Data related 'Refining the evolutionary tree of the horse Y chromosome'

Here we provide mapped reads of previously published 94 high-throughput sequenced horse samples (Felkel et al., 2019; Remer et al., 2022) and a donkey (Orlando et al., 2013). The raw data were mapped to the horse Y contigs (LipY764), horse X chromosome and mtDNA sequences. Only the reads mapped to the LipY764 contigs are given here. In addition, chrY reference, which was used for clustering the ancient horse samples mapped to this reference (Gaunitz et al., 2018; Fages et al., 2019), is provided in fasta format.