[Genome] regarding file SNP126orthoPanTro2RheMac2.txt

[Brooke Rhead]

Hello Saurabh,

The humanAllele field in snp126orthoPanTro2RheMac2 shows the allele in 
the reference genome, and the humanObserved field are the observed 
alleles at that position from dbSNP.  However, there is an inconsistency 
in the table (which we plan to fix in the future): the humanAllele field 
  always shows the base in the reference genome on the + strand, 
regardless of the strand that is listed in the 'humanStrand' field.  See 
more details in this previously answered question:

http://www.soe.ucsc.edu/pipermail/genome/2007-April/013360.html

On the other hand, the chimpAllele field shows the base in the chimp 
reference genome from the + strand when the chimpStrand field is +, and 
from the - strand when the chimpStrand field is - (the same is true for 
macaqueAllele and macaqueStrand).

I hope this information helps.  Please let us know if you have further 
questions.

--
Brooke Rhead
UCSC Genome Bioinformatics Group



saurabh wrote:
> Hi,
> 
> I downloaded the file SNP126orthoPanTro2RheMac2.txt giving the ancestral
> state of SNPs. I wanted to know the difference between the fields "human
> observed" and "human allele". Sometimes the "human allele" is different from
> the "human observed" irrespective of the strand.
> Which of these two ("human observed" or the "human allele") should be
> matched with the chimp allele to make sure that chimp has atleast one of the
> alleles segregating in humans?
> 
> With many thanks,
> saurabh
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