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 quality assigned by dbSNP
  
  • Weight can be 1, 2, 3 or 10.
  • Weight = 1 are the highest quality alignments.
  • Weight = 10 is excluded from the data set.
  • A filter on maximum weight value is supported, which defaults to 3.

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

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 where the alignments of the flanking sequences are adjacent or have a gap of more than one base are noted.
• 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; excpetions 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

• b125_SNPContigLoc.bcp.gz was used for coordinates, orientation, location type and the dbSNP reference allele.
• b125_SNPMapInfo.bcp.gz was used for alignment weights, filtering out alignments with weight = 0 or weight = 10.
• Class and observed polymorphism were obtained from the shared UniVariation.bcp.gz, using the univar_id from SNP.bcp.gz as an index.
• Functional classification 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 molecule type.

Coordinate Conversion

dbSnp chrom	UCSC chrom
chr2A	chr12
chr2B	chr13
chr3	chr2
chr4	chr3
chr5	chr4
chr6	chr5
chr7	chr6
chr8	chr7
chr9	chr11
chr10	chr8
chr11	chr9
chr12	chr10
chr13	chr14
chr14	chr15
chr15	chr16
chr16	chr18
chr17	chr19
chr18	chr17
chr19	chr20
chr20	chr21
chr21	chr22
chr22	chr23