Designing Efficient Spaced Seeds for SOLiD Read Mapping
Figure 7
Modeling matches (a), reading errors, SNPs (b), and indels (c). If we consider the costs 0, 2, 3, and 4, respectively: (a) the cost of a match is 0; (b) the cost of single mismatch is 2, and a mismatch that follows it has the cost 1, summing to 3 which is the cost of a SNP; (c) the cost of an indel is 4, and a subsequent mismatch is accepted at zero additional cost.