Table 2.

Classification of strain-variableORFs into species sets and phylogroups

Species profile	Phylogroup
	ROW*	RO	R8	R7	Total
Set 1: all species
1, 2, 3, 4, 5, 6, 7	29	15	30	1	75
Total	29	15	30	1	75
Set 2: TG + SFG
1, 2	0	0	1	3	4
1, 2, 3	1	0	2	0	3
1, 2, 3, 4, 5	0	0	1	0	1
1, 2, 3, 4, 6	0	0	1	0	1
1, 2, 3, 4, 5, 6	0	0	1	0	1
1, 2, 3, 4, 5, 7	3	0	1	0	4
1, 2, 3, 5, 6, 7	0	1	1	0	2
1, 2, 3, 6, 7	0	0	1	0	1
1, 2, 4	0	1	0	0	1
1, 2, 4, 5, 6	0	0	1	0	1
1, 2, 4, 5, 6, 7	0	0	2	0	2
1, 3, 4, 5, 6, 7	4	1	1	0	6
1, 3, 5, 6, 7	0	0	1	0	1
1, 4, 5, 6, 7	0	0	1	0	1
2, 3, 4, 5, 6, 7	0	1	0	0	1
2, 3, 5, 6, 7	0	0	1	0	1
Total	8	4	16	3	31
Set 3: SFG only
3, 4	2	4	19	3	28
3, 4, 5	0	0	3	0	3
3, 4, 5, 6, 7	16	6	53	1	76
3, 4, 5, 6	0	0	6	0	6
3, 4, 6	0	0	1	0	1
3, 4, 6, 7	0	0	1	0	1
3, 4, 7	0	0	1	0	1
3, 5	0	1	5	0	6
3, 5, 6	0	0	4	1	5
3, 5, 6, 7	4	2	17	2	25
3, 5, 7	0	0	3	0	3
3, 6	0	1	3	0	4
3, 6, 7	0	0	1	0	1
3, 7	0	0	2	2	4
4, 5	0	0	1	0	1
4, 5, 6	1	0	0	0	1
4, 5, 6, 7	1	1	3	0	5
5, 6	0	0	9	1	10
5, 6, 7	5	0	16	5	26
5, 7	0	0	3	2	5
6, 7	0	0	1	2	3
Total	29	15	152	19	215
Set 4: single species
1	1	4	2	2	9
3	21	5	69	20	115
4	1	0	11	1	13
5	0	0	3	1	4
6	0	0	2	1	3
7	0	1	3	0	4
Total	23	10	90	25	148
Grand total	89	44	288	48	469

Number abbreviations for species are as follows: 1, R. prowazekii; 2, R. typhi; 3, R. felis; 4, R. akari; 5, R. conorii; 6, R. sibirica; and 7, R. rickettsii. The phylogroup ROW* is a summary of ROW, RW, W, and OW. ORF, open reading frame; SFG, spotted fever group; TG, typhus group.