TABLE 5.

Variant SLV alleles among all CCs and singletons identified in the study collection and identification of the genetic events involved

ST of clonal ancestor	ST of SLV	Variant locus	Ancestral allele	SLV allele	No. of nucleotide differences	Other CC(s) containing SLV allele	Amino acid changea	Genetic eventb
1	83	gtr	2	1	7	CC1, CC2, CC21, S55	2 Syn + E→V, L→H, A→V, C→H, L→S	R
1	38	mut	2	5	4	CC11, CC33, CC49, CC66, S39, S82	1 Syn + A→S, I→T, E→K	R
2	80	arc	7	21	1	CC23	1 Syn	M
2	54	arc	7	1	13	CC1, CC42, S32, S44, S55, S60, S65, S73	10 Syn + K→E, I→V, K→Q	R
2	35	arc	7	2	14	CC21, S8	10 Syn + K→E, I→V, K→Q, E→K	R
2	67	gtr	2	18	1	None	D→H	M
2	76	mut	2	14	1	None	1 Syn	M
2	74	mut	2	12	2	None	1 Syn + S→C	R
2	43	pyr	4	1	2	CC1, CC21, CC42, S44, S8	2 Syn	R
2	22	tpi	1	7	1	None	T→S	M
2	75	tpi	1	13	1	CC42, S39	1 Syn	R
2	48	yqiL	1	4	6	CC11	6 Syn	R
2	45	arc	7	20	2	None	G→?	R
4	61	arc	1	2	1	CC21, S8	E→K	R
5	77	arc	1	23	1	None	1 Syn	M
5	87	arc	1	7	13	CC23	10 Syn + K→D, I→V, K→Q	R
5	57	mut	1	2	2	CC1, CC21, S44	1 Syn + Y→R	R
5	46	yqiL	1	7	1	None	Y→H	M
6	17	gtr	2	6	8	S44	2 Syn + V→A, E→V, A→V, P→T, C→H, L→S	R
6	5	gtr	2	1	7	CC1, CC21, S55	2 Syn + E→V, L→H, A→V, C→H, L→S	R
6	58	pyr	1	13	1	CC42, S39	Y→R	R
6	85	pyr	2	1	1	CC1, CC21, CC42, S8, S44	1 Syn	R
6	89	mut	2	1	2	CC2, CC23, CC42, S8, S32, S55, S90	A→S, I→L	R
10	41	yqiL	1	11	7	CC11, C66	1 Syn + Y→H, E→G, Y→C, L→S, F→C, I→T	R
11	53	pyr	3	11	2	CC49	2 Syn	R
11	71	tpi	4	1	3	CC1, CC2, CC21, CC66, S8, S44, S55, S60, S73	1 Syn, G→S, W→R	R
11	50	yqiL	11	4	1	CC2, S82	S→L	R
14	86	aro	1	2	1	CC1, CC21, CC49, S55, S72	I→K	R
17	69	aro	1	18	1	None	1 Syn	M
17	4	mut	2	6	1	S60, S73	1 Syn	R
20	34	tpi	1	13	1	CC42, S39	1 Syn	R
21	52	aro	1	2	1	CC1, CC2, CC49, S55, S72	I→K	R
22	70	pyr	4	14	1	None	I→N	M
23	79	arc	21	7	1	CC2	1 Syn	R
33	47	aro	10	1	13	CC2, CC11, CC21, CC23, CC49, S8, S32, S60, S90	8 Syn + R→S, Y→N, K→I, I→L, I→V	R
42	36	arc	1	11	1	None	V→L	M
43	51	yqiL	1	8	5	None	1 Syn + E→G, Y→C, I→T, Y→H	R
49	84	aro	1	2	1	CC1, CC2, CC21, S55, S72	I→K	R
49	64	pyr	3	11	2	CC11	2 Syn	R
50	62	aro	1	21	1	None	V→G	M
54	6	pyr	4	2	1	S55, S60 S73, S90	1 Syn	R
57	59	arc	1	2	1	CC21, S8	E-K	R
57	10	pyr	2	3	10	CC11, CC23, CC49, S32, S82	9 Syn + Y→R	R
59	81	aro	1	17	1	None	1 Syn	M
64	37	arc	12	18	1	None	I→Y	M
66	68	tpi	14	1	2	CC1, CC2, CC11, CC21, S8, S44, S55, S60, S73	2 Syn	M
75	63	arc	7	22	2	S39	N→H, I→M	R
80	78	tpi	1	13	1	CC42, S39	1 Syn	R
85	14	mut	2	1	2	CC23, CC42, S8, S32, S55, S90	1 Syn + A→S	R
85	20	yqiL	1	3	1	None	U→E	M
89	40	pyr	2	3	10	CC11, CC23, CC49, S32, S82	9 Syn + Y→R	R
89	88	yqiL	1	7	1	None	Y→H	M
Total		95 Syn + 71 Non-Syn	37R+15M

^aSyn, synonymous substitutions; Non-syn, nonsynonymous substitutions. Capital letters correspond to amino acids.

^bR, recombination event; M, mutation event.