The genomic distribution of population substructure in four populations using 8,525 autosomal SNPs

Table 1 Summary statistics for heterozygosity, branch lengths and F_ST.

Measure	Marker type	African-American	European-American	East Asian	Full F_ST
Heterozygosity¹	Autosomal	0.321 (0.027)	0.317 (0.031)	0.290 (0.035)	-
	X-linked	0.317 (0.028)	0.280 (0.038)	0.245 (0.041)	-
	p-value	0.180	1.6 × 10 ^-12	1.4 × 10 ^-15	-
LSBL raw dat ²	Autosomal	0.069 (0.014)	0.039 (0.010)	0.066 (0.015)	0.130
	X-linked	0.113 (0.031)	0.054 (0.017)	0.080 (0.023)	0.194
	p-value	5.5 × 10^-33	9.0 × 10^-7	0.0001	3.6 × 10^-63
LSBL adjusted³	Autosomal	0.114	0.046	0.055	0.163
	X-linked	0.170	0.063	0.068	0.242

¹Average (variance) for the unbiased heterozygosity calculated for n = 32,527 autosomal and n = 1,175 X-linked single nucleotide polymorphism (SNP) loci. Autosomal SNPs were compared with X-linked SNPs using a t-test and p-values are shown;
²Average (variance) for the locus-specific branch length and F_ST shown for n = 32,527 autosomal and n = 1,175 X-linked SNP loci. LSBL = locus-specific branch length;
³Admixture-adjusted average. African-American allele frequencies were adjusted to account for an average admixture level of 25 per cent European using the formula, p_Af= (p_AA- (m)p_EA)/(1 - m); where m is the admixture rate (25 per cent European), p_AAis the African-American allele frequency, p_EAis the European-American allele frequency and p_Afis the predicted African allele frequency.

ISSN: 1479-7364