Lee.pan.pro.renamed.fa.gz - Contains the protein models
SNPs_lee.id.biallic_maf_0.05_geno_0.1.vcf.gz - Contains the SNPs for the reference genome, filtered by MAF > 5% and Genotype missingness > 1%
Lee.pan.renamed.fa.gz - the Lee reference genome together with the additional pangenome contigs
soybean_pan_pav.matrix_gene.txt.gz - PAV matrix, one individual per column, one gene per row. 1 is present and 0 is missing.
Lee.pan.v1.renamed.gff.gz - the annotation in gff3 format