Tag-dependent quality filtering improves the mapping efficiency. Several entropy cutoffs were used to filter low-quality Rolexa-called tags and to reduce tags to higher scoring sub-tags. Solexa-called tags were filtered to the same length as the average length of the previous sets and to various average fast-q score. A. The actual coverage of the target genome as a function of the expected coverage (if all tags could have been mapped). B. The efficiency of the filtering in coverage ratio (actual number of nucleotides covered divided by expected number, X axis) and in tag mapping ratio (number of tags mapped to the genome divided by number of tags passing the quality filter, Y axis). Rolexa (red points) has superior efficiency to Solexa (green points) in all data sets. Points are labeled with the cutoffs used (see text): Rolexa cutoffs are either constant (2, 4, 6, 8), growing logarithmically (Log) or exponentially (Exp), Solexa cutoffs are indicated by two numbers, the length cutoff followed by the fast-q cutoff.