Genotype datasets of Mathieson et al. Nature, "Genome-wide patterns of selection in 230 ancient Eurasians", doi:10.1038/nature16152

1. Dataset used for population history analysis

Full dataset of 230 ancient individuals and Chimp, Human reference hg19, Ust_Ishim, Kostenki14, MA1.
  full230.geno
  full230.ind
  full230.snp

The full dataset includes 1233632 SNPs.
Population history analysis was not performed on this full set, but rather on the HOIll/HO subsets (Methods) as described below.

Auxiliary files:
  HOIll223.ind		223 individuals with population labels used for population history analysis
  HOIll223.snp		Set of SNPs used for population history analysis on ancient individuals alone
  HO223.snp		Set of SNPs used for population history analysis when co-analyzing ancient individuals with present-day Human Origins data.

Human Origins data on present-day humans (Lazaridis et al. Nature 2014) can be downloaded from the Reich lab website (http://genetics.med.harvard.edu/reich/Reich_Lab/Datasets.html).

2. Data used for selection analysis.

We merged the full230 data with 1000 Genomes phase 3 data downloaded from ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20130502/ on 17Sep14.

Auxilliary files:
  v81kg_europe2names.ind	230 Ancient samples plus 1000 Genomes samples analysed in the paper.
  v81kg_europe2names.snp	1131559 SNPs remaining after 1000 Genomes merge (includes monomorphic and ChrX SNPs).

To extract read counts for analysis, aligned bams are available from the European Nucleotide Archive (www.ebi.ac.uk/ena) under accession number PRJEB11450

3. Mitochondrial consensus sequences.

Directory:
 mtgens/*.fa
