1. A non-transitory computer-readable storage medium storing a computer-executable program product that determines a genotype of a sample of nucleic acid sequences, wherein the computer-executable program causes a computer to execute computer-executable code that comprises: computer-executable code that receives a first hybridization intensity indicating hybridization affinity between a first set of probes and a first allele, the first set of probes being complementary to a portion of the first allele; computer-executable code that receives a second hybridization intensity indicating hybridization affinity between a second set of probes and the first allele, the second set of probes having a single base mismatch with a portion of the first allele; computer-executable code that calculates a first difference between the first and second hybridization intensities; computer-executable code that receives a third hybridization intensity indicating hybridization affinity between a third set of probes and a second allele, the third set of probes being complementary to a portion of the second allele; computer-executable code that receives a fourth hybridization intensity indicating hybridization affinity between a fourth set of probes and the second allele, the fourth set of probes having a single base mismatch with a portion of the second allele; computer-executable code that calculates a second difference between the third and fourth hybridization intensities; computer-executable code that compares the first and second differences to calculate a ratio of the first difference to the second difference; and computer-executable code that uses principal component analysis to compare the ratio to ratios calculated according to the same procedure as the ratio, calculated for each of a plurality of individuals in a population in order to determine the genotype of the sample of nucleic acid sequences.