The paired-end contemporary DNA sequences were mapped to the human reference genome (GRCh37/hg19) or the revised Cambridge reference mitochondrial genome (32) using BWA version 0.6.2 (33). Duplicate sequences were then removed from Alignment/Map (SAM) files using SAMtools (35, 36). Using the mpileup command, with a maximum depth parameter of 1000, variant call format (VCF) files were generated for each chromosome separately. Using an awk command, indel variations were excluded. The VCF files of individual modern genomes were merged using VCFtools (37) after zipping and indexing using tabix.

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