Single nucleotide polymorphisms
Another level of comparing genomes is at the single nucleotide level. A single nucleotide polymorphism (SNP, pronounced "snip") is a difference of just one nucleotide in the DNA sequence. These differences may or may not result in a visible change in either the phenotype or the amino acid sequence.
SNPs are useful as markers as they are the most basic type possible. However developing SNP assays is complicated as a substantial amount of DNA sequencing is necessary. Most SNPs are of the "transition" type (ie a purine base to a purine base, or a pyrimidine to a pyrimidine. So T/C or A/G)
.........GACGTACGATCAGCCTTATGC....
.........GACATACGATCAGCCTTATGC....