Appendix 1—table 7. Predicted concordantly evolving pairs for the ML phylogeny of S-gene reconstructed by IQ-TREE.

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), FDR value corresponding to the p-value of the site pair obtained for the alternative phylogeny reconstructed by USHER and distances between sites on the protein structure 7JJJ (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	FDRfor the USHER tree	pdb distance
13	152	<2e-5	2,864	5	5	4	5	16	0,03
18	20	0,00008	1,661	3,5	3	3	28	8	1,19	3,62
20	26	<2e-5	1,985	4	3	3	8	12	0,36	15,19
20	417	0,00022	1,348	4	3	2	8	7	0,05	47,83
26	190	0,00018	1,029	4	4	3	12	3	0,06	18,40
63	64	0,00002	0,726	1	1	1	2	4	1,00	1,31
63	67	0,00008	0,726	1	1	1	2	5	1,00	9,38
63	69	0,00012	0,726	1	1	1	2	5	1,00	11,07
63	213	0,00004	0,681	1	1	1	2	3	0,01	13,51
64	67	0,00012	0,726	1	1	1	4	5	1,00	5,51
64	69	0,00014	0,726	1	1	1	4	5	1,00	7,05
67	69	<2e-5	1,101	2	2	2	5	5	0,55	3,59
69	70	<2e-5	1,125	2	2	2	5	4	0,01	1,30
70	144	<2e-5	1,301	3	3	3	4	5	0,01	14,03
76	490	0,00026	0,220	1	1	1	3	3	0,05	45,18
154	1071	<2e-5	1,767	4	2	3	5	5	0,25	95,13
155	157	<2e-5	1,113	2	2	2	3	11	0,53	3,74
189	356	0,00006	0,544	2	1	2	3	2	0,32	31,63
189	360	0,00016	0,544	2	1	2	3	3	0,07	29,89
190	417	0,0001	1,272	3	2	2	3	7	0,01	39,93
213	261	0,00008	0,562	1	1	1	3	2	0,37	11,10
259	261	<2e-5	1,350	1,5	2	1	4	2	0,05	3,81
262	272	<2e-5	1,183	4	4	1	9	2	0,94	31,42
356	357	0,00006	0,448	1	1	1	2	2	0,69	1,33
356	360	<2e-5	1,283	2,5	2	3	2	3	0,05	10,12
359	360	<2e-5	0,976	1,5	1	2	2	3	0,01	1,34
439	441	<2e-5	2,097	4	3	4	9	8	0,01	3,50
440	441	0,00014	1,505	3	3	3	12	8	0,01	1,33
440	442	<2e-5	2,476	3	2	3	12	6	0,01	3,92
440	443	0,00002	1,284	4	3	2	12	2	0,25	3,86
440	444	<2e-5	2,515	3,5	2	5	12	7	0,01	5,60
441	442	<2e-5	2,244	4	4	4	8	6	0,01	1,33
441	443	0,00002	1,281	5	4	2	8	2	0,02	3,23
441	444	<2e-5	3,492	5,5	4	4	8	7	0,01	2,60
442	443	0,00006	1,301	4	4	2	6	2	0,05	1,32
442	444	<2e-5	3,013	6	4	4	6	7	0,01	4,05
443	444	0,00008	1,043	2	2	2	2	7	0,03	1,32
484	655	0,00004	1,716	8	6	5	34	12	0,89	73,58
501	1118	0,00014	2,737	16	13	12	40	22	0,09	131,71
681	716	<2e-5	3,905	16,5	12	16	59	21	0,02
716	982	0,00002	2,001	15	9	11	21	15	0,01	81,66
716	1118	0,00004	2,382	13	8	12	21	22	0,01	22,29
859	950	<2e-5	2,219	5,5	4	5	11	9	0,01	15,17
982	1118	0,00014	1,637	15	11	8	15	22	0,01	94,63
1258	1259	0,00004	0,775	3	1	3	5	3	NA