Table 1.

SNP distribution after quality control and the minor allele frequency (MAF), observed (H_O), expected (H_E) heterozygosities and inbreeding coefficient (F) of Malawi, South African field (SAField), Zimbabwean chicken populations as well as the Naked Neck (NN), Potchefstroom Koekoek (PK), Ovambo (OV) and Venda (VD) conservation flocks from South Africa.

	Malawi	Zimbabwe	SAField	NN	PK	OV	VD
SNPs
Total	57,636	57,636	57,636	57,636	57,636	57,636	57,636
Sex chromosome	3202	3202	3202	3202	3202	3202	3202
Unmapped	172	172	172	172	172	172	172
Monomorphic	1992	1878	1501	4488	2341	4702	2975
MAF ≤0.02	3706	2409	2047	9648	5191	4317	5204
HWE (P ≥ 0.001)	207	278	193	102	109	101	77
Missing Gen > 0.05	1384	1338	2039	1048	2218	2284	1086
PARAMETERS
HO	0.62 ± 0.00	0.62 ± 0.03	0.62 ± 0.00	0.62 ± 0.00	0.62 ± 0.00	0.62 ± 0.00	0.62 ± 0.00
HE	0.68 ± 0.02	0.66 ± 0.04	0.65 ± 0.05	0.70 ± 0.14	0.68 ± 0.06	0.65 ± 0.01	0.71 ± 0.00
Mean MAF ±SD	0.27 ± 0.14	0.28 ± 0.13	0.29 ± 0.13	0.26 ± 0.14	0.26 ± 0.14	0.28 ± 0.13	0.24 ± 0.14
F*	0.15 ± 0.07	0.12 ± 0.12	0.07 ± 0.14	0.21 ± 0.03	0.14 ± 0.15	0.07 ± 0.04	0.24 ± 0.18

^*Inbreeding coefficients of all populations were significantly > 0 at P ≤ 0.05.