Table 3.

CpG Drive and Analysis of syn-SNV Changing CpG along the SARS-CoV-2 Genome.

					CpG↓SNV			CpG↑SNV
	L	CpG	CpG Drive	SNV	Tot	/SNV (%)	/CpGSNV (%)	Tot	/SNV (%)	/CpGSNV (%)
3′UTR	162	5	−0.87	81	18	22	90	2	2	10
			With counts	6,020	1,597	27	99	20	0.3	1
5′UTR	211	13	−1.67	56	19	34	95	1	2	5
			With counts	48,806	47,446	97	99	328	1	1
N	1,260	39	−0.95	115	24	21	75	8	7	25
			With counts	4,745	2,239	47	94	146	3	6
M	669	20	−1.00	58	12	21	86	2	4	14
			With counts	5,508	245	5	45	302	6	55
ORF10	117	5	−2.01	6	2	33	100	0	0	0
			With counts	233	14	60	100	0	0	0
ORF7a	366	7	−0.61	23	5	22	56	4	17	44
			With counts	544	243	45	88	33	6	12
ORF8	366	8	−0.82	25	5	20	63	3	12	38
			With counts	2,146	107	5	86	17	1	14
ORF3a	828	17	−0.62	54	10	19	67	5	9	33
			With counts	1,530	244	16	87	36	2	13
ORF1a	13,203	160	0.05	848	86	10	52	81	10	49
			With counts	79,937	3,930	5	72	1,560	2	28
ORF1b	8,088	115	0.003	432	47	11	48	52	12	53
			With counts	33,788	7,342	22	84	1,434	4	26
E	228	11	−1.84	10	1	10	100%	0	0	0
			With counts	311	69	22	100	0	0	0
S	3,822	29	0.61	223	16	7	47	18	8	53
			With counts	14,540	571	4	44	729	5	56
ORF6	186	1	0.18	10	0	0	0	2	20	100
			With counts	275	0	0	0	40	15	100
ORF7b	132	1	−0.28	9	0	0	0	2	22	100
			With counts	406	0	0	0	14	4	100

Note.—The table gives, for all the ORFs and the 5′ and 3′UTRs of SARS-CoV-2 ancestral genome, the length of the region (L), the number of CpG motifs (CpG), the CpG drive $(f_{\text{eq}}-f)$, the syn-SNV, and the total numbers and percentages of syn-SNV removing a CpG motif (CG↓) or adding it (CG↑), with respect to total number of syn-SNV (/SNV) or to the total number of syn-SNV affecting CpG (/CpGSNV). For the noncoding 5′ and 3′UTRs, all SNV are taken into account with no restriction to syn-SNV and the noncoding forces are used; the equilibrium force is −1.16 (and not −1.79 as for ORFs) releasing such constraint. UTRs and ORFs and are sorted according to the density of CpG removing SNV (CG↓ SNV/L). The regions underlined are the most reliable for statistical analysis as they present at least 20 syn-SNV. Numbers and percentages of SNV are given with and without taking into account SNV counts. Data from GISAID (Elbe and Buckland-Merrett 2017), see Materials and Methods for details on data analysis (last update October 05, 2020). Ancestral genome GISAID ID: EPI_ISL_406798. SNV with <5 counts are excluded from the data. ROC: Receiver Operating Characteristic; AUROC: Area Under the Receiver Operating Characteristic.