Question on Minor allele Frequency in dbSNP135

ngarg · 02-06-2012, 10:55 AM

hi All,

I am looking at dbSNP135 data and I have a question. In cases where dbsnp records have GMAF(Global Minor Allele Frequency), G5 and G5A values reported, it is safe to assume that the alternate/observed allele is always the minor allele? The allele frequencies reported in dbsnp135 use the 1000G phase 1 population

It is slighly confusing as there are some examples on the web where reference allele is a minor allele and used for reporting minor allele frequency
Example can be found at this link:
[URL="http://biostar.stackexchange.com/questions/15272/list-of-dbsnp-variants-where-reference-genome-has-minor-allele"]

I have searched the dbsnp website, but there is no explicit info on if "ref/alt" is the minor allele

Thanks,
Nriti

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02-06-2012, 10:55 AM	#1
ngarg Junior Member Location: CA, USA Join Date: Sep 2009 Posts: 2	Question on Minor allele Frequency in dbSNP135 hi All, I am looking at dbSNP135 data and I have a question. In cases where dbsnp records have GMAF(Global Minor Allele Frequency), G5 and G5A values reported, it is safe to assume that the alternate/observed allele is always the minor allele? The allele frequencies reported in dbsnp135 use the 1000G phase 1 population It is slighly confusing as there are some examples on the web where reference allele is a minor allele and used for reporting minor allele frequency Example can be found at this link: [URL="http://biostar.stackexchange.com/questions/15272/list-of-dbsnp-variants-where-reference-genome-has-minor-allele"] I have searched the dbsnp website, but there is no explicit info on if "ref/alt" is the minor allele Thanks, Nriti