Nucleotide misincorporation patterns observed with standard and optimized BWA mapping parameters for read mapping both the horse and the chicken genome. Nucleotide misincorporation patterns observed for alignments against the horse genome (EquCab2), when using the reads recovered from default or optimized BWA parameters are shown on the left and on the right, respectively. 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). Reads were considered when mapping uniquely both to the EquCab2 and galGal3 genomes but not against the human genome (assembly hg19) and showing mapping qualities of at least 25. Red: C → T. Blue: G → A. Pink: Insertions. Green: Deletions. Orange: Clipped bases. Grey: Other misincorporations.