breseq  version 0.35.4  revision f352f80f4bc9 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence	position	mutation	freq	annotation	gene	description
RA	5,144	G→A	94.3%	intergenic (+124/‑90)	thrC → / → yaaX	L‑threonine synthase/DUF2502 family putative periplasmic protein
RA	10,444	G→T	100%	F17L (TTC→TTA)	satP ←	succinate‑acetate transporter
RA	12,901	G→A	100%	D247N (GAT→AAT)	dnaK →	chaperone Hsp70, with co‑chaperone DnaJ
RA	15,125	G→T	18.4%	D320Y (GAT→TAT)	dnaJ →	chaperone Hsp40, DnaK co‑chaperone
RA	25,546	G→T	89.7%	D114Y (GAC→TAC)	lspA →	prolipoprotein signal peptidase (signal peptidase II)
RA	28,818	G→T	7.0%	D149Y (GAC→TAC)	dapB →	dihydrodipicolinate reductase
RA	29,139	G→T	93.6%	G256C (GGT→TGT)	dapB →	dihydrodipicolinate reductase
RA	41,442	G→T	28.1%	R164S (CGC→AGC)	caiT ←	putative transporter
RA	42,150	G→A	43.2%	intergenic (‑219/‑253)	caiT ← / → fixA	putative transporter/anaerobic carnitine reduction putative electron transfer flavoprotein subunit
RA	49,840	G→T	94.2%	A6A (GCG→GCT)	folA →	dihydrofolate reductase
RA	51,352	A→T	25.2%	G85G (GGT→GGA)	apaG ←	protein associated with Co2+ and Mg2+ efflux
RA	55,590	G→T	88.7%	T507K (ACG→AAG)	lptD ←	LPS assembly OM complex LptDE, beta‑barrel component
RA	56,677	G→T	94.8%	R145S (CGC→AGC)	lptD ←	LPS assembly OM complex LptDE, beta‑barrel component
RA	68,546	C→A	8.3%	R237S (CGC→AGC)	yabI →	DedA family inner membrane protein
RA	76,821	G→T	42.0%	G177G (GGC→GGA)	leuC ←	3‑isopropylmalate dehydratase large subunit
RA	80,123	C→T	89.7%	G25S (GGC→AGC)	leuL ←	leu operon leader peptide
RA	80,491	G→T	12.1%	intergenic (‑296/‑364)	leuL ← / → leuO	leu operon leader peptide/global transcription factor
RA	81,562	C→A	91.8%	I236I (ATC→ATA)	leuO →	global transcription factor
RA	85,890	G→T	33.8%	intergenic (+371/‑231)	cra → / → mraZ	transcriptional repressor‑activator for carbon metabolism/RsmH methytransferase inhibitor
RA	92,294	C→A	24.7%	R386R (CGC→CGA)	murF →	UDP‑N‑acetylmuramoyl‑tripeptide:D‑alanyl‑D‑ alanine ligase
RA	92,728	G→T	7.5%	L80L (CTG→CTT)	mraY →	phospho‑N‑acetylmuramoyl‑pentapeptide transferase
RA	93,391	G→T	42.6%	T301T (ACG→ACT)	mraY →	phospho‑N‑acetylmuramoyl‑pentapeptide transferase
RA	97,521	C→A	100%	A90A (GCC→GCA)	murC →	UDP‑N‑acetylmuramate:L‑alanine ligase
RA	97,893	T→A	29.3%	F214L (TTT→TTA)	murC →	UDP‑N‑acetylmuramate:L‑alanine ligase
RA	103,467	G→T	94.3%	D142Y (GAT→TAT)	lpxC →	UDP‑3‑O‑acyl N‑acetylglucosamine deacetylase
RA	104,561	G→T	94.0%	A124S (GCG→TCG)	secM →	regulator of secA translation
RA	104,582	A→T	35.6%	T131S (ACG→TCG)	secM →	regulator of secA translation
RA	109,800	A→T	5.4%	intergenic (‑94/‑131)	coaE ← / → guaC	dephospho‑CoA kinase/GMP reductase
RA	110,883	A→T	29.0%	Y318F (TAC→TTC)	guaC →	GMP reductase
RA	118,873	G→T	100%	D99Y (GAC→TAC)	pdhR →	pyruvate dehydrogenase complex repressor; autorepressor
RA	132,639	T→A	11.2%	T105S (ACG→TCG)	speE ←	spermidine synthase (putrescine aminopropyltransferase)
RA	134,028	G→T	47.8%	A153A (GCG→GCT)	cueO →	multicopper oxidase (laccase)
RA	134,652	G→T	23.9%	M361I (ATG→ATT)	cueO →	multicopper oxidase (laccase)
RA	142,460	T→A	93.0%	F298Y (TTC→TAC)	yadE →	putative polysaccharide deacetylase lipoprotein
RA	148,264	G→T	6.4%	A152E (GCA→GAA)	yadL ←	putative fimbrial‑like adhesin protein
RA	153,472	G→T	100%	intergenic (‑102/+268)	yadN ← / ← folK	putative fimbrial‑like adhesin protein/2‑amino‑4‑hydroxy‑6‑hydroxymethyldihyropteridine pyrophosphokinase
RA	158,287	C→A	94.9%	D78Y (GAC→TAC)	ligT ←	2'‑5' RNA ligase
RA	161,068	A→C	39.5%	intergenic (+47/‑149)	hrpB → / → mrcB	putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase
RA	172,107	G→T	29.2%	E172* (GAA→TAA)	clcA →	H(+)/Cl(‑) exchange transporter
RA	172,979	G→T	21.4%	A462A (GCG→GCT)	clcA →	H(+)/Cl(‑) exchange transporter
RA	176,783	G→T	49.9%	D354Y (GAT→TAT)	dgt →	deoxyguanosine triphosphate triphosphohydrolase
RA	176,864	C→T	24.9%	L381L (CTA→TTA)	dgt →	deoxyguanosine triphosphate triphosphohydrolase
RA	179,424	G→T	6.2%	D159Y (GAT→TAT)	cdaR →	carbohydrate diacid regulon transcriptional regulator; autoregulator
RA	183,669	C→A	27.4%	R490L (CGC→CTC)	glnD ←	uridylyltransferase
RA	186,279	A→T	35.2%	noncoding (81/136 nt)	tff →	novel sRNA, function unknown
RA	201,962	A→T	41.2%	D117V (GAT→GTT)	dnaE →	DNA polymerase III alpha subunit
RA	202,839	G→T	13.4%	E409D (GAG→GAT)	dnaE →	DNA polymerase III alpha subunit
RA	215,833	G→T	26.4%	N83K (AAC→AAA)	tsaA ←	tRNA‑Thr(GGU) m(6)t(6)A37 methyltransferase, SAM‑dependent
RA	217,932	A→C	46.2%	I59M (ATT→ATG)	metI ←	DL‑methionine transporter subunit
RA	230,579	C→T	100%	E231K (GAA→AAA)	gloB ←	hydroxyacylglutathione hydrolase
RA	232,860	G→T	94.6%	D103Y (GAT→TAT)	dnaQ →	DNA polymerase III epsilon subunit
RA	233,931	G→A	33.8%	S37N (AGT→AAT)	yafT →	lipoprotein
RA	234,994	G→T	13.4%	S77* (TCA→TAA)	ykfM ←	lethality reduction protein, putative inner membrane protein
RA	235,010	G→T	15.8%	L72I (CTT→ATT)	ykfM ←	lethality reduction protein, putative inner membrane protein
RA	235,019	C→A	24.3%	V69L (GTA→TTA)	ykfM ←	lethality reduction protein, putative inner membrane protein
RA	235,022	G→T	18.9%	H68N (CAT→AAT)	ykfM ←	lethality reduction protein, putative inner membrane protein
RA	236,234	A→T	44.4%	V148E (GTG→GAG)	yafV ←	putative NAD(P)‑binding C‑N hydrolase family amidase
RA	238,195	G→T	100%	V532V (GTC→GTA)	fadE ←	acyl coenzyme A dehydrogenase
RA	250,880	G→T	36.4%	P442T (CCG→ACG)	pepD ←	aminoacyl‑histidine dipeptidase (peptidase D)
RA	262,114	C→A	41.3%	D51Y (GAT→TAT)	yafY ←	lipoprotein, inner membrane; overproduction stimulates degP expression; CP4‑6 prophage
RA	274,735	A→T	90.5%	pseudogene (138/348 nt)	afuB ←	pseudogene, CP4‑6 prophage; ABC transporter permease family;Phage or Prophage Related
RA	279,334	C→A	25.0%	I141I (ATC→ATA)	yagF →	CP4‑6 prophage; dehydratase family protein
RA	283,636	A→C	6.8%	Q379H (CAA→CAC)	yagH →	CP4‑6 prophage; putative xylosidase/arabinosidase
RA	287,667	G→T	12.8%	pseudogene (553/828 nt)	yagJ →	CP4‑6 prophage; uncharacterized protein;Phage or Prophage Related
RA	291,453	A→T	29.1%	L452* (TTA→TAA)	intF ←	CP4‑6 prophage; putative phage integrase
RA	295,092	G→T	27.2%	G518G (GGC→GGA)	paoC ←	PaoABC aldehyde oxidoreductase, Moco‑containing subunit
RA	295,695	T→G	21.4%	E317D (GAA→GAC)	paoC ←	PaoABC aldehyde oxidoreductase, Moco‑containing subunit
RA	302,428	G→T	29.6%	P34Q (CCG→CAG)	ecpD ←	polymerized tip adhesin of ECP fibers
RA	307,454	G→A	8.5%	intergenic (‑407/‑369)	ecpR ← / → ykgL	putative transcriptional regulator for the ecp operon/uncharacterized protein
RA	312,532	G→A	93.3%	pseudogene (349/684 nt)	ykgA ←	pseudogene, AraC family;putative regulator; Not classified; putative ARAC‑type regulatory protein
RA	314,027	C→T	6.9%	E2K (GAA→AAA)	rclC ←	reactive chlorine species (RCS) stress resistance inner membrane protein
RA	317,205	G→A	40.3%	intergenic (+413/‑114)	rclR → / → ykgE	reactive chlorine species (RCS)‑specific activator of the rcl genes/cysteine‑rich LutA family protein; putative electron transport chain YkgEFG component
RA	320,920	G→A	100%	S52S (AGC→AGT)	ykgH ←	putative inner membrane protein
RA	321,223	C→A	92.5%	intergenic (‑148/+65)	ykgH ← / ← betA	putative inner membrane protein/choline dehydrogenase, a flavoprotein
RA	326,385	G→T	29.2%	P404P (CCG→CCT)	betT →	choline transporter of high affinity
RA	329,887	G→T	6.6%	I86I (ATC→ATA)	yahB ←	putative DNA‑bindng transcriptional regulator
RA	344,800	G→T	93.0%	E136D (GAG→GAT)	prpB →	2‑methylisocitrate lyase
RA	345,384	G→C	5.1%	intergenic (+101/‑339)	prpB → / → prpC	2‑methylisocitrate lyase/2‑methylcitrate synthase
RA	345,428	T→C	10.2%	intergenic (+145/‑295)	prpB → / → prpC	2‑methylisocitrate lyase/2‑methylcitrate synthase
RA	347,382	G→T	38.1%	E153* (GAA→TAA)	prpD →	2‑methylcitrate dehydratase
RA	360,114	A→T	5.5%	intergenic (‑48/+547)	lacZ ← / ← lacI	pseudogene, truncated/DNA‑binding transcriptional repressor
RA	360,173	C→A	7.6%	intergenic (‑107/+488)	lacZ ← / ← lacI	pseudogene, truncated/DNA‑binding transcriptional repressor
RA	360,181	G→C	7.1%	intergenic (‑115/+480)	lacZ ← / ← lacI	pseudogene, truncated/DNA‑binding transcriptional repressor
RA	360,752	A→G	100%	V331A (GTG→GCG)	lacI ←	DNA‑binding transcriptional repressor
RA	361,806	G→A	100%	intergenic (‑63/+14)	lacI ← / ← mhpR	DNA‑binding transcriptional repressor/mhp operon transcriptional activator
RA	362,159	G→T	94.3%	I165I (ATC→ATA)	mhpR ←	mhp operon transcriptional activator
RA	368,518	A→C	6.0%	R48R (AGA→CGA)	mhpF →	acetaldehyde‑CoA dehydrogenase II, NAD‑binding
RA	385,815	G→T	50.9%	pseudogene (109/1458 nt)	yaiT →	pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein
RA	386,569	C→A	8.6%	pseudogene (863/1458 nt)	yaiT →	pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein
RA	394,744	G→T	18.6%	R16S (CGC→AGC)	yaiY ←	DUF2755 family inner membrane protein
RA	396,883	A→G	85.2%	Q14Q (CAA→CAG)	iraP →	anti‑RssB factor, RpoS stabilzer during Pi starvation; anti‑adapter protein
RA	397,959	G→A	37.6%	A253T (GCG→ACG)	phoA →	bacterial alkaline phosphatase
RA	402,340	G→T	100%	V160V (GTG→GTT)	aroL →	shikimate kinase II
RA	406,075	C→A	94.3%	P159Q (CCG→CAG)	mak →	manno(fructo)kinase
RA	411,027	G→T	92.8%	L61L (CTC→CTA)	sbcC ←	exonuclease, dsDNA, ATP‑dependent
RA	414,179	G→T	17.8%	D279Y (GAT→TAT)	phoR →	sensory histidine kinase in two‑component regulatory system with PhoB
RA	421,799	C→A	88.9%	I69I (ATC→ATA)	tgt →	tRNA‑guanine transglycosylase
RA	423,068	C→A	10.0%	A109E (GCG→GAG)	yajC →	SecYEG protein translocase auxillary subunit
RA	425,143	G→T	51.4%	T61T (ACG→ACT)	secF →	SecYEG protein translocase auxillary subunit
RA	427,603	C→T	22.9%	intergenic (‑134/+165)	tsx ← / ← yajI	nucleoside channel, receptor of phage T6 and colicin K/putative lipoprotein
RA	433,551	G→T	93.2%	S14Y (TCC→TAC)	yajO ←	2‑carboxybenzaldehyde reductase
RA	434,663	A→C	92.0%	I324S (ATC→AGC)	dxs ←	1‑deoxyxylulose‑5‑phosphate synthase, thiamine triphosphate‑binding, FAD‑requiring
RA	435,336	G→T	100%	Q100K (CAG→AAG)	dxs ←	1‑deoxyxylulose‑5‑phosphate synthase, thiamine triphosphate‑binding, FAD‑requiring
RA	437,672	T→A	90.0%	V223E (GTG→GAG)	thiI →	tRNA s(4)U8 sulfurtransferase
RA	441,811	A→C	10.5%	I104M (ATT→ATG)	yajR ←	putative transporter
RA	444,489	G→A	92.2%	R537C (CGT→TGT)	cyoB ←	cytochrome o ubiquinol oxidase subunit I
RA	446,369	T→G	47.0%	Q233P (CAG→CCG)	cyoA ←	cytochrome o ubiquinol oxidase subunit II
RA	450,290	G→A	100%	intergenic (+45/‑299)	bolA → / → tig	stationary‑phase morphogene, transcriptional repressor for mreB; also regulator for dacA, dacC, and ampC/peptidyl‑prolyl cis/trans isomerase (trigger factor)
RA	451,853	C→A	30.5%	T422N (ACC→AAC)	tig →	peptidyl‑prolyl cis/trans isomerase (trigger factor)
RA	453,656	T→A	31.2%	S259T (TCC→ACC)	clpX →	ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease
RA	456,298	T→A	90.9%	L652Q (CTG→CAG)	lon →	DNA‑binding ATP‑dependent protease La
RA	456,588	G→T	93.3%	D749Y (GAC→TAC)	lon →	DNA‑binding ATP‑dependent protease La
RA	465,341	A→C	29.7%	I339L (ATT→CTT)	mdlA →	putative multidrug transporter subunit of ABC superfamily, ATP‑binding component
RA	469,916	Δ1 bp	5.3%	coding (702/861 nt)	tesB ←	acyl‑CoA thioesterase 2
RA	474,138	G→T	93.8%	intergenic (‑65/+99)	ylaB ← / ← ylaC	putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase/DUF1449 family inner membrane protein
RA	475,502	T→A	34.4%	intergenic (‑128/+44)	maa ← / ← hha	maltose O‑acetyltransferase/modulator of gene expression, with H‑NS
RA	475,805	C→A	92.9%	A120A (GCG→GCT)	tomB ←	Hha toxicity attenuator; conjugation‑related protein
RA	479,244	C→A	91.6%	A206S (GCC→TCC)	acrB ←	multidrug efflux system protein
RA	480,820	C→T	92.0%	D86N (GAC→AAC)	acrA ←	multidrug efflux system
RA	481,667	G→A	89.1%	A151T (GCG→ACG)	acrR →	transcriptional repressor
RA	486,912	C→A	26.8%	I15I (ATC→ATA)	apt →	adenine phosphoribosyltransferase
RA	509,737	G→A	44.0%	E97K (GAG→AAG)	cueR →	copper‑responsive regulon transcriptional regulator
RA	511,619	A→T	29.5%	Q82L (CAA→CTA)	fetA →	iron exporter, ATP‑binding subunit, ABC transporter FetAB subunit; peroxide resistance protein
RA	522,859	T→G	19.1%	S1381R (AGT→AGG)	rhsD →	Rhs family putative polymorphic toxin
RA	523,413	G→T	31.9%	pseudogene (6/708 nt)	rhsH →	pseudogene, Rhs familly protein
RA	523,947	G→A	16.7%	pseudogene (540/708 nt)	rhsH →	pseudogene, Rhs familly protein
RA	524,334:1	+T	100%	pseudogene (239/491 nt)	ybbD →	pseudogene
RA	527,186	T→A	8.9%	L164F (TTA→TTT)	allS ←	allD operon transcriptional activator
RA	530,466	C→A	100%	F365L (TTC→TTA)	gcl →	glyoxylate carboligase
RA	542,200	Δ1 bp	100%	coding (65/1668 nt)	fdrA →	putative NAD(P)‑binding acyl‑CoA synthetase
RA	546,491	G→T	91.3%	V199V (GTG→GTT)	ybcF →	putative carbonate kinase
RA	549,397	G→T	94.5%	intergenic (‑1/+2)	lpxH ← / ← ppiB	UDP‑2,3‑diacylglucosamine pyrophosphohydrolase/peptidyl‑prolyl cis‑trans isomerase B (rotamase B)
RA	552,831	A→T	33.4%	F123I (TTC→ATC)	folD ←	bifunctional 5,10‑methylene‑tetrahydrofolate dehydrogenase/ 5,10‑methylene‑tetrahydrofolate cyclohydrolase
RA	554,327	G→T	7.0%	intergenic (+117/‑103)	sfmA → / → sfmC	FimA homolog/putative periplasmic pilus chaperone
RA	557,303	A→T	30.8%	E717D (GAA→GAT)	sfmD →	putative outer membrane export usher protein
RA	557,592	G→T	40.9%	D814Y (GAC→TAC)	sfmD →	putative outer membrane export usher protein
RA	560,919	G→T	10.9%	V172V (GTC→GTA)	intD ←	DLP12 prophage; putative phage integrase
RA	568,464	G→T	5.5%	E30* (GAA→TAA)	ninE →	DLP12 prophage; conserved protein
RA	576,998	G→T	88.5%	pseudogene (189/309 nt)	aaaD →	pseudogene; DLP12 prophage; tail fiber assembly protein family;Phage or Prophage Related
RA	581,203	A→T	100%	intergenic (‑114/‑310)	ompT ← / → pauD	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)/tRNA‑OTHER
RA	583,341	T→G	91.6%	S33R (AGT→CGT)	ybcH ←	PRK09936 family protein
RA	598,081	G→T	7.5%	G223C (GGC→TGC)	pheP →	phenylalanine transporter
RA	607,931	G→A	91.4%	S7F (TCC→TTC)	fepA ←	iron‑enterobactin outer membrane transporter
RA	615,143	C→A	28.2%	T171T (ACG→ACT)	fepC ←	iron‑enterobactin transporter subunit
RA	619,048	C→A	44.9%	A307S (GCC→TCC)	fepB ←	iron‑enterobactin transporter subunit
RA	623,935	C→A	6.6%	I262I (ATC→ATA)	entB →	isochorismatase
RA	625,364	G→T	93.7%	G5G (GGG→GGT)	cstA →	carbon starvation protein involved in peptide utilization; APC peptide transporter family protein
RA	639,231	G→A	100%	L65F (CTT→TTT)	rnk ←	regulator of nucleoside diphosphate kinase
RA	647,234	C→T	36.8%	E27K (GAA→AAA)	citC ←	[citrate [pro‑3S]‑lyase] ligase
RA	647,422	G→T	100%	intergenic (‑110/‑269)	citC ← / → citA	[citrate [pro‑3S]‑lyase] ligase/sensory histidine kinase in two‑component regulatory system with CitB
RA	647,509	T→C	100%	intergenic (‑197/‑182)	citC ← / → citA	[citrate [pro‑3S]‑lyase] ligase/sensory histidine kinase in two‑component regulatory system with CitB
RA	648,056	C→A	94.1%	F122L (TTC→TTA)	citA →	sensory histidine kinase in two‑component regulatory system with CitB
RA	650,141	G→T	5.5%	V428V (GTC→GTA)	dcuC ←	anaerobic C4‑dicarboxylate transport
RA	651,654	A→G	6.2%	intergenic (‑230/‑359)	dcuC ← / → pagP	anaerobic C4‑dicarboxylate transport/phospholipid:lipid A palmitoyltransferase
RA	652,865	Δ1 bp	91.7%	coding (118/210 nt)	cspE →	constitutive cold shock family transcription antitermination protein; negative regulator of cspA transcription; RNA melting protein; ssDNA‑binding protein
RA	662,108	A→T	93.3%	V522V (GTT→GTA)	mrdA ←	transpeptidase involved in peptidoglycan synthesis (penicillin‑binding protein 2)
RA	662,631	C→A	100%	R348L (CGC→CTC)	mrdA ←	transpeptidase involved in peptidoglycan synthesis (penicillin‑binding protein 2)
RA	664,243	C→A	33.4%	D84Y (GAT→TAT)	rsfS ←	ribosomal silencing factor
RA	666,998	G→T	33.5%	L22I (CTT→ATT)	holA ←	DNA polymerase III, delta subunit
RA	667,348	G→T	40.4%	Q99K (CAG→AAG)	lptE ←	LPS assembly OM complex LptDE, lipoprotein component
RA	672,142	T→A	40.4%	intergenic (‑139/‑25)	ybeQ ← / → ybeR	Sel1 family TPR‑like repeat protein/uncharacterized protein
RA	689,079	C→A	10.1%	E445* (GAA→TAA)	miaB ←	tRNA‑i(6)A37 methylthiotransferase
RA	693,739	G→T	50.8%	H299N (CAC→AAC)	asnB ←	asparagine synthetase B
RA	705,588	C→A	92.5%	intergenic (+16/+68)	chiQ → / ← fur	chitosugar‑induced verified lipoprotein/ferric iron uptake regulon transcriptional repressor; autorepressor
RA	706,097	A→C	45.1%	T2T (ACT→ACG)  *29G (TGA→GGA)	fur ← uof ←	ferric iron uptake regulon transcriptional repressor; autorepressor ryhB‑regulated fur leader peptide
RA	706,185	A→G	9.6%	intergenic (‑4/+206)	uof ← / ← fldA	ryhB‑regulated fur leader peptide/flavodoxin 1
RA	723,846	A→C	29.8%	W115G (TGG→GGG)	kdpA ←	potassium translocating ATPase, subunit A
RA	724,813	A→T	92.4%	intergenic (+17/‑226)	ybfA → / → rhsC	DUF2517 family protein/Rhs family putative polymorphic toxin
RA	725,650	G→T	30.8%	P204P (CCG→CCT)	rhsC →	Rhs family putative polymorphic toxin
RA	729,149	G→A	6.3%	D1371N (GAT→AAT)	rhsC →	Rhs family putative polymorphic toxin
RA	729,456	G→A	52.5%	R75R (AGG→AGA)	ybfB →	putative membrane protein
RA	732,494	G→T	47.9%	pseudogene (214/1137 nt)	ybfL →	pseudogene, DDE domain transposase family;putative factor; Not classified; putative receptor protein
RA	735,817	G→T	31.2%	L285L (CTG→CTT)	phr →	deoxyribodipyrimidine photolyase, FAD‑binding
RA	742,840	G→T	23.4%	A129E (GCG→GAG)	abrB ←	regulator of aidB expression; inner membrane protein
RA	743,278	G→A	24.9%	intergenic (‑53/+99)	abrB ← / ← ybgO	regulator of aidB expression; inner membrane protein/putative fimbrial protein
RA	750,112	A→T	38.4%	intergenic (‑188/‑521)	gltA ← / → sdhC	citrate synthase/succinate dehydrogenase, membrane subunit, binds cytochrome b556
RA	754,572	G→T	91.4%	E137D (GAG→GAT)	sucA →	2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding
RA	757,353	A→T	28.4%	N126Y (AAT→TAT)	sucB →	dihydrolipoyltranssuccinase
RA	759,000	C→A	94.0%	F177L (TTC→TTA)	sucC →	succinyl‑CoA synthetase, beta subunit
RA	761,420	C→T	30.8%	intergenic (‑89/‑20)	mngR ← / → mngA	Transcriptional repressor for the mannosyl‑D‑glycerate catabolic operon/fused 2‑O‑a‑mannosyl‑D‑glycerate specific PTS enzymes: IIA component/IIB component/IIC component
RA	772,664	A→C	12.4%	K289N (AAA→AAC)	tolA →	membrane anchored protein in TolA‑TolQ‑TolR complex
RA	779,256	T→A	7.5%	I212N (ATC→AAC)	pnuC →	nicotinamide riboside transporter
RA	788,902	G→T	88.4%	R115S (CGT→AGT)	modF ←	fused molybdate transporter subunits of ABC superfamily: ATP‑binding components
RA	789,044	G→T	29.8%	I67I (ATC→ATA)	modF ←	fused molybdate transporter subunits of ABC superfamily: ATP‑binding components
RA	792,351	G→T	21.6%	A114A (GCG→GCT)	modC →	molybdate transporter subunit
RA	800,488	G→T	90.6%	V510V (GTG→GTT)	ybhJ →	putative hydratase
RA	800,779	G→T	100%	E607D (GAG→GAT)	ybhJ →	putative hydratase
RA	805,693	A→C	8.3%	E298D (GAA→GAC)	bioB →	biotin synthase
RA	816,095	T→A	8.2%	intergenic (+51/‑154)	ybhL → / → ybhM	UPF0005 family inner membrane protein/UPF0005 family inner membrane protein
RA	816,152	C→A	30.2%	intergenic (+108/‑97)	ybhL → / → ybhM	UPF0005 family inner membrane protein/UPF0005 family inner membrane protein
RA	816,292	A→T	43.8%	H15L (CAC→CTC)	ybhM →	UPF0005 family inner membrane protein
RA	818,362	G→T	33.8%	G278G (GGC→GGA)	clsB ←	cardiolipin synthase 2
RA	828,374	G→T	89.5%	V11V (GTC→GTA)	ybiA ←	DUF1768 family protein
RA	832,445	G→T	92.1%	P213P (CCG→CCT)	ybiC →	putative dehydrogenase
RA	843,299	C→A	94.9%	W54C (TGG→TGT)	glnH ←	glutamine transporter subunit
RA	851,782	A→T	26.9%	K122* (AAA→TAA)	ybiT →	putative transporter subunit of ABC superfamily: ATP‑binding component
RA	861,323	T→A	10.3%	S166S (TCA→TCT)	moeA ←	molybdopterin molybdenumtransferase; molybdopterin biosynthesis protein
RA	863,481	T→G	11.1%	L169R (CTC→CGC)	gsiA →	glutathione transporter ATP‑binding protein, ABC superfamily
RA	863,745	T→A	32.1%	F257Y (TTT→TAT)	gsiA →	glutathione transporter ATP‑binding protein, ABC superfamily
RA	868,473	A→C	10.2%	I13I (ATA→ATC)	yliE →	putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	868,897	G→T	33.9%	D155Y (GAC→TAC)	yliE →	putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	876,447	G→A	100%	D89N (GAT→AAT)	dacC →	D‑alanyl‑D‑alanine carboxypeptidase (penicillin‑binding protein 6a)
RA	877,482	C→A	28.8%	D237Y (GAT→TAT)	deoR ←	deoxyribose‑5‑phosphate‑inducible deoxyribose operon transcriptional repressor; repressor of nupG and tsx
RA	879,085	G→T	100%	intergenic (‑241/‑44)	ybjG ← / → mdfA	undecaprenyl pyrophosphate phosphatase/multidrug efflux system protein
RA	884,152	G→T	19.8%	S375* (TCG→TAG)	ybjL ←	putative transporter
RA	889,044	G→T	28.3%	intergenic (+155/‑196)	ybjN → / → potF	negative regulator of motility; multicopy suppressor of coaA(Ts)/putrescine transporter subunit: periplasmic‑binding component of ABC superfamily
RA	899,961	T→A	8.4%	intergenic (‑38/‑88)	ybjP ← / → ybjQ	lipoprotein/UPF0145 family protein
RA	907,596	G→T	38.6%	P4Q (CCA→CAA)	hcr ←	HCP oxidoreductase, NADH‑dependent
RA	925,160	G→T	89.0%	S420* (TCA→TAA)	cydD ←	fused glutathione, cysteine exporter subunits of ABC superfamily: membrane component/ATP‑binding component
RA	925,355	A→T	34.4%	L355Q (CTG→CAG)	cydD ←	fused glutathione, cysteine exporter subunits of ABC superfamily: membrane component/ATP‑binding component
RA	925,957	A→T	33.0%	I154I (ATT→ATA)	cydD ←	fused glutathione, cysteine exporter subunits of ABC superfamily: membrane component/ATP‑binding component
RA	943,573	G→T	92.8%	A297S (GCC→TCC)	ycaM →	putative transporter
RA	955,568	A→T	47.6%	intergenic (+17/‑152)	aroA → / → ycaL	5‑enolpyruvylshikimate‑3‑phosphate synthetase/putative peptidase‑related chaperone
RA	963,256	G→A	28.1%	D394N (GAT→AAT)	msbA →	fused lipid transporter subunits of ABC superfamily: membrane component/ATP‑binding component
RA	968,415	G→T	91.9%	S148* (TCG→TAG)	ycbC ←	DUF218 superfamily protein
RA	976,873	C→A	30.2%	A124E (GCG→GAG)	ldtD →	murein L,D‑transpeptidase
RA	991,460	A→T	7.9%	L314Q (CTG→CAG)	ssuA ←	aliphatic sulfonate binding protein, SsuABC ABC transporter
RA	997,965	G→T	47.0%	D235Y (GAT→TAT)	elfG →	putative fimbrial‑like adhesin protein
RA	1,024,703	G→T	49.6%	G241G (GGC→GGA)	rlmI ←	23S rRNA m(5)C1962 methyltransferase, SAM‑dependent
RA	1,048,928	C→A	93.3%	E903* (GAA→TAA)	torS ←	hybrid sensory histidine kinase in two‑component regulatory system with TorR
RA	1,049,407	G→T	90.1%	T743K (ACG→AAG)	torS ←	hybrid sensory histidine kinase in two‑component regulatory system with TorR
RA	1,073,243	C→A	27.5%	G366C (GGT→TGT)	putA ←	fused DNA‑binding transcriptional regulator/proline dehydrogenase/pyrroline‑5‑carboxylate dehydrogenase
RA	1,073,863	G→T	30.3%	S159* (TCG→TAG)	putA ←	fused DNA‑binding transcriptional regulator/proline dehydrogenase/pyrroline‑5‑carboxylate dehydrogenase
RA	1,077,911	A→C	100%	K71N (AAA→AAC)	efeO →	inactive ferrous ion transporter EfeUOB
RA	1,083,443	G→T	43.4%	S624* (TCG→TAG)	pgaB ←	poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine (PGA) N‑deacetylase outer membrane export lipoprotein
RA	1,084,103	A→T	88.9%	L404* (TTA→TAA)	pgaB ←	poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine (PGA) N‑deacetylase outer membrane export lipoprotein
RA	1,116,964	A→G	92.4%	intergenic (‑21/+53)	dinI ← / ← pyrC	DNA damage‑inducible protein I/dihydro‑orotase
RA	1,118,506	A→T	9.4%	L75Q (CTA→CAA)	yceB ←	lipoprotein, DUF1439 family
RA	1,132,494	T→A	27.3%	I255I (ATT→ATA)	flgI →	putative flagellar basal body protein
RA	1,151,750	G→T	91.6%	R178L (CGC→CTC)	holB →	DNA polymerase III, delta prime subunit
RA	1,152,278	G→T	90.9%	E16* (GAA→TAA)	ycfH →	putative DNase
RA	1,164,454	G→A	23.3%	intergenic (‑166/‑75)	ycfQ ← / → bhsA	repressor for bhsA(ycfR)/biofilm, cell surface and signaling protein
RA	1,173,073	T→A	30.2%	F100I (TTC→ATC)	lolE →	lipoprotein‑releasing system transmembrane protein
RA	1,175,193	A→T	29.7%	E36V (GAA→GTA)	cobB →	deacetylase of acs and cheY, chemotaxis regulator
RA	1,191,676	C→T	32.9%	H366H (CAC→CAT)	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,688	C→T	29.4%	T370T (ACC→ACT)	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,701	T→C	24.6%	L375L (TTA→CTA) ‡	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,703	A→G	24.1%	L375L (TTA→TTG) ‡	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,733	C→T	15.5%	N385N (AAC→AAT)	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,736	G→C	15.5%	A386A (GCG→GCC)	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,739	A→G	15.5%	K387K (AAA→AAG)	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,748	C→T	9.2%	T390T (ACC→ACT)	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,193,516	T→G	15.4%	N60H (AAT→CAT)	ymfE ←	e14 prophage; putative inner membrane protein
RA	1,193,873	G→T	93.3%	intergenic (‑180/‑278)	ymfE ← / → lit	e14 prophage; putative inner membrane protein/e14 prophage; cell death peptidase, inhibitor of T4 late gene expression
RA	1,204,284	C→A	68.8%	D98Y (GAT→TAT)	tfaE ←	e14 prophage; putative tail fiber assembly protein
RA	1,211,169	C→A	87.8%	intergenic (‑238/‑76)	bluF ← / → ycgZ	anti‑repressor for YcgE, blue light‑responsive; FAD‑binding; has c‑di‑GMP phosphodiesterase‑like EAL domain, but does not degrade c‑di‑GMP/RcsB connector protein for regulation of biofilm and acid‑resistance
RA	1,219,533	A→G	100%	intergenic (+170/+202)	ycgI → / ← minE	pseudogene/cell division topological specificity factor
RA	1,220,996	G→T	100%	R181R (CGG→AGG)	minC ←	cell division inhibitor
RA	1,224,292	G→A	94.3%	D8N (GAT→AAT)	ycgN →	UPF0153 family cysteine cluster protein
RA	1,226,292	T→A	93.5%	C24S (TGT→AGT)	umuD →	DNA polymerase V, subunit D
RA	1,227,613	C→A	37.1%	N324K (AAC→AAA)	umuC →	DNA polymerase V, subunit C
RA	1,228,591	G→T	93.1%	intergenic (‑105/+41)	dsbB ← / ← nhaB	oxidoreductase that catalyzes reoxidation of DsbA protein disulfide isomerase I/sodium:proton antiporter
RA	1,245,682	T→G	20.1%	T205P (ACC→CCC)	dhaK ←	dihydroxyacetone kinase, PTS‑dependent, dihydroxyacetone‑binding subunit
RA	1,251,120	T→A	32.4%	T97S (ACC→TCC)	ycgV ←	putative adhesin
RA	1,277,786	G→A	91.6%	D823N (GAC→AAC)	narG →	nitrate reductase 1, alpha subunit
RA	1,288,669	A→T	40.8%	intergenic (‑291/‑314)	hns ← / → tdk	global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
RA	1,301,604	A→T	7.1%	I433I (ATT→ATA)	clsA ←	cardiolipin synthase 1
RA	1,322,140	T→A	90.7%	T159S (ACG→TCG)	btuR ←	cob(I)yrinic acid a,c‑diamide adenosyltransferase
RA	1,330,955	G→T	43.6%	D290Y (GAT→TAT)	acnA →	aconitate hydratase 1
RA	1,334,048	G→T	37.3%	E154D (GAG→GAT)	pgpB →	phosphatidylglycerophosphatase B
RA	1,337,533	G→T	93.6%	A18E (GCA→GAA)	osmB ←	lipoprotein
RA	1,340,901	A→T	40.7%	S33S (TCT→TCA)	gmr ←	cyclic‑di‑GMP phosphodiesterase; csgD regulator; modulator of Rnase II stability
RA	1,365,283	G→T	90.8%	E271* (GAG→TAG)	ycjM →	alpha amylase catalytic domain family protein
RA	1,369,694	G→A	6.8%	D159N (GAT→AAT)	ycjQ →	putative Zn‑dependent NAD(P)‑binding oxidoreductase
JC JC	1,376,043	IS5 (–) +4 bp	100%	pseudogene (10‑13/126 nt)	ycjV →	pseudogene; putative ATP‑binding component of a transport system
RA	1,377,394	C→T	93.5%	A275A (GCG→GCA)	ycjW ←	LacI family putative transcriptional repressor
RA	1,386,008	G→T	90.3%	Q35K (CAG→AAG)	ycjY ←	S9 homolog non‑peptidase family protein
RA	1,388,406	G→T	100%	R308L (CGC→CTC)	mppA →	murein tripeptide (L‑ala‑gamma‑D‑glutamyl‑meso‑DAP) transporter subunit
RA	1,396,370	G→T	5.9%	N381K (AAC→AAA)	abgB ←	p‑aminobenzoyl‑glutamate hydrolase, B subunit
RA	1,417,454	C→A	32.3%	pseudogene (497/500 nt)	ydaW →	Rac prophage; pseudogene, DNA‑binding protein family;Phage or Prophage Related
RA	1,423,594	G→T	12.1%	D97Y (GAT→TAT)	stfR →	Rac prophage; putative tail fiber protein
RA	1,424,234	C→A	89.7%	S310* (TCA→TAA)	stfR →	Rac prophage; putative tail fiber protein
JC JC	1,428,894	IS2 (–) +5 bp	93.4%	intergenic (‑413/+317)	ynaE ← / ← ttcC	cold shock protein, Rac prophage/pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related
RA	1,429,000	C→A	8.5%	intergenic (‑519/+215)	ynaE ← / ← ttcC	cold shock protein, Rac prophage/pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related
RA	1,439,518	C→A	91.6%	S737S (TCC→TCA)	ydbH →	putative membrane‑anchored protein, function unknown
RA	1,443,093	C→A	28.7%	L440I (CTC→ATC)	feaB →	phenylacetaldehyde dehydrogenase
RA	1,443,196	A→T	34.2%	Q474L (CAG→CTG)	feaB →	phenylacetaldehyde dehydrogenase
RA	1,444,739	G→A	30.3%	P290S (CCC→TCC)	tynA ←	tyramine oxidase, copper‑requiring
RA	1,448,466	C→A	25.1%	Q95K (CAA→AAA)	paaA →	ring 1,2‑phenylacetyl‑CoA epoxidase subunit
RA	1,451,422	A→T	48.8%	T246S (ACG→TCG)	paaE →	ring 1,2‑phenylacetyl‑CoA epoxidase, NAD(P)H oxidoreductase component
RA	1,454,118	A→T	7.0%	I270F (ATT→TTT)	paaH →	3‑hydroxyadipyl‑CoA dehydrogenase, NAD+‑dependent
RA	1,454,724	G→T	92.0%	G472C (GGT→TGT)	paaH →	3‑hydroxyadipyl‑CoA dehydrogenase, NAD+‑dependent
RA	1,488,630	C→A	35.8%	T233T (ACG→ACT)	ydcI ←	putative DNA‑binding transcriptional regulator
RA	1,519,349	T→A	94.9%	K297* (AAA→TAA)	ansP ←	L‑asparagine transporter
RA	1,529,506	C→T	31.6%	G204S (GGC→AGC)	yddE ←	PhzC‑PhzF family protein
RA	1,533,556	G→T	29.8%	H1098N (CAC→AAC)	narZ ←	nitrate reductase 2 (NRZ), alpha subunit
RA	1,533,940	C→T	5.9%	A970T (GCG→ACG)	narZ ←	nitrate reductase 2 (NRZ), alpha subunit
RA	1,548,144	G→T	92.7%	intergenic (‑49/+85)	adhP ← / ← maeA	ethanol‑active dehydrogenase/acetaldehyde‑active reductase/malate dehydrogenase, (decarboxylating, NAD‑requiring) (malic enzyme)
RA	1,552,629	C→A	45.7%	D216Y (GAT→TAT)	ddpD ←	D,D‑dipeptide permease system, ATP‑binding component
RA	1,563,276	G→T	100%	H491N (CAC→AAC)	gadC ←	glutamate:gamma‑aminobutyric acid antiporter
RA	1,565,497	G→A	92.1%	S269L (TCG→TTG)	gadB ←	glutamate decarboxylase B, PLP‑dependent
RA	1,566,392	A→T	27.4%	intergenic (‑90/+272)	gadB ← / ← pqqL	glutamate decarboxylase B, PLP‑dependent/putative periplasmic M16 family zinc metalloendopeptidase
RA	1,575,339	G→T	92.5%	F481L (TTC→TTA)	ydeN ←	putative Ser‑type periplasmic non‑aryl sulfatase
RA	1,586,871	G→T	34.5%	intergenic (‑172/+51)	hipB ← / ← yneO	antitoxin of HipAB toxin‑antitoxin system/pseudogene, AidA homolog
RA	1,602,131	G→T	38.8%	D177Y (GAT→TAT)	tam →	trans‑aconitate methyltransferase
RA	1,603,440	G→A	91.9%	intergenic (‑161/+46)	yneE ← / ← uxaB	bestrophin family putative inner membrane protein/altronate oxidoreductase, NAD‑dependent
RA	1,604,418	C→A	7.4%	D174Y (GAC→TAC)	uxaB ←	altronate oxidoreductase, NAD‑dependent
RA	1,615,440	G→T	6.2%	intergenic (‑46/‑149)	eamA ← / → ydeE	cysteine and O‑acetyl‑L‑serine efflux system/putative transporter
RA	1,615,798	C→A	5.1%	F70L (TTC→TTA)	ydeE →	putative transporter
RA	1,620,961	T→G	89.1%	Q226P (CAA→CCA)	dcp ←	dipeptidyl carboxypeptidase II
RA	1,622,999	G→T	6.6%	D131Y (GAT→TAT)	rspR →	transcriptional repressor for rspAB
RA	1,625,116	T→A	5.8%	N19Y (AAC→TAC)	ydfI ←	putative NAD‑dependent D‑mannonate oxidoreductase
RA	1,628,207	G→A	100%	G110E (GGA→GAA)	pinQ →	Qin prophage; putative site‑specific recombinase
RA	1,647,785	T→C	16.7%	K130E (AAA→GAA)	rspB ←	putative Zn‑dependent NAD(P)‑binding oxidoreductase
RA	1,661,763	C→A	100%	P353P (CCG→CCT)	mlc ←	glucosamine anaerobic growth regulon transcriptional repressor; autorepressor
RA	1,673,380	T→A	5.4%	S233T (TCA→ACA) ‡	ydgH →	DUF1471 family periplasmic protein
RA	1,673,381	C→A	7.7%	S233* (TCA→TAA) ‡	ydgH →	DUF1471 family periplasmic protein
RA	1,689,180	T→G	45.9%	E383D (GAA→GAC)	uidA ←	beta‑D‑glucuronidase
RA	1,690,981	G→T	27.5%	A110E (GCG→GAG)	uidR ←	transcriptional repressor
RA	1,692,573	C→A	46.2%	D289Y (GAT→TAT)	malI ←	transcriptional repressor of Mal regulon
RA	1,696,612	A→T	94.9%	E41D (GAA→GAT)	add →	adenosine deaminase
RA	1,699,862	T→A	44.6%	L119* (TTG→TAG)	ydgK →	DUF2569 family inner membrane protein
RA	1,702,966	T→A	9.3%	R597R (CGT→CGA)	rsxC →	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA	1,703,062	T→A	13.6%	R629R (CGT→CGA)	rsxC →	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA	1,703,071	A→T	9.8%	A632A (GCA→GCT)	rsxC →	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA	1,703,101	C→G	10.8%	A642A (GCC→GCG)	rsxC →	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA	1,711,397	C→T	94.6%	R28Q (CGA→CAA)	tyrS ←	tyrosyl‑tRNA synthetase
RA	1,723,809	G→T	46.1%	E156* (GAA→TAA)	lhr →	putative ATP‑dependent helicase
RA	1,725,272	G→T	25.9%	A643A (GCG→GCT)	lhr →	putative ATP‑dependent helicase
RA	1,747,034	C→A	27.6%	D352Y (GAT→TAT)	ydhV ←	putative oxidoreductase subunit
RA	1,752,893	T→A	27.2%	P30P (CCA→CCT)	ldtE ←	murein L,D‑transpeptidase
RA	1,754,950	T→A	89.9%	I367F (ATT→TTT)	sufD ←	component of SufBCD Fe‑S cluster assembly scaffold
RA	1,764,150	G→T	45.5%	D274Y (GAT→TAT)	ydiK →	UPF0118 family inner membrane protein
RA	1,766,617	A→T	6.6%	intergenic (+75/‑152)	ydiM → / → ydiN	MFS superfamily sugar transport 1 family protein/MFS transporter superfamily protein
RA	1,767,963	C→A	41.9%	P399T (CCT→ACT)	ydiN →	MFS transporter superfamily protein
RA	1,770,281	T→A	94.9%	D146E (GAT→GAA)	ydiF →	putative acetyl‑CoA:acetoacetyl‑CoA transferase: alpha subunit/beta subunit
RA	1,777,451	C→A	40.3%	A55E (GCG→GAG)	fadK →	short chain acyl‑CoA synthetase, anaerobic
RA	1,791,509	C→A	32.9%	P231P (CCG→CCT)	pheT ←	phenylalanine tRNA synthetase, beta subunit
RA	1,795,267	A→T	37.9%	F521I (TTC→ATC)	thrS ←	threonyl‑tRNA synthetase
RA	1,796,428	C→A	6.9%	V134F (GTC→TTC)	thrS ←	threonyl‑tRNA synthetase
RA	1,798,834	G→A	34.8%	pseudogene (1060/1476 nt)	arpB →	pseudogene, ankyrin repeats
RA	1,802,047	G→A	94.7%	intergenic (+100/‑6)	ydiZ → / → yniA	uncharacterized protein/fructosamine kinase family protein
RA	1,803,109	C→T	47.9%	A128T (GCC→ACC)	yniB ←	putative inner membrane protein
RA	1,805,071	C→A	8.8%	intergenic (+13/‑120)	ydjM → / → ydjN	inner membrane protein regulated by LexA/putative transporter
RA	1,813,263	C→A	27.3%	E148* (GAG→TAG)	chbR ←	repressor of chb operon for N,N'‑diacetylchitobiose utilization
RA	1,821,696	A→T	42.2%	L274Q (CTG→CAG)	astB ←	succinylarginine dihydrolase
RA	1,823,835	A→C	7.6%	W53G (TGG→GGG)	astD ←	succinylglutamic semialdehyde dehydrogenase
RA	1,825,763	C→A	91.2%	A159A (GCG→GCT)	astC ←	succinylornithine transaminase, PLP‑dependent
RA	1,832,413	C→A	94.4%	L315L (CTC→CTA)	ynjC →	inner membrane putative ABC superfamily transporter permease
RA	1,833,730	C→A	93.5%	R3S (CGT→AGT)	ynjE →	molybdopterin synthase sulfurtransferase
RA	1,850,880	C→A	31.7%	V102V (GTG→GTT)	ydjH ←	putative kinase
RA	1,862,404	G→T	28.2%	E414* (GAA→TAA)	yeaG →	protein kinase, endogenous substrate unidentified; autokinase
RA	1,865,422	C→A	91.2%	R261R (CGA→AGA)	yeaI →	putative membrane‑anchored diguanylate cyclase
RA	1,867,537	C→A	6.9%	R414S (CGT→AGT)	yeaJ →	putative diguanylate cyclase
RA	1,868,749	A→C	25.8%	E47D (GAA→GAC)	yeaL →	UPF0756 family putative inner membrane protein
RA	1,872,520	G→T	92.2%	P183P (CCG→CCT)	yeaP →	diguanylate cyclase
RA	1,902,119	C→A	5.5%	intergenic (‑271/+399)	yobF ← / ← yebO	DUF2527 family heat‑induced protein/putative inner membrane protein
RA	1,909,342	T→A	100%	E150D (GAA→GAT)	proQ ←	RNA chaperone, putative ProP translation regulator
RA	1,942,066	G→T	32.2%	H115N (CAT→AAT)	yebC ←	UPF0082 family protein
RA	1,943,414	C→A	7.4%	D456Y (GAT→TAT)	aspS ←	aspartyl‑tRNA synthetase
RA	1,944,177	C→A	93.9%	L201L (CTG→CTT)	aspS ←	aspartyl‑tRNA synthetase
RA	1,948,050	C→A	20.9%	L118I (CTT→ATT)	cmoB →	tRNA (cmo5U34)‑carboxymethyltransferase, carboxy‑SAM‑dependent
RA	1,951,127	C→A	14.8%	A46A (GCG→GCT)	torZ ←	trimethylamine N‑oxide reductase system III, catalytic subunit
RA	1,959,915	C→A	47.1%	P178P (CCG→CCT)	flhB ←	flagellin export apparatus, substrate specificity protein
RA	1,969,291	G→T	93.0%	I97I (ATC→ATA)	cheA ←	fused chemotactic sensory histidine kinase in two‑component regulatory system with CheB and CheY: sensory histidine kinase/signal sensing protein
RA	1,973,690	A→G	6.2%	A468A (GCT→GCC)	otsA ←	trehalose‑6‑phosphate synthase
RA	1,975,265	C→A	28.1%	D202Y (GAT→TAT)	otsB ←	trehalose‑6‑phosphate phosphatase, biosynthetic
RA	1,979,691	C→A	7.4%	intergenic (‑82/‑715)	araF ← / → ftnB	L‑arabinose transporter subunit/ferritin B, putative ferrous iron reservoir
RA	1,984,987	C→A	45.8%	T38T (ACG→ACT)	yecA ←	UPF0149 family protein
RA	1,985,366	G→T	32.1%	noncoding (17/87 nt)	leuZ ←	tRNA‑Leu
RA	1,986,289	T→A	90.4%	N4Y (AAT→TAT)	pgsA ←	phosphatidylglycerophosphate synthetase
RA	1,991,843	G→A	30.3%	L40F (CTC→TTC)	yecS ←	ABC family putative inner membrane permease
RA	1,997,314	G→T	100%	intergenic (‑227/‑39)	fliC ← / → fliD	flagellar filament structural protein (flagellin)/flagellar filament capping protein
RA	1,999,632	G→T	87.3%	intergenic (+73/‑5)	fliT → / → amyA	putative flagellar synthesis and assembly chaperone/cytoplasmic alpha‑amylase
RA	2,007,547	C→A	34.4%	R280S (CGC→AGC)	fliF →	flagellar basal‑body MS‑ring and collar protein
RA	2,020,166	C→A	93.5%	D445Y (GAC→TAC)	yedQ ←	putative membrane‑anchored diguanylate cyclase
RA	2,030,998	C→A	12.4%	P212P (CCG→CCT)	yedV ←	putative sensory kinase in two‑component regulatory system with YedW
RA	2,035,090	C→A	90.3%	Q79K (CAG→AAG)	zinT →	zinc and cadmium binding protein, periplasmic
RA	2,040,800	C→A	34.6%	T794T (ACC→ACA)	yeeJ →	putative adhesin
RA	2,041,982	A→T	12.8%	S1188S (TCA→TCT)	yeeJ →	putative adhesin
RA	2,067,205	G→A	5.2%	G729D (GGC→GAC)	flu →	CP4‑44 prophage; antigen 43 (Ag43) phase‑variable biofilm formation autotransporter
RA	2,074,680	A→T	90.7%	W22R (TGG→AGG)	sbmC ←	DNA gyrase inhibitor
RA	2,077,212	A→T	48.3%	N326Y (AAT→TAT)	sbcB →	exodeoxyribonuclease I; exonuclease I
RA	2,098,995	C→A	100%	G182* (GGA→TGA)	wbbI ←	d‑Galf:alpha‑d‑Glc beta‑1,6‑galactofuranosyltransferase
RA	2,102,205	C→A	10.8%	V287V (GTG→GTT)	wzxB ←	putative polisoprenol‑linked O‑antigen transporter
RA	2,108,219:1	+A	100%	coding (1159/1395 nt)	wcaM ←	colanic acid biosynthesis protein
RA	2,110,346	G→A	46.5%	T88I (ACC→ATC)	wcaL ←	putative glycosyl transferase
RA	2,114,414	C→A	31.8%	V208F (GTC→TTC)	wcaJ ←	colanic biosynthesis UDP‑glucose lipid carrier transferase
RA	2,114,911	A→T	100%	L42Q (CTG→CAG)	wcaJ ←	colanic biosynthesis UDP‑glucose lipid carrier transferase
RA	2,115,361	C→A	32.6%	R367L (CGC→CTC)	cpsG ←	phosphomannomutase
RA	2,135,016	C→A	24.8%	V26V (GTG→GTT)	asmA ←	suppressor of OmpF assembly mutants; putative outer membrane protein assembly factor; inner membrane‑anchored periplasmic protein
RA	2,139,910	G→T	92.4%	R1055L (CGA→CTA)	yegE →	putative diguanylate cyclase
RA	2,144,474	C→A	93.3%	intergenic (‑8/‑192)	yegI ← / → yegJ	protein kinase‑related putative non‑specific DNA‑binding protein/uncharacterized protein
RA	2,148,615	C→A	26.5%	R373R (CGC→CGA)	mdtA →	multidrug efflux system, subunit A
RA	2,149,603	A→T	91.1%	E287V (GAA→GTA)	mdtB →	multidrug efflux system, subunit B
RA	2,162,105	T→A	27.5%	intergenic (‑318/‑88)	yegR ← / → yegS	uncharacterized protein/phosphatidylglycerol kinase, metal‑dependent
RA	2,163,087	C→A	29.3%	R299S (CGT→AGT)	yegS →	phosphatidylglycerol kinase, metal‑dependent
RA	2,168,487	A→T	48.6%	D14E (GAT→GAA)	gatA ←	galactitol‑specific enzyme IIA component of PTS
RA	2,168,795	C→A	100%	D336Y (GAT→TAT)	gatZ ←	D‑tagatose 1,6‑bisphosphate aldolase 2, subunit
RA	2,170,713	C→A	30.2%	intergenic (‑30/+278)	gatY ← / ← fbaB	D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I
RA	2,170,724	G→T	30.0%	intergenic (‑41/+267)	gatY ← / ← fbaB	D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I
RA	2,170,757	T→A	10.0%	intergenic (‑74/+234)	gatY ← / ← fbaB	D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I
RA	2,170,758	C→A	11.3%	intergenic (‑75/+233)	gatY ← / ← fbaB	D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I
RA	2,179,205	G→T	100%	A24E (GCG→GAG)	rcnR ←	transcriptional repressor of rcnA
RA	2,181,645	A→G	89.2%	N83N (AAT→AAC)	yehA ←	putative fimbrial‑like adhesin protein
RA	2,189,888	C→A	7.4%	intergenic (+76/‑65)	metG → / → yehH	methionyl‑tRNA synthetase/DUF4132 family pseudogene; defective yehI paralog; molybdate metabolism regulator, first fragment; molybdate metabolism regulator, second fragment 2; yehI' molR mutations have phenotypes and the N‑terminal molR fragment of yehI' may be expressed and may have retained or evolved MolR function
RA	2,191,496	C→A	23.6%	pseudogene (1544/2847 nt)	yehH →	DUF4132 family pseudogene; defective yehI paralog; molybdate metabolism regulator, first fragment; molybdate metabolism regulator, second fragment 2; yehI' molR mutations have phenotypes and the N‑terminal molR fragment of yehI' may be expressed and may have retained or evolved MolR function
RA	2,193,783	C→A	21.6%	A9E (GCG→GAG)	yehI →	DUF4132 domain‑containing protein
RA	2,194,695	T→A	94.4%	L313Q (CTA→CAA)	yehI →	DUF4132 domain‑containing protein
RA	2,195,449	A→T	93.0%	E564D (GAA→GAT)	yehI →	DUF4132 domain‑containing protein
RA	2,197,797	A→T	23.7%	intergenic (+29/‑278)	yehK → / → yehL	uncharacterized protein/putative ABC superfamily transporter ATP‑binding subunit
RA	2,209,162	C→A	42.1%	I9I (ATC→ATA)	yohO →	putative membrane protein
RA	2,216,296	C→A	91.5%	I211I (ATC→ATA)	dld →	D‑lactate dehydrogenase, FAD‑binding, NADH independent
RA	2,220,503	C→T	28.2%	V83M (GTG→ATG)	yohF ←	putative oxidoreductase
RA	2,223,247	C→T	39.3%	W206* (TGG→TGA)	dusC ←	tRNA‑dihydrouridine synthase C
RA	2,224,212	C→A	25.3%	P37Q (CCG→CAG)	yohJ →	UPF0299 family inner membrane protein
RA	2,225,190	C→T	87.6%	G231G (GGC→GGT)	yohK →	LrgB family inner membrane protein
RA	2,225,260	C→T	11.3%	intergenic (+67/‑63)	yohK → / → cdd	LrgB family inner membrane protein/cytidine/deoxycytidine deaminase
RA	2,233,142	A→T	9.8%	V229E (GTG→GAG)	mglB ←	methyl‑galactoside transporter subunit
RA	2,237,098	G→T	89.7%	H12N (CAT→AAT)	folE ←	GTP cyclohydrolase I
RA	2,240,361	C→A	5.9%	intergenic (‑113/+181)	cirA ← / ← lysP	colicin IA outer membrane receptor and translocator; ferric iron‑catecholate transporter/lysine transporter
RA	2,243,089	G→T	10.8%	I3I (ATC→ATA)	yeiE ←	putative DNA‑binding transcriptional regulator
RA	2,259,689	C→A	6.1%	intergenic (+188/‑35)	yeiP → / → yeiQ	elongation factor P‑like protein/putative NAD‑dependent D‑mannonate oxidoreductase
RA	2,263,137	C→A	42.9%	intergenic (+91/‑321)	lpxT → / → mepS	lipid A 1‑diphosphate synthase; undecaprenyl pyrophosphate:lipid A 1‑phosphate phosphotransferase/murein DD‑endopeptidase, space‑maker hydrolase, mutational suppressor of prc thermosensitivity, outer membrane lipoprotein
RA	2,264,143	G→A	95.0%	intergenic (+119/‑62)	mepS → / → rtn	murein DD‑endopeptidase, space‑maker hydrolase, mutational suppressor of prc thermosensitivity, outer membrane lipoprotein/resistance protein for phages lambda and N4, putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	2,270,338	T→A	32.3%	L187Q (CTG→CAG)	yejF →	microcin C transporter, ATP‑binding subunit; ABC family
RA	2,287,829	C→A	46.8%	S185S (TCG→TCT)	ccmF ←	heme lyase, CcmF subunit
RA	2,289,043	C→A	42.3%	W8L (TGG→TTG)	ccmD ←	cytochrome c biogenesis protein
RA	2,289,374	C→A	92.0%	V142V (GTG→GTT)	ccmC ←	heme exporter subunit
RA	2,292,271	A→T	8.7%	C263S (TGC→AGC)	napH ←	ferredoxin‑type protein essential for electron transfer from ubiquinol to periplasmic nitrate reductase (NapAB)
RA	2,294,769	C→A	5.6%	P488P (CCG→CCT)	napA ←	nitrate reductase, periplasmic, large subunit
RA	2,298,128	C→T	6.9%	intergenic (+256/+459)	eco → / ← mqo	ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA	2,303,070	T→G	100%	Q272P (CAG→CCG)	ada ←	fused DNA‑binding transcriptional dual regulator/O6‑methylguanine‑DNA methyltransferase
RA	2,303,607	A→C	9.2%	L93R (CTG→CGG)	ada ←	fused DNA‑binding transcriptional dual regulator/O6‑methylguanine‑DNA methyltransferase
RA	2,305,116	C→A	92.5%	intergenic (‑103/+9)	apbE ← / ← ompC	putative thiamine‑synthetic flavin transferase lipoprotein/outer membrane porin protein C
RA	2,305,135	T→C	92.1%	Y365C (TAC→TGC)	ompC ←	outer membrane porin protein C
RA	2,310,690	C→A	7.2%	R889L (CGC→CTC)	rcsC ←	hybrid sensory kinase in two‑component regulatory system with RcsB and YojN
RA	2,311,008	T→A	26.9%	H783L (CAC→CTC)	rcsC ←	hybrid sensory kinase in two‑component regulatory system with RcsB and YojN
RA	2,313,924	C→A	32.0%	R135S (CGC→AGC)	atoS →	sensory histidine kinase in two‑component regulatory system with AtoC
RA	2,330,502	C→A	91.4%	D800Y (GAT→TAT)	gyrA ←	DNA gyrase (type II topoisomerase), subunit A
RA	2,331,288	C→T	14.9%	D538N (GAT→AAT)	gyrA ←	DNA gyrase (type II topoisomerase), subunit A
RA	2,348,894	T→A	36.7%	V384E (GTG→GAG)	glpB →	sn‑glycerol‑3‑phosphate dehydrogenase (anaerobic), membrane anchor subunit
RA	2,352,573	C→A	92.0%	P353P (CCG→CCT)	rhmT ←	putative L‑rhamnonate transporter
RA	2,353,889	C→A	35.5%	V335V (GTG→GTT)	rhmD ←	L‑rhamnonate dehydratase
RA	2,359,673	G→T	92.5%	M89I (ATG→ATT)	arnB →	uridine 5'‑(beta‑1‑threo‑pentapyranosyl‑4‑ulose diphosphate) aminotransferase, PLP‑dependent
RA	2,362,338	T→A	89.7%	L274Q (CTG→CAG)	arnA →	fused UDP‑L‑Ara4N formyltransferase/UDP‑GlcA C‑4'‑decarboxylase
RA	2,366,555	T→G	24.0%	F62C (TTT→TGT)	arnF →	undecaprenyl phosphate‑alpha‑L‑ara4N exporter; flippase ArnEF subunit
RA	2,370,361:1	+G	91.8%	coding (711/759 nt)	menH ←	2‑succinyl‑6‑hydroxy‑2, 4‑cyclohexadiene‑1‑carboxylate synthase
RA	2,370,837	Δ1 bp	35.9%	coding (235/759 nt)	menH ←	2‑succinyl‑6‑hydroxy‑2, 4‑cyclohexadiene‑1‑carboxylate synthase
RA	2,370,987	C→A	92.8%	E29* (GAA→TAA)	menH ←	2‑succinyl‑6‑hydroxy‑2, 4‑cyclohexadiene‑1‑carboxylate synthase
RA	2,373,129	C→A	32.9%	D332Y (GAT→TAT)	menF ←	isochorismate synthase 2
RA	2,379,450	C→T	5.1%	P38S (CCT→TCT)	yfbL →	putative peptidase
RA	2,380,078	C→T	42.6%	S247F (TCT→TTT)	yfbL →	putative peptidase
RA	2,383,897	C→A	46.1%	R363L (CGC→CTC)	nuoN ←	NADH:ubiquinone oxidoreductase, membrane subunit N
RA	2,395,041	C→A	6.7%	R164L (CGG→CTG)	nuoE ←	NADH:ubiquinone oxidoreductase, chain E
RA	2,399,210	G→T	94.3%	S304* (TCA→TAA)	lrhA ←	transcriptional repressor of flagellar, motility and chemotaxis genes
RA	2,405,946	T→G	94.4%	Q43P (CAG→CCG)	yfbU ←	UPF0304 family protein
RA	2,407,678	T→A	28.5%	S244T (TCT→ACT)	ackA →	acetate kinase A and propionate kinase 2
RA	2,412,205	C→A	49.1%	D151Y (GAT→TAT)	yfcD ←	putative NUDIX hydrolase
RA	2,416,101	C→A	100%	intergenic (+21/+27)	yfcH → / ← yfcI	putative NAD‑dependent nucleotide‑sugar epimerase/transposase_31 family protein
RA	2,422,841	C→A	92.8%	D293Y (GAT→TAT)	purF ←	amidophosphoribosyltransferase
RA	2,424,074	C→T	92.9%	D57N (GAC→AAC)	cvpA ←	colicin V production membrane protein
RA	2,426,731	G→T	21.0%	I225I (ATC→ATA)	accD ←	acetyl‑CoA carboxylase, beta (carboxyltransferase) subunit
RA	2,442,770	A→C	31.6%	D253E (GAT→GAG)	yfcO ←	DUF2544 family putative outer membrane protein
RA	2,442,790	C→A	24.5%	D247Y (GAT→TAT)	yfcO ←	DUF2544 family putative outer membrane protein
RA	2,450,335	C→T	89.5%	intergenic (‑44/+159)	sixA ← / ← fadJ	phosphohistidine phosphatase/fused enoyl‑CoA hydratase and epimerase and isomerase/3‑hydroxyacyl‑CoA dehydrogenase
RA	2,450,346	G→T	90.8%	intergenic (‑55/+148)	sixA ← / ← fadJ	phosphohistidine phosphatase/fused enoyl‑CoA hydratase and epimerase and isomerase/3‑hydroxyacyl‑CoA dehydrogenase
RA	2,452,454	G→T	92.9%	P62Q (CCG→CAG)	fadJ ←	fused enoyl‑CoA hydratase and epimerase and isomerase/3‑hydroxyacyl‑CoA dehydrogenase
RA	2,453,358	G→T	29.0%	I197I (ATC→ATA)	fadI ←	beta‑ketoacyl‑CoA thiolase, anaerobic, subunit
RA	2,454,297	T→G	93.0%	E39D (GAA→GAC)	yfcZ ←	UPF0381 family protein
RA	2,456,282	C→A	35.1%	intergenic (+157/‑209)	fadL → / → yfdF	long‑chain fatty acid outer membrane transporter/uncharacterized protein
RA	2,463,906	C→A	22.5%	Q433K (CAA→AAA)	gtrS →	serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
RA	2,463,920	C→A	13.0%	D437E (GAC→GAA)	gtrS →	serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
RA	2,474,418	G→T	100%	S413* (TCA→TAA)	emrY ←	putative multidrug efflux system
RA	2,494,310	C→A	27.8%	T150K (ACG→AAG)	ypdB →	response regulator activating yhjX; pyruvate‑responsive YpdAB two‑component system
RA	2,495,918	C→A	32.6%	V683F (GTT→TTT)	fryA ←	putative PTS enzyme, Hpr component/enzyme I component/enzyme IIA component
RA	2,503,015	C→A	28.9%	intergenic (‑110/‑94)	glk ← / → yfeO	glucokinase/putative ion channel protein
RA	2,504,065	C→T	30.3%	G319G (GGC→GGT)	yfeO →	putative ion channel protein
RA	2,514,754	A→T	9.5%	intergenic (+67/+198)	lysV → / ← xapR	tRNA‑Lys/transcriptional activator of xapAB
RA	2,516,553	T→G	10.6%	E264D (GAA→GAC)	xapB ←	xanthosine transporter
RA	2,520,652	C→A	94.6%	I116I (ATC→ATA)	yfeH →	putative inorganic ion transporter
RA	2,526,023	T→A	7.7%	Y86N (TAC→AAC)	cysK →	cysteine synthase A, O‑acetylserine sulfhydrolase A subunit
RA	2,542,627	T→G	49.5%	I389M (ATT→ATG)	yfeW →	penicillin binding protein PBP4B; weak DD‑carboxypeptidase activity
RA	2,549,676	C→A	91.2%	L28L (CTG→CTT)	eutL ←	putative ethanol utilization carboxysome structural protein
RA	2,559,092	C→A	5.9%	A384A (GCG→GCT)	eutA ←	reactivating factor for ethanolamine ammonia lyase
RA	2,568,720	C→T	92.8%	A33T (GCC→ACC)	eutP ←	putative P‑loop NTPase ethanolamine utilization protein
RA	2,576,325	C→A	90.4%	E171D (GAG→GAT)	nudK ←	GDP‑mannose pyrophosphatase
RA	2,586,791	G→T	31.6%	G113G (GGC→GGA)	ypfH ←	palmitoyl‑CoA esterase activity, uncertain physiological substrate
RA	2,587,029:1	+G	92.3%	coding (101/699 nt)	ypfH ←	palmitoyl‑CoA esterase activity, uncertain physiological substrate
RA	2,589,933	G→A	94.0%	T55I (ACC→ATC)	ypfJ ←	putative neutral zinc metallopeptidase
RA	2,597,173	T→G	52.7%	L666R (CTG→CGG)	hyfB →	hydrogenase 4, membrane subunit
RA	2,598,312	C→A	6.6%	A48E (GCG→GAG)	hyfD →	hydrogenase 4, membrane subunit
RA	2,604,731	C→T	15.8%	R223W (CGG→TGG)	hyfI →	hydrogenase 4, Fe‑S subunit
RA	2,606,516	G→T	100%	D420Y (GAC→TAC)	hyfR →	hydrogenase‑4 transcriptional activator
RA	2,610,919	C→A	100%	intergenic (+3/‑18)	bepA → / → yfgD	periplasmic metalloprotease and chaperone for OM protein maintenance and assembly/putative oxidoreductase
RA	2,614,168	C→A	100%	D22Y (GAT→TAT)	upp ←	uracil phosphoribosyltransferase
RA	2,618,693	G→T	49.5%	E74* (GAA→TAA)	ppx →	exopolyphosphatase
RA	2,619,125	G→T	33.6%	G218C (GGT→TGT)	ppx →	exopolyphosphatase
RA	2,619,563	C→A	8.1%	R364R (CGA→AGA)	ppx →	exopolyphosphatase
RA	2,632,012	C→A	37.0%	intergenic (‑1/+10)	bamB ← / ← yfgM	BamABCDE complex OM biogenesis lipoprotein/putative anti‑RcsB factor
RA	2,651,665	G→T	91.1%	G210G (GGC→GGA)	hscA ←	DnaK‑like molecular chaperone specific for IscU
RA	2,664,115	C→A	25.9%	R123R (CGG→AGG)	hcaF →	3‑phenylpropionate dioxygenase, small (beta) subunit
RA	2,665,693	C→A	7.7%	G96G (GGC→GGA)	hcaD →	phenylpropionate dioxygenase, ferredoxin reductase subunit
RA	2,669,978	C→A	42.8%	A69A (GCG→GCT)	yphD ←	inner membrane putative ABC superfamily sugar transporter permease
RA	2,670,904	G→T	7.9%	R273S (CGC→AGC)	yphE ←	putative sugar transporter subunit of ABC superfamily, ATP‑binding component
RA	2,671,274	C→A	92.8%	T149T (ACG→ACT)	yphE ←	putative sugar transporter subunit of ABC superfamily, ATP‑binding component
RA	2,678,030	C→A	27.3%	A279A (GCG→GCT)	glyA ←	serine hydroxymethyltransferase
RA	2,678,315	C→A	5.1%	A184A (GCG→GCT)	glyA ←	serine hydroxymethyltransferase
RA	2,681,873	T→A	91.5%	Q97L (CAG→CTG)	glrR ←	response regulator regulating glmY sRNA in two‑component system with sensor protein GlrK
RA	2,683,707	G→T	7.9%	H251N (CAT→AAT)	glrK ←	sensor protein kinase regulating glmY sRNA in two‑component system with response regulator GlrR
RA	2,683,829	C→A	91.2%	R210L (CGT→CTT)	glrK ←	sensor protein kinase regulating glmY sRNA in two‑component system with response regulator GlrR
RA	2,692,793	C→A	44.3%	H226N (CAT→AAT)	yfhH →	putative DNA‑binding transcriptional regulator
RA	2,694,843	G→T	45.1%	I82I (ATC→ATA)	pdxJ ←	pyridoxine 5'‑phosphate synthase
RA	2,699,380	C→A	41.1%	P368P (CCG→CCT)	lepA ←	back‑translocating elongation factor EF4, GTPase
RA	2,715,643	G→T	93.2%	E778* (GAA→TAA)	pka →	protein lysine acetyltransferase
RA	2,719,426	T→C	100%	intergenic (‑321/+2)	kgtP ← / ← rrfG	alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon
RA	2,726,786	C→A	90.9%	A249A (GCG→GCT)	clpB ←	protein disaggregation chaperone
RA	2,733,753	C→T	100%	E253K (GAG→AAG)	aroF ←	3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, tyrosine‑repressible
RA	2,735,293	A→T	30.4%	I20I (ATA→ATT)	yfiR →	putative periplasmic inhibitor of YfiN activity
RA	2,749,134	C→A	9.1%	intergenic (+397/‑384)	smpB → / → intA	trans‑translation protein/CP4‑57 prophage; integrase
RA	2,757,927	A→T	9.6%	S196T (TCC→ACC)	yfjL ←	CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein
RA	2,761,733	T→A	39.0%	V222E (GTA→GAA)	yfjP →	CP4‑57 prophage; 50S ribosome‑binding GTPase family protein
RA	2,771,358	G→A	91.2%	intergenic (+217/+147)	ypjF → / ← ypjA	CP4‑57 prophage; toxin of the YpjF‑YfjZ toxin‑antitoxin system/adhesin‑like autotransporter
RA	2,778,281	C→T	30.4%	pseudogene (90/1374 nt)	ypjC ←	pseudogene
RA	2,779,067	C→A	94.0%	intergenic (‑697/+54)	ypjC ← / ← ileY	pseudogene/tRNA‑Ile
RA	2,803,846	C→A	7.2%	I48I (ATC→ATA)	ygaH →	putative L‑valine exporter, norvaline resistance protein
RA	2,806,531	T→G	7.9%	L186R (CTG→CGG)	emrB →	multidrug efflux system protein
RA	2,808,646	G→T	9.8%	R385S (CGC→AGC)	gshA ←	glutamate‑cysteine ligase
RA	2,825,783	C→T	100%	intergenic (‑135/‑52)	norR ← / → norV	anaerobic nitric oxide reductase DNA‑binding transcriptional activator/anaerobic nitric oxide reductase flavorubredoxin
RA	2,828,952	C→A	90.7%	T611T (ACG→ACT)	hypF ←	carbamoyl phosphate phosphatase and maturation protein for [NiFe] hydrogenases
RA	2,831,086	C→A	37.2%	E127* (GAA→TAA)	hydN ←	formate dehydrogenase‑H, [4Fe‑4S] ferredoxin subunit
RA	2,835,094	C→A	40.7%	P249Q (CCG→CAG)	ascB →	cryptic 6‑phospho‑beta‑glucosidase
RA	2,841,044	C→A	89.0%	A519A (GCG→GCT)	hycC ←	hydrogenase 3, membrane subunit
RA	2,846,112	C→A	42.0%	I206I (ATC→ATA)	hypD →	hydrogenase maturation protein
RA	2,850,790	C→A	91.4%	I113I (ATC→ATA)	mutS →	methyl‑directed mismatch repair protein
RA	2,860,460	G→T	27.6%	R151S (CGC→AGC)	rpoS ←	RNA polymerase, sigma S (sigma 38) factor
RA	2,873,087	G→T	90.5%	V15V (GTC→GTA)	ygbT ←	multifunctional endonuclease Cas1, CRISPR adaptation protein; DNA repair enzyme
RA	2,876,760	C→T	100%	G246G (GGG→GGA)	casA ←	CRISP RNA (crRNA) containing Cascade antiviral complex protein
RA	2,878,668	G→T	90.4%	V637V (GTC→GTA)	ygcB ←	R‑loop helicase‑annealase Cas3 needed for Cascade anti‑viral activity
RA	2,879,449	G→T	91.4%	S377* (TCA→TAA)	ygcB ←	R‑loop helicase‑annealase Cas3 needed for Cascade anti‑viral activity
RA	2,880,202	G→T	6.5%	S126* (TCA→TAA)	ygcB ←	R‑loop helicase‑annealase Cas3 needed for Cascade anti‑viral activity
RA	2,888,584	G→T	100%	I185I (ATC→ATA)	ygcQ ←	putative flavoprotein
RA	2,893,446	T→A	47.4%	K63* (AAA→TAA)	ygcW ←	putative dehydrogenase
RA	2,914,100	C→A	5.4%	A2A (GCG→GCT)	gudX ←	glucarate dehydratase‑related protein, substrate unknown
RA	2,931,717	C→A	92.9%	N307K (AAC→AAA)	fucK →	L‑fuculokinase
RA	2,932,832	C→A	24.3%	R36S (CGT→AGT)	fucR →	l‑fucose operon activator
RA	2,932,835	C→T	52.8%	R37C (CGC→TGC)	fucR →	l‑fucose operon activator
RA	2,934,843	G→T	93.2%	H50N (CAT→AAT)	ygdD ←	UPF0382 family inner membrane protein
RA	2,936,686	G→T	36.9%	intergenic (‑182/‑10)	ygdI ← / → csdA	DUF903 family verified lipoprotein/cysteine sulfinate desulfinase
RA	2,938,640	C→A	19.6%	D188Y (GAT→TAT)	tcdA ←	tRNA threonylcarbamoyladenosine dehydratase; sulfur acceptor for CsdA
RA	2,940,935	C→A	5.4%	intergenic (+3/‑31)	metW → / → metV	tRNA‑Met/tRNA‑Met
RA	2,957,480	C→A	27.6%	L19F (TTG→TTT)	ppdA ←	putative prepilin peptidase‑dependent protein
RA	2,959,004	G→A	92.9%	I131I (ATC→ATT)	lgt ←	phosphatidylglycerol‑prolipoprotein diacylglyceryl transferase
RA	2,960,251	C→A	8.0%	E515* (GAA→TAA)	ptsP ←	fused PTS enzyme: PEP‑protein phosphotransferase (enzyme I)/GAF domain containing protein
RA	2,960,829	C→A	15.7%	R322L (CGT→CTT)	ptsP ←	fused PTS enzyme: PEP‑protein phosphotransferase (enzyme I)/GAF domain containing protein
RA	2,961,385	C→A	15.9%	E137* (GAA→TAA)	ptsP ←	fused PTS enzyme: PEP‑protein phosphotransferase (enzyme I)/GAF domain containing protein
RA	2,962,962	T→A	43.8%	intergenic (‑626/‑59)	rppH ← / → mutH	RNA pyrophosphohydrolase/methyl‑directed mismatch repair protein
RA	2,967,572	A→G	33.2%	F601S (TTT→TCT)	aas ←	fused 2‑acylglycerophospho‑ethanolamine acyl transferase/acyl‑acyl carrier protein synthetase
RA	2,985,884	C→T	42.5%	I144I (ATC→ATT)	ygeH →	putative transcriptional regulator
RA	2,987,928	C→A	24.9%	pseudogene (524/633 nt)	ygeK ←	pseudogene; putative 2‑component transcriptional regulator
RA	2,988,505	C→A	5.2%	intergenic (‑54/+168)	ygeK ← / ← ygeN	pseudogene; putative 2‑component transcriptional regulator/pseudogene
RA	2,988,554	G→A	51.3%	intergenic (‑103/+119)	ygeK ← / ← ygeN	pseudogene; putative 2‑component transcriptional regulator/pseudogene
RA	2,989,295	C→A	91.9%	pseudogene (85/261 nt)	ygeN ←	pseudogene
RA	2,993,211	C→A	100%	V14L (GTG→TTG)	ygeR ←	LysM domain‑containing M23 family putative peptidase; septation lipoprotein
RA	2,993,699	C→A	84.2%	intergenic (‑449/‑5)	ygeR ← / → xdhA	LysM domain‑containing M23 family putative peptidase; septation lipoprotein/xanthine dehydrogenase, molybdenum binding subunit
RA	2,995,335	C→A	24.6%	V544V (GTC→GTA)	xdhA →	xanthine dehydrogenase, molybdenum binding subunit
RA	2,999,286	G→T	7.2%	intergenic (‑141/‑335)	ygeV ← / → ygeW	putative sigma‑54‑interacting transcriptional activator/putative carbamoyltransferase
RA	3,009,187	G→T	47.9%	intergenic (+90/‑232)	mocA → / → ygfK	CTP:molybdopterin cytidylyltransferase/putative Fe‑S subunit oxidoreductase subunit
RA	3,016,372	C→A	6.0%	F566L (TTC→TTA)	xdhD →	putative hypoxanthine oxidase, molybdopterin‑binding/Fe‑S binding
RA	3,017,285	G→T	92.5%	D871Y (GAC→TAC)	xdhD →	putative hypoxanthine oxidase, molybdopterin‑binding/Fe‑S binding
RA	3,019,203	G→T	33.1%	E27* (GAG→TAG)	guaD →	guanine deaminase
RA	3,022,877	G→T	6.0%	R472S (CGC→AGC)	ygfT ←	putative oxidoreductase, Fe‑S subunit/nucleotide‑binding subunit
RA	3,022,888	C→A	8.0%	R468L (CGG→CTG)	ygfT ←	putative oxidoreductase, Fe‑S subunit/nucleotide‑binding subunit
RA	3,024,081	A→C	55.1%	V70V (GTT→GTG)	ygfT ←	putative oxidoreductase, Fe‑S subunit/nucleotide‑binding subunit
RA	3,024,983	C→G	94.1%	G86G (GGC→GGG)	uacT →	uric acid permease
RA	3,025,678	A→T	36.5%	Q318L (CAA→CTA)	uacT →	uric acid permease
RA	3,028,224	G→T	28.7%	L104I (CTC→ATC)	lysS ←	lysine tRNA synthetase, constitutive
RA	3,030,181	G→T	45.0%	H429N (CAT→AAT)	recJ ←	ssDNA exonuclease, 5' ‑‑> 3'‑specific
RA	3,039,409	T→G	13.0%	intergenic (‑149/+118)	ygfF ← / ← gcvP	putative NAD(P)‑dependent oxidoreductase with NAD(P)‑binding Rossmann‑fold domain/glycine decarboxylase, PLP‑dependent, subunit (protein P) of glycine cleavage complex
RA	3,041,026	C→A	26.5%	D459Y (GAC→TAC)	gcvP ←	glycine decarboxylase, PLP‑dependent, subunit (protein P) of glycine cleavage complex
RA	3,044,281	G→A	26.5%	intergenic (‑255/+193)	gcvT ← / ← ubiI	aminomethyltransferase, tetrahydrofolate‑dependent, subunit (T protein) of glycine cleavage complex/2‑octaprenylphenol hydroxylase, FAD‑dependent
RA	3,044,464	G→A	100%	intergenic (‑438/+10)	gcvT ← / ← ubiI	aminomethyltransferase, tetrahydrofolate‑dependent, subunit (T protein) of glycine cleavage complex/2‑octaprenylphenol hydroxylase, FAD‑dependent
RA	3,048,247	A→T	8.8%	V186E (GTA→GAA)	ygfB ←	UPF0149 family protein
RA	3,049,577	T→G	18.9%	intergenic (+53/‑23)	ssrS → / → fau	6S RNA inhibits RNA polymerase promoter binding/5‑formyltetrahydrofolate cyclo‑ligase family protein
RA	3,049,645	G→A	22.6%	E16K (GAA→AAA)	fau →	5‑formyltetrahydrofolate cyclo‑ligase family protein
RA	3,055,069	C→A	30.0%	V287V (GTC→GTA)	scpA →	methylmalonyl‑CoA mutase
RA	3,058,692	C→T	35.2%	P178S (CCT→TCT)	scpC →	propionyl‑CoA:succinate CoA transferase
RA	3,058,769	C→T	44.7%	I203I (ATC→ATT)	scpC →	propionyl‑CoA:succinate CoA transferase
RA	3,064,483	C→A	21.0%	D41Y (GAC→TAC)	fbaA ←	fructose‑bisphosphate aldolase, class II
RA	3,064,914	G→T	85.3%	I356I (ATC→ATA)	pgk ←	phosphoglycerate kinase
RA	3,068,135	G→T	37.8%	F140L (TTC→TTA)	yggD ←	MtlR family putative transcriptional repressor
RA	3,072,314	C→A	6.5%	E126* (GAA→TAA)	cmtB ←	putative mannitol‑specific enzyme IIA component of PTS
RA	3,075,114	C→A	86.6%	intergenic (‑120/‑158)	tktA ← / → loiP	transketolase 1, thiamine triphosphate‑binding/Phe‑Phe periplasmic metalloprotease, OM lipoprotein; low salt‑inducible; heat shock protein that binds Era
RA	3,076,526	C→A	90.9%	D211Y (GAC→TAC)	speB ←	agmatinase
RA	3,080,618	T→A	93.7%	V185E (GTG→GAG)	metK →	S‑adenosylmethionine synthetase
RA	3,081,697	T→A	26.8%	C19S (TGC→AGC)	galP →	D‑galactose transporter
RA	3,088,065	C→A	42.6%	V125V (GTG→GTT)	yggR ←	putative PilT family AAA+ ATPase
RA	3,092,182	C→A	19.4%	C248F (TGT→TTT)	yggM ←	DUF1202 family putative secreted protein
RA	3,097,262	C→T	44.6%	F297F (TTC→TTT)	mutY →	adenine DNA glycosylase
RA	3,102,941	T→A	6.5%	S10R (AGT→AGA)	yqgA →	DUF554 family putative inner membrane protein
RA	3,104,247	C→A	25.8%	R80L (CGA→CTA)	yghD ←	putative membrane‑anchored secretion pathway M‑type protein
RA	3,110,751	C→A	93.3%	R574L (CGT→CTT)	yghJ ←	DUF4092 family putative lipoprotein peptidase
RA	3,111,434	C→A	91.1%	A346A (GCG→GCT)	yghJ ←	DUF4092 family putative lipoprotein peptidase
RA	3,120,216	C→A	100%	D389Y (GAT→TAT)	glcD ←	glycolate oxidase subunit, FAD‑linked
RA	3,132,601	T→G	27.4%	I172M (ATT→ATG)	yghU →	putative S‑transferase
RA	3,142,668	G→T	39.5%	L55I (CTC→ATC)	yqhA ←	UPF0114 family putative inner membrane protein
RA	3,144,158	C→A	91.5%	intergenic (+253/+19)	yghA → / ← exbD	putative oxidoreductase/membrane spanning protein in TonB‑ExbB‑ExbD complex
RA	3,162,420	G→T	15.5%	V57V (GTC→GTA)	ygiV ←	transcriptional repressor for mcbR biofilm gene
RA	3,164,230	C→A	44.6%	R130S (CGT→AGT)	qseC →	quorum sensing sensory histidine kinase in two‑component regulatory system with QseB
RA	3,173,669	G→T	100%	A189A (GCG→GCT)	ygiB →	DUF1190 family protein
RA	3,176,733	G→T	45.8%	intergenic (+51/+439)	zupT → / ← ribB	zinc transporter/3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase
RA	3,191,839	T→A	25.0%	N388Y (AAC→TAC)	glnE ←	fused deadenylyltransferase/adenylyltransferase for glutamine synthetase
RA	3,214,709	C→A	32.0%	intergenic (‑103/‑116)	ygjH ← / → ebgR	putative tRNA binding protein; putative tRNA corner chaperone/transcriptional repressor
RA	3,215,927	C→A	9.8%	intergenic (+119/‑65)	ebgR → / → ebgA	transcriptional repressor/evolved beta‑D‑galactosidase, alpha subunit
RA	3,217,289	A→T	46.6%	H433L (CAC→CTC)	ebgA →	evolved beta‑D‑galactosidase, alpha subunit
RA	3,224,927	C→A	100%	intergenic (+329/‑97)	ygjK → / → fadH	alpha‑glucosidase/2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked
RA	3,230,857	C→G	54.4%	A63G (GCC→GGC)	ygjR →	putative NAD(P)‑dependent dehydrogenase
RA	3,231,349	A→C	43.5%	Q227P (CAG→CCG)	ygjR →	putative NAD(P)‑dependent dehydrogenase
RA	3,237,654	C→A	29.8%	M149I (ATG→ATT)	uxaC ←	uronate isomerase
RA	3,245,848	G→T	91.6%	L62L (CTG→CTT)	yhaH →	DUF805 family inner membrane protein
RA	3,246,634	A→T	34.2%	intergenic (+8/+43)	yhaI → / ← yhaJ	DUF805 family inner membrane protein/LysR family putative transcriptional regulator
RA	3,252,258	C→A	100%	D251Y (GAT→TAT)	tdcG ←	L‑serine dehydratase 3, anaerobic
RA	3,253,531	A→T	17.7%	R749R (CGT→CGA)	tdcE ←	pyruvate formate‑lyase 4/2‑ketobutyrate formate‑lyase
RA	3,262,473	G→A	6.2%	V234I (GTC→ATC)	yhaC →	pentapetide repeats‑related protein
RA	3,263,466	G→T	28.5%	intergenic (+505/+109)	yhaC → / ← rnpB	pentapetide repeats‑related protein/RNase P, M1 RNA component
RA	3,266,646	C→A	86.2%	G91C (GGT→TGT)	garL ←	alpha‑dehydro‑beta‑deoxy‑D‑glucarate aldolase
RA	3,275,040	C→A	10.9%	intergenic (+56/‑295)	agaA → / → agaS	pseudogene, N‑acetylgalactosamine‑6‑phosphate deacetylase fragment; putative N‑acetylgalactosamine‑6‑phosphate deacetylase/tagatose‑6‑phosphate ketose/aldose isomerase
RA	3,292,677	G→T	5.4%	V115V (GTG→GTT)	yhbO →	stress‑resistance protein
RA	3,296,612	G→T	47.5%	A255A (GCG→GCT)	yhbV →	U32 peptidase family protein
RA	3,302,027	G→T	93.5%	S86* (TCG→TAG)	nlpI ←	lipoprotein involved in osmotic sensitivity and filamentation
RA	3,312,862	T→A	32.0%	R289R (CGT→CGA)	argG →	argininosuccinate synthetase
RA	3,314,870	C→A	88.4%	A35S (GCG→TCG)	yhbX ←	putative EptAB family phosphoethanolamine transferase, inner membrane protein
RA	3,329,704	G→T	26.0%	V50V (GTC→GTA)	murA ←	UDP‑N‑acetylglucosamine 1‑carboxyvinyltransferase
RA	3,332,963	C→A	28.7%	A154A (GCG→GCT)	mlaF ←	ABC transporter maintaining OM lipid asymmetry, ATP‑binding protein
RA	3,347,778	G→A	100%	intergenic (‑369/‑306)	yhcC ← / → gltB	putative Fe‑S oxidoreductase, Radical SAM superfamily protein/glutamate synthase, large subunit
RA	3,351,650	G→T	48.8%	E1189D (GAG→GAT)	gltB →	glutamate synthase, large subunit
RA	3,354,405	C→T	93.4%	intergenic (+430/‑130)	gltD → / → gltF	glutamate synthase, 4Fe‑4S protein, small subunit/periplasmic protein
RA	3,357,229	C→A	30.7%	S355* (TCG→TAG)	yhcD →	putative outer membrane fimbrial subunit usher protein
RA	3,365,607	G→T	93.6%	I109I (ATC→ATA)	nanT ←	sialic acid transporter
RA	3,372,048	C→A	7.9%	intergenic (‑38/+181)	rplM ← / ← yhcM	50S ribosomal subunit protein L13/putative AFG1‑like family P‑loop ATPase
RA	3,373,985	C→A	92.5%	intergenic (+37/‑117)	yhcB → / → degQ	DUF1043 family inner membrane‑anchored protein/serine endoprotease, periplasmic
RA	3,375,260	G→T	93.1%	D387Y (GAT→TAT)	degQ →	serine endoprotease, periplasmic
RA	3,380,174	C→A	29.7%	S458S (TCG→TCT)	aaeB ←	p‑hydroxybenzoic acid efflux system component
RA	3,386,672	C→A	28.8%	P982P (CCG→CCT)	yhdP ←	DUF3971‑AsmA2 domains protein
RA	3,392,594	A→C	10.4%	A248A (GCT→GCG)	mreC ←	cell wall structural complex MreBCD transmembrane component MreC
RA	3,396,082	G→T	93.1%	R204S (CGT→AGT)	csrD ←	targeting factor for csrBC sRNA degradation
RA	3,407,007	G→A	50.7%	intergenic (‑183/‑216)	acrS ← / → acrE	acrAB operon transcriptional repressor/cytoplasmic membrane lipoprotein
RA	3,407,008	G→A	6.1%	intergenic (‑184/‑215)	acrS ← / → acrE	acrAB operon transcriptional repressor/cytoplasmic membrane lipoprotein
RA	3,411,136	G→T	6.6%	A915A (GCG→GCT)	acrF →	multidrug efflux system protein
RA	3,416,890	T→G	5.1%	noncoding (12/120 nt)	rrfF ←	5S ribosomal RNA of rrnD operon
RA	3,437,010	C→A	9.7%	V149V (GTG→GTT)	secY ←	preprotein translocase membrane subunit
RA	3,437,638	G→T	27.1%	G87G (GGC→GGA)	rplO ←	50S ribosomal subunit protein L15
RA	3,439,443	G→T	8.1%	I19I (ATC→ATA)	rplF ←	50S ribosomal subunit protein L6
RA	3,440,151	G→T	100%	I31I (ATC→ATA)	rpsN ←	30S ribosomal subunit protein S14
RA	3,440,444	G→T	100%	S118S (TCC→TCA)	rplE ←	50S ribosomal subunit protein L5
RA	3,440,832	T→C	92.2%	N99D (AAC→GAC)	rplX ←	50S ribosomal subunit protein L24
RA	3,447,853	A→T	7.7%	V302E (GTA→GAA)	gspA ←	general secretory pathway component, cryptic
RA	3,455,867	C→A	100%	I55I (ATC→ATA)	gspJ →	putative general secretory pathway component, cryptic
RA	3,467,941	C→T	6.3%	intergenic (‑30/+96)	rpsL ← / ← tusB	30S ribosomal subunit protein S12/mnm(5)‑s(2)U34‑tRNA synthesis 2‑thiolation protein
RA	3,473,139	G→T	94.3%	I276I (ATC→ATA)	kefB ←	potassium:proton antiporter
RA	3,479,769	A→T	91.8%	E97D (GAA→GAT)	crp →	cAMP‑activated global transcription factor, mediator of catabolite repression
RA	3,483,095	C→A	28.9%	V149F (GTT→TTT)	argD ←	bifunctional acetylornithine aminotransferase/ succinyldiaminopimelate aminotransferase
RA	3,488,966	G→C	94.3%	A533P (GCC→CCC)	nirB →	nitrite reductase, large subunit, NAD(P)H‑binding
RA	3,489,397	C→A	87.4%	F676L (TTC→TTA)	nirB →	nitrite reductase, large subunit, NAD(P)H‑binding
RA	3,498,214	T→G	5.2%	intergenic (+72/+80)	frlR → / ← yhfS	putative DNA‑binding transcriptional regulator/FNR‑regulated pyridoxal phosphate‑dependent aminotransferase family protein
RA	3,501,571	C→A	91.7%	G127C (GGC→TGC)	php ←	phosphotriesterase homology protein
RA	3,504,143	G→T	47.7%	R65S (CGT→AGT)	yhfX ←	putative pyridoxal 5'‑phosphate binding protein
RA	3,504,943	C→A	11.1%	R254L (CGA→CTA)	yhfZ ←	putative DNA‑binding transcriptional regulator
RA	3,507,749	G→T	92.7%	H224N (CAT→AAT)	rpe ←	D‑ribulose‑5‑phosphate 3‑epimerase
RA	3,510,311	C→A	30.1%	G119C (GGT→TGT)	damX ←	cell division protein that binds to the septal ring
RA	3,513,424	A→T	46.8%	V213V (GTT→GTA)	hofQ ←	DNA catabolic putative fimbrial transporter
RA	3,519,657	G→T	100%	intergenic (‑149/‑171)	nudE ← / → yrfF	adenosine nucleotide hydrolase; substrates include Ap3A, Ap2A, ADP‑ribose, NADH/inner membrane protein
RA	3,525,950	C→T	34.7%	intergenic (‑152/‑227)	yhgE ← / → pck	DUF4153 family putative inner membrane protein/phosphoenolpyruvate carboxykinase
RA	3,538,325	G→T	14.5%	A29S (GCC→TCC)	gntX →	DNA catabolic protein
RA	3,542,744	T→A	5.4%	Q229L (CAG→CTG)	malQ ←	4‑alpha‑glucanotransferase (amylomaltase)
RA	3,543,959	G→T	95.0%	A625E (GCG→GAG)	malP ←	maltodextrin phosphorylase
RA	3,551,503	T→C	8.6%	intergenic (‑65/‑124)	rtcB ← / → rtcR	RNA‑splicing ligase/sigma 54‑dependent transcriptional regulator of rtcBA expression
RA	3,559,170	C→A	8.4%	D258Y (GAT→TAT)	glgP ←	glycogen phosphorylase
RA	3,561,574	C→A	93.8%	W372L (TGG→TTG)	glgC ←	glucose‑1‑phosphate adenylyltransferase
RA	3,575,640	C→A	5.7%	L140I (CTT→ATT)	yhhZ →	putative Hcp1 family polymorphic toxin protein; putative colicin‑like DNase/tRNase activity
RA	3,580,673	G→T	21.0%	R124I (AGA→ATA)	yhhA →	DUF2756 family protein
RA	3,585,079	C→A	31.2%	A203S (GCC→TCC)	ugpB ←	glycerol‑3‑phosphate transporter subunit
RA	3,588,904	A→T	36.3%	L287Q (CTG→CAG)	livH ←	leucine/isoleucine/valine transporter subunit
RA	3,598,440	C→A	32.4%	N34K (AAC→AAA)	yhhL →	DUF1145 family protein
RA	3,632,600	T→G	27.2%	intergenic (+99/+145)	pitA → / ← uspB	phosphate transporter, low‑affinity; tellurite importer/universal stress (ethanol tolerance) protein B
RA	3,639,551	C→A	26.8%	T269T (ACC→ACA)	rlmJ →	23S rRNA m(6)A2030 methyltransferase, SAM‑dependent
RA	3,656,367	C→A	5.0%	A865E (GCG→GAG)	mdtF →	anaerobic multidrug efflux transporter, ArcA‑regulated
RA	3,662,660	T→C	89.9%	intergenic (‑112/‑292)	yhjA ← / → treF	putative cytochrome C peroxidase/cytoplasmic trehalase
RA	3,679,301	T→G	92.1%	Q1078P (CAG→CCG)	bcsC ←	cellulose synthase subunit
RA	3,679,324	C→A	92.7%	M1070I (ATG→ATT)	bcsC ←	cellulose synthase subunit
RA	3,680,910	G→T	90.1%	H542N (CAT→AAT)	bcsC ←	cellulose synthase subunit
RA	3,689,369	C→A	6.6%	A59A (GCG→GCT)	yhjR ←	DUF2629 family protein
RA	3,698,875	G→T	45.8%	F92L (TTC→TTA)	dppB ←	dipeptide/heme transporter
RA	3,701,561	G→A	24.5%	intergenic (‑496/+415)	dppA ← / ← proK	dipeptide transporter/tRNA‑Pro
RA	3,703,272	C→A	32.0%	A188A (GCG→GCT)	eptB ←	KDO phosphoethanolamine transferase, Ca(2+)‑inducible
RA	3,717,788	C→A	91.9%	P297P (CCG→CCT)	glyQ ←	glycine tRNA synthetase, alpha subunit
RA	3,718,959	C→A	39.7%	L38F (TTG→TTT)	ysaB ←	uncharacterized protein
RA	3,730,615	C→A	34.2%	intergenic (‑78/‑242)	bax ← / → malS	putative glucosaminidase/alpha‑amylase
RA	3,738,431	C→A	94.5%	P90T (CCA→ACA)	yiaN →	2,3‑diketo‑L‑gulonate TRAP transporter large permease protein
RA	3,759,388	C→A	32.8%	N1282K (AAC→AAA)	rhsA →	Rhs family protein, putative polymorphic toxin; putative polysaccharide synthesis/export protein; putative neighboring cell growth inhibitor
RA	3,767,000	G→T	43.2%	D454Y (GAC→TAC)	mtlA →	fused mannitol‑specific PTS enzymes: IIA components/IIB components/IIC components
RA	3,769,093	C→A	11.6%	T54T (ACC→ACA)	mtlR →	mannitol operon repressor
RA	3,774,382	T→G	7.7%	intergenic (+5/‑193)	lldD → / → trmL	L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent
RA	3,779,281	C→G	6.5%	A221G (GCT→GGT)	gpmM →	phosphoglycero mutase III, cofactor‑independent
RA	3,779,319	G→T	9.0%	E234* (GAA→TAA)	gpmM →	phosphoglycero mutase III, cofactor‑independent
RA	3,785,915	G→T	90.9%	intergenic (‑4/+271)	kbl ← / ← yibB	glycine C‑acetyltransferase/YibB family protein, function unknown
RA	3,791,588	T→A	29.9%	intergenic (+21/+11)	waaL → / ← waaU	O‑antigen ligase/lipopolysaccharide core biosynthesis
RA	3,802,238	A→T	7.2%	A113A (GCA→GCT)	waaA →	3‑deoxy‑D‑manno‑octulosonic‑acid transferase (KDO transferase)
RA	3,804,099	G→T	7.1%	F138L (TTC→TTA)	mutM ←	formamidopyrimidine/5‑formyluracil/ 5‑hydroxymethyluracil DNA glycosylase
RA	3,810,195	C→A	93.1%	R54S (CGT→AGT)	yicC →	UPF0701 family protein
RA	3,814,302	T→A	35.6%	S77C (AGC→TGC)	ligB ←	DNA ligase, NAD(+)‑dependent
RA	3,816,601	A→T	94.2%	H281L (CAC→CTC)	spoT →	bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase
RA	3,818,010	C→A	93.3%	H46N (CAT→AAT)	trmH →	tRNA mG18‑2'‑O‑methyltransferase, SAM‑dependent
RA	3,822,339	A→C	14.2%	Q12P (CAA→CCA) ‡	xanP →	xanthine permease
RA	3,822,340	A→C	9.4%	Q12H (CAA→CAC) ‡	xanP →	xanthine permease
RA	3,825,702	C→A	93.7%	K732N (AAG→AAT)	yicI ←	putative alpha‑glucosidase
RA	3,828,206	T→A	21.2%	S362C (AGT→TGT)	yicJ ←	putative transporter
RA	3,830,197	C→A	92.3%	intergenic (+281/‑116)	yicT → / → setC	pseudogene/putative arabinose efflux transporter
RA	3,830,311	G→T	92.2%	intergenic (+395/‑2)	yicT → / → setC	pseudogene/putative arabinose efflux transporter
RA	3,835,154	G→A	31.6%	intergenic (‑55/+156)	nepI ← / ← yicN	putative transporter/DUF1198 family protein
RA	3,846,307	C→A	27.4%	A14A (GCG→GCT)	ivbL ←	ilvB operon leader peptide
RA	3,851,275	G→T	30.1%	H164N (CAT→AAT)	yidJ ←	sulfatase/phosphatase superfamily protein
RA	3,860,159	C→A	100%	P33P (CCG→CCT)	ibpB ←	heat shock chaperone
RA	3,860,327	C→A	48.8%	intergenic (‑70/+42)	ibpB ← / ← ibpA	heat shock chaperone/heat shock chaperone
RA	3,860,653	C→A	46.3%	E44* (GAA→TAA)	ibpA ←	heat shock chaperone
RA	3,865,120	C→A	42.3%	intergenic (‑30/+90)	dgoT ← / ← dgoD	D‑galactonate transporter/galactonate dehydratase
RA	3,870,977	T→A	5.5%	intergenic (‑152/+88)	yidB ← / ← gyrB	DUF937 family protein/DNA gyrase, subunit B
RA	3,894,614	C→A	25.0%	A323S (GCA→TCA)	bglH ←	carbohydrate‑specific outer membrane porin, cryptic
RA	3,896,189	G→T	6.8%	T291T (ACC→ACA)	bglB ←	cryptic phospho‑beta‑glucosidase B
RA	3,898,349	G→A	5.7%	F203F (TTC→TTT)	bglF ←	fused beta‑glucoside‑specific PTS enzymes: IIA component/IIB component/IIC component
RA	3,906,384	G→T	6.4%	I215I (ATC→ATA)	glmS ←	L‑glutamine:D‑fructose‑6‑phosphate aminotransferase
RA	3,910,894	C→A	93.0%	M244I (ATG→ATT)	atpG ←	F1 sector of membrane‑bound ATP synthase, gamma subunit
RA	3,916,052	C→A	30.1%	intergenic (‑252/+365)	atpI ← / ← rsmG	ATP synthase, membrane‑bound accessory factor/16S rRNA m(7)G527 methyltransferase, SAM‑dependent; glucose‑inhibited cell‑division protein
RA	3,916,830	C→A	91.2%	D71Y (GAT→TAT)	rsmG ←	16S rRNA m(7)G527 methyltransferase, SAM‑dependent; glucose‑inhibited cell‑division protein
RA	3,917,548	C→A	7.0%	S482S (TCG→TCT)	mnmG ←	5‑methylaminomethyl‑2‑thiouridine modification at tRNA U34
RA	3,923,028	C→A	45.4%	D476Y (GAC→TAC)	ravA ←	hexameric AAA+ MoxR family ATPase, putative molecular chaperone
RA	3,926,831	G→T	100%	D41Y (GAT→TAT)	rbsD →	putative cytoplasmic sugar‑binding protein
RA	3,927,972	G→T	41.2%	E279* (GAA→TAA)	rbsA →	fused D‑ribose transporter subunits of ABC superfamily: ATP‑binding components
RA	3,933,680	G→T	25.8%	S98* (TCG→TAG)	hsrA ←	putative multidrug or homocysteine efflux system
RA	3,935,100	G→T	41.1%	intergenic (‑413/‑68)	yieP ← / → rrsC	putative transcriptional regulator/16S ribosomal RNA of rrnC operon
RA	3,944,000	T→A	5.6%	pseudogene (81/984 nt)	ilvG →	pseudogene, acetolactate synthase 2 large subunit, valine‑insensitive; acetolactate synthase II, large subunit, cryptic, interrupted
RA	3,950,395	C→A	30.6%	E262D (GAG→GAT)	ilvY ←	transcriptional activator of ilvC; autorepressor
RA	3,952,658	C→T	29.8%	D443D (GAC→GAT)	ilvC →	ketol‑acid reductoisomerase, NAD(P)‑binding
RA	3,952,817	T→G	8.9%	intergenic (+12/+75)	ilvC → / ← ppiC	ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C)
RA	3,956,662	T→G	8.1%	S310R (AGC→CGC)	gpp ←	guanosine pentaphosphatase/exopolyphosphatase
RA	3,960,036	G→A	89.3%	R87H (CGC→CAC)	rho →	transcription termination factor
RA	3,966,854	C→A	91.6%	R325S (CGT→AGT)	rffG →	dTDP‑glucose 4,6‑dehydratase
RA	3,967,474	G→T	43.5%	A169A (GCG→GCT)	rffH →	glucose‑1‑phosphate thymidylyltransferase
RA	3,969,710	G→T	91.2%	G25C (GGT→TGT)	wzxE →	O‑antigen translocase
RA	3,970,026	C→A	21.0%	A130D (GCC→GAC)	wzxE →	O‑antigen translocase
RA	3,988,075	T→A	93.2%	V65E (GTG→GAG)	yifL →	putative lipoprotein
RA	3,994,076	A→T	93.4%	L114* (TTA→TAA)	yigE ←	DUF2233 family protein
RA	3,994,247	A→T	94.6%	V57E (GTG→GAG)	yigE ←	DUF2233 family protein
RA	3,998,903	C→A	5.1%	L228I (CTC→ATC)	pldA →	outer membrane phospholipase A
RA	4,009,108	A→T	15.2%	L141* (TTA→TAA)	ysgA ←	putative carboxymethylenebutenolidase
RA	4,009,667	T→C	9.0%	intergenic (‑138/‑124)	ysgA ← / → udp	putative carboxymethylenebutenolidase/uridine phosphorylase
RA	4,009,705	G→A	93.9%	intergenic (‑176/‑86)	ysgA ← / → udp	putative carboxymethylenebutenolidase/uridine phosphorylase
RA	4,024,827	G→T	49.0%	D103Y (GAT→TAT)	pepQ →	proline dipeptidase
RA	4,035,421	G→T	46.7%	intergenic (‑62/‑8)	mobA ← / → yihD	molybdopterin‑guanine dinucleotide synthase/DUF1040 protein YihD
RA	4,039,399	G→T	8.7%	F188L (TTC→TTA)	yihG ←	inner membrane protein, inner membrane acyltransferase
RA	4,046,172	A→T	43.9%	K256N (AAA→AAT)	hemN →	coproporphyrinogen III oxidase, SAM and NAD(P)H dependent, oxygen‑independent
RA	4,056,018	T→A	92.1%	F138I (TTC→ATC)	yihN →	MFS transporter family protein
RA	4,062,424	G→T	93.0%	I71I (ATC→ATA)	yihQ ←	alpha‑glucosidase
RA	4,066,133	T→G	100%	S267R (AGC→CGC)	yihU ←	gamma‑hydroxybutyrate dehydrogenase, NADH‑dependent
RA	4,068,208	C→A	94.4%	G60G (GGC→GGA)	yihW →	DeoR family putative transcriptional regulator
RA	4,076,055	T→G	12.4%	Q22P (CAG→CCG)	fdoH ←	formate dehydrogenase‑O, Fe‑S subunit
RA	4,094,362	C→A	91.7%	W181L (TGG→TTG)	cpxA ←	sensory histidine kinase in two‑component regulatory system with CpxR
RA	4,096,555	G→T	6.6%	S53S (TCG→TCT)	fieF →	ferrous iron and zinc transporter
RA	4,097,822	G→T	100%	E115* (GAA→TAA)	pfkA →	6‑phosphofructokinase I
RA	4,105,186	C→A	16.6%	D108Y (GAT→TAT)	glpX ←	fructose 1,6‑bisphosphatase II
RA	4,122,248	A→T	46.4%	intergenic (+53/‑296)	metL → / → metF	Bifunctional aspartokinase/homoserine dehydrogenase 2/5,10‑methylenetetrahydrofolate reductase
RA	4,127,022	T→G	92.8%	E188D (GAA→GAC)	yijF ←	DUF1287 family protein
RA	4,143,375	A→G	8.2%	intergenic (‑349/+249)	ppc ← / ← argE	phosphoenolpyruvate carboxylase/acetylornithine deacetylase
RA	4,143,605	G→T	32.0%	intergenic (‑579/+19)	ppc ← / ← argE	phosphoenolpyruvate carboxylase/acetylornithine deacetylase
RA	4,150,197	G→T	26.6%	H174Q (CAC→CAA)	sthA ←	pyridine nucleotide transhydrogenase, soluble
RA	4,163,570	T→A	31.9%	I187I (ATT→ATA)	birA →	bifunctional biotin‑[acetylCoA carboxylase] holoenzyme synthetase/ DNA‑binding transcriptional repressor, bio‑5'‑AMP‑binding
RA	4,167,908	T→A	10.5%	W80R (TGG→AGG)	nusG →	transcription termination factor
RA	4,173,145	A→T	46.4%	Q658L (CAG→CTG)	rpoB →	RNA polymerase, beta subunit
RA	4,176,823	G→T	94.3%	D516Y (GAC→TAC)	rpoC →	RNA polymerase, beta prime subunit
RA	4,178,758	G→T	33.2%	G1161C (GGT→TGT)	rpoC →	RNA polymerase, beta prime subunit
RA	4,183,054	C→A	5.7%	A151S (GCG→TCG)	thiF ←	adenylyltransferase, modifies ThiS C‑terminus
RA	4,207,552	G→T	43.7%	M172I (ATG→ATT)	aceA →	isocitrate lyase
RA	4,207,558	G→T	31.5%	A174A (GCG→GCT)	aceA →	isocitrate lyase
RA	4,211,576	G→T	94.0%	S280R (AGC→AGA)	arpA ←	ankyrin repeat protein
RA	4,211,803	G→A	89.6%	P205S (CCT→TCT)	arpA ←	ankyrin repeat protein
RA	4,214,563	A→T	50.5%	T270S (ACC→TCC)	metH →	homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent
RA	4,218,928	G→A	32.9%	E424K (GAA→AAA)	yjbB →	putative Na+/Pi‑cotransporter
RA	4,219,081	C→A	10.9%	R475S (CGC→AGC)	yjbB →	putative Na+/Pi‑cotransporter
RA	4,220,948	G→T	29.4%	D223Y (GAT→TAT)	rluF →	23S rRNA pseudouridine(2604) synthase
RA	4,230,913	A→T	100%	W424R (TGG→AGG)	xylE ←	D‑xylose transporter
RA	4,234,527	C→G	13.3%	L159L (CTG→CTC)	malF ←	maltose transporter subunit
RA	4,235,869	G→T	45.8%	A160E (GCG→GAG)	malE ←	maltose transporter subunit
RA	4,241,633	C→T	31.9%	pseudogene (745/1323 nt)	yjbI →	pseudogene, SopA‑related, pentapeptide repeats‑containing
RA	4,242,509	C→T	42.8%	L26F (CTC→TTC)	ubiC →	chorismate‑‑pyruvate lyase
RA	4,257,593	C→T	20.8%	N184N (AAC→AAT)	tyrB →	tyrosine aminotransferase, tyrosine‑repressible, PLP‑dependent
RA	4,265,064	C→A	90.3%	intergenic (‑95/‑335)	yjcB ← / → yjcC	putative inner membrane protein/putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	4,268,967	A→T	10.6%	S187S (TCA→TCT)	yjcD →	inner membrane putative guanine permease
RA	4,271,906	C→T	34.4%	E366E (GAG→GAA)	yjcF ←	pentapeptide repeats protein
RA	4,273,297	A→T	33.7%	W512R (TGG→AGG)	actP ←	acetate transporter
RA	4,274,926	A→C	93.4%	I72M (ATT→ATG)	yjcH ←	DUF485 family inner membrane protein
RA	4,275,142	C→A	93.1%	intergenic (‑1/+199)	yjcH ← / ← acs	DUF485 family inner membrane protein/acetyl‑CoA synthetase
RA	4,286,118	A→G	6.4%	intergenic (+396/+135)	gltP → / ← yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA	4,290,080	G→T	94.1%	I256I (ATC→ATA)	mdtP ←	outer membrane factor of efflux pump
RA	4,297,485	G→C	39.4%	G44G (GGC→GGG)	alsK ←	D‑allose kinase
RA	4,297,846	C→A	94.8%	M150I (ATG→ATT)	alsE ←	allulose‑6‑phosphate 3‑epimerase
RA	4,300,333	T→A	37.1%	E155D (GAA→GAT)	alsA ←	fused D‑allose transporter subunits of ABC superfamily: ATP‑binding components
RA	4,303,614	T→A	93.7%	*150R (TGA→AGA)	rpiB →	ribose 5‑phosphate isomerase B/allose 6‑phosphate isomerase
RA	4,304,132	G→T	8.4%	intergenic (+118/+29)	yjdP → / ← phnP	putative periplasmic protein/5‑phospho‑alpha‑D‑ribosyl 1,2‑cyclic phosphate phosphodiesterase
RA	4,308,395	G→T	31.0%	H63N (CAC→AAC)	phnK ←	carbon‑phosphorus lyase complex subunit, putative ATP transporter ATP‑binding protein
RA	4,320,106	T→A	13.3%	intergenic (+51/‑213)	yjcZ → / → proP	YjcZ family protein, mutational suppressor of yhjH motility mutation/proline/glycine betaine transporter
RA	4,330,426	Δ1 bp	100%	intergenic (‑88/+111)	adiA ← / ← melR	arginine decarboxylase/melibiose operon transcriptional regulator; autoregulator
RA	4,335,195	G→T	18.9%	L61I (CTC→ATC)	yjdF ←	DUF2238 family inner membrane protein
RA	4,336,681	A→T	33.6%	Y155N (TAC→AAC)	fumB ←	anaerobic class I fumarate hydratase (fumarase B)
RA	4,338,712	T→A	11.9%	intergenic (‑151/+420)	dcuB ← / ← dcuR	C4‑dicarboxylate transporter, anaerobic; DcuS co‑sensor/response regulator in two‑component regulatory system with DcuS
RA	4,341,023	A→T	92.9%	Y153N (TAC→AAC)	dcuS ←	sensory histidine kinase in two‑component regulatory system with DcuR, regulator of anaerobic fumarate respiration
RA	4,345,995	C→A	29.4%	V78V (GTG→GTT)	dtpC ←	dipeptide and tripeptide permease
RA	4,354,610	A→T	29.1%	W84R (TGG→AGG)	dsbD ←	fused thiol:disulfide interchange protein: activator of DsbC/conserved protein
RA	4,355,606	G→T	5.6%	H329N (CAT→AAT)	dcuA ←	C4‑dicarboxylate antiporter
RA	4,358,920	G→T	49.1%	R147L (CGC→CTC)	fxsA →	suppressor of F exclusion of phage T7
RA	4,372,891	A→T	32.1%	A144A (GCA→GCT)	epmA →	Elongation Factor P Lys34 lysyltransferase
RA	4,376,178	C→A	48.7%	E1004* (GAA→TAA)	mscM ←	mechanosensitive channel protein, miniconductance
RA	4,378,778	G→T	43.6%	S137* (TCG→TAG)	mscM ←	mechanosensitive channel protein, miniconductance
RA	4,382,399	A→C	5.8%	intergenic (+35/‑1)	glyX → / → glyY	tRNA‑Gly/tRNA‑Gly
RA	4,388,902	G→T	94.7%	A558A (GCG→GCT)	mutL →	methyl‑directed mismatch repair protein
RA	4,394,875	G→T	46.2%	A124A (GCG→GCT)	purA →	adenylosuccinate synthetase
RA	4,396,598	A→T	94.2%	E43V (GAA→GTA)	rnr →	exoribonuclease R, RNase R
RA	4,396,680	C→A	5.3%	F70L (TTC→TTA)	rnr →	exoribonuclease R, RNase R
RA	4,402,850	G→T	39.6%	L2L (CTG→CTT)	yjfC →	ATP‑Grasp family ATPase
RA	4,402,870	G→T	6.3%	R9L (CGA→CTA)	yjfC →	ATP‑Grasp family ATPase
RA	4,405,735	G→T	32.1%	intergenic (+18/+99)	aidB → / ← yjfN	DNA alkylation damage repair protein; flavin‑containing DNA binding protein, weak isovaleryl CoA dehydrogenase/DUF1471 family periplasmic protein
RA	4,407,307	A→T	21.4%	H180L (CAC→CTC)	yjfP →	acyl CoA esterase
RA	4,411,145	T→G	9.2%	L450R (CTG→CGG)	ulaA →	L‑ascorbate‑specific enzyme IIC permease component of PTS
RA	4,417,551	A→C	91.6%	pseudogene (41/402 nt)	ytfA →	pseudogene, related to transcriptional regulators
RA	4,421,791	G→T	32.0%	R4S (CGC→AGC)	ytfE ←	iron‑sulfur cluster repair protein RIC
RA	4,427,761	G→T	7.5%	A80S (GCC→TCC)	ytfI →	uncharacterized protein
RA	4,428,092	G→T	51.7%	G190V (GGA→GTA)	ytfI →	uncharacterized protein
RA	4,440,321	C→A	32.8%	I181I (ATC→ATA)	ytfQ →	galactofuranose binding proteint: periplasmic‑binding component of ABC superfamily
RA	4,442,597	G→T	12.6%	A70A (GCG→GCT)	ytfT →	inner membrane putative ABC superfamily sugar transporter permease
RA	4,458,254	T→A	93.8%	V271V (GTT→GTA)	mgtA →	magnesium transporter
RA	4,458,609	G→T	100%	D390Y (GAT→TAT)	mgtA →	magnesium transporter
RA	4,465,836	C→T	18.8%	L195L (CTA→TTA)	yjgL →	uncharacterized protein
RA	4,468,165	A→G	90.6%	intergenic (‑37/‑125)	argI ← / → rraB	ornithine carbamoyltransferase 1/protein inhibitor of RNase E
RA	4,469,550	G→A	92.2%	A2T (GCT→ACT)	yjgN →	DUF898 family inner membrane protein
RA	4,470,017	G→A	89.9%	M157I (ATG→ATA)	yjgN →	DUF898 family inner membrane protein
RA	4,470,873	G→T	43.4%	R928S (CGT→AGT)	valS ←	valyl‑tRNA synthetase
RA	4,473,750	G→T	9.5%	F116L (TTC→TTA)	holC ←	DNA polymerase III, chi subunit
RA	4,474,526	C→A	6.8%	D415Y (GAC→TAC)	pepA ←	multifunctional aminopeptidase A: a cyteinylglycinase, transcription regulator and site‑specific recombination factor
RA	4,481,249	A→T	24.9%	V365E (GTG→GAG)	idnT ←	L‑idonate and D‑gluconate transporter
RA	4,494,721	G→A	43.0%	A283T (GCC→ACC)	yjhB →	putative transporter
RA	4,495,560	A→T	30.0%	N153Y (AAC→TAC)	yjhC →	putative oxidoreductase
RA	4,497,253	G→T	8.9%	pseudogene (240/255 nt)	insO →	pseudogene, IS911 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related
RA	4,512,693	T→A	92.4%	K407* (AAG→TAG)	yjhG ←	putative dehydratase
RA	4,515,068	G→T	17.8%	L185I (CTT→ATT)	yjhI ←	putative DNA‑binding transcriptional regulator
RA	4,523,001	T→A	42.6%	intergenic (‑1/+55)	yjhP ← / ← yjhQ	putative methyltransferase/putative acetyltransferase
RA	4,525,234	G→A	93.9%	pseudogene (415/1029 nt)	yjhR →	pseudogene, helicase family; putative frameshift suppressor
RA	4,529,263	A→T	9.2%	L19* (TTA→TAA)	nanC ←	N‑acetylnuraminic acid outer membrane channel protein
RA	4,530,002	C→A	8.0%	intergenic (‑684/‑772)	nanC ← / → fimB	N‑acetylnuraminic acid outer membrane channel protein/tyrosine recombinase/inversion of on/off regulator of fimA
RA	4,531,143	A→T	100%	I124F (ATT→TTT)	fimB →	tyrosine recombinase/inversion of on/off regulator of fimA
RA	4,531,451	A→G	9.6%	intergenic (+75/‑403)	fimB → / → fimE	tyrosine recombinase/inversion of on/off regulator of fimA/tyrosine recombinase/inversion of on/off regulator of fimA
RA	4,541,449	A→T	40.9%	intergenic (‑336/‑4)	gntP ← / → uxuA	fructuronate transporter/mannonate hydrolase
RA	4,555,156	G→T	90.2%	A171E (GCG→GAG)	yjiM ←	putative 2‑hydroxyglutaryl‑CoA dehydratase
RA	4,555,620	T→G	30.7%	E16D (GAA→GAC)	yjiM ←	putative 2‑hydroxyglutaryl‑CoA dehydratase
RA	4,562,043	C→A	93.5%	intergenic (+311/‑188)	yjiS → / → yjiT	DUF1127 family protein/pseudogene
RA	4,565,742	C→A	29.0%	pseudogene (2007/2937 nt)	yjiV →	pseudogene; conserved hypothetical protein
RA	4,571,233	G→A	45.6%	S16F (TCT→TTT)	hsdS ←	specificity determinant for hsdM and hsdR
RA	4,584,381	G→T	93.0%	I53I (ATC→ATA)	yjjL ←	L‑galactonate transporter
RA	4,584,756	A→T	48.6%	*305K (TAA→AAA)	yjjM ←	yjjMN operon transcriptional activator
RA	4,585,338	A→T	90.1%	S111T (TCT→ACT)	yjjM ←	yjjMN operon transcriptional activator
RA	4,590,074	A→C	27.5%	V240G (GTA→GGA)	dnaC ←	DNA biosynthesis protein
RA	4,591,139	C→A	47.4%	D66Y (GAT→TAT)	dnaT ←	DNA biosynthesis protein (primosomal protein I)
RA	4,596,243	T→A	45.1%	intergenic (‑25/+243)	leuQ ← / ← rsmC	tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase, SAM‑dependent
RA	4,603,125	A→C	8.0%	T300P (ACG→CCG)	yjjU →	putative patatin‑like family phospholipase
RA	4,603,144	C→A	7.6%	T306N (ACT→AAT)	yjjU →	putative patatin‑like family phospholipase
RA	4,604,397	G→A	5.5%	intergenic (+320/+100)	yjjV → / ← yjjW	putative DNase/putative pyruvate formate lyase activating enzyme
RA	4,612,781	C→A	31.3%	A399E (GCG→GAG)	yjjJ →	putative protein kinase
RA	4,617,009	G→T	32.7%	A427A (GCG→GCT)	radA →	DNA repair protein
RA	4,624,581	C→A	8.1%	E183* (GAA→TAA)	rob ←	right oriC‑binding transcriptional activator, AraC family
RA	4,625,288	T→C	87.4%	intergenic (‑161/‑50)	rob ← / → creA	right oriC‑binding transcriptional activator, AraC family/putative periplasmic protein
RA	4,629,649	A→T	30.8%	Y159N (TAC→AAC)	arcA ←	response regulator in two‑component regulatory system with ArcB or CpxA

Unassigned missing coverage evidence
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	CP009273	373891	375071	1181	133 [128]	[127] 129	frmA–[frmR]	frmA,[frmR]
*	*	÷	CP009273	4100629	4101480	852	132 [128]	[128] 129	tpiA	tpiA

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	360104 =	280 (1.010)	204 (0.740)	117/278	NT	42.1%	intergenic (‑38/+557)	lacZ/lacI	pseudogene, truncated/DNA‑binding transcriptional repressor
	?	CP009273	= 360286	NA (NA)					intergenic (‑220/+375)	lacZ/lacI	pseudogene, truncated/DNA‑binding transcriptional repressor
*	?	CP009273	= 360278	NA (NA)	4386 (16.840) +TTAATTAA	195/262	NT	94.2%	intergenic (‑212/+383)	lacZ/lacI	pseudogene, truncated/DNA‑binding transcriptional repressor
	?	CP009273	= 361823	287 (1.040)					coding (831/834 nt)	mhpR	mhp operon transcriptional activator
*	?	CP009273	360652 =	359 (1.300)	4385 (23.790) +46 bp	186/186	NT	95.6%	intergenic (‑586/+9)	lacZ/lacI	pseudogene, truncated/DNA‑binding transcriptional repressor
	?	CP009273	= 1317577	252 (0.910)					coding (101/882 nt)	yciV	PHP domain protein
*	?	CP009273	376716 =	NA (NA)	230 (0.830)	127/278	NT	94.7%	intergenic (‑1/‑91)	yaiX/insC1	pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase/IS2 repressor TnpA
	?	CP009273	566411 =	13 (0.050)					coding (63/552 nt)	ybcL	inactive polymorphonuclear leukocyte migration suppressor; DLP12 prophage; secreted protein, UPF0098 family
*	?	CP009273	= 378046	NA (NA)	203 (0.730)	107/278	NT	94.0%	intergenic (+11/+1)	insD1/yaiX	IS2 transposase TnpB/pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase
	?	CP009273	= 566415	13 (0.050)					coding (67/552 nt)	ybcL	inactive polymorphonuclear leukocyte migration suppressor; DLP12 prophage; secreted protein, UPF0098 family
*	?	CP009273	1203246 =	33 (0.120)	70 (0.290)	49/246	NT	66.3%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	CP009273	1205075 =	42 (0.170)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	CP009273	= 1203261	33 (0.120)	118 (0.480)	63/246	NT	76.8%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	CP009273	= 1205058	42 (0.170)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	CP009273	1635219 =	9 (0.030)	190 (0.700)	106/274	NT	95.5%	intergenic (‑377/+377)	essQ/cspB	Qin prophage; putative S lysis protein/Qin prophage; cold shock protein
	?	CP009273	= 2063752	NA (NA)					noncoding (1/1331 nt)	IS2	repeat region
*	?	CP009273	= 1635223	9 (0.030)	228 (0.820)	114/278	NT	96.2%	intergenic (‑381/+373)	essQ/cspB	Qin prophage; putative S lysis protein/Qin prophage; cold shock protein
	?	CP009273	= 1645805	NA (NA)					intergenic (+11/‑3)	insD1/intQ	IS2 transposase TnpB;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related/pseudogene, Qin prophage; phage integrase family;Phage or Prophage Related
*	?	CP009273	= 1645805	NA (NA)	19 (0.070)	13/278	NT	6.7%	intergenic (+11/‑3)	insD1/intQ	IS2 transposase TnpB;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related/pseudogene, Qin prophage; phage integrase family;Phage or Prophage Related
	?	CP009273	2310157 =	263 (0.950)					coding (502/651 nt)	rcsB	response regulator in two‑component regulatory system with RcsC and YojN
*	?	CP009273	= 2283592	NA (NA)	14 (0.050)	7/278	NT	7.0%	noncoding (1/1195 nt)	IS5	repeat region
	?	CP009273	= 3795905	181 (0.670)					coding (514/1020 nt)	waaR	UDP‑D‑galactose:(glucosyl)lipopolysaccharide‑ alpha‑1,3‑D‑galactosyltransferase
*	?	CP009273	= 3180783	NA (NA)	108 (0.400)	64/274	NT	47.9%	pseudogene (4/2445 nt)	yqiG	pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein
	?	CP009273	= 3833569	119 (0.430)					intergenic (‑216/‑6)	nlpA/yicS	cytoplasmic membrane lipoprotein‑28/putative periplasmic protein
*	?	CP009273	3833562 =	118 (0.430)	105 (0.380)	69/276	NT	47.3%	intergenic (‑209/‑13)	nlpA/yicS	cytoplasmic membrane lipoprotein‑28/putative periplasmic protein
	?	CP009273	4487999 =	NA (NA)					intergenic (+242/‑90)	intB/insC1	pseudogene, integrase homology;IS, phage, Tn; Phage‑related functions and prophages; KpLE2 phage‑like element; P4‑like integrase/IS2 repressor TnpA