. 2013 Jul 25;8(7):e70147. doi: 10.1371/journal.pone.0070147

Table 2. High-confidence candidates for pathoadaptive mutations.

	Lineage	Pos Start	Pos End	Ref	Variant	# Reads	% Different	Gene affected	AA sequence^a	Function
Chromosome	DA5822	328501	328501	A	–	21	52%	STM0286	Frameshift	Putative cytoplasmic protein, mutation fuses STM0286 to STM0287 (putative periplasmic protein)
	DA5803 DA5816	392852	392852	A	G	28	11%	STM0350.S	L342P (455)	Outer membrane efflux-like protein^b
	DA5803	1099934	1099934	C	T	18	22%	STM1007	I54V (79)	Hypothetical protein
	DA5816	1318652	1318652	A	T	21	57%	*phoQ*	L13Q (487)	Transmembrane sensor kinase, regulates resonse to low Mg²⁺ and cationic peptides
	DA5894	1852977	1852977	T	C	13	31%			Intergenic
	DA5915	2242837	2242837	C	A	28	11%	stcD	D335Y (335)	Putative outer membrane lipoprotein
	DA5915	2942948	2942948	T	C	24	37%			Intergenic, between gapP and gabT
	DA5810	2947501	2947503	TTC	–	25	60%	*stpA*	ΔE42 (42/134)	DNA binding protein, nucleoid associated. Represses RpoS regulon, homolog of H-NS
	DA5822	3804942	3804942	C	A	37	30%	yhjS	Truncation (93/523)	bcsE homolog, required for cellulose biofilm synthesis
	DA5822	3807045	3807045	G	A	32	22%	yhjU	Truncation (209/559)	Putative cellulose biosynthesis protein
	DA5816	4402521	4402521	C	T	22	14%	aceB	Synonymous	Malate synthase
pSLT	DA5803 DA5816	35606	35606	A	G	47	15%	rlgA	M>T (391/554)	Putative integrase protein

Reference>Variant (position in protein/total protein length).

Variant also found in DA5822 but not called as high-confidence (3 non-duplicate reads).