[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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