The Copper Age settlements in the area of Botai in Northern Kazakhstan (3500-2700 BC) represent the hitherto oldest known sites of horse domestication (Brown & Anthony 1998, Outram 2009), one of the key events that lead to the rapid emergence of successful steppe pastoralist societies. This in turn had profound consequences on the spread of human populations, cultures and languages during the Bronze Age (Allentoft et al. 2015, Haak et al. 2015). This data set aims to include a mixture of deep (~20x) and moderate (~6x) coverage whole genome sequences from ancient samples to address the genetic relationships between the Botai population, the contemporary Bronze Age Yamnaya population, the Saami, and the previously sequenced Upper Paleolithic Mal'ta individual (Raghavan et al. 2014). This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/