Table 2.

Additional B. pertussis, B. bronchiseptica, and B. parapertussis HPTs analyzed in this study

	B. pertussis Tohama I		B. bronchiseptica RB50		B. parapertussis 12822
HPT numa	ORFb	Allelec	ORF	Allele	ORF	Allele	Gene	Base	Poly-morphicd	Loce	Promoter overlapf	Functional categoryf
47	BP0059	8	BB0530	6	BPP0525	6		C/G	y	C		Global regulatory functions
81	BP1877	6	BB2995	6	BPP3029	6	bvgS	C/G	n	C		Global regulatory functions
57	BP3651	8	BB0066	6	BPP0066	6		C/G	y	I	H	Cell envelope
85	BP3783	6	BB4890	6	BPP4304	6	ptxA	C/G	n	I	K	Periplasmic/exported/lipoproteins

^a HPT number is an arbitrarily assigned unique ID. Table is sorted by order in the B. bronchiseptica RB50 genome.

^b Identifier of ORF that is either contains or is downstream of the HPT. Empty cell indicates that no orthologous sequence exists in that genome.

^c Numbers are length of HPTs. Sequences are given when the tract contains a substitution relative to alleles in the other genomes.

^d "y" denotes HPT length polymorphism among the three sequenced genomes.

^e "I", located in intergenic region; "C", located in coding sequence

^f Probability that the HPT overlaps a promoter coded as follows: H, high; K, known to overlap experimentally defined promoter.

Values were determined only for coding HPTs. See Methods for definitions of classes.

^g Functional categories from MultiFun classification system as assigned by Parkhill, et al. [3]