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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).