Interpreting the MGI Mouse SNPs Legend
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This help document describes the following sections of the MGI Mouse SNPs legend:

See also:

RefSNPs (rs) vs. Submitted SNPs (ss)

RefSNP Reference SNP (rs). dbSNP maps each submitted SNP assay (ss) to the genome and assigns a RefSNP accession ID (rs#) to each submitted SNP assay. Submitted SNPs that map to the same location are clustered into the same RefSNP and have the same rs#.
Assay ID Assay ID (ss) assigned by dbSNP. Bold: Exemplar (or representative) ss.
The rs reference flanking sequence is derived from the submitted flanking sequence for the exemplar ss.
Submitter
SNP ID
Assay ID assigned by the submitter.
rs orient Orientation of the rs reference flanking sequence relative to the mouse genome sequence (f-forward, r-reverse).
ss orient Orientation of the ss flanking sequence relative to the rs reference flanking sequence (f-forward, r-reverse).

Function Classes

Notes on Function Classes

dbSNP Function Classes

ClassThe variation is ...
Coding-NonSynonymousIn the coding region; change in amino acid sequence.
Coding-SynonymousIn the coding region; no change in amino acid sequence.
IntronIn the intron, except the first or last two bases of the intron.
Locus-RegionIn an untranscribed region flanking a gene (2 kb 5' or 0.5 kb 3').
Splice-SiteIn the first or last two bases of an intron.
mRNA-UTRIn the transcript but not in the coding region interval. (UTR is untranslated region).
Contig-ReferenceIdentical to the contig nucleotide.
CodingIn the coding region; specific function class unknown.
Coding-ExceptionIn the coding region; function class unknown due to exon alignment error.
Non-coding-Transcript-VariantIn a non-coding transcript.

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MGI Function Classes

The following are MGI function classes that appear when genome coordinates are "in sync"
(see Understanding Mouse SNP Coordinate Discrepancies for details).

ClassThe variation ...
Locus region (upstream)1Is an annotation that falls upstream of the annotated gene.
Locus region (downstream)1Is an annotation that falls downstream of the annotated gene.
within X kb upstreamLies within the distance indicated, upstream from the gene's 5' coordinate.
within X kb downstreamLies within the distance indicated, downstream from the gene's 3' coordinate.
within coordinatesLies within the MGI coordinate range of the gene and has no dbSNP annotation.
1 Note: If a SNP has the dbSNP Function Class annotation of Locus-Region for a gene and the coordinates for that SNP fall within the MGI coordinate range of this gene, then the MGI Function Class is Locus region, without (upstream) or (downstream) qualifiers.

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Variation Types

SNPSingle Nucleotide Polymorphism
IN-DELInsertion/Deletion Polymorphism
NamedNamed/Characterized Insertion Variant
MixedTwo or more Variation Types
MNPMultiple Nucleotide Polymorphism
STRShort Tandem Repeat or Microsatellite
NoneNo Variation Detected
Note: MGI queries display only the dbSNP variation types present in the mouse SNP data.
See SNP Terms and Concepts for definitions of the dbSNP variation types.

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Strain Alleles

 A   C   G   T 
Nucleotide values (no conflict for the strain)
 - 
(dash) indicates a deletion for that strain relative to some other strain.
 i   j   k 
Single letter insertion codes indicate noted insertion sequences defined in the Insertions column (see below).
   
(blank cell) means that no allele data are available for that strain.
STRAIN
Reference Strain Selected (SNP results summary pages only).
 S 
Same allele value as in the reference strain (SNP results summary pages only).
 D 
Different allele value from that in the reference strain (SNP results summary pages only).
 A   C   G   T 
(underlined) Nucleotide value conflict for the strain; consensus value determined by majority.
 ? 
The consensus value is ambiguous because there is a nucleotide value conflict for the strain.
Insertions Insertion allele sequences for single-letter insertion codes.
Allele Summary Summary of observed allele values from all strains for the RefSNP (SNP results summary pages only).

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