Uganda's indigenous goats are characterised based on ethnic communities that raise them, average mature weight, and hair coat characteristics. Uganda's indigenous goats have  been genotyped based on the Goat_IGGC_65K_v2 illumina chip to study their population structure and genetic characteristics. Information generated from this data is vital for the sustainable utilisation, development, and conservation of Uganda's goat genetic resources.

The data was collected from genomic DNA extracted from ear tissue samples of 1032 indigenous goats from different agro-ecological zones of Uganda.  The study aimed to characterise the genetic diversity, population structure and signatures of selection of indigenous goats in different agroecological zones of Uganda. Indigenous goats were identified in their known phenotypic/ ethnic classifications of Mubende, Kigezi and Small East African goats in all the 10 agroecologies. Ear tissue samples were collected from each goat using the allflex tissue sampling system that allows for no cross contamination as each sample self locks in a single use tube after it is collected. Genomic DNA was extracted from each sample using the TANBEAD automated DNA extraction system with the 6T2 total tissue DNA extraction kit. DNA samples were genotyped based on the Goat_IGGC_65K_v2 illumina chip. 

Data processing

After genotyping, 59725 SNPs from 1032 genotypes were received in PLINK format. The data was opened in Tassel Version 5.2 and saved as VCF format for further processing. The near complete goat genome (ARS1) was used as reference to align all the SNPs to the right chromosomes and chromosome positions using R  (version 4.3.3) software. The final data set was saved as a VCF file for analysis.