We imputed a total of 31,326,389 markers (29,890,747 SNPs and 1,435,642 indels) and the majority (69%) of these had a MAF≤0.01. The average imputation quality score by minor frequency for each platform family is shown in Fig 2 and the distribution of imputation quality score for rare (MAF≤0.01) variants is shown in S1 Table. The imputation quality was very similar across all three datasets (S1–S3 Figs) with 49–51% of markers having an imputation quality score ≥0.3. When restricting to markers with MAF>0.01 (~10 million), 92–94% of the markers had a quality score ≥0.3, compared to 29–32% of markers with MAF≤0.01. After filtering markers based on MAF (>0.01) and imputation r-sq (≥0.3), approximately 9.8 million markers were available for analysis.
