Description

This track consolidates all the Simple Nucleotide Polymorphisms into a single track.

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 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 displayed on this page 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 NIH's dbSNP for providing the public data, which are available from dbSnp at the NCBI.