Displaying Genotype Data: Visual Genotypes

The display and interpretation of large genotype data sets can be simplified by using a graphical display. We have found it useful to present complete raw datasets of individuals' genotype data using a display format called a visual genotype (VG) (see Nickerson et al., Nature Genetics, 19:233-240, 1998, and Rieder et al., Nature Genetics, 22:59-60, 1999). This format presents all data in an array of samples (rows) x polymorphic sites (columns) and encodes each diallelic polymorphism according to a general color scheme where:

blue - homozygous genotype for the common allele

red - heterozygous genotype (both common and rare allele)

yellow - homozygous genotype for the rare allele

gray - missing data (N)

This array format allows one to visually inspect the data across both individual's diplotypes and polymorphic sites to make comparisons.

We have established a specific format for the uploading of genotype data. See below for complete formatting guidelines.

Displaying Your Own Data
Using this page you are able to upload a file (using the browse button to find a file on your own computer) and have a visual genotype produced. This image will appear in a separate browser window.

Displaying PGA Finished Data
You are also able to directly view data from our Finished Genes list and interactively display these visual genotypes. Select the "Finished Genes on our Server" button and use the drop-down list to select a gene.

Display Options
The format of the visual genotype can be adjusted by filtering out polymorphisms below a minimum allele frequency. This is simply done by entering your minimum cutoff in the Rare Allele Percentage box.
In order to cluster sites, we calculate r² for all pairs of sites in a file, and then cluster sites such that sites with similar patterns of genotype (high r²) are shown near one another. We use an unweighted average linkage algorithm (UPGMA) to generate a hierarchical tree of cluster relationships (see more on VG2 site clustering).

How to Save A Visual Genotype Image

1. Move the mouse pointer over the image you wish to save.
2. Press right mouse button.
3. Move the pointer over "Save Image As..." (Netscape) or "Save Picture As..." (Internet Explorer)
4. Choose target directory to save to and type in desired filename.
5. Click "Ok" button.

Formatting Guidelines

Genotype Date Format:

This file must be a tab-delimited file with four fields on each line, in the format:

<Site Position><tab><Sample ID><tab><Allele 1><tab><Allele 2>

e.g.

200 IND1 A A

This line would represent a polymorphism at posit