Extended Data Fig. 10: Visualisation of sequence imputation allelic R-squared statistics by minor allele frequency, dominance effect sizes, and dominance p-values in the GWAS dataset.
From: Non-additive association analysis using proxy phenotypes identifies novel cattle syndromes
Plots showing imputation allelic R2 (AR2) values of genotypes from the discovery population, where AR2 is taken to reflect accuracy of imputation, representing the squared correlation between the allele dosage with the highest posterior probability and the true allele dosage35. a, Box plots showing distributions of AR2 within different MAF classes for the 16,128,757 sequence variants used for GWAS. Box plots show median (centre line), interquartile range (box limits), and upper and lower whiskers (maxima and minima data points). b, Plot showing absolute dominance effect size (Effect size, kg) for genome-wide significant variants (P < 5 × 10−8) from the bodyweight GWAS, visualised by AR2. Also indicated are the candidate causative mutations of interest; effects are expressed as allele substitutions and thus represent half the effect observed in homozygous mutant individuals c, Scatter/density plot showing relationship between P-value and AR2 for the sequence variants tested in the bodyweight GWAS (dominance model), with mutations of interest also indicated.
