genotype_file_MER_Geraldesetal2012.csv

The file genotype_file_MER_Geraldesetal2012.csv contains the genotyping data used in Geraldes et al. 2012 "A 34K SNP genotyping array for Populus trichocarpa: Design, application to the study of natural populations and transferability to other Populus species". The file contains genotypes for 32,683 loci in 72 accessions. These loci were genotyped with the 34K Populus SNP array described in this manuscript. Details regarding each locus and the genotyping methods can be found in the manuscript. The file contains 32,684 lines and 73 fields per line separated with commas (.csv). The first line is a header line. The first field reads "SNP" and indicates that for each line, the first field contains the name of the Single Nucleotide Polymorphism (SNP). This name has three parts separated with underscores, where the first part is always "scaffold", the second part is the linkage group to which the locus is mapped and the last part is the location (in base pairs) in that linkage group. All names refer to version 2 of the Populus trichocarpa genome available at http://www.phytozome.net/. Each following field in line one, is the name of the accession genotyped. Accession details are provided in Geraldes et al 2012. Each subsequent line has the genotypes for each individual/locus. Each genotype is followed by a "|" and a number ranging from 0 to 1. This number is the GenCall Score, a measure of the confidence in the genotytpe call. Details are in Geraldes et al. 2012. If the Gencall Score is <0.15, the genotype is considered missing and is represented by "--". Other missing genotypes are indicated with #NA.