This track shows locations of Single Nucleotide Polymorphisms detected by aligning reads from random genomic clones from a diverse pool of human DNA against the genome.
Thanks to the SNP Consortium and NIH for providing this data.
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The SNPs in this track include all of the polymorphisms that can be mapped against the current assembly. This includes known point mutations (Single Nucleotide Polymorphisms), insertions, deletions, and segmental mutations from the current build of dbSNP. There are three major cases that are not mapped and/or annotated:
a. Submissions that are completely masked as repetitive elements. These are dropped from any further computations. This set of refSNPs are dumped in chromosome "rs_chMasked" on the dbSNP ftp site.
b. 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.
c. 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 so some of these are probably lost. This approach was chosen to avoid false annotation of variation in inappropriate locations.
The dbSNP ftp site can be found at ftp://ftp.ncbi.nih.gov/snp/.
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