[ensembl-dev] variation synonyms

[Will McLaren]

Hi Andrea,

Aside from a little confusion over IDs here, I think what you are seeing is
a consequence of lag between dbSNP and Ensembl.

Ensembl has dbSNP version 130 for cow:

mysql> select name, version from source;
+-------+---------+
| name  | version |
+-------+---------+
| dbSNP |     130 |
+-------+---------+
1 row in set (0.00 sec)

What you see on dbSNP's website is version 131.

rs43654640 is given as having a position of 1955248; this is the same
position as was given for rs43654637 in version 130, hence they are merged.

It looks like the position for rs43654637 has now changed to 1955254, so
when we import dbSNP 131 they should appear as separate SNPs.

We merge SNPs based on positions (almost always provided to us by dbSNP); we
do not explicitly consider the flanking sequence here for speed.

Will

On 4 January 2011 15:40, Andrea Edwards <edwardsa at cs.man.ac.uk> wrote:

> Happy New Year esteemed bioinformaticians
>
> I have a question about variation synonyms
>
> As you know, 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
>
> Variation_id in ensembl (e!60_37e) = 2092683
> variation name = dbSNP id  = rs43654637
> This variation maps to 11[1955348] in dbSNP(v131) 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.Why are these 2 snps classed as
> synonyms?
>
> thanks a lot
>
>
>
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