When you run a GWAS using FarmCPU via GAPIT or MVP, you get an 'effect' reported per SNP (a number somewhere around -1 to +1, with a bunch of outliers).
I've looked at the papers and the GAPIT forum but I'm not understanding what the effect itself reports. Is it the effect of the minor allele? The major allele? The entire SNP in the model? And is that effect measured in the same unit as the associated phenotype, i.e., if I have a plant height phenotype around 50 cm, does a SNP with an effect of +5 lead to a 5cm higher plant in the model?