The reference assembly the 1000 genomes project has mapped sequence data to has changed over the course of the project.
For the pilot phase we mapped data to NCBI36. A copy of our reference fasta file can be found on the ftp site.
For the phase1 analysis we mapped to GRCh37. Our fasta file which can be found here called human_g1k_v37.fasta.gz, it contains the autosomes, X, Y and MT but no haplotype sequence or EBV
For the final round of alignments the sequence data will be mapped to a set of sequences derived from the GRCh37 assembly. This GRCh37-derived alignment set includes chromosomal plus unlocalized and unplaced contigs, the rCRS mitochondrial sequence (AC:NC_012920), Human herpesvirus 4 type 1 (AC:NC_007605) and decoy sequence derived from HuRef, Human Bac and Fosmid clones and NA12878. These files are available in phase2_reference_assembly_sequence on the ftp site. All human variant coordinates reported by the 1000 Genomes project are in GRCh37 coordinates.