breseq  version 0.33.1  revision 8505477f25b3 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence	position	mutation	freq	annotation	gene	description
RA	287	Δ1 bp	10.2%	intergenic (+32/‑50)	thrL → / → thrA	thr operon leader peptide/Bifunctional aspartokinase/homoserine dehydrogenase 1
RA	291	A→T	9.6%	intergenic (+36/‑46)	thrL → / → thrA	thr operon leader peptide/Bifunctional aspartokinase/homoserine dehydrogenase 1
RA	293:1	+G	10.2%	intergenic (+38/‑44)	thrL → / → thrA	thr operon leader peptide/Bifunctional aspartokinase/homoserine dehydrogenase 1
RA	9,907	A→C	10.2%	intergenic (+14/+21)	mog → / ← satP	molybdochelatase incorporating molybdenum into molybdopterin/succinate‑acetate transporter
RA	9,908	G→T	10.2%	intergenic (+15/+20)	mog → / ← satP	molybdochelatase incorporating molybdenum into molybdopterin/succinate‑acetate transporter
RA	22,773	A→T	5.8%	E128V (GAA→GTA)	ileS →	isoleucyl‑tRNA synthetase
RA	22,776	A→T	5.6%	Y129F (TAC→TTC)	ileS →	isoleucyl‑tRNA synthetase
RA	53,376	G→A	8.4%	P14L (CCC→CTC)	pdxA ←	4‑hydroxy‑L‑threonine phosphate dehydrogenase, NAD‑dependent
RA	53,379	T→C	7.9%	E13G (GAG→GGG)	pdxA ←	4‑hydroxy‑L‑threonine phosphate dehydrogenase, NAD‑dependent
RA	78,830	T→A	10.7%	intergenic (+31/+18)	setA → / ← leuD	broad specificity sugar efflux system/3‑isopropylmalate dehydratase small subunit
RA	78,831	T→A	10.7%	intergenic (+32/+17)	setA → / ← leuD	broad specificity sugar efflux system/3‑isopropylmalate dehydratase small subunit
RA	83,587	A→C	11.0%	intergenic (‑58/+35)	leuA ← / ← leuL	2‑isopropylmalate synthase/leu operon leader peptide
RA	83,590	G→T	10.1%	intergenic (‑61/+32)	leuA ← / ← leuL	2‑isopropylmalate synthase/leu operon leader peptide
RA	111,013	G→A	9.8%	intergenic (+29/‑31)	secA → / → mutT	preprotein translocase subunit, ATPase/dGTP‑preferring nucleoside triphosphate pyrophosphohydrolase
RA	111,016	T→C	10.5%	intergenic (+32/‑28)	secA → / → mutT	preprotein translocase subunit, ATPase/dGTP‑preferring nucleoside triphosphate pyrophosphohydrolase
RA	120,154	Δ1 bp	6.8%	intergenic (+19/+24)	ampE → / ← aroP	ampicillin resistance inner membrane protein; putative signaling protein in beta‑lactamase regulation/aromatic amino acid transporter
RA	120,158:1	+A	7.2%	intergenic (+23/+20)	ampE → / ← aroP	ampicillin resistance inner membrane protein; putative signaling protein in beta‑lactamase regulation/aromatic amino acid transporter
RA	143,533	T→C	5.5%	L252P (CTG→CCG) ‡	yadG →	putative ABC transporter ATPase
RA	143,534	G→A	5.5%	L252L (CTG→CTA) ‡	yadG →	putative ABC transporter ATPase
RA	146,289	G→T	5.6%	V403V (GTG→GTT)	yadE →	putative polysaccharide deacetylase lipoprotein
RA	146,291	G→C	5.7%	S404T (AGT→ACT)	yadE →	putative polysaccharide deacetylase lipoprotein
RA	146,293	A→C	5.8%	N405H (AAC→CAC)	yadE →	putative polysaccharide deacetylase lipoprotein
RA	151,519	A→C	6.0%	I27M (ATT→ATG)	yadK ←	putative fimbrial‑like adhesin protein
RA	151,522	G→T	6.0%	A26A (GCC→GCA)	yadK ←	putative fimbrial‑like adhesin protein
RA	164,620	C→T	7.3%	intergenic (+86/‑110)	hrpB → / → mrcB	putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase
RA	164,621	A→G	7.4%	intergenic (+87/‑109)	hrpB → / → mrcB	putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase
RA	191,720	G→A	5.4%	intergenic (+12/‑135)	tsf → / → pyrH	translation elongation factor EF‑Ts/uridylate kinase
RA	191,739	T→C	6.3%	intergenic (+31/‑116)	tsf → / → pyrH	translation elongation factor EF‑Ts/uridylate kinase
RA	208,552	T→A	11.5%	L1143I (TTA→ATA)	dnaE →	DNA polymerase III alpha subunit
RA	242,344	C→G	5.7%	P320P (CCG→CCC)	fadE ←	acyl coenzyme A dehydrogenase
RA	252,589	G→C	5.8%	A97P (GCA→CCA)	yafO →	mRNA interferase toxin of the YafO‑YafN toxin‑antitoxin system
RA	252,594	G→C	5.7%	W98C (TGG→TGC)	yafO →	mRNA interferase toxin of the YafO‑YafN toxin‑antitoxin system
MC JC	257,908	Δ776 bp	100%		[crl]	[crl]
RA	285,882	T→G	8.5%	I163S (ATC→AGC)	yagG →	CP4‑6 prophage; putative sugar transporter
RA	285,887	C→A	7.9%	L165M (CTG→ATG)	yagG →	CP4‑6 prophage; putative sugar transporter
RA	287,395	G→C	7.3%	E203Q (GAG→CAG) ‡	yagH →	CP4‑6 prophage; putative xylosidase/arabinosidase
RA	287,396	A→T	6.9%	E203V (GAG→GTG) ‡	yagH →	CP4‑6 prophage; putative xylosidase/arabinosidase
RA	287,397	G→C	6.9%	E203D (GAG→GAC) ‡	yagH →	CP4‑6 prophage; putative xylosidase/arabinosidase
RA	314,255	T→C	5.6%	intergenic (‑450/‑102)	ykgP ← / → eaeH	pseudogene, oxidoreductase family/pseudogene, attaching and effacing protein homology;factor; Not classified
RA	314,258	G→A	5.8%	intergenic (‑453/‑99)	ykgP ← / → eaeH	pseudogene, oxidoreductase family/pseudogene, attaching and effacing protein homology;factor; Not classified
RA	328,375	A→C	7.2%	I120S (ATC→AGC)	betB ←	betaine aldehyde dehydrogenase, NAD‑dependent
RA	328,377	C→G	7.3%	L119L (CTG→CTC) ‡	betB ←	betaine aldehyde dehydrogenase, NAD‑dependent
RA	328,379	G→T	7.3%	L119M (CTG→ATG) ‡	betB ←	betaine aldehyde dehydrogenase, NAD‑dependent
RA	344,705	A→T	5.0%	K177I (AAA→ATA)	yahL →	uncharacterized protein
RA	404,113	A→C	5.3%	A137A (GCA→GCC)	yaiC →	diguanylate cyclase, cellulose regualtor
RA	404,115	G→C	5.1%	G138A (GGC→GCC)	yaiC →	diguanylate cyclase, cellulose regualtor
RA	404,117	G→T	5.1%	G139C (GGC→TGC)	yaiC →	diguanylate cyclase, cellulose regualtor
RA	414,827	A→C	5.7%	I309M (ATT→ATG)	sbcC ←	exonuclease, dsDNA, ATP‑dependent
RA	454,853	T→C	12.3%	intergenic (+64/‑280)	bolA → / → tig	stationary‑phase morphogene, transcriptional repressor for mreB; also regulator for dacA, dacC, and ampC/peptidyl‑prolyl cis/trans isomerase (trigger factor)
RA	454,856	G→A	13.0%	intergenic (+67/‑277)	bolA → / → tig	stationary‑phase morphogene, transcriptional repressor for mreB; also regulator for dacA, dacC, and ampC/peptidyl‑prolyl cis/trans isomerase (trigger factor)
RA	464,354	C→A	5.1%	intergenic (+46/‑48)	ybaV → / → fadM	putative competence‑suppressing periplasmic helix‑hairpin‑helix DNA‑binding protein/long‑chain acyl‑CoA thioesterase III
RA	475,971	C→G	12.5%	intergenic (+20/+11)	ybaY → / ← ybaZ	outer membrane lipoprotein/excision repair protein, alkyltransferase‑like protein ATL
RA	475,972	C→G	13.1%	intergenic (+21/+10)	ybaY → / ← ybaZ	outer membrane lipoprotein/excision repair protein, alkyltransferase‑like protein ATL
RA	481,225	T→G	9.6%	intergenic (‑517/+29)	tomB ← / ← acrB	Hha toxicity attenuator; conjugation‑related protein/multidrug efflux system protein
RA	481,228	C→A	9.6%	intergenic (‑520/+26)	tomB ← / ← acrB	Hha toxicity attenuator; conjugation‑related protein/multidrug efflux system protein
RA	533,846	T→C	5.2%	intergenic (+20/‑70)	allR → / → gcl	glyoxylate‑inducible transcriptional repressor of all and gcl operons/glyoxylate carboligase
RA	533,849	G→A	5.4%	intergenic (+23/‑67)	allR → / → gcl	glyoxylate‑inducible transcriptional repressor of all and gcl operons/glyoxylate carboligase
RA	543,091	G→C	7.5%	intergenic (+58/+170)	glxK → / ← allE	glycerate kinase II/S‑ureidoglycine aminohydrolase
RA	543,094	G→C	7.5%	intergenic (+61/+167)	glxK → / ← allE	glycerate kinase II/S‑ureidoglycine aminohydrolase
RA	603,391	C→G	9.2%	intergenic (+56/+25)	pheP → / ← ybdG	phenylalanine transporter/mechanosensitive channel protein, miniconductance
RA	603,393	T→A	9.2%	intergenic (+58/+23)	pheP → / ← ybdG	phenylalanine transporter/mechanosensitive channel protein, miniconductance
RA	603,395	C→G	9.1%	intergenic (+60/+21)	pheP → / ← ybdG	phenylalanine transporter/mechanosensitive channel protein, miniconductance
RA	650,529	G→A	7.5%	R85R (CGC→CGT)	citD ←	citrate lyase, acyl carrier (gamma) subunit
RA	650,532	T→C	7.2%	A84A (GCA→GCG)	citD ←	citrate lyase, acyl carrier (gamma) subunit
RA	672,110	G→A	5.4%	T26I (ACC→ATC)	lptE ←	LPS assembly OM complex LptDE, lipoprotein component
RA	672,113	T→C	5.3%	D25G (GAT→GGT)	lptE ←	LPS assembly OM complex LptDE, lipoprotein component
RA	681,694	A→G	5.8%	intergenic (+31/+29)	djlC → / ← hscC	J domain‑containing HscC co‑chaperone; Hsc56/Hsp70 family chaperone Hsc62; RpoD‑binding transcription inhibitor
RA	681,699	T→A	5.3%	intergenic (+36/+24)	djlC → / ← hscC	J domain‑containing HscC co‑chaperone; Hsc56/Hsp70 family chaperone Hsc62; RpoD‑binding transcription inhibitor
RA	681,700	T→A	5.3%	intergenic (+37/+23)	djlC → / ← hscC	J domain‑containing HscC co‑chaperone; Hsc56/Hsp70 family chaperone Hsc62; RpoD‑binding transcription inhibitor
RA	681,705	C→T	5.7%	intergenic (+42/+18)	djlC → / ← hscC	J domain‑containing HscC co‑chaperone; Hsc56/Hsp70 family chaperone Hsc62; RpoD‑binding transcription inhibitor
RA	699,556	C→T	9.3%	intergenic (‑379/+18)	asnB ← / ← umpH	asparagine synthetase B/UMP phosphatase
RA	699,559	A→G	8.7%	intergenic (‑382/+15)	asnB ← / ← umpH	asparagine synthetase B/UMP phosphatase
RA	710,170	C→T	8.9%	intergenic (+54/+30)	chiQ → / ← fur	chitosugar‑induced verified lipoprotein/ferric iron uptake regulon transcriptional repressor; autorepressor
RA	710,173	A→G	8.7%	intergenic (+57/+27)	chiQ → / ← fur	chitosugar‑induced verified lipoprotein/ferric iron uptake regulon transcriptional repressor; autorepressor
RA	756,643	T→A	5.5%	I246N (ATT→AAT)	sdhA →	succinate dehydrogenase, flavoprotein subunit
RA	774,356	C→G	5.6%	P16P (CCC→CCG)	ybgE →	putative inner membrane protein in cydABX‑ybgE operon
RA	774,358	T→A	5.5%	L17Q (CTG→CAG)	ybgE →	putative inner membrane protein in cydABX‑ybgE operon
RA	781,668	C→T	6.1%	intergenic (+16/‑417)	lysQ → / → nadA	tRNA‑Lys/quinolinate synthase, subunit A
RA	781,670	A→T	6.2%	intergenic (+18/‑415)	lysQ → / → nadA	tRNA‑Lys/quinolinate synthase, subunit A
RA	781,672	A→G	6.2%	intergenic (+20/‑413)	lysQ → / → nadA	tRNA‑Lys/quinolinate synthase, subunit A
RA	781,824	C→T	5.6%	intergenic (+172/‑261)	lysQ → / → nadA	tRNA‑Lys/quinolinate synthase, subunit A
RA	781,826	A→T	5.5%	intergenic (+174/‑259)	lysQ → / → nadA	tRNA‑Lys/quinolinate synthase, subunit A
RA	781,828	A→G	5.5%	intergenic (+176/‑257)	lysQ → / → nadA	tRNA‑Lys/quinolinate synthase, subunit A
RA	782,999	T→G	5.7%	L305L (CTT→CTG)	nadA →	quinolinate synthase, subunit A
RA	783,000	C→A	5.6%	Q306K (CAG→AAG)	nadA →	quinolinate synthase, subunit A
RA	847,213	A→T	6.8%	intergenic (‑94/+45)	glnP ← / ← glnH	glutamine transporter subunit/glutamine transporter subunit
RA	847,214	T→A	7.1%	intergenic (‑95/+44)	glnP ← / ← glnH	glutamine transporter subunit/glutamine transporter subunit
RA	847,215	A→T	7.2%	intergenic (‑96/+43)	glnP ← / ← glnH	glutamine transporter subunit/glutamine transporter subunit
RA	850,993	T→C	5.9%	intergenic (+28/+21)	ompX → / ← opgE	outer membrane protein X/OPG biosynthetic transmembrane phosphoethanolamine transferase
RA	850,995	T→G	5.8%	intergenic (+30/+19)	ompX → / ← opgE	outer membrane protein X/OPG biosynthetic transmembrane phosphoethanolamine transferase
RA	850,996	C→A	5.8%	intergenic (+31/+18)	ompX → / ← opgE	outer membrane protein X/OPG biosynthetic transmembrane phosphoethanolamine transferase
RA	850,998	G→A	5.2%	intergenic (+33/+16)	ompX → / ← opgE	outer membrane protein X/OPG biosynthetic transmembrane phosphoethanolamine transferase
RA	857,576	T→C	8.5%	intergenic (+21/+220)	ybiT → / ← ybiU	ABC‑F family putative regulatory ATPase/DUF1479 family protein
RA	857,578	C→G	8.6%	intergenic (+23/+218)	ybiT → / ← ybiU	ABC‑F family putative regulatory ATPase/DUF1479 family protein
RA	857,580	G→A	9.1%	intergenic (+25/+216)	ybiT → / ← ybiU	ABC‑F family putative regulatory ATPase/DUF1479 family protein
RA	866,388	A→T	6.0%	intergenic (‑24/‑180)	moeA ← / → iaaA	molybdopterin molybdenumtransferase; molybdopterin biosynthesis protein/Isoaspartyl peptidase
RA	866,393	A→T	6.0%	intergenic (‑29/‑175)	moeA ← / → iaaA	molybdopterin molybdenumtransferase; molybdopterin biosynthesis protein/Isoaspartyl peptidase
RA	897,968:1	+A	5.5%	intergenic (+39/‑21)	potI → / → ybjO	putrescine ABC transporter permease/DUF2593 family inner membrane protein
RA	897,973	Δ1 bp	5.2%	intergenic (+44/‑16)	potI → / → ybjO	putrescine ABC transporter permease/DUF2593 family inner membrane protein
RA	915,080	G→C	8.0%	intergenic (‑223/+272)	ybjE ← / ← aqpZ	putative transporter/aquaporin Z
RA	915,081	G→C	8.0%	intergenic (‑224/+271)	ybjE ← / ← aqpZ	putative transporter/aquaporin Z
RA	940,751	T→C	7.4%	intergenic (+31/‑208)	serS → / → dmsA	seryl‑tRNA synthetase/dimethyl sulfoxide reductase, anaerobic, subunit A
RA	940,754	G→A	8.1%	intergenic (+34/‑205)	serS → / → dmsA	seryl‑tRNA synthetase/dimethyl sulfoxide reductase, anaerobic, subunit A
RA	958,769	C→G	7.9%	intergenic (+28/‑43)	serC → / → aroA	3‑phosphoserine/phosphohydroxythreonine aminotransferase/5‑enolpyruvylshikimate‑3‑phosphate synthetase
RA	958,771	A→T	8.0%	intergenic (+30/‑41)	serC → / → aroA	3‑phosphoserine/phosphohydroxythreonine aminotransferase/5‑enolpyruvylshikimate‑3‑phosphate synthetase
RA	958,773	C→G	7.9%	intergenic (+32/‑39)	serC → / → aroA	3‑phosphoserine/phosphohydroxythreonine aminotransferase/5‑enolpyruvylshikimate‑3‑phosphate synthetase
RA	968,406	G→A	6.1%	R14Q (CGG→CAG)	lpxK →	lipid A 4'kinase
RA	968,409	T→A	6.1%	L15Q (CTA→CAA)	lpxK →	lipid A 4'kinase
RA	968,412	T→A	6.3%	L16* (TTG→TAG)	lpxK →	lipid A 4'kinase
RA	968,415	T→C	6.3%	L17P (CTG→CCG)	lpxK →	lipid A 4'kinase
RA	987,560	G→C	5.4%	intergenic (‑578/+25)	ompF ← / ← asnS	outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
RA	987,561	G→C	5.3%	intergenic (‑579/+24)	ompF ← / ← asnS	outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
RA	993,258	G→T	5.0%	intergenic (+24/+19)	pepN → / ← ssuB	aminopeptidase N/aliphatic sulfonate ABC transporter ATPase
RA	993,259	C→T	5.1%	intergenic (+25/+18)	pepN → / ← ssuB	aminopeptidase N/aliphatic sulfonate ABC transporter ATPase
RA	1,015,912	T→A	12.4%	intergenic (+30/+40)	rmf → / ← fabA	ribosome modulation factor/beta‑hydroxydecanoyl thioester dehydrase
RA	1,018,983	A→T	7.4%	intergenic (+46/+30)	matP → / ← ompA	Ter macrodomain organizer matS‑binding protein/outer membrane protein A (3a;II*;G;d)
RA	1,018,986	A→T	7.5%	intergenic (+49/+27)	matP → / ← ompA	Ter macrodomain organizer matS‑binding protein/outer membrane protein A (3a;II*;G;d)
RA	1,041,937	T→G	7.0%	intergenic (+22/+93)	appA → / ← etk	phosphoanhydride phosphorylase/tyrosine‑protein kinase, role in O‑antigen capsule formation
RA	1,041,940	C→A	7.0%	intergenic (+25/+90)	appA → / ← etk	phosphoanhydride phosphorylase/tyrosine‑protein kinase, role in O‑antigen capsule formation
RA	1,075,515	G→T	5.5%	A1123E (GCG→GAG)	putA ←	fused DNA‑binding transcriptional regulator/proline dehydrogenase/pyrroline‑5‑carboxylate dehydrogenase
RA	1,075,518	A→C	5.3%	L1122R (CTC→CGC)	putA ←	fused DNA‑binding transcriptional regulator/proline dehydrogenase/pyrroline‑5‑carboxylate dehydrogenase
RA	1,097,480	A→C	8.0%	intergenic (+651/+85)	ycdU → / ← serX	putative inner membrane protein/tRNA‑Ser
RA	1,100,789	G→T	5.8%	intergenic (+2/+62)	ycdZ → / ← csgG	DUF1097 family inner membrane protein/curli production assembly/transport outer membrane lipoprotein
RA	1,100,791	G→C	5.8%	intergenic (+4/+60)	ycdZ → / ← csgG	DUF1097 family inner membrane protein/curli production assembly/transport outer membrane lipoprotein
RA	1,100,793	A→C	6.0%	intergenic (+6/+58)	ycdZ → / ← csgG	DUF1097 family inner membrane protein/curli production assembly/transport outer membrane lipoprotein
RA	1,113,544	G→A	5.5%	intergenic (+138/‑35)	opgH → / → yceK	OPG biosynthetic ACP‑dependent transmembrane UDP‑glucose beta‑1,2 glycosyltransferase; nutrient‑dependent cell size regulator, FtsZ assembly antagonist/outer membrane integrity lipoprotein
RA	1,113,546	T→A	5.6%	intergenic (+140/‑33)	opgH → / → yceK	OPG biosynthetic ACP‑dependent transmembrane UDP‑glucose beta‑1,2 glycosyltransferase; nutrient‑dependent cell size regulator, FtsZ assembly antagonist/outer membrane integrity lipoprotein
RA	1,113,548	T→C	5.6%	intergenic (+142/‑31)	opgH → / → yceK	OPG biosynthetic ACP‑dependent transmembrane UDP‑glucose beta‑1,2 glycosyltransferase; nutrient‑dependent cell size regulator, FtsZ assembly antagonist/outer membrane integrity lipoprotein
RA	1,147,548	T→G	5.1%	intergenic (+8/‑73)	rpmF → / → plsX	50S ribosomal subunit protein L32/putative phosphate acyltransferase
RA	1,147,549	C→A	5.3%	intergenic (+9/‑72)	rpmF → / → plsX	50S ribosomal subunit protein L32/putative phosphate acyltransferase
RA	1,153,208	T→C	5.4%	intergenic (+28/‑92)	fabF → / → pabC	3‑oxoacyl‑[acyl‑carrier‑protein] synthase II/4‑amino‑4‑deoxychorismate lyase component of para‑aminobenzoate synthase multienzyme complex
RA	1,153,213	T→A	5.5%	intergenic (+33/‑87)	fabF → / → pabC	3‑oxoacyl‑[acyl‑carrier‑protein] synthase II/4‑amino‑4‑deoxychorismate lyase component of para‑aminobenzoate synthase multienzyme complex
RA	1,153,214	T→A	5.8%	intergenic (+34/‑86)	fabF → / → pabC	3‑oxoacyl‑[acyl‑carrier‑protein] synthase II/4‑amino‑4‑deoxychorismate lyase component of para‑aminobenzoate synthase multienzyme complex
RA	1,153,219	G→A	6.0%	intergenic (+39/‑81)	fabF → / → pabC	3‑oxoacyl‑[acyl‑carrier‑protein] synthase II/4‑amino‑4‑deoxychorismate lyase component of para‑aminobenzoate synthase multienzyme complex
RA	1,159,335	G→T	7.1%	intergenic (+33/+27)	ptsG → / ← fhuE	fused glucose‑specific PTS enzymes: IIB component/IIC component/ferric‑rhodotorulic acid outer membrane transporter
RA	1,159,336	A→C	7.1%	intergenic (+34/+26)	ptsG → / ← fhuE	fused glucose‑specific PTS enzymes: IIB component/IIC component/ferric‑rhodotorulic acid outer membrane transporter
RA	1,174,077	G→A	7.3%	intergenic (‑113/+15)	mfd ← / ← ycfT	transcription‑repair coupling factor/inner membrane protein
RA	1,174,080	T→C	7.2%	intergenic (‑116/+12)	mfd ← / ← ycfT	transcription‑repair coupling factor/inner membrane protein
RA	1,174,501	A→T	5.6%	L222Q (CTG→CAG)	ycfT ←	inner membrane protein
RA	1,174,504	A→T	5.6%	L221Q (CTG→CAG)	ycfT ←	inner membrane protein
RA	1,196,803	A→C	5.7%	intergenic (+430/+64)	icd → / ← ymfD	isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase/e14 prophage; putative SAM‑dependent methyltransferase
RA	1,196,804	G→T	6.0%	intergenic (+431/+63)	icd → / ← ymfD	isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase/e14 prophage; putative SAM‑dependent methyltransferase
RA	1,202,957	G→T	5.1%	intergenic (‑24/‑67)	cohE ← / → croE	e14 prophage; repressor protein phage e14/e14 prophage; putative DNA‑binding transcriptional regulator
RA	1,211,610	A→G	11.9%	intergenic (+33/+70)	icdC → / ← iraM	pseudogene, isocitrate dehydrogenase C‑terminal gene fragment; idcC' is a 54 codon 3' gene fragment created during e14 prophage insertion/RpoS stabilzer during Mg starvation, anti‑RssB factor
RA	1,211,612	A→T	11.9%	intergenic (+35/+68)	icdC → / ← iraM	pseudogene, isocitrate dehydrogenase C‑terminal gene fragment; idcC' is a 54 codon 3' gene fragment created during e14 prophage insertion/RpoS stabilzer during Mg starvation, anti‑RssB factor
RA	1,211,614	C→T	11.9%	intergenic (+37/+66)	icdC → / ← iraM	pseudogene, isocitrate dehydrogenase C‑terminal gene fragment; idcC' is a 54 codon 3' gene fragment created during e14 prophage insertion/RpoS stabilzer during Mg starvation, anti‑RssB factor
RA	1,224,239	A→T	6.2%	intergenic (+332/+40)	ycgI → / ← minE	pseudogene/cell division topological specificity factor
RA	1,224,242	A→T	5.0%	intergenic (+335/+37)	ycgI → / ← minE	pseudogene/cell division topological specificity factor
RA	1,232,481	C→T	5.2%	intergenic (+27/+19)	umuC → / ← dsbB	translesion error‑prone DNA polymerase V subunit; DNA polymerase activity/oxidoreductase that catalyzes reoxidation of DsbA protein disulfide isomerase I
RA	1,260,901	C→T	8.0%	intergenic (‑98/+27)	dauA ← / ← prs	C4‑dicarboxylic acid transporter/phosphoribosylpyrophosphate synthase
RA	1,260,904	A→G	7.9%	intergenic (‑101/+24)	dauA ← / ← prs	C4‑dicarboxylic acid transporter/phosphoribosylpyrophosphate synthase
JC JC	1,293,015	IS1 (+) +8 bp	10.5%	intergenic (‑93/‑505)	hns ← / → tdk	global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
JC JC	1,293,124	IS5 (+) +4 bp	6.4%	intergenic (‑202/‑400)	hns ← / → tdk	global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
JC JC	1,293,196	IS5 (+) +4 bp	7.4%	intergenic (‑274/‑328)	hns ← / → tdk	global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
RA	1,304,469	C→G	5.1%	R212R (CGC→CGG)	oppC →	oligopeptide ABC transporter permease
RA	1,304,474	T→A	5.4%	I214N (ATT→AAT)	oppC →	oligopeptide ABC transporter permease
RA	1,304,479	C→G	5.6%	P216A (CCG→GCG)	oppC →	oligopeptide ABC transporter permease
RA	1,306,787	G→A	7.3%	intergenic (+19/+34)	oppF → / ← yciU	oligopeptide ABC transporter ATPase/UPF0263 family protein
RA	1,306,788	T→C	7.3%	intergenic (+20/+33)	oppF → / ← yciU	oligopeptide ABC transporter ATPase/UPF0263 family protein
RA	1,311,830	A→G	11.0%	intergenic (+22/+18)	tonB → / ← yciA	membrane spanning protein in TonB‑ExbB‑ExbD transport complex/acyl‑CoA esterase
RA	1,311,831	C→T	11.0%	intergenic (+23/+17)	tonB → / ← yciA	membrane spanning protein in TonB‑ExbB‑ExbD transport complex/acyl‑CoA esterase
RA	1,324,839	G→T	5.4%	E32* (GAA→TAA)	yciQ →	enhancer of membrane protein expression; putative inner membrane protein
RA	1,330,396:1	+T	5.3%	intergenic (+15/+21)	sohB → / ← yciN	inner membrane protein, S49 peptidase family protein/DUF2498 protein YciN
RA	1,330,399	A→T	5.2%	intergenic (+18/+18)	sohB → / ← yciN	inner membrane protein, S49 peptidase family protein/DUF2498 protein YciN
RA	1,330,402	Δ1 bp	5.3%	intergenic (+21/+15)	sohB → / ← yciN	inner membrane protein, S49 peptidase family protein/DUF2498 protein YciN
RA	1,344,033	A→G	6.9%	L105P (CTG→CCG)	yciT ←	global regulator of transcription; DeoR family
RA	1,344,036	G→C	7.1%	T104S (ACT→AGT)	yciT ←	global regulator of transcription; DeoR family
RA	1,344,039	C→T	6.9%	R103Q (CGG→CAG)	yciT ←	global regulator of transcription; DeoR family
RA	1,354,220	C→A	5.2%	G100V (GGT→GTT)	sapC ←	antimicrobial peptide transport ABC transporter permease
RA	1,354,223	A→G	5.2%	V99A (GTG→GCG) ‡	sapC ←	antimicrobial peptide transport ABC transporter permease
RA	1,354,224	C→T	5.1%	V99M (GTG→ATG) ‡	sapC ←	antimicrobial peptide transport ABC transporter permease
RA	1,370,026	T→A	6.1%	intergenic (+23/‑190)	pspE → / → ycjM	thiosulfate:cyanide sulfurtransferase (rhodanese)/alpha amylase catalytic domain family protein
RA	1,370,029	T→A	6.0%	intergenic (+26/‑187)	pspE → / → ycjM	thiosulfate:cyanide sulfurtransferase (rhodanese)/alpha amylase catalytic domain family protein
RA	1,382,000	C→T	6.0%	C18C (TGC→TGT)	ompG →	outer membrane porin G
RA	1,382,003	A→G	6.1%	A19A (GCA→GCG)	ompG →	outer membrane porin G
RA	1,388,283	C→T	8.6%	intergenic (+22/+22)	tyrR → / ← tpx	aromatic amino acid biosynthesis and transport regulon transcriptional regulator; autorepressor; ATPase; phosphatase/lipid hydroperoxide peroxidase
RA	1,388,284	A→T	7.8%	intergenic (+23/+21)	tyrR → / ← tpx	aromatic amino acid biosynthesis and transport regulon transcriptional regulator; autorepressor; ATPase; phosphatase/lipid hydroperoxide peroxidase
RA	1,388,285	A→G	8.2%	intergenic (+24/+20)	tyrR → / ← tpx	aromatic amino acid biosynthesis and transport regulon transcriptional regulator; autorepressor; ATPase; phosphatase/lipid hydroperoxide peroxidase
RA	1,413,964	C→T	5.8%	intergenic (‑37/+20)	ralR ← / ← recT	Rac prophage; restriction alleviation protein/Rac prophage; recombination and repair protein
RA	1,413,966	T→A	5.8%	intergenic (‑39/+18)	ralR ← / ← recT	Rac prophage; restriction alleviation protein/Rac prophage; recombination and repair protein
RA	1,413,968	A→G	5.8%	intergenic (‑41/+16)	ralR ← / ← recT	Rac prophage; restriction alleviation protein/Rac prophage; recombination and repair protein
RA	1,449,050	T→A	7.2%	intergenic (+32/+26)	feaB → / ← tynA	phenylacetaldehyde dehydrogenase/tyramine oxidase, copper‑requiring
RA	1,462,028	G→A	7.1%	G379D (GGT→GAT) ‡	paaJ →	3‑oxoadipyl‑CoA/3‑oxo‑5,6‑dehydrosuberyl‑CoA thiolase
RA	1,462,029	T→C	6.9%	G379G (GGT→GGC) ‡	paaJ →	3‑oxoadipyl‑CoA/3‑oxo‑5,6‑dehydrosuberyl‑CoA thiolase
RA	1,483,343	G→C	5.0%	V95L (GTG→CTG)	hrpA →	putative ATP‑dependent helicase
RA	1,498,892	A→T	7.5%	intergenic (+17/‑46)	ydcH → / → rimL	DUF465 family protein/ribosomal‑protein‑L7/L12‑serine acetyltransferase
RA	1,498,894	C→G	7.5%	intergenic (+19/‑44)	ydcH → / → rimL	DUF465 family protein/ribosomal‑protein‑L7/L12‑serine acetyltransferase
RA	1,498,896	A→T	7.4%	intergenic (+21/‑42)	ydcH → / → rimL	DUF465 family protein/ribosomal‑protein‑L7/L12‑serine acetyltransferase
RA	1,517,481	C→G	6.2%	R31R (CGC→CGG)	ydcX →	DUF2566 family protein
RA	1,517,484	C→G	6.5%	I32M (ATC→ATG)	ydcX →	DUF2566 family protein
RA	1,541,077	G→C	6.4%	A505G (GCC→GGC)	narZ ←	nitrate reductase 2 (NRZ), alpha subunit
RA	1,552,388	T→C	5.7%	intergenic (+397/+10)	fdnI → / ← yddM	formate dehydrogenase‑N, cytochrome B556 (gamma) subunit, nitrate‑inducible/putative DNA‑binding transcriptional regulator
RA	1,557,194	A→C	7.1%	L282R (CTG→CGG)	ddpF ←	D,D‑dipeptide ABC transporter ATPase
RA	1,557,197	G→T	7.2%	P281Q (CCG→CAG)	ddpF ←	D,D‑dipeptide ABC transporter ATPase
RA	1,603,724	A→C	8.2%	T236P (ACC→CCC)	lsrC →	autoinducer 2 import system permease protein
RA	1,603,735	G→T	8.0%	G239G (GGG→GGT)	lsrC →	autoinducer 2 import system permease protein
RA	1,608,704	A→G	5.2%	S107P (TCG→CCG)	yneE ←	bestrophin family putative inner membrane protein
RA	1,608,707	C→T	5.4%	D106N (GAT→AAT)	yneE ←	bestrophin family putative inner membrane protein
RA	1,620,224	C→G	5.1%	intergenic (+17/+14)	marB → / ← eamA	periplasmic mar operon regulator/cysteine and O‑acetyl‑L‑serine efflux system
RA	1,620,227	C→G	5.3%	intergenic (+20/+11)	marB → / ← eamA	periplasmic mar operon regulator/cysteine and O‑acetyl‑L‑serine efflux system
RA	1,674,955	A→T	6.7%	intergenic (+8/+17)	tqsA → / ← pntB	pheromone AI‑2 transporter/pyridine nucleotide transhydrogenase, beta subunit
RA	1,674,958	A→T	6.8%	intergenic (+11/+14)	tqsA → / ← pntB	pheromone AI‑2 transporter/pyridine nucleotide transhydrogenase, beta subunit
RA	1,685,527	A→G	100%	G354G (GGT→GGC)	fumC ←	fumarate hydratase (fumarase C),aerobic Class II
RA	1,689,817	C→A	6.0%	intergenic (+66/‑35)	manA → / → ydgA	mannose‑6‑phosphate isomerase/DUF945 family protein
RA	1,689,819	A→T	5.9%	intergenic (+68/‑33)	manA → / → ydgA	mannose‑6‑phosphate isomerase/DUF945 family protein
RA	1,689,821	T→G	6.0%	intergenic (+70/‑31)	manA → / → ydgA	mannose‑6‑phosphate isomerase/DUF945 family protein
RA	1,703,251	A→T	6.3%	intergenic (+17/+17)	add → / ← ydgJ	adenosine deaminase/putative oxidoreductase
RA	1,703,252	A→T	6.3%	intergenic (+18/+16)	add → / ← ydgJ	adenosine deaminase/putative oxidoreductase
RA	1,747,025	G→C	9.0%	intergenic (+20/‑106)	ydhR → / → ydhS	putative monooxygenase/putative oxidoreductase
RA	1,747,027	T→A	9.0%	intergenic (+22/‑104)	ydhR → / → ydhS	putative monooxygenase/putative oxidoreductase
RA	1,747,029	G→C	9.0%	intergenic (+24/‑102)	ydhR → / → ydhS	putative monooxygenase/putative oxidoreductase
RA	1,757,688	T→A	14.0%	intergenic (+31/+33)	lpp → / ← ldtE	murein lipoprotein/murein L,D‑transpeptidase
RA	1,764,687	T→C	6.8%	intergenic (‑301/+26)	sufA ← / ← rydB	Fe‑S cluster assembly protein/novel sRNA, function unknown
RA	1,764,701	G→A	6.1%	intergenic (‑315/+12)	sufA ← / ← rydB	Fe‑S cluster assembly protein/novel sRNA, function unknown
RA	1,770,203	T→A	6.1%	intergenic (+17/‑169)	ydiK → / → rprA	UPF0118 family inner membrane protein/sRNA antisense activator for RpoS translation, Hfq‑dependent
RA	1,770,204	C→G	5.5%	intergenic (+18/‑168)	ydiK → / → rprA	UPF0118 family inner membrane protein/sRNA antisense activator for RpoS translation, Hfq‑dependent
RA	1,770,205	T→A	5.5%	intergenic (+19/‑167)	ydiK → / → rprA	UPF0118 family inner membrane protein/sRNA antisense activator for RpoS translation, Hfq‑dependent
RA	1,793,668	C→A	6.2%	E148* (GAA→TAA)	btuE ←	glutathione peroxidase
RA	1,795,227	A→T	12.2%	intergenic (‑75/+26)	btuC ← / ← ihfA	vitamin B12 ABC transporter permease/integration host factor (IHF), DNA‑binding protein, alpha subunit
RA	1,795,228	G→C	12.3%	intergenic (‑76/+25)	btuC ← / ← ihfA	vitamin B12 ABC transporter permease/integration host factor (IHF), DNA‑binding protein, alpha subunit
RA	1,795,229	A→T	12.3%	intergenic (‑77/+24)	btuC ← / ← ihfA	vitamin B12 ABC transporter permease/integration host factor (IHF), DNA‑binding protein, alpha subunit
RA	1,799,370	Δ1 bp	5.7%	intergenic (‑100/+23)	pheM ← / ← rplT	phenylalanyl‑tRNA synthetase operon leader peptide/50S ribosomal subunit protein L20
RA	1,799,374:1	+T	5.7%	intergenic (‑104/+19)	pheM ← / ← rplT	phenylalanyl‑tRNA synthetase operon leader peptide/50S ribosomal subunit protein L20
RA	1,808,680	T→A	7.1%	intergenic (+24/+17)	yniA → / ← yniB	fructosamine kinase family protein/putative inner membrane protein
RA	1,808,682	C→G	7.2%	intergenic (+26/+15)	yniA → / ← yniB	fructosamine kinase family protein/putative inner membrane protein
RA	1,808,684	T→A	7.1%	intergenic (+28/+13)	yniA → / ← yniB	fructosamine kinase family protein/putative inner membrane protein
RA	1,810,062	T→C	7.3%	intergenic (+14/‑149)	yniC → / → ydjM	2‑deoxyglucose‑6‑P phosphatase/inner membrane protein regulated by LexA
RA	1,810,065	T→G	7.3%	intergenic (+17/‑146)	yniC → / → ydjM	2‑deoxyglucose‑6‑P phosphatase/inner membrane protein regulated by LexA
RA	1,810,066	C→A	7.2%	intergenic (+18/‑145)	yniC → / → ydjM	2‑deoxyglucose‑6‑P phosphatase/inner membrane protein regulated by LexA
RA	1,810,069	G→A	7.4%	intergenic (+21/‑142)	yniC → / → ydjM	2‑deoxyglucose‑6‑P phosphatase/inner membrane protein regulated by LexA
RA	1,850,715	Δ1 bp	6.6%	intergenic (+22/‑145)	sppA → / → ansA	protease IV (signal peptide peptidase)/cytoplasmic L‑asparaginase 1
RA	1,850,719:1	+T	6.6%	intergenic (+26/‑141)	sppA → / → ansA	protease IV (signal peptide peptidase)/cytoplasmic L‑asparaginase 1
RA	1,856,333	T→G	8.3%	E199A (GAG→GCG) ‡	ydjH ←	putative kinase
RA	1,856,334	C→A	8.3%	E199* (GAG→TAG) ‡	ydjH ←	putative kinase
RA	1,864,758	G→A	6.9%	intergenic (+24/+24)	yeaD → / ← yeaE	D‑hexose‑6‑phosphate epimerase‑like protein/aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent
RA	1,864,763	A→T	6.6%	intergenic (+29/+19)	yeaD → / ← yeaE	D‑hexose‑6‑phosphate epimerase‑like protein/aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent
RA	1,864,768	T→C	7.4%	intergenic (+34/+14)	yeaD → / ← yeaE	D‑hexose‑6‑phosphate epimerase‑like protein/aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent
RA	1,865,682	G→C	7.8%	intergenic (‑46/+44)	yeaE ← / ← mipA	aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent/scaffolding protein for murein synthesizing machinery
RA	1,883,027	C→G	7.1%	intergenic (+30/‑161)	dmlA → / → yeaV	D‑malate oxidase, NAD‑dependent; putative tartrate dehydrogenase/putative transporter
RA	1,901,029	Δ1 bp	5.7%	coding (557/1557 nt)	yoaE ←	putative membrane protein/conserved protein
RA	1,901,034	C→G	5.7%	T184T (ACG→ACC)	yoaE ←	putative membrane protein/conserved protein
RA	1,901,038:1	+T	5.8%	coding (548/1557 nt)	yoaE ←	putative membrane protein/conserved protein
RA	1,926,891	G→C	5.1%	S650* (TCA→TGA)	ptrB ←	protease II
RA	1,977,223:1	+A	7.5%	intergenic (‑84/+43)	motA ← / ← flhC	proton conductor component of flagella motor/flagellar class II regulon transcriptional activator, with FlhD
RA	1,977,227	T→A	8.4%	intergenic (‑88/+39)	motA ← / ← flhC	proton conductor component of flagella motor/flagellar class II regulon transcriptional activator, with FlhD
RA	1,977,230	Δ1 bp	8.4%	intergenic (‑91/+36)	motA ← / ← flhC	proton conductor component of flagella motor/flagellar class II regulon transcriptional activator, with FlhD
MC JC	1,978,503	Δ776 bp	100%		insB1–insA	insB1, insA
RA	1,985,112	C→G	13.7%	intergenic (‑43/+27)	araG ← / ← araF	L‑arabinose ABC transporter ATPase/L‑arabinose ABC transporter periplasmic binding protein
RA	1,987,442	Δ1 bp	6.3%	intergenic (+14/+65)	ftnB → / ← yecJ	ferritin B, putative ferrous iron reservoir/DUF2766 family protein
RA	1,987,450:1	+A	6.8%	intergenic (+22/+57)	ftnB → / ← yecJ	ferritin B, putative ferrous iron reservoir/DUF2766 family protein
RA	2,009,731	A→G	7.8%	intergenic (+19/‑90)	yedF → / → yedK	putative TusA family sulfurtransferase/DUF159 family protein
RA	2,009,732	C→G	7.2%	intergenic (+20/‑89)	yedF → / → yedK	putative TusA family sulfurtransferase/DUF159 family protein
RA	2,009,733	C→T	8.0%	intergenic (+21/‑88)	yedF → / → yedK	putative TusA family sulfurtransferase/DUF159 family protein
RA	2,028,158	G→C	7.0%	intergenic (‑141/+30)	yedQ ← / ← yodC	putative membrane‑anchored diguanylate cyclase/uncharacterized protein
RA	2,028,159	T→A	7.0%	intergenic (‑142/+29)	yedQ ← / ← yodC	putative membrane‑anchored diguanylate cyclase/uncharacterized protein
RA	2,028,160	G→C	7.5%	intergenic (‑143/+28)	yedQ ← / ← yodC	putative membrane‑anchored diguanylate cyclase/uncharacterized protein
RA	2,079,004	G→C	9.5%	intergenic (+73/+28)	yoeF → / ← yeeX	pseudogene, CP4‑44 putative prophage remnant;Phage or Prophage Related/UPF0265 family protein
RA	2,089,854	A→T	6.5%	intergenic (‑141/‑142)	yefM ← / → hisL	antitoxin of the YoeB‑YefM toxin‑antitoxin system/his operon leader peptide
RA	2,145,313	C→A	100%	S683Y (TCC→TAC)	yegE →	putative diguanylate cyclase
RA	2,173,361	Δ2 bp	100%	pseudogene (1‑2/442 nt)	gatC ←	pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC
RA	2,177,332	C→T	9.1%	intergenic (‑128/+180)	gatY ← / ← fbaB	D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I
RA	2,177,337	G→T	9.0%	intergenic (‑133/+175)	gatY ← / ← fbaB	D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I
RA	2,177,340	A→C	9.0%	intergenic (‑136/+172)	gatY ← / ← fbaB	D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I
RA	2,177,345	A→G	9.3%	intergenic (‑141/+167)	gatY ← / ← fbaB	D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I
RA	2,187,314	C→G	9.4%	intergenic (+16/+66)	rcnB → / ← yehA	periplasmic modulator of Ni and Co efflux/putative fimbrial‑like adhesin protein
RA	2,255,991	A→T	5.5%	K213* (AAA→TAA) ‡	yeiL →	putative transcriptional regulator
RA	2,255,992	A→T	5.5%	K213I (AAA→ATA) ‡	yeiL →	putative transcriptional regulator
RA	2,270,602	T→C	10.5%	intergenic (+57/‑124)	mepS → / → rtn	murein DD‑endopeptidase, space‑maker hydrolase, mutational suppressor of prc thermosensitivity, outer membrane lipoprotein, weak murein LD‑carboxypeptidase/resistance protein for phages lambda and N4, putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	2,270,605	G→A	10.6%	intergenic (+60/‑121)	mepS → / → rtn	murein DD‑endopeptidase, space‑maker hydrolase, mutational suppressor of prc thermosensitivity, outer membrane lipoprotein, weak murein LD‑carboxypeptidase/resistance protein for phages lambda and N4, putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	2,282,830	T→C	5.3%	intergenic (+29/+110)	rplY → / ← yejK	50S ribosomal subunit protein L25/spermidine nucleoid‑associated protein
RA	2,282,831	C→G	5.3%	intergenic (+30/+109)	rplY → / ← yejK	50S ribosomal subunit protein L25/spermidine nucleoid‑associated protein
RA	2,282,832	C→G	5.9%	intergenic (+31/+108)	rplY → / ← yejK	50S ribosomal subunit protein L25/spermidine nucleoid‑associated protein
RA	2,282,833	G→A	5.4%	intergenic (+32/+107)	rplY → / ← yejK	50S ribosomal subunit protein L25/spermidine nucleoid‑associated protein
RA	2,286,311	C→G	6.5%	intergenic (+24/+79)	proL → / ← yejO	tRNA‑Pro/pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system
RA	2,286,313	T→A	6.5%	intergenic (+26/+77)	proL → / ← yejO	tRNA‑Pro/pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system
RA	2,286,315	C→G	6.4%	intergenic (+28/+75)	proL → / ← yejO	tRNA‑Pro/pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system
RA	2,305,085	A→G	23.2%	intergenic (+692/+23)	eco → / ← mqo	ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA	2,305,086	C→G	23.2%	intergenic (+693/+22)	eco → / ← mqo	ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA	2,305,087	C→T	23.1%	intergenic (+694/+21)	eco → / ← mqo	ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA	2,314,800	A→C	8.3%	Q438P (CAG→CCG) ‡	rcsD →	phosphotransfer intermediate protein in two‑component regulatory system with RcsBC
RA	2,314,801	G→T	8.0%	Q438H (CAG→CAT) ‡	rcsD →	phosphotransfer intermediate protein in two‑component regulatory system with RcsBC
RA	2,318,095	C→G	100%	L594F (TTG→TTC)	rcsC ←	hybrid sensory kinase in two‑component regulatory system with RcsB and YojN
RA	2,364,995	T→G	7.7%	intergenic (+16/+23)	nudI → / ← ais	nucleoside triphosphatase/putative LPS core heptose(II)‑phosphate phosphatase
RA	2,364,998	C→A	7.6%	intergenic (+19/+20)	nudI → / ← ais	nucleoside triphosphatase/putative LPS core heptose(II)‑phosphate phosphatase
RA	2,383,956	A→T	7.6%	intergenic (+32/+39)	elaD → / ← yfbK	protease, capable of cleaving an AMC‑ubiquitin model substrate/Von Willebrand factor domain putative lipoprotein
RA	2,383,959	A→T	7.6%	intergenic (+35/+36)	elaD → / ← yfbK	protease, capable of cleaving an AMC‑ubiquitin model substrate/Von Willebrand factor domain putative lipoprotein
RA	2,391,414	C→G	6.2%	R31P (CGA→CCA)	nuoN ←	NADH:ubiquinone oxidoreductase, membrane subunit N
RA	2,391,417	C→G	6.3%	W30S (TGG→TCG)	nuoN ←	NADH:ubiquinone oxidoreductase, membrane subunit N
RA	2,414,689	C→G	5.3%	intergenic (+17/‑58)	ackA → / → pta	acetate kinase A and propionate kinase 2/phosphate acetyltransferase
RA	2,415,725	C→A	6.2%	L327M (CTG→ATG) ‡	pta →	phosphate acetyltransferase
RA	2,415,726	T→G	5.8%	L327R (CTG→CGG) ‡	pta →	phosphate acetyltransferase
RA	2,430,144	G→C	5.7%	A32G (GCC→GGC)	purF ←	amidophosphoribosyltransferase
RA	2,440,295	A→T	6.3%	intergenic (‑175/+90)	yfcJ ← / ← fabB	putative arabinose efflux transporter/3‑oxoacyl‑[acyl‑carrier‑protein] synthase I
RA	2,440,296	T→G	6.3%	intergenic (‑176/+89)	yfcJ ← / ← fabB	putative arabinose efflux transporter/3‑oxoacyl‑[acyl‑carrier‑protein] synthase I
RA	2,440,297	C→A	6.3%	intergenic (‑177/+88)	yfcJ ← / ← fabB	putative arabinose efflux transporter/3‑oxoacyl‑[acyl‑carrier‑protein] synthase I
RA	2,440,298	A→T	6.2%	intergenic (‑178/+87)	yfcJ ← / ← fabB	putative arabinose efflux transporter/3‑oxoacyl‑[acyl‑carrier‑protein] synthase I
RA	2,462,677	A→T	6.0%	intergenic (+31/‑335)	fadL → / → yfdF	long‑chain fatty acid outer membrane transporter/uncharacterized protein
RA	2,462,678	T→A	5.7%	intergenic (+32/‑334)	fadL → / → yfdF	long‑chain fatty acid outer membrane transporter/uncharacterized protein
RA	2,462,679	A→T	5.8%	intergenic (+33/‑333)	fadL → / → yfdF	long‑chain fatty acid outer membrane transporter/uncharacterized protein
RA	2,474,878	T→C	8.0%	intergenic (+22/‑106)	yfdQ → / → yfdR	CPS‑53 (KpLE1) prophage; uncharacterized protein/CPS‑53 (KpLE1) prophage; conserved protein
RA	2,474,881	G→A	8.7%	intergenic (+25/‑103)	yfdQ → / → yfdR	CPS‑53 (KpLE1) prophage; uncharacterized protein/CPS‑53 (KpLE1) prophage; conserved protein
RA	2,521,344	C→T	6.8%	intergenic (+16/+249)	lysV → / ← xapR	tRNA‑Lys/transcriptional activator of xapAB
RA	2,521,346	A→T	6.6%	intergenic (+18/+247)	lysV → / ← xapR	tRNA‑Lys/transcriptional activator of xapAB
RA	2,521,348	A→G	6.7%	intergenic (+20/+245)	lysV → / ← xapR	tRNA‑Lys/transcriptional activator of xapAB
RA	2,536,047	T→G	100%	F72V (TTT→GTT)	crr →	glucose‑specific enzyme IIA component of PTS
RA	2,561,205	A→T	5.4%	intergenic (+307/‑163)	yffL → / → yffM	CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein
RA	2,561,206	A→T	6.0%	intergenic (+308/‑162)	yffL → / → yffM	CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein
RA	2,587,131	G→C	5.4%	Q467H (CAG→CAC)	narQ →	sensory histidine kinase in two‑component regulatory system with NarP
RA	2,587,132	G→C	5.4%	V468L (GTG→CTG)	narQ →	sensory histidine kinase in two‑component regulatory system with NarP
RA	2,596,873	Δ1 bp	8.9%	intergenic (‑136/+32)	ypfJ ← / ← purC	putative neutral zinc metallopeptidase/phosphoribosylaminoimidazole‑succinocarboxamide synthetase
RA	2,596,878:1	+G	8.4%	intergenic (‑141/+27)	ypfJ ← / ← purC	putative neutral zinc metallopeptidase/phosphoribosylaminoimidazole‑succinocarboxamide synthetase
RA	2,622,348:1	+A	7.0%	coding (115/639 nt)	purN →	phosphoribosylglycinamide formyltransferase 1
RA	2,622,354	Δ1 bp	7.1%	coding (121/639 nt)	purN →	phosphoribosylglycinamide formyltransferase 1
RA	2,632,584	A→T	6.7%	intergenic (‑49/+20)	guaA ← / ← guaB	GMP synthetase (glutamine aminotransferase)/IMP dehydrogenase
RA	2,632,586	G→C	6.7%	intergenic (‑51/+18)	guaA ← / ← guaB	GMP synthetase (glutamine aminotransferase)/IMP dehydrogenase
RA	2,632,588	A→T	6.7%	intergenic (‑53/+16)	guaA ← / ← guaB	GMP synthetase (glutamine aminotransferase)/IMP dehydrogenase
RA	2,637,234	C→A	6.4%	K41N (AAG→AAT) ‡	der ←	GTPase; multicopy suppressor of ftsJ
RA	2,637,235	T→G	6.5%	K41T (AAG→ACG) ‡	der ←	GTPase; multicopy suppressor of ftsJ
RA	2,637,444	A→G	6.0%	intergenic (‑88/+30)	der ← / ← bamB	GTPase; multicopy suppressor of ftsJ/BamABCDE complex OM biogenesis lipoprotein
RA	2,640,666	A→C	5.1%	intergenic (‑91/+20)	hisS ← / ← ispG	histidyl tRNA synthetase/1‑hydroxy‑2‑methyl‑2‑(E)‑butenyl 4‑diphosphate synthase
RA	2,640,668	G→T	5.1%	intergenic (‑93/+18)	hisS ← / ← ispG	histidyl tRNA synthetase/1‑hydroxy‑2‑methyl‑2‑(E)‑butenyl 4‑diphosphate synthase
RA	2,653,367	G→A	8.5%	intergenic (+28/‑488)	sseA → / → ryfA	3‑mercaptopyruvate sulfurtransferase/novel sRNA, function unknown
RA	2,653,372	T→C	9.1%	intergenic (+33/‑483)	sseA → / → ryfA	3‑mercaptopyruvate sulfurtransferase/novel sRNA, function unknown
RA	2,660,612	T→A	5.0%	Y307F (TAC→TTC)	iscS ←	cysteine desulfurase (tRNA sulfurtransferase), PLP‑dependent
RA	2,691,169	A→T	9.9%	noncoding (172/184 nt)	glmY ←	sRNA activator of glmS mRNA, glmZ processing antagonist
RA	2,691,171	T→A	9.7%	noncoding (170/184 nt)	glmY ←	sRNA activator of glmS mRNA, glmZ processing antagonist
RA	2,691,173	A→T	9.8%	noncoding (168/184 nt)	glmY ←	sRNA activator of glmS mRNA, glmZ processing antagonist
RA	2,704,304	A→G	10.1%	intergenic (‑241/+31)	rnc ← / ← lepB	RNase III/leader peptidase (signal peptidase I)
RA	2,704,306	A→T	10.0%	intergenic (‑243/+29)	rnc ← / ← lepB	RNase III/leader peptidase (signal peptidase I)
RA	2,704,308	C→T	9.9%	intergenic (‑245/+27)	rnc ← / ← lepB	RNase III/leader peptidase (signal peptidase I)
RA	2,706,121:1	+T	5.2%	coding (1004/1800 nt)	lepA ←	back‑translocating elongation factor EF4, GTPase
RA	2,706,134	Δ1 bp	6.6%	coding (991/1800 nt)	lepA ←	back‑translocating elongation factor EF4, GTPase
RA	2,716,030	T→G	6.9%	intergenic (+20/+36)	eamB → / ← grcA	cysteine and O‑acetylserine exporter/autonomous glycyl radical cofactor
RA	2,716,033	C→A	6.4%	intergenic (+23/+33)	eamB → / ← grcA	cysteine and O‑acetylserine exporter/autonomous glycyl radical cofactor
RA	2,724,412	A→T	5.2%	A95A (GCA→GCT)	yfiM →	putative lipoprotein
RA	2,731,073	A→T	8.2%	noncoding (85/1542 nt)	rrsG ←	16S ribosomal RNA of rrnG operon
RA	2,731,074	A→T	7.9%	noncoding (84/1542 nt)	rrsG ←	16S ribosomal RNA of rrnG operon
RA	2,736,911	C→T	5.9%	intergenic (+28/‑243)	bamD → / → raiA	BamABCDE complex OM biogenesis lipoprotein/cold shock protein associated with 30S ribosomal subunit
RA	2,736,913	T→A	5.6%	intergenic (+30/‑241)	bamD → / → raiA	BamABCDE complex OM biogenesis lipoprotein/cold shock protein associated with 30S ribosomal subunit
RA	2,736,914	T→A	5.7%	intergenic (+31/‑240)	bamD → / → raiA	BamABCDE complex OM biogenesis lipoprotein/cold shock protein associated with 30S ribosomal subunit
RA	2,736,916	A→G	6.2%	intergenic (+33/‑238)	bamD → / → raiA	BamABCDE complex OM biogenesis lipoprotein/cold shock protein associated with 30S ribosomal subunit
RA	2,750,073	G→T	7.9%	intergenic (+13/+42)	yfjD → / ← grpE	UPF0053 family inner membrane protein/heat shock protein
RA	2,750,078	T→G	8.1%	intergenic (+18/+37)	yfjD → / ← grpE	UPF0053 family inner membrane protein/heat shock protein
RA	2,750,081	C→A	8.1%	intergenic (+21/+34)	yfjD → / ← grpE	UPF0053 family inner membrane protein/heat shock protein
RA	2,750,086	A→C	8.3%	intergenic (+26/+29)	yfjD → / ← grpE	UPF0053 family inner membrane protein/heat shock protein
RA	2,761,620	T→G	6.9%	K641Q (AAG→CAG)	yfjK ←	radiation resistance protein; DEAD/H helicase‑like protein; CP4‑57 putative defective prophage
RA	2,761,623	C→A	6.8%	V640L (GTA→TTA)	yfjK ←	radiation resistance protein; DEAD/H helicase‑like protein; CP4‑57 putative defective prophage
RA	2,775,093	G→A	5.3%	intergenic (+72/‑452)	yfjW → / → ypjI	CP4‑57 prophage; putative inner membrane protein/pseudogene, CP4‑57 putative prophage remnant;Phage or Prophage Related
RA	2,796,375	T→A	6.4%	I138F (ATT→TTT)	ygaU ←	uncharacterized protein
RA	2,800,515	C→A	6.0%	intergenic (+40/‑208)	ygaM → / → nrdH	putative membrane‑anchored DUF883 family ribosome‑binding protein/hydrogen donor for NrdEF electron transport system; glutaredoxin‑like protein
RA	2,800,517	T→A	5.9%	intergenic (+42/‑206)	ygaM → / → nrdH	putative membrane‑anchored DUF883 family ribosome‑binding protein/hydrogen donor for NrdEF electron transport system; glutaredoxin‑like protein
RA	2,800,519	T→G	5.8%	intergenic (+44/‑204)	ygaM → / → nrdH	putative membrane‑anchored DUF883 family ribosome‑binding protein/hydrogen donor for NrdEF electron transport system; glutaredoxin‑like protein
RA	2,801,056	A→T	5.7%	N31I (AAT→ATT)	nrdI →	NrdEF cluster assembly flavodoxin
RA	2,807,091	T→C	5.4%	intergenic (+17/‑41)	proW → / → proX	glycine betaine/proline ABC transporter permease/glycine betaine/proline ABC transporter periplasmic binding protein; cold shock protein
RA	2,807,093	A→T	5.1%	intergenic (+19/‑39)	proW → / → proX	glycine betaine/proline ABC transporter permease/glycine betaine/proline ABC transporter periplasmic binding protein; cold shock protein
RA	2,807,095	G→A	5.1%	intergenic (+21/‑37)	proW → / → proX	glycine betaine/proline ABC transporter permease/glycine betaine/proline ABC transporter periplasmic binding protein; cold shock protein
RA	2,810,872	C→T	5.2%	H35Y (CAC→TAC) ‡	mprA →	transcriptional repressor of microcin B17 synthesis and multidrug efflux
RA	2,810,873	A→G	5.2%	H35R (CAC→CGC) ‡	mprA →	transcriptional repressor of microcin B17 synthesis and multidrug efflux
RA	2,818,392	A→T	5.9%	intergenic (‑118/+81)	argY ← / ← argV	tRNA‑Arg/tRNA‑Arg
RA	2,818,393	A→T	6.4%	intergenic (‑119/+80)	argY ← / ← argV	tRNA‑Arg/tRNA‑Arg
RA	2,838,222	A→T	7.4%	intergenic (‑117/+32)	hydN ← / ← ascG	formate dehydrogenase‑H, [4Fe‑4S] ferredoxin subunit/asc operon transcriptional repressor; prpBC operon repressor
RA	2,838,231	A→T	6.7%	intergenic (‑126/+23)	hydN ← / ← ascG	formate dehydrogenase‑H, [4Fe‑4S] ferredoxin subunit/asc operon transcriptional repressor; prpBC operon repressor
RA	2,866,487	G→C	6.9%	intergenic (+22/+72)	ygbN → / ← rpoS	putative transporter/RNA polymerase, sigma S (sigma 38) factor
RA	2,866,488	G→C	6.9%	intergenic (+23/+71)	ygbN → / ← rpoS	putative transporter/RNA polymerase, sigma S (sigma 38) factor
RA	2,873,915	A→G	5.8%	H26H (CAT→CAC) ‡	cysC ←	adenosine 5'‑phosphosulfate kinase
RA	2,873,917	G→C	5.9%	H26D (CAT→GAT) ‡	cysC ←	adenosine 5'‑phosphosulfate kinase
RA	2,873,919	C→T	6.0%	G25D (GGT→GAT)	cysC ←	adenosine 5'‑phosphosulfate kinase
RA	2,898,535	T→C	6.7%	K295R (AAG→AGG)	ygcU ←	putative FAD‑linked oxidoreductase
RA	2,898,541	A→T	6.5%	I293N (ATT→AAT)	ygcU ←	putative FAD‑linked oxidoreductase
RA	2,898,547	G→A	5.3%	P291L (CCT→CTT)	ygcU ←	putative FAD‑linked oxidoreductase
RA	2,900,322	C→T	8.0%	intergenic (‑49/‑270)	ygcW ← / → yqcE	putative SDR family oxidoreductase/putative MFS transporter, inner membrane protein
RA	2,900,324	G→T	8.1%	intergenic (‑51/‑268)	ygcW ← / → yqcE	putative SDR family oxidoreductase/putative MFS transporter, inner membrane protein
RA	2,900,327	A→C	7.9%	intergenic (‑54/‑265)	ygcW ← / → yqcE	putative SDR family oxidoreductase/putative MFS transporter, inner membrane protein
RA	2,902,494	G→T	5.5%	G200V (GGA→GTA) ‡	ygcE →	putative kinase
RA	2,902,495	A→C	5.1%	G200G (GGA→GGC) ‡	ygcE →	putative kinase
RA	2,918,017	C→T	6.2%	intergenic (+204/+28)	barA → / ← gudD	hybrid sensory histidine kinase, in two‑component regulatory system with UvrY/D‑glucarate dehydratase 1
RA	2,918,019	G→T	6.1%	intergenic (+206/+26)	barA → / ← gudD	hybrid sensory histidine kinase, in two‑component regulatory system with UvrY/D‑glucarate dehydratase 1
RA	2,918,020	A→C	6.1%	intergenic (+207/+25)	barA → / ← gudD	hybrid sensory histidine kinase, in two‑component regulatory system with UvrY/D‑glucarate dehydratase 1
RA	2,918,022	A→G	6.1%	intergenic (+209/+23)	barA → / ← gudD	hybrid sensory histidine kinase, in two‑component regulatory system with UvrY/D‑glucarate dehydratase 1
RA	2,961,248	A→T	6.5%	L394Q (CTG→CAG)	recC ←	exonuclease V (RecBCD complex), gamma chain
RA	2,961,251	A→T	6.6%	L393Q (CTG→CAG)	recC ←	exonuclease V (RecBCD complex), gamma chain
RA	2,971,146	T→C	6.7%	intergenic (+13/‑125)	ygdQ → / → ygdR	UPF0053 family inner membrane protein/DUF903 family verified lipoprotein
RA	2,971,151	T→C	6.5%	intergenic (+18/‑120)	ygdQ → / → ygdR	UPF0053 family inner membrane protein/DUF903 family verified lipoprotein
RA	2,971,154	G→A	6.9%	intergenic (+21/‑117)	ygdQ → / → ygdR	UPF0053 family inner membrane protein/DUF903 family verified lipoprotein
RA	2,971,159	G→A	6.3%	intergenic (+26/‑112)	ygdQ → / → ygdR	UPF0053 family inner membrane protein/DUF903 family verified lipoprotein
RA	2,976,320	T→G	7.7%	noncoding (66/82 nt)	omrB ←	sRNA antisense regulator downregulates OM proteins and curli; positively regulated by OmpR/EnvZ, Hfq‑dependent
RA	2,976,321	C→A	7.8%	noncoding (65/82 nt)	omrB ←	sRNA antisense regulator downregulates OM proteins and curli; positively regulated by OmpR/EnvZ, Hfq‑dependent
RA	2,980,742	A→G	5.7%	intergenic (‑107/+22)	ygeA ← / ← araE	Asp/Glu_racemase family protein/arabinose transporter
RA	2,980,744	A→T	5.9%	intergenic (‑109/+20)	ygeA ← / ← araE	Asp/Glu_racemase family protein/arabinose transporter
RA	2,980,746	C→T	6.1%	intergenic (‑111/+18)	ygeA ← / ← araE	Asp/Glu_racemase family protein/arabinose transporter
RA	3,020,510	G→T	9.9%	intergenic (+21/‑30)	ssnA → / → ygfM	putative chlorohydrolase/aminohydrolase/putative oxidoreductase
RA	3,020,511	C→G	9.8%	intergenic (+22/‑29)	ssnA → / → ygfM	putative chlorohydrolase/aminohydrolase/putative oxidoreductase
RA	3,020,512	A→C	9.9%	intergenic (+23/‑28)	ssnA → / → ygfM	putative chlorohydrolase/aminohydrolase/putative oxidoreductase
RA	3,033,624	A→G	5.4%	intergenic (+11/+33)	idi → / ← lysS	isopentenyl diphosphate isomerase/lysine tRNA synthetase, constitutive
RA	3,033,627	T→A	5.3%	intergenic (+14/+30)	idi → / ← lysS	isopentenyl diphosphate isomerase/lysine tRNA synthetase, constitutive
RA	3,033,628	T→A	6.1%	intergenic (+15/+29)	idi → / ← lysS	isopentenyl diphosphate isomerase/lysine tRNA synthetase, constitutive
RA	3,033,631	C→T	5.4%	intergenic (+18/+26)	idi → / ← lysS	isopentenyl diphosphate isomerase/lysine tRNA synthetase, constitutive
RA	3,037,956	A→C	8.3%	W51G (TGG→GGG)	recJ ←	ssDNA exonuclease, 5' ‑‑> 3'‑specific
RA	3,037,957	G→T	8.6%	P50P (CCC→CCA)	recJ ←	ssDNA exonuclease, 5' ‑‑> 3'‑specific
RA	3,056,125	G→T	5.6%	noncoding (143/183 nt)	ssrS →	6S RNA inhibits RNA polymerase promoter binding
RA	3,066,299:1	+G	5.7%	coding (875/897 nt)	ygfI ←	putative DNA‑binding transcriptional regulator
RA	3,066,307	Δ1 bp	5.1%	coding (867/897 nt)	ygfI ←	putative DNA‑binding transcriptional regulator
RA	3,066,308	A→T	5.9%	I289N (ATT→AAT) ‡	ygfI ←	putative DNA‑binding transcriptional regulator
RA	3,066,309	T→A	5.3%	I289F (ATT→TTT) ‡	ygfI ←	putative DNA‑binding transcriptional regulator
RA	3,066,310	A→T	5.9%	H288Q (CAT→CAA)	ygfI ←	putative DNA‑binding transcriptional regulator
RA	3,066,319	Δ1 bp	7.1%	coding (855/897 nt)	ygfI ←	putative DNA‑binding transcriptional regulator
RA	3,067,320	A→T	7.9%	intergenic (‑147/+20)	ygfI ← / ← yggE	putative DNA‑binding transcriptional regulator/oxidative stress defense protein
RA	3,067,323	A→T	7.7%	intergenic (‑150/+17)	ygfI ← / ← yggE	putative DNA‑binding transcriptional regulator/oxidative stress defense protein
RA	3,101,541	G→C	7.5%	P28R (CCG→CGG)	yggN ←	DUF2884 family putative periplasmic protein
RA	3,114,881	A→C	6.1%	L1411R (CTG→CGG) ‡	sslE ←	putative secreted and surface‑associated lipoprotein mucinase
RA	3,114,882	G→T	6.6%	L1411M (CTG→ATG) ‡	sslE ←	putative secreted and surface‑associated lipoprotein mucinase
RA	3,124,932	G→C	5.0%	C176W (TGC→TGG)	glcF ←	glycolate oxidase 4Fe‑4S iron‑sulfur cluster subunit
RA	3,156,590	C→A	6.1%	intergenic (+72/‑33)	yqhD → / → dkgA	aldehyde reductase, NADPH‑dependent/2,5‑diketo‑D‑gluconate reductase A
RA	3,156,591	T→G	5.9%	intergenic (+73/‑32)	yqhD → / → dkgA	aldehyde reductase, NADPH‑dependent/2,5‑diketo‑D‑gluconate reductase A
RA	3,180,497	Δ1 bp	8.3%	coding (77/1161 nt)	ygiC →	ATP‑Grasp family ATPase
RA	3,180,505	G→T	11.1%	E29* (GAG→TAG) ‡	ygiC →	ATP‑Grasp family ATPase
RA	3,180,506	A→C	11.1%	E29A (GAG→GCG) ‡	ygiC →	ATP‑Grasp family ATPase
RA	3,180,513:1	+A	5.9%	coding (93/1161 nt)	ygiC →	ATP‑Grasp family ATPase
RA	3,183,345:1	+T	6.9%	intergenic (+22/+468)	zupT → / ← ribB	zinc transporter/3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase
RA	3,183,350	Δ1 bp	6.8%	intergenic (+27/+463)	zupT → / ← ribB	zinc transporter/3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase
RA	3,239,609	T→G	8.9%	intergenic (+64/‑335)	alx → / → sstT	putative membrane‑bound redox modulator/sodium:serine/threonine symporter
RA	3,239,610	C→G	9.0%	intergenic (+65/‑334)	alx → / → sstT	putative membrane‑bound redox modulator/sodium:serine/threonine symporter
RA	3,239,611	C→A	8.6%	intergenic (+66/‑333)	alx → / → sstT	putative membrane‑bound redox modulator/sodium:serine/threonine symporter
RA	3,250,989	G→C	5.6%	intergenic (+35/‑35)	yqjF → / → yqjG	putative quinol oxidase subunit/putative S‑transferase
RA	3,250,990	A→T	5.7%	intergenic (+36/‑34)	yqjF → / → yqjG	putative quinol oxidase subunit/putative S‑transferase
RA	3,250,991	A→T	5.5%	intergenic (+37/‑33)	yqjF → / → yqjG	putative quinol oxidase subunit/putative S‑transferase
RA	3,250,992	G→C	5.5%	intergenic (+38/‑32)	yqjF → / → yqjG	putative quinol oxidase subunit/putative S‑transferase
RA	3,276,890	G→A	5.1%	intergenic (+37/‑112)	garD → / → prlF	D‑galactarate dehydrogenase/antitoxin of the SohA(PrlF)‑YhaV toxin‑antitoxin system
RA	3,288,032	C→A	6.6%	intergenic (+22/‑58)	yraH → / → yraI	putative fimbrial‑like adhesin protein/putative periplasmic pilin chaperone
RA	3,288,033	T→G	6.5%	intergenic (+23/‑57)	yraH → / → yraI	putative fimbrial‑like adhesin protein/putative periplasmic pilin chaperone
RA	3,313,207	G→A	6.7%	intergenic (‑29/+135)	rbfA ← / ← infB	30s ribosome binding factor/translation initiation factor IF‑2
RA	3,313,208	T→A	6.9%	intergenic (‑30/+134)	rbfA ← / ← infB	30s ribosome binding factor/translation initiation factor IF‑2
RA	3,313,209	T→C	6.8%	intergenic (‑31/+133)	rbfA ← / ← infB	30s ribosome binding factor/translation initiation factor IF‑2
RA	3,324,952	A→G	8.6%	intergenic (‑41/+49)	folP ← / ← ftsH	7,8‑dihydropteroate synthase/protease, ATP‑dependent zinc‑metallo
RA	3,324,955	A→G	8.6%	intergenic (‑44/+46)	folP ← / ← ftsH	7,8‑dihydropteroate synthase/protease, ATP‑dependent zinc‑metallo
RA	3,324,956	C→T	8.6%	intergenic (‑45/+45)	folP ← / ← ftsH	7,8‑dihydropteroate synthase/protease, ATP‑dependent zinc‑metallo
RA	3,324,959	C→T	8.3%	intergenic (‑48/+42)	folP ← / ← ftsH	7,8‑dihydropteroate synthase/protease, ATP‑dependent zinc‑metallo
RA	3,328,182	A→T	9.4%	intergenic (+99/+57)	yhbY → / ← greA	RNA binding protein associated with pre‑50S ribosomal subunits/transcript cleavage factor
RA	3,328,183	T→A	9.0%	intergenic (+100/+56)	yhbY → / ← greA	RNA binding protein associated with pre‑50S ribosomal subunits/transcript cleavage factor
RA	3,328,184	A→T	9.0%	intergenic (+101/+55)	yhbY → / ← greA	RNA binding protein associated with pre‑50S ribosomal subunits/transcript cleavage factor
RA	3,332,822	G→A	5.9%	intergenic (‑87/+40)	yhbE ← / ← rpmA	EamA family inner membrane putative transporter/50S ribosomal subunit protein L27
RA	3,332,823	T→C	5.9%	intergenic (‑88/+39)	yhbE ← / ← rpmA	EamA family inner membrane putative transporter/50S ribosomal subunit protein L27
RA	3,334,703	A→G	7.8%	intergenic (+22/‑206)	ispB → / → sfsB	octaprenyl diphosphate synthase/malPQ operon transcriptional activator
RA	3,334,704	G→C	7.8%	intergenic (+23/‑205)	ispB → / → sfsB	octaprenyl diphosphate synthase/malPQ operon transcriptional activator
RA	3,334,705	C→T	7.8%	intergenic (+24/‑204)	ispB → / → sfsB	octaprenyl diphosphate synthase/malPQ operon transcriptional activator
RA	3,350,678	Δ1 bp	5.1%	noncoding (102/121 nt)	arcZ →	sRNA positive antisense regulator of rpoS; binds Hfq
RA	3,350,682:1	+A	5.1%	noncoding (106/121 nt)	arcZ →	sRNA positive antisense regulator of rpoS; binds Hfq
RA	3,360,643	T→A	5.8%	intergenic (+27/‑533)	gltD → / → gltF	glutamate synthase, 4Fe‑4S protein, small subunit/periplasmic protein
RA	3,360,644	G→C	5.9%	intergenic (+28/‑532)	gltD → / → gltF	glutamate synthase, 4Fe‑4S protein, small subunit/periplasmic protein
RA	3,360,645	T→A	5.7%	intergenic (+29/‑531)	gltD → / → gltF	glutamate synthase, 4Fe‑4S protein, small subunit/periplasmic protein
RA	3,368,219	G→A	6.2%	T131T (ACG→ACA)	yhcG →	DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily
RA	3,368,220	C→G	5.6%	L132V (CTG→GTG) ‡	yhcG →	DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily
RA	3,368,221	T→C	5.4%	L132P (CTG→CCG) ‡	yhcG →	DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily
RA	3,400,846	A→T	6.5%	I81N (ATC→AAC)	mreB ←	cell wall structural complex MreBCD, actin‑like component MreB
RA	3,400,849	A→T	6.6%	V80D (GTT→GAT)	mreB ←	cell wall structural complex MreBCD, actin‑like component MreB
RA	3,407,293	T→A	5.9%	intergenic (+27/‑82)	accC → / → yhdT	acetyl‑CoA carboxylase, biotin carboxylase subunit/DUF997 family putative inner membrane protein
RA	3,407,294	T→A	5.9%	intergenic (+28/‑81)	accC → / → yhdT	acetyl‑CoA carboxylase, biotin carboxylase subunit/DUF997 family putative inner membrane protein
RA	3,407,295	T→A	5.9%	intergenic (+29/‑80)	accC → / → yhdT	acetyl‑CoA carboxylase, biotin carboxylase subunit/DUF997 family putative inner membrane protein
RA	3,423,383	A→G	9.7%	intergenic (+189/+40)	yhdZ → / ← rrfF	putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon
RA	3,437,908	T→A	6.3%	intergenic (+14/‑116)	trkA → / → mscL	NAD‑binding component of TrK potassium transporter/mechanosensitive channel protein, high conductance
RA	3,437,909	A→T	6.3%	intergenic (+15/‑115)	trkA → / → mscL	NAD‑binding component of TrK potassium transporter/mechanosensitive channel protein, high conductance
RA	3,437,910	A→T	6.3%	intergenic (+16/‑114)	trkA → / → mscL	NAD‑binding component of TrK potassium transporter/mechanosensitive channel protein, high conductance
RA	3,437,911	T→A	6.2%	intergenic (+17/‑113)	trkA → / → mscL	NAD‑binding component of TrK potassium transporter/mechanosensitive channel protein, high conductance
RA	3,439,588	G→C	8.4%	intergenic (‑79/+28)	yhdN ← / ← rplQ	DUF1992 family protein/50S ribosomal subunit protein L17
RA	3,439,589	G→C	7.8%	intergenic (‑80/+27)	yhdN ← / ← rplQ	DUF1992 family protein/50S ribosomal subunit protein L17
RA	3,453,174	C→T	5.4%	G33S (GGT→AGT)	rpsJ ←	30S ribosomal subunit protein S10
RA	3,471,366	A→G	5.3%	intergenic (‑37/+34)	tufA ← / ← fusA	translation elongation factor EF‑Tu 1/protein chain elongation factor EF‑G, GTP‑binding
RA	3,476,585	G→A	5.7%	intergenic (‑145/+22)	yheO ← / ← fkpA	putative PAS domain‑containing DNA‑binding transcriptional regulator/FKBP‑type peptidyl‑prolyl cis‑trans isomerase (rotamase)
RA	3,476,586	T→C	5.5%	intergenic (‑146/+21)	yheO ← / ← fkpA	putative PAS domain‑containing DNA‑binding transcriptional regulator/FKBP‑type peptidyl‑prolyl cis‑trans isomerase (rotamase)
RA	3,486,217	A→C	5.1%	Q33P (CAG→CCG) ‡	crp →	cAMP‑activated global transcription factor, mediator of catabolite repression
RA	3,486,218	G→T	5.6%	Q33H (CAG→CAT) ‡	crp →	cAMP‑activated global transcription factor, mediator of catabolite repression
RA	3,560,455:1	+G	100%	intergenic (‑2/+1)	glpR ← / ← glpR	pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon
RA	3,642,358	T→A	6.9%	intergenic (+27/+22)	dtpB → / ← rsmJ	dipeptide and tripeptide permease B/16S rRNA m(2)G1516 methyltransferase, SAM‑dependent
RA	3,642,361	T→A	6.2%	intergenic (+30/+19)	dtpB → / ← rsmJ	dipeptide and tripeptide permease B/16S rRNA m(2)G1516 methyltransferase, SAM‑dependent
RA	3,657,599	T→A	7.0%	intergenic (+32/+387)	hdeD → / ← arrS	acid‑resistance membrane protein/antisense sRNA ArrS, function unknown
RA	3,657,601	G→C	7.6%	intergenic (+34/+385)	hdeD → / ← arrS	acid‑resistance membrane protein/antisense sRNA ArrS, function unknown
RA	3,657,603	T→A	7.1%	intergenic (+36/+383)	hdeD → / ← arrS	acid‑resistance membrane protein/antisense sRNA ArrS, function unknown
RA	3,708,427	G→A	7.9%	intergenic (‑722/+189)	dppA ← / ← proK	dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro
RA	3,708,428	T→A	8.0%	intergenic (‑723/+188)	dppA ← / ← proK	dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro
RA	3,708,429	T→C	8.0%	intergenic (‑724/+187)	dppA ← / ← proK	dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro
RA	3,708,595	G→A	5.7%	intergenic (‑890/+21)	dppA ← / ← proK	dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro
RA	3,708,596	T→A	5.6%	intergenic (‑891/+20)	dppA ← / ← proK	dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro
RA	3,708,597	T→C	5.5%	intergenic (‑892/+19)	dppA ← / ← proK	dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro
RA	3,714,163:1	+T	5.0%	coding (2232/2334 nt)	bisC ←	biotin sulfoxide reductase
RA	3,714,168	Δ1 bp	5.1%	coding (2227/2334 nt)	bisC ←	biotin sulfoxide reductase
RA	3,720,294	T→C	5.5%	intergenic (+33/+154)	cspA → / ← hokA	RNA chaperone and antiterminator, cold‑inducible/toxic polypeptide, small
RA	3,720,299	T→A	5.3%	intergenic (+38/+149)	cspA → / ← hokA	RNA chaperone and antiterminator, cold‑inducible/toxic polypeptide, small
RA	3,720,300	T→A	5.3%	intergenic (+39/+148)	cspA → / ← hokA	RNA chaperone and antiterminator, cold‑inducible/toxic polypeptide, small
RA	3,720,305	G→A	5.2%	intergenic (+44/+143)	cspA → / ← hokA	RNA chaperone and antiterminator, cold‑inducible/toxic polypeptide, small
RA	3,722,300	G→T	5.3%	intergenic (+195/+28)	sokA → / ← glyS	pseudogene, sRNA antisense regulator blocking mokA/hokA translation/glycine tRNA synthetase, beta subunit
RA	3,722,301	A→C	5.2%	intergenic (+196/+27)	sokA → / ← glyS	pseudogene, sRNA antisense regulator blocking mokA/hokA translation/glycine tRNA synthetase, beta subunit
RA	3,774,207	C→T	6.6%	intergenic (+13/‑217)	mtlA → / → mtlD	mannitol‑specific PTS enzyme: IIA, IIB and IIC components/mannitol‑1‑phosphate dehydrogenase, NAD‑dependent
RA	3,774,214	C→T	6.6%	intergenic (+20/‑210)	mtlA → / → mtlD	mannitol‑specific PTS enzyme: IIA, IIB and IIC components/mannitol‑1‑phosphate dehydrogenase, NAD‑dependent
RA	3,774,215	A→G	6.7%	intergenic (+21/‑209)	mtlA → / → mtlD	mannitol‑specific PTS enzyme: IIA, IIB and IIC components/mannitol‑1‑phosphate dehydrogenase, NAD‑dependent
RA	3,774,222	A→G	6.5%	intergenic (+28/‑202)	mtlA → / → mtlD	mannitol‑specific PTS enzyme: IIA, IIB and IIC components/mannitol‑1‑phosphate dehydrogenase, NAD‑dependent
RA	3,781,051	C→G	7.5%	intergenic (+34/‑164)	lldD → / → trmL	L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent
RA	3,790,300	A→T	6.2%	intergenic (‑219/+20)	waaH ← / ← tdh	LPS(HepIII)‑glucuronic acid glycosyltransferase/L‑threonine 3‑dehydrogenase, NAD(P)‑binding
RA	3,790,303	A→T	6.2%	intergenic (‑222/+17)	waaH ← / ← tdh	LPS(HepIII)‑glucuronic acid glycosyltransferase/L‑threonine 3‑dehydrogenase, NAD(P)‑binding
RA	3,798,234	A→T	5.5%	intergenic (+27/+5)	waaL → / ← waaU	O‑antigen ligase/lipopolysaccharide core biosynthesis
RA	3,798,235	A→T	5.6%	intergenic (+28/+4)	waaL → / ← waaU	O‑antigen ligase/lipopolysaccharide core biosynthesis
RA	3,853,674	G→T	5.6%	intergenic (+32/‑248)	tisB → / → emrD	toxic membrane persister formation peptide, LexA‑regulated/multidrug efflux system protein
RA	3,853,675	A→T	5.3%	intergenic (+33/‑247)	tisB → / → emrD	toxic membrane persister formation peptide, LexA‑regulated/multidrug efflux system protein
RA	3,853,676	A→T	5.5%	intergenic (+34/‑246)	tisB → / → emrD	toxic membrane persister formation peptide, LexA‑regulated/multidrug efflux system protein
RA	3,853,677	A→C	5.5%	intergenic (+35/‑245)	tisB → / → emrD	toxic membrane persister formation peptide, LexA‑regulated/multidrug efflux system protein
RA	3,886,756	G→A	7.1%	intergenic (+34/‑72)	yidC → / → mnmE	membrane protein insertase/tRNA U34 5‑methylaminomethyl‑2‑thiouridine modification GTPase
RA	3,886,757	T→C	7.1%	intergenic (+35/‑71)	yidC → / → mnmE	membrane protein insertase/tRNA U34 5‑methylaminomethyl‑2‑thiouridine modification GTPase
RA	3,891,502	C→G	5.0%	intergenic (+19/‑113)	tnaB → / → mdtL	tryptophan transporter of low affinity/multidrug efflux system protein
RA	3,900,410	A→T	5.1%	P56P (CCT→CCA)	yieL ←	putative xylanase
RA	3,900,542	A→T	5.3%	I12I (ATT→ATA)	yieL ←	putative xylanase
RA	3,900,545	A→T	5.3%	A11A (GCT→GCA)	yieL ←	putative xylanase
RA	3,938,255	T→A	7.4%	L10Q (CTG→CAG)	rbsR →	transcriptional repressor of ribose metabolism
RA	3,959,515	T→A	8.6%	intergenic (+70/+17)	ilvC → / ← ppiC	ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C)
RA	3,971,996	T→A	9.6%	L246Q (CTG→CAG)	wecC →	UDP‑N‑acetyl‑D‑mannosaminuronic acid dehydrogenase
RA	3,981,102	T→A	7.2%	V72V (GTT→GTA)	yifK →	putative APC family amino acid transporter
RA	3,993,296	T→C	5.0%	L715P (CTG→CCG)	cyaA →	adenylate cyclase
RA	4,008,408	A→G	5.9%	intergenic (+31/+31)	rhtC → / ← rhtB	threonine efflux pump/homoserine, homoserine lactone and S‑methyl‑methionine efflux pump
RA	4,008,409	A→C	6.0%	intergenic (+32/+30)	rhtC → / ← rhtB	threonine efflux pump/homoserine, homoserine lactone and S‑methyl‑methionine efflux pump
RA	4,008,415	T→A	5.8%	intergenic (+38/+24)	rhtC → / ← rhtB	threonine efflux pump/homoserine, homoserine lactone and S‑methyl‑methionine efflux pump
RA	4,008,416	T→A	5.8%	intergenic (+39/+23)	rhtC → / ← rhtB	threonine efflux pump/homoserine, homoserine lactone and S‑methyl‑methionine efflux pump
RA	4,017,216:1	+A	7.3%	intergenic (+24/‑117)	udp → / → rmuC	uridine phosphorylase/DNA recombination protein
RA	4,017,222	Δ1 bp	7.6%	intergenic (+30/‑111)	udp → / → rmuC	uridine phosphorylase/DNA recombination protein
RA	4,049,986	G→T	8.9%	noncoding (88/109 nt)	spf →	Spot 42 sRNA antisense regulator of galK translation, Hfq‑dependent
RA	4,049,989	A→C	9.0%	noncoding (91/109 nt)	spf →	Spot 42 sRNA antisense regulator of galK translation, Hfq‑dependent
RA	4,051,259	G→T	5.5%	noncoding (224/245 nt)	csrC →	CsrC sRNA sequesters CsrA, a carbon flux regulator
RA	4,051,262	A→C	5.2%	noncoding (227/245 nt)	csrC →	CsrC sRNA sequesters CsrA, a carbon flux regulator
RA	4,060,261	G→T	11.4%	intergenic (+31/‑186)	typA → / → yihL	GTP‑binding protein/putative DNA‑binding transcriptional regulator
RA	4,060,264	A→C	11.4%	intergenic (+34/‑183)	typA → / → yihL	GTP‑binding protein/putative DNA‑binding transcriptional regulator
RA	4,062,371	A→T	5.6%	N42I (AAT→ATT)	yihN →	MFS transporter family protein
RA	4,082,696	G→C	6.4%	Q22E (CAG→GAG)	fdoH ←	formate dehydrogenase‑O, Fe‑S subunit
RA	4,110,717	A→T	6.7%	intergenic (+32/+23)	cdh → / ← tpiA	CDP‑diacylglycerol phosphotidylhydrolase/triosephosphate isomerase
RA	4,110,719	G→C	6.7%	intergenic (+34/+21)	cdh → / ← tpiA	CDP‑diacylglycerol phosphotidylhydrolase/triosephosphate isomerase
RA	4,110,721	A→T	6.7%	intergenic (+36/+19)	cdh → / ← tpiA	CDP‑diacylglycerol phosphotidylhydrolase/triosephosphate isomerase
RA	4,116,516	G→T	55.4%	T236K (ACG→AAG)	glpK ←	glycerol kinase
RA	4,116,536	G→T	43.4%	N229K (AAC→AAA)	glpK ←	glycerol kinase
RA	4,117,059	G→C	7.5%	A55G (GCC→GGC)	glpK ←	glycerol kinase
RA	4,127,251	C→T	6.3%	intergenic (+26/+35)	rpmE → / ← yiiX	50S ribosomal subunit protein L31/putative lipid binding hydrolase, DUF830 family protein
RA	4,127,252	A→G	6.2%	intergenic (+27/+34)	rpmE → / ← yiiX	50S ribosomal subunit protein L31/putative lipid binding hydrolase, DUF830 family protein
RA	4,177,171	T→A	9.0%	intergenic (+43/‑187)	tufB → / → secE	translation elongation factor EF‑Tu 2/preprotein translocase membrane subunit
RA	4,177,172	T→A	8.1%	intergenic (+44/‑186)	tufB → / → secE	translation elongation factor EF‑Tu 2/preprotein translocase membrane subunit
JC	4,186,098	+TCCGCTGGT	16.8%	coding (749/4224 nt)	rpoC →	RNA polymerase, beta prime subunit
RA	4,208,230	T→A	14.0%	noncoding (84/1542 nt)	rrsE →	16S ribosomal RNA of rrnE operon
RA	4,208,231	T→A	14.0%	noncoding (85/1542 nt)	rrsE →	16S ribosomal RNA of rrnE operon
RA	4,213,131	C→T	5.8%	noncoding (92/120 nt)	rrfE →	5S ribosomal RNA of rrnE operon
RA	4,223,854	T→C	6.3%	R9R (CGT→CGC)	metH →	homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent
RA	4,223,855	G→A	6.3%	A10T (GCG→ACG)	metH →	homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent
RA	4,227,550	G→A	6.0%	intergenic (+39/‑181)	metH → / → yjbB	homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent/putative Na+/Pi‑cotransporter
RA	4,227,555	A→T	7.0%	intergenic (+44/‑176)	metH → / → yjbB	homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent/putative Na+/Pi‑cotransporter
RA	4,227,560	T→C	6.7%	intergenic (+49/‑171)	metH → / → yjbB	homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent/putative Na+/Pi‑cotransporter
RA	4,235,579	G→A	5.1%	intergenic (+172/‑327)	pgi → / → yjbE	glucosephosphate isomerase/extracellular polysaccharide production threonine‑rich protein
RA	4,235,581	T→A	5.1%	intergenic (+174/‑325)	pgi → / → yjbE	glucosephosphate isomerase/extracellular polysaccharide production threonine‑rich protein
RA	4,235,583	T→C	5.1%	intergenic (+176/‑323)	pgi → / → yjbE	glucosephosphate isomerase/extracellular polysaccharide production threonine‑rich protein
RA	4,261,358	T→A	5.2%	intergenic (+52/‑311)	yjbM → / → dusA	uncharacterized protein/tRNA‑dihydrouridine synthase A
RA	4,261,359	T→A	5.2%	intergenic (+53/‑310)	yjbM → / → dusA	uncharacterized protein/tRNA‑dihydrouridine synthase A
RA	4,272,377	T→G	5.8%	S499R (AGC→CGC)	uvrA ←	ATPase and DNA damage recognition protein of nucleotide excision repair excinuclease UvrABC
RA	4,272,378	C→A	5.7%	A498A (GCG→GCT)	uvrA ←	ATPase and DNA damage recognition protein of nucleotide excision repair excinuclease UvrABC
RA	4,274,740	G→A	6.5%	intergenic (+79/+20)	ssb → / ← yjcB	single‑stranded DNA‑binding protein/putative inner membrane protein
RA	4,274,742	T→A	6.5%	intergenic (+81/+18)	ssb → / ← yjcB	single‑stranded DNA‑binding protein/putative inner membrane protein
RA	4,274,744	T→C	6.4%	intergenic (+83/+16)	ssb → / ← yjcB	single‑stranded DNA‑binding protein/putative inner membrane protein
RA	4,291,512	G→A	6.2%	M1M (GTG→ATG) †‡	nrfE →	heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfE
RA	4,291,513	T→C	6.2%	M1A (GTG→GCG) †‡	nrfE →	heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfE
RA	4,295,955	G→A	5.3%	intergenic (+161/+481)	gltP → / ← yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA	4,295,956	C→A	5.4%	intergenic (+162/+480)	gltP → / ← yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA	4,296,060	C→T	23.5%	intergenic (+266/+376)	gltP → / ← yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA	4,296,380:1	+CG	100%	intergenic (+586/+56)	gltP → / ← yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA	4,307,294	A→T	8.6%	L169Q (CTG→CAG)	alsK ←	D‑allose kinase
RA	4,307,298	G→A	8.8%	P168S (CCC→TCC)	alsK ←	D‑allose kinase
RA	4,314,233	A→T	5.3%	intergenic (+36/+111)	yjdP → / ← phnP	putative periplasmic protein/5‑phospho‑alpha‑D‑ribosyl 1,2‑cyclic phosphate phosphodiesterase
RA	4,332,868	G→T	7.4%	R135R (CGC→CGA)	basS ←	sensory histidine kinase in two‑component regulatory system with BasR
RA	4,332,871	A→C	7.0%	S134R (AGT→AGG)	basS ←	sensory histidine kinase in two‑component regulatory system with BasR
RA	4,356,445	A→T	8.2%	intergenic (‑34/+25)	dtpC ← / ← cadA	dipeptide and tripeptide permease/lysine decarboxylase, acid‑inducible
RA	4,356,446	A→T	8.7%	intergenic (‑35/+24)	dtpC ← / ← cadA	dipeptide and tripeptide permease/lysine decarboxylase, acid‑inducible
RA	4,366,854	T→G	12.5%	intergenic (‑81/+37)	dcuA ← / ← aspA	C4‑dicarboxylate antiporter/aspartate ammonia‑lyase
RA	4,366,855	C→A	12.8%	intergenic (‑82/+36)	dcuA ← / ← aspA	C4‑dicarboxylate antiporter/aspartate ammonia‑lyase
RA	4,376,280	G→A	6.4%	intergenic (+15/‑37)	efp → / → ecnA	polyproline‑specific translation elongation factor EF‑P/entericidin A membrane lipoprotein, antidote entericidin B
RA	4,376,291	T→C	6.1%	intergenic (+26/‑26)	efp → / → ecnA	polyproline‑specific translation elongation factor EF‑P/entericidin A membrane lipoprotein, antidote entericidin B
RA	4,376,819	A→T	5.1%	intergenic (+120/‑56)	ecnB → / → sugE	entericidin B membrane lipoprotein/multidrug efflux system protein
RA	4,376,822	A→T	5.1%	intergenic (+123/‑53)	ecnB → / → sugE	entericidin B membrane lipoprotein/multidrug efflux system protein
RA	4,392,506	C→G	7.6%	noncoding (35/76 nt)	glyX →	tRNA‑Gly
RA	4,395,454	T→C	5.4%	C463C (TGT→TGC)	nnr →	bifunctional NAD(P)H‑hydrate repair enzyme; C‑terminal domain ADP‑dependent (S)‑NAD(P)H‑hydrate dehydratase and N‑terminal domain NAD(P)H‑hydrate epimerase
RA	4,395,455	G→A	5.4%	A464T (GCA→ACA)	nnr →	bifunctional NAD(P)H‑hydrate repair enzyme; C‑terminal domain ADP‑dependent (S)‑NAD(P)H‑hydrate dehydratase and N‑terminal domain NAD(P)H‑hydrate epimerase
RA	4,409,402	Δ1 bp	5.3%	coding (128/732 nt)	rlmB →	23S rRNA mG2251 2'‑O‑ribose methyltransferase, SAM‑dependent
RA	4,409,407	T→A	5.4%	S45T (TCT→ACT)	rlmB →	23S rRNA mG2251 2'‑O‑ribose methyltransferase, SAM‑dependent
RA	4,409,410:1	+A	5.6%	coding (136/732 nt)	rlmB →	23S rRNA mG2251 2'‑O‑ribose methyltransferase, SAM‑dependent
RA	4,424,465	G→T	6.0%	intergenic (+79/+51)	ulaF → / ← yjfY	L‑ribulose 5‑phosphate 4‑epimerase/YhcN family protein, periplasmic
RA	4,424,468	A→C	6.2%	intergenic (+82/+48)	ulaF → / ← yjfY	L‑ribulose 5‑phosphate 4‑epimerase/YhcN family protein, periplasmic
RA	4,426,592	T→A	10.6%	intergenic (+35/+36)	rplI → / ← yjfZ	50S ribosomal subunit protein L9/uncharacterized protein
RA	4,479,012	A→T	7.5%	intergenic (+123/+22)	rraB → / ← yjgM	protein inhibitor of RNase E/GNAT family putative N‑acetyltransferase
RA	4,479,016	G→C	8.0%	intergenic (+127/+18)	rraB → / ← yjgM	protein inhibitor of RNase E/GNAT family putative N‑acetyltransferase
RA	4,479,020	A→T	8.2%	intergenic (+131/+14)	rraB → / ← yjgM	protein inhibitor of RNase E/GNAT family putative N‑acetyltransferase
RA	4,496,511	A→G	5.8%	intergenic (+22/‑164)	leuX → / → intB	tRNA‑Leu/pseudogene, integrase homology;IS, phage, Tn; Phage‑related functions and prophages; KpLE2 phage‑like element; P4‑like integrase
RA	4,496,512	C→T	5.8%	intergenic (+23/‑163)	leuX → / → intB	tRNA‑Leu/pseudogene, integrase homology;IS, phage, Tn; Phage‑related functions and prophages; KpLE2 phage‑like element; P4‑like integrase
RA	4,512,350:1	+G	6.9%	coding (65/957 nt)	fecD ←	ferric citrate ABC transporter permease
RA	4,520,500	Δ1 bp	8.5%	intergenic (‑176/+171)	yjhU ← / ← yjhF	putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter
RA	4,520,504:1	+T	8.5%	intergenic (‑180/+167)	yjhU ← / ← yjhF	putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter
RA	4,548,914	G→C	5.5%	G36A (GGT→GCT)	fimH →	minor component of type 1 fimbriae
RA	4,548,917	G→C	5.6%	G37A (GGC→GCC)	fimH →	minor component of type 1 fimbriae
RA	4,548,920	G→C	5.4%	S38T (AGC→ACC)	fimH →	minor component of type 1 fimbriae
RA	4,549,932	T→A	5.1%	intergenic (+222/+21)	fimH → / ← gntP	minor component of type 1 fimbriae/fructuronate transporter

Unassigned missing coverage evidence
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	3423744–3424234	3424556–3424238	5–813	87 [85]	[84] 92	[rrfD]–[rrlD]	[rrfD],[rrlD]

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 53968	109 (0.640)	9 (0.050)	9/248	NT	7.6%	coding (735/1287 nt)	surA	peptidyl‑prolyl cis‑trans isomerase (PPIase)
	?	NC_000913	= 53983	114 (0.690)					coding (720/1287 nt)	surA	peptidyl‑prolyl cis‑trans isomerase (PPIase)
*	?	NC_000913	= 224065	NA (NA)	9 (0.060)	6/242	NT	NA	noncoding (295/1542 nt)	rrsH	16S ribosomal RNA of rrnH operon
	?	NC_000913	= 224074	NA (NA)					noncoding (304/1542 nt)	rrsH	16S ribosomal RNA of rrnH operon
*	?	NC_000913	225078 =	NA (NA)	25 (0.150)	15/242	NT	NA	noncoding (1308/1542 nt)	rrsH	16S ribosomal RNA of rrnH operon
	?	NC_000913	225100 =	NA (NA)					noncoding (1330/1542 nt)	rrsH	16S ribosomal RNA of rrnH operon
*	?	NC_000913	274620 =	NA (NA)	5 (0.030)	4/238	NT	NA	noncoding (530/1195 nt)	IS5	repeat region
	?	NC_000913	274663 =	NA (NA)					noncoding (487/1195 nt)	IS5	repeat region
*	?	NC_000913	= 315852	NA (NA)	18 (0.110)	11/248	NT	NA	noncoding (624/1255 nt)	IS3	repeat region
	?	NC_000913	= 315875	NA (NA)					noncoding (647/1255 nt)	IS3	repeat region
*	?	NC_000913	349605 =	NA (NA)	7 (0.040)	7/242	NT	NA	noncoding (1/365 nt)	REP25 (repetitive extragenic palindromic) element; contains 8 REP sequences	REP25 (repetitive extragenic palindromic) element; contains 8 REP sequences
	?	NC_000913	349637 =	NA (NA)					noncoding (33/365 nt)	REP25 (repetitive extragenic palindromic) element; contains 8 REP sequences	REP25 (repetitive extragenic palindromic) element; contains 8 REP sequences
*	?	NC_000913	349884 =	154 (0.900)	12 (0.070)	8/242	NT	7.8%	noncoding (280/365 nt)	REP25 (repetitive extragenic palindromic) element; contains 8 REP sequences	REP25 (repetitive extragenic palindromic) element; contains 8 REP sequences
	?	NC_000913	349916 =	139 (0.860)					noncoding (312/365 nt)	REP25 (repetitive extragenic palindromic) element; contains 8 REP sequences	REP25 (repetitive extragenic palindromic) element; contains 8 REP sequences
*	?	NC_000913	381663 =	NA (NA)	3 (0.020)	3/242	NT	NA	noncoding (404/1331 nt)	IS2	repeat region
	?	NC_000913	381703 =	NA (NA)					noncoding (444/1331 nt)	IS2	repeat region
*	?	NC_000913	= 381669	NA (NA)	6 (0.040)	5/242	NT	NA	noncoding (410/1331 nt)	IS2	repeat region
	?	NC_000913	= 381695	NA (NA)					noncoding (436/1331 nt)	IS2	repeat region
*	?	NC_000913	= 399026	NA (NA)	11 (0.070)	8/242	NT	NA	coding (308/309 nt)	yaiY	DUF2755 family inner membrane protein
	?	NC_000913	= 399047	NA (NA)					coding (287/309 nt)	yaiY	DUF2755 family inner membrane protein
*	?	NC_000913	762803 =	NA (NA)	7 (0.040) +CTACG	6/246	NT	5.5%	noncoding (42/167 nt)	REP68 (repetitive extragenic palindromic) element; contains 4 REP sequences	REP68 (repetitive extragenic palindromic) element; contains 4 REP sequences
	?	NC_000913	3708527 =	126 (0.740)					intergenic (‑822/+89)	dppA/proK	dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro
*	?	NC_000913	900753 =	NA (NA)	4 (0.020)	4/242	NT	NA	noncoding (5/87 nt)	REP83 (repetitive extragenic palindromic) element; contains 2 REP sequences	REP83 (repetitive extragenic palindromic) element; contains 2 REP sequences
	?	NC_000913	900783 =	NA (NA)					noncoding (35/87 nt)	REP83 (repetitive extragenic palindromic) element; contains 2 REP sequences	REP83 (repetitive extragenic palindromic) element; contains 2 REP sequences
*	?	NC_000913	= 937227	NA (NA)	7 (0.040)	7/240	NT	NA	noncoding (4/36 nt)	REP85 (repetitive extragenic palindromic) element; contains 1 REP sequences	REP85 (repetitive extragenic palindromic) element; contains 1 REP sequences
	?	NC_000913	= 937259	NA (NA)					noncoding (36/36 nt)	REP85 (repetitive extragenic palindromic) element; contains 1 REP sequences	REP85 (repetitive extragenic palindromic) element; contains 1 REP sequences
*	?	NC_000913	1097106 =	101 (0.590)	8 (0.050)	3/240	NT	11.1%	intergenic (+277/+459)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
	?	NC_000913	1097283 =	33 (0.210)					intergenic (+454/+282)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
*	?	NC_000913	1097275 =	41 (0.240)	21 (0.130)	12/240	NT	37.0%	intergenic (+446/+290)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
	?	NC_000913	1097476 =	33 (0.210)					intergenic (+647/+89)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
*	?	NC_000913	1207790 =	61 (0.360)	83 (0.560)	64/224	NT	58.6%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	64 (0.430)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1207805	62 (0.360)	71 (0.480)	54/224	NT	54.6%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	64 (0.430)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1299498	0 (0.000)	181 (1.090)	109/248	NT	100%	intergenic (+253/‑1684)	ychE/oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
	?	NC_000913	1300698 =	0 (0.000)					intergenic (+1453/‑484)	ychE/oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
*	?	NC_000913	= 1886825	107 (0.630)	5 (0.030)	5/234	NT	5.0%	intergenic (+15/+39)	yeaX/rnd	putative YeaWX dioxygenase beta subunit, reductase component/ribonuclease D
	?	NC_000913	= 1886846	92 (0.590)					intergenic (+36/+18)	yeaX/rnd	putative YeaWX dioxygenase beta subunit, reductase component/ribonuclease D
*	?	NC_000913	1911650 =	136 (0.800)	12 (0.080)	11/232	NT	9.0%	intergenic (+1/+45)	yebQ/htpX	putative transporter/putative endopeptidase
	?	NC_000913	1911680 =	118 (0.760)					intergenic (+31/+15)	yebQ/htpX	putative transporter/putative endopeptidase
*	?	NC_000913	= 2025238	158 (0.920)	9 (0.060)	7/236	NT	5.5%	noncoding (76/87 nt)	dsrA	sRNA antisense regulator enhances translation of RpoS, Hfq‑dependent
	?	NC_000913	= 2025243	164 (1.040)					noncoding (71/87 nt)	dsrA	sRNA antisense regulator enhances translation of RpoS, Hfq‑dependent
*	?	NC_000913	2118562 =	161 (0.940)	10 (0.060)	9/242	NT	6.5%	noncoding (97/186 nt)	REP144 (repetitive extragenic palindromic) element; contains 4 REP sequences	REP144 (repetitive extragenic palindromic) element; contains 4 REP sequences
	?	NC_000913	2118594 =	135 (0.840)					noncoding (129/186 nt)	REP144 (repetitive extragenic palindromic) element; contains 4 REP sequences	REP144 (repetitive extragenic palindromic) element; contains 4 REP sequences
*	?	NC_000913	2304817 =	NA (NA)	12 (0.070)	8/242	NT	16.6%	noncoding (401/655 nt)	REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences	REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences
	?	NC_000913	2304948 =	64 (0.370)					noncoding (532/655 nt)	REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences	REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences
*	?	NC_000913	2460605 =	130 (0.760)	13 (0.080)	6/238	NT	10.2%	intergenic (‑136/+45)	fadI/yfcZ	beta‑ketoacyl‑CoA thiolase, anaerobic, subunit/UPF0381 family protein
	?	NC_000913	2460634 =	108 (0.680)					intergenic (‑165/+16)	fadI/yfcZ	beta‑ketoacyl‑CoA thiolase, anaerobic, subunit/UPF0381 family protein
*	?	NC_000913	= 2473342	126 (0.740)	8 (0.050)	6/244	NT	6.0%	pseudogene (244/708 nt)	oweS	pseudogene, CPS‑53 (KpLE1) prophage; bacteriophage replication protein O family;Phage or Prophage Related
	?	NC_000913	= 2473353	131 (0.800)					pseudogene (233/708 nt)	oweS	pseudogene, CPS‑53 (KpLE1) prophage; bacteriophage replication protein O family;Phage or Prophage Related
*	?	NC_000913	2539608 =	NA (NA)	9 (0.060)	7/244	NT	NA	noncoding (2/36 nt)	REP175 (repetitive extragenic palindromic) element; contains 1 REP sequences	REP175 (repetitive extragenic palindromic) element; contains 1 REP sequences
	?	NC_000913	2539638 =	NA (NA)					noncoding (32/36 nt)	REP175 (repetitive extragenic palindromic) element; contains 1 REP sequences	REP175 (repetitive extragenic palindromic) element; contains 1 REP sequences
*	?	NC_000913	2726200 =	NA (NA)	61 (0.370)	13/244	NT	NA	intergenic (‑12/+81)	rrfG/rrlG	5S ribosomal RNA of rrnG operon/23S ribosomal RNA of rrnG operon
	?	NC_000913	2726224 =	NA (NA)					intergenic (‑36/+57)	rrfG/rrlG	5S ribosomal RNA of rrnG operon/23S ribosomal RNA of rrnG operon
*	?	NC_000913	= 3042439	NA (NA)	4 (0.020)	4/242	NT	NA	noncoding (119/155 nt)	REP210 (repetitive extragenic palindromic) element; contains 3 REP sequences	REP210 (repetitive extragenic palindromic) element; contains 3 REP sequences
	?	NC_000913	= 3042471	NA (NA)					noncoding (151/155 nt)	REP210 (repetitive extragenic palindromic) element; contains 3 REP sequences	REP210 (repetitive extragenic palindromic) element; contains 3 REP sequences
*	?	NC_000913	3289918 =	163 (0.950)	10 (0.060)	7/242	NT	6.4%	coding (1105/2517 nt)	yraJ	putative outer membrane protein
	?	NC_000913	3289945 =	138 (0.850)					coding (1132/2517 nt)	yraJ	putative outer membrane protein
*	?	NC_000913	3423376 =	137 (0.800)	30 (0.190) +TTGATGT	8/242	NT	19.2%	intergenic (+182/+47)	yhdZ/rrfF	putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon
	?	NC_000913	= 4213155	130 (0.760)					noncoding (116/120 nt)	rrfE	5S ribosomal RNA of rrnE operon
*	?	NC_000913	= 3620350	NA (NA)	7 (0.040)	6/244	NT	100%	coding (1159/4236 nt)	rhsB	Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
	?	NC_000913	= 3620425	0 (0.000)					coding (1234/4236 nt)	rhsB	Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
*	?	NC_000913	3701833 =	185 (1.080)	9 (0.060)	11/242	NT	5.2%	coding (1271/1272 nt)	yhjV	putative transporter
	?	NC_000913	3701858 =	153 (0.950)					intergenic (+24/+6)	yhjV/dppF	putative transporter/dipeptide/heme ABC transporter ATPas
*	?	NC_000913	3721045 =	258 (1.510)	623 (3.680)	189/254	NT	75.2%	noncoding (413/1443 nt)	IS150	repeat region
	?	NC_000913	= 3839774	154 (0.910)					coding (220/819 nt)	nlpA	cytoplasmic membrane lipoprotein‑28
*	?	NC_000913	3811200 =	663 (3.880)	45 (0.290)	24/232	NT	7.2%	intergenic (‑48/+50)	mutM/rpmG	formamidopyrimidine/5‑formyluracil/ 5‑hydroxymethyluracil DNA glycosylase/50S ribosomal subunit protein L33
	?	NC_000913	3811236 =	561 (3.620)					intergenic (‑84/+14)	mutM/rpmG	formamidopyrimidine/5‑formyluracil/ 5‑hydroxymethyluracil DNA glycosylase/50S ribosomal subunit protein L33
*	?	NC_000913	3895222 =	152 (0.890)	11 (0.070)	10/232	NT	7.7%	intergenic (+4/+50)	chrR/adeP	chromate reductase, Class I, flavoprotein/adenine permease, high affinity; adenine:H+ symporter
	?	NC_000913	3895257 =	127 (0.820)					intergenic (+39/+15)	chrR/adeP	chromate reductase, Class I, flavoprotein/adenine permease, high affinity; adenine:H+ symporter
*	?	NC_000913	3943467 =	NA (NA)	24 (0.150)	12/244	NT	18.1%	noncoding (33/76 nt)	gltU	tRNA‑Glu
	?	NC_000913	3943474 =	114 (0.670)					noncoding (40/76 nt)	gltU	tRNA‑Glu
*	?	NC_000913	= 3955396	126 (0.740)	7 (0.040)	7/244	NT	5.4%	coding (66/1545 nt)	ilvA	l‑threonine dehydratase, biosynthetic; also known as threonine deaminase
	?	NC_000913	= 3955414	126 (0.770)					coding (84/1545 nt)	ilvA	l‑threonine dehydratase, biosynthetic; also known as threonine deaminase
*	?	NC_000913	= 4168341	86 (0.500)	6 (0.040)	4/236	NT	8.0%	intergenic (+141/‑31)	rrsB/gltT	16S ribosomal RNA of rrnB operon/tRNA‑Glu
	?	NC_000913	= 4168363	58 (0.370)					intergenic (+163/‑9)	rrsB/gltT	16S ribosomal RNA of rrnB operon/tRNA‑Glu
*	?	NC_000913	4295868 =	NA (NA)	13 (0.080)	6/242	NT	10.8%	noncoding (34/600 nt)	RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites	RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites
	?	NC_000913	4295948 =	114 (0.670)					noncoding (114/600 nt)	RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites	RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites
*	?	NC_000913	4542682 =	100 (0.590)	11 (0.070)	11/238	NT	8.2%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	153 (0.960)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	= 4542690	104 (0.610)	8 (0.050)	8/238	NT	6.0%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	153 (0.960)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)