README

The methods used to generate these data can be found in Leiboff et al. (2015) [doi:10.1038/ncomms9974] and Goiffon et al. (2017) [doi:10.1534/genetics.116.197103]. More information on the Shoot Apical Meristem (SAM) Diversity Panel is in Leiboff et al.

phased_SAM.vcf.gz :
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This file contains imputed and phased single nucleotide polymorphisms for the SAM Diversity Panel. Imputation and phasing was performed using Beagle 5.0 [https://faculty.washington.edu/browning/beagle/beagle.html]. 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 and https://github.com/samtools/hts-specs].

genetic_map.csv :
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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 SAM volume (see Leiboff et al.) 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 = Effect - estimated marker effect (um^3)