README.txt

nam_thin_phased.vcf.gz :
-------------------
This file contains imputed and phased single nucleotide polymorphisms for the 
Nested Association Mapping popoulation. Imputation and phasing was performed 
using Beagle 5.0 [https://faculty.washington.edu/browning/beagle/beagle.html]. 
SNPs were thinned using the 'indep-pairwise' function of PLINKv1.90b 
[https://www.cog-genomics.org/plink2] with a window size of 250 kb, a step size 
of 50 SNPs, and an LD threshold of 0.6. The file is block gzipped and can be 
inflated using bgzip [http://www.htslib.org/]. The file is in VCF4.1 format 
[https://samtools.github.io/hts-specs/VCFv4.1.pdf]. For more information on the 
construction of the SNP file, see Kusmec et al. (2017).

thinned_map.csv :
-----------------
This file contains genetic map information for the SNPs in the marker file. 
Recombination rates are calculated using Haldane's mapping function. Marker 
effect estimates were calculated using ear height and total kernel weight (see 
Kusmec et al. (2017) and Yang et al. (2018)) and the BayesB algorithm.

Columns:
1 = Marker - marker ID (Chr_Physical)
2 = Chr - chromosome
3 = Physical - physical position (bp)
4 = Genetic - genetic position (cM)
5 = RecombRate - recombination rate
6 = EHT - estimated effect on ear height (cm)
7 = TKW - estimated effect on total kernel weight (g)

References :
------------
Kusmec, A., S. Srinivasan, D. Nettleton, and P.S. Schnable. (2017) "Distinct 
   genetic architectures of mean phenotypes and plasticities in Zea mays." 
  Nature Plants, 3(9): 715-23.
Yang, J., C.-T. Yeh, R.K. Ramamurthy, X. Qi, R.L. Fernando, J.C.M. Dekkers, 
   D.J. Garrick, D. Nettleton, and P.S. Schnable. (2018) "Empirical comparisons 
   of different statistical models to identify and validate kernel row number-
   associated variants from structured multi-parent mapping populations of 
   maize." G3: Genes, Genomes, Genetics, 8(11): 3567-75.