Our results highlight a number of general conclusions. First, when rare variants are discovered through re-sequencing, RVT1, based on the proportion of rare variants at which an individual carries minor alleles, is always at least as powerful as RVT2, based on the presence/absence of minor alleles. The difference in power between the two tests is most noticeable when the trait mean is determined by the proportion of causal variants at which a minor allele is present, which is not surprising, since this model is assumed by RVT1 (Supplementary Fig. 2). However, even when the trait mean is determined by the presence or absence of a minor allele at any causal variant, RVT1 is generally more powerful than RVT2. This would suggest that RVT2 is less robust to the presence of minor alleles at non-causal rare variants than is RVT1.
