Sequence reads from fossil material mapped by Stampy (Lunter & Gerton 2010) to the human genome (hg18) and the Cambridge reference mtDNA sequence (rCRS) in binary alignment format (BAM). r1 refers to libraries amplified with Phusion polymerase and r2 to r7 refers to libraries amplified by Hifi polymerase. Duplicates were removed using rmdup in the samtools suite (Li et al. 2010). For more details and sample description see supplementary material in Skoglund et al. (submitted). For more information, contact: pontus.skoglund@ebc.uu.se