Table 2. Identified SNPs defining the Lineage 1.0/2.0 divergence (Top) and the Bovine-associated/Poultry-associated divergence (Bottom).

S = synonymous mutation. NS = non-synonymous mutation.

Lineage 1.0 / 2.0	Locus Tag a	Annotation b	Genome Position a	nt Lineage 2.0	nt Lineage 1.0	Substitution c	aa Lineage 2.0	aa Lineage 1.0	aa Position a	Method
	intergenic		528068	C	T					1, 2, 3
	SeKA_A1002	LysR substrate binding domain protein	953413	A	G	S	Leu	Leu	223	1, 2, 3
	SeKA_A1027	nitrite extrusion protein 2	984718	C	T	S	Pro	Pro	288	1, 2, 3
	intergenic		1032798	A	G					2, 3
	SeKA_A1948	amidophosphoribosyltransferase	1876321	G	A	S	Ala	Ala	288	1, 2, 3
	intergenic		2432705	T	G					1, 2, 3
	intergenic		3169966	T	G					1, 2, 3
	SeKA_A4700	propionate—CoA ligase	4587482	A	C	NS	Asn	Thr	240	2, 3
Bovine / Poultry	Locus Tag a	Annotation b	Genome Position a	nt Poultry-associated	nt Bovine-associated	Substitution c	aa Poultry	aa Bovine	aa Position	Method
	SeKA_A1094	protein YdcF	1055798	T	C	NS	Thr	Ala	43	1, 2, 3
	SeKA_A2591	hemolysin-3	2519134	A	C	NS	Phe	Val	32	3
	SeKA_A2812	methyltransferase family protein	2713142	G	A	NS	Ser	Leu	39	1, 2, 3
	SeKA_A4467	carbonate dehydratase	4347265	G	T	NS	Ala	Asp	22	1, 2, 3

^a = Locus/Position in S. Kentucky CVM29188

^b = Annotation in S. Kentucky CVM29188 (accession no. ABAK02000001.1)

^c = S(synonymous), NS(nonsynonymous)

1 = Parsnp

2 = Lyve-SET

3 = CFSAN SNP Pipeline