MGI 5.12 MGI-Interpreting the MGI Mouse SNPs Legend

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

RefSNPs (rs) vs. Submitted SNPs (ss)
Function Classes

Notes on Function Classes
dbSNP Function Classes
MGI Function Classes

Variation Types
Strain Alleles

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).

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, NCBI, or VEGA 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.

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.

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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)¹ Is an annotation that falls upstream of the annotated gene.

Locus region (downstream)¹ Is an annotation that falls downstream of the annotated gene.

within X kb upstream Lies within the distance indicated, upstream from the gene's 5' coordinate.

within X kb downstream Lies within the distance indicated, downstream from the gene's 3' coordinate.

within coordinates Lies within the MGI coordinate range of the gene and has no dbSNP annotation.

Class	The variation ...
Locus region (upstream)¹	Is an annotation that falls upstream of the annotated gene.
Locus region (downstream)¹	Is an annotation that falls downstream of the annotated gene.
within X kb upstream	Lies within the distance indicated, upstream from the gene's 5' coordinate.
within X kb downstream	Lies within the distance indicated, downstream from the gene's 3' coordinate.
within coordinates	Lies 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

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

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: 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.

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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