Nucleotide misincorporation patterns observed with standard and optimized BWA mapping parameters. Nucleotide misincorporation patterns observed when using the reads recovered from default or optimized BWA parameters are shown on the left and in the middle columns respectively. Nucleotide misincorporation patterns observed on the fraction of high-quality hits identified only with the optimized set of parameters are shown on the right. For both Illumina and Helicos sequencing data, the seed was disabled in the optimized set of mapping parameters (−l 1024). For Helicos tSMS reads, we further increased the maximum number of gap opens to 2 (−o 2) as well as the edit distance (−n 0.03) and allowed for indels at read termini (−i 0). Red: C → T. Blue: G → A. Pink: Insertions. Green: Deletions. Orange: Clipped bases. Grey: Other misincorporations.