Table 1. Summary of ORF variability.

Genomes	Orthologous scaffolds*	No. of ORF alignments†	Nucleotide difference, %	Amino acid difference, %	Ka/Ks
Pairwise comparisons
B31 and JD1	Main chromosome	705 (88.6%)	0.4615	0.4618	0.1353
	lp54,cp26,cp9,lp17,lp25,lp28-2,lp28-4,lp38,lp36	100 (42.0%)	0.8131	0.9553	0.2003
B31 and N40	Main chromosome	706 (88.7%)	0.5706	0.5681	0.1344
	lp54,cp26,lp25,lp28-3,lp28-4,lp36	146 (84.4%)	2.0342	3.0364	0.3999
JD1 and N40	Main chromosome	692 (86.9%)	0.6083	0.5882	0.1279
	lp54,cp26,lp25,lp28-4,lp36	83 (55.3%)	1.8611	2.6895	0.3577
HDNPs vs. non-HDNPs on lp54 and cp26
B31 and N40	BBA24,68,69,70	4 (7.0%)	24.7	42.6	0.7145
	Rest of lp54	45 (78.9%)	0.3380	0.4334	0.1937
	ospC	1 (3.8%)	17.1	25.8	0.5750
	Rest of cp26	22 (84.6%)	0.7832	0.7457	0.1236

^*Orthologous genome segments, B31 nomenclature (23, 24).

^†No. of alignments of orthologous ORFs, given as percentage of total ≥250-bp ORFs predicted on B31 chromosome or plasmids.