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# filename in this repository: description
glyma.Wm82.gnm2.div.Valliyodan_Brown_2021.Soy106.vcf.gz: Genotype information in vcf format for 106 accessions from USB-funded project; from Valliyodan et al Sci Rep 2016.
glyma.Wm82.gnm2.div.Valliyodan_Brown_2021.USB-15x.vcf.gz: Genotype information in vcf format for 284 accessions sequenced at 15x coverage from USB-funded project.
glyma.Wm82.gnm2.div.Valliyodan_Brown_2021.USB-40x.vcf.gz: Genotype information in vcf format for 46 accessions sequenced at 40x coverage from USB-funded project. 
glyma.Wm82.gnm2.div.Valliyodan_Brown_2021.USB481.vcf.gz: Genotype informaiton in vcf format for all 481 accessions from USB-funded project
glyma.Wm82.gnm2.div.Valliyodan_Brown_2021.USB481_nosoja.vcf.gz: Combined genotype information, in vcf format, for all USB lines excluding the Sjoa lines from USB funded project. 
glyma.Wm82.gnm2.div.Valliyodan_Brown_2021.USB481_list.txt.gz: Table containing the PI names, common names, maturity group, and county of origin for the 481 accessions. 
glyma.Wm82.gnm2.div.Valliyodan_Brown_2021.snpEff.gff3.gz: SnpEff results using the SNPs from the glyma.Wm82.gnm2.div.G787.USB481.vcf file as input. Output was converted to GFF file format.  
glyma.Wm82.gnm2.div.Valliyodan_Brown_2021.sampled_25Kpos.fna.gz: Aligned SNP data for USB481 data, based on SNPs sampled at one SNP per 25kb
glyma.Wm82.gnm2.div.Valliyodan_Brown_2021.sampled_25Kpos.nh.txt.gz: Phylogenetic tree (newick format) of SNP data for USB481 data, based on SNPs sampled at one SNP per 25kb
glyma.Wm82.gnm2.div.Valliyodan_Brown_2021.sampled_25Kpos.pxml.txt.gz: Phylogenetic tree (phyloxml format; colored) of SNP data for USB481 data, based on SNPs sampled at one SNP per 25kb
glyma.Wm82.gnm2.div.Valliyodan_Brown_2021.USB481.vcf.gz.tbi: indexed VCF file glyma.Wm82.gnm2.div.G787.USB481.vcf.gz using tabix. 
glyma.Wm82.gnm2.div.Valliyodan_Brown_2021.snpEff_Gsoja.gff.gz: Output from snpEff program using SNPs from the glyma.Wm82.div.G787.Soja.vcf.gz file as input. Output from SnpEff was converted to GFF file format. 
glyma.Wm82.gnm2.div.Valliyodan_Brown_2021.snpEff_Gmax.gff.gz: Output from SnpEff program using SNPs from the glyma.Wm82.div.G787.USB481_nosoja.vcf.gz file as input. Output from SnpEff was coverted to GFF file format.