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SNP Selection Criteria

Category 1 "verified"

This contains all SNPs for which we have allele frequency or genotyping data. This includes SNPs from the TSC allele frequency project, as well as SNPs characterized by JSNP. These SNPs were generated from those rs clusters in which at least one of the SNPs in the cluster contains genotype or allele frequency data and the minor allele must have been seen in at least two individuals.

Category 2 "two-hit"

These are true double-hit SNPs, produced in collaboration with Jim Mullikin and Sarah Hunt. A double-hit SNP must be seen twice, in two different DNA samples which must have produced two alleles. TSC trace data was only allowed to contribute one hit per allele because the individual source DNA for a trace could not be identified.

Category 3 "jsnp-verified/perlegen-verified"

This category contains two groups: SNPs that JSNP certifies are likely to be real based on manual inspection of their data (but have not been genotyped), and SNPs that Perlegen verified independently.

Category 4 "bac-overlap"

These are SNPs from BAC overlaps that do not fall into category 1 or 2 above.

Category 5 "tsc-overlap"

These are SNPs from the TSC project (http://snp.cshl.org), discovered using reduced-representation shotgun (RRS) sequencing.

Other categories

"cSNP": coding SNPs, according to NCBI analysis

"non-validated": Other non-EST SNPs.


Last updated : snp_categories.html,v 1.7 2003/12/12 16:13:34 fiona Exp

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