[ensembl-dev] Can a SNP span 366bp ?

Will McLaren wm2 at ebi.ac.uk
Fri Jul 6 09:47:51 BST 2012


Hi Ben,

This variant has been flagged as failed:

http://www.ensembl.org/Homo_sapiens/Variation/Summary?source=dbSNP;v=rs11553164;vdb=variation

Check the failed_variation and failed_description tables in MySQL, or
use $v->get_all_failed_descriptions on a variation object.

Cheers

Will

On 6 July 2012 09:43, Benoît Ballester <benoit.ballester at inserm.fr> wrote:
> Hi,
>
> I am fetching variants for some slices using the API (v65).
> But for a given slice (22:24309259-24309271) I find this variant rs11553164 (T/C) which span 366bp !
>
> rs11553164      T/C     22      24309211        24309576        1       SNP     dbSNP   ESSENTIAL_SPLICE_SITE
>
> I am probably missing something obvious, but how come this SNP (T/C) can spread 366bp ?
> I would expect the usual 1bp, I find this is a bit confusing.
>
>
>
> #-- the same apply in v67
> anonymous at ensembldb.ensembl.org [homo_sapiens_variation_65_37]> SELECT  v.name, sq.name as chr, vf.seq_region_start, vf.seq_region_end FROM variation v, variation_feature vf, seq_region sq  WHERE v.variation_id=vf.variation_id  AND sq.seq_region_id = vf.seq_region_id AND v.name = "rs11553164";
> +------------+-----+------------------+----------------+
> | name       | chr | seq_region_start | seq_region_end |
> +------------+-----+------------------+----------------+
> | rs11553164 | 22  |         24309211 |       24309576 |
> | rs11553164 | 22  |         24316130 |       24316495 |
> +------------+-----+------------------+----------------+
>
>
> Thanks for the feedback,
>
> Ben
>
>
> --
> Benoît Ballester, PhD
> Inserm U1090, TAGC
> Marseille - France
> +33 4 91 82 87 39
>
>
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