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
-log
10
scale if selected in the process
dialog
. The
x
-axis plots the estimate of the minor allele
genotype
effect for each marker. When the
trait
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.
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
-log
10
-converted p-values, markers above this line are significant; for
p
-values on the original scale, markers below the line are significant.
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
.