Annotation Group Results (Marker Properties)

An Annotation Group Plots tab is shown below:

The Annotation Group Results tab contains the following elements:

•

One or more P-Value Plots.

When there are multiple annotation groups, there is a separate Annotation Group Results tab for each annotation group. In this example there are two annotation groups, CandGene 1 and CandGene 2. The CandGene 1 Results tab is shown above.

This tab contains one or more p-value plots. The y-axis variable is the p-value from the HWE test, converted to the -log or -log10 scale if selected in the process dialog. The x-axis plots location of the marker according to the annotation location variable within the annotation group. A horizontal reference line is drawn as a red, dashed line at the significance level that was specified. For -log- or -log10-converted p-values, markers above this line are significant; for p-values on the original scale, markers below the line are significant.

If any BY variables were selected, a separate chart is displayed for each BY group.

•

MAF and Missing Genotype Proportion Distributions.

For the given annotation group, the distribution of MAF and missing genotype proportion across the markers in the annotation group are displayed, using histograms and quantile information.

If any By Variables were selected, separate distributions are displayed for each BY group.

These results can give guidance on values to set for the Filters for Markers cutoffs to be used to filter markers/individuals in the Action Buttons pane.