[Genome] snps128

[Ann Zweig]

Hello Yu,

	We create the SNP128 track from data available through dbSNP at NCBI.  NCBI 
doesn't give avHet and avHetSE for most SNPs -- this page has an
explanation:

http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helpsnpfaq.section.Content.Heterozygosity_Data

click on the second question to expand the answer:
-----------------------------------------------------------------------
Q: We have sequenced a cDNA containing a base change that corresponds
to a SNP in the SNP database, yet dbSNP shows no heterozygosity data
for this SNP. Why is this?

We compute heterozygosity at dbSNP based on submitted allele frequency
for the SNP. In the case of an example SNP, say rs4779794, the
frequency data were not directly submitted, so we were unable to
compute the heterozygosity value.
-----------------------------------------------------------------------


Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu

Please feel free to search the Genome mailing list archives by visiting our home 
page, clicking on "Contact Us", then typing a word or phrase into the search 
box.  On that same page
(http://genome.ucsc.edu/contacts.html), you can subscribe to the Genome mailing 
list.




Yuan Jian wrote:
> Hi UCSC,
>    
>   I downloaded SNPs128 from UCSC. 
>   the most columns of avHet avHetSE are zero.
>   but I want to get a table with genotype frequency for all alleles.
>   which table should I download?
>    
>   Yu
>    
>    
> 
>        
> ---------------------------------
> You rock. That's why Blockbuster's offering you one month of Blockbuster Total Access, No Cost.
>        
> ---------------------------------
> You rock. That's why Blockbuster's offering you one month of Blockbuster Total Access, No Cost.
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome