SNPs Track Settings
 
Simple Nucleotide Polymorphisms (dbSNP build 125)   (All Variation and Repeats tracks)

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Data last updated at UCSC: 2006-04-25

Description

This track contains dbSNP build 125, available from ftp.ncbi.nih.gov/snp.

Interpreting and Configuring the Graphical Display

Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases.

The configuration categories reflect the following definitions (not all categories apply to this assembly):

  • Location Type: Describes the alignment of the flanking sequence
    • Range - the flank alignments leave a gap of 2 or more bases in the reference assembly
    • Exact - the flank alignments leave exactly one base between them
    • Between - the flank alignments are contiguous; the variation is an insertion
    • RangeInsertion - the flank alignments surround a distinct polymorphism between the submitted sequence and reference assembly; the submitted sequence is shorter
    • RangeSubstitution - the flank alignments surround a distinct polymorphism between the submitted sequence and reference assembly; the submitted sequence and the reference assembly sequence are of equal length
    • RangeDeletion - the flank alignments surround a distinct polymorphism between the submitted sequence and reference assembly; the submitted sequence is longer
  • Class: Describes the observed alleles
    • Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles)
    • In-del - insertion/deletion (applies to RangeInsertion, RangeSubstitution, RangeDeletion)
    • Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)'
    • Microsatellite - the observed allele from dbSNP is variation in counts of short tandem repeats
    • Named - the observed allele from dbSNP is given as a text name
    • No Variation - no variation asserted for sequence
    • Mixed - the cluster contains submissions from multiple classes
    • Multiple Nucleotide Polymorphism - alleles of the same length, length > 1, and from set of {A,T,C,G}
    • Insertion - the polymorphism is an insertion relative to the reference assembly
    • Deletion - the polymorphism is a deletion relative to the reference assembly
    • Unknown - no classification provided by data contributor
  • Validation: Method used to validate the variant (each variant may be validated by more than one method)
    • By Frequency - at least one submitted SNP in cluster has frequency data submitted
    • By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method
    • By Submitter - at least one submitter SNP in cluster was validated by independent assay
    • By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes
    • By HapMap - validated by HapMap project
    • Unknown - no validation has been reported for this variant
  • Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts.
    • Locus Region - variation is 3' to and within 500 bases of a transcript, or is 5' to and within 2000 bases of a transcript (dbSNP term: locus; Sequence Ontology term: feature_variant)
    • Coding - Synonymous - no change in peptide for allele with respect to the reference assembly (dbSNP term: coding-synon; Sequence Ontology term: synonymous_variant)
    • Coding - Non-Synonymous - change in peptide for allele with respect to the reference assembly (dbSNP term: coding-nonsynon; Sequence Ontology term: protein_altering_variant)
    • Untranslated - variation is in a transcript, but not in a coding region interval (dbSNP term: untranslated; Sequence Ontology term: UTR_variant)
    • Intron - variation is in an intron, but not in the first two or last two bases of the intron (dbSNP term: intron; Sequence Ontology term: intron_variant)
    • Splice Site - variation is in the first two or last two bases of an intron (dbSNP term: splice-site; Sequence Ontology term: splice_site_variant)
    • Reference (coding) - one of the observed alleles of a SNP in a coding region matches the reference assembly (cds-reference) Sequence Ontology term: coding_sequence_variant)
    • Unknown - no known functional classification
  • Molecule Type: Sample used to find this variant
    • Genomic - variant discovered using a genomic template
    • cDNA - variant discovered using a cDNA template
    • Unknown - sample type not known
  • Average heterozygosity: Calculated by dbSNP as described here
    • Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions.
  • Weight: Alignment count
    • Weight can be 1, 2, 3 or 10.
    • Weight = 10 is excluded from the data set.
    • A filter on maximum weight value is supported, which defaults to 3.
    • Alignments to chrN_random are not included.

You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, but can sometimes give a bit more detail (e.g. more detail about how close a near-gene SNP is to a nearby gene).

Insertions/Deletions

dbSNP uses a class called 'in-del'. This has been split into the 'insertion' and 'deletion' categories, based on location type. The location types 'range' and 'exact' are deletions relative to the reference assembly. The location type 'between' indicates insertions relative to the reference assembly. For the new location types, the class 'in-del' is preserved.

UCSC Annotations

In addition to presenting the dbSNP data, the following annotations are provided:

  • The size of the dbSNP reference allele is checked to see if it matches the coordinate span; exceptions are noted.
  • The dbSNP reference allele is compared to the UCSC reference allele, and a note is made if the dbSNP reference allele is the reverse complement of the UCSC reference allele.
  • Single-base substitutions are noted where the alignments of the flanking sequences are adjacent or have a gap of more than one base.
  • A note is made if the observed alleles are not available from the rs_fasta files.
  • Observed alleles with an unexpected format are noted.
  • The length of the observed alleles is checked for consistency with location types; exceptions are noted.
  • Single-base substitutions are checked to see that one of the observed alleles matches the reference allele; exceptions are noted.
  • Simple deletions are checked to see that the observed allele matches the reference allele; exceptions are noted.
  • Tri-allelic and quad-allelic single-base substitutions are noted.
  • Variants that have multiple mappings are noted.

Data Sources

  • Coordinates, orientation, location type and dbSNP reference allele data were obtained from b125_SNPContigLoc.bcp.gz.
  • b125_SNPMapInfo.bcp.gz provided the alignment weights; alignments with weight = 10 were filtered out.
  • Functional classification information was obtained from b125_SNPContigLocusId.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms.
  • Validation status and heterozygosity were obtained from SNP.bcp.gz.
  • The header lines in the rs_fasta files were used for class, observed polymorphism and molecule type.