TABLE 1.

Nucleotide diversity and Pi(a)/Pi(s) ratio for C. trachomatis TrpR-, TrpB-, and TrpA-coding sequences (CDS) for ocular, urogenital/rectal, and LGV strains based on phylogenetic lineages^a

CDS	No. of haplotypes	Haplotype diversity (Hd)	Ct lineage	No. of sequences	No. of polymorphic segregating sites (Ss)	Synonymous nucleotide diversity (Pi(s); Jukes-Cantor corrected)	Nonsynonymous nucleotide diversity (Pi(a); Jukes-Cantor corrected)	Pi(a)/Pi(s) ratio	No. of synonymous substitutions	No. of nonsynonymous substitutions
trpR	10	0.2889	Ocular	79	1	0	0.00011	0	0	1
			Urogenital/rectal	455	14	0.00179	0.00101	0.564	4	9
			LGV	70	0	0	0	0	0	0
trpB	26	0.4844	Ocular	79	36	0.00075	0.00164	2.182	16	20
			Urogenital/rectal	455	20	0.00126	0.00092	0.726	9	11
			LGV	70	1	0	0	0	1	0
trpA	19	0.5883	Ocular	79	8	0.00074	0.00164	2.212	3	5
			Urogenital/rectal	455	16	0.00158	0.00209	1.317	6	10
			LGV	70	0	0	0	0	0	0

^aNote that TrpR-, TrpB-, and TrpA-CDS were extracted from individual strains and segregated into ocular, urogenital, rectal, and LGV disease groups; TrpA-CDSs from urogenital strains were further segregated into vaginal and urethral strains. Diversity metrics were calculated in DnaSP6 using the MAFFT alignment (see Materials and Methods).