This Help document answers the following questions about a marker summary report:

• What determines the content of this report?
• What's the difference between the narrow search and the broad search?
• What should the summary report contain?
• What determines the sort order on a summary page?

See also:

• Using the Genes and Markers Query Form
• Using the Marker Detail Report

What determines the content of this report?

The marker summary content depends on the button you click on the Genes and Markers Query Form (cM, Nomenclature, or Genome Coordinates) and your choice in the Search box next to the Symbol/Name field. There are two types of searches: narrow and broad.

What's the difference between the narrow search and the broad search?

The narrow search is on current gene symbols or names. The broad search includes current as well as old symbols or names, plus any synonyms, alleles, or orthologs.

What should the summary report contain?

• At the top of the Genes and Markers Query Results - Summary report is a summary of your query parameters. For example:

	Genome Coordinates:	between 7.427 and 7.428 Mbp
	Sort:	by Genome Coordinates
	Display Limit:	equals 100

• Beneath the summary is information about the amount of data found. For example:

3 matching items displayed.

If your display limit was 100, and this sentence is 100 matching items displayed, you many want to go back to the query form and set the display to either 500 or No limit in order to see all results (or you could refine the query to yield fewer results).

• Beneath the statment are the following columns, with a row for each matching item.

Field	Description
Chr	If known, the chromosome to which the marker is assigned.
cM	Marker's centimorgan position.
Genome Coordinate (strand)	Marker's coordinates on the mouse genome assembly sequence map, and the strand location of the coordinates in parentheses. Plus (+) is = 5' to 3'. Minus (-) is 3' to 5'.
Symbol, Name	Marker symbol and name, linked to the MGI marker detail page.
Matching Text	Type of information contained in the database and the text that it matches. The tool searches for items containing a match in the following order: current symbol, current name, allele symbol, allele name, withdrawn symbol, withdrawn name, human ortholog symbol, human ortholog name, other ortholog symbol.

Note: If you use the narrow search (gene symbols/names), the Matching Text field does not appear on the Genes and Markers Query Results - Summary report.

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What determines the sort order on a summary page?

1. The Nomenclature sort (the default) is the result of the interaction of two hierarchies: primary and secondary. The first items to appear in summary report are any results that equal your search criteria, in secondary hierarchy order. Next all results that begin with your search criteria appear, in the same order. Finally, all results containing your criteria appear, again in the same order.
   • Primary
     1. equals
     2. begins
     3. contains
   • Secondary:
     1. current symbols
     2. current names
     3. allele symbols
     4. allele names
     5. old (withdrawn) symbols
     6. old (withdrawn) names
     7. synonyms
     8. human ortholog symbols
     9. human ortholog names
     10. other orthologs
   
   
2. The cM sort order is:
   • First by chromosome.
   • Second by cM position in ascending order. Markers with a syntenic cM position (or with no cM position value) appear at the end of each chromosome's list, ordered alphabetically by symbol.
   
   
3. Genome coordinates sort order is:
   • First by chromosome.
   • Second by genome coordinates.
   • Third by symbol/name.