Rolexa base-calling increases the coverage. Black: Solexa base calling, blue: Rolexa base calling using only the ACGT alphabet (most probable base calling), green: Rolexa base calling using IUPAC codes, red: Rolexa base calling with IUPAC codes and tag length optimization. Numbers in the right margin are the number of matching tags in millions. Sequence tags were sorted by decreasing quality (fast-q) and unique exact matches on the reference phiX174 genome were searched. Vertical axis shows the proportion of tags finding an exact match.