Popgen: Difference between revisions
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Open the result in the PopGen tool to see results in tabular and graphical form. | Open the result in the PopGen tool to see results in tabular and graphical form. | ||
[[File:popgen_example_table.png|thumb|left|400px|Example table of summary statistics]] | [[File:popgen_example_table.png|thumb|left|400px|Example table of summary statistics]] | ||
[[File:popgen_example_plot.png|thumb|left|300px|Example plot of selected summary statistics]] | [[File:popgen_example_plot.png|thumb|left|300px|Example plot of selected summary statistics]] | ||
Revision as of 18:49, 9 February 2016
CoGe can generate basic population genetics summary statistics given a GVCF input file and an annotated 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 estimator (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".
3. Open the finished result
Open the result in the PopGen tool to see results in tabular and graphical form.
