Two contrasts were examined, each with the Wald test: the major homozygote (Hom1) against the heterozygote (Het); and the major homozygote against the minor homozygote (Hom2). Statistical tests were reduced by only testing markers with an MAF>1% and eliminating the Hom2 against the Het as the power of these tests is very low due to small numbers in one of the genotype classes. FDR q-values were calculated using the method of Storey and Tibshirani [54].
