[Genome] query regarding chimp alleles

[Brooke Rhead]

Hello Aradhita,

The reference alleles for human SNPs are taken from the same strand as 
the SNPs.  Most of the SNPs in SNP 128 on human are on the positive 
strand (About 10.6 million + strand SNPs vs. 1.6 million - strand SNPs), 
so most alleles reported will be from the + strand.  If you have found 
cases where this does not appear to be true, please send us an example, 
and we can look for an explanation.

The same is logic is used for displaying chimp alleles: the allele 
reported is talem from the strand reported.  So, if an allele is given 
as G for both human and chimp, the allele is conserved, regardless of 
the strand on which the allele resides.

--
Brooke Rhead
UCSC Genome Bioinformatics Group


Aradhita Baral wrote:
> Hello
> I have a query regarding the allele given for chimp in the database.I
> understand that the UCSC allele given for human SNP, belongs to the +ve
strand,irrespective of the SNP strand.Is it the same case for Chimp.For
example if an allele is given as G for both human and chimp but strands
are different,then is the allele conserved or is there a change.
  thanks and regards
> Aradhita Baral
> senior Research Fellow
> Institute of Genomics and Integrative Biology
> New Delhi
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