Table 1.

NGS error rate and imputation error matrices

Real	Called (NGS)			Imputed
	RR	RA	AA	RR	RA	AA
RR	1 − λ/5	λ/5	0	1 − α	α/2	α/2
RA	λ	1 − 2λ	λ	α/2	1 − α	α/2
AA	0	λ/5	1 − λ/5	α/2	α/2	1 − α

R: reference allele; A: alternative allele; λ: base NGS genotyping error rate; α: imputation error rate. The Table shows the probability of a true genotype being called or imputed for each of the three possible genotypes; for instance, under this model, a true heterozygous genotype RA has a probability λ of being called as homozygous RR or AA and 2λ of being wrongly called.