Parameter and file settings for STRUCTURE analysis

Data Information

Number of Individuals: 977
Number of Loci: 17
Ploidy: 2
Missing Data is Represented by: -9


Data Format

Data Contains Individual Labels 
Data Contains Population Identifiers 
Data Contains USEPOPINFO Selection Flags 
Data File Strores Data for Individuals in a Single Line 

Running Length          

Length of Burnin Period: 100000
Number of MCMC Reps after Burnin: 1000000

Ancestry Model Info          

Use Prior Population Information to Assist Clustering           
* GENSBACK  = 2
* MIGRPRIOR = 0.05
* For Individuals without population information data, use    
Admixture Model            
** Infer Alpha
** Initial Value of ALPHA (Dirichlet Parameter for Degree of Admixture):  1.0
** Use Same Alpha for all Populations
** Use a Uniform Prior for Alpha
*** Maximum Value for Alpha: 10.0
*** SD of Proposal for Updating Alpha: 0.025

Frequency Model Info   

Allele Frequencies are Correlated among Pops
* Assume Different Values of Fst for Different Subpopulations
* Prior Mean of Fst for Pops: 0.01
* Prior SD   of Fst for Pops: 0.05
* Use Constant Lambda (Allele Frequencies Parameter) 
* Value of Lambda: 1.0


Advanced Options   

Update Allele Frequencies using Individuals with POPFLAG=1 ONLY
Estimate the Probability of the Data Under the Model 
Collect Data About the Distribution of Ancestry Coefficients Q for each Individual
* Distribution of Q values is Stored as a Histogram with 1000 Boxes
* Size of the Displayed Probability Interval on Q: 0.9
Frequency of Metropolis update for Q: 10