Wepresent the high-quality genome sequence of a 45,000-year-old modern human male from Siberia. This individual derives from a population that lived before¿or simultaneously with¿the separation of the populations in western and eastern Eurasia and carries a similar amount of Neanderthal ancestry as present-day Eurasians. However, the genomic segments of Neanderthal ancestry are substantially longer than those observed in present-day individuals, indicating that Neanderthal gene flow into the ancestors of this individual occurred 7,000¿13,000 years before he lived. We estimate an autosomal mutation rate of 0.4 x 10-9 to 0.6x10-9 per site per year, a Y chromosomal mutation rate of 0.7x10-9 to 0.9x10-9 per site per year based on the additional substitutions that have occurred in present-day non- Africans compared to this genome, and a mitochondrial mutation rate of 1.8x10-8 to 3.2x10-8 per site per year based on the age of the bone.