Secondary_E&R_Sim Files

#Anna Maria Langmüller
#Vetmeduni Vienna
#05/2021
#Secondary E&R Sim
#README: processed-simulations

This folder contains the processed simulations needed for the statistical analysis

main.txt
	crossing schemes= 1:1, 1:few, 1:many, dil:st, dil:mt
	N= 300, 1200, 4800, 19200
	generation= 20 (1:1 & dil:mt), 60
	replicates= 5
	2000 simulations per experimental design
	
S-30replicates.txt
	crossing schemes= 1:1, 1:1few, 1:many, dil:st, dil:mt
	N= 300
	generation= 60
	replicates= 30
	100 simulations per experimental design 
	
S-1to1Versions.txt
	crossing schemes= 1:1_1f1nf, 1:1_2f
	N= 300, 1200, 4800, 19200
	generation= 60
	replicates= 5
	whole chromosome 2L is analysed
	2000 simulations per experimental design 
	
S-1to1Versions-window.txt
	crossing schemes= 1:1_2f 
	N= 300, 1200, 4800, 19200
	generation= 60
	replicates= 5
	1:1_2f analysis is restricted to a 1 Mb window around the target of interest
	
Each text file contains the following columns (n=19):

meanAF= 	average starting frequency of the focal target
mix=		ID for simulated selection scenario (i.e., SNP file)
design= 	variable indicating the simulated crossing scheme & population size 
chr=		chromosome, here always 2L
pos=		position of the selected SNP
ad=		ancestral/derived allele (derived = selected SNP)
s=		selection coefficient of the selected SNP
h=		dominance coefficient of the selected SNP
cmhO=		CMH statistic of the selected SNP
trgt=		ID for selected SNP (i.e., chr[.]pos)
rankO=		rank of the selected SNP
ties=		string containing number of ties (i.e., number of "-")
tiespos= 	position of the ties (given by IDs, separated by "-")
dsnp= 		Distance to SNP with highest CMH test statistic in SNPs
dbp= 		Distance to SNP with highest CMH test statistic in base pairs
g=		Number of simulated generations
pos_max=	Position of SNP with the highest Chi^2 statistic in the primary E&R (only defined in dil:st and dil:mt)
rawdesign= 	crossing scheme
N= 		population size