Figure 3

PARSESNP output for the rice target OsDREB showing mutations discovered in both test populations. At top, the gene model is shown in red with boxes corresponding to exons and lines for introns. Green boxes represent protein homology block alignments automatically generated using the SIFT program. Triangles indicate the location and type of mutation found. The red triangle denotes a nonsense mutation, the purple a silent change, and black triangles represent missense changes. The table summarizes the position and nucleotide change of each mutation, and the respective effect on the protein sequence (* indicates premature stop codon, = indicates a silent change, and letters indicate the amino acid according to single letter code). Restriction endonuclease sites that are either gained or lost due to the mutation are also listed and can be used for downstream genotyping. Missense changes are provided with PSSM and SIFT scores [46,47]. Scores are listed in red when the change is predicted to be damaging.