TABLE 3 

Homoplasic SNPs

PositionaLocus tag(s)GeneBranchesbBootstrapcChangedProduct
(distance to ATG in bp)
Functional categoryLocalizationeBvgf
612075BP0607gpm2 (1, 3)99SilentPhosphoglycerate
mutase 1
Energy metabolismCytoplasmic
667028BP06582 (1, 19)55Q30Putative dehydrogenaseMiscellaneousCytoplasmic
925864BP08882 (7, 1)100SilentGntR family
transcriptional regulator
RegulationCytoplasmic
997017BP0958cysM5 (1, 1, 4, 2, 1)100G247ECysteine synthase BAmino acid
biosynthesis
Cytoplasmic
11093101064BPmaeB2 (6, 1)100SilentNADP-dependent malic
enzyme
Central/intermediary
metabolism
Cytoplasmic
11093121064BPmaeB2 (6, 1)100Q28PNADP-dependent malic
enzyme
Central/intermediary
metabolism
Cytoplasmic
11759561119BPfim22 (7, 9)100R177KSerotype 2 fimbrial
subunit precursor
Virulence-
associated genes
Extracellular+
15655291487BPsmoM2 (1, 4)100R176KPutative periplasmic
solute-binding protein
Transport/binding
proteins
Unknown+
16479891568BPfim32 (1, 1)98T130ASerotype 3 fimbrial
subunit precursor
Virulence-
associated genes
Extracellular+
2018882BP1914P2 (1, 2)100IntergenicTransposase for IS1663
(321)
Phage or transposon
related
Unknown
BP1915P2 (1, 2)100IntergenicConserved hypothetical
protein (23)
Conserved
hypothetical
Unknown
2213448BP2090P2 (8, 1)100IntergenicABC transporter
substrate-binding protein
(306)
Transport/binding
proteins
Periplasmic
BP2091P2 (8, 1)100IntergenicDioxygenase hydroxylase
component (53)
Small molecule
degradation
Cytoplasmic
23743222249BPbscI2 (1, 97)60Y114CType III secretion proteinVirulence-
associated genes
Unknown+
3041105BP2862P2 (6, 1)100IntergenicConserved hypothetical
protein (174)
UnknownUnknown
BP2863P2 (6, 1)100IntergenicConserved hypothetical
protein (148)
UnknownCytoplasmic
3251279BP3052P2 (6, 2)100IntergenicPutative gamma-
glutamyl transpeptidase
(242)
MiscellaneousPeriplasmic
39920643789BPptlB2 (1, 1)69SilentPertussis toxin transport
protein
Virulence-
associated genes
CM+
  • a Position in reference genome B. pertussis Tohama I.

  • b Number of branches in which the homoplasic SNP occurred (number of strains/branch).

  • c Number of trees in which SNP is homoplasic (100 trees tested).

  • d Change in amino acid.

  • e Subcellular localization: CM, cytoplasmic membrane.

  • f Regulation by Bvg: + activated; − repressed; blank cells, not activated or repressed.