Table 1.

Estimates of imputation accuracy for all four VNTRs (and one moderating SNP) using the FTP and CADD/GADD datasets as reference panels for one another. Here, we restricted comparisons to imputed genotypes with probabilities of at least 0.99. See Supplemental Table 1–6 for full details on each locus

Locus	Target	Reference	True risk variant freq.	Minimac3 INFO score	Imputed risk variant freq.	Empirical r2	Genotype match rate
DRD4 VNTR	CADD/GADD	FTP	0.207	0.913	0.182	0.961	0.988
DRD4 VNTR	FTP	CADD/GADD	0.198	0.973	0.174	0.977	0.993
MAOA VNTR females	CADD/GADD	FTP	0.392	0.965	0.396	0.642	0.838
MAOA VNTR females	FTP	CADD/GADD	0.352	0.946	0.340	0.959	0.981
MAOA VNTR males	CADD/GADD	FTP	0.177	0.946	0.159	0.665	0.919
MAOA VNTR males	FTP	CADD/GADD	0.383	0.934	0.353	0.954	0.989
SLC6A3 VNTR	CADD/GADD	FTP	0.762	0.945	0.800	0.728	0.898
SLC6A3 VNTR	FTP	CADD/GADD	0.757	0.960	0.767	0.990	0.996
SLC6A4 5HTTLPR	CADD/GADD	FTP	0.531	0.926	0.535	0.873	0.936
SLC6A4 5HTTLPR	FTP	CADD/GADD	0.591	0.940	0.593	0.932	0.966
SLC6A4 SNP (rs25531)	CADD/GADD	FTP	0.939	0.952	0.957	0.626	0.961
SLC6A4 SNP (rs25531)	FTP	CADD/GADD	0.930	0.974	0.934	0.737	0.968