The International Union of Pure and Applied Chemistry (IUPAC) has defined a standard representation of DNA bases by single characters that specify either a single base (e.g. G for guanine, A for adenine) or a set of bases (e.g. R for either G or A). UCSC uses these single character codes to represent multiple observed alleles of single-base polymorphisms.
| Symbol | Bases | Origin of designation |
|---|---|---|
| G | G | Guanine |
| A | A | Adenine |
| T | T | Thymine |
| C | C | Cytosine |
| R | G or A | puRine |
| Y | T or C | pYrimidine |
| M | A or C | aMino |
| K | G or T | Keto |
| S | G or C | Strong interaction (3 H bonds) |
| W | A or T | Weak interaction (2 H bonds) |
| H | A or C or T | not-G, H follows G in the alphabet |
| B | G or T or C | not-A, B follows A |
| V | G or C or A | not-T (not-U), V follows U |
| D | G or A or T | not-C, D follows C |
| N | G or A or T or C | aNy |