Summary

This page hosts the genetic marker and phenotypic data from Wright, Horsnell et al. (underprep). This version of the data has been through a quality control pipeline outlined in the paper.

Data Download

The QC’d genotype data can be downloaded here. The zip folder includes the following files:

  • dataset.map.csv the physical positions for 11,051 SNP markers
  • dataset.1.NAM.mapped.csv the genotypes across 11,051 markers for 2637 SHW NAM individuals
  • dataset.1.NAM.mapped.with.parents.csvthe genotypes across 11,051 markers for 2637 SHW NAM individuals + 54 primary SHW parents and Robigus
  • dataset.2.NAM.mapped.skim100 is dataset.1.NAM.mapped.csv skimmed with an absolute Pearson correlation (r) of 1
  • dataset.3.NAM.mapped.skim80 is dataset.1.NAM.mapped.csv skimmed with r = 0.80
  • NIAB.WW.SHW.NAM.pedigree.info.csv contains the pedigree information for the population
  • genotype.population.numbers.csv contains the nested population number of each genotype

The data is in numeric format and was converted from the original axiom call codes format (AA, AB, BB and NoCall) using the following conversion:

"NoCall" = NA "AA" = 0 "AB" = 1 "BB" = 2

The phenotypic data from the six trials used in the paper can be downloaded here.

The raw and unedited version of the genotype data can be downloaded from here. This zip folder includes the following files:

  • full.markers.winter.shw.nam.v1.csv the dataset with NIAB codes.
  • GRUvs.NIAB.code.conversion.csv a conversion file to link up the Academic and Breeders’ toolkit lines with the NIAB codes. See here for more info on these toolkits.

Contact

For queries on the data and usage please contact:

  • tally.wright@niab.com and richard.horsnell@niab.com