This data was funded in part by the Bill & Melinda Gates Foundation and with UK aid from the UK Foreign, Commonwealth and Development Office (Grant Agreement OPP1127286) under the auspices of the Centre for Tropical Livestock Genetics and Health (CTLGH), established jointly by the University of Edinburgh, SRUC (Scotland's Rural College), and the International Livestock Research Institute. The findings and conclusions contained within are those of the authors and do not necessarily reflect positions or policies of the Bill & Melinda Gates Foundation nor the UK Government

Whole genome sequence variants (SNPs) from forty samples of each Ethiopian Boran, N'Dama and Holstein cattle breeds which were utilised in the Assessment of genotyping array performance for genome-wide association studies and imputation in African cattle study by Riggio et al., 2022, (in review). The NDama sequences included samples from Guinea (n =21), Nigeria (n =10) and Senegal (n = 9); and the Boran samples from Ethiopia (n = 30) and Kenya (n = 10). Variants discovery followed the protocol described in the Material and Method section of the paper.