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This document answers the following questions about the allele summary page:

• When does an allele summary appear?
• What should show up on this page?
• How do I interpret an allele summary page?
• Why do some alleles have observed phenotypes and genotypes and some do not?
• What if my query returns no results?

See also:

• MGI Glossary (unfamiliar terms or acronyms)
• Using the Phenotypes, Alleles, and Disease Models Query Form
• Understanding Phenotypic Allele Detail Pages

When does an allele summary appear?

The Phenotypic Alleles Query Results -- Summary appears when a query on the Phenotypes, Alleles, and Disease Models Query Form returns any alleles.

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What should show up on this page?

A search for alleles results in a summary listing of any "hits" with links to detail records. The Query Summary at the top of the Phenotypic Alleles summary reiterates the search parameters that produced the report and contains:

• the Phenotype/Disease term(s) searched for (MP terms, synonyms IDs, and notes; human disease terms and IDs)
• the sort order (i.e., by allele symbol, allele name, category, or chromosome)
• the display limit (the number next to Maximum Returned on the query form) (Note: you can change this number for a subsequent query, if your results seem too large or small)

You'll find a line of text near the top that reports the number of unique alleles matching your query, and, in parentheses, the number of genes or markers represented by those alleles. For example, if a query returns three different alleles of the same marker, this line would read
3 matching Alleles (1 Gene/Marker represented)

Table columns summarize information about the alleles matching your query. Your sort option (from the query form) determines the presentation order. The results appear in some or all of the following fields (depending on your query form choices).

Field	Description
Allele Symbol Gene; Allele Name [Camera icon]	Official symbol for the allele, linked to its Phenotypic Allele Detail page. Name for the allele. If a camera icon appears, click it to view any associated image(s).
Chr	Chromosome of the marker that the allele is associated with.
Synonyms	Any synonyms for the allele.
Category	Specific allele type (e.g., knockout, targeted)
Observed Phenotypes in Mouse	Affected Anatomical Systems High level terms chosen from the Phenotype Selection List pop-up (when you click Anatomical Systems Affected by Phenotypes on the Phenotypes, Alleles, and Disease Models Query Form). Similar Human Diseases Human disease terms and IDs found by the query, based on your entry in the Phenotype/Disease box on the query form.
Allelic Composition (Genetic Background)	Allele pairs that contribute to the genotype and the mouse strain background. Each allele is linked to its corresponding Phenotypic Allele Detail page. Beneath the allele pairs, in parentheses, the strain involved in the genetic background appears; e.g., (involves: 129/Sv * C57BL/6) or (not specified). Involves Indicates that the strains listed (separated by asterisks) contributed to the genetic background of the specimen; additional unspecified strains may also be part of the specimen's genetic background. Either Indicates that more than one genetic background appears in a reference, but the background of the specimen is unspecified.

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How do I interpret an allele summary page?

• To view the additional data for a given allele, click the allele symbol (in the Allele column) to go to its Phenotypic Allele Detail page.
• To view the additional data for a genotype, click on either of the allele symbols in the Allelic Composition (Genetic Background) column to go to each page.

After reviewing the summary information, you may want to run your query again, and change the...

• number next to Maximum Returned on the query form (e.g., if the number of query results is too large or too small.)
• Sort by option; for example, you may want results ordered by allele name or chromosome or category rather than by the default sort order, allele symbol.
• information in the Phenotypes box; for example, you may want to search the MP Ontology terms and IDs and select a more specific term than one from the high-level phenotype term list or add a human disease term to your query.

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Why do some alleles have observed phenotypes and genotypes and some do not?

The vocabulary is annotated at the genotype level. If an allele either does not yet have a genotype or has a genotype with no annotations, the Observed Phenotypes in Mouse and Allelic Composition fields are blank. However, if your search terms match a combination of genotype and text in the Additional Information field, the query returns that data.

For example, on the Phenotypes, Alleles, and Disease Models Query Form:

In the Phenotype/Disease box, you enter ...	The query returns...	Why?
superimposed aqueductal stenosis	One allele (oh) with no observed effects or allelic composition (genetic background).	The match is in the Additional Information section.
aqueductal stenosis	Two alleles (hhy and oh). Hhy returns data in the Observed Phenotypes in Mouse and Allelic Composition (Genetic Background) columns.	Hhy is annotated to the term.

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What if my query returns no results?

See What if my query returns no results? in Using the Phenotypes, Alleles, and Disease Models Query Form.

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