Whole genome sequencing data of 14 indigenous Greek goats

Goat farming is a significant livestock sector in Greece, which holds the largest population of goats in the European Union. This population is mainly composed of the Eghoria and Skopelos indigenous breeds, the first of which is characterized by great phenotypic diversity, while the second presents a more uniform phenotype. Both breeds are characterized by high levels of genetic diversity. However, data regarding their genetic structure are scarce, usually concerning a limited number of genetic loci. Here, we present the first whole genome sequencing data generated for 14 indigenous Greek goats. In total, 66.5 Gb of data were produced on a NovaSeq. 6000 Illumina sequencer, corresponding to 3.18X average coverage. After quality filtering, >99.7% of sequences mapped successfully to the goat reference genome. Variant calling identified approximately 14 million autosomal variants of high-quality. These data can be used for the genetic improvement of the national herd through selective breeding schemes and, subsequently, improve the sustainability of the sector.