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	86.7%	intergenic (+124/‑90)	thrC → / → yaaX	L‑threonine synthase/DUF2502 family putative periplasmic protein
RA	10,444	G→T	82.4%	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	85.0%	D114Y (GAC→TAC)	lspA →	prolipoprotein signal peptidase (signal peptidase II)
RA	28,818	G→T	17.2%	D149Y (GAC→TAC)	dapB →	dihydrodipicolinate reductase
RA	29,139	G→T	84.0%	G256C (GGT→TGT)	dapB →	dihydrodipicolinate reductase
RA	37,692	G→T	8.7%	Q45K (CAG→AAG)	caiC ←	putative crotonobetaine/carnitine‑CoA ligase
RA	41,442	G→T	9.9%	R164S (CGC→AGC)	caiT ←	putative transporter
RA	49,840	G→T	80.0%	A6A (GCG→GCT)	folA →	dihydrofolate reductase
RA	55,590	G→T	84.0%	T507K (ACG→AAG)	lptD ←	LPS assembly OM complex LptDE, beta‑barrel component
RA	56,677	G→T	88.0%	R145S (CGC→AGC)	lptD ←	LPS assembly OM complex LptDE, beta‑barrel component
RA	68,547	G→T	13.0%	R237L (CGC→CTC)	yabI →	DedA family inner membrane protein
RA	80,123	C→T	64.6%	G25S (GGC→AGC)	leuL ←	leu operon leader peptide
RA	81,562	C→A	87.5%	I236I (ATC→ATA)	leuO →	global transcription factor
RA	85,890	G→T	17.1%	intergenic (+371/‑231)	cra → / → mraZ	transcriptional repressor‑activator for carbon metabolism/RsmH methytransferase inhibitor
RA	91,849	G→T	16.3%	R238L (CGT→CTT)	murF →	UDP‑N‑acetylmuramoyl‑tripeptide:D‑alanyl‑D‑ alanine ligase
RA	97,521	C→A	82.0%	A90A (GCC→GCA)	murC →	UDP‑N‑acetylmuramate:L‑alanine ligase
RA	103,467	G→T	90.7%	D142Y (GAT→TAT)	lpxC →	UDP‑3‑O‑acyl N‑acetylglucosamine deacetylase
RA	104,561	G→T	84.9%	A124S (GCG→TCG)	secM →	regulator of secA translation
RA	104,582	A→T	5.3%	T131S (ACG→TCG)	secM →	regulator of secA translation
RA	107,704	C→A	14.9%	V58V (GTC→GTA)	mutT →	nucleoside triphosphate pyrophosphohydrolase, marked preference for dGTP
RA	109,800	A→T	42.2%	intergenic (‑94/‑131)	coaE ← / → guaC	dephospho‑CoA kinase/GMP reductase
RA	118,873	G→T	89.8%	D99Y (GAC→TAC)	pdhR →	pyruvate dehydrogenase complex repressor; autorepressor
RA	132,639	T→A	15.5%	T105S (ACG→TCG)	speE ←	spermidine synthase (putrescine aminopropyltransferase)
RA	134,028	G→T	5.7%	A153A (GCG→GCT)	cueO →	multicopper oxidase (laccase)
RA	142,460	T→A	89.5%	F298Y (TTC→TAC)	yadE →	putative polysaccharide deacetylase lipoprotein
RA	153,472	G→T	87.1%	intergenic (‑102/+268)	yadN ← / ← folK	putative fimbrial‑like adhesin protein/2‑amino‑4‑hydroxy‑6‑hydroxymethyldihyropteridine pyrophosphokinase
RA	158,287	C→A	85.7%	D78Y (GAC→TAC)	ligT ←	2'‑5' RNA ligase
RA	158,587	G→T	12.5%	intergenic (‑69/‑5)	ligT ← / → hrpB	2'‑5' RNA ligase/putative ATP‑dependent helicase
RA	166,356	C→A	11.1%	S31* (TCG→TAG)	fhuC →	iron‑hydroxamate transporter subunit
RA	169,092	T→G	6.2%	L382V (TTG→GTG)	fhuB →	fused iron‑hydroxamate transporter subunits of ABC superfamily: membrane components
RA	179,424	G→T	14.7%	D159Y (GAT→TAT)	cdaR →	carbohydrate diacid regulon transcriptional regulator; autoregulator
RA	181,035	C→A	5.4%	P174P (CCG→CCT)	yaeI ←	phosphodiesterase with model substrate bis‑pNPP
RA	186,279	A→T	25.8%	noncoding (81/136 nt)	tff →	novel sRNA, function unknown
RA	186,633	C→A	10.4%	F91L (TTC→TTA)	rpsB →	30S ribosomal subunit protein S2
RA	205,796	C→A	14.3%	P230Q (CCG→CAG)	accA →	acetyl‑CoA carboxylase, carboxytransferase, alpha subunit
RA	230,579	C→T	100%	E231K (GAA→AAA)	gloB ←	hydroxyacylglutathione hydrolase
RA	232,860	G→T	85.8%	D103Y (GAT→TAT)	dnaQ →	DNA polymerase III epsilon subunit
RA	233,931	G→A	25.7%	S37N (AGT→AAT)	yafT →	lipoprotein
RA	234,984	G→T	16.0%	I80I (ATC→ATA) ‡	ykfM ←	lethality reduction protein, putative inner membrane protein
RA	234,985	A→T	9.9%	I80N (ATC→AAC) ‡	ykfM ←	lethality reduction protein, putative inner membrane protein
RA	234,990	G→T	13.4%	F78L (TTC→TTA)	ykfM ←	lethality reduction protein, putative inner membrane protein
RA	234,994	G→T	24.1%	S77* (TCA→TAA)	ykfM ←	lethality reduction protein, putative inner membrane protein
RA	235,010	G→T	17.6%	L72I (CTT→ATT)	ykfM ←	lethality reduction protein, putative inner membrane protein
RA	235,019	C→A	20.3%	V69L (GTA→TTA)	ykfM ←	lethality reduction protein, putative inner membrane protein
RA	235,022	G→T	25.4%	H68N (CAT→AAT)	ykfM ←	lethality reduction protein, putative inner membrane protein
RA	235,035	G→T	12.4%	S63S (TCC→TCA) ‡	ykfM ←	lethality reduction protein, putative inner membrane protein
RA	235,036	G→T	14.5%	S63Y (TCC→TAC) ‡	ykfM ←	lethality reduction protein, putative inner membrane protein
RA	236,191	G→T	14.4%	V162V (GTC→GTA)	yafV ←	putative NAD(P)‑binding C‑N hydrolase family amidase
RA	236,234	A→T	6.7%	V148E (GTG→GAG)	yafV ←	putative NAD(P)‑binding C‑N hydrolase family amidase
RA	238,195	G→T	86.1%	V532V (GTC→GTA)	fadE ←	acyl coenzyme A dehydrogenase
RA	250,880	G→T	11.2%	P442T (CCG→ACG)	pepD ←	aminoacyl‑histidine dipeptidase (peptidase D)
RA	262,114	C→A	10.0%	D51Y (GAT→TAT)	yafY ←	lipoprotein, inner membrane; overproduction stimulates degP expression; CP4‑6 prophage
RA	266,079	G→T	12.5%	pseudogene (91/258 nt)	insN →	pseudogene, IS911 transposase A;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related
RA	274,735	A→T	86.6%	pseudogene (138/348 nt)	afuB ←	pseudogene, CP4‑6 prophage; ABC transporter permease family;Phage or Prophage Related
RA	283,636	A→C	6.1%	Q379H (CAA→CAC)	yagH →	CP4‑6 prophage; putative xylosidase/arabinosidase
RA	295,695	T→G	14.5%	E317D (GAA→GAC)	paoC ←	PaoABC aldehyde oxidoreductase, Moco‑containing subunit
RA	306,772	C→A	18.1%	L92F (TTG→TTT)	ecpR ←	putative transcriptional regulator for the ecp operon
RA	307,454	G→A	16.2%	intergenic (‑407/‑369)	ecpR ← / → ykgL	putative transcriptional regulator for the ecp operon/uncharacterized protein
JC JC	308,665	IS2 (–) +5 bp	13.9%	intergenic (‑177/+183)	ykgM ← / ← ykgR	50S ribosomal protein L31 type B; alternative L31 utilized during zinc limitation/uncharacterized protein
RA	312,532	G→A	90.4%	pseudogene (349/684 nt)	ykgA ←	pseudogene, AraC family;putative regulator; Not classified; putative ARAC‑type regulatory protein
RA	317,205	G→A	6.7%	intergenic (+413/‑114)	rclR → / → ykgE	reactive chlorine species (RCS)‑specific activator of the rcl genes/cysteine‑rich LutA family protein; putative electron transport chain YkgEFG component
RA	320,920	G→A	89.3%	S52S (AGC→AGT)	ykgH ←	putative inner membrane protein
RA	321,223	C→A	85.1%	intergenic (‑148/+65)	ykgH ← / ← betA	putative inner membrane protein/choline dehydrogenase, a flavoprotein
RA	344,800	G→T	70.4%	E136D (GAG→GAT)	prpB →	2‑methylisocitrate lyase
RA	345,428	T→C	5.9%	intergenic (+145/‑295)	prpB → / → prpC	2‑methylisocitrate lyase/2‑methylcitrate synthase
RA	347,382	G→T	22.5%	E153* (GAA→TAA)	prpD →	2‑methylcitrate dehydratase
RA	347,652	G→T	16.6%	E243* (GAA→TAA)	prpD →	2‑methylcitrate dehydratase
RA	348,024	G→T	13.2%	E367* (GAG→TAG)	prpD →	2‑methylcitrate dehydratase
RA	353,486	A→T	6.3%	intergenic (+321/+16)	codA → / ← cynR	cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor
RA	353,489	C→T	6.2%	intergenic (+324/+13)	codA → / ← cynR	cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor
RA	359,604	T→A	11.1%	pseudogene (463/1125 nt)	lacZ ←	pseudogene, truncated
RA	360,157	T→G	5.8%	intergenic (‑91/+504)	lacZ ← / ← lacI	pseudogene, truncated/DNA‑binding transcriptional repressor
RA	360,752	A→G	100%	V331A (GTG→GCG)	lacI ←	DNA‑binding transcriptional repressor
RA	361,454	G→T	14.0%	S97* (TCG→TAG)	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	86.4%	I165I (ATC→ATA)	mhpR ←	mhp operon transcriptional activator
RA	396,883	A→G	66.4%	Q14Q (CAA→CAG)	iraP →	anti‑RssB factor, RpoS stabilzer during Pi starvation; anti‑adapter protein
RA	402,340	G→T	89.2%	V160V (GTG→GTT)	aroL →	shikimate kinase II
RA	404,324	C→A	15.1%	pseudogene (260/342 nt)	ykiA →	pseudogene
RA	405,332	C→A	20.5%	P48P (CCG→CCT)	rdgC ←	nucleoid‑associated ssDNA and dsDNA binding protein; competitive inhibitor of RecA function
RA	405,758	G→T	20.0%	A53A (GCG→GCT)	mak →	manno(fructo)kinase
RA	406,075	C→A	88.0%	P159Q (CCG→CAG)	mak →	manno(fructo)kinase
RA	410,300	C→A	23.0%	A304S (GCG→TCG)	sbcC ←	exonuclease, dsDNA, ATP‑dependent
RA	411,027	G→T	86.6%	L61L (CTC→CTA)	sbcC ←	exonuclease, dsDNA, ATP‑dependent
RA	415,698	G→T	12.6%	V218F (GTT→TTT)	brnQ →	branched‑chain amino acid transport system 2 carrier protein; LIV‑II transport system for Ile, Leu, and Val
RA	417,789	G→T	11.6%	D450Y (GAT→TAT)	proY →	proline‑specific permease
RA	418,995	T→G	8.6%	L341R (CTG→CGG)	malZ →	maltodextrin glucosidase
RA	421,799	C→A	80.4%	I69I (ATC→ATA)	tgt →	tRNA‑guanine transglycosylase
RA	423,068	C→A	18.5%	A109E (GCG→GAG)	yajC →	SecYEG protein translocase auxillary subunit
RA	425,143	G→T	10.3%	T61T (ACG→ACT)	secF →	SecYEG protein translocase auxillary subunit
RA	433,551	G→T	86.8%	S14Y (TCC→TAC)	yajO ←	2‑carboxybenzaldehyde reductase
RA	434,663	A→C	87.5%	I324S (ATC→AGC)	dxs ←	1‑deoxyxylulose‑5‑phosphate synthase, thiamine triphosphate‑binding, FAD‑requiring
RA	435,336	G→T	87.5%	Q100K (CAG→AAG)	dxs ←	1‑deoxyxylulose‑5‑phosphate synthase, thiamine triphosphate‑binding, FAD‑requiring
RA	437,672	T→A	87.7%	V223E (GTG→GAG)	thiI →	tRNA s(4)U8 sulfurtransferase
RA	441,811	A→C	14.5%	I104M (ATT→ATG)	yajR ←	putative transporter
RA	444,489	G→A	89.8%	R537C (CGT→TGT)	cyoB ←	cytochrome o ubiquinol oxidase subunit I
RA	451,853	C→A	26.5%	T422N (ACC→AAC)	tig →	peptidyl‑prolyl cis/trans isomerase (trigger factor)
RA	453,656	T→A	5.5%	S259T (TCC→ACC)	clpX →	ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease
RA	456,298	T→A	86.6%	L652Q (CTG→CAG)	lon →	DNA‑binding ATP‑dependent protease La
RA	456,588	G→T	87.9%	D749Y (GAC→TAC)	lon →	DNA‑binding ATP‑dependent protease La
RA	462,448	C→A	21.3%	L107L (CTG→CTT)	ybaE ←	putative ABC superfamily transporter periplasmic‑binding protein
RA	469,770	C→A	7.3%	R283L (CGT→CTT)	tesB ←	acyl‑CoA thioesterase 2
RA	474,138	G→T	89.3%	intergenic (‑65/+99)	ylaB ← / ← ylaC	putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase/DUF1449 family inner membrane protein
RA	475,502	T→A	5.7%	intergenic (‑128/+44)	maa ← / ← hha	maltose O‑acetyltransferase/modulator of gene expression, with H‑NS
RA	475,805	C→A	88.7%	A120A (GCG→GCT)	tomB ←	Hha toxicity attenuator; conjugation‑related protein
RA	479,244	C→A	85.4%	A206S (GCC→TCC)	acrB ←	multidrug efflux system protein
RA	480,820	C→T	90.1%	D86N (GAC→AAC)	acrA ←	multidrug efflux system
RA	481,667	G→A	87.7%	A151T (GCG→ACG)	acrR →	transcriptional repressor
RA	511,619	A→T	7.1%	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	18.4%	L164F (TTA→TTT)	allS ←	allD operon transcriptional activator
RA	530,466	C→A	89.5%	F365L (TTC→TTA)	gcl →	glyoxylate carboligase
RA	535,649	G→A	5.3%	A349A (GCG→GCA)	allB →	allantoinase
RA	542,200	Δ1 bp	85.8%	coding (65/1668 nt)	fdrA →	putative NAD(P)‑binding acyl‑CoA synthetase
RA	546,491	G→T	89.9%	V199V (GTG→GTT)	ybcF →	putative carbonate kinase
RA	549,397	G→T	85.8%	intergenic (‑1/+2)	lpxH ← / ← ppiB	UDP‑2,3‑diacylglucosamine pyrophosphohydrolase/peptidyl‑prolyl cis‑trans isomerase B (rotamase B)
RA	552,831	A→T	6.7%	F123I (TTC→ATC)	folD ←	bifunctional 5,10‑methylene‑tetrahydrofolate dehydrogenase/ 5,10‑methylene‑tetrahydrofolate cyclohydrolase
RA	557,592	G→T	7.8%	D814Y (GAC→TAC)	sfmD →	putative outer membrane export usher protein
RA	560,919	G→T	21.7%	V172V (GTC→GTA)	intD ←	DLP12 prophage; putative phage integrase
RA	564,590	G→T	10.3%	G78V (GGA→GTA)	ybcK →	DLP12 prophage; putative recombinase
RA	572,364	G→A	20.1%	intergenic (‑83/‑490)	nmpC ← / → essD	DLP12 prophage; truncated outer membrane porin (pseudogene);IS, phage, Tn; Phage or Prophage Related; outer membrane porin protein; locus of qsr prophage/DLP12 prophage; putative phage lysis protein
RA	576,183	G→T	8.8%	intergenic (‑282/‑107)	ylcI ← / → nohD	DUF3950 family protein, DLP12 prophage/DLP12 prophage; DNA packaging protein
RA	576,998	G→T	87.7%	pseudogene (189/309 nt)	aaaD →	pseudogene; DLP12 prophage; tail fiber assembly protein family;Phage or Prophage Related
RA	581,203	A→T	81.4%	intergenic (‑114/‑310)	ompT ← / → pauD	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)/tRNA‑OTHER
RA	583,341	T→G	93.8%	S33R (AGT→CGT)	ybcH ←	PRK09936 family protein
RA	607,931	G→A	84.4%	S7F (TCC→TTC)	fepA ←	iron‑enterobactin outer membrane transporter
RA	609,813	C→A	13.0%	G67G (GGC→GGA)	entF →	enterobactin synthase multienzyme complex component, ATP‑dependent
RA	619,048	C→A	5.7%	A307S (GCC→TCC)	fepB ←	iron‑enterobactin transporter subunit
RA	625,364	G→T	79.9%	G5G (GGG→GGT)	cstA →	carbon starvation protein involved in peptide utilization; APC peptide transporter family protein
RA	639,231	G→A	85.6%	L65F (CTT→TTT)	rnk ←	regulator of nucleoside diphosphate kinase
RA	647,422	G→T	76.5%	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	86.8%	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	87.4%	F122L (TTC→TTA)	citA →	sensory histidine kinase in two‑component regulatory system with CitB
RA	650,141	G→T	10.0%	V428V (GTC→GTA)	dcuC ←	anaerobic C4‑dicarboxylate transport
RA	651,654	A→G	15.9%	intergenic (‑230/‑359)	dcuC ← / → pagP	anaerobic C4‑dicarboxylate transport/phospholipid:lipid A palmitoyltransferase
RA	652,865	Δ1 bp	86.9%	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	86.5%	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	666,998	G→T	8.6%	L22I (CTT→ATT)	holA ←	DNA polymerase III, delta subunit
RA	667,017	T→G	12.8%	E15D (GAA→GAC)	holA ←	DNA polymerase III, delta subunit
RA	667,638	C→A	13.7%	R2L (CGA→CTA)	lptE ←	LPS assembly OM complex LptDE, lipoprotein component
RA	672,142	T→A	5.6%	intergenic (‑139/‑25)	ybeQ ← / → ybeR	Sel1 family TPR‑like repeat protein/uncharacterized protein
RA	681,257	C→A	12.2%	V43V (GTG→GTT)	gltK ←	glutamate, aspartate ABC transporter permease subunit
RA	681,488	G→T	7.9%	T213N (ACC→AAC)	gltJ ←	glutamate, aspartate ABC transporter permease subunit
RA	689,079	C→A	8.2%	E445* (GAA→TAA)	miaB ←	tRNA‑i(6)A37 methylthiotransferase
RA	697,299	G→T	12.8%	N303K (AAC→AAA)	nagA ←	N‑acetylglucosamine‑6‑phosphate deacetylase
RA	698,274	C→T	14.2%	G265D (GGT→GAT)	nagB ←	glucosamine‑6‑phosphate deaminase
RA	699,801	G→T	15.1%	P134P (CCG→CCT)	nagE →	fused N‑acetyl glucosamine specific PTS enzyme: IIC, IIB, and IIA components
RA	704,018	G→T	10.4%	D77Y (GAT→TAT)	chiP →	chitoporin, uptake of chitosugars
RA	705,588	C→A	86.4%	intergenic (+16/+68)	chiQ → / ← fur	chitosugar‑induced verified lipoprotein/ferric iron uptake regulon transcriptional repressor; autorepressor
RA	706,097	A→C	7.2%	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	18.2%	intergenic (‑4/+206)	uof ← / ← fldA	ryhB‑regulated fur leader peptide/flavodoxin 1
RA	715,467	A→T	12.6%	F150L (TTT→TTA)	speF ←	ornithine decarboxylase isozyme, inducible
RA	724,813	A→T	82.7%	intergenic (+17/‑226)	ybfA → / → rhsC	DUF2517 family protein/Rhs family putative polymorphic toxin
RA	725,650	G→T	7.8%	P204P (CCG→CCT)	rhsC →	Rhs family putative polymorphic toxin
RA	732,494	G→T	8.8%	pseudogene (214/1137 nt)	ybfL →	pseudogene, DDE domain transposase family;putative factor; Not classified; putative receptor protein
RA	733,191	A→T	16.1%	pseudogene (911/1137 nt)	ybfL →	pseudogene, DDE domain transposase family;putative factor; Not classified; putative receptor protein
RA	735,322	G→T	23.0%	A120A (GCG→GCT)	phr →	deoxyribodipyrimidine photolyase, FAD‑binding
RA	739,280	A→C	18.5%	S78R (AGC→CGC)	ybgJ →	putative allophanate hydrolase, subunit 1
RA	743,278	G→A	10.9%	intergenic (‑53/+99)	abrB ← / ← ybgO	regulator of aidB expression; inner membrane protein/putative fimbrial protein
RA	750,112	A→T	5.8%	intergenic (‑188/‑521)	gltA ← / → sdhC	citrate synthase/succinate dehydrogenase, membrane subunit, binds cytochrome b556
RA	754,572	G→T	81.3%	E137D (GAG→GAT)	sucA →	2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding
RA	759,000	C→A	84.1%	F177L (TTC→TTA)	sucC →	succinyl‑CoA synthetase, beta subunit
RA	777,514	G→T	17.4%	intergenic (+406/‑27)	lysQ → / → nadA	tRNA‑Lys/quinolinate synthase, subunit A
RA	781,965	G→T	11.9%	E293* (GAA→TAA)	aroG →	3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, phenylalanine repressible
RA	788,902	G→T	81.7%	R115S (CGT→AGT)	modF ←	fused molybdate transporter subunits of ABC superfamily: ATP‑binding components
RA	800,488	G→T	83.8%	V510V (GTG→GTT)	ybhJ →	putative hydratase
RA	800,779	G→T	87.0%	E607D (GAG→GAT)	ybhJ →	putative hydratase
RA	805,693	A→C	6.8%	E298D (GAA→GAC)	bioB →	biotin synthase
RA	808,977	G→T	13.4%	intergenic (+574/‑5)	bioD → / → uvrB	dethiobiotin synthetase/excinulease of nucleotide excision repair, DNA damage recognition component
RA	812,743	G→T	13.0%	D82Y (GAT→TAT)	moaA →	molybdopterin biosynthesis protein A
RA	816,078	C→G	7.4%	intergenic (+34/‑171)	ybhL → / → ybhM	UPF0005 family inner membrane protein/UPF0005 family inner membrane protein
RA	816,095	T→A	5.2%	intergenic (+51/‑154)	ybhL → / → ybhM	UPF0005 family inner membrane protein/UPF0005 family inner membrane protein
RA	816,292	A→T	6.2%	H15L (CAC→CTC)	ybhM →	UPF0005 family inner membrane protein
RA	828,374	G→T	92.4%	V11V (GTC→GTA)	ybiA ←	DUF1768 family protein
RA	832,445	G→T	88.4%	P213P (CCG→CCT)	ybiC →	putative dehydrogenase
RA	833,437	G→A	13.4%	intergenic (‑56/+209)	ybiJ ← / ← ybiI	DUF1471 family putative periplasmic protein/DksA‑type zinc finger protein
RA	833,711	C→A	19.6%	D68Y (GAT→TAT)	ybiI ←	DksA‑type zinc finger protein
RA	843,299	C→A	76.6%	W54C (TGG→TGT)	glnH ←	glutamine transporter subunit
RA	844,378	C→A	8.1%	intergenic (‑11/+288)	dps ← / ← rhtA	Fe‑binding and storage protein; stress‑inducible DNA‑binding protetin/threonine and homoserine efflux system
RA	853,232	C→A	14.9%	intergenic (+221/+20)	ybiT → / ← ybiU	putative transporter subunit of ABC superfamily: ATP‑binding component/DUF1479 family protein
RA	861,323	T→A	13.3%	S166S (TCA→TCT)	moeA ←	molybdopterin molybdenumtransferase; molybdopterin biosynthesis protein
RA	862,542	A→T	15.6%	E173D (GAA→GAT)	iaaA →	Isoaspartyl peptidase
RA	863,481	T→G	20.6%	L169R (CTC→CGC)	gsiA →	glutathione transporter ATP‑binding protein, ABC superfamily
RA	868,473	A→C	10.0%	I13I (ATA→ATC)	yliE →	putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	876,447	G→A	88.2%	D89N (GAT→AAT)	dacC →	D‑alanyl‑D‑alanine carboxypeptidase (penicillin‑binding protein 6a)
RA	877,482	C→A	7.5%	D237Y (GAT→TAT)	deoR ←	deoxyribose‑5‑phosphate‑inducible deoxyribose operon transcriptional repressor; repressor of nupG and tsx
RA	879,085	G→T	87.7%	intergenic (‑241/‑44)	ybjG ← / → mdfA	undecaprenyl pyrophosphate phosphatase/multidrug efflux system protein
RA	881,695	T→A	11.7%	L367F (TTA→TTT)	ybjJ ←	putative transporter
RA	896,109	T→C	18.8%	intergenic (‑78/+213)	artJ ← / ← artM	arginine binding protein, periplasmic/arginine transporter subunit
RA	899,961	T→A	14.1%	intergenic (‑38/‑88)	ybjP ← / → ybjQ	lipoprotein/UPF0145 family protein
RA	910,654	C→G	11.4%	intergenic (‑341/+154)	ybjE ← / ← aqpZ	putative transporter/aquaporin Z
RA	925,160	G→T	85.7%	S420* (TCA→TAA)	cydD ←	fused glutathione, cysteine exporter subunits of ABC superfamily: membrane component/ATP‑binding component
RA	925,355	A→T	7.5%	L355Q (CTG→CAG)	cydD ←	fused glutathione, cysteine exporter subunits of ABC superfamily: membrane component/ATP‑binding component
RA	925,957	A→T	6.8%	I154I (ATT→ATA)	cydD ←	fused glutathione, cysteine exporter subunits of ABC superfamily: membrane component/ATP‑binding component
RA	943,573	G→T	67.1%	A297S (GCC→TCC)	ycaM →	putative transporter
RA	955,568	A→T	6.0%	intergenic (+17/‑152)	aroA → / → ycaL	5‑enolpyruvylshikimate‑3‑phosphate synthetase/putative peptidase‑related chaperone
RA	968,415	G→T	85.0%	S148* (TCG→TAG)	ycbC ←	DUF218 superfamily protein
RA	973,038	G→T	13.6%	A419A (GCG→GCT)	mukB →	chromosome condensin MukBEF, ATPase and DNA‑binding subunit
RA	988,954	C→A	11.8%	G183C (GGC→TGC)	ssuB ←	alkanesulfonate transporter subunit
RA	991,460	A→T	15.1%	L314Q (CTG→CAG)	ssuA ←	aliphatic sulfonate binding protein, SsuABC ABC transporter
RA	993,869	C→T	14.7%	intergenic (+6/‑77)	elfA → / → elfD	laminin‑binding fimbrin subunit/putative periplasmic pilin chaperone
RA	997,965	G→T	10.0%	D235Y (GAT→TAT)	elfG →	putative fimbrial‑like adhesin protein
RA	1,020,762	C→A	17.3%	A279E (GCG→GAG)	helD →	DNA helicase IV
RA	1,042,107	G→T	15.9%	T432K (ACA→AAA)	gfcD ←	putative O‑antigen capsule production periplasmic protein
RA	1,045,159	C→A	15.0%	L14F (TTG→TTT)	gfcA ←	O‑antigen capsule production threonine‑rich inner membrane protein
RA	1,048,928	C→A	66.4%	E903* (GAA→TAA)	torS ←	hybrid sensory histidine kinase in two‑component regulatory system with TorR
RA	1,049,407	G→T	86.7%	T743K (ACG→AAG)	torS ←	hybrid sensory histidine kinase in two‑component regulatory system with TorR
RA	1,077,911	A→C	90.3%	K71N (AAA→AAC)	efeO →	inactive ferrous ion transporter EfeUOB
RA	1,083,443	G→T	8.0%	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	62.6%	L404* (TTA→TAA)	pgaB ←	poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine (PGA) N‑deacetylase outer membrane export lipoprotein
RA	1,086,516	T→A	15.9%	V410V (GTA→GTT)	pgaA ←	biofilm adhesin polysaccharide PGA secretin; OM porin; poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine export protein
RA	1,116,964	A→G	88.9%	intergenic (‑21/+53)	dinI ← / ← pyrC	DNA damage‑inducible protein I/dihydro‑orotase
RA	1,151,750	G→T	86.0%	R178L (CGC→CTC)	holB →	DNA polymerase III, delta prime subunit
RA	1,152,278	G→T	86.5%	E16* (GAA→TAA)	ycfH →	putative DNase
RA	1,169,335	G→T	18.8%	T29K (ACG→AAG)	mfd ←	transcription‑repair coupling factor
RA	1,170,302	G→T	17.5%	A107E (GCG→GAG)	ycfT ←	inner membrane protein
RA	1,181,431	G→T	9.6%	E44D (GAG→GAT)	pepT →	peptidase T
RA	1,191,676	C→T	17.3%	H366H (CAC→CAT)	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,688	C→T	13.3%	T370T (ACC→ACT)	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,701	T→C	12.1%	L375L (TTA→CTA) ‡	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,703	A→G	12.2%	L375L (TTA→TTG) ‡	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,733	C→T	7.4%	N385N (AAC→AAT)	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,736	G→C	7.4%	A386A (GCG→GCC)	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,739	A→G	5.7%	K387K (AAA→AAG)	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,193,516	T→G	24.3%	N60H (AAT→CAT)	ymfE ←	e14 prophage; putative inner membrane protein
RA	1,193,873	G→T	86.9%	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	9.5%	S15* (TCA→TAA)	lit →	e14 prophage; cell death peptidase, inhibitor of T4 late gene expression
RA	1,211,169	C→A	84.0%	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	1,212,835	G→A	5.1%	G18S (GGT→AGT)	ycgG →	putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	1,219,533	A→G	88.4%	intergenic (+170/+202)	ycgI → / ← minE	pseudogene/cell division topological specificity factor
RA	1,220,996	G→T	87.5%	R181R (CGG→AGG)	minC ←	cell division inhibitor
RA	1,224,292	G→A	87.4%	D8N (GAT→AAT)	ycgN →	UPF0153 family cysteine cluster protein
RA	1,226,292	T→A	92.4%	C24S (TGT→AGT)	umuD →	DNA polymerase V, subunit D
RA	1,227,613	C→A	5.1%	N324K (AAC→AAA)	umuC →	DNA polymerase V, subunit C
RA	1,228,591	G→T	86.2%	intergenic (‑105/+41)	dsbB ← / ← nhaB	oxidoreductase that catalyzes reoxidation of DsbA protein disulfide isomerase I/sodium:proton antiporter
RA	1,251,120	T→A	6.0%	T97S (ACC→TCC)	ycgV ←	putative adhesin
RA	1,277,786	G→A	82.9%	D823N (GAC→AAC)	narG →	nitrate reductase 1, alpha subunit
RA	1,288,669	A→T	8.3%	intergenic (‑291/‑314)	hns ← / → tdk	global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
RA	1,301,604	A→T	18.3%	I433I (ATT→ATA)	clsA ←	cardiolipin synthase 1
RA	1,320,990	A→T	12.4%	intergenic (+92/‑119)	yciQ → / → rluB	enhancer of membrane protein expression; putative inner membrane protein/23S rRNA pseudouridine(2605) synthase
RA	1,322,140	T→A	89.3%	T159S (ACG→TCG)	btuR ←	cob(I)yrinic acid a,c‑diamide adenosyltransferase
RA	1,327,148	T→G	15.8%	V615G (GTA→GGA)	topA →	DNA topoisomerase I, omega subunit
RA	1,329,391	G→A	14.2%	S4N (AGT→AAT)	ymiA →	uncharacterized protein
RA	1,337,533	G→T	87.6%	A18E (GCA→GAA)	osmB ←	lipoprotein
RA	1,345,484	A→C	9.4%	intergenic (‑188/+180)	fabI ← / ← ycjD	enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent/DUF559 family endonuclease‑related protein
RA	1,345,918	C→A	15.8%	D34Y (GAT→TAT)	ycjD ←	DUF559 family endonuclease‑related protein
RA	1,365,283	G→T	90.9%	E271* (GAG→TAG)	ycjM →	alpha amylase catalytic domain family protein
RA	1,369,694	G→A	19.5%	D159N (GAT→AAT)	ycjQ →	putative Zn‑dependent NAD(P)‑binding oxidoreductase
JC JC	1,376,043	IS5 (–) +4 bp	86.3%	pseudogene (10‑13/126 nt)	ycjV →	pseudogene; putative ATP‑binding component of a transport system
RA	1,377,394	C→T	90.0%	A275A (GCG→GCA)	ycjW ←	LacI family putative transcriptional repressor
RA	1,385,964	T→G	11.7%	Q49H (CAA→CAC)	ycjY ←	S9 homolog non‑peptidase family protein
RA	1,386,008	G→T	87.7%	Q35K (CAG→AAG)	ycjY ←	S9 homolog non‑peptidase family protein
RA	1,388,406	G→T	85.9%	R308L (CGC→CTC)	mppA →	murein tripeptide (L‑ala‑gamma‑D‑glutamyl‑meso‑DAP) transporter subunit
RA	1,396,370	G→T	5.2%	N381K (AAC→AAA)	abgB ←	p‑aminobenzoyl‑glutamate hydrolase, B subunit
RA	1,397,285	G→T	11.9%	I76I (ATC→ATA)	abgB ←	p‑aminobenzoyl‑glutamate hydrolase, B subunit
RA	1,414,576	C→T	13.7%	intergenic (‑78/‑46)	racR ← / → ydaS	Rac prophage; putative DNA‑binding transcriptional regulator/Rac prophage; putative DNA‑binding transcriptional regulator
RA	1,424,234	C→A	83.2%	S310* (TCA→TAA)	stfR →	Rac prophage; putative tail fiber protein
JC JC	1,428,894	IS2 (–) +5 bp	85.6%	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	9.3%	intergenic (‑519/+215)	ynaE ← / ← ttcC	cold shock protein, Rac prophage/pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related
RA	1,430,082	A→C	8.4%	F357V (TTC→GTC)	ompN ←	outer membrane pore protein N, non‑specific
RA	1,438,433	G→T	13.1%	D376Y (GAT→TAT)	ydbH →	putative membrane‑anchored protein, function unknown
RA	1,439,234	G→T	14.7%	D643Y (GAT→TAT)	ydbH →	putative membrane‑anchored protein, function unknown
RA	1,439,518	C→A	66.8%	S737S (TCC→TCA)	ydbH →	putative membrane‑anchored protein, function unknown
RA	1,443,093	C→A	8.6%	L440I (CTC→ATC)	feaB →	phenylacetaldehyde dehydrogenase
RA	1,444,739	G→A	5.5%	P290S (CCC→TCC)	tynA ←	tyramine oxidase, copper‑requiring
RA	1,450,710	A→T	13.0%	T8T (ACA→ACT)	paaE →	ring 1,2‑phenylacetyl‑CoA epoxidase, NAD(P)H oxidoreductase component
RA	1,451,422	A→T	6.3%	T246S (ACG→TCG)	paaE →	ring 1,2‑phenylacetyl‑CoA epoxidase, NAD(P)H oxidoreductase component
RA	1,454,724	G→T	71.7%	G472C (GGT→TGT)	paaH →	3‑hydroxyadipyl‑CoA dehydrogenase, NAD+‑dependent
RA	1,460,887	G→C	6.7%	pseudogene (1239/2513 nt)	ydbA →	pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA	1,460,896	C→T	6.5%	pseudogene (1248/2513 nt)	ydbA →	pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA	1,477,840	G→T	6.0%	D175Y (GAC→TAC)	hrpA →	putative ATP‑dependent helicase
RA	1,481,732	G→A	15.9%	A81T (GCC→ACC)	ydcF →	DUF218 superfamily protein, SAM‑binding
RA	1,515,250	G→T	5.7%	V691V (GTC→GTA)	yncD ←	putative iron outer membrane transporter
RA	1,516,408	T→G	5.8%	E305D (GAA→GAC)	yncD ←	putative iron outer membrane transporter
RA	1,519,349	T→A	94.8%	K297* (AAA→TAA)	ansP ←	L‑asparagine transporter
RA	1,541,486	A→T	11.8%	intergenic (‑60/‑172)	yddG ← / → fdnG	aromatic amino acid exporter/formate dehydrogenase‑N, alpha subunit, nitrate‑inducible
RA	1,545,377	T→A	13.4%	G220G (GGT→GGA)	fdnH →	formate dehydrogenase‑N, Fe‑S (beta) subunit, nitrate‑inducible
RA	1,548,144	G→T	89.5%	intergenic (‑49/+85)	adhP ← / ← maeA	ethanol‑active dehydrogenase/acetaldehyde‑active reductase/malate dehydrogenase, (decarboxylating, NAD‑requiring) (malic enzyme)
RA	1,554,204	A→T	17.8%	L328* (TTG→TAG)	ddpB ←	D‑ala‑D‑ala transporter subunit
RA	1,555,972	T→A	13.2%	D256V (GAT→GTT)	ddpA ←	D‑ala‑D‑a la transporter subunit
RA	1,558,906	G→T	9.7%	A362E (GCG→GAG)	dosP ←	oxygen sensor, c‑di‑GMP phosphodiesterase, heme‑regulated; cold‑ and stationary phase‑induced bioflim regulator
RA	1,563,276	G→T	86.3%	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	6.3%	intergenic (‑90/+272)	gadB ← / ← pqqL	glutamate decarboxylase B, PLP‑dependent/putative periplasmic M16 family zinc metalloendopeptidase
RA	1,575,339	G→T	79.2%	F481L (TTC→TTA)	ydeN ←	putative Ser‑type periplasmic non‑aryl sulfatase
RA	1,602,131	G→T	5.5%	D177Y (GAT→TAT)	tam →	trans‑aconitate methyltransferase
RA	1,603,440	G→A	77.5%	intergenic (‑161/+46)	yneE ← / ← uxaB	bestrophin family putative inner membrane protein/altronate oxidoreductase, NAD‑dependent
RA	1,604,418	C→A	9.4%	D174Y (GAC→TAC)	uxaB ←	altronate oxidoreductase, NAD‑dependent
RA	1,605,093	A→T	12.9%	intergenic (‑156/+71)	uxaB ← / ← yneF	altronate oxidoreductase, NAD‑dependent/putative membrane‑bound diguanylate cyclase
RA	1,605,117	A→C	15.2%	intergenic (‑180/+47)	uxaB ← / ← yneF	altronate oxidoreductase, NAD‑dependent/putative membrane‑bound diguanylate cyclase
RA	1,610,407	C→T	10.0%	P130S (CCC→TCC)	yneK →	uncharacterized protein
RA	1,612,820	T→A	7.6%	S116C (AGT→TGT)	marC ←	UPF0056 family inner membrane protein
RA	1,620,961	T→G	84.5%	Q226P (CAA→CCA)	dcp ←	dipeptidyl carboxypeptidase II
RA	1,628,207	G→A	86.6%	G110E (GGA→GAA)	pinQ →	Qin prophage; putative site‑specific recombinase
RA	1,661,763	C→A	88.4%	P353P (CCG→CCT)	mlc ←	glucosamine anaerobic growth regulon transcriptional repressor; autorepressor
RA	1,663,893	C→T	16.4%	intergenic (‑44/‑63)	ynfL ← / → ynfM	LysR family putative transcriptional regulator/putative arabinose efflux transporter
RA	1,673,421	T→A	11.0%	T246T (ACT→ACA)	ydgH →	DUF1471 family periplasmic protein
RA	1,690,805	C→A	13.8%	D169Y (GAT→TAT)	uidR ←	transcriptional repressor
RA	1,696,612	A→T	86.7%	E41D (GAA→GAT)	add →	adenosine deaminase
RA	1,698,876	G→T	16.6%	A23A (GCG→GCT)	blr →	beta‑lactam resistance membrane protein; divisome‑associated protein
RA	1,699,862	T→A	6.8%	L119* (TTG→TAG)	ydgK →	DUF2569 family inner membrane protein
RA	1,701,282	A→C	9.3%	Q36P (CAG→CCG)	rsxC →	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA	1,703,015	G→C	6.4%	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	10.1%	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	10.2%	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	6.0%	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	90.4%	R28Q (CGA→CAA)	tyrS ←	tyrosyl‑tRNA synthetase
RA	1,752,953	C→A	5.6%	T10T (ACG→ACT)	ldtE ←	murein L,D‑transpeptidase
RA	1,754,950	T→A	77.2%	I367F (ATT→TTT)	sufD ←	component of SufBCD Fe‑S cluster assembly scaffold
RA	1,764,150	G→T	7.1%	D274Y (GAT→TAT)	ydiK →	UPF0118 family inner membrane protein
RA	1,766,617	A→T	17.2%	intergenic (+75/‑152)	ydiM → / → ydiN	MFS superfamily sugar transport 1 family protein/MFS transporter superfamily protein
RA	1,770,281	T→A	83.8%	D146E (GAT→GAA)	ydiF →	putative acetyl‑CoA:acetoacetyl‑CoA transferase: alpha subunit/beta subunit
RA	1,773,528	C→A	5.5%	E11* (GAA→TAA)	ydiP ←	putative DNA‑binding transcriptional regulator
RA	1,781,314	T→A	17.9%	N19I (AAT→ATT)	ppsA ←	phosphoenolpyruvate synthase
RA	1,784,363	C→A	13.0%	R380L (CGT→CTT)	ydiU ←	UPF0061 family protein
RA	1,796,428	C→A	12.0%	V134F (GTC→TTC)	thrS ←	threonyl‑tRNA synthetase
RA	1,796,460	C→A	14.1%	R123L (CGG→CTG)	thrS ←	threonyl‑tRNA synthetase
RA	1,798,834	G→A	7.0%	pseudogene (1060/1476 nt)	arpB →	pseudogene, ankyrin repeats
RA	1,802,047	G→A	90.2%	intergenic (+100/‑6)	ydiZ → / → yniA	uncharacterized protein/fructosamine kinase family protein
RA	1,803,109	C→T	6.4%	A128T (GCC→ACC)	yniB ←	putative inner membrane protein
RA	1,805,071	C→A	12.4%	intergenic (+13/‑120)	ydjM → / → ydjN	inner membrane protein regulated by LexA/putative transporter
RA	1,821,696	A→T	11.7%	L274Q (CTG→CAG)	astB ←	succinylarginine dihydrolase
RA	1,823,835	A→C	7.3%	W53G (TGG→GGG)	astD ←	succinylglutamic semialdehyde dehydrogenase
RA	1,825,763	C→A	65.8%	A159A (GCG→GCT)	astC ←	succinylornithine transaminase, PLP‑dependent
RA	1,828,918	C→A	13.2%	V182V (GTC→GTA)	ydjY →	putative ferrodoxin‑like lipoprotein
RA	1,832,413	C→A	89.3%	L315L (CTC→CTA)	ynjC →	inner membrane putative ABC superfamily transporter permease
RA	1,833,730	C→A	86.3%	R3S (CGT→AGT)	ynjE →	molybdopterin synthase sulfurtransferase
RA	1,840,083	C→A	17.5%	D379Y (GAT→TAT)	topB ←	DNA topoisomerase III
RA	1,848,731	C→A	15.4%	A127A (GCG→GCT)	ydjF ←	putative DNA‑binding transcriptional regulator
RA	1,859,031	A→C	7.7%	intergenic (+40/+8)	yeaD → / ← yeaE	D‑hexose‑6‑phosphate epimerase‑like protein/aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent
RA	1,865,422	C→A	88.4%	R261R (CGA→AGA)	yeaI →	putative membrane‑anchored diguanylate cyclase
RA	1,867,537	C→A	10.2%	R414S (CGT→AGT)	yeaJ →	putative diguanylate cyclase
RA	1,872,520	G→T	88.4%	P183P (CCG→CCT)	yeaP →	diguanylate cyclase
RA	1,886,360	G→T	17.9%	A378E (GCG→GAG)	yoaA ←	putative ATP‑dependent helicase, DinG family
RA	1,909,342	T→A	89.4%	E150D (GAA→GAT)	proQ ←	RNA chaperone, putative ProP translation regulator
RA	1,942,066	G→T	21.0%	H115N (CAT→AAT)	yebC ←	UPF0082 family protein
RA	1,944,177	C→A	90.0%	L201L (CTG→CTT)	aspS ←	aspartyl‑tRNA synthetase
RA	1,959,915	C→A	6.8%	P178P (CCG→CCT)	flhB ←	flagellin export apparatus, substrate specificity protein
RA	1,969,291	G→T	89.2%	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	1,986,289	T→A	83.7%	N4Y (AAT→TAT)	pgsA ←	phosphatidylglycerophosphate synthetase
RA	1,997,314	G→T	66.3%	intergenic (‑227/‑39)	fliC ← / → fliD	flagellar filament structural protein (flagellin)/flagellar filament capping protein
RA	1,999,334	T→A	5.3%	I47I (ATT→ATA)	fliT →	putative flagellar synthesis and assembly chaperone
RA	1,999,632	G→T	69.5%	intergenic (+73/‑5)	fliT → / → amyA	putative flagellar synthesis and assembly chaperone/cytoplasmic alpha‑amylase
RA	2,007,547	C→A	5.2%	R280S (CGC→AGC)	fliF →	flagellar basal‑body MS‑ring and collar protein
RA	2,020,166	C→A	88.8%	D445Y (GAC→TAC)	yedQ ←	putative membrane‑anchored diguanylate cyclase
RA	2,028,807	G→T	19.5%	intergenic (+83/‑509)	yedS → / → hchA	pseudogene, outer membrane protein homology; putative outer membrane protein/glyoxalase III and Hsp31 molecular chaperone
RA	2,030,998	C→A	11.9%	P212P (CCG→CCT)	yedV ←	putative sensory kinase in two‑component regulatory system with YedW
RA	2,035,090	C→A	66.4%	Q79K (CAG→AAG)	zinT →	zinc and cadmium binding protein, periplasmic
RA	2,041,982	A→T	17.8%	S1188S (TCA→TCT)	yeeJ →	putative adhesin
RA	2,067,205	G→A	5.4%	G729D (GGC→GAC)	flu →	CP4‑44 prophage; antigen 43 (Ag43) phase‑variable biofilm formation autotransporter
RA	2,073,386	C→T	13.3%	S229S (TCG→TCA)	yeeA ←	putative transporter, FUSC family inner membrane protein
RA	2,074,680	A→T	88.7%	W22R (TGG→AGG)	sbmC ←	DNA gyrase inhibitor
RA	2,077,212	A→T	7.0%	N326Y (AAT→TAT)	sbcB →	exodeoxyribonuclease I; exonuclease I
RA	2,098,995	C→A	84.9%	G182* (GGA→TGA)	wbbI ←	d‑Galf:alpha‑d‑Glc beta‑1,6‑galactofuranosyltransferase
RA	2,102,205	C→A	14.2%	V287V (GTG→GTT)	wzxB ←	putative polisoprenol‑linked O‑antigen transporter
RA	2,102,807	C→T	15.9%	A87T (GCG→ACG)	wzxB ←	putative polisoprenol‑linked O‑antigen transporter
RA	2,103,588	A→T	11.9%	V11E (GTG→GAG)	rfbC ←	dTDP‑4‑deoxyrhamnose‑3,5‑epimerase
RA	2,108,219:1	+A	100%	coding (1159/1395 nt)	wcaM ←	colanic acid biosynthesis protein
RA	2,111,193	G→T	20.3%	A231A (GCC→GCA)	wcaK ←	colanic acid biosynthesis protein
RA	2,114,911	A→T	86.1%	L42Q (CTG→CAG)	wcaJ ←	colanic biosynthesis UDP‑glucose lipid carrier transferase
RA	2,123,590	A→T	13.5%	V257E (GTG→GAG)	wcaD ←	putative colanic acid polymerase
RA	2,126,692	T→A	11.9%	T63S (ACT→TCT)	wcaA ←	putative glycosyl transferase
RA	2,139,910	G→T	92.1%	R1055L (CGA→CTA)	yegE →	putative diguanylate cyclase
RA	2,144,474	C→A	86.6%	intergenic (‑8/‑192)	yegI ← / → yegJ	protein kinase‑related putative non‑specific DNA‑binding protein/uncharacterized protein
RA	2,148,624	A→C	15.2%	T376T (ACA→ACC)	mdtA →	multidrug efflux system, subunit A
RA	2,149,603	A→T	63.0%	E287V (GAA→GTA)	mdtB →	multidrug efflux system, subunit B
RA	2,161,404	T→A	12.5%	intergenic (‑109/+66)	yegZ ← / ← yegR	pseudogene, gpD phage P2‑like protein D/uncharacterized protein
RA	2,168,487	A→T	56.5%	D14E (GAT→GAA)	gatA ←	galactitol‑specific enzyme IIA component of PTS
RA	2,168,795	C→A	84.0%	D336Y (GAT→TAT)	gatZ ←	D‑tagatose 1,6‑bisphosphate aldolase 2, subunit
RA	2,168,986	C→A	12.9%	R272L (CGC→CTC)	gatZ ←	D‑tagatose 1,6‑bisphosphate aldolase 2, subunit
RA	2,170,708	G→T	10.3%	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	20.0%	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	23.7%	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	10.3%	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	10.8%	intergenic (‑75/+233)	gatY ← / ← fbaB	D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I
RA	2,172,457	C→A	14.9%	S53* (TCG→TAG)	yegT →	nucleoside transporter, low affinity
RA	2,178,937	A→T	10.1%	intergenic (‑157/+66)	thiM ← / ← rcnR	hydoxyethylthiazole kinase/transcriptional repressor of rcnA
RA	2,179,205	G→T	86.6%	A24E (GCG→GAG)	rcnR ←	transcriptional repressor of rcnA
RA	2,181,645	A→G	71.7%	N83N (AAT→AAC)	yehA ←	putative fimbrial‑like adhesin protein
RA	2,189,888	C→A	19.3%	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	2,192,382	C→A	18.0%	pseudogene (2430/2847 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	90.9%	L313Q (CTA→CAA)	yehI →	DUF4132 domain‑containing protein
RA	2,195,449	A→T	84.4%	E564D (GAA→GAT)	yehI →	DUF4132 domain‑containing protein
RA	2,196,227	T→A	13.0%	W824R (TGG→AGG)	yehI →	DUF4132 domain‑containing protein
RA	2,204,551	T→G	5.5%	pseudogene (1973/2001 nt)	yehQ →	pseudogene
RA	2,216,296	C→A	81.8%	I211I (ATC→ATA)	dld →	D‑lactate dehydrogenase, FAD‑binding, NADH independent
RA	2,220,503	C→T	8.9%	V83M (GTG→ATG)	yohF ←	putative oxidoreductase
RA	2,223,247	C→T	9.3%	W206* (TGG→TGA)	dusC ←	tRNA‑dihydrouridine synthase C
RA	2,225,190	C→T	79.7%	G231G (GGC→GGT)	yohK →	LrgB family inner membrane protein
RA	2,225,260	C→T	13.1%	intergenic (+67/‑63)	yohK → / → cdd	LrgB family inner membrane protein/cytidine/deoxycytidine deaminase
RA	2,228,226	T→G	12.5%	F239V (TTC→GTC)	preT →	dihydropyrimidine dehydrogenase, NADH‑dependent, subunit N
RA	2,233,142	A→T	13.4%	V229E (GTG→GAG)	mglB ←	methyl‑galactoside transporter subunit
RA	2,237,098	G→T	90.6%	H12N (CAT→AAT)	folE ←	GTP cyclohydrolase I
RA	2,243,089	G→T	18.7%	I3I (ATC→ATA)	yeiE ←	putative DNA‑binding transcriptional regulator
RA	2,259,689	C→A	14.1%	intergenic (+188/‑35)	yeiP → / → yeiQ	elongation factor P‑like protein/putative NAD‑dependent D‑mannonate oxidoreductase
RA	2,264,143	G→A	87.5%	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	2,289,043	C→A	7.7%	W8L (TGG→TTG)	ccmD ←	cytochrome c biogenesis protein
RA	2,289,374	C→A	83.8%	V142V (GTG→GTT)	ccmC ←	heme exporter subunit
RA	2,292,271	A→T	18.1%	C263S (TGC→AGC)	napH ←	ferredoxin‑type protein essential for electron transfer from ubiquinol to periplasmic nitrate reductase (NapAB)
RA	2,294,769	C→A	6.5%	P488P (CCG→CCT)	napA ←	nitrate reductase, periplasmic, large subunit
RA	2,298,277	T→C	6.7%	intergenic (+405/+310)	eco → / ← mqo	ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA	2,298,393	A→G	5.3%	intergenic (+521/+194)	eco → / ← mqo	ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA	2,303,070	T→G	85.8%	Q272P (CAG→CCG)	ada ←	fused DNA‑binding transcriptional dual regulator/O6‑methylguanine‑DNA methyltransferase
RA	2,303,607	A→C	8.9%	L93R (CTG→CGG)	ada ←	fused DNA‑binding transcriptional dual regulator/O6‑methylguanine‑DNA methyltransferase
RA	2,305,116	C→A	84.5%	intergenic (‑103/+9)	apbE ← / ← ompC	putative thiamine‑synthetic flavin transferase lipoprotein/outer membrane porin protein C
RA	2,305,135	T→C	84.6%	Y365C (TAC→TGC)	ompC ←	outer membrane porin protein C
RA	2,319,347	G→T	12.2%	V371V (GTG→GTT)	atoE →	short chain fatty acid transporter
RA	2,320,247	G→T	14.2%	P220P (CCG→CCT)	atoB →	acetyl‑CoA acetyltransferase
RA	2,327,398	C→A	5.7%	pseudogene (484/4605 nt)	yfaS ←	pseudogene, bacterial alpha2‑macroglobulin YfaS variant family; putative membrane protein
RA	2,330,502	C→A	70.5%	D800Y (GAT→TAT)	gyrA ←	DNA gyrase (type II topoisomerase), subunit A
RA	2,332,648	C→A	5.5%	A84A (GCG→GCT)	gyrA ←	DNA gyrase (type II topoisomerase), subunit A
RA	2,341,252	C→A	16.0%	I130I (ATC→ATA)	nrdB →	ribonucleoside‑diphosphate reductase 1, beta subunit, ferritin‑like protein
RA	2,346,194	T→A	8.7%	I23I (ATT→ATA)	glpA →	sn‑glycerol‑3‑phosphate dehydrogenase (anaerobic), large subunit, FAD/NAD(P)‑binding
RA	2,352,573	C→A	87.0%	P353P (CCG→CCT)	rhmT ←	putative L‑rhamnonate transporter
RA	2,353,889	C→A	19.2%	V335V (GTG→GTT)	rhmD ←	L‑rhamnonate dehydratase
RA	2,359,673	G→T	87.1%	M89I (ATG→ATT)	arnB →	uridine 5'‑(beta‑1‑threo‑pentapyranosyl‑4‑ulose diphosphate) aminotransferase, PLP‑dependent
RA	2,362,338	T→A	85.0%	L274Q (CTG→CAG)	arnA →	fused UDP‑L‑Ara4N formyltransferase/UDP‑GlcA C‑4'‑decarboxylase
RA	2,370,361:1	+G	84.6%	coding (711/759 nt)	menH ←	2‑succinyl‑6‑hydroxy‑2, 4‑cyclohexadiene‑1‑carboxylate synthase
RA	2,370,837	Δ1 bp	5.6%	coding (235/759 nt)	menH ←	2‑succinyl‑6‑hydroxy‑2, 4‑cyclohexadiene‑1‑carboxylate synthase
RA	2,370,987	C→A	87.3%	E29* (GAA→TAA)	menH ←	2‑succinyl‑6‑hydroxy‑2, 4‑cyclohexadiene‑1‑carboxylate synthase
RA	2,391,622	C→A	6.4%	A675S (GCT→TCT)	nuoG ←	NADH:ubiquinone oxidoreductase, chain G
RA	2,395,041	C→A	18.1%	R164L (CGG→CTG)	nuoE ←	NADH:ubiquinone oxidoreductase, chain E
RA	2,398,940	C→A	18.4%	intergenic (‑389/+242)	nuoA ← / ← lrhA	NADH:ubiquinone oxidoreductase, membrane subunit A/transcriptional repressor of flagellar, motility and chemotaxis genes
RA	2,399,210	G→T	87.8%	S304* (TCA→TAA)	lrhA ←	transcriptional repressor of flagellar, motility and chemotaxis genes
RA	2,405,946	T→G	83.7%	Q43P (CAG→CCG)	yfbU ←	UPF0304 family protein
RA	2,407,678	T→A	7.4%	S244T (TCT→ACT)	ackA →	acetate kinase A and propionate kinase 2
RA	2,416,101	C→A	89.7%	intergenic (+21/+27)	yfcH → / ← yfcI	putative NAD‑dependent nucleotide‑sugar epimerase/transposase_31 family protein
RA	2,417,989	C→T	15.6%	intergenic (‑1/+7)	hisP ← / ← hisM	histidine/lysine/arginine/ornithine transporter subunit/histidine/lysine/arginine/ornithine transporter subunit
RA	2,422,841	C→A	85.7%	D293Y (GAT→TAT)	purF ←	amidophosphoribosyltransferase
RA	2,424,074	C→T	80.8%	D57N (GAC→AAC)	cvpA ←	colicin V production membrane protein
RA	2,441,337	C→A	18.6%	D195Y (GAC→TAC)	prmB ←	N5‑glutamine methyltransferase
RA	2,444,315	C→A	17.4%	E80D (GAG→GAT)	yfcQ ←	putative fimbrial‑like adhesin protein
RA	2,450,335	C→T	89.9%	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	89.9%	intergenic (‑55/+148)	sixA ← / ← fadJ	phosphohistidine phosphatase/fused enoyl‑CoA hydratase and epimerase and isomerase/3‑hydroxyacyl‑CoA dehydrogenase
RA	2,450,550	C→A	16.6%	E697* (GAG→TAG)	fadJ ←	fused enoyl‑CoA hydratase and epimerase and isomerase/3‑hydroxyacyl‑CoA dehydrogenase
RA	2,452,454	G→T	85.0%	P62Q (CCG→CAG)	fadJ ←	fused enoyl‑CoA hydratase and epimerase and isomerase/3‑hydroxyacyl‑CoA dehydrogenase
RA	2,454,297	T→G	88.2%	E39D (GAA→GAC)	yfcZ ←	UPF0381 family protein
RA	2,463,906	C→A	23.7%	Q433K (CAA→AAA)	gtrS →	serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
RA	2,463,910	G→T	15.7%	R434I (AGA→ATA)	gtrS →	serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
RA	2,471,682	A→C	18.3%	E119D (GAA→GAC)	dsdX →	D‑serine transporter
RA	2,474,418	G→T	89.4%	S413* (TCA→TAA)	emrY ←	putative multidrug efflux system
RA	2,486,801	A→T	10.6%	intergenic (‑68/+445)	frc ← / ← yfdX	formyl‑CoA transferase, NAD(P)‑binding/uncharacterized protein
RA	2,489,031	C→A	16.6%	intergenic (‑260/‑93)	yfdY ← / → lpxP	DUF2545 family putative inner membrane protein/palmitoleoyl‑acyl carrier protein (ACP)‑dependent acyltransferase
RA	2,495,918	C→A	10.7%	V683F (GTT→TTT)	fryA ←	putative PTS enzyme, Hpr component/enzyme I component/enzyme IIA component
RA	2,507,141	C→A	17.1%	I207I (ATC→ATA)	nupC →	nucleoside (except guanosine) transporter
RA	2,510,074	C→A	15.9%	R413L (CGA→CTA)	yfeA ←	putative diguanylate cyclase
RA	2,516,553	T→G	15.3%	E264D (GAA→GAC)	xapB ←	xanthosine transporter
RA	2,516,871	A→T	16.6%	S158R (AGT→AGA)	xapB ←	xanthosine transporter
RA	2,520,652	C→A	87.9%	I116I (ATC→ATA)	yfeH →	putative inorganic ion transporter
RA	2,523,881	T→A	17.2%	S238C (AGC→TGC)	zipA ←	FtsZ stabilizer
RA	2,526,023	T→A	14.0%	Y86N (TAC→AAC)	cysK →	cysteine synthase A, O‑acetylserine sulfhydrolase A subunit
RA	2,544,917	C→A	12.0%	D57Y (GAT→TAT)	yfeZ ←	inner membrane protein
RA	2,549,676	C→A	84.4%	L28L (CTG→CTT)	eutL ←	putative ethanol utilization carboxysome structural protein
RA	2,559,092	C→A	20.6%	A384A (GCG→GCT)	eutA ←	reactivating factor for ethanolamine ammonia lyase
RA	2,568,720	C→T	88.9%	A33T (GCC→ACC)	eutP ←	putative P‑loop NTPase ethanolamine utilization protein
RA	2,570,684	A→T	20.1%	I351I (ATT→ATA)	maeB ←	malic enzyme: putative oxidoreductase/putative phosphotransacetylase
RA	2,573,363	C→A	14.6%	V123V (GTC→GTA)	tktB →	transketolase 2, thiamine triphosphate‑binding
RA	2,576,325	C→A	91.5%	E171D (GAG→GAT)	nudK ←	GDP‑mannose pyrophosphatase
RA	2,580,299	G→T	14.6%	D404Y (GAT→TAT)	narQ →	sensory histidine kinase in two‑component regulatory system with NarP (NarL)
RA	2,587,029:1	+G	86.4%	coding (101/699 nt)	ypfH ←	palmitoyl‑CoA esterase activity, uncertain physiological substrate
RA	2,589,150	C→A	11.7%	L23L (CTG→CTT)	tmcA ←	elongator methionine tRNA (ac4C34) acetyltransferase
RA	2,589,933	G→A	85.3%	T55I (ACC→ATC)	ypfJ ←	putative neutral zinc metallopeptidase
RA	2,594,253	C→A	14.1%	F139L (TTC→TTA)	bcp →	peroxiredoxin; thiol peroxidase, thioredoxin‑dependent
RA	2,601,829	T→G	6.1%	S518S (TCT→TCG)	hyfF →	hydrogenase 4, membrane subunit
RA	2,601,887	C→A	15.9%	L14L (CTC→CTA)	hyfG →	hydrogenase 4, subunit
RA	2,606,516	G→T	85.4%	D420Y (GAC→TAC)	hyfR →	hydrogenase‑4 transcriptional activator
RA	2,610,919	C→A	87.6%	intergenic (+3/‑18)	bepA → / → yfgD	periplasmic metalloprotease and chaperone for OM protein maintenance and assembly/putative oxidoreductase
RA	2,614,168	C→A	86.2%	D22Y (GAT→TAT)	upp ←	uracil phosphoribosyltransferase
RA	2,618,693	G→T	9.0%	E74* (GAA→TAA)	ppx →	exopolyphosphatase
RA	2,619,125	G→T	23.9%	G218C (GGT→TGT)	ppx →	exopolyphosphatase
RA	2,651,665	G→T	88.8%	G210G (GGC→GGA)	hscA ←	DnaK‑like molecular chaperone specific for IscU
RA	2,665,693	C→A	21.3%	G96G (GGC→GGA)	hcaD →	phenylpropionate dioxygenase, ferredoxin reductase subunit
RA	2,670,904	G→T	9.9%	R273S (CGC→AGC)	yphE ←	putative sugar transporter subunit of ABC superfamily, ATP‑binding component
RA	2,671,274	C→A	87.7%	T149T (ACG→ACT)	yphE ←	putative sugar transporter subunit of ABC superfamily, ATP‑binding component
RA	2,681,873	T→A	89.7%	Q97L (CAG→CTG)	glrR ←	response regulator regulating glmY sRNA in two‑component system with sensor protein GlrK
RA	2,683,829	C→A	89.3%	R210L (CGT→CTT)	glrK ←	sensor protein kinase regulating glmY sRNA in two‑component system with response regulator GlrR
RA	2,684,556	C→A	13.5%	noncoding (144/184 nt)	glmY ←	sRNA activator of glmS mRNA, glmZ processing antagonist
RA	2,687,651	C→A	6.4%	G418C (GGC→TGC)	purL ←	phosphoribosylformyl‑glycineamide synthetase
RA	2,692,793	C→A	5.4%	H226N (CAT→AAT)	yfhH →	putative DNA‑binding transcriptional regulator
RA	2,693,726	C→T	13.5%	intergenic (‑170/‑153)	shoB ← / → ohsC	toxic membrane protein/sRNA antisense regulator of shoB toxin
RA	2,694,843	G→T	7.1%	I82I (ATC→ATA)	pdxJ ←	pyridoxine 5'‑phosphate synthase
RA	2,715,643	G→T	88.5%	E778* (GAA→TAA)	pka →	protein lysine acetyltransferase
RA	2,719,426	T→C	100%	intergenic (‑321/+2)	kgtP ← / ← rrfG	alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon
RA	2,726,786	C→A	86.3%	A249A (GCG→GCT)	clpB ←	protein disaggregation chaperone
RA	2,733,461	T→A	18.6%	Q350L (CAG→CTG)	aroF ←	3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, tyrosine‑repressible
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	5.1%	I20I (ATA→ATT)	yfiR →	putative periplasmic inhibitor of YfiN activity
RA	2,738,911	C→A	12.9%	D123Y (GAT→TAT)	rimM ←	16S rRNA processing protein
RA	2,742,459	T→A	16.4%	A109A (GCT→GCA)	yfjD →	UPF0053 family inner membrane protein
RA	2,748,452	T→C	5.2%	F66F (TTT→TTC)	smpB →	trans‑translation protein
RA	2,757,927	A→T	17.8%	S196T (TCC→ACC)	yfjL ←	CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein
RA	2,761,733	T→A	7.1%	V222E (GTA→GAA)	yfjP →	CP4‑57 prophage; 50S ribosome‑binding GTPase family protein
RA	2,766,733	C→T	10.0%	D19D (GAC→GAT)	yfjW →	CP4‑57 prophage; putative inner membrane protein
RA	2,771,358	G→A	86.1%	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	86.1%	intergenic (‑697/+54)	ypjC ← / ← ileY	pseudogene/tRNA‑Ile
RA	2,792,237	T→A	16.9%	intergenic (‑383/‑286)	stpA ← / → alaE	DNA binding protein, nucleoid‑associated/alanine exporter, alanine‑inducible, stress‑responsive
RA	2,803,846	C→A	17.0%	I48I (ATC→ATA)	ygaH →	putative L‑valine exporter, norvaline resistance protein
RA	2,806,531	T→G	16.3%	L186R (CTG→CGG)	emrB →	multidrug efflux system protein
RA	2,808,646	G→T	15.4%	R385S (CGC→AGC)	gshA ←	glutamate‑cysteine ligase
RA	2,816,762	C→A	12.9%	G123C (GGC→TGC)	recA ←	DNA recombination and repair protein; ssDNA‑dependent ATPase; synaptase; ssDNA and dsDNA binding protein forming filaments; ATP‑dependent homologous DNA strand exchanger; recombinase A; LexA autocleavage cofactor
RA	2,825,783	C→T	88.2%	intergenic (‑135/‑52)	norR ← / → norV	anaerobic nitric oxide reductase DNA‑binding transcriptional activator/anaerobic nitric oxide reductase flavorubredoxin
RA	2,828,952	C→A	84.8%	T611T (ACG→ACT)	hypF ←	carbamoyl phosphate phosphatase and maturation protein for [NiFe] hydrogenases
RA	2,831,086	C→A	7.2%	E127* (GAA→TAA)	hydN ←	formate dehydrogenase‑H, [4Fe‑4S] ferredoxin subunit
RA	2,835,094	C→A	5.9%	P249Q (CCG→CAG)	ascB →	cryptic 6‑phospho‑beta‑glucosidase
RA	2,841,044	C→A	87.2%	A519A (GCG→GCT)	hycC ←	hydrogenase 3, membrane subunit
RA	2,842,318	T→A	12.0%	N95Y (AAC→TAC)	hycC ←	hydrogenase 3, membrane subunit
RA	2,850,790	C→A	83.6%	I113I (ATC→ATA)	mutS →	methyl‑directed mismatch repair protein
RA	2,860,407	C→A	15.4%	P168P (CCG→CCT)	rpoS ←	RNA polymerase, sigma S (sigma 38) factor
RA	2,872,873	C→A	5.0%	A87S (GCT→TCT)	ygbT ←	multifunctional endonuclease Cas1, CRISPR adaptation protein; DNA repair enzyme
RA	2,873,087	G→T	85.6%	V15V (GTC→GTA)	ygbT ←	multifunctional endonuclease Cas1, CRISPR adaptation protein; DNA repair enzyme
RA	2,874,470	A→T	11.3%	V344V (GTT→GTA)	casC ←	CRISP RNA (crRNA) containing Cascade antiviral complex protein
RA	2,876,760	C→T	90.3%	G246G (GGG→GGA)	casA ←	CRISP RNA (crRNA) containing Cascade antiviral complex protein
RA	2,878,668	G→T	85.2%	V637V (GTC→GTA)	ygcB ←	R‑loop helicase‑annealase Cas3 needed for Cascade anti‑viral activity
RA	2,879,449	G→T	77.5%	S377* (TCA→TAA)	ygcB ←	R‑loop helicase‑annealase Cas3 needed for Cascade anti‑viral activity
RA	2,886,177	C→A	12.3%	L54L (CTC→CTA)	ygcN →	putative oxidoreductase
RA	2,888,584	G→T	88.8%	I185I (ATC→ATA)	ygcQ ←	putative flavoprotein
RA	2,889,967	T→A	12.2%	A421A (GCA→GCT)	ygcS ←	putative transporter
RA	2,894,015	G→T	16.0%	S22I (AGT→ATT)	yqcE →	MFS transporter family protein
RA	2,915,010	C→A	7.4%	T150T (ACG→ACT)	gudP ←	putative D‑glucarate transporter
RA	2,923,089	C→A	15.2%	S52* (TCG→TAG)	sdaB →	L‑serine dehydratase 2
RA	2,923,478	C→A	5.5%	Q182K (CAG→AAG)	sdaB →	L‑serine dehydratase 2
RA	2,931,717	C→A	88.5%	N307K (AAC→AAA)	fucK →	L‑fuculokinase
RA	2,934,843	G→T	83.4%	H50N (CAT→AAT)	ygdD ←	UPF0382 family inner membrane protein
RA	2,936,686	G→T	20.8%	intergenic (‑182/‑10)	ygdI ← / → csdA	DUF903 family verified lipoprotein/cysteine sulfinate desulfinase
RA	2,945,504	C→A	16.5%	R106L (CGT→CTT)	recD ←	exonuclease V (RecBCD complex), alpha chain
RA	2,946,267	G→T	13.0%	I1032I (ATC→ATA)	recB ←	exonuclease V (RecBCD complex), beta subunit
RA	2,959,004	G→A	83.4%	I131I (ATC→ATT)	lgt ←	phosphatidylglycerol‑prolipoprotein diacylglyceryl transferase
RA	2,960,651	A→T	19.4%	R381R (CGT→CGA)	ptsP ←	fused PTS enzyme: PEP‑protein phosphotransferase (enzyme I)/GAF domain containing protein
RA	2,966,053	A→C	14.5%	L390R (CTG→CGG)	lplT ←	lysophospholipid transporter
RA	2,967,572	A→G	6.9%	F601S (TTT→TCT)	aas ←	fused 2‑acylglycerophospho‑ethanolamine acyl transferase/acyl‑acyl carrier protein synthetase
RA	2,969,747	C→A	7.1%	intergenic (‑3/‑211)	omrB ← / → galR	sRNA antisense regulator downregulates OM proteins and curli; positively regulated by OmpR/EnvZ, Hfq‑dependent/galactose‑inducible d‑galactose regulon transcriptional repressor; autorepressor
RA	2,969,827	A→T	17.7%	intergenic (‑83/‑131)	omrB ← / → galR	sRNA antisense regulator downregulates OM proteins and curli; positively regulated by OmpR/EnvZ, Hfq‑dependent/galactose‑inducible d‑galactose regulon transcriptional repressor; autorepressor
RA	2,979,736	T→G	21.7%	P177P (CCT→CCG)	yqeG →	putative transporter
RA	2,985,884	C→T	9.7%	I144I (ATC→ATT)	ygeH →	putative transcriptional regulator
RA	2,988,554	G→A	7.1%	intergenic (‑103/+119)	ygeK ← / ← ygeN	pseudogene; putative 2‑component transcriptional regulator/pseudogene
RA	2,989,041	T→A	12.8%	pseudogene (79/447 nt)	ygeN ←	pseudogene
RA	2,989,295	C→A	89.4%	pseudogene (85/261 nt)	ygeN ←	pseudogene
RA	2,993,211	C→A	87.0%	V14L (GTG→TTG)	ygeR ←	LysM domain‑containing M23 family putative peptidase; septation lipoprotein
RA	2,993,699	C→A	88.4%	intergenic (‑449/‑5)	ygeR ← / → xdhA	LysM domain‑containing M23 family putative peptidase; septation lipoprotein/xanthine dehydrogenase, molybdenum binding subunit
RA	3,011,240	G→T	14.3%	D608Y (GAT→TAT)	ygfK →	putative Fe‑S subunit oxidoreductase subunit
RA	3,014,214	G→T	13.7%	E106* (GAA→TAA)	ygfM →	putative oxidoreductase
RA	3,016,372	C→A	19.5%	F566L (TTC→TTA)	xdhD →	putative hypoxanthine oxidase, molybdopterin‑binding/Fe‑S binding
RA	3,017,285	G→T	89.3%	D871Y (GAC→TAC)	xdhD →	putative hypoxanthine oxidase, molybdopterin‑binding/Fe‑S binding
RA	3,022,888	C→A	6.5%	R468L (CGG→CTG)	ygfT ←	putative oxidoreductase, Fe‑S subunit/nucleotide‑binding subunit
RA	3,024,081	A→C	7.4%	V70V (GTT→GTG)	ygfT ←	putative oxidoreductase, Fe‑S subunit/nucleotide‑binding subunit
RA	3,024,983	C→G	86.7%	G86G (GGC→GGG)	uacT →	uric acid permease
RA	3,025,678	A→T	27.9%	Q318L (CAA→CTA)	uacT →	uric acid permease
RA	3,030,073	C→A	13.5%	E465* (GAA→TAA)	recJ ←	ssDNA exonuclease, 5' ‑‑> 3'‑specific
RA	3,039,409	T→G	12.0%	intergenic (‑149/+118)	ygfF ← / ← gcvP	putative NAD(P)‑dependent oxidoreductase with NAD(P)‑binding Rossmann‑fold domain/glycine decarboxylase, PLP‑dependent, subunit (protein P) of glycine cleavage complex
RA	3,044,464	G→A	85.1%	intergenic (‑438/+10)	gcvT ← / ← ubiI	aminomethyltransferase, tetrahydrofolate‑dependent, subunit (T protein) of glycine cleavage complex/2‑octaprenylphenol hydroxylase, FAD‑dependent
RA	3,045,365	A→T	13.6%	L104L (CTT→CTA)	ubiI ←	2‑octaprenylphenol hydroxylase, FAD‑dependent
RA	3,048,037	C→A	15.9%	G55C (GGC→TGC)	pepP ←	proline aminopeptidase P II
RA	3,055,069	C→A	7.1%	V287V (GTC→GTA)	scpA →	methylmalonyl‑CoA mutase
RA	3,058,692	C→T	7.0%	P178S (CCT→TCT)	scpC →	propionyl‑CoA:succinate CoA transferase
RA	3,058,769	C→T	6.2%	I203I (ATC→ATT)	scpC →	propionyl‑CoA:succinate CoA transferase
RA	3,064,914	G→T	68.0%	I356I (ATC→ATA)	pgk ←	phosphoglycerate kinase
RA	3,067,329	A→G	10.2%	intergenic (‑279/+6)	epd ← / ← yggC	D‑erythrose 4‑phosphate dehydrogenase/putative PanK family P‑loop kinase
RA	3,068,135	G→T	5.6%	F140L (TTC→TTA)	yggD ←	MtlR family putative transcriptional repressor
RA	3,071,726	A→T	14.0%	C165S (TGT→AGT)	cmtA ←	putative mannitol‑specific PTS enzymes: IIB component/IIC component
RA	3,072,314	C→A	14.2%	E126* (GAA→TAA)	cmtB ←	putative mannitol‑specific enzyme IIA component of PTS
RA	3,072,825	G→T	9.4%	intergenic (‑136/+178)	cmtB ← / ← tktA	putative mannitol‑specific enzyme IIA component of PTS/transketolase 1, thiamine triphosphate‑binding
RA	3,075,114	C→A	85.7%	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	82.9%	D211Y (GAC→TAC)	speB ←	agmatinase
RA	3,080,618	T→A	85.3%	V185E (GTG→GAG)	metK →	S‑adenosylmethionine synthetase
RA	3,088,065	C→A	7.9%	V125V (GTG→GTT)	yggR ←	putative PilT family AAA+ ATPase
RA	3,088,780	C→A	5.8%	I108I (ATC→ATA)	yggS →	UPF0001 family protein, PLP‑binding
RA	3,097,262	C→T	6.9%	F297F (TTC→TTT)	mutY →	adenine DNA glycosylase
RA	3,101,591	A→T	16.0%	F308L (TTT→TTA)	speC ←	ornithine decarboxylase, constitutive
RA	3,110,751	C→A	89.8%	R574L (CGT→CTT)	yghJ ←	DUF4092 family putative lipoprotein peptidase
RA	3,111,434	C→A	83.0%	A346A (GCG→GCT)	yghJ ←	DUF4092 family putative lipoprotein peptidase
RA	3,113,832	C→G	13.6%	W269C (TGG→TGC)	glcA ←	glycolate transporter
RA	3,120,216	C→A	83.4%	D389Y (GAT→TAT)	glcD ←	glycolate oxidase subunit, FAD‑linked
RA	3,127,390	G→A	11.8%	intergenic (‑74/‑100)	yghS ← / → yghT	putative ATP‑binding protein/putative ATP‑binding protein
RA	3,127,766	C→A	12.0%	R93S (CGC→AGC)	yghT →	putative ATP‑binding protein
RA	3,142,668	G→T	5.4%	L55I (CTC→ATC)	yqhA ←	UPF0114 family putative inner membrane protein
RA	3,144,158	C→A	93.6%	intergenic (+253/+19)	yghA → / ← exbD	putative oxidoreductase/membrane spanning protein in TonB‑ExbB‑ExbD complex
RA	3,148,927	G→T	20.1%	E72* (GAA→TAA)	yqhD →	aldehyde reductase, NADPH‑dependent
RA	3,164,230	C→A	5.1%	R130S (CGT→AGT)	qseC →	quorum sensing sensory histidine kinase in two‑component regulatory system with QseB
RA	3,173,669	G→T	84.8%	A189A (GCG→GCT)	ygiB →	DUF1190 family protein
RA	3,174,875	C→A	17.1%	R366S (CGT→AGT)	ygiC →	ATP‑Grasp family ATPase
RA	3,176,733	G→T	6.2%	intergenic (+51/+439)	zupT → / ← ribB	zinc transporter/3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase
RA	3,183,817	C→A	6.1%	T193K (ACG→AAG)	yqiH →	putative periplasmic pilin chaperone
RA	3,191,701	C→A	13.3%	E434* (GAA→TAA)	glnE ←	fused deadenylyltransferase/adenylyltransferase for glutamine synthetase
RA	3,193,086	A→T	13.7%	I413I (ATT→ATA)	ygiF ←	inorganic triphosphatase
RA	3,201,433	C→A	19.8%	I17I (ATC→ATA)	ttdT →	L‑tartrate/succinate antiporte
RA	3,204,684	C→T	18.5%	F73F (TTC→TTT)	dnaG →	DNA primase
RA	3,204,711	C→A	5.2%	F82L (TTC→TTA)	dnaG →	DNA primase
RA	3,204,985	G→T	5.3%	G174C (GGC→TGC)	dnaG →	DNA primase
RA	3,215,927	C→A	13.4%	intergenic (+119/‑65)	ebgR → / → ebgA	transcriptional repressor/evolved beta‑D‑galactosidase, alpha subunit
RA	3,217,289	A→T	7.7%	H433L (CAC→CTC)	ebgA →	evolved beta‑D‑galactosidase, alpha subunit
RA	3,224,927	C→A	85.0%	intergenic (+329/‑97)	ygjK → / → fadH	alpha‑glucosidase/2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked
RA	3,230,857	C→G	8.3%	A63G (GCC→GGC)	ygjR →	putative NAD(P)‑dependent dehydrogenase
RA	3,231,349	A→C	7.5%	Q227P (CAG→CCG)	ygjR →	putative NAD(P)‑dependent dehydrogenase
RA	3,231,558	C→A	14.2%	H297N (CAT→AAT)	ygjR →	putative NAD(P)‑dependent dehydrogenase
RA	3,243,876	C→A	16.4%	intergenic (+141/‑45)	yqjK → / → yqjF	uncharacterized protein/putative quinol oxidase subunit
RA	3,245,848	G→T	90.2%	L62L (CTG→CTT)	yhaH →	DUF805 family inner membrane protein
RA	3,246,327	C→T	14.8%	R20C (CGT→TGT)	yhaI →	DUF805 family inner membrane protein
RA	3,246,634	A→T	5.2%	intergenic (+8/+43)	yhaI → / ← yhaJ	DUF805 family inner membrane protein/LysR family putative transcriptional regulator
RA	3,252,258	C→A	85.3%	D251Y (GAT→TAT)	tdcG ←	L‑serine dehydratase 3, anaerobic
RA	3,259,317	C→A	10.6%	R24L (CGA→CTA)	tdcB ←	L‑threonine dehydratase, catabolic
RA	3,263,315	T→C	6.8%	intergenic (+354/+260)	yhaC → / ← rnpB	pentapetide repeats‑related protein/RNase P, M1 RNA component
RA	3,266,646	C→A	87.8%	G91C (GGT→TGT)	garL ←	alpha‑dehydro‑beta‑deoxy‑D‑glucarate aldolase
RA	3,275,040	C→A	7.0%	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	3,281,016	T→G	22.2%	C78G (TGC→GGC)	yraH →	putative fimbrial‑like adhesin protein
RA	3,296,612	G→T	5.5%	A255A (GCG→GCT)	yhbV →	U32 peptidase family protein
RA	3,302,027	G→T	83.5%	S86* (TCG→TAG)	nlpI ←	lipoprotein involved in osmotic sensitivity and filamentation
RA	3,308,528	T→A	12.6%	V282V (GTA→GTT)	infB ←	translation initiation factor IF‑2
RA	3,312,862	T→A	7.8%	R289R (CGT→CGA)	argG →	argininosuccinate synthetase
RA	3,314,870	C→A	88.6%	A35S (GCG→TCG)	yhbX ←	putative EptAB family phosphoethanolamine transferase, inner membrane protein
RA	3,316,817	C→A	14.2%	G205C (GGT→TGT)	glmM ←	phosphoglucosamine mutase
RA	3,332,543	C→A	16.9%	R22L (CGG→CTG)	mlaE ←	ABC transporter maintaining OM lipid asymmetry, inner membrane permease protein
RA	3,343,353	C→A	10.1%	D156Y (GAT→TAT)	elbB ←	isoprenoid biosynthesis protein with amidotransferase‑like domain
RA	3,347,778	G→A	87.7%	intergenic (‑369/‑306)	yhcC ← / → gltB	putative Fe‑S oxidoreductase, Radical SAM superfamily protein/glutamate synthase, large subunit
RA	3,354,405	C→T	89.0%	intergenic (+430/‑130)	gltD → / → gltF	glutamate synthase, 4Fe‑4S protein, small subunit/periplasmic protein
RA	3,360,610	C→T	12.3%	T109I (ACC→ATC)	yhcF →	putative transcriptional regulator
RA	3,365,527	C→T	12.0%	S136N (AGC→AAC)	nanT ←	sialic acid transporter
RA	3,365,607	G→T	85.7%	I109I (ATC→ATA)	nanT ←	sialic acid transporter
RA	3,372,048	C→A	20.9%	intergenic (‑38/+181)	rplM ← / ← yhcM	50S ribosomal subunit protein L13/putative AFG1‑like family P‑loop ATPase
RA	3,373,985	C→A	88.0%	intergenic (+37/‑117)	yhcB → / → degQ	DUF1043 family inner membrane‑anchored protein/serine endoprotease, periplasmic
RA	3,374,389	C→A	18.1%	I96I (ATC→ATA)	degQ →	serine endoprotease, periplasmic
RA	3,375,260	G→T	83.7%	D387Y (GAT→TAT)	degQ →	serine endoprotease, periplasmic
RA	3,380,174	C→A	6.2%	S458S (TCG→TCT)	aaeB ←	p‑hydroxybenzoic acid efflux system component
RA	3,385,479	C→G	9.7%	intergenic (‑92/+338)	tldD ← / ← yhdP	putative peptidase/DUF3971‑AsmA2 domains protein
RA	3,385,571	C→G	6.4%	intergenic (‑184/+246)	tldD ← / ← yhdP	putative peptidase/DUF3971‑AsmA2 domains protein
RA	3,385,669	A→T	5.8%	intergenic (‑282/+148)	tldD ← / ← yhdP	putative peptidase/DUF3971‑AsmA2 domains protein
RA	3,396,082	G→T	85.0%	R204S (CGT→AGT)	csrD ←	targeting factor for csrBC sRNA degradation
RA	3,400,740	A→T	5.9%	T3S (ACT→TCT)	yhdT →	DUF997 family putative inner membrane protein
RA	3,407,008	G→A	13.5%	intergenic (‑184/‑215)	acrS ← / → acrE	acrAB operon transcriptional repressor/cytoplasmic membrane lipoprotein
RA	3,437,010	C→A	20.1%	V149V (GTG→GTT)	secY ←	preprotein translocase membrane subunit
RA	3,439,422	G→T	9.4%	I26I (ATC→ATA)	rplF ←	50S ribosomal subunit protein L6
RA	3,440,151	G→T	91.3%	I31I (ATC→ATA)	rpsN ←	30S ribosomal subunit protein S14
RA	3,440,444	G→T	88.2%	S118S (TCC→TCA)	rplE ←	50S ribosomal subunit protein L5
RA	3,440,832	T→C	83.3%	N99D (AAC→GAC)	rplX ←	50S ribosomal subunit protein L24
RA	3,447,853	A→T	17.2%	V302E (GTA→GAA)	gspA ←	general secretory pathway component, cryptic
RA	3,452,752	T→A	12.9%	V352E (GTG→GAG)	gspE →	general secretory pathway component, cryptic
RA	3,455,867	C→A	90.7%	I55I (ATC→ATA)	gspJ →	putative general secretory pathway component, cryptic
RA	3,466,358	C→A	8.8%	A172A (GCG→GCT)	fusA ←	protein chain elongation factor EF‑G, GTP‑binding
RA	3,467,734	C→A	15.1%	G60C (GGT→TGT)	rpsL ←	30S ribosomal subunit protein S12
RA	3,473,139	G→T	92.1%	I276I (ATC→ATA)	kefB ←	potassium:proton antiporter
RA	3,479,542	C→A	17.1%	H22N (CAT→AAT)	crp →	cAMP‑activated global transcription factor, mediator of catabolite repression
RA	3,479,769	A→T	68.3%	E97D (GAA→GAT)	crp →	cAMP‑activated global transcription factor, mediator of catabolite repression
RA	3,483,095	C→A	10.0%	V149F (GTT→TTT)	argD ←	bifunctional acetylornithine aminotransferase/ succinyldiaminopimelate aminotransferase
RA	3,488,961	T→A	17.7%	L531Q (CTG→CAG)	nirB →	nitrite reductase, large subunit, NAD(P)H‑binding
RA	3,488,966	G→C	90.5%	A533P (GCC→CCC)	nirB →	nitrite reductase, large subunit, NAD(P)H‑binding
RA	3,489,397	C→A	67.7%	F676L (TTC→TTA)	nirB →	nitrite reductase, large subunit, NAD(P)H‑binding
RA	3,501,571	C→A	82.7%	G127C (GGC→TGC)	php ←	phosphotriesterase homology protein
RA	3,504,943	C→A	12.7%	R254L (CGA→CTA)	yhfZ ←	putative DNA‑binding transcriptional regulator
RA	3,507,749	G→T	67.7%	H224N (CAT→AAT)	rpe ←	D‑ribulose‑5‑phosphate 3‑epimerase
RA	3,510,311	C→A	10.0%	G119C (GGT→TGT)	damX ←	cell division protein that binds to the septal ring
RA	3,512,114	C→A	6.5%	E104* (GAA→TAA)	aroK ←	shikimate kinase I
RA	3,513,424	A→T	5.4%	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	5.5%	V210V (GTC→GTA)	yrfF →	inner membrane protein
RA	3,525,215	A→C	8.8%	L195R (CTG→CGG)	yhgE ←	DUF4153 family putative inner membrane protein
RA	3,525,258	T→G	5.8%	T181P (ACC→CCC)	yhgE ←	DUF4153 family putative inner membrane protein
RA	3,530,608	G→T	7.2%	A146A (GCG→GCT)	greB →	transcript cleavage factor
RA	3,538,254	C→A	13.2%	P5Q (CCG→CAG)	gntX →	DNA catabolic protein
RA	3,543,959	G→T	85.0%	A625E (GCG→GAG)	malP ←	maltodextrin phosphorylase
RA	3,544,759	C→A	5.3%	V358V (GTG→GTT)	malP ←	maltodextrin phosphorylase
RA	3,546,323	C→A	9.5%	intergenic (‑491/‑121)	malP ← / → malT	maltodextrin phosphorylase/mal regulon transcriptional activator
RA	3,549,415	T→G	16.6%	Q265P (CAG→CCG)	rtcA ←	RNA 3'‑terminal phosphate cyclase
RA	3,551,373	T→G	9.6%	V22V (GTA→GTC)	rtcB ←	RNA‑splicing ligase
RA	3,551,503	T→C	20.5%	intergenic (‑65/‑124)	rtcB ← / → rtcR	RNA‑splicing ligase/sigma 54‑dependent transcriptional regulator of rtcBA expression
RA	3,559,170	C→A	6.3%	D258Y (GAT→TAT)	glgP ←	glycogen phosphorylase
RA	3,561,574	C→A	86.2%	W372L (TGG→TTG)	glgC ←	glucose‑1‑phosphate adenylyltransferase
RA	3,569,056	C→A	13.5%	intergenic (+32/+25)	yhgN → / ← gntU	UPF0056 family inner membrane protein/gluconate transporter, low affinity GNT 1 system
RA	3,585,079	C→A	6.7%	A203S (GCC→TCC)	ugpB ←	glycerol‑3‑phosphate transporter subunit
RA	3,586,143	C→A	17.6%	D219Y (GAT→TAT)	livF ←	leucine/isoleucine/valine transporter subunit
RA	3,612,224	G→T	7.3%	D93Y (GAC→TAC)	nikR →	transcriptional repressor, Ni‑binding
RA	3,619,105	T→A	19.1%	A353A (GCA→GCT)	yhhJ ←	inner membrane putative ABC transporter permease
RA	3,625,721	A→T	21.6%	I77N (ATT→AAT)	yhiJ ←	DUF4049 family protein
RA	3,626,023	G→T	5.8%	intergenic (‑73/+189)	yhiJ ← / ← yhiL	DUF4049 family protein/pseudogene, DUF4049 family protein
RA	3,627,639	G→A	16.8%	pseudogene (180/1194 nt)	yhiL ←	pseudogene, DUF4049 family protein
RA	3,639,551	C→A	24.6%	T269T (ACC→ACA)	rlmJ →	23S rRNA m(6)A2030 methyltransferase, SAM‑dependent
RA	3,640,495	T→G	17.4%	T279T (ACT→ACG)	gor →	glutathione oxidoreductase
RA	3,642,278	T→C	10.0%	intergenic (+37/‑17)	arsR → / → arsB	arsenical resistance operon transcriptional repressor; autorepressor/arsenite/antimonite transporter
RA	3,647,598	G→T	7.6%	R93L (CGA→CTA)	slp →	outer membrane lipoprotein
RA	3,662,660	T→C	86.3%	intergenic (‑112/‑292)	yhjA ← / → treF	putative cytochrome C peroxidase/cytoplasmic trehalase
RA	3,665,617	C→A	13.3%	intergenic (‑363/‑157)	yhjB ← / → yhjC	putative DNA‑binding transcriptional response regulator/LysR family putative transcriptional regulator
RA	3,679,301	T→G	88.5%	Q1078P (CAG→CCG)	bcsC ←	cellulose synthase subunit
RA	3,679,324	C→A	89.5%	M1070I (ATG→ATT)	bcsC ←	cellulose synthase subunit
RA	3,680,910	G→T	82.8%	H542N (CAT→AAT)	bcsC ←	cellulose synthase subunit
RA	3,695,997	C→A	19.9%	E78* (GAG→TAG)	dppF ←	dipeptide transporter
RA	3,698,594	A→C	17.2%	L186R (CTA→CGA)	dppB ←	dipeptide/heme transporter
RA	3,700,154	G→T	18.4%	L304L (CTC→CTA)	dppA ←	dipeptide transporter
RA	3,714,588	T→A	12.3%	Y11N (TAT→AAT)	insK →	IS150 transposase B
RA	3,717,788	C→A	84.3%	P297P (CCG→CCT)	glyQ ←	glycine tRNA synthetase, alpha subunit
RA	3,718,959	C→A	8.1%	L38F (TTG→TTT)	ysaB ←	uncharacterized protein
RA	3,721,485	T→G	10.2%	Y416S (TAC→TCC)	xylB ←	xylulokinase
RA	3,730,615	C→A	7.3%	intergenic (‑78/‑242)	bax ← / → malS	putative glucosaminidase/alpha‑amylase
RA	3,738,431	C→A	84.3%	P90T (CCA→ACA)	yiaN →	2,3‑diketo‑L‑gulonate TRAP transporter large permease protein
RA	3,774,382	T→G	12.7%	intergenic (+5/‑193)	lldD → / → trmL	L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent
RA	3,785,915	G→T	85.3%	intergenic (‑4/+271)	kbl ← / ← yibB	glycine C‑acetyltransferase/YibB family protein, function unknown
RA	3,786,717	G→T	16.3%	N109K (AAC→AAA)	yibB ←	YibB family protein, function unknown
JC JC	3,795,902	IS5 (+) +4 bp	10.2%	coding (514‑517/1020 nt)	waaR ←	UDP‑D‑galactose:(glucosyl)lipopolysaccharide‑ alpha‑1,3‑D‑galactosyltransferase
RA	3,802,238	A→T	20.3%	A113A (GCA→GCT)	waaA →	3‑deoxy‑D‑manno‑octulosonic‑acid transferase (KDO transferase)
RA	3,810,195	C→A	88.3%	R54S (CGT→AGT)	yicC →	UPF0701 family protein
RA	3,814,302	T→A	25.7%	S77C (AGC→TGC)	ligB ←	DNA ligase, NAD(+)‑dependent
RA	3,816,601	A→T	85.6%	H281L (CAC→CTC)	spoT →	bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase
RA	3,818,010	C→A	85.7%	H46N (CAT→AAT)	trmH →	tRNA mG18‑2'‑O‑methyltransferase, SAM‑dependent
RA	3,822,274	T→A	9.9%	intergenic (‑249/‑31)	gltS ← / → xanP	glutamate transporter/xanthine permease
RA	3,822,339	A→C	10.0%	Q12P (CAA→CCA) ‡	xanP →	xanthine permease
RA	3,822,340	A→C	17.2%	Q12H (CAA→CAC) ‡	xanP →	xanthine permease
RA	3,822,345	T→G	9.7%	V14G (GTT→GGT)	xanP →	xanthine permease
RA	3,825,702	C→A	92.0%	K732N (AAG→AAT)	yicI ←	putative alpha‑glucosidase
RA	3,829,464	T→G	16.7%	intergenic (‑175/‑118)	yicJ ← / → selC	putative transporter/tRNA‑Sec
RA	3,830,197	C→A	87.8%	intergenic (+281/‑116)	yicT → / → setC	pseudogene/putative arabinose efflux transporter
RA	3,830,311	G→T	93.3%	intergenic (+395/‑2)	yicT → / → setC	pseudogene/putative arabinose efflux transporter
RA	3,837,117	A→T	15.4%	N11K (AAT→AAA)	yicO ←	putative adenine permease
RA	3,844,906	G→T	12.1%	S413S (TCC→TCA)	ilvB ←	acetolactate synthase 2 large subunit
RA	3,856,944	C→A	13.0%	pseudogene (20/1617 nt)	glvC ←	pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component
RA	3,860,159	C→A	87.9%	P33P (CCG→CCT)	ibpB ←	heat shock chaperone
RA	3,870,977	T→A	7.3%	intergenic (‑152/+88)	yidB ← / ← gyrB	DUF937 family protein/DNA gyrase, subunit B
RA	3,876,681	T→A	17.1%	T137S (ACG→TCG)	dnaA ←	chromosomal replication initiator protein DnaA, DNA‑binding transcriptional dual regulator
RA	3,886,876	T→A	6.0%	L251Q (CTG→CAG)	yidZ →	putative DNA‑binding transcriptional regulator
RA	3,896,189	G→T	17.9%	T291T (ACC→ACA)	bglB ←	cryptic phospho‑beta‑glucosidase B
RA	3,910,894	C→A	88.3%	M244I (ATG→ATT)	atpG ←	F1 sector of membrane‑bound ATP synthase, gamma subunit
RA	3,911,514	G→T	13.6%	R38S (CGC→AGC)	atpG ←	F1 sector of membrane‑bound ATP synthase, gamma subunit
RA	3,914,395	T→A	9.6%	Q52L (CAG→CTG)	atpE ←	F0 sector of membrane‑bound ATP synthase, subunit c
RA	3,916,052	C→A	20.7%	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	86.0%	D71Y (GAT→TAT)	rsmG ←	16S rRNA m(7)G527 methyltransferase, SAM‑dependent; glucose‑inhibited cell‑division protein
RA	3,917,548	C→A	18.2%	S482S (TCG→TCT)	mnmG ←	5‑methylaminomethyl‑2‑thiouridine modification at tRNA U34
RA	3,917,940	C→A	11.8%	D352Y (GAC→TAC)	mnmG ←	5‑methylaminomethyl‑2‑thiouridine modification at tRNA U34
RA	3,923,028	C→A	9.8%	D476Y (GAC→TAC)	ravA ←	hexameric AAA+ MoxR family ATPase, putative molecular chaperone
RA	3,926,831	G→T	67.3%	D41Y (GAT→TAT)	rbsD →	putative cytoplasmic sugar‑binding protein
RA	3,930,175	A→T	11.2%	N180Y (AAT→TAT)	rbsB →	D‑ribose transporter subunit
RA	3,958,909	C→T	13.4%	G28R (GGG→AGG)	rhlB ←	ATP‑dependent RNA helicase
RA	3,960,036	G→A	92.9%	R87H (CGC→CAC)	rho →	transcription termination factor
RA	3,966,854	C→A	86.6%	R325S (CGT→AGT)	rffG →	dTDP‑glucose 4,6‑dehydratase
RA	3,967,474	G→T	7.3%	A169A (GCG→GCT)	rffH →	glucose‑1‑phosphate thymidylyltransferase
RA	3,969,710	G→T	71.6%	G25C (GGT→TGT)	wzxE →	O‑antigen translocase
RA	3,975,006	G→T	5.8%	V254F (GTT→TTT)	yifK →	putative APC family amino acid transporter
RA	3,976,846	A→T	15.9%	S177C (AGC→TGC)	aslB →	putative AslA‑specific sulfatase‑maturating enzyme
RA	3,988,075	T→A	80.3%	V65E (GTG→GAG)	yifL →	putative lipoprotein
RA	3,994,076	A→T	85.1%	L114* (TTA→TAA)	yigE ←	DUF2233 family protein
RA	3,994,247	A→T	87.9%	V57E (GTG→GAG)	yigE ←	DUF2233 family protein
RA	3,999,937	A→T	6.6%	S238S (TCA→TCT)	recQ →	ATP‑dependent DNA helicase
RA	4,009,667	T→C	6.5%	intergenic (‑138/‑124)	ysgA ← / → udp	putative carboxymethylenebutenolidase/uridine phosphorylase
RA	4,009,705	G→A	90.6%	intergenic (‑176/‑86)	ysgA ← / → udp	putative carboxymethylenebutenolidase/uridine phosphorylase
RA	4,034,740	G→T	14.4%	T18T (ACC→ACA)	mobB ←	molybdopterin‑guanine dinucleotide biosynthesis protein B
RA	4,039,399	G→T	18.0%	F188L (TTC→TTA)	yihG ←	inner membrane protein, inner membrane acyltransferase
RA	4,056,018	T→A	87.4%	F138I (TTC→ATC)	yihN →	MFS transporter family protein
RA	4,062,424	G→T	82.6%	I71I (ATC→ATA)	yihQ ←	alpha‑glucosidase
RA	4,063,530	A→C	16.6%	C78G (TGT→GGT)	yihR ←	mutarotase superfamily protein, YihR family
RA	4,066,133	T→G	84.3%	S267R (AGC→CGC)	yihU ←	gamma‑hydroxybutyrate dehydrogenase, NADH‑dependent
RA	4,068,208	C→A	88.9%	G60G (GGC→GGA)	yihW →	DeoR family putative transcriptional regulator
RA	4,080,315	C→A	14.1%	intergenic (+106/‑47)	fdhD → / → yiiG	formate dehydrogenase formation protein/DUF3829 family lipoprotein
RA	4,080,364	G→T	7.6%	M1M (ATG→ATT) †	yiiG →	DUF3829 family lipoprotein
RA	4,094,362	C→A	88.8%	W181L (TGG→TTG)	cpxA ←	sensory histidine kinase in two‑component regulatory system with CpxR
RA	4,097,822	G→T	89.2%	E115* (GAA→TAA)	pfkA →	6‑phosphofructokinase I
RA	4,110,209	G→T	16.9%	L23L (CTC→CTA)	menA ←	1,4‑dihydroxy‑2‑naphthoate octaprenyltransferase
RA	4,118,851	G→T	8.8%	T84T (ACG→ACT)	metB →	cystathionine gamma‑synthase, PLP‑dependent
RA	4,122,248	A→T	7.2%	intergenic (+53/‑296)	metL → / → metF	Bifunctional aspartokinase/homoserine dehydrogenase 2/5,10‑methylenetetrahydrofolate reductase
RA	4,127,022	T→G	89.4%	E188D (GAA→GAC)	yijF ←	DUF1287 family protein
RA	4,134,054	G→T	13.9%	A44A (GCG→GCT)	pflD →	putative glycine radical domain‑containing pyruvate formate‑lyase
RA	4,143,375	A→G	6.0%	intergenic (‑349/+249)	ppc ← / ← argE	phosphoenolpyruvate carboxylase/acetylornithine deacetylase
RA	4,163,211	A→T	14.3%	N68Y (AAT→TAT)	birA →	bifunctional biotin‑[acetylCoA carboxylase] holoenzyme synthetase/ DNA‑binding transcriptional repressor, bio‑5'‑AMP‑binding
RA	4,163,570	T→A	9.6%	I187I (ATT→ATA)	birA →	bifunctional biotin‑[acetylCoA carboxylase] holoenzyme synthetase/ DNA‑binding transcriptional repressor, bio‑5'‑AMP‑binding
RA	4,167,908	T→A	19.0%	W80R (TGG→AGG)	nusG →	transcription termination factor
RA	4,172,704	T→G	18.5%	L511R (CTG→CGG)	rpoB →	RNA polymerase, beta subunit
RA	4,173,582	T→A	16.3%	F804I (TTC→ATC)	rpoB →	RNA polymerase, beta subunit
RA	4,176,823	G→T	88.8%	D516Y (GAC→TAC)	rpoC →	RNA polymerase, beta prime subunit
RA	4,178,758	G→T	22.2%	G1161C (GGT→TGT)	rpoC →	RNA polymerase, beta prime subunit
RA	4,211,576	G→T	87.1%	S280R (AGC→AGA)	arpA ←	ankyrin repeat protein
RA	4,211,803	G→A	86.4%	P205S (CCT→TCT)	arpA ←	ankyrin repeat protein
RA	4,219,081	C→A	19.4%	R475S (CGC→AGC)	yjbB →	putative Na+/Pi‑cotransporter
RA	4,230,913	A→T	87.0%	W424R (TGG→AGG)	xylE ←	D‑xylose transporter
RA	4,235,869	G→T	7.6%	A160E (GCG→GAG)	malE ←	maltose transporter subunit
RA	4,236,535	T→A	6.7%	intergenic (‑188/‑177)	malE ← / → malK	maltose transporter subunit/fused maltose transport subunit, ATP‑binding component of ABC superfamily/regulatory protein
RA	4,250,378	A→T	11.4%	I44L (ATA→TTA)	yjbL →	uncharacterized protein
RA	4,251,224	C→A	16.1%	S233* (TCG→TAG)	yjbM →	uncharacterized protein
RA	4,257,197	G→T	7.5%	A52A (GCG→GCT)	tyrB →	tyrosine aminotransferase, tyrosine‑repressible, PLP‑dependent
RA	4,260,359	G→T	18.3%	R65L (CGT→CTT)	yjbQ →	thiamine phosphate synthase
RA	4,265,064	C→A	85.3%	intergenic (‑95/‑335)	yjcB ← / → yjcC	putative inner membrane protein/putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	4,268,967	A→T	14.0%	S187S (TCA→TCT)	yjcD →	inner membrane putative guanine permease
RA	4,269,705	C→A	7.3%	V433V (GTC→GTA)	yjcD →	inner membrane putative guanine permease
RA	4,273,297	A→T	8.3%	W512R (TGG→AGG)	actP ←	acetate transporter
RA	4,274,926	A→C	89.7%	I72M (ATT→ATG)	yjcH ←	DUF485 family inner membrane protein
RA	4,275,123	G→T	17.0%	Q7K (CAG→AAG)	yjcH ←	DUF485 family inner membrane protein
RA	4,275,142	C→A	57.9%	intergenic (‑1/+199)	yjcH ← / ← acs	DUF485 family inner membrane protein/acetyl‑CoA synthetase
RA	4,285,857	T→C	5.9%	intergenic (+135/+396)	gltP → / ← yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA	4,286,817	G→T	13.9%	A42A (GCC→GCA)	yjcO ←	Sel1 family TPR‑like repeat protein
RA	4,290,080	G→T	86.8%	I256I (ATC→ATA)	mdtP ←	outer membrane factor of efflux pump
RA	4,297,485	G→C	7.3%	G44G (GGC→GGG)	alsK ←	D‑allose kinase
RA	4,297,846	C→A	88.8%	M150I (ATG→ATT)	alsE ←	allulose‑6‑phosphate 3‑epimerase
RA	4,300,333	T→A	7.1%	E155D (GAA→GAT)	alsA ←	fused D‑allose transporter subunits of ABC superfamily: ATP‑binding components
RA	4,303,614	T→A	87.9%	*150R (TGA→AGA)	rpiB →	ribose 5‑phosphate isomerase B/allose 6‑phosphate isomerase
RA	4,304,132	G→T	14.6%	intergenic (+118/+29)	yjdP → / ← phnP	putative periplasmic protein/5‑phospho‑alpha‑D‑ribosyl 1,2‑cyclic phosphate phosphodiesterase
RA	4,309,623	C→A	5.8%	A286A (GCG→GCT)	phnI ←	ribophosphonate triphosphate synthase complex putative catalytic subunit
RA	4,330,426	Δ1 bp	100%	intergenic (‑88/+111)	adiA ← / ← melR	arginine decarboxylase/melibiose operon transcriptional regulator; autoregulator
RA	4,338,712	T→A	16.5%	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	78.5%	Y153N (TAC→AAC)	dcuS ←	sensory histidine kinase in two‑component regulatory system with DcuR, regulator of anaerobic fumarate respiration
RA	4,347,057	C→A	13.1%	D460Y (GAT→TAT)	cadA ←	lysine decarboxylase, acid‑inducible
RA	4,354,610	A→T	24.1%	W84R (TGG→AGG)	dsbD ←	fused thiol:disulfide interchange protein: activator of DsbC/conserved protein
RA	4,357,204	A→T	6.5%	L314Q (CTG→CAG)	aspA ←	aspartate ammonia‑lyase
RA	4,358,920	G→T	8.0%	R147L (CGC→CTC)	fxsA →	suppressor of F exclusion of phage T7
RA	4,372,891	A→T	7.3%	A144A (GCA→GCT)	epmA →	Elongation Factor P Lys34 lysyltransferase
RA	4,376,178	C→A	12.1%	E1004* (GAA→TAA)	mscM ←	mechanosensitive channel protein, miniconductance
RA	4,382,314	A→T	5.4%	noncoding (26/76 nt)	glyX →	tRNA‑Gly
RA	4,386,747	G→T	10.7%	R289L (CGT→CTT)	amiB →	N‑acetylmuramoyl‑l‑alanine amidase II
RA	4,388,902	G→T	82.8%	A558A (GCG→GCT)	mutL →	methyl‑directed mismatch repair protein
RA	4,394,875	G→T	8.1%	A124A (GCG→GCT)	purA →	adenylosuccinate synthetase
RA	4,396,598	A→T	84.5%	E43V (GAA→GTA)	rnr →	exoribonuclease R, RNase R
RA	4,405,735	G→T	7.8%	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	7.7%	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	10.7%	L450R (CTG→CGG)	ulaA →	L‑ascorbate‑specific enzyme IIC permease component of PTS
RA	4,415,892	G→T	19.7%	intergenic (+9/‑33)	rpsR → / → rplI	30S ribosomal subunit protein S18/50S ribosomal subunit protein L9
RA	4,417,551	A→C	83.7%	pseudogene (41/402 nt)	ytfA →	pseudogene, related to transcriptional regulators
RA	4,429,361	G→T	5.2%	intergenic (‑282/‑43)	ytfJ ← / → ytfK	putative transcriptional regulator/DUF1107 family protein
RA	4,458,254	T→A	88.0%	V271V (GTT→GTA)	mgtA →	magnesium transporter
RA	4,458,609	G→T	88.2%	D390Y (GAT→TAT)	mgtA →	magnesium transporter
RA	4,459,683	A→T	11.9%	N748Y (AAC→TAC)	mgtA →	magnesium transporter
RA	4,462,966	A→T	18.3%	Y21N (TAT→AAT)	yjgH ←	UPF0131 family protein
RA	4,468,165	A→G	87.7%	intergenic (‑37/‑125)	argI ← / → rraB	ornithine carbamoyltransferase 1/protein inhibitor of RNase E
RA	4,469,550	G→A	92.2%	A2T (GCT→ACT)	yjgN →	DUF898 family inner membrane protein
RA	4,470,017	G→A	91.6%	M157I (ATG→ATA)	yjgN →	DUF898 family inner membrane protein
RA	4,472,200	A→T	11.1%	S485S (TCT→TCA)	valS ←	valyl‑tRNA synthetase
RA	4,474,526	C→A	7.7%	D415Y (GAC→TAC)	pepA ←	multifunctional aminopeptidase A: a cyteinylglycinase, transcription regulator and site‑specific recombination factor
RA	4,484,059	G→T	11.9%	F55L (TTC→TTA)	idnD ←	L‑idonate 5‑dehydrogenase, NAD‑binding
RA	4,495,560	A→T	14.1%	N153Y (AAC→TAC)	yjhC →	putative oxidoreductase
RA	4,497,253	G→T	13.4%	pseudogene (240/255 nt)	insO →	pseudogene, IS911 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related
RA	4,512,693	T→A	85.1%	K407* (AAG→TAG)	yjhG ←	putative dehydratase
RA	4,515,655	C→A	11.9%	intergenic (‑35/+268)	yjhI ← / ← sgcR	putative DNA‑binding transcriptional regulator/putative DNA‑binding transcriptional regulator
RA	4,518,741	T→A	5.9%	intergenic (‑7/+6)	sgcQ ← / ← sgcC	putative nucleoside triphosphatase/putative PTS system EIIC permease component
RA	4,520,215	T→A	14.8%	N46Y (AAC→TAC)	sgcB ←	putative enzyme IIB component of PTS
RA	4,523,001	T→A	8.6%	intergenic (‑1/+55)	yjhP ← / ← yjhQ	putative methyltransferase/putative acetyltransferase
RA	4,525,234	G→A	86.5%	pseudogene (415/1029 nt)	yjhR →	pseudogene, helicase family; putative frameshift suppressor
RA	4,529,263	A→T	8.2%	L19* (TTA→TAA)	nanC ←	N‑acetylnuraminic acid outer membrane channel protein
RA	4,529,483	A→T	13.4%	intergenic (‑165/‑1291)	nanC ← / → fimB	N‑acetylnuraminic acid outer membrane channel protein/tyrosine recombinase/inversion of on/off regulator of fimA
RA	4,529,937	C→T	7.4%	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	14.2%	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	86.2%	I124F (ATT→TTT)	fimB →	tyrosine recombinase/inversion of on/off regulator of fimA
RA	4,541,449	A→T	5.9%	intergenic (‑336/‑4)	gntP ← / → uxuA	fructuronate transporter/mannonate hydrolase
RA	4,554,534	G→T	14.4%	A378A (GCC→GCA)	yjiM ←	putative 2‑hydroxyglutaryl‑CoA dehydratase
RA	4,555,156	G→T	82.7%	A171E (GCG→GAG)	yjiM ←	putative 2‑hydroxyglutaryl‑CoA dehydratase
RA	4,561,347	A→T	17.7%	I15I (ATT→ATA)	yjiR ←	putative DNA‑binding transcriptional regulator/putative aminotransferase
RA	4,562,043	C→A	95.0%	intergenic (+311/‑188)	yjiS → / → yjiT	DUF1127 family protein/pseudogene
RA	4,584,381	G→T	89.8%	I53I (ATC→ATA)	yjjL ←	L‑galactonate transporter
RA	4,585,338	A→T	67.9%	S111T (TCT→ACT)	yjjM ←	yjjMN operon transcriptional activator
RA	4,598,924	A→T	15.7%	K154N (AAA→AAT)	yjjG →	dUMP phosphatase
RA	4,616,297	C→A	5.7%	S190* (TCG→TAG)	radA →	DNA repair protein
RA	4,616,972	G→T	16.7%	R415L (CGA→CTA)	radA →	DNA repair protein
RA	4,624,581	C→A	24.2%	E183* (GAA→TAA)	rob ←	right oriC‑binding transcriptional activator, AraC family
RA	4,625,288	T→C	68.3%	intergenic (‑161/‑50)	rob ← / → creA	right oriC‑binding transcriptional activator, AraC family/putative periplasmic protein
RA	4,629,649	A→T	19.4%	Y159N (TAC→AAC)	arcA ←	response regulator in two‑component regulatory system with ArcB or CpxA
RA	4,629,850	C→T	7.6%	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	373849	375108	1260	162 [161]	[161] 164	frmA–[frmR]	frmA,[frmR]
*	*	÷	CP009273	4100621	4101509	889	162 [155]	[159] 163	tpiA	tpiA

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	360104 =	208 (0.810)	166 (0.650)	94/278	NT	44.4%	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)	9004 (37.390) +TTAATTAA	196/262	NT	97.7%	intergenic (‑212/+383)	lacZ/lacI	pseudogene, truncated/DNA‑binding transcriptional repressor
	?	CP009273	= 361823	230 (0.900)					coding (831/834 nt)	mhpR	mhp operon transcriptional activator
*	?	CP009273	360652 =	319 (1.250)	8788 (51.560) +46 bp	186/186	NT	97.9%	intergenic (‑586/+9)	lacZ/lacI	pseudogene, truncated/DNA‑binding transcriptional repressor
	?	CP009273	= 1317577	236 (0.920)					coding (101/882 nt)	yciV	PHP domain protein
*	?	CP009273	376716 =	NA (NA)	215 (0.840)	122/278	NT	93.1%	intergenic (‑1/‑91)	yaiX/insC1	pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase/IS2 repressor TnpA
	?	CP009273	566411 =	16 (0.060)					coding (63/552 nt)	ybcL	inactive polymorphonuclear leukocyte migration suppressor; DLP12 prophage; secreted protein, UPF0098 family
*	?	CP009273	= 378046	NA (NA)	228 (0.890)	127/278	NT	93.4%	intergenic (+11/+1)	insD1/yaiX	IS2 transposase TnpB/pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase
	?	CP009273	= 566415	16 (0.060)					coding (67/552 nt)	ybcL	inactive polymorphonuclear leukocyte migration suppressor; DLP12 prophage; secreted protein, UPF0098 family
*	?	CP009273	1203246 =	89 (0.350)	99 (0.440)	58/246	NT	55.8%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	CP009273	1205075 =	78 (0.350)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	CP009273	= 1203261	87 (0.340)	107 (0.470)	60/246	NT	58.0%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	CP009273	= 1205058	78 (0.350)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	CP009273	= 1282540	92 (0.360)	7 (0.030)	5/238	NT	5.9%	noncoding (153/171 nt)	rttR	rtT sRNA, processed from tyrT transcript
	?	CP009273	1283013 =	145 (0.660)					noncoding (66/85 nt)	tyrT	tRNA‑Tyr
*	?	CP009273	1635219 =	34 (0.130)	186 (0.740)	116/274	NT	84.5%	intergenic (‑377/+377)	essQ/cspB	Qin prophage; putative S lysis protein/Qin prophage; cold shock protein
	?	CP009273	= 2063752	NA (NA)					noncoding (1/1331 nt)	IS2	repeat region
*	?	CP009273	= 1635223	34 (0.130)	170 (0.660)	105/278	NT	83.3%	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)	15 (0.060)	13/278	NT	7.2%	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 =	194 (0.760)					coding (502/651 nt)	rcsB	response regulator in two‑component regulatory system with RcsC and YojN
*	?	CP009273	= 2310161	200 (0.780)	22 (0.090)	16/278	NT	9.9%	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	= 3180783	NA (NA)	18 (0.070)	16/274	NT	8.1%	pseudogene (4/2445 nt)	yqiG	pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein
	?	CP009273	= 3833569	208 (0.810)					intergenic (‑216/‑6)	nlpA/yicS	cytoplasmic membrane lipoprotein‑28/putative periplasmic protein
*	?	CP009273	3833562 =	218 (0.850)	13 (0.050)	8/276	NT	5.7%	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