--  HapMap data release #20, January 2005, on NCBI B35 assembly, dbSNP b125   --

This release includes all data from phases I+II of the project.  This
data now contains SNPs in NCBI Build 35 positions.

To generate the mapping, SNPs were only included when they had
consistent mappings from dbSNP against build 34 from two mappings done
at dbSNP, and also mapped to the same chromosome in Build 35.  This
has resulted in some SNPs being not present in this release, however
the will be recovered in the next release.  For details on the
excluded SNPs, and the reasons, see the file 'excluded_SNPs.txt' in
the 'genotypes/2006-01/excluded_snps/' directory.  30,828 SNPs have
been excluded from release 20 for the reasons listed in this file.

Hapmap.org has ongoing work to remap all the assays back to the
genome, which will be the "Gold Standard" release.  In this release,
assays were not specifically QC'd against the genomic location.  While
the mapping protocol outlined above should catch most problematic
SNPs, it remains possible that there are a few SNPs where the assay
does not map properly against Build 35.  The next release (coming
shortly) will fix any potential problems in this area.

Data specific to Phase II is marked with the protocol LSID of
'urn:lsid:perlegen.hapmap.org:Protocol:Genotyping_1.0.0:2' in the genotype
release files.  For the CEU and YRI plates in Phase II, duplicate samples
were not genotyped.  The 'NN' on the '.dup' samples is a place holder.  
The QC-p flag was adjusted to not count these duplicate sample on Phase
II.  For Phase II, there is a new JPT sample 'NA19012'.  For all the Phase
I data, a 'NN' was added for this sample, and genotypes were not attempted
on this sample.  This is a placeholder to keep the file columns aligned.

The release includes mitochondria genotypes.  Positions of these markers 
are express relative to the Human Mitochondrial DNA Revised Cambridge 
Reference Sequence.  See http://www.mitomap.org/mitoseq.html.  Details on 
the polymorphic positions can be seen at mtDB - Human Mitochondrial Genome 
Database <http://www.genpat.uu.se/mtDB/>.

The HapMap database is updated with data submitted to the DCC
by centers funded by agencies in the UK, Japan, US, China and Canada.
New data are submitted to NCBI's dbSNP database within days and should
become available also at http://www.ncbi.nih.gov/SNP/ soon thereafter,
once NCBI has incorporated this submission into the next build of
dbSNP.  

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