Appendix 1—table 9. Predicted discordantly evolving pairs for the MP phylogeny of S-gene reconstructed by USHER.

The characteristics of predicted site pairs for the estimated FDR≤10% are shown: the positions of sites on the primary sequence of S-protein (site1 and site2), the upper p-values (p-value), values of the epistatic statistic (epistat), numbers of consecutive pairs of mutations (#consec. pairs of mutations), numbers of mutations in consecutive pairs of sites (#mut. in consec. pairs in site1 and site2) and total numbers of mutations on the internal tree branches in sites (#mut. in site1 and site2), indicator variable that marks whether a site pairs is also within the set of predictions for the ML phylogeny reconstructed by IQ-TREE for the same FDR threshold (IQ-TREE tree) and distances between sites on the protein structure (pdb distance).

site1	site2	p-value	epistat	#consec. pairs of mut.	#mut. in consec. pairs in site1	#mut. in consec. pairs in site2	#mut. in site1	#mut. in site2	IQ-TREE	pdb distance
18	681	0,00344	0,102	5,5	5	4	22	62	0
222	501	0,00314	0,019	1	1	1	12	46	1	55,44
439	501	0,00286	0	0	0	0	10	46	0	5,16
440	501	0,0019	0	0	0	0	12	46	0	9,47
440	681	0,00274	0,008	1	1	1	12	62	1
484	982	0,0021	0,020	3	3	3	43	18	0	35,42
501	675	0,00136	0,025	1	1	1	46	22	1	84,98
501	677	0,0001	0,023	2	2	2	46	33	1	88,2
570	677	0,00226	0,011	1	1	1	19	33	0	44,77
614	653	0,00022	0,037	4	1	4	10	5	1	15,47
675	716	0,00568	0	0	0	0	22	21	0	38,15
675	1118	0,00524	0	0	0	0	22	19	0	58,84
677	681	0,00264	0,098	3	3	3	33	62	0
677	716	0,00102	0,011	1	1	1	33	21	0	42,93
677	982	0,00152	0,004	1	1	1	33	18	0	54,37
677	1118	0,00066	0,002	1	1	1	33	19	0	64,36