Annotation Group Plots/All Markers Plots (Linkage Disequilibrium)

An Annotation Group Plots tab is shown below:

When no annotation variables are specified, this plot is labeled as the All Markers Plots tab

The Annotation Group Plots/All Markers Plots tabs, contain the following elements:

•	One or more triangular LD plots ( top ).

This scatter plot has marker positions along both axes, with a point at each marker pair, colored by the p-value range for its LD coefficient. The legend to the right of the plot indicates the colors associated with each value.. Along the diagonal (indicated by the dotted line ¹ ), where the same marker is represented on the x and y axes, this p -value corresponds to the test for Hardy-Weinberg equilibrium (HWE) instead. Note : If any BY variables were selected, a separate plot is displayed for each BY group .

•	One or more contour plots ( bottom ).

A contour plot of the LD measure is included on this tab when Dprime or CorrCoeff is selected for the Measure for LD Contour Plot option. As with the previous plot(s), the axes represent the marker positions and a legend showing the color for the LD measure ranges is to the plot's right. This plot is symmetric along the 45 degree line (indicated by the dotted line). Note : If any By Variables were selected, a separate plot is displayed for each BY group.

These plots, along with the interactive LD plot drill-downs, give you several ways of viewing the LD for your data in the different annotation groups so that you can see the extent of LD for this sample.

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The dotted lines shown in these plots were added to the graphics for illustration purposes only. These lines are not generally included in the plots.