Variants

	A	B	C	D	E	F	G	H	I	J	K	L	M	N	O	P	Q	R	S	T	U	V	W	X	Y	Z	AB	AC	AD	AE	AF	AG	AH	AI
1		# SNPs	/4	coding	all	all	spacer	in coding (dN SNP) mutations										in all (dN+dS SNP) mutations					among c>u
2				trans/c>u	trans/c>u	dN/dS		c>u	u>c	a>g	g>a	trans	->in spike	ratio	->->in rbd	ratio		c>u	u>c	a>g	g>a	(transversions)	a/u upstream	c/g upstream	a/u downstream	c/g downstream	canva thing	/4
3	wild-type, early 2020‡	32	8.00	0.58	0.22	0.73	0	40	10	7	19	23					early 2020	119	32	28	29	26	71	29	78	22	89	22.25	12	3	8	8	8	8
4	19b to B.1	7	1.75	0.00	0.00	0.75	0	2	0	1	0	0	0		0		19b to B.1	4	2	1	0	0	3	1	3	1	4	1	3	0.75	8	8	8	8
5	"C.1," SA summer 2020	8	2.00	1.00	0.50	0.60	0	1	0	0	1	1	0		0		"C.1"	4	0	0	2	2					4	1	2	0.5	8	8	8	8
6	alpha*	18	4.50	1.75	0.88	2.60	0	4	1	1	0	7	5	0.71	1	0.14	alpha*	8	2	1	0	7	6	2	5	3	8	2	3	0.75	8	8	8	8
7	beta**	13	3.25	1.00	1.00	3.33	0	4	0	1	1	4	2	0.50	1	0.25	beta**	5	0	2	1	5	3	1	3	1	5	1.25	3	0.75	8	8	8	8
8	B.1.1.28.2	11	2.75	4.00	1.00	1.20	0	1	0	0	1	4	1	0.25	0	0.00	B.1.1.28.2	4	1	1	1	4					4	1	3	0.75	8	8	8	8
9	gamma	25	6.25	1.80	1.38	2.13	0	5	1	0	2	9	6	0.67	2	0.22	gamma	8	2	2	2	11	5	1	5	1	8	2	6	1.5	8	8	8	8
10	delta	15	3.75	1.67	2.33	6.50	0	3	2	1	2	5	4	0.80	1	0.20	delta	3	2	1	2	7	2	1	3	0	3	0.75	5	1.25	8	8	8	8
11	eta	21	5.25	0.40	0.33	1.10	0	5	2	1	1	2	1	0.50	0	0.00	eta	9	3	4	2	3	7	2	8	1	9	2.25	9	2.25	8	8	8	8
12	lambda	17	4.25	1.25	0.75	2.40	0	4	2	0	1	5	3	0.60	1	0.20	lambda	8	2	0	1	6					8	2	3	0.75	8	8	8	8
13	BA.0	33	8.25	2.33	1.78	5.60	0	6	2	3	3	14	11	0.79	5	0.36	BA.0	9	2	3	3	16	7	3	5	5	9	2.25	8	2	8	8	8	8
14	BA.1 (post BA.0)	15	3.75	1.00	1.00	6.50	0	3	1	3	3	3	2	0.67	1	0.33	BA.1	4	1	3	3	4	2	2	4	0	4	1	7	1.75	8	8	8	8
15	BA.2 (post BA.0)*	24	6.00	0.50	0.31	2.43	0	8	0	1	4	4	2	0.50	1	0.25	BA.2	13	0	3	4	4	12	1	12	1	13	3.25	7	1.75	8	8	8	8
16	mice serial passage	19	4.75	5.00	1.40	0.90	0	1	3	0	0	5	4	0.80	4	0.80	mice	5	5	2	0	7					5	1.25	7	1.75	8	8	8	8
17																	As in "early 2020" example, most c>u SNPs happen in c's before or after a's and u's. Except for BA.0 and BA.1, the VOCs obey this pattern, indicating that the c>u's they do have likely originate in "normal" conditions. Delta remains a peculiar case here, for likely having the most transmission before identification but the least c>u.
18
19	‡coding mutation rates derived from Fig 5, converted to percentage. With all mutation rates, creativity was required for scaling transversions since nothing is provided for them in Fig 2. I decided to set a sum for all mutations of 234 based on the .73 dN/dS ratio (taking directly from Simmonds' own calculation in Fig1, using highest basket), while scaling transversions discretely using the transversion dN/dS from the VOCs (as Simmonds comments that synonymous transversions were not common, nor would one expect them to be outside of the UTR). With overall - modeled transversion = 209, the values from Fig 2 were scaled accordingly.
20	*triple-SNP's censored, as these likely originate in weird DEL/INS or TRS-B recombs
21	**K417N censored, as appeared after first squences in August (removing K417N diminishes the overall transversion signal and also removes a spike/rbd transversion)
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