README Version: 0.1 (2024-02-09)

This README file was generated on 2024-02-09 by THERAROZ Adelaide.

# GENERAL INFORMATION

## Dataset title : The genetic consequences of being marginal: a case study in maritime pine
 
## DOI: https://doi.org/10.57745/SPUDQQ
 
## Contact address : adelaide.theraroz@inrae.fr and santiago.gonzalez-martinez@inrae.fr


# METHODOLOGICAL INFORMATION

## Description of sources and methods used to collect and generate data:

DNA was extracted using the DNeasy 96 plant kit (QIAGEN, Germany), following the manufacturer’s instructions. All the samples were genotyped for SNPs using the multispecies 4TREE Axiom array (Thermo Fisher Scientific, USA). Only SNPs with high-quality scoring following the Best Practices Workflow implemented in the Axiom™ Analysis Suite v5.2 were selected and filtered by missing data (<30%), yielding a total of 10,185 SNPs. Contains Affymetrix SNP codes.


## Other contextual information :

Format file: genepop 
SNPs encoding: 2-digits numbers
Number of populations: 82 (codes with "bis" mean that the same population has been genotyped twice (different stands)) Number of individuals: 1.510  
Number of individuals: 1.510


# OVERVIEW OF DATA AND FILES


## File naming convention :  POPGEN_FILTERED_Affx.gen
POPGEN (FORMAT)
FILTERED (Filtered by missing data)
Affx (with Affymetrix SNPs codes)



# SPECIFIC DATA INFORMATION :

## List of variables/column headers :
Cf genepop format

------------- The file starts here ---------------- 
Informative sentence
Affx-979041050
Affx-979041051
Affx-979041053
Affx-979041054
Affx-979041055
Affx-979041057
Affx-979041058
... (locus codes)
POP (Population 1 starts)
GIR01 , 0303 0303 0103 0101 0303 0303 0404 ... (Population GIR, individual 01, and genotypes for each locus encoded in 2-digits) 
GIR02 , 0303 0303 0303 0101 0103 0303 0104 ... (Population GIR, individual 02, and genotypes for each locus)
POP (Population 2 starts)
PDL01 ,  0303 0101 0303 0101 0303 0303 0104 ... (Population PDL, individual 01, and genotypes for each locus)
PDL02 ,  0303 0103 0103 0101 0303 0303 0101 ... (Population PDL, individual 02, and genotypes for each locus)
...
------------- The file ends here -------------------



## Missing values code :
0000


## Additional information :

This dataset was used to carry out a population genetics study.