A method for determining a frequency of single nucleotide polymorphism (SNP) within genomic DNA includes providing genomic DNA of each of a plurality of different organisms. The genomic DNA of each organism includes first and second portions, e.g., first and second strands. First and second amplicons are prepared from the genomic DNA of each organism. The first amplicon corresponds to the first portion of the genomic DNA and the second amplicon corresponds to the second portion of the genomic DNA.A plurality of duplexes is prepared from the first and second amplicons of the genomic DNA of each organism. At least some of the duplexes include a portion of one of the first amplicons and a portion of one of the second amplicons.The duplexes are subjected to temperature gradient electrophoresis to obtain first electrophoresis data indicative of the rate of SNP at a first location in the genomic DNA of the plurality of organisms.