Information of the contents of pilot_data directory

Files 						 Contents
----------------------		--------------------------------------------------------------
sequence.index			meta information of the three 1000Genomes Project Pilot study files
			

SRP000031.sequence.index	meta information of 1000Genomes Project Pilot 1 study files
SRP000032.sequence.index	meta information of 1000Genomes Project Pilot 2 study files	
SRP000033.sequence.index	meta information of 1000Genomes Project Pilot 3 study files

(See ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/README.sequence.index for fuller description
sequence.index file contents and format.)
	

alignment.index			meta information of all bam and bai files in /data directory

(See ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/README.alignment.index for fuller description
alignment.index file contents and format.)



Directory      					 Contents
----------------------		--------------------------------------------------------------
data     			contains a subdirectory per individual of the project. Each
				individual directory contains series of subdirectories for different
				data sets like sequence reads, sequence alignments etc.


release				subdirectories contain intermediate release of results from the
				1000genomes project.
				See individual README files in each subdirectory for a description
				of contents.   


technical/reference		This directory contains the two (male and female) human genome reference
				assemblies used by the 1000genomes project. These are in gzipped, fasta format.
				Files reporting b129 snp positions on reference NCBI36.3 


technical/reference/ancestral_alignments
				This directory contains the ancestral sequence for each human base (in human 
				coordinates) as defined by the 4-way EPO alignments 
				(ftp://ftp.ensembl.org/pub/release-54/emf/ensembl-compara/epo_4_catarrhini/).
				


technical/working		subdirectories contain intermediate sequence.index files.
				pilot3_alignment_20090722 directory contains a number of July 2009 pilot 3
				bam and indexed bam files.