Interpreting mismatches between reads in base- and color-space. (a,b) Base call error simulation in Illumina and SOLiD reads reflecting one mismatch with respect to the reference from which they are simulated in their respective base- and color-space. (b) A naïve conversion of color read to base space, for the purpose of mapping against the base space reference, is not recommended as a single color base error will introduce cascading mismatches in base space. (c) A bisulfite conversion in base space will introduce two adjacent mismatches in its equivalent representation in color space.
Lim et al. Genome Biology 2012 13:R82 doi:10.1186/gb-2012-13-10-r82