Genome Scanner

This tool is designed to assist researchers in selecting polymorphic markers for a genome scan of a cross between two strains. It uses the Allele Characterization Project dataset in combination with various genetic and Radiation Hybrid maps.

Select Cross, map, desired bin size and chromosome
Cross X
Available Maps at RGD
Bin Size (cM for Genetic maps, cR for RH maps)
Output options
Highlight allele size differences between bp and bp
Autoselect one polymorphic marker in each bin within this range
Output Content
Output Format

Genome Scanner Instructions

Based on the selected Genetic or RH map, markers that are polymorphic are organized into bins based on the desired scan resolution. For example, to pick polymorphic markers for a 10cM genome scan you would select a 10cM bin size and you could then pick one marker from each 10cM bin and thereby get coverage of the desired chromosome(s) at the desired resolution.

Basic Steps:

  1. Select the two strains to be crossed
  2. Select a map to base the genome scan bin interval upon
  3. Select the desired bin size (genome scan resolution). 10cM works well for scans based on genetic maps, 50cR is best for scans based on RH maps.
  4. Pick one or more chromosomes to scan
  5. Leave all other options, click Generate Genome Scanner Output buton

Explanation of the Output Options

  • Highlight allele size differences graphically indicates polymorphic markers with size differences within the selected size range. This facilitates the selection of markers with suitably spaced alleles for your specific detection system (gel, capillary, etc.)
  • Autoselect - turning this feature on will cause the program to automatically select the first polymorphic marker in each bin with an allele size difference within the size range.
  • Only Show Markers in this range causes the polymorphic markers outside of the size range to be hidden from view.
  • Output Content - A Chromosome Statistics table has been added to show various statistics including the number of polymorphic markers and the corresponding polymorphism percentage for the chromosome. This table and the genome scan results can be displayed together or separately.
    NB These statistics are unaffected by any settings in the marker size difference range
  • Output Format - Output can be in HTML or CSV (Comma separated values, suitable for import into MS Excel, etc.)


RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.