Table 1.

Summary of imputation reference panels compared in our study

Reference panel	Samples	Sites (millions)	Ancestry distribution	Panel content	Phasing and imputation
AGR	4,956	93	predominantly Africana	chr1-22 and X; biallelic SNPs only	EAGLE2+ PBWT
TOPMed	97,256	308	multi-ethnic	chr1-22 and X; SNPs and indels	EAGLE2+ Minimac4
KGP_S	2,504	85	multi-ethnic	chr1-22 and X; SNPs and indels	EAGLE2+ PBWT
KGP_M	2,504	49	multi-ethnic	chr1-22 and X; SNPs and indels	EAGLE2+ Minimac4
HRC	32,470	40	predominantly European	chr1-22 and X; SNPs only	EAGLE2+ PBWT

Panel codes: AGR, African Genome Resource hosted at the Sanger Imputation Server (SIS); KGP_S, 1000 Genomes Project hosted at the SIS; HRC, Haplo-type Reference Consortium hosted at the SIS; KGP_M, 1000 Genomes Project hosted at the Michigan Imputation Server; TOPMed, hosted at the TOPMed Imputation Server.

^aPopulations from Uganda, Ethiopia, Egypt, and Nama from South Africa and the 1000 Genomes Project.