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

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


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.

Marsh et al. BMC Microbiology 2011 11:77   doi:10.1186/1471-2180-11-77

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