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== Frequently asked Questions ==
== Frequently asked Questions ==
=== Effect allele ==
=== Effect allele ===
Q. Which allele is effect allele?
Q. Which allele is effect allele?
A. EMMAX simply follows the encoding scheme of .tped file in additive model. So whichever allele encoded as 1 in the .tped file, it will be the effect allele (usually the major allele)
A. EMMAX simply follows the encoding scheme of .tped file in additive model. So whichever allele encoded as 1 in the .tped file, it will be the effect allele (usually the major allele)
