Table 2.

Synonymous SNPs and less significant non-synonymous SNPs identified by GWAS.

-log10(P)	Genomic position	Locus including or closest to the SNP	Gene name	Description	Function	Variant associated with gastric cancer	Position in the gene	Amino acid change	Corresponding locus in the strain 26695
4.7	485 026	HPF57_0479 [483 859–485079] (-)	ispDF	bifunctional 2-C-methyl-d-erythritol 4-phosphate cytidylyltransferase/2-C-methyl-d-erythritol 2,4-cyclodiphosphate synthase protein for isoprenoid synthesis	isoprenoid synthesis	T	54	–	HP1020
4.6	549 551	HPF57_0538 [549 128–550432] (+)	pgbA	plasminogen binding protein	anti-immunity	C	424	–	HP0508
4.5	163 266	HPF57_0158 [162 843–164288] (-)	lldF	L-lactate dehydrogenase to pyruvate	anaerobic catabolism	C	1023	–	HP0138
4.5	713 996	HPF57_0678 [711 939–714599] (+)	bamA	outer membrane protein assembly factor; surface antigen D15	assembly of outer membrane β-barrel proteins	C	2058	–	HP0655
4.4	101 839	HPF57_0101 [101 587–103584] (-)	rpoD	RNA polymerase sigma factor σ70	transcription initiation	C	1746	–	HP0088
4.2	389 519	HPF57_0382 [389 375–390157] (-)	nadE	NH3-dependent NAD+ synthetase	NAD synthesis	G	639	–	HP0329
4.2	598 098	HPF57_0574 [594 999–598511] (+)	cagA	cytotoxin-associated gene A	interferences with signal transduction	G	3100	A1034T,X,S	HP0547
4.2	146 365	HPF57_0139 [145 564–146508] (-)	ctbP	human C-terminal binding protein homolog	interference with gene expression? oncoprotein?	G	144	E48EDX	HP0096
4.1	1 102 964	HPF57_1035 [1 102 345– 1 103 568] (+)	zmp	zinc-metallo protease acting on isoprenylated protein		A	620	K207R	HP0382
4.1	1 292 278	HPF57_1206 [1 292 110– 1 293 132] (-)	holA	DNA polymerase III subunit delta	DNA replication	G	855	–	HP1247
4.1	1 111 855	HPF57_1042 [1 111 772– 1 112 203] (+)	hemX	haem interaction		C	84	–	HP0375
4.1	686 823	HPF57_0653 [686 461–688509] (+)	mdr	modification-specific restriction	restriction	C	363	–	no ortholog

position in F57 reference genome.