Fig. 1

Metrics for the assessment of imputation quality and accuracy by individuals and by SNPs. The first upper panel depicts an example of a toy genotyping matrix containing the allelic doses, with markers in columns and individuals in rows. First two individuals correspond to complete genotypes from sequences; next two to sequences with masked positions to be imputed for quality assessment; and last individual to one genotype from the SNP array. The lower panel represents the two simplified genotyping matrices respectively with real and imputed genotypes. Associated boxes contain the different metrics that were used in the study: to the right and across markers (columns), the metrics by individual; at the bottom and across individuals (rows), it can be found the metrics by marker. The expressions for Prop-like metrics contain the following variables: gij the observed allelic dosage (0,1,2) of the SNP i in individual j; \(\hat {g}ij\) the imputed allelic dosage (0,1,2) from FImpute; M the total number of SNP; Ni the number of individuals with called genotypes for SNP i; p(AA)_refi, p(AB)_refi, and p(BB)_refi are the observed frequencies for genotypes AA, AB, and BB for SNP i in the reference and p(AA)_vali, p(AB)_vali, and p(BB)_vali are the predicted genotypic frequencies in the testing population for SNP i