The fixed-effects portion of the model was used for testing the association between a single SNP and BSA. The SNP was treated in R as a factor with three levels (categories), which is similar to coding the major homozygotes as 1/1, the heterozygotes as 0/1, and the minor homozygotes as 0/0. For each SNP, two tests were performed to determine if a given genotype class differed in its average phenotype from the other genotypes. The test compared (a) the major homozygotes (1/1) and the heterozygotes (0/1), and (b) the major homozygotes (1/1) and the minor homozygotes (0/0). Tests (a) and (b) were performed by testing the significance of the regression coefficients from zero, of the heterozygote term and the minor homozygote term, while holding the major homozygote coefficient constant at zero. For rare SNPs, minor homozygote individuals are often not present in the sample, in which case, only test (a) was available for the SNP. In all cases, the Wald test was used to examine the significance of the regression coefficients.
