Table 2.

Post imputation marker filtering by MAF and HWE for self-reported census race and genetic population assignment for an example GWAS of unrelated individuals using 17,461,305 imputed variants.

Group	n	min. MAF	MAF fail	HWE fail	MAF/HWE fail
ALL	5880	0.0034	77,826	2,716,350	2,794,175
WHT	3002	0.0067	6,965,188	10,004	6,974,728
EUR	2972	0.0067	7,036,314	9,308	7,045,613
BLK	1202	0.0166	3,333,134	4,169	3,337,283
AFR	1329	0.0150	2,973,215	4,579	2,977,773
ASN	921	0.0217	9,182,668	143,288	9,325,808
EAS	552	0.0362	10,561,171	2,829	10,563,961
SAS	447	0.0447	10,093,522	1,774	10,095,181
HSP	357	0.0560	10,450,319	925	10,451,231
AMR	580	0.0345	9,402,185	2,229	9,404,397
Analysis	nmax	nmin	nmedian	Total SNPs
ALL	5880	–	–	14,667,130
Census Race	5482	1,202	4,204	16,377,112
Pop. Match	5880	1,027	4,104	16,597,801

Note: SNP = single nucleotide polymorphism, n = sample size, min. MAF = minimum minor allele frequency where at least 40 minor alleles are observed in the sample, MAF pass = number of SNPs passed MAF, HWE = number of SNPs passed Hardy Weinberg Equilibrium threshold, Total fail = number of SNPs failing MAF or HWE threshold, ALL = all data available for genetic analysis, WHT = self-identified census race (SIA) white, EUR = matched to 1KGP European population, BLK = SIA black/African American, AFR = matched to 1KGP African population, ASN = SIA Asian, EAS = matched to 1KGP East Asian population, SAS = matched to 1KGP South Asian population, HSP = SIA Hispanic/Latino, AMR = matched to 1KGP Americas population, Census Race = total sample available for analysis using SIA, Pop. Match = total sample available for analysis using genetic population assignment, Analysis = ALL is all subjects analyzed together, Census Race or Pop. Match is each group analyzed separately and then meta-analyzed, n_max = maximum number of individuals in analysis, n_min and n_median are the minimum and median number of individuals available per meta-analysis, Total SNPs = total SNPs available for genome-wide association analysis.