certainty or so. We don't recommend these types of measures because they are not very meaningful when comparing markers with different allele frequencies (for example, if a marker has an allele frequency of <5%, it should be possible to achieve 90% accuracy by simply assigning the most common genotype to every individual). Instead, we typically recommend measures that try to capture the correlation between imputed genotype calls and the true underlying genotypes – typically expressed as an r2 coefficient. Most often these measures are calculated by comparing the variance in a set of imputed allele counts to theoretical expectations based on Hardy-Weinberg equilibrium (because imputed allele counts for poorly imputed markers show less variability than expected based on allele frequency).
