[Genome] snps128

[Brooke Rhead]

Hi Yu,

You may also be interested in the information in the HapMap SNPs track, 
which contains about four million SNPs that were genotyped in four 
populations (click on the track name to read more details; also see: 
http://www.hapmap.org/).  This track contains allele frequency data for 
each of the four populations.

The tables that contain information on each of the populations are:

hapmapSnpsCEU
hapmapSnpsCHB
hapmapSnpsJPT
hapmapSnpsYRI

There is also a summary table:

hapmapAllelesSummary

The 'score' field of hapmapAllelesSummary is a calculation of 
heterozygosity over all four populations.  Note that this is not exactly 
the same as the average heterozygosity calculated by dbSNP (described 
here: http://www.ncbi.nlm.nih.gov/SNP/Hetfreq.html).  The heterozygosity 
calculated for the HapMap SNPs track is computed by UCSC as 2*p*q (*1000 
for bed scoring), where p is (allele1 / total) and q is (allele2 / 
total).  A score of 500 in the hapmapAllelesSummary.score field 
corresponds to a heterozygosity of 50%.

--
Brooke Rhead
UCSC Genome Bioinformatics Group


Ann Zweig wrote:
> 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 
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> 
> 
> 
> 
> 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
>>    
>>    
>>
>>        
>> ---------------------------------
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>>        
>> ---------------------------------
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