The Modern Human Variants track shows variant calls made from sequence reads of eleven individuals mapped to the $organism genome. The purpose of this track is to put the divergence of the Denisova genome into perspective with regard to present-day humans.
DNA was obtained for each of ten individuals from the CEPH-Human Genome Diversity Panel (HGDP):
Variant Call Format (VCF) files were enhanced by adding information from Ensembl Compara EPO alignments of 6 primates and of 35 Eutherian mammals, phastCons conservation scores generated using EPO alignments, 1000 Genomes Project integrated variant call files, University of Washington background selection scores, ENCODE/Duke Uniqueness of 20mers (see the Mapability track), segmental duplications from the Eichler lab (see the Segmental Dups track), and samtools mpileup summaries of mapped reads.
Thanks to the Max Planck Institute for Evolutionary Anthropology for providing the variant-only VCF files used for this track.
Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Prüfer K, de Filippo C et al. A High-Coverage Genome Sequence from an Archaic Denisovan Individual. Science. 2012 Aug 31. [Epub ahead of print] supplementary online materials, Note 6