Popgen

CoGe can generate basic population genetics summary statistics given a GVCF input file and an annotated genome.

Note: This tool is in Beta Testing. If you use it and have feedback, please email us.

Summary Statistics

These summary statistics are computed per feature overall (gene, CDS, etc) and by 0/4-fold degeneracy (for CDS only):

• Nucleotide diversity (pi) - average number of pairwise differences between variant sequences
• Watterson's estimator (theta)
• Tajima's D

Steps

1. Load a GVCF file

See the LoadExperiment tool for loading a GCVF file against an existing genome in CoGe.

2. Analyze Diversity

Once the GVCF experiment is loaded, navigate to the experiment view and select "Analyze Diversity".

3. Open the finished result

Open the result in the PopGen tool to see results in tabular and graphical form.

Example table of summary statistics

Example plot of selected summary statistics

Troubleshooting

No results

Check that the chromosome/contig names in your GVCF data file exactly match those for the genome.