MOESM1 of Parsing the synonymous mutations in the maize genome: isoaccepting mutations are more advantageous in regions with codon co-occurrence bias

Additional file 1: Figure S1. Locations of the CDS sequence files of the plant species used in this study. The basic statistics such as the number of genes and codons in maize, and the numbers of detected different mutation types in maize are also displayed. Figure S2. An example of how to define the isoaccepting codon(s) of a given codon. The four Ala codons are taken as an example. Figure S3. The observed patterns are robust when excluding the CpG regions as a confounding factor. Only mutations outside the CpG regions were considered in this case. Significance was defined by Fisher’s exact test and the Wilcoxon rank sum test. Figure S4. Linkage disequilibrium (LD) analysis of the pairwise mutation sites called from the RNA-seq data. An example of a (pairwise) linkage plot is shown for 13 mutation sites in gene Zm00001d031523_T001. The positions of these mutation sites are given in the plot.