TABLE 2.

Summary of nucleotide sequence variation in sampled regions of the C. trachomatis genome^a

Group and locus	Size (bp)	Δnt	%nt	Δrep	%rep	pars	π	πs	πa	πs/πa
Housekeeping genes
ssb	54	0	0.0	0	0.0	0	0.000	0.000	0.000
pepA	84	2	2.4	1	3.6	2	0.010	0.027	0.005	5.94
araD	337	3	0.9	3	2.7	2	0.002	0.000	0.002	0.00
adk	313	0	0.0	0	0.0	0	0.000	0.000	0.000
hemZ	297	2	0.7	2	2.0	1	0.001	0.000	0.002	0.00
gap	328	2	0.6	1	0.9	2	0.002	0.005	0.001	3.89
thdF	39	0	0.0	0	0.0	0	0.000	0.000	0.000
uvrC	289	0	0.0	0	0.0		0.000	0.000	0.000
mrsA	334	3	0.9	1	0.9	1	0.002	0.003	0.003	1.00
Total	2,073	12	0.6	8	1.2	8	0.002	0.002	0.001	1.65
Intergenic noncoding
ssb-pepA	342	17	4.9			15	0.014	0.014
rpoB-r17	342	10	2.9			6	0.009	0.009
rs4-yceA	266	4	1.5			3	0.004	0.004
thdF-psdD	237	6	2.5			5	0.007	0.007
glyQ-pgsA	425	4	0.9			4	0.003	0.003
Total	1,612	41	2.5			33	0.007	0.007
porB	1,023	11	1.1	8c	2.3	9	0.003	0.003	0.003	0.86
ompA	1,194	334	27.7	99	24.9	301	0.121	0.289	0.069	4.20
pmp genesb
pmpH	2,988	263	8.8	76	7.6	258	0.037	0.101	0.015	6.55
pmpE	2,826	172	6.1	63	6.6	160	0.026	0.061	0.015	3.91
pmpI	2,538	46	1.8	21	2.5	36	0.006	0.012	0.003	3.69
pmpC	5,355	86	1.6	64	3.6	72	0.005	0.005	0.005	1.05

^aΔnt, number of polymorphic nucleotide sites; %nt, percent nucleotide sites polymorphic; Δrep, number of polymorphic sites resulting in an amino acid replacement; %rep, percent sites with replacement; pars, parsimony informative sites; π, π_s, and π_a, average p-distances at all sites, synonymous sites, and nonsynonymous sites, respectively.

^bAnalyses based on published nucleotide sequence data (15, 48); these sequences represent the same serovars as used in this study, but some sequences come from different strains.

^cThis includes one substitution resulting in a premature stop codon.