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Table 3 Summary of nucleotide sequence variation between the MC/Mars Bar koala C. pecorum type strain and non-koala C. pecorum strains in sampled regions of the C. pecorum genome

From: Novel molecular markers of Chlamydia pecorum genetic diversity in the koala (Phascolarctos cinereus)

Group and locus N Size (bp) AlleleNo. Δnt %nt π Δrep %rep Δnon-rep %non-rep dN/dS D Pars D.I.
Housekeeping Genes
16S rRNA 2 1549 2 2 0.130 0.001 N/A N/A N/A N/A N/A N/A 0 N/A
16S/23S intergenic spacer 2 225 1 0 0.000 0 N/A N/A N/A N/A N/A N/A 0 N/A
Membrane Proteins
ompA 20 1170 13 122 10.430 0.162 72 59.020 21 17.210 0.170 1.734 111 0.910
omcB 2 1675 2 8 0.420 0.004 7 87.500 1 12.500 2.150 N/A 0 N/A
pmpD 2 4145 2 20 0.480 0.005 13 65.000 5 25.000 0.670 N/A 0 N/A
incA 20 984 17 116 11.790 0.656 78 67.240 19 16.380 1.540 0.703 59 0.980
copN 20 1191 9 9 0.760 0.008 9 55.560 5 44.440 0.550 1.163 7 0.880
Potential Virulence Genes
tarP 2 2604 2 56 2.150 0.029 37 66.070 19 33.903 0.660 N/A 0 N/A
MACPF 2 2346 2 7 0.300 0.003 5 71.430 2 28.570 0.730 N/A 0 N/A
ORF663 20 552 18 66 11.960 0.741 29 43.940 23 34.850 1.350 0.381 48 0.980
  1. N: no. of C. pecorum sequences analysed; Allele no.: no. of unique sequences according to gene; Δnt: number of polymorphic nucleotide sites; %nt: percent nucleotide sites polymorphic; π: average p-distance at all sites; Δrep: number of polymorphic sites resulting in an amino acid replacement; %rep: percent sites with replacement; Δnon-rep: number of polymorphic sites not resulting in an amino acid replacement (synonymous changes); %non-rep: percent sites with non-replacement; dN/dS: ratio of the number of non-synonymous (dN) to synonymous (dS) substitutions per site; D: Tajima's test for neutrality; Pars: parsimony-informative sites; D.I.: discrimination index; D: Tajima's test for neutrality.