IGV can display genome-wide association study (GWAS) data as a Manhattan plot. Data formats are described here.

Manhattan plot#

The GWAS Manhattan plot represents the significance of the association between a SNP or haplotype and the trait being measured. The Y-axis shows -log10 transformed P values, which represent the strength of association.

The size of a data point in the plot and its vertical position in the plot relate directly to its significance: the larger the point and the higher the point on the Y-axis, the more significant the association with the trait. You can see the point size difference in the following screenshot of data on chromosome 1.

As in other parts of IGV, clicking on a data point (or hovering over it if you have set the info popup text to display on hover rather than click) allows you to see a pop-up containing the data specifically associated with that point. You can see the pop-up for the topmost data point in this image. Note that the point's vertical position is associated with its P value.

Plot attributes#

Color scheme

The points in the plot are colored by chromosome. Options for the color scheme include:

To change the color scheme:

To change the colors used by each scheme:

Point size

The size of a data point in the plot relates directly to its significance.

To change the size of the data points:

Data scale

To define the scale of the plot's Y-axis: