Table 2. SNV genotyping set: East African sample SNV statistics.

	EAC01	EAC02	EAC03
Genotyped loci	55,399	55,399	55,399
Total SNVs	23,379	20,734	20,934
SNVs covered >5 reads	19,667	19,623	20,110
Homozygous SNVs	11,064	19,365	19,807
Heterozygous SNVs	8,603	258	303
% Heterozygous	43.74%	1.31%	1.51%
Fws	0.51	0.97	0.94
% Heterozygous SNVs in variable regions	15.65%	35.37%	41.45%
% Genome consisting of variable regions	11.97%	11.97%	11.97%
# SNVs in coding regionsa	10,401	9,102	9,147
# Synonymous SNVsa	4,248	3,674	3,682
# Non-synonymous SNVsa	6,153	5,428	5,465
Base pairs per SNVa	967	1,091	1,080
% SNVs in coding regionsa	44.5%	43.9%	43.7%
% of genome consisting of coding regionsb	54.6%	54.6%	54.6%

^aOnly homozygous SNVs are used in the calculation.

^bGenome size - 22,621,101 bp; Coding regions - 12,348,368 bp.