A Plots of Runs (Chromosome) tab is shown below:
The Plots of Runs (Chromosome) tab is created for each value of the Chromosome variable selected in the process dialog and contains the following elements:
The y-axis of this plot represents the Run Length for each run and the x-axis has the chromosome location. If you zoom in far enough (using JMPs 
tool), you can see what looks like a point on the plot is actually made up of points for each SNP included in the run all with the same y-axis value. This number of points is the same as the Run Length.
tool), you can see what looks like a point on the plot is actually made up of points for each SNP included in the run all with the same y-axis value. This number of points is the same as the Run Length. The Data Filter on the right can be used to restrict the display to run lengths in a certain range.
You can select a run or individual SNP points then click on the button to bring up a cell plot view of the offspring genotypes at the selected SNPs. An example of this plot (for the run circled in the figure above) is shown below:
