Interpreting the MGI Mouse SNPs Results Table

This help document describes the following sections of the MGI Mouse SNPs Results Table:

• RefSNPs (rs) vs. Submitted SNPs (ss)
• Function Classes
  • Notes on Function Classes
  • dbSNP Function Classes
  • MGI Function Classes
• Variation Types
• Strain Alleles

See also:

• SNP Terms and Concepts
• Interpreting a Mouse SNP Summary
• Interpreting Mouse SNP Details
• Interpreting the SNP Data in MGI
• Understanding Mouse SNP Coordinate Discrepancies
• My query returned no results. Why?

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

• A class does not appear on MGI queries unless it is annotated to mouse SNPs. One exception, Contig-Reference, does not appear on the Mouse SNP Query Form but does appear on Mouse SNP Detail reports.
• The coordinates for an MGI gene are obtained from either Ensembl, or NCBI gene model annotations of the genome assembly. Occasionally the gene model used for MGI gene coordinates differs from the gene model used by dbSNP to annotate SNP Function Classes. This can give rise to Function Class annotation discrepancies between dbSNP and MGI. For example, a SNP may be annotated to a gene as Locus-Region by dbSNP which implies that it is located outside of the transcribed region for the gene, yet that SNP may fall within the coordinate range (within coordinates) of the gene in MGI.

dbSNP Function Classes

Class	The variation is ...
Coding-NonSynonymous	In the coding region; change in amino acid sequence.
Coding-Synonymous	In the coding region; no change in amino acid sequence.
Intron	In the intron, except the first or last two bases of the intron.
Locus-Region	In an untranscribed region flanking a gene (2 kb 5' or 0.5 kb 3').
Splice-Site	In the first or last two bases of an intron.
mRNA-UTR	In the transcript but not in the coding region interval. (UTR is untranslated region).
Contig-Reference	Identical to the contig nucleotide.
Coding	In the coding region; specific function class unknown.
Coding-Exception	In the coding region; function class unknown due to exon alignment error.
Non-coding-Transcript-Variant	In 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).

Class	The variation ...
Locus-Region upstream	Is an annotation that falls upstream of the annotated gene.
Locus-Region downstream	Is an annotation that falls downstream of the annotated gene.
x bp upstream	Lies within the distance indicated, upstream from the gene's 5' coordinate.
x bp downstream	Lies within the distance indicated, downstream from the gene's 3' coordinate.
within coordinates of	Lies within the MGI coordinate range of the gene and has no dbSNP annotation.
x bp proximal	Lies within the distance indicated, in the proximal direction from the feature's most proximal coordinate. Applies only to SNPs associated with genome features that do not have a defined transcriptional orientation (strand).
x bp distal	Lies within the distance indicated, in the distal direction from the feature's most distal coordinate. Applies only to SNPs associated with genome features that do not have a defined transcriptional orientation (strand).
Locus-Region proximal	Is an annotation that falls near a genome feature in the proximal direction. Applies only to SNPs with dbSNP-assigned Locus-Region annotations to genome features that do not have a defined transcriptional orientation (strand).
Locus-Region distal	Is an annotation that falls near a genome feature in the distal direction. Applies only to SNPs with dbSNP-assigned Locus-Region annotations to genome features that do not have a defined transcriptional orientation (strand).

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Variation Types

SNP	Single Nucleotide Polymorphism
IN-DEL	Insertion/Deletion Polymorphism
Named	Named/Characterized Insertion Variant
Mixed	Two or more Variation Types
MNP	Multiple Nucleotide Polymorphism
STR	Short Tandem Repeat or Microsatellite
None	No Variation Detected

Note: Note: MGI SNP queries return only RefSNPs with Variation Type = "SNP". RefSNPs with other variation types can be accessed by searching with the RefSNP ID using the Quick Search tool.
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.
	Reference Strain Selected (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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