Genomic analyses of the Chlamydia trachomatis core genome show an association between chromosomal genome, plasmid type and disease

Table 2 Polymorphism analysis and allelic variance of the plasmid genes derived from 157 Chlamydia trachomatis isolates

				Overall Mean Distance (pairwise deletion; bootstrap = 1000 replicates)
				Nucleotide				Amino Acid				P-distance; Non- and Synonymous substitutions
Gene (ORF)^a	Length (bp)^b	No. alleles	No. polymorphic sites	No. of differences	[SE]	P-distance	[SE]	No. of differences	[SE]	P-distance	[SE]	Mean dS	[SE]	Mean dN	[SE]	dN/dS^c
pgp1 (ORF3)	1356	12	18	4.965	1.402	0.004	0.001	1.602	0.682	0.004	0.002	0.007	0.002	0.002	0.001	0.286
pgp2 (ORF4)	1065	14	20	4.420	1.125	0.004	0.001	1.043	0.553	0.003	0.002	0.009	0.003	0.001	0.001	0.111
pgp3 (ORF5)	795	12	23	6.133	1.488	0.008	0.002	4.172	1.122	0.016	0.004	0.007	0.003	0.007	0.002	1.000
pgp4 (ORF6)	309	3	2	0.363	0.262	0.001	0.001	0.243	0.239	0.002	0.002	0.001	0.001	0.001	0.001	1.000
pgp5 (ORF7)	795	13	15	2.720	0.934	0.003	0.001	2.111	0.872	0.008	0.003	0.002	0.001	0.004	0.002	2.000
pgp6 (ORF8)	744	17	20	3.003	1.020	0.004	0.001	1.415	0.648	0.006	0.003	0.006	0.003	0.003	0.001	0.500
pgp7 (ORF1)	918	13	23	4.523	1.227	0.005	0.001	1.715	0.739	0.006	0.002	0.010	0.004	0.002	0.001	0.200
pgp8 (ORF2)	993	11	18	4.346	1.223	0.004	0.001	0.476	0.428	0.001	0.001	0.012	0.004	0.001	0.001	0.083

^aORFs designation according to Thomas et al., 1997. Microbiology. 143, 1847–1854
^bLength in base pairs relative to the sequence of the plasmid of the E/Bour strain (GenBank No. HE603212)
^cThe value of dN/dS > 1 obtained for pgp5 was not statistically significant by the Z-test of positive selection

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