This directory contains the SNP calls and hapotypes for the 1000 Genomes Pilot 1 release of April 2009.

There are separate files for each population: CEU, YRI and JPTCHB.

In each case, there is a site file, e.g. CEU.sites.2009_04, with typical line:

1	211	A	G	0.201754

<chromosome>, <position>, <ref base>, <non-reference (variant) base>, <inferred non-reference allele frequency>

and a haplotype file, e.g. CEU.hap, with typical line

1	211	aaaaagaaaaaaAAaaaaaagggaaaggGAaaAAAAaaaaaaaaggagaaaggaaaagaaaaggagaaaaAAaaAAaaaaagaagaaaaaaaaaaaAAAGaagaaaAAgagaga

<chromosome>, <position>, 2N*haplotype calls

where the first two calls correspond to the phased alleles of first
sample, calls three and four to the phased alleles of the second
sample etc.

The sample order is given in CEU.Samples etc., which have one line per sample as below:

NA06985
NA06986
NA06994
...

Quang Le <lsq@sanger.ac.uk> and Richard Durbin <rd@sanger.ac.uk>