Popgen

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

Summary Statistics

Summary statistics 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 theta
• Tajima's D

Steps

1. Load a GVCF file

See the LoadExperiment tool to load a GCVF file against an existing genome in CoGe.

2. Analyze Diversity

In the resulting experiment's menu select "Analyze Diversity".

Diversity analysis menu option

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