When the Trend test is performed, a scatter plot shows the p-values and estimates of minor allele genotype effect for the Trend test, for all annotation groups. The y-axis variable of this scatter plot is the p-value from the trend test, converted to the -log or -log10 scale if selected in the process dialog. The x-axis plots the estimate of the minor allele genotype effect for each marker. When the traits is binary, this is the same value as the log odds ratio, so this plot is identical to the Odds Ratio Volcano Plots (shown on the All P-Value Plots tab)with all annotation groups overlaid onto a single plot. When the trait is continuous, this is the fixed effect estimate for the genotype variable in the trend test (treating genotype as a continuous variable). A positive value on the x-axis indicates a positive correlation of the number of minor alleles for that marker's genotype with the trait.
When the Genotype test is performed and the Output genotype LS means and diffs check box is checked (not done in this example), this tab will contain two more volcano plots displaying the p-value versus the estimate for the LS diff between genotypes 0 and 1, and genotypes 0 and 2. The y-axis variable of this scatter plot is the p-value for the LS diff, converted to the -log or -log10 scale if selected in the process dialog. The x-axis plots the estimate of the LS diff for each marker.
For all volcano plots, 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.
The Local Data Filter to the right of the plot can be used to display a single annotation group at a time. Note however that this does not actually select markers for the drill-down buttons. Markers can be selected either by clicking on annotation groups in the legend below the plot or by selecting points in the plot using left-click with the mouse. If any BY variables were selected, a separate set of plots is displayed for each BY group.