IGD - Index of Genetic Differentiation

Download IGD        Sample input file     PDF manual

This program is based on calculation proposed by Pojskic (2005) and Pojskic et al. (2013). The purpose of this measurment is to estimate deviation of each locus Fst (Gst, Theta) from overall value. Analyze of index of genetic differentiation (I) is performed  according to (FSTk-FST)/FST, where FSTk is value for individual locus and FST for all loci. Index for each locus shows intensity and direction of deviation from overall value. Statistical probability is estimated by permutation. In this way you can make assessment of the relevance impact of each locus genetic differentiation to the overall genetic differentiation.

Relative genetic differentiation (R) is proportion of each locus Fst deviation into total deviation (all observed loci from overall Fst value). It expressed as percentage.

 

 

 

Sample input file

 

Sample of result

 

 

                                         Fig.- BarChart - Index of  Genetic Differentiation                                                                                 Fig.- PieChart - Relative Genetic Differentiation

 

 

How to citate IGD

Pojskic N, Sator E. 2013. IGD: Index of Genetic Differentiation. INGEB, University of Sarajevo.


Reference

Bosanski:

Pojskić N (2005): Polimorfizam mikrosatelitnih markera nuklearnog genoma u bh. populacijama salmonida. Doktorska teza, Prirodno-matematički fakultet, Univerzitet u Sarajevu, COBISS.BH-ID: 16348934

Pojskic N, Silajdzic E, Kalamujic B, Kapur-Pojskic L, Lasic L, Tulic U, Hadziselimovic R. 2013. Polymorphic Alu insertions in human populations of Bosnia and Herzegovina. Annals of Human Biology
40(2): 181–185.


English:

Pojskić N (2005): Polymorphism of microsatellite markers in the nuclear genome within BH populations of salmonids. PhD. thesis, Faculty of Science, University of Sarajevo, COBISS.BH-ID: 16348934

Pojskic N, Silajdzic E, Kalamujic B, Kapur-Pojskic L, Lasic L, Tulic U, Hadziselimovic R. 2013. Polymorphic Alu insertions in human populations of Bosnia and Herzegovina. Annals of Human Biology
40(2): 181–185.