Fig 5. Sites embedding antigenic signals beyond the envelope protein.

Prediction performance of downsampled NS2A sites concatenated with E when randomly downsampled to a) 60 sites and b) 30 sites contrasted against when concatenated with random sites from other proteins. c) Distribution of frequencies at which sites showed non-zero effect given being sampled in the two downsampling schemes. Black lines link frequencies of the same sites. d) Performance when concatenating the 62 sites which >99% of the times sampled was estimated to have non-zero effect size when adjusted for E in both schemes (red) compared against the same sites but permuted (yellow), and sites from other proteins of the same length (gray). Permutation was done by permuting residues observed at each site across viruses to conserve its diversity.