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Table 8 Intragenic and intergenic recombination in six L. pneumophila genomes predicted on individual genes and on combined data using six different methods

From: Extensive recombination events and horizontal gene transfer shaped the Legionella pneumophila genomes

   

Detection Method

Data set

Event Number

Putative recombinant sequences

RDP

GENECONV

Boot

scan

Max

chi

Chimaera

SiSscan

metG

1

Lorraine, Lens

NS

NS

NS

Yes

Yes

Yes

dnaX

1

Philadelphia

NS

NS

Yes

Yes

Yes

Yes

 

2

Lens, Lorraine

NS

NS

NS

Yes

Yes

Yes

proS

1

HL06041035

Yes

Yes

Yes

Yes

Yes

Yes

 

2

Philadelphia

NS

Yes

NS

Yes

Yes

Yes

cysS

1

Philadelphia

NS

NS

NS

Yes

Yes

NS

lig

1

Lorraine

NS

Yes

Yes

NS

NS

NS

uvrC

1

Lens,Philadelphia, Lorraine

NS

NS

NS

Yes

Yes

Yes

flh

1

Lens

NS

NS

Yes

Yes

Yes

Yes

 

2

Paris, HL06041035

NS

NS

NS

Yes

Yes

Yes

pgk

1

Lens

NS

NS

NS

Yes

Yes

Yes

atpD

1

Corby

NS

NS

NS

Yes

Yes

Yes

Concatenated

1

Philadelphia

Yes

Yes

Yes

Yes

Yes

Yes

 

2

Philadelphia

Yes

Yes

Yes

Yes

Yes

Yes

 

3

HL06041035

Yes

Yes

Yes

Yes

Yes

Yes

 

4

HL06041035

Yes

Yes

Yes

Yes

Yes

Yes

 

5

Philadelphia, Corby, Lorraine

Yes

Yes

Yes

Yes

Yes

Yes

 

6

Lens

Yes

Yes

Yes

Yes

Yes

Yes

 

7

Paris, HL06041035

Yes

NS

NS

Yes

Yes

NS

 

8

Paris

Yes

Yes

Yes

Yes

Yes

Yes

 

9

Lens

Yes

Yes

NS

Yes

Yes

Yes

 

10

Lens

Yes

Yes

Yes

Yes

Yes

NS

 

11

HL06041035

Yes

Yes

NS

Yes

NS

NS

 

12

Paris, HL06041035

Yes

Yes

Yes

Yes

Yes

Yes

 

13

HL06041035, Lens

NS

Yes

NS

Yes

Yes

Yes

 

14

Lens, Lorraine

Yes

NS

NS

Yes

Yes

NS

 

15

Paris, HL06041035

Yes

Yes

NS

Yes

Yes

NS

 

16

Corby

Yes

NS

NS

Yes

Yes

NS

 

17

Lens

NS

Yes

NS

Yes

Yes

NS

 

18

HL06041035, Paris

Yes

NS

NS

Yes

Yes

Yes

 

19

Corby

Yes

NS

NS

Yes

Yes

NS

 

20

Lorraine

Yes

Yes

NS

NS

NS

Yes

 

21

Lens

Yes

NS

Yes

NS

NS

Yes

 

22

Corby

Yes

NS

Yes

Yes

NS

Yes

 

23

Lens

NS

Yes

NS

Yes

NS

NS

 

24

Lens

NS

Yes

NS

Yes

NS

Yes

 

25

Philadelphia

Yes

NS

NS

Yes

Yes

Yes

  1. NS = non significant result. Yes = significant result with p-value ≤0.05 (where P is the highest acceptable probability value of recombination occurrence).