost any answers about the Watson GTF question back to BioStar as well, I was just trying not to leave unanswered questions laying around :)