Table 1.

Number of animals and SNPs excluded and remaining after quality control procedures on genotype data

Breed	n	Excluded SNPsa SNP CR < 0.95	MAF < 0.05	HWE	Total	Remaining SNPs
Boer	13	2577	5280	208	7323	46 024
Karamojong	15	2640	5687	358	7803	45 544
Kigezi	29	1977	6139	543	7793	45 554
Mubende	29	2260	4922	767	7034	46 313
Small East African	29	2523	5669	589	7818	45 529
Sebei	29	2429	4824	469	6826	46 521
Merged	144	2093	3500	2817	7242	46 105

N, number of animals; CR, call rate; MAF, minor allele frequency; HWE, chi square test for Hardy‐Weinberg equilibrium (P‐value < 0.001).

^aSome SNPs were excluded due to more than a single criterion.