This directory contains a series of ancillary data associated with the phase1 analysis 

ancestral_alignments, Ancestral fasta files based on a 32 way alignment from Ensembl 59 based on the
Enredo Pecan Ortheus pipeline

axiom_genotypes, Genotypes from the Affymetrix Axiom platform for 1000 genomes samples

cryptic_relation_analysis, The results of the Cryptic Relatedness Analysis performed by Jim Nemesh
at the Broad Insititute

excluded_indel_sites, The list of indels which were excluded from the v3 integrated variant release

exome_pull_down, The target coordinates used for both variant calling and the downstream analysis
of the exome data

omni_haplotypes, Genotypes from the Illumina Omni 2.5M Chip for 1000 genomes individuals

accessible_genome_masks, Mask files defining which regions of the genome are more or less
accessible to the next generation methods used by the 1000 Genomes
Project

variant_gerp_scores, Conservation scores for all snp and indel variant sites

highly_differentiated_sites, An excel spreadsheets listing highly differentiated sites
both between super populations and between sub populations within a super population