Linkage Map

The Linkage Map tab is shown below:

The <Linkage Map> tab contains the following elements:

•	One Genetic Distances for Linkage Groups plot.

This plot displays the position of markers ( y -axis) versus the chromosome index ( x -axis) for each chromosome. Each colored filled-circle represents a marker on the chromosome.

A chromosome index for the consensus map is defined as a concatenation of the input linkage group name, a dot, the word Consensus (if the map is a consensus output), a dot, and the maximum interval window used to build the consensus map (if the map is a consensus output). For example, if the input linkage group name is 1H and the map is a consensus output build with maximum interval window of 2, then the chromosome index is 1H.Consensus.mw2 .

Chromosome indexes for the original input linkage groups are likewise defined, however, with the word Consensus replaced by the name of the input map file, and without maximum interval window. For example, if an input linkage group has name 1H , and it is coming from an input file named mb.sas7bdat , then its chromosome index is 1H.mb .

Select points in one or more chromosomes and click Linkage Map Viewer to launch the Linkage Map Viewer process to visualize the selected chromosomes. Likewise, select points in two or more chromosomes and click Compare Linkage Maps to launch the Compare Linkage Maps process to compare all pairwise selected chromosomes.

•	One Data Filter.

The JMP Data Filter has also been embedded into this tabbed view to use for interactively selecting points in the plots.