Table 1 Metrics used to calculate genetic diversity
From: RepeatAnalyzer: a tool for analysing and managing short-sequence repeat data
Metric Name | Formula | Significance |
|---|---|---|
GD2 | \( \left(\frac{Total\ \#\ Unique\ SSRs}{\# Strains}\right)\times 100 \) | Defined in [31] |
GD2b | \( \frac{Total\ \#\ Unique\ SSRs}{\#\ Genotypes} \) | Modified version of GD2, calculable in RepeatAnalyzer |
GDM1-Local | \( Avg\left(\frac{\#\ Unique\ SSRs\ in\ Genotype\ i}{Length\left( Genotype\ i\right)}\right) \) | Ratio of unique repeats in each strain in the region |
GDM1-Global | \( \frac{Total\ \#\ Unique\ SSRs}{Total\ Length\left( All\ Genotypes\right)} \) | Ratio of unique repeats across the region as a whole |
GDM2-Local | \( Avg\left( Deviation\left(\frac{Frequency\left(SSR\ i\ in\ Genotype\ j\right)}{Length\left( Genotype\ j\right)}\right)\right) \) | Variation in how often repeats occur within strains in the region |
GDM2-Global | \( Deviation\left(\frac{Frequency\left(SSR\ i\right)}{Total\ Length\left( All\ Genotypes\right)}\right) \) | Variation in how often repeats occur in the region as a whole |