Apparent polyploid levels based on comparing simulated to observed cluster locations. Points for plots in upper row are the simulated cluster center locations for the given genotype where A = (#A_alleles * Intensity_per_A_allele) + Background_Intensity and B = (#B_alleles * Intensity_per_B_allele) + Background_Intensity. Intensity_per_A_allele = Intensity_per_B_allele = Background_Intensity = 100. The #A_alleles and #B_alleles are the counts of each allele in the given genotype. Points for plots in lower row are the observed contrast vs size values for each sample. Each column in 4A, 4B, and 4C is a SNP locus at a different polyploid level. An “X” is drawn over subgenome genotypes to indicate effective absence. A vertical bar is drawn at contrast = zero. A: The 2x/diploid-like cluster pattern. Alleles segregate in one subgenome and are effectively absent in the other three subgenomes. The AB cluster is centered ~ contrast = zero and the homozygous BB and AA genotype clusters have negative and positive contrast values, respectively, in the simulated and observed cluster patterns. B: The 4x/allo-tetraploid-like cluster pattern. Alleles segregate in one subgenome, are fixed in another subgenome, and are effectively absent in the other two subgenomes. One of the genotype clusters AABB, is centered near contrast = zero and the other two genotype clusters are offset to negative contrast values in both the simulated and observed cluster patterns, and correspond to one subgenome being fixed for the B-allele. C: The 8x/allo-octoploid-like pattern. Alleles segregate in one subgenome, and are fixed in at least two other subgenomes. Simulation is shown for allo-octoploid genotypes, where alleles segregate in one subgenome and three other subgenomes are present and fixed for the same allele. The pattern is the same as that for the 4x locus, except that all genotype clusters are offset to the positive (subgenomes are fixed for the A-allele) or negative (subgenomes are fixed for the B-allele, shown) contrast values.