A portion of the Manhattan Plot tab is shown below:
When there are multiple annotation plotting groups such as chromosomes, a Manhattan plot is used to show p-values for all genes (or other type of annotation analysis groups) from a particular type of test in a single scatter plot.
The Y-axis variable is the p-value from the association test, converted to the -log or -log10 scale if selected in the process dialog. The X-axis plots the genes in cumulative order, according to the location of the first SNP in the gene, within and across annotation plotting groups.
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, genes above this line are significant; for p-values on the original scale, genes below the line are significant.
A separate plot is created for each association test performed (plots for two different tests are shown above), and for each trait and the overall MANOVA test, and if any BY variables were selected, a separate chart is displayed for each BY group as well.
On this plot or any of the other p-value plots, you can mouse-over any of the points on the plot to see the marker's label( SNP ID, for example). When an annotation accession variable is specified when running the process, you can select a point and click on any of the Annotation action buttons - GenBank Nucleotide, UniGene Database, AceView Database, or dbSNP - to link directly to the corresponding website to view extensive annotation information about the gene's first locus.