TABLE 3.

Coding region SNVs in CT9 strains P590 and P589 and CT76 strains P665 and P666^a

CT	Ref nt	Alt nt	Mutation type	Impact	Gene name	Ref aa	Alt aa	aa position	Protein length	Function
CT9	A	C	Missense	Moderate	L_00407	Ser	Arg	22	470	Putative ATPase, hypothetical protein
	A	C	Missense	Moderate	L_00407	Asn	Thr	282	470	Putative ATPase, hypothetical protein
	G	T	Missense	Moderate	L_00640	Pro	Thr	513	844	Translation initiation factor IF-2
	A	C	Stop lost	High	L_00728	Ter	Ser	229	228	Outer membrane protein P1, long-chain fatty acid outer membrane transporter
	T	C	Missense	Moderate	L_01000	Asn	Asp	59	137	Phage GP46 family protein, hypothetical protein
	A	G	Missense	Moderate	L_01011	Ser	Pro	91	101	Putative uncharacterized protein, putative protein
	C	A	Missense	Moderate	L_01014	Glu	Asp	131	161	Phage virion morphogenesis protein
	T	C	Missense	Moderate	L_01016	Asn	Asp	521	546	Putative uncharacterized protein, hypothetical protein
	TG	CA	Missense	Moderate	L_01016	Lys	Glu	514	546	Putative uncharacterized protein, hypothetical protein
CT76	AGGA	AA	Frameshift	High	L_00010	Gly	FS	140	258	Hypothetical protein
	A	C	Missense	Moderate	L_00404	Lys	Thr	413	1046	Outer membrane receptor protein, putative Fe transport, hemoglobin/ hemoglobin-haptoglobin binding protein B
	CT	CTCGAT	Frameshift and stop lost	High	L_00626	Ter	FS	168	167	Outer membrane protein P1, long-chain fatty acid outer membrane transporter
	T	C	Noncoding transcript	Modifier	L_00890					rRNA
	A	C	Missense	Moderate	L_00973	Tyr	Asp	345	366	Outer membrane protein P2 precursor
	C	T	Missense	Moderate	L_00973	Gly	Ser	93	366	Outer membrane protein P2 precursor
	A	C	Missense	Moderate	L_01164	Gln	Pro	288	704	Guanosine-3',5'-bis 3'- pyrophosphohydrolase
	C	T	Missense	Moderate	L_01164	Pro	Leu	402	704	Guanosine-3',5'-bis 3'- pyrophosphohydrolase
	T	A	Noncoding transcript	Modifier	L_01171					rRNA
	A	T	Noncoding transcript	Modifier	L_01171					rRNA
	T	G	Missense	Moderate	L_01757	Ser	Ala	322	366	Histidinol-phosphate aminotransferase 2

^ant, nucleotide; Ref, reference; Alt, alternative; aa, amino acid; FS, frameshift. The CT9 strain P589 contained each SNV; P590 contained none of them, it was used as reference. CT76 strain P666 contained each SNV; P665 contained none of them, it was used as reference.