Description

This track consolidates all the Simple Nucleotide Polymorphisms into a single track. It is the union of the Overlap SNPs, Random SNPs, Affymetrix 120K SNP, and Affymetrix 10K SNP tracks that previously existed in the Genome Browser.

Variant Sources

The Random variants were detected by aligning reads from random genomic clones from a diverse pool of human DNA against the genome.
(These were previously located in the Random SNPs track.)
The Mixed variants were detected by both clone overlaps and the random genomic clones.
(These were previously located in the Random SNPs track.)
The BAC Overlaps variants were detected primarily by looking at overlaps between clones that cover the same region of the genome.
(These were previously located in the Overlap SNPs track.)
The Other variants were found using alternative methods.
(These were previously located in the Overlap SNPs track.)
The Affymetrix Genotyping Array 10K variants are those Single Nucleotide Polymorphisms that have been included in the Affymetrix 10K SNP Genotyping Array.
(These were previously located in the Affymetrix 10K SNP track.)
The Affymetrix Genotyping Array 120K variants are those Single Nucleotide Polymorphisms that have been included in the Affymetrix 120K SNP Genotyping Array.
(These were previously located in the Affymetrix 120K SNP track.)

Variant Types

Single Nucleotide Polymorphisms: variants where the two alleles are each a single base long.
Insertions and Deletions: variants where one allele contains no bases.
Segmental Mutations: variants with multiple nucleotide differences.

Filtering

The SNPs in this track include all known polymorphisms that can be mapped against the current assembly. These include known point mutations (Single Nucleotide Polymorphisms), insertions, deletions, and segmental mutations from the current build of dbSnp, which is shown in the Genome Browser release log.

There are three major cases that are not mapped and/or annotated:

Submissions that are completely masked as repetitive elements. These are dropped from any further computations. This set of reference SNPs is can be found in chromosome "rs_chMasked" on the dbSNP ftp site.
Submissions that are defined in a cDNA context with extensive splicing. These SNPs are typically annotated on refSeq mRNAs through a separate annotation process. Effort is being made to reverse map these variations back to contig coordinates, but that has not been implemented. For now, you can find this set of variations in "rs_chNotOn" on the dbSNP ftp site.
Submissions with excessive hits to the genome. Variations with 3+ hits to the genome are not included in the tracks, but are available in "rs_chMulti" on the dbSNP ftp site.

The heuristics for the non-SNP variations (i.e. named elements and STRs) are quite conservative; therefore, some of these are probably lost. This approach was chosen to avoid false annotation of variation in inappropriate locations.

Supporting Details

Positional information can be found in the annotations section of the Genome Browser downloads page, which is organized by species and assembly. Non-positional information can be found in the shared data section of the same page, where it is split into tables by organism: dbSnpRsHg for Human, dbSnpRsMm for Mouse, and dbSnpRsRn for Rat.

Credits

Thanks to the SNP Consortium and NIH for providing the public data, which are available from dbSnp at NCBI.

Thanks to Perlegen Sciences, Inc. for providing additional SNPs from their database. Additional information about the Perlegen SNP discovery process can be found in Patil, N. (2001) Blocks of Limited Haplotype Diversity Revealed by High-Resolution Scanning of Human Chromosome 21. Science 294:1719-1723.

Thanks to Affymetrix, Inc. for developing the genotyping arrays. For more details on this genotyping assay, please see the supplemental information on the Affymetrix 10K SNP and Affymetrix 120K SNP products. Additional information, including genotyping data, is available from the details pages for the Affymetrix 120K SNP and Affymetrix 10K SNP tracks.

Terms of Use for the Affymetrix data

Please see the Terms and Conditions page on the Affymetrix website for restrictions on the use of their data.