[ensembl-dev] Dense SNP region in Mus_musculus.gvf?
Anja Thormann
anja at ebi.ac.uk
Tue Apr 23 10:35:36 BST 2013
Hello Zhaojun,
The region you are looking at is highly repetitive which makes variant calling difficult and which could be the reason
for many co-located variants. To answer your second question: There are no variants reported for the strains in the selected region.
Hope this helps.
Kind regards,
Anja
On 22 Apr 2013, at 20:17, Zhaojun Zhang wrote:
>
>
> Hi,
>
> I am working on the GVF database of Ensembl, recently. I downloaded the newest version of GVF file from the website.
>
> And I found out there is chromosome 14:19415857-19418930 is a very dense SNV region, and also several SNVs are located at the exact same location. Is it normal?
>
> You could use "head -n 28042193 Mus_musculus.gvf | tail -n 100" to check out the region.
>
> However, I could not see any variants in resequencing query:
>
> http://useast.ensembl.org/Mus_musculus/Location/SequenceAlignment?db=core;g=ENSMUSG00000095280;r=14:19415857-19418930;t=ENSMUST00000177817
>
> Best,
> Zhaojun.
>
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