Figure 2

Explanation of unphased genotypes. The example shows an unphased tetraploid genotype at the top, which consists of three different alleles at the first SNP site and two different alleles at the remaining sites. In the second table, the given genotype is given in its vector representation. Different nucleotides at different SNP sites may be encoded by identical numbers, which depends on the allele composition of the SNP sites. There is an exponential number of possible haplotype explanations for one unphased genotype. Below, three of the possible haplotype explanations are shown. The first explanation can be resolved directly from the vector representation of the unphased genotype. The second explanation is resolved by randomly permutating the allele arrangement of the SNP sites. Finally, the third explanation is outstanding since it uses only three different haplotypes. Note that at least the first SNP site of the example will be further encoded as described in "Extension to SAT model for polyallelic polyploids".