[ensembl-dev] Allele table in Variation DB

[Will McLaren]

Hi Stuart,

Most of our data is imported from dbSNP, as is the case with this allele data.

I can only assume the C row is included in dbSNP for completeness
since there are other sample_ids that do have frequencies for C.

I agree though on the face of it there is not much point in the row
being there; we may look into deleting these rows.

Thanks

Will

On 16 May 2011 11:28, Stuart Meacham <sm766 at cam.ac.uk> wrote:
> Hi there,
>
> I was wondering why you get entries like this in the allele table:
>
> select allele_id, allele, frequency, count from allele where variation_id =
> 4843210 and subsnp_id = 231810106 and sample_id = 12131;
> +-----------+--------+-----------+-------+
> | allele_id | allele | frequency | count |
> +-----------+--------+-----------+-------+
> | 401222449 | A      |  0.558333 |    67 |
> | 401222450 | C      |  0        |    0  |
> | 401222451 | G      |  0.441667 |    53 |
> +-----------+--------+-----------+-------+
>
> What is the point of the C allele entry? What exactly does it mean?
>
> Cheers
>
> Stuart
>
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