Figure 4.

Concordance of the binomial- and parsimony-based methods for MCS detection. (A) Venn diagram showing the relationship of MCS bases detected by the binomial- (yellow circle) and parsimony- (purple circle) based methods, with the bases detected by both methods shown in brown. Also indicated is the total number of MCS bases in each category. (B) Scatter plots showing the relationship of the conservation scores calculated by each method for bases residing in different types of sequence. Each point represents a base that falls within coding sequence (orange), ARs (green), UTRs (light blue), or non-coding sequence (dark blue), with its position on the x- and y-axes reflecting the conservation score calculated by the binomial- and parsimony-based methods, respectively. The boundaries of each rectangular area (color coded to match the Venn diagram in A) correspond to the established conservation score threshold for each method (see Figs. 1, 2). The indicated percentages reflect the fraction of bases of the indicated type of sequence falling within that area. For visual clarity, every tenth base is plotted; however, the indicated percentages reflect all bases.