TABLE 2.

Unique and pair-specific SNPs in H. pylori reisolates from infected volunteers^a

Functional category and no.	Strain(s)	Position	From > to	Type	ORF	HP no.
Energy metabolism
1	78A3	317530	c > t	Nonsynonymous	pgi	HP1166
2	87A3	622512	c > t	Nonsynonymous	hydA	HP0631
3	8A3, 8C10	1407887	c > t	Nonsynonymous	putA	HP0056
Cell envelope, transport, and binding proteins
4	12C8	33480	a > g	Nonsynonymous	copA	HP1503
5	81A1	34327	t > c	Nonsynonymous	copA	HP1503
6	29A2	231005	g > a	Nonsynonymous	babA	HP1243
7	8C10	231370	c > a	Stop	babA	HP1243
8	8A3	232590	g > a	Nonsynonymous	babA	HP1243
9	87A3	896139	c > a	Nonsynonymous	oppB	HP1251
10	119C10	1185884	g > a	Nonsynonymous	rfaC	HP0279
11	119A2	1211998	g > a	Nonsynonymous	oppC	HP0251
12	125A3	1213476	g > a	Nonsynonymous	oppD	HP0250
13	78A3	1213737	g > t	Stop	oppD	HP0250
14	87A3	1213789	g > a	Nonsynonymous	oppD	HP0250
DNA metabolism
15	12A3	815510	t > c	Synonymous	uvrC	HP0821
Protein synthesis
16	29C8	1336072	c > t	Nonsynonymous	thrS	HP0123
Regulatory functions
17	103A4	1298936	c > t	Nonsynonymous	arcS	HP0164
Unknown and hypothetical
18	125C7	166082	c > t	Nonsynonymous	NA	HP0953
19	29C8	332008	a > g	Nonsynonymous	NA	HP1154
20	103C8	426225	c > t	Nonsynonymous	NA	HP0394
21	103C8	1303279	c > t	Nonsynonymous	hcpD	HP0160
22	48A2, 48C8	1331716	c > t	Nonsynonymous	NA	HP0130
23	103C8	1560203	g > a	Nonsynonymous	NA	HP1533
Noncoding regions
24	119A2	472706	c > t		Intergenic
25	125C7	925414	c > t		Intergenic

^aPosition refers to the location of the SNPs in the reference genome of clone H1. HP no. refers to the reference strain H. pylori 26695. ORF, open reading frame; NA, not available.