TASSEL Tutorial Data sets

File name	Type	Format	Description
d8_sequence.phy	Genotype	Phylip Alignment	Sequence of dwarf8 gene with 2466 sites on 91 maize inbred lines. The data was described by the paper on the association between Dwarf8 and flowering time.
mdp_genotype.hmp.txt	Genotype	Hapmap	3093 SNPs on 281 maize association inbred lines. The data was created by the PANZEA project funded by NSF. Details of the data can be found at http://www.panzea.org.
mdp_genotype.plk.ped, mdp_genotype.plk.map	Genotype	Plink	Same As Above
mdp_genotype.vcf	Genotype	VCF	Same As Above
mdp_kinship.txt	Kinship	Numerical Square Matrix	Kinship created by Yu et al.
mdp_population_structure.txt	Population structure	Numerical Trait Data	Population Structure of 282 maize inbred lines.
mdp_traits.txt	Phenotype	Numerical Trait Data	Three phenotypes, including flowering time, on 282 maize inbred lines.
mdp_phenotype.txt	Phenotype	Numerical Phenotype Data	Three phenotypes, one factor (location), and three covariates (population structure) on 282 maize inbred lines
282_GBS2.7_Depth7Mask.h5		HDF5	2.7 build GBS file that genotypes have been masked at sites with physical positions divisible by 7, and have a read depth of 7. 282 maize inbred lines. They are masked by simply setting to missing. The masked genotypes are held in corresponding files with the phase "maskKey", which have all genotypes set to missing except the ones that are masked.
NAM_RILs1-5_GBS2.7_Depth7Mask.h5		HDF5	Same as above but with NAM RIL families 1-5

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