TABLE 2.

Twenty mutations identified in genomes of D-EC and D-LC compared to C. trachomatis D/UW-3/CX^a

SNP locationb	Gene	Reference D/UW-3/CX		D-EC		D-LC
		Gene start position	Gene stop position	nt change	aa change	nt change	aa change
30572	CT025	29069	29941	C → G	Thr → Ser	C → G	Thr → Ser
55047	CT049	54113	55585	G → C	Gly → Ala	G → C	Gly → Ala
55099	CT049	54113	55585	A → G	None	A → G	None
152276	CT135	152143	153225	None	None	ΔT	Frameshift
152686	CT135	152143	153225	::T	Frameshift	None	None
403784	CT352	403499	403804	A → C	Ile → Leu	A → C	Ile → Leu
450477	CT394	449841	451019	A → G	Lys → Glu	A → G	Lys → Glu
517109	IGc (CT446-CT447)	516946	519105	G → T	None	G → T	None
588168	CT511	587942	588376	G → T	Thr → Lys	G → T	Thr → Lys
621054	CT551	620037	621068	::G	Frameshift	::G	Frameshift
628883	IG (CT556-CT557)	628808	630414	C → T	None	C → T	None
706330	CT621	704354	706852	T → C	Thr → Ala	T → C	Thr → Ala
717493	CT630	717087	717770	T → C	Gln → Arg	T → C	Gln → Arg
720059	IG (CT632-CT633)	719973	721287	A → T	None	A → T	None
727542	CT638	726792	727559	::G	Frameshift	::G	Frameshift
733706	CT640	730899	733913	T → C	Thr → Ala	T → C	Thr → Ala
752502	IG (CT655-CT656)	752365	753143	::C	None	::C	None
858691	23S rRNA	878039	880902	G → A	None	G → A	None
858694	23S rRNA	878039	880902	G → A	None	G → A	None
858698	23S rRNA	878039	880902	ΔC	None	ΔC	None

^aBoldface type indicates unique mutations identified in D-EC and D-LC. nt, nucleotide; aa, amino acid; ::, insertion; Δ, deletion.

^bSNP location refers to the location of the mutation in the reference D/UW-3/CX genome; for a single base pair insertion, the location of the preceding nucleotide is given.

^cIG, intergenic region and adjacent ORFs.