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# filename in this repository: description
glyma.Wm82.gnm2.div.Song_Hyten_2015.vcf.gz.tbi: Indexed VCF file using tabix
glyma.Wm82.gnm2.div.Song_Hyten_2015.hmp.gz: HapMap file of the whole U.S. germplasm collection genotyped with SoySNP50K against Williams82 Reference genome a2 (Wm82.a2.v1)                    
glyma.Wm82.gnm2.div.Song_Hyten_2015.Flapjack.txt.gz: Text file containing genotype information of each soybean accession. Columns are ssIDs and rows are Accessions. To be used with glysp.mixed.div2.892R.Wm82.a2.markerMap.txt as input into the Flapjack Program 
glyma.Wm82.gnm2.div.Song_Hyten_2015.markerMap.txt.gz: Text file containing ssIDs and their positions in Wm82.a2.v1 reference genome. To be used with glysp.mixed.div2.892R.Wm82.a2.Flapjack.txt.gz as input into the Flapjack Program
glyma.Wm82.gnm2.div.Song_Hyten_2015.PIconversion.txt.gz: Text file containing the PI# for each accession in the U.S. germplasm collection and what the common name is in the second column.
glyma.Wm82.gnm2.div.Song_Hyten_2015.AlleleCount.tsv.gz: Tab separated file containing allele counts for each cultivar in the dataset.