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	92.2%	intergenic (+124/‑90)	thrC → / → yaaX	L‑threonine synthase/DUF2502 family putative periplasmic protein
RA	8,598	G→T	6.4%	D121Y (GAT→TAT)	talB →	transaldolase B
RA	10,444	G→T	89.0%	F17L (TTC→TTA)	satP ←	succinate‑acetate transporter
RA	12,901	G→A	100%	D247N (GAT→AAT)	dnaK →	chaperone Hsp70, with co‑chaperone DnaJ
RA	25,546	G→T	89.4%	D114Y (GAC→TAC)	lspA →	prolipoprotein signal peptidase (signal peptidase II)
RA	28,818	G→T	23.5%	D149Y (GAC→TAC)	dapB →	dihydrodipicolinate reductase
RA	29,139	G→T	91.0%	G256C (GGT→TGT)	dapB →	dihydrodipicolinate reductase
RA	31,177	G→T	11.5%	D121Y (GAT→TAT)	carB →	carbamoyl‑phosphate synthase large subunit
RA	41,442	G→T	17.0%	R164S (CGC→AGC)	caiT ←	putative transporter
RA	42,150	G→A	50.0%	intergenic (‑219/‑253)	caiT ← / → fixA	putative transporter/anaerobic carnitine reduction putative electron transfer flavoprotein subunit
RA	49,840	G→T	88.2%	A6A (GCG→GCT)	folA →	dihydrofolate reductase
RA	55,590	G→T	89.9%	T507K (ACG→AAG)	lptD ←	LPS assembly OM complex LptDE, beta‑barrel component
RA	56,677	G→T	92.2%	R145S (CGC→AGC)	lptD ←	LPS assembly OM complex LptDE, beta‑barrel component
RA	76,821	G→T	9.1%	G177G (GGC→GGA)	leuC ←	3‑isopropylmalate dehydratase large subunit
RA	80,123	C→T	90.8%	G25S (GGC→AGC)	leuL ←	leu operon leader peptide
RA	81,562	C→A	100%	I236I (ATC→ATA)	leuO →	global transcription factor
RA	85,890	G→T	23.1%	intergenic (+371/‑231)	cra → / → mraZ	transcriptional repressor‑activator for carbon metabolism/RsmH methytransferase inhibitor
RA	92,294	C→A	12.5%	R386R (CGC→CGA)	murF →	UDP‑N‑acetylmuramoyl‑tripeptide:D‑alanyl‑D‑ alanine ligase
RA	92,728	G→T	9.7%	L80L (CTG→CTT)	mraY →	phospho‑N‑acetylmuramoyl‑pentapeptide transferase
RA	93,391	G→T	44.1%	T301T (ACG→ACT)	mraY →	phospho‑N‑acetylmuramoyl‑pentapeptide transferase
RA	97,521	C→A	92.9%	A90A (GCC→GCA)	murC →	UDP‑N‑acetylmuramate:L‑alanine ligase
RA	97,893	T→A	9.2%	F214L (TTT→TTA)	murC →	UDP‑N‑acetylmuramate:L‑alanine ligase
RA	103,467	G→T	90.6%	D142Y (GAT→TAT)	lpxC →	UDP‑3‑O‑acyl N‑acetylglucosamine deacetylase
RA	104,561	G→T	100%	A124S (GCG→TCG)	secM →	regulator of secA translation
RA	104,582	A→T	14.4%	T131S (ACG→TCG)	secM →	regulator of secA translation
RA	109,050	C→T	5.0%	E13K (GAA→AAA)	zapD ←	FtsZ stabilizer
RA	109,800	A→T	20.6%	intergenic (‑94/‑131)	coaE ← / → guaC	dephospho‑CoA kinase/GMP reductase
RA	118,873	G→T	91.7%	D99Y (GAC→TAC)	pdhR →	pyruvate dehydrogenase complex repressor; autorepressor
RA	132,084	C→T	5.0%	intergenic (‑15/+1)	speD ← / ← speE	S‑adenosylmethionine decarboxylase/spermidine synthase (putrescine aminopropyltransferase)
RA	132,639	T→A	26.2%	T105S (ACG→TCG)	speE ←	spermidine synthase (putrescine aminopropyltransferase)
RA	134,028	G→T	49.3%	A153A (GCG→GCT)	cueO →	multicopper oxidase (laccase)
RA	134,652	G→T	14.4%	M361I (ATG→ATT)	cueO →	multicopper oxidase (laccase)
RA	142,460	T→A	94.6%	F298Y (TTC→TAC)	yadE →	putative polysaccharide deacetylase lipoprotein
RA	148,264	G→T	11.9%	A152E (GCA→GAA)	yadL ←	putative fimbrial‑like adhesin protein
RA	153,472	G→T	92.7%	intergenic (‑102/+268)	yadN ← / ← folK	putative fimbrial‑like adhesin protein/2‑amino‑4‑hydroxy‑6‑hydroxymethyldihyropteridine pyrophosphokinase
RA	158,287	C→A	93.8%	D78Y (GAC→TAC)	ligT ←	2'‑5' RNA ligase
RA	161,068	A→C	40.4%	intergenic (+47/‑149)	hrpB → / → mrcB	putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase
RA	172,107	G→T	22.7%	E172* (GAA→TAA)	clcA →	H(+)/Cl(‑) exchange transporter
RA	176,783	G→T	38.5%	D354Y (GAT→TAT)	dgt →	deoxyguanosine triphosphate triphosphohydrolase
RA	179,424	G→T	23.8%	D159Y (GAT→TAT)	cdaR →	carbohydrate diacid regulon transcriptional regulator; autoregulator
RA	186,279	A→T	19.2%	noncoding (81/136 nt)	tff →	novel sRNA, function unknown
RA	201,962	A→T	51.5%	D117V (GAT→GTT)	dnaE →	DNA polymerase III alpha subunit
RA	209,853	G→T	5.9%	D346Y (GAT→TAT)	tilS →	tRNA(Ile)‑lysidine synthetase
RA	215,833	G→T	13.7%	N83K (AAC→AAA)	tsaA ←	tRNA‑Thr(GGU) m(6)t(6)A37 methyltransferase, SAM‑dependent
RA	217,932	A→C	50.1%	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	93.7%	D103Y (GAT→TAT)	dnaQ →	DNA polymerase III epsilon subunit
RA	233,931	G→A	11.3%	S37N (AGT→AAT)	yafT →	lipoprotein
RA	234,985	A→T	9.0%	I80N (ATC→AAC)	ykfM ←	lethality reduction protein, putative inner membrane protein
RA	234,994	G→T	18.8%	S77* (TCA→TAA)	ykfM ←	lethality reduction protein, putative inner membrane protein
RA	235,010	G→T	16.0%	L72I (CTT→ATT)	ykfM ←	lethality reduction protein, putative inner membrane protein
RA	235,019	C→A	14.3%	V69L (GTA→TTA)	ykfM ←	lethality reduction protein, putative inner membrane protein
RA	236,234	A→T	50.4%	V148E (GTG→GAG)	yafV ←	putative NAD(P)‑binding C‑N hydrolase family amidase
RA	238,195	G→T	93.7%	V532V (GTC→GTA)	fadE ←	acyl coenzyme A dehydrogenase
RA	245,779	C→A	6.5%	pseudogene (779/1713 nt)	lfhA ←	pseudogene, flagellar system protein, promoterless fragment; flagellar biosynthesis
RA	250,880	G→T	18.2%	P442T (CCG→ACG)	pepD ←	aminoacyl‑histidine dipeptidase (peptidase D)
RA	251,998	T→C	7.3%	K69R (AAA→AGA)	pepD ←	aminoacyl‑histidine dipeptidase (peptidase D)
RA	262,114	C→A	48.5%	D51Y (GAT→TAT)	yafY ←	lipoprotein, inner membrane; overproduction stimulates degP expression; CP4‑6 prophage
RA	266,189	C→A	6.9%	pseudogene (201/258 nt)	insN →	pseudogene, IS911 transposase A;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related
RA	274,735	A→T	91.4%	pseudogene (138/348 nt)	afuB ←	pseudogene, CP4‑6 prophage; ABC transporter permease family;Phage or Prophage Related
RA	280,268	G→T	8.4%	A453S (GCC→TCC)	yagF →	CP4‑6 prophage; dehydratase family protein
RA	287,084	C→A	6.7%	intergenic (‑27/‑31)	insA ← / → yagJ	IS1 repressor TnpA/CP4‑6 prophage; uncharacterized protein;Phage or Prophage Related
RA	295,092	G→T	13.5%	G518G (GGC→GGA)	paoC ←	PaoABC aldehyde oxidoreductase, Moco‑containing subunit
RA	295,695	T→G	17.0%	E317D (GAA→GAC)	paoC ←	PaoABC aldehyde oxidoreductase, Moco‑containing subunit
RA	307,454	G→A	29.0%	intergenic (‑407/‑369)	ecpR ← / → ykgL	putative transcriptional regulator for the ecp operon/uncharacterized protein
RA	310,098	C→A	5.3%	pseudogene (31/872 nt)	eaeH →	pseudogene, attaching and effacing protein homology;factor; Not classified
RA	312,532	G→A	94.1%	pseudogene (349/684 nt)	ykgA ←	pseudogene, AraC family;putative regulator; Not classified; putative ARAC‑type regulatory protein
RA	314,027	C→T	11.1%	E2K (GAA→AAA)	rclC ←	reactive chlorine species (RCS) stress resistance inner membrane protein
RA	314,223	G→T	5.2%	S19Y (TCC→TAC)	rclB ←	reactive chlorine species (RCS) stress resistance periplasmic protein
RA	317,205	G→A	39.0%	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	320,430	A→T	18.5%	Y216N (TAC→AAC)	ykgH ←	putative inner membrane protein
RA	320,920	G→A	90.7%	S52S (AGC→AGT)	ykgH ←	putative inner membrane protein
RA	321,223	C→A	94.1%	intergenic (‑148/+65)	ykgH ← / ← betA	putative inner membrane protein/choline dehydrogenase, a flavoprotein
RA	326,385	G→T	10.2%	P404P (CCG→CCT)	betT →	choline transporter of high affinity
RA	329,887	G→T	11.2%	I86I (ATC→ATA)	yahB ←	putative DNA‑bindng transcriptional regulator
RA	344,800	G→T	91.3%	E136D (GAG→GAT)	prpB →	2‑methylisocitrate lyase
RA	345,428	T→C	7.7%	intergenic (+145/‑295)	prpB → / → prpC	2‑methylisocitrate lyase/2‑methylcitrate synthase
RA	347,382	G→T	13.3%	E153* (GAA→TAA)	prpD →	2‑methylcitrate dehydratase
RA	349,845	T→A	8.0%	F477I (TTT→ATT)	prpE →	propionate‑‑CoA ligase
RA	353,335	T→G	6.1%	intergenic (+170/+167)	codA → / ← cynR	cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor
RA	353,486	A→T	5.8%	intergenic (+321/+16)	codA → / ← cynR	cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor
RA	353,489	C→T	5.8%	intergenic (+324/+13)	codA → / ← cynR	cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor
RA	360,154	T→G	6.4%	intergenic (‑88/+507)	lacZ ← / ← lacI	pseudogene, truncated/DNA‑binding transcriptional repressor
RA	360,156	C→G	6.9%	intergenic (‑90/+505)	lacZ ← / ← lacI	pseudogene, truncated/DNA‑binding transcriptional repressor
RA	360,157	T→G	9.3%	intergenic (‑91/+504)	lacZ ← / ← lacI	pseudogene, truncated/DNA‑binding transcriptional repressor
RA	360,165	G→C	8.6%	intergenic (‑99/+496)	lacZ ← / ← lacI	pseudogene, truncated/DNA‑binding transcriptional repressor
RA	360,172	T→A	7.6%	intergenic (‑106/+489)	lacZ ← / ← lacI	pseudogene, truncated/DNA‑binding transcriptional repressor
RA	360,173	C→A	7.5%	intergenic (‑107/+488)	lacZ ← / ← lacI	pseudogene, truncated/DNA‑binding transcriptional repressor
RA	360,181	G→C	8.6%	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	91.6%	I165I (ATC→ATA)	mhpR ←	mhp operon transcriptional activator
RA	370,428	T→C	5.6%	intergenic (+91/‑487)	mhpE → / → mhpT	4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter
RA	385,815	G→T	45.9%	pseudogene (109/1458 nt)	yaiT →	pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein
RA	396,883	A→G	90.0%	Q14Q (CAA→CAG)	iraP →	anti‑RssB factor, RpoS stabilzer during Pi starvation; anti‑adapter protein
RA	397,959	G→A	39.4%	A253T (GCG→ACG)	phoA →	bacterial alkaline phosphatase
RA	402,340	G→T	93.8%	V160V (GTG→GTT)	aroL →	shikimate kinase II
RA	406,075	C→A	88.6%	P159Q (CCG→CAG)	mak →	manno(fructo)kinase
RA	411,027	G→T	92.1%	L61L (CTC→CTA)	sbcC ←	exonuclease, dsDNA, ATP‑dependent
RA	421,799	C→A	87.5%	I69I (ATC→ATA)	tgt →	tRNA‑guanine transglycosylase
RA	423,068	C→A	23.1%	A109E (GCG→GAG)	yajC →	SecYEG protein translocase auxillary subunit
RA	425,143	G→T	50.7%	T61T (ACG→ACT)	secF →	SecYEG protein translocase auxillary subunit
RA	433,551	G→T	91.9%	S14Y (TCC→TAC)	yajO ←	2‑carboxybenzaldehyde reductase
RA	434,663	A→C	92.7%	I324S (ATC→AGC)	dxs ←	1‑deoxyxylulose‑5‑phosphate synthase, thiamine triphosphate‑binding, FAD‑requiring
RA	435,336	G→T	94.1%	Q100K (CAG→AAG)	dxs ←	1‑deoxyxylulose‑5‑phosphate synthase, thiamine triphosphate‑binding, FAD‑requiring
RA	437,076	A→T	5.5%	K24N (AAA→AAT)	thiI →	tRNA s(4)U8 sulfurtransferase
RA	437,672	T→A	89.9%	V223E (GTG→GAG)	thiI →	tRNA s(4)U8 sulfurtransferase
RA	441,811	A→C	20.7%	I104M (ATT→ATG)	yajR ←	putative transporter
RA	444,489	G→A	94.1%	R537C (CGT→TGT)	cyoB ←	cytochrome o ubiquinol oxidase subunit I
RA	446,369	T→G	46.0%	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	15.4%	T422N (ACC→AAC)	tig →	peptidyl‑prolyl cis/trans isomerase (trigger factor)
RA	453,656	T→A	21.4%	S259T (TCC→ACC)	clpX →	ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease
RA	456,298	T→A	94.5%	L652Q (CTG→CAG)	lon →	DNA‑binding ATP‑dependent protease La
RA	456,588	G→T	90.1%	D749Y (GAC→TAC)	lon →	DNA‑binding ATP‑dependent protease La
RA	465,341	A→C	14.9%	I339L (ATT→CTT)	mdlA →	putative multidrug transporter subunit of ABC superfamily, ATP‑binding component
RA	469,770	C→A	17.9%	R283L (CGT→CTT)	tesB ←	acyl‑CoA thioesterase 2
RA	474,138	G→T	90.9%	intergenic (‑65/+99)	ylaB ← / ← ylaC	putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase/DUF1449 family inner membrane protein
RA	475,502	T→A	15.7%	intergenic (‑128/+44)	maa ← / ← hha	maltose O‑acetyltransferase/modulator of gene expression, with H‑NS
RA	475,805	C→A	86.1%	A120A (GCG→GCT)	tomB ←	Hha toxicity attenuator; conjugation‑related protein
RA	479,244	C→A	93.3%	A206S (GCC→TCC)	acrB ←	multidrug efflux system protein
RA	480,820	C→T	89.8%	D86N (GAC→AAC)	acrA ←	multidrug efflux system
RA	481,667	G→A	92.2%	A151T (GCG→ACG)	acrR →	transcriptional repressor
RA	486,912	C→A	7.9%	I15I (ATC→ATA)	apt →	adenine phosphoribosyltransferase
RA	509,737	G→A	45.1%	E97K (GAG→AAG)	cueR →	copper‑responsive regulon transcriptional regulator
RA	511,619	A→T	11.5%	Q82L (CAA→CTA)	fetA →	iron exporter, ATP‑binding subunit, ABC transporter FetAB subunit; peroxide resistance protein
RA	524,334:1	+T	100%	pseudogene (239/491 nt)	ybbD →	pseudogene
RA	527,186	T→A	21.7%	L164F (TTA→TTT)	allS ←	allD operon transcriptional activator
RA	530,466	C→A	92.2%	F365L (TTC→TTA)	gcl →	glyoxylate carboligase
RA	542,200	Δ1 bp	89.2%	coding (65/1668 nt)	fdrA →	putative NAD(P)‑binding acyl‑CoA synthetase
RA	546,491	G→T	93.1%	V199V (GTG→GTT)	ybcF →	putative carbonate kinase
RA	549,397	G→T	92.4%	intergenic (‑1/+2)	lpxH ← / ← ppiB	UDP‑2,3‑diacylglucosamine pyrophosphohydrolase/peptidyl‑prolyl cis‑trans isomerase B (rotamase B)
RA	551,838	G→T	6.7%	R58S (CGC→AGC)	ybcI ←	DUF457 family inner membrane protein
RA	552,831	A→T	18.3%	F123I (TTC→ATC)	folD ←	bifunctional 5,10‑methylene‑tetrahydrofolate dehydrogenase/ 5,10‑methylene‑tetrahydrofolate cyclohydrolase
RA	554,327	G→T	11.4%	intergenic (+117/‑103)	sfmA → / → sfmC	FimA homolog/putative periplasmic pilus chaperone
RA	557,303	A→T	10.2%	E717D (GAA→GAT)	sfmD →	putative outer membrane export usher protein
RA	557,592	G→T	44.3%	D814Y (GAC→TAC)	sfmD →	putative outer membrane export usher protein
RA	560,919	G→T	24.3%	V172V (GTC→GTA)	intD ←	DLP12 prophage; putative phage integrase
RA	567,543	G→T	6.9%	D212Y (GAT→TAT)	ybcM →	DLP12 prophage; putative DNA‑binding transcriptional regulator
RA	568,464	G→T	23.6%	E30* (GAA→TAA)	ninE →	DLP12 prophage; conserved protein
RA	574,515	C→A	6.3%	intergenic (‑166/+125)	borD ← / ← ybcV	DLP12 prophage; putative lipoprotein/DLP12 prophage; uncharacterized protein
RA	576,998	G→T	91.4%	pseudogene (189/309 nt)	aaaD →	pseudogene; DLP12 prophage; tail fiber assembly protein family;Phage or Prophage Related
RA	581,203	A→T	93.4%	intergenic (‑114/‑310)	ompT ← / → pauD	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)/tRNA‑OTHER
RA	583,341	T→G	94.9%	S33R (AGT→CGT)	ybcH ←	PRK09936 family protein
RA	594,191	C→T	7.2%	R8C (CGC→TGC)	cusA →	copper/silver efflux system, membrane component
RA	598,081	G→T	8.9%	G223C (GGC→TGC)	pheP →	phenylalanine transporter
RA	602,045	C→A	7.6%	L265L (CTG→CTT)	ybdK ←	weak gamma‑glutamyl:cysteine ligase
RA	607,931	G→A	100%	S7F (TCC→TTC)	fepA ←	iron‑enterobactin outer membrane transporter
RA	619,048	C→A	50.7%	A307S (GCC→TCC)	fepB ←	iron‑enterobactin transporter subunit
RA	623,935	C→A	7.7%	I262I (ATC→ATA)	entB →	isochorismatase
RA	625,364	G→T	87.9%	G5G (GGG→GGT)	cstA →	carbon starvation protein involved in peptide utilization; APC peptide transporter family protein
RA	639,231	G→A	89.8%	L65F (CTT→TTT)	rnk ←	regulator of nucleoside diphosphate kinase
RA	647,234	C→T	32.9%	E27K (GAA→AAA)	citC ←	[citrate [pro‑3S]‑lyase] ligase
RA	647,422	G→T	87.0%	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	94.1%	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	14.4%	V428V (GTC→GTA)	dcuC ←	anaerobic C4‑dicarboxylate transport
RA	651,654	A→G	24.6%	intergenic (‑230/‑359)	dcuC ← / → pagP	anaerobic C4‑dicarboxylate transport/phospholipid:lipid A palmitoyltransferase
RA	652,865	Δ1 bp	89.3%	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	90.5%	V522V (GTT→GTA)	mrdA ←	transpeptidase involved in peptidoglycan synthesis (penicillin‑binding protein 2)
RA	662,631	C→A	91.2%	R348L (CGC→CTC)	mrdA ←	transpeptidase involved in peptidoglycan synthesis (penicillin‑binding protein 2)
RA	664,243	C→A	18.4%	D84Y (GAT→TAT)	rsfS ←	ribosomal silencing factor
RA	666,998	G→T	22.8%	L22I (CTT→ATT)	holA ←	DNA polymerase III, delta subunit
RA	667,348	G→T	40.2%	Q99K (CAG→AAG)	lptE ←	LPS assembly OM complex LptDE, lipoprotein component
RA	672,142	T→A	47.4%	intergenic (‑139/‑25)	ybeQ ← / → ybeR	Sel1 family TPR‑like repeat protein/uncharacterized protein
RA	689,079	C→A	20.1%	E445* (GAA→TAA)	miaB ←	tRNA‑i(6)A37 methylthiotransferase
RA	693,739	G→T	34.7%	H299N (CAC→AAC)	asnB ←	asparagine synthetase B
RA	705,588	C→A	85.6%	intergenic (+16/+68)	chiQ → / ← fur	chitosugar‑induced verified lipoprotein/ferric iron uptake regulon transcriptional repressor; autorepressor
RA	706,097	A→C	50.7%	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	25.1%	intergenic (‑4/+206)	uof ← / ← fldA	ryhB‑regulated fur leader peptide/flavodoxin 1
RA	723,846	A→C	17.0%	W115G (TGG→GGG)	kdpA ←	potassium translocating ATPase, subunit A
RA	724,813	A→T	92.9%	intergenic (+17/‑226)	ybfA → / → rhsC	DUF2517 family protein/Rhs family putative polymorphic toxin
RA	725,650	G→T	18.8%	P204P (CCG→CCT)	rhsC →	Rhs family putative polymorphic toxin
RA	729,149	G→A	9.5%	D1371N (GAT→AAT)	rhsC →	Rhs family putative polymorphic toxin
RA	729,456	G→A	42.1%	R75R (AGG→AGA)	ybfB →	putative membrane protein
RA	732,494	G→T	40.6%	pseudogene (214/1137 nt)	ybfL →	pseudogene, DDE domain transposase family;putative factor; Not classified; putative receptor protein
RA	735,817	G→T	12.5%	L285L (CTG→CTT)	phr →	deoxyribodipyrimidine photolyase, FAD‑binding
RA	743,278	G→A	17.7%	intergenic (‑53/+99)	abrB ← / ← ybgO	regulator of aidB expression; inner membrane protein/putative fimbrial protein
RA	750,112	A→T	16.1%	intergenic (‑188/‑521)	gltA ← / → sdhC	citrate synthase/succinate dehydrogenase, membrane subunit, binds cytochrome b556
RA	753,205	C→A	6.1%	Q21K (CAG→AAG)	sdhB →	succinate dehydrogenase, FeS subunit
RA	754,572	G→T	91.1%	E137D (GAG→GAT)	sucA →	2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding
RA	757,353	A→T	12.1%	N126Y (AAT→TAT)	sucB →	dihydrolipoyltranssuccinase
RA	759,000	C→A	93.6%	F177L (TTC→TTA)	sucC →	succinyl‑CoA synthetase, beta subunit
RA	780,465	G→T	9.4%	I103I (ATC→ATA)	ybgS ←	putative periplasmic protein
RA	788,902	G→T	94.0%	R115S (CGT→AGT)	modF ←	fused molybdate transporter subunits of ABC superfamily: ATP‑binding components
RA	789,044	G→T	14.2%	I67I (ATC→ATA)	modF ←	fused molybdate transporter subunits of ABC superfamily: ATP‑binding components
RA	792,351	G→T	11.8%	A114A (GCG→GCT)	modC →	molybdate transporter subunit
RA	800,488	G→T	88.3%	V510V (GTG→GTT)	ybhJ →	putative hydratase
RA	800,779	G→T	89.9%	E607D (GAG→GAT)	ybhJ →	putative hydratase
RA	805,693	A→C	13.3%	E298D (GAA→GAC)	bioB →	biotin synthase
RA	816,292	A→T	19.7%	H15L (CAC→CTC)	ybhM →	UPF0005 family inner membrane protein
RA	828,374	G→T	91.6%	V11V (GTC→GTA)	ybiA ←	DUF1768 family protein
RA	832,445	G→T	88.5%	P213P (CCG→CCT)	ybiC →	putative dehydrogenase
RA	843,299	C→A	90.7%	W54C (TGG→TGT)	glnH ←	glutamine transporter subunit
RA	851,782	A→T	15.3%	K122* (AAA→TAA)	ybiT →	putative transporter subunit of ABC superfamily: ATP‑binding component
RA	861,323	T→A	27.7%	S166S (TCA→TCT)	moeA ←	molybdopterin molybdenumtransferase; molybdopterin biosynthesis protein
RA	863,481	T→G	19.5%	L169R (CTC→CGC)	gsiA →	glutathione transporter ATP‑binding protein, ABC superfamily
RA	863,745	T→A	10.9%	F257Y (TTT→TAT)	gsiA →	glutathione transporter ATP‑binding protein, ABC superfamily
RA	868,473	A→C	25.5%	I13I (ATA→ATC)	yliE →	putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	868,897	G→T	17.1%	D155Y (GAC→TAC)	yliE →	putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	876,447	G→A	92.6%	D89N (GAT→AAT)	dacC →	D‑alanyl‑D‑alanine carboxypeptidase (penicillin‑binding protein 6a)
RA	877,482	C→A	14.7%	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	889,044	G→T	15.4%	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	23.8%	intergenic (‑38/‑88)	ybjP ← / → ybjQ	lipoprotein/UPF0145 family protein
RA	907,596	G→T	6.7%	P4Q (CCA→CAA)	hcr ←	HCP oxidoreductase, NADH‑dependent
RA	925,160	G→T	93.3%	S420* (TCA→TAA)	cydD ←	fused glutathione, cysteine exporter subunits of ABC superfamily: membrane component/ATP‑binding component
RA	925,355	A→T	18.1%	L355Q (CTG→CAG)	cydD ←	fused glutathione, cysteine exporter subunits of ABC superfamily: membrane component/ATP‑binding component
RA	925,957	A→T	15.4%	I154I (ATT→ATA)	cydD ←	fused glutathione, cysteine exporter subunits of ABC superfamily: membrane component/ATP‑binding component
RA	943,573	G→T	88.8%	A297S (GCC→TCC)	ycaM →	putative transporter
RA	955,568	A→T	48.7%	intergenic (+17/‑152)	aroA → / → ycaL	5‑enolpyruvylshikimate‑3‑phosphate synthetase/putative peptidase‑related chaperone
RA	958,417	A→T	7.6%	N323Y (AAC→TAC)	rpsA →	30S ribosomal subunit protein S1
RA	958,850	C→A	9.2%	T467N (ACC→AAC)	rpsA →	30S ribosomal subunit protein S1
RA	963,256	G→A	12.8%	D394N (GAT→AAT)	msbA →	fused lipid transporter subunits of ABC superfamily: membrane component/ATP‑binding component
RA	968,415	G→T	91.4%	S148* (TCG→TAG)	ycbC ←	DUF218 superfamily protein
RA	976,873	C→A	16.2%	A124E (GCG→GAG)	ldtD →	murein L,D‑transpeptidase
RA	987,780	C→A	8.4%	A568E (GCG→GAG)	pepN →	aminopeptidase N
RA	991,460	A→T	24.5%	L314Q (CTG→CAG)	ssuA ←	aliphatic sulfonate binding protein, SsuABC ABC transporter
RA	997,965	G→T	41.3%	D235Y (GAT→TAT)	elfG →	putative fimbrial‑like adhesin protein
RA	1,024,703	G→T	46.1%	G241G (GGC→GGA)	rlmI ←	23S rRNA m(5)C1962 methyltransferase, SAM‑dependent
RA	1,048,928	C→A	90.6%	E903* (GAA→TAA)	torS ←	hybrid sensory histidine kinase in two‑component regulatory system with TorR
RA	1,049,407	G→T	92.7%	T743K (ACG→AAG)	torS ←	hybrid sensory histidine kinase in two‑component regulatory system with TorR
RA	1,073,243	C→A	7.5%	G366C (GGT→TGT)	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	48.6%	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	88.5%	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	90.6%	intergenic (‑21/+53)	dinI ← / ← pyrC	DNA damage‑inducible protein I/dihydro‑orotase
RA	1,121,219	G→T	5.5%	E68* (GAA→TAA)	rimJ →	ribosomal‑protein‑S5‑alanine N‑acetyltransferase
RA	1,132,494	T→A	15.7%	I255I (ATT→ATA)	flgI →	putative flagellar basal body protein
RA	1,151,750	G→T	90.9%	R178L (CGC→CTC)	holB →	DNA polymerase III, delta prime subunit
RA	1,152,278	G→T	92.0%	E16* (GAA→TAA)	ycfH →	putative DNase
RA	1,175,193	A→T	15.8%	E36V (GAA→GTA)	cobB →	deacetylase of acs and cheY, chemotaxis regulator
RA	1,181,431	G→T	20.5%	E44D (GAG→GAT)	pepT →	peptidase T
RA	1,191,676	C→T	44.1%	H366H (CAC→CAT)	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,688	C→T	41.2%	T370T (ACC→ACT)	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,701	T→C	36.5%	L375L (TTA→CTA) ‡	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,703	A→G	36.3%	L375L (TTA→TTG) ‡	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,733	C→T	23.4%	N385N (AAC→AAT)	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,736	G→C	23.3%	A386A (GCG→GCC)	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,739	A→G	21.4%	K387K (AAA→AAG)	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,748	C→T	17.6%	T390T (ACC→ACT)	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,760	G→A	10.9%	E394E (GAG→GAA)	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,193,516	T→G	52.4%	N60H (AAT→CAT)	ymfE ←	e14 prophage; putative inner membrane protein
RA	1,193,873	G→T	90.2%	intergenic (‑180/‑278)	ymfE ← / → lit	e14 prophage; putative inner membrane protein/e14 prophage; cell death peptidase, inhibitor of T4 late gene expression
RA	1,194,194	C→A	32.9%	S15* (TCA→TAA)	lit →	e14 prophage; cell death peptidase, inhibitor of T4 late gene expression
RA	1,204,284	C→A	15.3%	D98Y (GAT→TAT)	tfaE ←	e14 prophage; putative tail fiber assembly protein
RA	1,211,169	C→A	92.8%	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	94.0%	intergenic (+170/+202)	ycgI → / ← minE	pseudogene/cell division topological specificity factor
RA	1,220,996	G→T	93.2%	R181R (CGG→AGG)	minC ←	cell division inhibitor
RA	1,224,292	G→A	93.4%	D8N (GAT→AAT)	ycgN →	UPF0153 family cysteine cluster protein
RA	1,226,292	T→A	93.7%	C24S (TGT→AGT)	umuD →	DNA polymerase V, subunit D
RA	1,227,613	C→A	19.9%	N324K (AAC→AAA)	umuC →	DNA polymerase V, subunit C
RA	1,228,591	G→T	94.4%	intergenic (‑105/+41)	dsbB ← / ← nhaB	oxidoreductase that catalyzes reoxidation of DsbA protein disulfide isomerase I/sodium:proton antiporter
RA	1,251,120	T→A	24.0%	T97S (ACC→TCC)	ycgV ←	putative adhesin
RA	1,259,548	G→T	6.5%	D127Y (GAT→TAT)	hemA →	glutamyl tRNA reductase
RA	1,277,786	G→A	92.5%	D823N (GAC→AAC)	narG →	nitrate reductase 1, alpha subunit
RA	1,282,421	A→T	10.9%	intergenic (+439/+101)	narI → / ← rttR	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
RA	1,282,578	T→G	13.1%	noncoding (115/171 nt) R19R (AGG→CGG)	rttR ← tpr ←	rtT sRNA, processed from tyrT transcript protamine‑like protein
RA	1,288,669	A→T	41.6%	intergenic (‑291/‑314)	hns ← / → tdk	global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
RA	1,301,604	A→T	20.5%	I433I (ATT→ATA)	clsA ←	cardiolipin synthase 1
RA	1,320,508	C→T	6.1%	T502T (ACC→ACT)	yciQ →	enhancer of membrane protein expression; putative inner membrane protein
RA	1,322,140	T→A	92.0%	T159S (ACG→TCG)	btuR ←	cob(I)yrinic acid a,c‑diamide adenosyltransferase
RA	1,330,955	G→T	45.6%	D290Y (GAT→TAT)	acnA →	aconitate hydratase 1
RA	1,334,048	G→T	11.7%	E154D (GAG→GAT)	pgpB →	phosphatidylglycerophosphatase B
RA	1,337,533	G→T	89.0%	A18E (GCA→GAA)	osmB ←	lipoprotein
RA	1,340,901	A→T	20.9%	S33S (TCT→TCA)	gmr ←	cyclic‑di‑GMP phosphodiesterase; csgD regulator; modulator of Rnase II stability
RA	1,345,951	G→A	6.3%	L23F (CTC→TTC)	ycjD ←	DUF559 family endonuclease‑related protein
RA	1,365,283	G→T	100%	E271* (GAG→TAG)	ycjM →	alpha amylase catalytic domain family protein
RA	1,369,694	G→A	28.7%	D159N (GAT→AAT)	ycjQ →	putative Zn‑dependent NAD(P)‑binding oxidoreductase
JC JC	1,376,043	IS5 (–) +4 bp	88.9%	pseudogene (10‑13/126 nt)	ycjV →	pseudogene; putative ATP‑binding component of a transport system
RA	1,377,394	C→T	100%	A275A (GCG→GCA)	ycjW ←	LacI family putative transcriptional repressor
RA	1,386,008	G→T	100%	Q35K (CAG→AAG)	ycjY ←	S9 homolog non‑peptidase family protein
RA	1,388,406	G→T	90.1%	R308L (CGC→CTC)	mppA →	murein tripeptide (L‑ala‑gamma‑D‑glutamyl‑meso‑DAP) transporter subunit
RA	1,396,370	G→T	18.8%	N381K (AAC→AAA)	abgB ←	p‑aminobenzoyl‑glutamate hydrolase, B subunit
RA	1,417,454	C→A	13.9%	pseudogene (497/500 nt)	ydaW →	Rac prophage; pseudogene, DNA‑binding protein family;Phage or Prophage Related
RA	1,424,234	C→A	91.3%	S310* (TCA→TAA)	stfR →	Rac prophage; putative tail fiber protein
JC JC	1,428,894	IS2 (–) +5 bp	91.9%	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	18.3%	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	84.4%	S737S (TCC→TCA)	ydbH →	putative membrane‑anchored protein, function unknown
RA	1,443,093	C→A	15.9%	L440I (CTC→ATC)	feaB →	phenylacetaldehyde dehydrogenase
RA	1,443,196	A→T	10.2%	Q474L (CAG→CTG)	feaB →	phenylacetaldehyde dehydrogenase
RA	1,444,739	G→A	13.5%	P290S (CCC→TCC)	tynA ←	tyramine oxidase, copper‑requiring
RA	1,451,422	A→T	39.2%	T246S (ACG→TCG)	paaE →	ring 1,2‑phenylacetyl‑CoA epoxidase, NAD(P)H oxidoreductase component
RA	1,454,724	G→T	90.2%	G472C (GGT→TGT)	paaH →	3‑hydroxyadipyl‑CoA dehydrogenase, NAD+‑dependent
RA	1,460,593	C→G	6.0%	pseudogene (945/2513 nt)	ydbA →	pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA	1,460,752	C→T	6.6%	pseudogene (1104/2513 nt)	ydbA →	pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA	1,460,761	A→G	6.7%	pseudogene (1113/2513 nt)	ydbA →	pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA	1,460,819	G→A	8.2%	pseudogene (1171/2513 nt)	ydbA →	pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA	1,488,630	C→A	18.5%	T233T (ACG→ACT)	ydcI ←	putative DNA‑binding transcriptional regulator
RA	1,519,349	T→A	100%	K297* (AAA→TAA)	ansP ←	L‑asparagine transporter
RA	1,533,940	C→T	7.4%	A970T (GCG→ACG)	narZ ←	nitrate reductase 2 (NRZ), alpha subunit
RA	1,548,144	G→T	93.7%	intergenic (‑49/+85)	adhP ← / ← maeA	ethanol‑active dehydrogenase/acetaldehyde‑active reductase/malate dehydrogenase, (decarboxylating, NAD‑requiring) (malic enzyme)
RA	1,552,629	C→A	42.5%	D216Y (GAT→TAT)	ddpD ←	D,D‑dipeptide permease system, ATP‑binding component
RA	1,563,276	G→T	93.8%	H491N (CAC→AAC)	gadC ←	glutamate:gamma‑aminobutyric acid antiporter
RA	1,565,497	G→A	100%	S269L (TCG→TTG)	gadB ←	glutamate decarboxylase B, PLP‑dependent
RA	1,566,392	A→T	24.6%	intergenic (‑90/+272)	gadB ← / ← pqqL	glutamate decarboxylase B, PLP‑dependent/putative periplasmic M16 family zinc metalloendopeptidase
RA	1,575,339	G→T	93.5%	F481L (TTC→TTA)	ydeN ←	putative Ser‑type periplasmic non‑aryl sulfatase
RA	1,586,871	G→T	9.4%	intergenic (‑172/+51)	hipB ← / ← yneO	antitoxin of HipAB toxin‑antitoxin system/pseudogene, AidA homolog
RA	1,602,131	G→T	20.5%	D177Y (GAT→TAT)	tam →	trans‑aconitate methyltransferase
RA	1,603,440	G→A	92.2%	intergenic (‑161/+46)	yneE ← / ← uxaB	bestrophin family putative inner membrane protein/altronate oxidoreductase, NAD‑dependent
RA	1,604,418	C→A	25.1%	D174Y (GAC→TAC)	uxaB ←	altronate oxidoreductase, NAD‑dependent
RA	1,615,440	G→T	7.5%	intergenic (‑46/‑149)	eamA ← / → ydeE	cysteine and O‑acetyl‑L‑serine efflux system/putative transporter
RA	1,618,147	A→T	5.4%	intergenic (‑40/+215)	dgcZ ← / ← ydeI	diguanylate cyclase, zinc‑sensing/hydrogen peroxide resistance OB fold protein; putative periplasmic protein
RA	1,620,961	T→G	90.7%	Q226P (CAA→CCA)	dcp ←	dipeptidyl carboxypeptidase II
RA	1,623,050	G→T	12.6%	D148Y (GAC→TAC)	rspR →	transcriptional repressor for rspAB
RA	1,625,116	T→A	10.6%	N19Y (AAC→TAC)	ydfI ←	putative NAD‑dependent D‑mannonate oxidoreductase
RA	1,628,207	G→A	95.0%	G110E (GGA→GAA)	pinQ →	Qin prophage; putative site‑specific recombinase
RA	1,648,870	A→T	9.9%	W177R (TGG→AGG)	rspA ←	bifunctional D‑altronate/D‑mannonate dehydratase
RA	1,661,763	C→A	92.3%	P353P (CCG→CCT)	mlc ←	glucosamine anaerobic growth regulon transcriptional repressor; autorepressor
RA	1,689,180	T→G	45.5%	E383D (GAA→GAC)	uidA ←	beta‑D‑glucuronidase
RA	1,692,573	C→A	43.8%	D289Y (GAT→TAT)	malI ←	transcriptional repressor of Mal regulon
RA	1,696,612	A→T	91.2%	E41D (GAA→GAT)	add →	adenosine deaminase
RA	1,699,862	T→A	44.4%	L119* (TTG→TAG)	ydgK →	DUF2569 family inner membrane protein
RA	1,701,282	A→C	6.0%	Q36P (CAG→CCG)	rsxC →	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA	1,702,966	T→A	10.6%	R597R (CGT→CGA)	rsxC →	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA	1,703,015	G→C	7.1%	E614Q (GAA→CAA)	rsxC →	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA	1,703,062	T→A	13.9%	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	11.5%	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	7.6%	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	100%	R28Q (CGA→CAA)	tyrS ←	tyrosyl‑tRNA synthetase
RA	1,723,809	G→T	53.7%	E156* (GAA→TAA)	lhr →	putative ATP‑dependent helicase
RA	1,754,950	T→A	93.3%	I367F (ATT→TTT)	sufD ←	component of SufBCD Fe‑S cluster assembly scaffold
RA	1,764,150	G→T	44.8%	D274Y (GAT→TAT)	ydiK →	UPF0118 family inner membrane protein
RA	1,766,617	A→T	23.0%	intergenic (+75/‑152)	ydiM → / → ydiN	MFS superfamily sugar transport 1 family protein/MFS transporter superfamily protein
RA	1,770,281	T→A	93.7%	D146E (GAT→GAA)	ydiF →	putative acetyl‑CoA:acetoacetyl‑CoA transferase: alpha subunit/beta subunit
RA	1,777,451	C→A	43.1%	A55E (GCG→GAG)	fadK →	short chain acyl‑CoA synthetase, anaerobic
RA	1,791,509	C→A	12.5%	P231P (CCG→CCT)	pheT ←	phenylalanine tRNA synthetase, beta subunit
RA	1,795,267	A→T	13.5%	F521I (TTC→ATC)	thrS ←	threonyl‑tRNA synthetase
RA	1,796,428	C→A	7.5%	V134F (GTC→TTC)	thrS ←	threonyl‑tRNA synthetase
RA	1,798,834	G→A	18.2%	pseudogene (1060/1476 nt)	arpB →	pseudogene, ankyrin repeats
RA	1,802,047	G→A	100%	intergenic (+100/‑6)	ydiZ → / → yniA	uncharacterized protein/fructosamine kinase family protein
RA	1,803,109	C→T	49.2%	A128T (GCC→ACC)	yniB ←	putative inner membrane protein
RA	1,805,071	C→A	18.2%	intergenic (+13/‑120)	ydjM → / → ydjN	inner membrane protein regulated by LexA/putative transporter
RA	1,813,263	C→A	9.8%	E148* (GAG→TAG)	chbR ←	repressor of chb operon for N,N'‑diacetylchitobiose utilization
RA	1,821,696	A→T	48.3%	L274Q (CTG→CAG)	astB ←	succinylarginine dihydrolase
RA	1,823,835	A→C	7.8%	W53G (TGG→GGG)	astD ←	succinylglutamic semialdehyde dehydrogenase
RA	1,825,763	C→A	90.7%	A159A (GCG→GCT)	astC ←	succinylornithine transaminase, PLP‑dependent
RA	1,829,162	T→A	7.1%	V33D (GTC→GAC)	ydjZ →	TVP38/TMEM64 family inner membrane protein
RA	1,832,413	C→A	90.3%	L315L (CTC→CTA)	ynjC →	inner membrane putative ABC superfamily transporter permease
RA	1,833,730	C→A	94.0%	R3S (CGT→AGT)	ynjE →	molybdopterin synthase sulfurtransferase
RA	1,850,797	C→A	8.1%	R130L (CGG→CTG)	ydjH ←	putative kinase
RA	1,850,880	C→A	18.1%	V102V (GTG→GTT)	ydjH ←	putative kinase
RA	1,862,404	G→T	9.6%	E414* (GAA→TAA)	yeaG →	protein kinase, endogenous substrate unidentified; autokinase
RA	1,865,422	C→A	100%	R261R (CGA→AGA)	yeaI →	putative membrane‑anchored diguanylate cyclase
RA	1,867,537	C→A	20.0%	R414S (CGT→AGT)	yeaJ →	putative diguanylate cyclase
RA	1,872,520	G→T	100%	P183P (CCG→CCT)	yeaP →	diguanylate cyclase
RA	1,909,342	T→A	93.4%	E150D (GAA→GAT)	proQ ←	RNA chaperone, putative ProP translation regulator
RA	1,942,066	G→T	18.6%	H115N (CAT→AAT)	yebC ←	UPF0082 family protein
RA	1,944,177	C→A	89.4%	L201L (CTG→CTT)	aspS ←	aspartyl‑tRNA synthetase
RA	1,959,915	C→A	46.7%	P178P (CCG→CCT)	flhB ←	flagellin export apparatus, substrate specificity protein
RA	1,969,291	G→T	92.2%	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	5.6%	A468A (GCT→GCC)	otsA ←	trehalose‑6‑phosphate synthase
RA	1,984,987	C→A	51.3%	T38T (ACG→ACT)	yecA ←	UPF0149 family protein
RA	1,986,289	T→A	89.4%	N4Y (AAT→TAT)	pgsA ←	phosphatidylglycerophosphate synthetase
RA	1,997,314	G→T	92.3%	intergenic (‑227/‑39)	fliC ← / → fliD	flagellar filament structural protein (flagellin)/flagellar filament capping protein
RA	1,999,098	C→A	6.6%	V105V (GTC→GTA)	fliS →	flagellar protein potentiates polymerization
RA	1,999,632	G→T	92.3%	intergenic (+73/‑5)	fliT → / → amyA	putative flagellar synthesis and assembly chaperone/cytoplasmic alpha‑amylase
RA	2,007,547	C→A	17.6%	R280S (CGC→AGC)	fliF →	flagellar basal‑body MS‑ring and collar protein
RA	2,020,166	C→A	94.4%	D445Y (GAC→TAC)	yedQ ←	putative membrane‑anchored diguanylate cyclase
RA	2,030,998	C→A	15.6%	P212P (CCG→CCT)	yedV ←	putative sensory kinase in two‑component regulatory system with YedW
RA	2,035,090	C→A	90.6%	Q79K (CAG→AAG)	zinT →	zinc and cadmium binding protein, periplasmic
RA	2,038,804	C→A	13.2%	P129Q (CCG→CAG)	yeeJ →	putative adhesin
RA	2,040,800	C→A	14.1%	T794T (ACC→ACA)	yeeJ →	putative adhesin
RA	2,041,982	A→T	25.4%	S1188S (TCA→TCT)	yeeJ →	putative adhesin
RA	2,067,205	G→A	15.6%	G729D (GGC→GAC)	flu →	CP4‑44 prophage; antigen 43 (Ag43) phase‑variable biofilm formation autotransporter
RA	2,074,680	A→T	89.9%	W22R (TGG→AGG)	sbmC ←	DNA gyrase inhibitor
RA	2,077,212	A→T	44.0%	N326Y (AAT→TAT)	sbcB →	exodeoxyribonuclease I; exonuclease I
RA	2,098,995	C→A	87.6%	G182* (GGA→TGA)	wbbI ←	d‑Galf:alpha‑d‑Glc beta‑1,6‑galactofuranosyltransferase
RA	2,102,205	C→A	28.0%	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	2,109,267	A→T	6.6%	I37I (ATT→ATA)	wcaM ←	colanic acid biosynthesis protein
RA	2,110,346	G→A	43.5%	T88I (ACC→ATC)	wcaL ←	putative glycosyl transferase
RA	2,114,911	A→T	93.1%	L42Q (CTG→CAG)	wcaJ ←	colanic biosynthesis UDP‑glucose lipid carrier transferase
RA	2,115,361	C→A	10.0%	R367L (CGC→CTC)	cpsG ←	phosphomannomutase
RA	2,139,910	G→T	100%	R1055L (CGA→CTA)	yegE →	putative diguanylate cyclase
RA	2,144,474	C→A	94.6%	intergenic (‑8/‑192)	yegI ← / → yegJ	protein kinase‑related putative non‑specific DNA‑binding protein/uncharacterized protein
RA	2,149,603	A→T	91.0%	E287V (GAA→GTA)	mdtB →	multidrug efflux system, subunit B
RA	2,163,087	C→A	11.4%	R299S (CGT→AGT)	yegS →	phosphatidylglycerol kinase, metal‑dependent
RA	2,168,487	A→T	41.3%	D14E (GAT→GAA)	gatA ←	galactitol‑specific enzyme IIA component of PTS
RA	2,168,795	C→A	88.7%	D336Y (GAT→TAT)	gatZ ←	D‑tagatose 1,6‑bisphosphate aldolase 2, subunit
RA	2,170,707	C→A	16.1%	intergenic (‑24/+284)	gatY ← / ← fbaB	D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I
RA	2,170,708	G→T	15.8%	intergenic (‑25/+283)	gatY ← / ← fbaB	D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I
RA	2,170,713	C→A	32.2%	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	36.7%	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	10.4%	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	7.2%	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	90.9%	A24E (GCG→GAG)	rcnR ←	transcriptional repressor of rcnA
RA	2,181,645	A→G	88.7%	N83N (AAT→AAC)	yehA ←	putative fimbrial‑like adhesin protein
RA	2,189,888	C→A	23.3%	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	6.4%	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	2,194,695	T→A	93.7%	L313Q (CTA→CAA)	yehI →	DUF4132 domain‑containing protein
RA	2,195,449	A→T	92.7%	E564D (GAA→GAT)	yehI →	DUF4132 domain‑containing protein
RA	2,197,797	A→T	9.3%	intergenic (+29/‑278)	yehK → / → yehL	uncharacterized protein/putative ABC superfamily transporter ATP‑binding subunit
RA	2,209,162	C→A	40.6%	I9I (ATC→ATA)	yohO →	putative membrane protein
RA	2,216,296	C→A	100%	I211I (ATC→ATA)	dld →	D‑lactate dehydrogenase, FAD‑binding, NADH independent
RA	2,220,503	C→T	17.6%	V83M (GTG→ATG)	yohF ←	putative oxidoreductase
RA	2,223,247	C→T	39.3%	W206* (TGG→TGA)	dusC ←	tRNA‑dihydrouridine synthase C
RA	2,225,190	C→T	100%	G231G (GGC→GGT)	yohK →	LrgB family inner membrane protein
RA	2,225,260	C→T	20.4%	intergenic (+67/‑63)	yohK → / → cdd	LrgB family inner membrane protein/cytidine/deoxycytidine deaminase
RA	2,233,142	A→T	19.1%	V229E (GTG→GAG)	mglB ←	methyl‑galactoside transporter subunit
RA	2,237,098	G→T	93.3%	H12N (CAT→AAT)	folE ←	GTP cyclohydrolase I
RA	2,240,361	C→A	10.8%	intergenic (‑113/+181)	cirA ← / ← lysP	colicin IA outer membrane receptor and translocator; ferric iron‑catecholate transporter/lysine transporter
RA	2,243,089	G→T	25.0%	I3I (ATC→ATA)	yeiE ←	putative DNA‑binding transcriptional regulator
RA	2,259,689	C→A	20.4%	intergenic (+188/‑35)	yeiP → / → yeiQ	elongation factor P‑like protein/putative NAD‑dependent D‑mannonate oxidoreductase
RA	2,263,137	C→A	45.0%	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	2,263,171	T→C	5.8%	intergenic (+125/‑287)	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	90.5%	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	19.0%	L187Q (CTG→CAG)	yejF →	microcin C transporter, ATP‑binding subunit; ABC family
RA	2,278,791	A→C	8.0%	I313L (ATC→CTC)	yejM →	essential inner membrane DUF3413 domain‑containing protein; lipid A production and membrane permeability factor
RA	2,287,829	C→A	44.5%	S185S (TCG→TCT)	ccmF ←	heme lyase, CcmF subunit
RA	2,289,043	C→A	57.1%	W8L (TGG→TTG)	ccmD ←	cytochrome c biogenesis protein
RA	2,289,374	C→A	91.4%	V142V (GTG→GTT)	ccmC ←	heme exporter subunit
RA	2,292,271	A→T	24.7%	C263S (TGC→AGC)	napH ←	ferredoxin‑type protein essential for electron transfer from ubiquinol to periplasmic nitrate reductase (NapAB)
RA	2,294,769	C→A	13.2%	P488P (CCG→CCT)	napA ←	nitrate reductase, periplasmic, large subunit
RA	2,298,128	C→T	9.2%	intergenic (+256/+459)	eco → / ← mqo	ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA	2,303,070	T→G	91.7%	Q272P (CAG→CCG)	ada ←	fused DNA‑binding transcriptional dual regulator/O6‑methylguanine‑DNA methyltransferase
RA	2,303,607	A→C	9.3%	L93R (CTG→CGG)	ada ←	fused DNA‑binding transcriptional dual regulator/O6‑methylguanine‑DNA methyltransferase
RA	2,305,116	C→A	90.1%	intergenic (‑103/+9)	apbE ← / ← ompC	putative thiamine‑synthetic flavin transferase lipoprotein/outer membrane porin protein C
RA	2,305,135	T→C	91.6%	Y365C (TAC→TGC)	ompC ←	outer membrane porin protein C
RA	2,310,690	C→A	11.7%	R889L (CGC→CTC)	rcsC ←	hybrid sensory kinase in two‑component regulatory system with RcsB and YojN
RA	2,313,924	C→A	21.1%	R135S (CGC→AGC)	atoS →	sensory histidine kinase in two‑component regulatory system with AtoC
RA	2,330,502	C→A	86.8%	D800Y (GAT→TAT)	gyrA ←	DNA gyrase (type II topoisomerase), subunit A
RA	2,348,894	T→A	52.7%	V384E (GTG→GAG)	glpB →	sn‑glycerol‑3‑phosphate dehydrogenase (anaerobic), membrane anchor subunit
RA	2,352,573	C→A	88.1%	P353P (CCG→CCT)	rhmT ←	putative L‑rhamnonate transporter
RA	2,353,889	C→A	17.7%	V335V (GTG→GTT)	rhmD ←	L‑rhamnonate dehydratase
RA	2,359,673	G→T	89.9%	M89I (ATG→ATT)	arnB →	uridine 5'‑(beta‑1‑threo‑pentapyranosyl‑4‑ulose diphosphate) aminotransferase, PLP‑dependent
RA	2,360,045	C→A	11.8%	V213V (GTC→GTA)	arnB →	uridine 5'‑(beta‑1‑threo‑pentapyranosyl‑4‑ulose diphosphate) aminotransferase, PLP‑dependent
RA	2,362,338	T→A	100%	L274Q (CTG→CAG)	arnA →	fused UDP‑L‑Ara4N formyltransferase/UDP‑GlcA C‑4'‑decarboxylase
RA	2,370,361:1	+G	89.2%	coding (711/759 nt)	menH ←	2‑succinyl‑6‑hydroxy‑2, 4‑cyclohexadiene‑1‑carboxylate synthase
RA	2,370,837	Δ1 bp	20.8%	coding (235/759 nt)	menH ←	2‑succinyl‑6‑hydroxy‑2, 4‑cyclohexadiene‑1‑carboxylate synthase
RA	2,370,987	C→A	90.6%	E29* (GAA→TAA)	menH ←	2‑succinyl‑6‑hydroxy‑2, 4‑cyclohexadiene‑1‑carboxylate synthase
RA	2,379,450	C→T	6.8%	P38S (CCT→TCT)	yfbL →	putative peptidase
RA	2,380,078	C→T	37.7%	S247F (TCT→TTT)	yfbL →	putative peptidase
RA	2,383,897	C→A	47.9%	R363L (CGC→CTC)	nuoN ←	NADH:ubiquinone oxidoreductase, membrane subunit N
RA	2,395,041	C→A	20.9%	R164L (CGG→CTG)	nuoE ←	NADH:ubiquinone oxidoreductase, chain E
RA	2,399,210	G→T	90.0%	S304* (TCA→TAA)	lrhA ←	transcriptional repressor of flagellar, motility and chemotaxis genes
RA	2,405,946	T→G	92.9%	Q43P (CAG→CCG)	yfbU ←	UPF0304 family protein
RA	2,407,678	T→A	15.3%	S244T (TCT→ACT)	ackA →	acetate kinase A and propionate kinase 2
RA	2,412,205	C→A	46.5%	D151Y (GAT→TAT)	yfcD ←	putative NUDIX hydrolase
RA	2,416,101	C→A	88.6%	intergenic (+21/+27)	yfcH → / ← yfcI	putative NAD‑dependent nucleotide‑sugar epimerase/transposase_31 family protein
RA	2,422,841	C→A	94.9%	D293Y (GAT→TAT)	purF ←	amidophosphoribosyltransferase
RA	2,424,074	C→T	88.9%	D57N (GAC→AAC)	cvpA ←	colicin V production membrane protein
RA	2,442,770	A→C	9.8%	D253E (GAT→GAG)	yfcO ←	DUF2544 family putative outer membrane protein
RA	2,450,335	C→T	94.4%	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	94.5%	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	90.7%	P62Q (CCG→CAG)	fadJ ←	fused enoyl‑CoA hydratase and epimerase and isomerase/3‑hydroxyacyl‑CoA dehydrogenase
RA	2,454,297	T→G	91.8%	E39D (GAA→GAC)	yfcZ ←	UPF0381 family protein
RA	2,456,282	C→A	12.2%	intergenic (+157/‑209)	fadL → / → yfdF	long‑chain fatty acid outer membrane transporter/uncharacterized protein
RA	2,463,906	C→A	21.6%	Q433K (CAA→AAA)	gtrS →	serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
RA	2,463,910	G→T	16.5%	R434I (AGA→ATA)	gtrS →	serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
RA	2,474,418	G→T	89.9%	S413* (TCA→TAA)	emrY ←	putative multidrug efflux system
RA	2,495,918	C→A	17.0%	V683F (GTT→TTT)	fryA ←	putative PTS enzyme, Hpr component/enzyme I component/enzyme IIA component
RA	2,503,813	A→C	7.1%	A235A (GCA→GCC)	yfeO →	putative ion channel protein
RA	2,504,065	C→T	12.7%	G319G (GGC→GGT)	yfeO →	putative ion channel protein
RA	2,516,553	T→G	20.5%	E264D (GAA→GAC)	xapB ←	xanthosine transporter
RA	2,520,652	C→A	93.6%	I116I (ATC→ATA)	yfeH →	putative inorganic ion transporter
RA	2,526,023	T→A	26.7%	Y86N (TAC→AAC)	cysK →	cysteine synthase A, O‑acetylserine sulfhydrolase A subunit
RA	2,542,627	T→G	49.0%	I389M (ATT→ATG)	yfeW →	penicillin binding protein PBP4B; weak DD‑carboxypeptidase activity
RA	2,545,908	C→A	8.3%	G66G (GGC→GGA)	amiA →	N‑acetylmuramoyl‑l‑alanine amidase I
RA	2,549,676	C→A	88.3%	L28L (CTG→CTT)	eutL ←	putative ethanol utilization carboxysome structural protein
RA	2,559,092	C→A	24.7%	A384A (GCG→GCT)	eutA ←	reactivating factor for ethanolamine ammonia lyase
RA	2,568,720	C→T	92.4%	A33T (GCC→ACC)	eutP ←	putative P‑loop NTPase ethanolamine utilization protein
RA	2,573,363	C→A	24.4%	V123V (GTC→GTA)	tktB →	transketolase 2, thiamine triphosphate‑binding
RA	2,576,325	C→A	92.6%	E171D (GAG→GAT)	nudK ←	GDP‑mannose pyrophosphatase
RA	2,586,791	G→T	10.3%	G113G (GGC→GGA)	ypfH ←	palmitoyl‑CoA esterase activity, uncertain physiological substrate
RA	2,587,029:1	+G	90.8%	coding (101/699 nt)	ypfH ←	palmitoyl‑CoA esterase activity, uncertain physiological substrate
RA	2,589,933	G→A	93.4%	T55I (ACC→ATC)	ypfJ ←	putative neutral zinc metallopeptidase
RA	2,597,173	T→G	43.6%	L666R (CTG→CGG)	hyfB →	hydrogenase 4, membrane subunit
RA	2,606,516	G→T	91.8%	D420Y (GAC→TAC)	hyfR →	hydrogenase‑4 transcriptional activator
RA	2,610,919	C→A	91.8%	intergenic (+3/‑18)	bepA → / → yfgD	periplasmic metalloprotease and chaperone for OM protein maintenance and assembly/putative oxidoreductase
RA	2,614,168	C→A	90.6%	D22Y (GAT→TAT)	upp ←	uracil phosphoribosyltransferase
RA	2,618,693	G→T	44.0%	E74* (GAA→TAA)	ppx →	exopolyphosphatase
RA	2,619,125	G→T	19.1%	G218C (GGT→TGT)	ppx →	exopolyphosphatase
RA	2,619,563	C→A	8.4%	R364R (CGA→AGA)	ppx →	exopolyphosphatase
RA	2,632,012	C→A	46.6%	intergenic (‑1/+10)	bamB ← / ← yfgM	BamABCDE complex OM biogenesis lipoprotein/putative anti‑RcsB factor
RA	2,651,665	G→T	90.4%	G210G (GGC→GGA)	hscA ←	DnaK‑like molecular chaperone specific for IscU
RA	2,655,934	A→C	5.3%	intergenic (‑444/+8)	iscR ← / ← trmJ	isc operon transcriptional repressor; suf operon transcriptional activator; oxidative stress‑ and iron starvation‑inducible; autorepressor/tRNA mC32,mU32 2'‑O‑methyltransferase, SAM‑dependent
RA	2,656,833	A→C	14.3%	A11A (GCA→GCC)	suhB →	inositol monophosphatase
RA	2,665,693	C→A	17.6%	G96G (GGC→GGA)	hcaD →	phenylpropionate dioxygenase, ferredoxin reductase subunit
RA	2,669,978	C→A	46.7%	A69A (GCG→GCT)	yphD ←	inner membrane putative ABC superfamily sugar transporter permease
RA	2,670,904	G→T	15.8%	R273S (CGC→AGC)	yphE ←	putative sugar transporter subunit of ABC superfamily, ATP‑binding component
RA	2,671,274	C→A	88.4%	T149T (ACG→ACT)	yphE ←	putative sugar transporter subunit of ABC superfamily, ATP‑binding component
RA	2,674,117	C→A	15.1%	R663L (CGC→CTC)	yphG ←	DUF4380 domain‑containing TPR repeat protein
RA	2,678,030	C→A	20.4%	A279A (GCG→GCT)	glyA ←	serine hydroxymethyltransferase
RA	2,678,315	C→A	16.2%	A184A (GCG→GCT)	glyA ←	serine hydroxymethyltransferase
RA	2,681,873	T→A	91.6%	Q97L (CAG→CTG)	glrR ←	response regulator regulating glmY sRNA in two‑component system with sensor protein GlrK
RA	2,683,829	C→A	91.5%	R210L (CGT→CTT)	glrK ←	sensor protein kinase regulating glmY sRNA in two‑component system with response regulator GlrR
RA	2,692,793	C→A	44.4%	H226N (CAT→AAT)	yfhH →	putative DNA‑binding transcriptional regulator
RA	2,694,843	G→T	44.5%	I82I (ATC→ATA)	pdxJ ←	pyridoxine 5'‑phosphate synthase
RA	2,695,549	C→A	6.2%	E94* (GAA→TAA)	recO ←	gap repair protein
RA	2,699,380	C→A	46.6%	P368P (CCG→CCT)	lepA ←	back‑translocating elongation factor EF4, GTPase
RA	2,711,673	A→C	9.8%	V72G (GTT→GGT)	yfiF ←	putative methyltransferase
RA	2,715,643	G→T	91.6%	E778* (GAA→TAA)	pka →	protein lysine acetyltransferase
RA	2,719,197	C→A	12.1%	intergenic (‑92/+231)	kgtP ← / ← rrfG	alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon
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	86.0%	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	19.5%	I20I (ATA→ATT)	yfiR →	putative periplasmic inhibitor of YfiN activity
RA	2,749,134	C→A	7.1%	intergenic (+397/‑384)	smpB → / → intA	trans‑translation protein/CP4‑57 prophage; integrase
RA	2,757,927	A→T	24.0%	S196T (TCC→ACC)	yfjL ←	CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein
RA	2,761,733	T→A	17.5%	V222E (GTA→GAA)	yfjP →	CP4‑57 prophage; 50S ribosome‑binding GTPase family protein
RA	2,771,358	G→A	94.8%	intergenic (+217/+147)	ypjF → / ← ypjA	CP4‑57 prophage; toxin of the YpjF‑YfjZ toxin‑antitoxin system/adhesin‑like autotransporter
RA	2,779,067	C→A	85.4%	intergenic (‑697/+54)	ypjC ← / ← ileY	pseudogene/tRNA‑Ile
RA	2,803,846	C→A	22.4%	I48I (ATC→ATA)	ygaH →	putative L‑valine exporter, norvaline resistance protein
RA	2,806,531	T→G	24.2%	L186R (CTG→CGG)	emrB →	multidrug efflux system protein
RA	2,808,646	G→T	17.3%	R385S (CGC→AGC)	gshA ←	glutamate‑cysteine ligase
RA	2,811,275	T→G	11.7%	intergenic (‑56/+143)	argQ ← / ← argZ	tRNA‑Arg/tRNA‑Arg
RA	2,813,731	G→T	12.1%	A547E (GCG→GAG)	alaS ←	alanyl‑tRNA synthetase
RA	2,825,783	C→T	90.2%	intergenic (‑135/‑52)	norR ← / → norV	anaerobic nitric oxide reductase DNA‑binding transcriptional activator/anaerobic nitric oxide reductase flavorubredoxin
RA	2,828,952	C→A	92.6%	T611T (ACG→ACT)	hypF ←	carbamoyl phosphate phosphatase and maturation protein for [NiFe] hydrogenases
RA	2,831,086	C→A	54.7%	E127* (GAA→TAA)	hydN ←	formate dehydrogenase‑H, [4Fe‑4S] ferredoxin subunit
RA	2,835,094	C→A	45.4%	P249Q (CCG→CAG)	ascB →	cryptic 6‑phospho‑beta‑glucosidase
RA	2,835,291	T→G	10.1%	C315G (TGC→GGC)	ascB →	cryptic 6‑phospho‑beta‑glucosidase
RA	2,841,044	C→A	87.5%	A519A (GCG→GCT)	hycC ←	hydrogenase 3, membrane subunit
RA	2,846,112	C→A	35.1%	I206I (ATC→ATA)	hypD →	hydrogenase maturation protein
RA	2,850,790	C→A	89.0%	I113I (ATC→ATA)	mutS →	methyl‑directed mismatch repair protein
RA	2,871,412	T→G	8.3%	intergenic (+435/+516)	iap → / ← ygbF	aminopeptidase in alkaline phosphatase isozyme conversion/CRISPR adaptation ssRNA endonuclease
RA	2,873,087	G→T	92.3%	V15V (GTC→GTA)	ygbT ←	multifunctional endonuclease Cas1, CRISPR adaptation protein; DNA repair enzyme
RA	2,876,760	C→T	92.7%	G246G (GGG→GGA)	casA ←	CRISP RNA (crRNA) containing Cascade antiviral complex protein
RA	2,878,668	G→T	92.6%	V637V (GTC→GTA)	ygcB ←	R‑loop helicase‑annealase Cas3 needed for Cascade anti‑viral activity
RA	2,879,449	G→T	86.6%	S377* (TCA→TAA)	ygcB ←	R‑loop helicase‑annealase Cas3 needed for Cascade anti‑viral activity
RA	2,880,202	G→T	9.8%	S126* (TCA→TAA)	ygcB ←	R‑loop helicase‑annealase Cas3 needed for Cascade anti‑viral activity
RA	2,888,584	G→T	93.4%	I185I (ATC→ATA)	ygcQ ←	putative flavoprotein
RA	2,893,446	T→A	42.2%	K63* (AAA→TAA)	ygcW ←	putative dehydrogenase
RA	2,908,686	G→T	10.7%	E91* (GAA→TAA)	barA →	hybrid sensory histidine kinase, in two‑component regulatory system with UvrY
RA	2,915,010	C→A	14.5%	T150T (ACG→ACT)	gudP ←	putative D‑glucarate transporter
RA	2,931,717	C→A	88.6%	N307K (AAC→AAA)	fucK →	L‑fuculokinase
RA	2,932,832	C→A	12.1%	R36S (CGT→AGT)	fucR →	l‑fucose operon activator
RA	2,932,835	C→T	44.7%	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	15.2%	intergenic (‑182/‑10)	ygdI ← / → csdA	DUF903 family verified lipoprotein/cysteine sulfinate desulfinase
RA	2,957,480	C→A	12.2%	L19F (TTG→TTT)	ppdA ←	putative prepilin peptidase‑dependent protein
RA	2,959,004	G→A	89.7%	I131I (ATC→ATT)	lgt ←	phosphatidylglycerol‑prolipoprotein diacylglyceryl transferase
RA	2,959,786	C→A	8.0%	E670* (GAA→TAA)	ptsP ←	fused PTS enzyme: PEP‑protein phosphotransferase (enzyme I)/GAF domain containing protein
RA	2,962,962	T→A	48.4%	intergenic (‑626/‑59)	rppH ← / → mutH	RNA pyrophosphohydrolase/methyl‑directed mismatch repair protein
RA	2,967,572	A→G	20.6%	F601S (TTT→TCT)	aas ←	fused 2‑acylglycerophospho‑ethanolamine acyl transferase/acyl‑acyl carrier protein synthetase
RA	2,985,884	C→T	46.0%	I144I (ATC→ATT)	ygeH →	putative transcriptional regulator
RA	2,988,554	G→A	56.9%	intergenic (‑103/+119)	ygeK ← / ← ygeN	pseudogene; putative 2‑component transcriptional regulator/pseudogene
RA	2,989,295	C→A	100%	pseudogene (85/261 nt)	ygeN ←	pseudogene
RA	2,993,211	C→A	94.2%	V14L (GTG→TTG)	ygeR ←	LysM domain‑containing M23 family putative peptidase; septation lipoprotein
RA	2,993,699	C→A	100%	intergenic (‑449/‑5)	ygeR ← / → xdhA	LysM domain‑containing M23 family putative peptidase; septation lipoprotein/xanthine dehydrogenase, molybdenum binding subunit
RA	2,999,286	G→T	11.9%	intergenic (‑141/‑335)	ygeV ← / → ygeW	putative sigma‑54‑interacting transcriptional activator/putative carbamoyltransferase
RA	3,007,414	A→C	9.6%	L62R (CTT→CGT)	yqeB ←	XdhC‑CoxI family protein with NAD(P)‑binding Rossman fold
RA	3,009,187	G→T	49.8%	intergenic (+90/‑232)	mocA → / → ygfK	CTP:molybdopterin cytidylyltransferase/putative Fe‑S subunit oxidoreductase subunit
RA	3,016,372	C→A	30.3%	F566L (TTC→TTA)	xdhD →	putative hypoxanthine oxidase, molybdopterin‑binding/Fe‑S binding
RA	3,017,285	G→T	89.2%	D871Y (GAC→TAC)	xdhD →	putative hypoxanthine oxidase, molybdopterin‑binding/Fe‑S binding
RA	3,019,203	G→T	11.9%	E27* (GAG→TAG)	guaD →	guanine deaminase
RA	3,022,877	G→T	11.6%	R472S (CGC→AGC)	ygfT ←	putative oxidoreductase, Fe‑S subunit/nucleotide‑binding subunit
RA	3,022,888	C→A	19.0%	R468L (CGG→CTG)	ygfT ←	putative oxidoreductase, Fe‑S subunit/nucleotide‑binding subunit
RA	3,024,081	A→C	44.4%	V70V (GTT→GTG)	ygfT ←	putative oxidoreductase, Fe‑S subunit/nucleotide‑binding subunit
RA	3,024,983	C→G	94.2%	G86G (GGC→GGG)	uacT →	uric acid permease
RA	3,025,678	A→T	20.2%	Q318L (CAA→CTA)	uacT →	uric acid permease
RA	3,028,266	C→A	7.0%	D90Y (GAC→TAC)	lysS ←	lysine tRNA synthetase, constitutive
RA	3,029,817	A→T	12.7%	V550E (GTG→GAG)	recJ ←	ssDNA exonuclease, 5' ‑‑> 3'‑specific
RA	3,030,181	G→T	47.6%	H429N (CAT→AAT)	recJ ←	ssDNA exonuclease, 5' ‑‑> 3'‑specific
RA	3,035,672	C→A	5.7%	intergenic (+20/+176)	ygfZ → / ← yqfA	iron‑sulfur cluster repair protein, plumbagin resistance/hemolysin III family HylIII inner membrane protein
RA	3,039,409	T→G	11.5%	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	3,044,464	G→A	90.6%	intergenic (‑438/+10)	gcvT ← / ← ubiI	aminomethyltransferase, tetrahydrofolate‑dependent, subunit (T protein) of glycine cleavage complex/2‑octaprenylphenol hydroxylase, FAD‑dependent
RA	3,049,716	A→T	5.2%	V39V (GTA→GTT)	fau →	5‑formyltetrahydrofolate cyclo‑ligase family protein
RA	3,049,730	A→T	7.1%	D44V (GAT→GTT)	fau →	5‑formyltetrahydrofolate cyclo‑ligase family protein
RA	3,051,954	G→A	5.1%	intergenic (‑185/+71)	serA ← / ← rpiA	D‑3‑phosphoglycerate dehydrogenase/ribose 5‑phosphate isomerase, constitutive
RA	3,055,069	C→A	21.2%	V287V (GTC→GTA)	scpA →	methylmalonyl‑CoA mutase
RA	3,058,692	C→T	14.7%	P178S (CCT→TCT)	scpC →	propionyl‑CoA:succinate CoA transferase
RA	3,058,769	C→T	45.8%	I203I (ATC→ATT)	scpC →	propionyl‑CoA:succinate CoA transferase
RA	3,064,914	G→T	86.2%	I356I (ATC→ATA)	pgk ←	phosphoglycerate kinase
RA	3,068,135	G→T	19.9%	F140L (TTC→TTA)	yggD ←	MtlR family putative transcriptional repressor
RA	3,072,314	C→A	19.4%	E126* (GAA→TAA)	cmtB ←	putative mannitol‑specific enzyme IIA component of PTS
RA	3,075,114	C→A	94.3%	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	93.4%	D211Y (GAC→TAC)	speB ←	agmatinase
RA	3,080,618	T→A	90.3%	V185E (GTG→GAG)	metK →	S‑adenosylmethionine synthetase
RA	3,088,065	C→A	42.0%	V125V (GTG→GTT)	yggR ←	putative PilT family AAA+ ATPase
RA	3,092,496	C→A	6.9%	V143V (GTG→GTT)	yggM ←	DUF1202 family putative secreted protein
RA	3,097,262	C→T	43.7%	F297F (TTC→TTT)	mutY →	adenine DNA glycosylase
RA	3,102,941	T→A	12.8%	S10R (AGT→AGA)	yqgA →	DUF554 family putative inner membrane protein
RA	3,110,751	C→A	93.6%	R574L (CGT→CTT)	yghJ ←	DUF4092 family putative lipoprotein peptidase
RA	3,111,434	C→A	92.5%	A346A (GCG→GCT)	yghJ ←	DUF4092 family putative lipoprotein peptidase
RA	3,120,216	C→A	88.8%	D389Y (GAT→TAT)	glcD ←	glycolate oxidase subunit, FAD‑linked
RA	3,132,601	T→G	14.1%	I172M (ATT→ATG)	yghU →	putative S‑transferase
RA	3,142,668	G→T	41.5%	L55I (CTC→ATC)	yqhA ←	UPF0114 family putative inner membrane protein
RA	3,144,158	C→A	85.7%	intergenic (+253/+19)	yghA → / ← exbD	putative oxidoreductase/membrane spanning protein in TonB‑ExbB‑ExbD complex
RA	3,164,230	C→A	44.7%	R130S (CGT→AGT)	qseC →	quorum sensing sensory histidine kinase in two‑component regulatory system with QseB
RA	3,173,669	G→T	88.2%	A189A (GCG→GCT)	ygiB →	DUF1190 family protein
RA	3,176,733	G→T	47.5%	intergenic (+51/+439)	zupT → / ← ribB	zinc transporter/3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase
RA	3,215,927	C→A	22.9%	intergenic (+119/‑65)	ebgR → / → ebgA	transcriptional repressor/evolved beta‑D‑galactosidase, alpha subunit
RA	3,217,289	A→T	55.5%	H433L (CAC→CTC)	ebgA →	evolved beta‑D‑galactosidase, alpha subunit
RA	3,224,927	C→A	94.0%	intergenic (+329/‑97)	ygjK → / → fadH	alpha‑glucosidase/2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked
RA	3,230,857	C→G	44.9%	A63G (GCC→GGC)	ygjR →	putative NAD(P)‑dependent dehydrogenase
RA	3,231,349	A→C	39.2%	Q227P (CAG→CCG)	ygjR →	putative NAD(P)‑dependent dehydrogenase
RA	3,245,848	G→T	91.1%	L62L (CTG→CTT)	yhaH →	DUF805 family inner membrane protein
RA	3,246,634	A→T	16.5%	intergenic (+8/+43)	yhaI → / ← yhaJ	DUF805 family inner membrane protein/LysR family putative transcriptional regulator
RA	3,252,258	C→A	92.4%	D251Y (GAT→TAT)	tdcG ←	L‑serine dehydratase 3, anaerobic
RA	3,263,315	T→C	5.3%	intergenic (+354/+260)	yhaC → / ← rnpB	pentapetide repeats‑related protein/RNase P, M1 RNA component
RA	3,263,502	C→T	5.8%	intergenic (+541/+73)	yhaC → / ← rnpB	pentapetide repeats‑related protein/RNase P, M1 RNA component
RA	3,266,646	C→A	92.6%	G91C (GGT→TGT)	garL ←	alpha‑dehydro‑beta‑deoxy‑D‑glucarate aldolase
RA	3,275,040	C→A	19.0%	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	3,296,612	G→T	42.7%	A255A (GCG→GCT)	yhbV →	U32 peptidase family protein
RA	3,302,027	G→T	91.2%	S86* (TCG→TAG)	nlpI ←	lipoprotein involved in osmotic sensitivity and filamentation
RA	3,312,862	T→A	17.4%	R289R (CGT→CGA)	argG →	argininosuccinate synthetase
RA	3,314,870	C→A	87.0%	A35S (GCG→TCG)	yhbX ←	putative EptAB family phosphoethanolamine transferase, inner membrane protein
RA	3,320,198	C→A	6.9%	D33Y (GAT→TAT)	ftsH ←	protease, ATP‑dependent zinc‑metallo
RA	3,332,963	C→A	8.0%	A154A (GCG→GCT)	mlaF ←	ABC transporter maintaining OM lipid asymmetry, ATP‑binding protein
RA	3,347,778	G→A	94.6%	intergenic (‑369/‑306)	yhcC ← / → gltB	putative Fe‑S oxidoreductase, Radical SAM superfamily protein/glutamate synthase, large subunit
RA	3,351,650	G→T	44.5%	E1189D (GAG→GAT)	gltB →	glutamate synthase, large subunit
RA	3,354,405	C→T	92.8%	intergenic (+430/‑130)	gltD → / → gltF	glutamate synthase, 4Fe‑4S protein, small subunit/periplasmic protein
RA	3,357,229	C→A	13.7%	S355* (TCG→TAG)	yhcD →	putative outer membrane fimbrial subunit usher protein
RA	3,365,607	G→T	91.6%	I109I (ATC→ATA)	nanT ←	sialic acid transporter
RA	3,372,048	C→A	31.5%	intergenic (‑38/+181)	rplM ← / ← yhcM	50S ribosomal subunit protein L13/putative AFG1‑like family P‑loop ATPase
RA	3,373,985	C→A	92.0%	intergenic (+37/‑117)	yhcB → / → degQ	DUF1043 family inner membrane‑anchored protein/serine endoprotease, periplasmic
RA	3,375,260	G→T	88.7%	D387Y (GAT→TAT)	degQ →	serine endoprotease, periplasmic
RA	3,380,174	C→A	21.8%	S458S (TCG→TCT)	aaeB ←	p‑hydroxybenzoic acid efflux system component
RA	3,385,487	A→T	5.9%	intergenic (‑100/+330)	tldD ← / ← yhdP	putative peptidase/DUF3971‑AsmA2 domains protein
RA	3,385,702	A→C	6.5%	intergenic (‑315/+115)	tldD ← / ← yhdP	putative peptidase/DUF3971‑AsmA2 domains protein
RA	3,386,303	A→T	17.2%	I1105I (ATT→ATA)	yhdP ←	DUF3971‑AsmA2 domains protein
RA	3,386,672	C→A	9.0%	P982P (CCG→CCT)	yhdP ←	DUF3971‑AsmA2 domains protein
RA	3,396,082	G→T	94.1%	R204S (CGT→AGT)	csrD ←	targeting factor for csrBC sRNA degradation
RA	3,397,642	C→A	5.6%	S267* (TCA→TAA)	acuI →	putative acryloyl‑CoA reductase
RA	3,407,007	G→A	37.5%	intergenic (‑183/‑216)	acrS ← / → acrE	acrAB operon transcriptional repressor/cytoplasmic membrane lipoprotein
RA	3,407,008	G→A	27.9%	intergenic (‑184/‑215)	acrS ← / → acrE	acrAB operon transcriptional repressor/cytoplasmic membrane lipoprotein
RA	3,411,136	G→T	11.1%	A915A (GCG→GCT)	acrF →	multidrug efflux system protein
RA	3,416,890	T→G	7.4%	noncoding (12/120 nt)	rrfF ←	5S ribosomal RNA of rrnD operon
RA	3,437,010	C→A	26.8%	V149V (GTG→GTT)	secY ←	preprotein translocase membrane subunit
RA	3,440,151	G→T	91.9%	I31I (ATC→ATA)	rpsN ←	30S ribosomal subunit protein S14
RA	3,440,444	G→T	93.9%	S118S (TCC→TCA)	rplE ←	50S ribosomal subunit protein L5
RA	3,440,832	T→C	93.7%	N99D (AAC→GAC)	rplX ←	50S ribosomal subunit protein L24
RA	3,447,853	A→T	30.5%	V302E (GTA→GAA)	gspA ←	general secretory pathway component, cryptic
RA	3,455,867	C→A	86.1%	I55I (ATC→ATA)	gspJ →	putative general secretory pathway component, cryptic
RA	3,462,472	G→T	5.5%	G247G (GGC→GGA)	chiA ←	periplasmic endochitinase
RA	3,467,941	C→T	7.8%	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	100%	I276I (ATC→ATA)	kefB ←	potassium:proton antiporter
RA	3,479,769	A→T	89.3%	E97D (GAA→GAT)	crp →	cAMP‑activated global transcription factor, mediator of catabolite repression
RA	3,483,095	C→A	14.5%	V149F (GTT→TTT)	argD ←	bifunctional acetylornithine aminotransferase/ succinyldiaminopimelate aminotransferase
RA	3,488,966	G→C	91.1%	A533P (GCC→CCC)	nirB →	nitrite reductase, large subunit, NAD(P)H‑binding
RA	3,489,397	C→A	91.8%	F676L (TTC→TTA)	nirB →	nitrite reductase, large subunit, NAD(P)H‑binding
RA	3,490,359	C→T	7.9%	intergenic (+123/‑3)	nirD → / → nirC	nitrite reductase, NAD(P)H‑binding, small subunit/nitrite transporter
RA	3,498,239	A→C	6.8%	intergenic (+97/+55)	frlR → / ← yhfS	putative DNA‑binding transcriptional regulator/FNR‑regulated pyridoxal phosphate‑dependent aminotransferase family protein
RA	3,501,571	C→A	93.5%	G127C (GGC→TGC)	php ←	phosphotriesterase homology protein
RA	3,504,143	G→T	51.8%	R65S (CGT→AGT)	yhfX ←	putative pyridoxal 5'‑phosphate binding protein
RA	3,504,943	C→A	29.9%	R254L (CGA→CTA)	yhfZ ←	putative DNA‑binding transcriptional regulator
RA	3,507,749	G→T	93.5%	H224N (CAT→AAT)	rpe ←	D‑ribulose‑5‑phosphate 3‑epimerase
RA	3,510,311	C→A	12.0%	G119C (GGT→TGT)	damX ←	cell division protein that binds to the septal ring
RA	3,513,424	A→T	43.9%	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	3,520,457	C→A	5.7%	V210V (GTC→GTA)	yrfF →	inner membrane protein
RA	3,525,215	A→C	11.6%	L195R (CTG→CGG)	yhgE ←	DUF4153 family putative inner membrane protein
RA	3,525,950	C→T	9.5%	intergenic (‑152/‑227)	yhgE ← / → pck	DUF4153 family putative inner membrane protein/phosphoenolpyruvate carboxykinase
RA	3,542,744	T→A	11.3%	Q229L (CAG→CTG)	malQ ←	4‑alpha‑glucanotransferase (amylomaltase)
RA	3,543,959	G→T	93.4%	A625E (GCG→GAG)	malP ←	maltodextrin phosphorylase
RA	3,548,048	T→A	7.8%	S535R (AGT→AGA)	malT →	mal regulon transcriptional activator
RA	3,551,503	T→C	22.0%	intergenic (‑65/‑124)	rtcB ← / → rtcR	RNA‑splicing ligase/sigma 54‑dependent transcriptional regulator of rtcBA expression
RA	3,561,574	C→A	92.2%	W372L (TGG→TTG)	glgC ←	glucose‑1‑phosphate adenylyltransferase
RA	3,585,079	C→A	16.0%	A203S (GCC→TCC)	ugpB ←	glycerol‑3‑phosphate transporter subunit
RA	3,588,904	A→T	11.2%	L287Q (CTG→CAG)	livH ←	leucine/isoleucine/valine transporter subunit
RA	3,607,530	G→T	9.2%	Q168H (CAG→CAT)	nikA →	nickel‑binding, heme‑binding periplasmic protein
RA	3,632,600	T→G	20.0%	intergenic (+99/+145)	pitA → / ← uspB	phosphate transporter, low‑affinity; tellurite importer/universal stress (ethanol tolerance) protein B
RA	3,639,551	C→A	19.7%	T269T (ACC→ACA)	rlmJ →	23S rRNA m(6)A2030 methyltransferase, SAM‑dependent
RA	3,643,207	C→A	7.7%	L305I (CTT→ATT)	arsB →	arsenite/antimonite transporter
RA	3,656,367	C→A	12.8%	A865E (GCG→GAG)	mdtF →	anaerobic multidrug efflux transporter, ArcA‑regulated
RA	3,661,524	C→T	7.6%	G342D (GGC→GAC)	yhjA ←	putative cytochrome C peroxidase
RA	3,662,660	T→C	90.8%	intergenic (‑112/‑292)	yhjA ← / → treF	putative cytochrome C peroxidase/cytoplasmic trehalase
RA	3,679,301	T→G	94.7%	Q1078P (CAG→CCG)	bcsC ←	cellulose synthase subunit
RA	3,679,324	C→A	100%	M1070I (ATG→ATT)	bcsC ←	cellulose synthase subunit
RA	3,680,910	G→T	91.5%	H542N (CAT→AAT)	bcsC ←	cellulose synthase subunit
RA	3,698,875	G→T	49.1%	F92L (TTC→TTA)	dppB ←	dipeptide/heme transporter
RA	3,701,561	G→A	13.6%	intergenic (‑496/+415)	dppA ← / ← proK	dipeptide transporter/tRNA‑Pro
RA	3,703,272	C→A	21.3%	A188A (GCG→GCT)	eptB ←	KDO phosphoethanolamine transferase, Ca(2+)‑inducible
RA	3,711,401	T→A	7.7%	N244K (AAT→AAA)	ghrB →	glyoxylate/hydroxypyruvate reductase B
RA	3,717,788	C→A	93.1%	P297P (CCG→CCT)	glyQ ←	glycine tRNA synthetase, alpha subunit
RA	3,718,959	C→A	17.7%	L38F (TTG→TTT)	ysaB ←	uncharacterized protein
RA	3,730,615	C→A	16.5%	intergenic (‑78/‑242)	bax ← / → malS	putative glucosaminidase/alpha‑amylase
RA	3,738,431	C→A	92.4%	P90T (CCA→ACA)	yiaN →	2,3‑diketo‑L‑gulonate TRAP transporter large permease protein
RA	3,759,388	C→A	18.5%	N1282K (AAC→AAA)	rhsA →	Rhs family protein, putative polymorphic toxin; putative polysaccharide synthesis/export protein; putative neighboring cell growth inhibitor
RA	3,765,316	T→C	10.1%	intergenic (‑212/‑325)	yibI ← / → mtlA	DUF3302 family inner membrane protein/fused mannitol‑specific PTS enzymes: IIA components/IIB components/IIC components
RA	3,767,000	G→T	31.1%	D454Y (GAC→TAC)	mtlA →	fused mannitol‑specific PTS enzymes: IIA components/IIB components/IIC components
RA	3,779,281	C→G	8.1%	A221G (GCT→GGT)	gpmM →	phosphoglycero mutase III, cofactor‑independent
RA	3,785,915	G→T	94.6%	intergenic (‑4/+271)	kbl ← / ← yibB	glycine C‑acetyltransferase/YibB family protein, function unknown
RA	3,791,588	T→A	18.6%	intergenic (+21/+11)	waaL → / ← waaU	O‑antigen ligase/lipopolysaccharide core biosynthesis
JC JC	3,795,902	IS5 (+) +4 bp	8.1%	coding (514‑517/1020 nt)	waaR ←	UDP‑D‑galactose:(glucosyl)lipopolysaccharide‑ alpha‑1,3‑D‑galactosyltransferase
RA	3,802,238	A→T	25.7%	A113A (GCA→GCT)	waaA →	3‑deoxy‑D‑manno‑octulosonic‑acid transferase (KDO transferase)
RA	3,810,195	C→A	92.8%	R54S (CGT→AGT)	yicC →	UPF0701 family protein
RA	3,814,302	T→A	23.9%	S77C (AGC→TGC)	ligB ←	DNA ligase, NAD(+)‑dependent
RA	3,816,601	A→T	92.8%	H281L (CAC→CTC)	spoT →	bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase
RA	3,818,010	C→A	93.9%	H46N (CAT→AAT)	trmH →	tRNA mG18‑2'‑O‑methyltransferase, SAM‑dependent
RA	3,822,339	A→C	10.2%	Q12P (CAA→CCA) ‡	xanP →	xanthine permease
RA	3,822,340	A→C	12.0%	Q12H (CAA→CAC) ‡	xanP →	xanthine permease
RA	3,825,702	C→A	94.2%	K732N (AAG→AAT)	yicI ←	putative alpha‑glucosidase
RA	3,830,197	C→A	91.3%	intergenic (+281/‑116)	yicT → / → setC	pseudogene/putative arabinose efflux transporter
RA	3,830,311	G→T	93.4%	intergenic (+395/‑2)	yicT → / → setC	pseudogene/putative arabinose efflux transporter
RA	3,835,154	G→A	11.6%	intergenic (‑55/+156)	nepI ← / ← yicN	putative transporter/DUF1198 family protein
RA	3,860,159	C→A	100%	P33P (CCG→CCT)	ibpB ←	heat shock chaperone
RA	3,860,327	C→A	49.7%	intergenic (‑70/+42)	ibpB ← / ← ibpA	heat shock chaperone/heat shock chaperone
RA	3,860,653	C→A	43.8%	E44* (GAA→TAA)	ibpA ←	heat shock chaperone
RA	3,865,120	C→A	42.7%	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	3,896,189	G→T	31.8%	T291T (ACC→ACA)	bglB ←	cryptic phospho‑beta‑glucosidase B
RA	3,897,991	C→A	5.1%	D323Y (GAC→TAC)	bglF ←	fused beta‑glucoside‑specific PTS enzymes: IIA component/IIB component/IIC component
RA	3,901,867	T→G	9.1%	intergenic (‑141/+42)	pstB ← / ← pstA	phosphate transporter subunit/phosphate transporter subunit
RA	3,906,261	C→A	11.9%	E256D (GAG→GAT)	glmS ←	L‑glutamine:D‑fructose‑6‑phosphate aminotransferase
RA	3,910,894	C→A	91.9%	M244I (ATG→ATT)	atpG ←	F1 sector of membrane‑bound ATP synthase, gamma subunit
RA	3,914,395	T→A	20.1%	Q52L (CAG→CTG)	atpE ←	F0 sector of membrane‑bound ATP synthase, subunit c
RA	3,915,091	C→A	8.0%	T107T (ACG→ACT)	atpB ←	F0 sector of membrane‑bound ATP synthase, subunit a
RA	3,916,052	C→A	16.9%	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	94.4%	D71Y (GAT→TAT)	rsmG ←	16S rRNA m(7)G527 methyltransferase, SAM‑dependent; glucose‑inhibited cell‑division protein
RA	3,917,548	C→A	26.6%	S482S (TCG→TCT)	mnmG ←	5‑methylaminomethyl‑2‑thiouridine modification at tRNA U34
RA	3,923,028	C→A	51.2%	D476Y (GAC→TAC)	ravA ←	hexameric AAA+ MoxR family ATPase, putative molecular chaperone
RA	3,926,831	G→T	92.6%	D41Y (GAT→TAT)	rbsD →	putative cytoplasmic sugar‑binding protein
RA	3,927,972	G→T	43.8%	E279* (GAA→TAA)	rbsA →	fused D‑ribose transporter subunits of ABC superfamily: ATP‑binding components
RA	3,935,100	G→T	46.2%	intergenic (‑413/‑68)	yieP ← / → rrsC	putative transcriptional regulator/16S ribosomal RNA of rrnC operon
RA	3,950,395	C→A	11.6%	E262D (GAG→GAT)	ilvY ←	transcriptional activator of ilvC; autorepressor
RA	3,952,658	C→T	15.8%	D443D (GAC→GAT)	ilvC →	ketol‑acid reductoisomerase, NAD(P)‑binding
RA	3,956,662	T→G	10.1%	S310R (AGC→CGC)	gpp ←	guanosine pentaphosphatase/exopolyphosphatase
RA	3,960,036	G→A	94.2%	R87H (CGC→CAC)	rho →	transcription termination factor
RA	3,966,854	C→A	87.6%	R325S (CGT→AGT)	rffG →	dTDP‑glucose 4,6‑dehydratase
RA	3,967,474	G→T	48.8%	A169A (GCG→GCT)	rffH →	glucose‑1‑phosphate thymidylyltransferase
RA	3,969,710	G→T	89.6%	G25C (GGT→TGT)	wzxE →	O‑antigen translocase
RA	3,988,075	T→A	94.1%	V65E (GTG→GAG)	yifL →	putative lipoprotein
RA	3,994,076	A→T	93.1%	L114* (TTA→TAA)	yigE ←	DUF2233 family protein
RA	3,994,247	A→T	93.4%	V57E (GTG→GAG)	yigE ←	DUF2233 family protein
RA	3,997,389	C→A	11.3%	M50I (ATG→ATT)	rarD ←	putative chloramphenical resistance permease
RA	3,998,903	C→A	6.1%	L228I (CTC→ATC)	pldA →	outer membrane phospholipase A
RA	4,009,667	T→C	17.7%	intergenic (‑138/‑124)	ysgA ← / → udp	putative carboxymethylenebutenolidase/uridine phosphorylase
RA	4,009,705	G→A	94.0%	intergenic (‑176/‑86)	ysgA ← / → udp	putative carboxymethylenebutenolidase/uridine phosphorylase
RA	4,024,827	G→T	46.1%	D103Y (GAT→TAT)	pepQ →	proline dipeptidase
RA	4,035,421	G→T	50.6%	intergenic (‑62/‑8)	mobA ← / → yihD	molybdopterin‑guanine dinucleotide synthase/DUF1040 protein YihD
RA	4,039,399	G→T	25.2%	F188L (TTC→TTA)	yihG ←	inner membrane protein, inner membrane acyltransferase
RA	4,046,172	A→T	39.4%	K256N (AAA→AAT)	hemN →	coproporphyrinogen III oxidase, SAM and NAD(P)H dependent, oxygen‑independent
RA	4,056,018	T→A	91.9%	F138I (TTC→ATC)	yihN →	MFS transporter family protein
RA	4,062,424	G→T	90.9%	I71I (ATC→ATA)	yihQ ←	alpha‑glucosidase
RA	4,066,133	T→G	93.9%	S267R (AGC→CGC)	yihU ←	gamma‑hydroxybutyrate dehydrogenase, NADH‑dependent
RA	4,068,208	C→A	92.7%	G60G (GGC→GGA)	yihW →	DeoR family putative transcriptional regulator
RA	4,094,362	C→A	100%	W181L (TGG→TTG)	cpxA ←	sensory histidine kinase in two‑component regulatory system with CpxR
RA	4,096,555	G→T	8.6%	S53S (TCG→TCT)	fieF →	ferrous iron and zinc transporter
RA	4,097,822	G→T	93.1%	E115* (GAA→TAA)	pfkA →	6‑phosphofructokinase I
RA	4,108,097	A→C	6.9%	intergenic (‑79/‑346)	glpF ← / → zapB	glycerol facilitator/FtsZ stabilizer; septal ring assembly factor, stimulates cell division
RA	4,112,557	T→G	5.8%	K237N (AAA→AAC)	ftsN ←	essential cell division protein
RA	4,122,248	A→T	46.3%	intergenic (+53/‑296)	metL → / → metF	Bifunctional aspartokinase/homoserine dehydrogenase 2/5,10‑methylenetetrahydrofolate reductase
RA	4,127,022	T→G	92.9%	E188D (GAA→GAC)	yijF ←	DUF1287 family protein
RA	4,143,375	A→G	6.6%	intergenic (‑349/+249)	ppc ← / ← argE	phosphoenolpyruvate carboxylase/acetylornithine deacetylase
RA	4,143,544	C→T	5.0%	intergenic (‑518/+80)	ppc ← / ← argE	phosphoenolpyruvate carboxylase/acetylornithine deacetylase
RA	4,143,605	G→T	15.5%	intergenic (‑579/+19)	ppc ← / ← argE	phosphoenolpyruvate carboxylase/acetylornithine deacetylase
RA	4,144,697	C→A	13.2%	A27S (GCA→TCA)	argE ←	acetylornithine deacetylase
RA	4,158,047	G→T	13.4%	noncoding (1461/1542 nt)	rrsB →	16S ribosomal RNA of rrnB operon
RA	4,163,151	G→T	5.3%	V48F (GTT→TTT)	birA →	bifunctional biotin‑[acetylCoA carboxylase] holoenzyme synthetase/ DNA‑binding transcriptional repressor, bio‑5'‑AMP‑binding
RA	4,163,570	T→A	18.0%	I187I (ATT→ATA)	birA →	bifunctional biotin‑[acetylCoA carboxylase] holoenzyme synthetase/ DNA‑binding transcriptional repressor, bio‑5'‑AMP‑binding
RA	4,167,908	T→A	25.5%	W80R (TGG→AGG)	nusG →	transcription termination factor
RA	4,173,145	A→T	46.6%	Q658L (CAG→CTG)	rpoB →	RNA polymerase, beta subunit
RA	4,176,823	G→T	100%	D516Y (GAC→TAC)	rpoC →	RNA polymerase, beta prime subunit
RA	4,178,758	G→T	15.8%	G1161C (GGT→TGT)	rpoC →	RNA polymerase, beta prime subunit
RA	4,183,054	C→A	16.4%	A151S (GCG→TCG)	thiF ←	adenylyltransferase, modifies ThiS C‑terminus
RA	4,207,552	G→T	47.8%	M172I (ATG→ATT)	aceA →	isocitrate lyase
RA	4,207,558	G→T	8.9%	A174A (GCG→GCT)	aceA →	isocitrate lyase
RA	4,211,576	G→T	100%	S280R (AGC→AGA)	arpA ←	ankyrin repeat protein
RA	4,211,803	G→A	100%	P205S (CCT→TCT)	arpA ←	ankyrin repeat protein
RA	4,214,563	A→T	43.2%	T270S (ACC→TCC)	metH →	homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent
RA	4,218,928	G→A	9.4%	E424K (GAA→AAA)	yjbB →	putative Na+/Pi‑cotransporter
RA	4,219,081	C→A	24.5%	R475S (CGC→AGC)	yjbB →	putative Na+/Pi‑cotransporter
RA	4,230,913	A→T	92.8%	W424R (TGG→AGG)	xylE ←	D‑xylose transporter
RA	4,235,869	G→T	44.0%	A160E (GCG→GAG)	malE ←	maltose transporter subunit
RA	4,241,633	C→T	14.6%	pseudogene (745/1323 nt)	yjbI →	pseudogene, SopA‑related, pentapeptide repeats‑containing
RA	4,242,509	C→T	42.7%	L26F (CTC→TTC)	ubiC →	chorismate‑‑pyruvate lyase
RA	4,265,064	C→A	87.4%	intergenic (‑95/‑335)	yjcB ← / → yjcC	putative inner membrane protein/putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	4,268,967	A→T	28.7%	S187S (TCA→TCT)	yjcD →	inner membrane putative guanine permease
RA	4,271,906	C→T	16.8%	E366E (GAG→GAA)	yjcF ←	pentapeptide repeats protein
RA	4,273,297	A→T	18.9%	W512R (TGG→AGG)	actP ←	acetate transporter
RA	4,274,926	A→C	94.6%	I72M (ATT→ATG)	yjcH ←	DUF485 family inner membrane protein
RA	4,275,142	C→A	90.8%	intergenic (‑1/+199)	yjcH ← / ← acs	DUF485 family inner membrane protein/acetyl‑CoA synthetase
RA	4,285,893	A→C	5.7%	intergenic (+171/+360)	gltP → / ← yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA	4,286,214	T→C	6.6%	intergenic (+492/+39)	gltP → / ← yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA	4,290,080	G→T	100%	I256I (ATC→ATA)	mdtP ←	outer membrane factor of efflux pump
RA	4,297,485	G→C	50.2%	G44G (GGC→GGG)	alsK ←	D‑allose kinase
RA	4,297,846	C→A	94.6%	M150I (ATG→ATT)	alsE ←	allulose‑6‑phosphate 3‑epimerase
RA	4,300,333	T→A	19.9%	E155D (GAA→GAT)	alsA ←	fused D‑allose transporter subunits of ABC superfamily: ATP‑binding components
RA	4,303,614	T→A	93.2%	*150R (TGA→AGA)	rpiB →	ribose 5‑phosphate isomerase B/allose 6‑phosphate isomerase
RA	4,304,132	G→T	20.4%	intergenic (+118/+29)	yjdP → / ← phnP	putative periplasmic protein/5‑phospho‑alpha‑D‑ribosyl 1,2‑cyclic phosphate phosphodiesterase
RA	4,308,395	G→T	19.3%	H63N (CAC→AAC)	phnK ←	carbon‑phosphorus lyase complex subunit, putative ATP transporter ATP‑binding protein
RA	4,315,905	T→G	6.1%	intergenic (‑347/+311)	yjdN ← / ← yjdM	metalloprotein superfamily protein/zinc‑ribbon family protein
RA	4,330,426	Δ1 bp	100%	intergenic (‑88/+111)	adiA ← / ← melR	arginine decarboxylase/melibiose operon transcriptional regulator; autoregulator
RA	4,333,431	C→A	11.9%	I82I (ATC→ATA)	melB →	melibiose:sodium symporter
RA	4,336,681	A→T	14.5%	Y155N (TAC→AAC)	fumB ←	anaerobic class I fumarate hydratase (fumarase B)
RA	4,338,712	T→A	21.6%	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	92.3%	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	13.6%	V78V (GTG→GTT)	dtpC ←	dipeptide and tripeptide permease
RA	4,354,610	A→T	16.7%	W84R (TGG→AGG)	dsbD ←	fused thiol:disulfide interchange protein: activator of DsbC/conserved protein
RA	4,355,606	G→T	7.1%	H329N (CAT→AAT)	dcuA ←	C4‑dicarboxylate antiporter
RA	4,358,920	G→T	57.1%	R147L (CGC→CTC)	fxsA →	suppressor of F exclusion of phage T7
RA	4,371,380	G→T	7.9%	G252G (GGC→GGA)	frdA ←	fumarate reductase (anaerobic) catalytic and NAD/flavoprotein subunit
RA	4,372,891	A→T	13.6%	A144A (GCA→GCT)	epmA →	Elongation Factor P Lys34 lysyltransferase
RA	4,373,797	T→C	15.7%	L48L (TTA→CTA)	yjeM →	putative transporter
RA	4,376,178	C→A	46.2%	E1004* (GAA→TAA)	mscM ←	mechanosensitive channel protein, miniconductance
RA	4,378,778	G→T	46.2%	S137* (TCG→TAG)	mscM ←	mechanosensitive channel protein, miniconductance
RA	4,386,747	G→T	8.5%	R289L (CGT→CTT)	amiB →	N‑acetylmuramoyl‑l‑alanine amidase II
RA	4,388,902	G→T	91.9%	A558A (GCG→GCT)	mutL →	methyl‑directed mismatch repair protein
RA	4,394,875	G→T	44.6%	A124A (GCG→GCT)	purA →	adenylosuccinate synthetase
RA	4,396,598	A→T	100%	E43V (GAA→GTA)	rnr →	exoribonuclease R, RNase R
RA	4,396,680	C→A	9.4%	F70L (TTC→TTA)	rnr →	exoribonuclease R, RNase R
RA	4,402,850	G→T	42.5%	L2L (CTG→CTT)	yjfC →	ATP‑Grasp family ATPase
RA	4,402,870	G→T	11.1%	R9L (CGA→CTA)	yjfC →	ATP‑Grasp family ATPase
RA	4,405,735	G→T	17.8%	intergenic (+18/+99)	aidB → / ← yjfN	DNA alkylation damage repair protein; flavin‑containing DNA binding protein, weak isovaleryl CoA dehydrogenase/DUF1471 family periplasmic protein
RA	4,405,747	G→T	21.4%	intergenic (+30/+87)	aidB → / ← yjfN	DNA alkylation damage repair protein; flavin‑containing DNA binding protein, weak isovaleryl CoA dehydrogenase/DUF1471 family periplasmic protein
RA	4,411,145	T→G	17.7%	L450R (CTG→CGG)	ulaA →	L‑ascorbate‑specific enzyme IIC permease component of PTS
RA	4,413,467	G→T	7.5%	D269Y (GAT→TAT)	ulaE →	L‑xylulose 5‑phosphate 3‑epimerase
RA	4,417,551	A→C	89.1%	pseudogene (41/402 nt)	ytfA →	pseudogene, related to transcriptional regulators
RA	4,427,761	G→T	8.9%	A80S (GCC→TCC)	ytfI →	uncharacterized protein
RA	4,428,092	G→T	45.6%	G190V (GGA→GTA)	ytfI →	uncharacterized protein
RA	4,429,851	C→A	7.7%	P394P (CCG→CCT)	ytfL ←	UPF0053 family inner membrane protein
RA	4,439,193	C→A	8.1%	V93F (GTT→TTT)	ppa ←	inorganic pyrophosphatase
RA	4,440,321	C→A	14.8%	I181I (ATC→ATA)	ytfQ →	galactofuranose binding proteint: periplasmic‑binding component of ABC superfamily
RA	4,458,254	T→A	91.5%	V271V (GTT→GTA)	mgtA →	magnesium transporter
RA	4,458,609	G→T	93.4%	D390Y (GAT→TAT)	mgtA →	magnesium transporter
RA	4,462,966	A→T	26.7%	Y21N (TAT→AAT)	yjgH ←	UPF0131 family protein
RA	4,468,165	A→G	94.0%	intergenic (‑37/‑125)	argI ← / → rraB	ornithine carbamoyltransferase 1/protein inhibitor of RNase E
RA	4,469,550	G→A	87.8%	A2T (GCT→ACT)	yjgN →	DUF898 family inner membrane protein
RA	4,470,017	G→A	92.2%	M157I (ATG→ATA)	yjgN →	DUF898 family inner membrane protein
RA	4,470,873	G→T	48.5%	R928S (CGT→AGT)	valS ←	valyl‑tRNA synthetase
RA	4,474,526	C→A	16.8%	D415Y (GAC→TAC)	pepA ←	multifunctional aminopeptidase A: a cyteinylglycinase, transcription regulator and site‑specific recombination factor
RA	4,481,249	A→T	21.3%	V365E (GTG→GAG)	idnT ←	L‑idonate and D‑gluconate transporter
RA	4,494,721	G→A	45.5%	A283T (GCC→ACC)	yjhB →	putative transporter
RA	4,495,560	A→T	20.1%	N153Y (AAC→TAC)	yjhC →	putative oxidoreductase
RA	4,497,253	G→T	24.1%	pseudogene (240/255 nt)	insO →	pseudogene, IS911 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related
RA	4,512,693	T→A	91.5%	K407* (AAG→TAG)	yjhG ←	putative dehydratase
RA	4,518,092	A→C	8.0%	L215V (TTG→GTG)	sgcQ ←	putative nucleoside triphosphatase
RA	4,523,001	T→A	44.6%	intergenic (‑1/+55)	yjhP ← / ← yjhQ	putative methyltransferase/putative acetyltransferase
RA	4,525,234	G→A	95.0%	pseudogene (415/1029 nt)	yjhR →	pseudogene, helicase family; putative frameshift suppressor
RA	4,529,263	A→T	17.2%	L19* (TTA→TAA)	nanC ←	N‑acetylnuraminic acid outer membrane channel protein
RA	4,529,937	C→T	17.0%	intergenic (‑619/‑837)	nanC ← / → fimB	N‑acetylnuraminic acid outer membrane channel protein/tyrosine recombinase/inversion of on/off regulator of fimA
RA	4,530,002	C→A	22.2%	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	92.8%	I124F (ATT→TTT)	fimB →	tyrosine recombinase/inversion of on/off regulator of fimA
RA	4,531,451	A→G	7.3%	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	49.1%	intergenic (‑336/‑4)	gntP ← / → uxuA	fructuronate transporter/mannonate hydrolase
RA	4,541,609	G→T	5.6%	E53* (GAA→TAA)	uxuA →	mannonate hydrolase
RA	4,555,156	G→T	89.6%	A171E (GCG→GAG)	yjiM ←	putative 2‑hydroxyglutaryl‑CoA dehydratase
RA	4,562,043	C→A	100%	intergenic (+311/‑188)	yjiS → / → yjiT	DUF1127 family protein/pseudogene
RA	4,565,742	C→A	8.0%	pseudogene (2007/2937 nt)	yjiV →	pseudogene; conserved hypothetical protein
RA	4,569,865	G→T	5.4%	intergenic (+137/+20)	symR → / ← hsdS	sRNA antisense regulator destabilizing divergent and overlapping symE mRNA/specificity determinant for hsdM and hsdR
RA	4,571,233	G→A	46.7%	S16F (TCT→TTT)	hsdS ←	specificity determinant for hsdM and hsdR
RA	4,584,381	G→T	91.7%	I53I (ATC→ATA)	yjjL ←	L‑galactonate transporter
RA	4,584,756	A→T	32.6%	*305K (TAA→AAA)	yjjM ←	yjjMN operon transcriptional activator
RA	4,585,338	A→T	89.0%	S111T (TCT→ACT)	yjjM ←	yjjMN operon transcriptional activator
RA	4,590,074	A→C	15.0%	V240G (GTA→GGA)	dnaC ←	DNA biosynthesis protein
RA	4,591,139	C→A	47.6%	D66Y (GAT→TAT)	dnaT ←	DNA biosynthesis protein (primosomal protein I)
RA	4,594,244	T→G	12.8%	L90V (TTA→GTA)	bglJ →	bgl operon transcriptional activator
RA	4,596,243	T→A	44.1%	intergenic (‑25/+243)	leuQ ← / ← rsmC	tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase, SAM‑dependent
RA	4,624,581	C→A	19.3%	E183* (GAA→TAA)	rob ←	right oriC‑binding transcriptional activator, AraC family
RA	4,625,288	T→C	89.8%	intergenic (‑161/‑50)	rob ← / → creA	right oriC‑binding transcriptional activator, AraC family/putative periplasmic protein
RA	4,628,095	G→T	6.7%	R34L (CGT→CTT)	creD →	inner membrane protein
RA	4,629,649	A→T	16.3%	Y159N (TAC→AAC)	arcA ←	response regulator in two‑component regulatory system with ArcB or CpxA
RA	4,629,850	C→T	15.3%	G92S (GGC→AGC)	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	373840	375095	1256	152 [148]	[150] 151	frmA–[frmR]	frmA,[frmR]
*	*	÷	CP009273	4100615	4101517	903	152 [150]	[149] 154	tpiA	tpiA

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	360104 =	212 (0.840)	167 (0.660)	93/278	NT	44.1%	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)	4676 (19.740) +TTAATTAA	195/262	NT	94.8%	intergenic (‑212/+383)	lacZ/lacI	pseudogene, truncated/DNA‑binding transcriptional repressor
	?	CP009273	= 361823	270 (1.070)					coding (831/834 nt)	mhpR	mhp operon transcriptional activator
*	?	CP009273	360652 =	306 (1.220)	4526 (27.000) +46 bp	184/186	NT	96.1%	intergenic (‑586/+9)	lacZ/lacI	pseudogene, truncated/DNA‑binding transcriptional repressor
	?	CP009273	= 1317577	245 (0.970)					coding (101/882 nt)	yciV	PHP domain protein
*	?	CP009273	376716 =	NA (NA)	204 (0.810)	123/278	NT	96.2%	intergenic (‑1/‑91)	yaiX/insC1	pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase/IS2 repressor TnpA
	?	CP009273	566411 =	8 (0.030)					coding (63/552 nt)	ybcL	inactive polymorphonuclear leukocyte migration suppressor; DLP12 prophage; secreted protein, UPF0098 family
*	?	CP009273	= 378046	NA (NA)	230 (0.910)	134/278	NT	96.6%	intergenic (+11/+1)	insD1/yaiX	IS2 transposase TnpB/pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase
	?	CP009273	= 566415	8 (0.030)					coding (67/552 nt)	ybcL	inactive polymorphonuclear leukocyte migration suppressor; DLP12 prophage; secreted protein, UPF0098 family
*	?	CP009273	1203246 =	57 (0.230)	37 (0.170)	26/246	NT	40.4%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	CP009273	1205075 =	59 (0.270)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	CP009273	= 1203261	59 (0.230)	67 (0.300)	42/246	NT	54.7%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	CP009273	= 1205058	59 (0.270)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	CP009273	1635219 =	13 (0.050)	189 (0.760)	104/274	NT	93.6%	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	11 (0.040)	251 (1.000)	135/278	NT	95.8%	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)	21 (0.080)	15/278	NT	9.2%	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 =	207 (0.820)					coding (502/651 nt)	rcsB	response regulator in two‑component regulatory system with RcsC and YojN
*	?	CP009273	= 2310161	204 (0.810)	16 (0.060)	12/278	NT	7.3%	coding (506/651 nt)	rcsB	response regulator in two‑component regulatory system with RcsC and YojN
	?	CP009273	= 2991050	NA (NA)					noncoding (1/1331 nt)	IS2	repeat region
*	?	CP009273	= 2811301	169 (0.670)	24 (0.110)	17/238	NT	12.9%	intergenic (‑82/+117)	argQ/argZ	tRNA‑Arg/tRNA‑Arg
	?	CP009273	2811851 =	180 (0.840)					noncoding (58/77 nt)	argV	tRNA‑Arg
*	?	CP009273	= 3180783	NA (NA)	111 (0.450)	71/274	NT	47.2%	pseudogene (4/2445 nt)	yqiG	pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein
	?	CP009273	= 3833569	126 (0.500)					intergenic (‑216/‑6)	nlpA/yicS	cytoplasmic membrane lipoprotein‑28/putative periplasmic protein
*	?	CP009273	3833562 =	130 (0.520)	86 (0.340)	65/276	NT	40.0%	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