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	9,907	A→C	8.8%	intergenic (+14/+21)	mog → / ← satP	molybdochelatase incorporating molybdenum into molybdopterin/succinate‑acetate transporter
RA	9,908	G→T	8.7%	intergenic (+15/+20)	mog → / ← satP	molybdochelatase incorporating molybdenum into molybdopterin/succinate‑acetate transporter
RA	53,376	G→A	6.0%	P14L (CCC→CTC)	pdxA ←	4‑hydroxy‑L‑threonine phosphate dehydrogenase, NAD‑dependent
RA	53,379	T→C	5.6%	E13G (GAG→GGG)	pdxA ←	4‑hydroxy‑L‑threonine phosphate dehydrogenase, NAD‑dependent
RA	72,198	A→G	5.3%	intergenic (+83/+31)	yabI → / ← thiQ	DedA family inner membrane protein/thiamine/thiamine pyrophosphate ABC transporter ATPase
RA	72,199	A→C	5.1%	intergenic (+84/+30)	yabI → / ← thiQ	DedA family inner membrane protein/thiamine/thiamine pyrophosphate ABC transporter ATPase
RA	72,205	T→G	5.8%	intergenic (+90/+24)	yabI → / ← thiQ	DedA family inner membrane protein/thiamine/thiamine pyrophosphate ABC transporter ATPase
RA	72,206	C→A	5.7%	intergenic (+91/+23)	yabI → / ← thiQ	DedA family inner membrane protein/thiamine/thiamine pyrophosphate ABC transporter ATPase
RA	83,587	A→C	9.8%	intergenic (‑58/+35)	leuA ← / ← leuL	2‑isopropylmalate synthase/leu operon leader peptide
RA	83,590	G→T	9.7%	intergenic (‑61/+32)	leuA ← / ← leuL	2‑isopropylmalate synthase/leu operon leader peptide
RA	111,013	G→A	7.1%	intergenic (+29/‑31)	secA → / → mutT	preprotein translocase subunit, ATPase/dGTP‑preferring nucleoside triphosphate pyrophosphohydrolase
RA	111,016	T→C	7.9%	intergenic (+32/‑28)	secA → / → mutT	preprotein translocase subunit, ATPase/dGTP‑preferring nucleoside triphosphate pyrophosphohydrolase
RA	120,154	Δ1 bp	7.0%	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	7.1%	intergenic (+23/+20)	ampE → / ← aroP	ampicillin resistance inner membrane protein; putative signaling protein in beta‑lactamase regulation/aromatic amino acid transporter
RA	151,519	A→C	6.9%	I27M (ATT→ATG)	yadK ←	putative fimbrial‑like adhesin protein
RA	151,522	G→T	6.7%	A26A (GCC→GCA)	yadK ←	putative fimbrial‑like adhesin protein
RA	164,557	G→C	6.5%	intergenic (+23/‑173)	hrpB → / → mrcB	putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase
RA	164,558	T→A	6.5%	intergenic (+24/‑172)	hrpB → / → mrcB	putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase
RA	164,620	C→T	7.7%	intergenic (+86/‑110)	hrpB → / → mrcB	putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase
RA	164,621	A→G	8.9%	intergenic (+87/‑109)	hrpB → / → mrcB	putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase
RA	167,917	A→C	6.7%	Q145P (CAG→CCG) ‡	fhuA →	ferrichrome outer membrane transporter
RA	167,918	G→C	6.8%	Q145H (CAG→CAC) ‡	fhuA →	ferrichrome outer membrane transporter
RA	167,919	G→T	6.8%	G146C (GGC→TGC)	fhuA →	ferrichrome outer membrane transporter
RA	201,032	G→A	5.5%	G21D (GGC→GAC)	lpxD →	UDP‑3‑O‑(3‑hydroxymyristoyl)‑glucosamine N‑acyltransferase
RA	208,552	T→A	5.3%	L1143I (TTA→ATA)	dnaE →	DNA polymerase III alpha subunit
RA	254,228	A→T	5.2%	intergenic (+26/+31)	prfH → / ← pepD	pseudogene, RF‑1 domain family; probable peptide chain release factor/aminoacyl‑histidine dipeptidase (peptidase D)
RA	254,233	A→T	5.2%	intergenic (+31/+26)	prfH → / ← pepD	pseudogene, RF‑1 domain family; probable peptide chain release factor/aminoacyl‑histidine dipeptidase (peptidase D)
MC JC	257,908	Δ776 bp	100%		[crl]	[crl]
RA	292,302	C→G	5.2%	intergenic (+71/+20)	yagJ → / ← yagK	CP4‑6 prophage; uncharacterized protein;Phage or Prophage Related/CP4‑6 prophage; conserved protein
RA	314,255	T→C	6.1%	intergenic (‑450/‑102)	ykgP ← / → eaeH	pseudogene, oxidoreductase family/pseudogene, attaching and effacing protein homology;factor; Not classified
RA	314,258	G→A	6.1%	intergenic (‑453/‑99)	ykgP ← / → eaeH	pseudogene, oxidoreductase family/pseudogene, attaching and effacing protein homology;factor; Not classified
RA	373,332	C→G	5.1%	P138A (CCA→GCA)	mhpF →	acetaldehyde‑CoA dehydrogenase II, NAD‑binding
RA	385,724	T→A	5.9%	W165R (TGG→AGG)	tauA →	taurine ABC transporter periplasmic binding protein
RA	443,022	G→A	8.0%	intergenic (+25/+29)	thiI → / ← yajL	tRNA s(4)U8 sulfurtransferase/oxidative‑stress‑resistance chaperone
RA	443,023	T→C	8.3%	intergenic (+26/+28)	thiI → / ← yajL	tRNA s(4)U8 sulfurtransferase/oxidative‑stress‑resistance chaperone
RA	454,853	T→C	9.1%	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	9.7%	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	475,971	C→G	11.7%	intergenic (+20/+11)	ybaY → / ← ybaZ	outer membrane lipoprotein/excision repair protein, alkyltransferase‑like protein ATL
RA	475,972	C→G	12.1%	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	9.8%	intergenic (‑520/+26)	tomB ← / ← acrB	Hha toxicity attenuator; conjugation‑related protein/multidrug efflux system protein
RA	533,846	T→C	7.4%	intergenic (+20/‑70)	allR → / → gcl	glyoxylate‑inducible transcriptional repressor of all and gcl operons/glyoxylate carboligase
RA	533,849	G→A	7.0%	intergenic (+23/‑67)	allR → / → gcl	glyoxylate‑inducible transcriptional repressor of all and gcl operons/glyoxylate carboligase
RA	543,091	G→C	5.2%	intergenic (+58/+170)	glxK → / ← allE	glycerate kinase II/S‑ureidoglycine aminohydrolase
RA	543,094	G→C	5.1%	intergenic (+61/+167)	glxK → / ← allE	glycerate kinase II/S‑ureidoglycine aminohydrolase
RA	543,207	A→T	5.3%	intergenic (+174/+54)	glxK → / ← allE	glycerate kinase II/S‑ureidoglycine aminohydrolase
RA	543,210	A→T	5.3%	intergenic (+177/+51)	glxK → / ← allE	glycerate kinase II/S‑ureidoglycine aminohydrolase
RA	594,950	T→G	5.0%	H165P (CAT→CCT)	cusR ←	response regulator in two‑component regulatory system with CusS
RA	595,519	T→A	5.8%	intergenic (‑76/‑81)	cusR ← / → cusC	response regulator in two‑component regulatory system with CusS/copper/silver efflux system, outer membrane component
RA	595,520	T→A	5.7%	intergenic (‑77/‑80)	cusR ← / → cusC	response regulator in two‑component regulatory system with CusS/copper/silver efflux system, outer membrane component
RA	603,391	C→G	5.4%	intergenic (+56/+25)	pheP → / ← ybdG	phenylalanine transporter/mechanosensitive channel protein, miniconductance
RA	603,393	T→A	5.5%	intergenic (+58/+23)	pheP → / ← ybdG	phenylalanine transporter/mechanosensitive channel protein, miniconductance
RA	603,395	C→G	6.0%	intergenic (+60/+21)	pheP → / ← ybdG	phenylalanine transporter/mechanosensitive channel protein, miniconductance
RA	644,030	A→G	6.2%	intergenic (‑63/+167)	rnk ← / ← rna	regulator of nucleoside diphosphate kinase/ribonuclease I
RA	644,034	T→C	5.6%	intergenic (‑67/+163)	rnk ← / ← rna	regulator of nucleoside diphosphate kinase/ribonuclease I
RA	644,036	A→T	5.9%	intergenic (‑69/+161)	rnk ← / ← rna	regulator of nucleoside diphosphate kinase/ribonuclease I
RA	644,038	G→A	5.9%	intergenic (‑71/+159)	rnk ← / ← rna	regulator of nucleoside diphosphate kinase/ribonuclease I
RA	644,042	C→T	6.0%	intergenic (‑75/+155)	rnk ← / ← rna	regulator of nucleoside diphosphate kinase/ribonuclease I
RA	647,575	A→C	5.2%	V154G (GTC→GGC)	citX ←	apo‑citrate lyase phosphoribosyl‑dephospho‑CoA transferase
RA	657,531	T→G	9.5%	intergenic (+30/+24)	cspE → / ← flc	constitutive cold shock family transcription antitermination protein; negative regulator of cspA transcription; RNA melting protein; ssDNA‑binding protein/fluoride efflux channel, dual topology membrane protein
RA	657,533	A→T	9.4%	intergenic (+32/+22)	cspE → / ← flc	constitutive cold shock family transcription antitermination protein; negative regulator of cspA transcription; RNA melting protein; ssDNA‑binding protein/fluoride efflux channel, dual topology membrane protein
RA	657,535	C→A	9.3%	intergenic (+34/+20)	cspE → / ← flc	constitutive cold shock family transcription antitermination protein; negative regulator of cspA transcription; RNA melting protein; ssDNA‑binding protein/fluoride efflux channel, dual topology membrane protein
RA	672,110	G→A	6.3%	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	699,556	C→T	8.8%	intergenic (‑379/+18)	asnB ← / ← umpH	asparagine synthetase B/UMP phosphatase
RA	699,559	A→G	8.8%	intergenic (‑382/+15)	asnB ← / ← umpH	asparagine synthetase B/UMP phosphatase
RA	710,170	C→T	10.1%	intergenic (+54/+30)	chiQ → / ← fur	chitosugar‑induced verified lipoprotein/ferric iron uptake regulon transcriptional repressor; autorepressor
RA	710,173	A→G	8.8%	intergenic (+57/+27)	chiQ → / ← fur	chitosugar‑induced verified lipoprotein/ferric iron uptake regulon transcriptional repressor; autorepressor
RA	725,276	G→A	5.2%	Y587Y (TAC→TAT)	kdpB ←	potassium translocating ATPase, subunit B
RA	729,376	G→T	7.6%	intergenic (+36/‑207)	ybfA → / → rhsC	DUF2517 family protein/Rhs protein with putative toxin domain; putative neighboring cell growth inhibitor
RA	729,377	A→T	9.1%	intergenic (+37/‑206)	ybfA → / → rhsC	DUF2517 family protein/Rhs protein with putative toxin domain; putative neighboring cell growth inhibitor
RA	729,379	A→C	8.7%	intergenic (+39/‑204)	ybfA → / → rhsC	DUF2517 family protein/Rhs protein with putative toxin domain; putative neighboring cell growth inhibitor
RA	770,679	G→T	7.5%	intergenic (+68/‑779)	mngB → / → cydA	alpha‑mannosidase/cytochrome d terminal oxidase, subunit I
RA	770,682	A→C	7.0%	intergenic (+71/‑776)	mngB → / → cydA	alpha‑mannosidase/cytochrome d terminal oxidase, subunit I
RA	773,138	G→A	5.3%	G33S (GGC→AGC)	cydB →	cytochrome d terminal oxidase, subunit II
RA	773,553	T→C	6.0%	L171P (CTG→CCG) ‡	cydB →	cytochrome d terminal oxidase, subunit II
RA	773,554	G→A	6.0%	L171L (CTG→CTA) ‡	cydB →	cytochrome d terminal oxidase, subunit II
RA	774,356	C→G	7.4%	P16P (CCC→CCG)	ybgE →	putative inner membrane protein in cydABX‑ybgE operon
RA	774,358	T→A	7.0%	L17Q (CTG→CAG)	ybgE →	putative inner membrane protein in cydABX‑ybgE operon
RA	782,999	T→G	5.5%	L305L (CTT→CTG)	nadA →	quinolinate synthase, subunit A
RA	783,000	C→A	5.3%	Q306K (CAG→AAG)	nadA →	quinolinate synthase, subunit A
RA	805,312	G→T	5.0%	E604* (GAG→TAG) ‡	ybhJ →	aconitase family protein
RA	805,313	A→C	5.2%	E604A (GAG→GCG) ‡	ybhJ →	aconitase family protein
RA	832,252	T→A	6.7%	intergenic (+16/+216)	rhlE → / ← ybiA	ATP‑dependent RNA helicase/DUF1768 family protein
RA	832,253	A→T	6.9%	intergenic (+17/+215)	rhlE → / ← ybiA	ATP‑dependent RNA helicase/DUF1768 family protein
RA	832,254	T→A	7.1%	intergenic (+18/+214)	rhlE → / ← ybiA	ATP‑dependent RNA helicase/DUF1768 family protein
RA	847,213	A→T	11.5%	intergenic (‑94/+45)	glnP ← / ← glnH	glutamine transporter subunit/glutamine transporter subunit
RA	847,214	T→A	11.5%	intergenic (‑95/+44)	glnP ← / ← glnH	glutamine transporter subunit/glutamine transporter subunit
RA	847,215	A→T	11.5%	intergenic (‑96/+43)	glnP ← / ← glnH	glutamine transporter subunit/glutamine transporter subunit
RA	850,993	T→C	5.6%	intergenic (+28/+21)	ompX → / ← opgE	outer membrane protein X/OPG biosynthetic transmembrane phosphoethanolamine transferase
RA	850,995	T→G	5.6%	intergenic (+30/+19)	ompX → / ← opgE	outer membrane protein X/OPG biosynthetic transmembrane phosphoethanolamine transferase
RA	850,996	C→A	5.5%	intergenic (+31/+18)	ompX → / ← opgE	outer membrane protein X/OPG biosynthetic transmembrane phosphoethanolamine transferase
RA	850,998	G→A	5.6%	intergenic (+33/+16)	ompX → / ← opgE	outer membrane protein X/OPG biosynthetic transmembrane phosphoethanolamine transferase
RA	857,576	T→C	6.3%	intergenic (+21/+220)	ybiT → / ← ybiU	ABC‑F family putative regulatory ATPase/DUF1479 family protein
RA	857,578	C→G	6.8%	intergenic (+23/+218)	ybiT → / ← ybiU	ABC‑F family putative regulatory ATPase/DUF1479 family protein
RA	857,580	G→A	6.5%	intergenic (+25/+216)	ybiT → / ← ybiU	ABC‑F family putative regulatory ATPase/DUF1479 family protein
RA	892,455	G→C	7.1%	V163V (GTG→GTC)	rimK →	ribosomal protein S6 modification protein
RA	892,457	T→A	6.5%	I164N (ATT→AAT)	rimK →	ribosomal protein S6 modification protein
RA	892,459	G→C	6.5%	D165H (GAC→CAC)	rimK →	ribosomal protein S6 modification protein
RA	897,968:1	+A	5.7%	intergenic (+39/‑21)	potI → / → ybjO	putrescine ABC transporter permease/DUF2593 family inner membrane protein
RA	897,973	Δ1 bp	5.4%	intergenic (+44/‑16)	potI → / → ybjO	putrescine ABC transporter permease/DUF2593 family inner membrane protein
RA	915,080	G→C	10.8%	intergenic (‑223/+272)	ybjE ← / ← aqpZ	putative transporter/aquaporin Z
RA	915,081	G→C	10.8%	intergenic (‑224/+271)	ybjE ← / ← aqpZ	putative transporter/aquaporin Z
RA	940,751	T→C	9.4%	intergenic (+31/‑208)	serS → / → dmsA	seryl‑tRNA synthetase/dimethyl sulfoxide reductase, anaerobic, subunit A
RA	940,754	G→A	9.3%	intergenic (+34/‑205)	serS → / → dmsA	seryl‑tRNA synthetase/dimethyl sulfoxide reductase, anaerobic, subunit A
RA	958,769	C→G	7.6%	intergenic (+28/‑43)	serC → / → aroA	3‑phosphoserine/phosphohydroxythreonine aminotransferase/5‑enolpyruvylshikimate‑3‑phosphate synthetase
RA	958,771	A→T	7.6%	intergenic (+30/‑41)	serC → / → aroA	3‑phosphoserine/phosphohydroxythreonine aminotransferase/5‑enolpyruvylshikimate‑3‑phosphate synthetase
RA	958,773	C→G	8.2%	intergenic (+32/‑39)	serC → / → aroA	3‑phosphoserine/phosphohydroxythreonine aminotransferase/5‑enolpyruvylshikimate‑3‑phosphate synthetase
RA	987,560	G→C	6.6%	intergenic (‑578/+25)	ompF ← / ← asnS	outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
RA	987,561	G→C	7.5%	intergenic (‑579/+24)	ompF ← / ← asnS	outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
RA	993,259	C→T	5.0%	intergenic (+25/+18)	pepN → / ← ssuB	aminopeptidase N/aliphatic sulfonate ABC transporter ATPase
RA	1,007,813	T→C	5.0%	intergenic (‑213/‑31)	ycbX ← / → rlmL	6‑N‑hydroxylaminopurine detoxification oxidoreductase/23S rRNA m(2)G2445 and m(7)G2069 methyltransferases, SAM‑dependent
RA	1,007,816	G→A	5.1%	intergenic (‑216/‑28)	ycbX ← / → rlmL	6‑N‑hydroxylaminopurine detoxification oxidoreductase/23S rRNA m(2)G2445 and m(7)G2069 methyltransferases, SAM‑dependent
RA	1,015,912	T→A	14.9%	intergenic (+30/+40)	rmf → / ← fabA	ribosome modulation factor/beta‑hydroxydecanoyl thioester dehydrase
RA	1,018,983	A→T	9.0%	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	9.0%	intergenic (+49/+27)	matP → / ← ompA	Ter macrodomain organizer matS‑binding protein/outer membrane protein A (3a;II*;G;d)
RA	1,038,117	C→G	5.3%	H126Q (CAC→CAG)	cbdA →	cytochrome bd‑II oxidase, subunit I
RA	1,038,118	C→G	5.5%	L127V (CTG→GTG)	cbdA →	cytochrome bd‑II oxidase, subunit I
RA	1,041,937	T→G	6.8%	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	1,052,257	C→T	6.2%	intergenic (+17/+32)	gnsA → / ← yccM	putative phosphatidylethanolamine synthesis regulator/putative 4Fe‑4S membrane protein
RA	1,113,544	G→A	6.8%	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	6.4%	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	6.3%	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	1,141,148	C→T	5.5%	intergenic (+162/+34)	flgL → / ← rne	flagellar hook‑filament junction protein/endoribonuclease; RNA‑binding protein;RNA degradosome binding protein
RA	1,141,150	G→A	5.7%	intergenic (+164/+32)	flgL → / ← rne	flagellar hook‑filament junction protein/endoribonuclease; RNA‑binding protein;RNA degradosome binding protein
RA	1,141,151	T→C	5.8%	intergenic (+165/+31)	flgL → / ← rne	flagellar hook‑filament junction protein/endoribonuclease; RNA‑binding protein;RNA degradosome binding protein
RA	1,141,153	A→G	5.7%	intergenic (+167/+29)	flgL → / ← rne	flagellar hook‑filament junction protein/endoribonuclease; RNA‑binding protein;RNA degradosome binding protein
RA	1,147,548	T→G	5.0%	intergenic (+8/‑73)	rpmF → / → plsX	50S ribosomal subunit protein L32/putative phosphate acyltransferase
RA	1,159,335	G→T	6.6%	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	6.6%	intergenic (+34/+26)	ptsG → / ← fhuE	fused glucose‑specific PTS enzymes: IIB component/IIC component/ferric‑rhodotorulic acid outer membrane transporter
RA	1,169,380	T→C	6.7%	intergenic (+50/+32)	bhsA → / ← ldtC	biofilm, cell surface and signaling protein/L,D‑transpeptidase linking Lpp to murein
RA	1,169,382	C→G	6.8%	intergenic (+52/+30)	bhsA → / ← ldtC	biofilm, cell surface and signaling protein/L,D‑transpeptidase linking Lpp to murein
RA	1,169,384	G→A	6.9%	intergenic (+54/+28)	bhsA → / ← ldtC	biofilm, cell surface and signaling protein/L,D‑transpeptidase linking Lpp to murein
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	7.3%	intergenic (‑116/+12)	mfd ← / ← ycfT	transcription‑repair coupling factor/inner membrane protein
RA	1,202,957	G→T	5.2%	intergenic (‑24/‑67)	cohE ← / → croE	e14 prophage; repressor protein phage e14/e14 prophage; putative DNA‑binding transcriptional regulator
RA	1,202,961	A→C	5.3%	intergenic (‑28/‑63)	cohE ← / → croE	e14 prophage; repressor protein phage e14/e14 prophage; putative DNA‑binding transcriptional regulator
RA	1,211,610	A→G	6.4%	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	6.4%	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	6.4%	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	9.0%	intergenic (+332/+40)	ycgI → / ← minE	pseudogene/cell division topological specificity factor
RA	1,224,242	A→T	9.0%	intergenic (+335/+37)	ycgI → / ← minE	pseudogene/cell division topological specificity factor
RA	1,233,154	T→A	8.9%	intergenic (‑124/+22)	dsbB ← / ← nhaB	oxidoreductase that catalyzes reoxidation of DsbA protein disulfide isomerase I/sodium:proton antiporter
RA	1,233,157	T→A	9.2%	intergenic (‑127/+19)	dsbB ← / ← nhaB	oxidoreductase that catalyzes reoxidation of DsbA protein disulfide isomerase I/sodium:proton antiporter
RA	1,292,472	G→A	6.5%	intergenic (+107/+37)	galU → / ← hns	glucose‑1‑phosphate uridylyltransferase/global DNA‑binding transcriptional dual regulator H‑NS
RA	1,292,473	C→G	6.4%	intergenic (+108/+36)	galU → / ← hns	glucose‑1‑phosphate uridylyltransferase/global DNA‑binding transcriptional dual regulator H‑NS
RA	1,292,474	T→C	6.6%	intergenic (+109/+35)	galU → / ← hns	glucose‑1‑phosphate uridylyltransferase/global DNA‑binding transcriptional dual regulator H‑NS
RA	1,306,787	G→A	5.2%	intergenic (+19/+34)	oppF → / ← yciU	oligopeptide ABC transporter ATPase/UPF0263 family protein
RA	1,311,830	A→G	8.4%	intergenic (+22/+18)	tonB → / ← yciA	membrane spanning protein in TonB‑ExbB‑ExbD transport complex/acyl‑CoA esterase
RA	1,311,831	C→T	8.5%	intergenic (+23/+17)	tonB → / ← yciA	membrane spanning protein in TonB‑ExbB‑ExbD transport complex/acyl‑CoA esterase
RA	1,315,796	A→G	6.6%	intergenic (‑26/+60)	yciF ← / ← yciG	putative rubrerythrin/ferritin‑like metal‑binding protein/KGG family protein
RA	1,315,800	A→G	8.2%	intergenic (‑30/+56)	yciF ← / ← yciG	putative rubrerythrin/ferritin‑like metal‑binding protein/KGG family protein
RA	1,315,803	C→T	8.3%	intergenic (‑33/+53)	yciF ← / ← yciG	putative rubrerythrin/ferritin‑like metal‑binding protein/KGG family protein
RA	1,315,807	C→T	8.2%	intergenic (‑37/+49)	yciF ← / ← yciG	putative rubrerythrin/ferritin‑like metal‑binding protein/KGG family protein
RA	1,324,837	A→C	6.0%	Y31S (TAT→TCT) ‡	yciQ →	enhancer of membrane protein expression; putative inner membrane protein
RA	1,324,838	T→A	6.0%	Y31* (TAT→TAA) ‡	yciQ →	enhancer of membrane protein expression; putative inner membrane protein
RA	1,324,839	G→T	5.7%	E32* (GAA→TAA)	yciQ →	enhancer of membrane protein expression; putative inner membrane protein
RA	1,344,033	A→G	6.3%	L105P (CTG→CCG)	yciT ←	global regulator of transcription; DeoR family
RA	1,344,036	G→C	6.3%	T104S (ACT→AGT)	yciT ←	global regulator of transcription; DeoR family
RA	1,344,039	C→T	6.1%	R103Q (CGG→CAG)	yciT ←	global regulator of transcription; DeoR family
RA	1,354,220	C→A	6.0%	G100V (GGT→GTT)	sapC ←	antimicrobial peptide transport ABC transporter permease
RA	1,354,223	A→G	6.1%	V99A (GTG→GCG) ‡	sapC ←	antimicrobial peptide transport ABC transporter permease
RA	1,354,224	C→T	6.1%	V99M (GTG→ATG) ‡	sapC ←	antimicrobial peptide transport ABC transporter permease
RA	1,354,227	T→G	5.7%	T98P (ACC→CCC)	sapC ←	antimicrobial peptide transport ABC transporter permease
RA	1,388,283	C→T	6.0%	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	6.1%	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	6.2%	intergenic (+24/+20)	tyrR → / ← tpx	aromatic amino acid biosynthesis and transport regulon transcriptional regulator; autorepressor; ATPase; phosphatase/lipid hydroperoxide peroxidase
RA	1,426,417	T→C	5.1%	intergenic (+335/‑37)	ydaY → / → tmpR	pseudogene, Rac prophage;Phage or Prophage Related/Rac prophage; pseudogene, tail protein family;Phage or Prophage Related; putative alpha helix protein
RA	1,426,418	T→G	5.1%	intergenic (+336/‑36)	ydaY → / → tmpR	pseudogene, Rac prophage;Phage or Prophage Related/Rac prophage; pseudogene, tail protein family;Phage or Prophage Related; putative alpha helix protein
RA	1,426,422	G→A	5.0%	intergenic (+340/‑32)	ydaY → / → tmpR	pseudogene, Rac prophage;Phage or Prophage Related/Rac prophage; pseudogene, tail protein family;Phage or Prophage Related; putative alpha helix protein
RA	1,449,050	T→A	12.0%	intergenic (+32/+26)	feaB → / ← tynA	phenylacetaldehyde dehydrogenase/tyramine oxidase, copper‑requiring
RA	1,498,892	A→T	7.7%	intergenic (+17/‑46)	ydcH → / → rimL	DUF465 family protein/ribosomal‑protein‑L7/L12‑serine acetyltransferase
RA	1,498,894	C→G	7.7%	intergenic (+19/‑44)	ydcH → / → rimL	DUF465 family protein/ribosomal‑protein‑L7/L12‑serine acetyltransferase
RA	1,498,896	A→T	7.7%	intergenic (+21/‑42)	ydcH → / → rimL	DUF465 family protein/ribosomal‑protein‑L7/L12‑serine acetyltransferase
RA	1,543,229	G→T	6.4%	L278M (CTG→ATG)	narU ←	nitrate/nitrite transporter
RA	1,543,230	C→G	6.4%	M277I (ATG→ATC) ‡	narU ←	nitrate/nitrite transporter
RA	1,543,231	A→C	6.5%	M277R (ATG→AGG) ‡	narU ←	nitrate/nitrite transporter
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	1,572,928	C→G	5.9%	A759P (GCA→CCA)	pqqL ←	putative periplasmic M16 family zinc metalloendopeptidase
RA	1,603,724	A→C	9.0%	T236P (ACC→CCC)	lsrC →	autoinducer 2 import system permease protein
RA	1,603,735	G→T	8.8%	G239G (GGG→GGT)	lsrC →	autoinducer 2 import system permease protein
RA	1,666,466	T→G	7.2%	Y384* (TAT→TAG)	clcB →	H(+)/Cl(‑) exchange transporter
RA	1,666,468	A→T	6.9%	Q385L (CAG→CTG)	clcB →	H(+)/Cl(‑) exchange transporter
RA	1,666,470	C→A	7.7%	L386I (CTA→ATA)	clcB →	H(+)/Cl(‑) exchange transporter
RA	1,685,527	A→G	100%	G354G (GGT→GGC)	fumC ←	fumarate hydratase (fumarase C),aerobic Class II
RA	1,689,817	C→A	7.7%	intergenic (+66/‑35)	manA → / → ydgA	mannose‑6‑phosphate isomerase/DUF945 family protein
RA	1,689,819	A→T	7.7%	intergenic (+68/‑33)	manA → / → ydgA	mannose‑6‑phosphate isomerase/DUF945 family protein
RA	1,689,821	T→G	7.7%	intergenic (+70/‑31)	manA → / → ydgA	mannose‑6‑phosphate isomerase/DUF945 family protein
RA	1,693,417	G→C	5.2%	L283V (CTG→GTG)	uidB ←	glucuronide transporter
RA	1,698,585	T→G	6.9%	E199A (GAA→GCA)	malI ←	transcriptional repressor of Mal regulon
RA	1,698,587	T→A	7.0%	A198A (GCA→GCT) ‡	malI ←	transcriptional repressor of Mal regulon
RA	1,698,589	C→A	6.9%	A198S (GCA→TCA) ‡	malI ←	transcriptional repressor of Mal regulon
RA	1,701,108	A→T	8.9%	N51I (AAT→ATT)	malY →	PLP‑dependent beta‑cystathionase and maltose regulon regulator
RA	1,736,097	T→A	5.8%	intergenic (+138/+24)	sodB → / ← ydhP	superoxide dismutase, Fe/putative MFS transporter, inner membrane protein
RA	1,736,100	T→A	5.9%	intergenic (+141/+21)	sodB → / ← ydhP	superoxide dismutase, Fe/putative MFS transporter, inner membrane protein
RA	1,764,701	G→A	5.2%	intergenic (‑315/+12)	sufA ← / ← rydB	Fe‑S cluster assembly protein/novel sRNA, function unknown
RA	1,770,203	T→A	12.2%	intergenic (+17/‑169)	ydiK → / → rprA	UPF0118 family inner membrane protein/sRNA antisense activator for RpoS translation, Hfq‑dependent
RA	1,770,204	C→G	12.2%	intergenic (+18/‑168)	ydiK → / → rprA	UPF0118 family inner membrane protein/sRNA antisense activator for RpoS translation, Hfq‑dependent
RA	1,770,205	T→A	13.0%	intergenic (+19/‑167)	ydiK → / → rprA	UPF0118 family inner membrane protein/sRNA antisense activator for RpoS translation, Hfq‑dependent
RA	1,795,227	A→T	6.1%	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	6.1%	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	6.1%	intergenic (‑77/+24)	btuC ← / ← ihfA	vitamin B12 ABC transporter permease/integration host factor (IHF), DNA‑binding protein, alpha subunit
RA	1,797,388	G→T	5.4%	P186Q (CCG→CAG)	pheT ←	phenylalanine tRNA synthetase, beta subunit
RA	1,797,391	A→C	5.4%	L185R (CTG→CGG)	pheT ←	phenylalanine tRNA synthetase, beta subunit
RA	1,799,370	Δ1 bp	9.0%	intergenic (‑100/+23)	pheM ← / ← rplT	phenylalanyl‑tRNA synthetase operon leader peptide/50S ribosomal subunit protein L20
RA	1,799,374:1	+T	8.8%	intergenic (‑104/+19)	pheM ← / ← rplT	phenylalanyl‑tRNA synthetase operon leader peptide/50S ribosomal subunit protein L20
RA	1,806,390	G→A	5.2%	L7L (TTG→TTA)	pfkB →	6‑phosphofructokinase II
RA	1,823,335	G→C	12.5%	intergenic (+50/‑180)	nadE → / → cho	NAD synthetase, NH3/glutamine‑dependent/endonuclease of nucleotide excision repair
RA	1,823,338	G→C	13.1%	intergenic (+53/‑177)	nadE → / → cho	NAD synthetase, NH3/glutamine‑dependent/endonuclease of nucleotide excision repair
RA	1,829,328	C→G	5.8%	G136A (GGC→GCC)	astD ←	succinylglutamic semialdehyde dehydrogenase
RA	1,829,334	G→T	6.0%	P134Q (CCG→CAG)	astD ←	succinylglutamic semialdehyde dehydrogenase
RA	1,864,758	G→A	5.2%	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	5.8%	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	5.6%	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	8.6%	intergenic (‑46/+44)	yeaE ← / ← mipA	aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent/scaffolding protein for murein synthesizing machinery
RA	1,868,859	Δ1 bp	5.8%	intergenic (+17/‑96)	yeaG → / → yeaH	protein kinase, endogenous substrate unidentified; autokinase/UPF0229 family protein
RA	1,868,865:1	+G	5.9%	intergenic (+23/‑90)	yeaG → / → yeaH	protein kinase, endogenous substrate unidentified; autokinase/UPF0229 family protein
RA	1,880,851	T→A	7.4%	intergenic (‑92/+35)	leuE ← / ← dmlR	leucine efflux protein/transcriptional activator of dmlA
RA	1,880,852	T→A	7.4%	intergenic (‑93/+34)	leuE ← / ← dmlR	leucine efflux protein/transcriptional activator of dmlA
RA	1,881,358	T→A	6.2%	D151V (GAC→GTC)	dmlR ←	transcriptional activator of dmlA
RA	1,883,027	C→G	10.4%	intergenic (+30/‑161)	dmlA → / → yeaV	D‑malate oxidase, NAD‑dependent; putative tartrate dehydrogenase/putative transporter
RA	1,888,030	A→T	6.2%	intergenic (‑39/+31)	rnd ← / ← fadD	ribonuclease D/acyl‑CoA synthetase (long‑chain‑fatty‑acid‑‑CoA ligase)
RA	1,888,032	T→A	6.1%	intergenic (‑41/+29)	rnd ← / ← fadD	ribonuclease D/acyl‑CoA synthetase (long‑chain‑fatty‑acid‑‑CoA ligase)
RA	1,888,034	A→T	6.2%	intergenic (‑43/+27)	rnd ← / ← fadD	ribonuclease D/acyl‑CoA synthetase (long‑chain‑fatty‑acid‑‑CoA ligase)
RA	1,910,295	A→T	5.8%	D7V (GAC→GTC)	yebQ →	putative transporter
RA	1,932,094	C→G	7.2%	intergenic (+35/+21)	purT → / ← eda	phosphoribosylglycinamide formyltransferase 2/KHG/KDPG aldolase; 2‑dehydro‑3‑deoxy‑phosphogluconate/4‑hydroxy‑2‑ oxoglutarate aldolase
RA	1,932,095	T→A	7.1%	intergenic (+36/+20)	purT → / ← eda	phosphoribosylglycinamide formyltransferase 2/KHG/KDPG aldolase; 2‑dehydro‑3‑deoxy‑phosphogluconate/4‑hydroxy‑2‑ oxoglutarate aldolase
RA	1,932,096	C→G	7.0%	intergenic (+37/+19)	purT → / ← eda	phosphoribosylglycinamide formyltransferase 2/KHG/KDPG aldolase; 2‑dehydro‑3‑deoxy‑phosphogluconate/4‑hydroxy‑2‑ oxoglutarate aldolase
RA	1,944,233	G→T	6.0%	intergenic (+34/+113)	znuB → / ← ruvB	zinc ABC transporter permease/ATP‑dependent DNA helicase, component of RuvABC resolvasome
RA	1,944,234	A→C	5.8%	intergenic (+35/+112)	znuB → / ← ruvB	zinc ABC transporter permease/ATP‑dependent DNA helicase, component of RuvABC resolvasome
RA	1,944,240	T→G	5.8%	intergenic (+41/+106)	znuB → / ← ruvB	zinc ABC transporter permease/ATP‑dependent DNA helicase, component of RuvABC resolvasome
RA	1,944,241	T→C	5.3%	intergenic (+42/+105)	znuB → / ← ruvB	zinc ABC transporter permease/ATP‑dependent DNA helicase, component of RuvABC resolvasome
RA	1,952,587	T→A	5.8%	W108R (TGG→AGG)	yecN →	MAPEG family inner membrane protein
MC JC	1,978,503	Δ776 bp	100%		insB1–insA	insB1, insA
RA	1,985,112	C→G	14.5%	intergenic (‑43/+27)	araG ← / ← araF	L‑arabinose ABC transporter ATPase/L‑arabinose ABC transporter periplasmic binding protein
RA	1,987,442	Δ1 bp	6.9%	intergenic (+14/+65)	ftnB → / ← yecJ	ferritin B, putative ferrous iron reservoir/DUF2766 family protein
RA	1,987,450:1	+A	6.5%	intergenic (+22/+57)	ftnB → / ← yecJ	ferritin B, putative ferrous iron reservoir/DUF2766 family protein
RA	2,032,336	G→C	8.8%	intergenic (‑19/+48)	dcm ← / ← yedJ	DNA cytosine methyltransferase/putative HD superfamily phosphohydrolase
RA	2,079,004	G→C	8.4%	intergenic (+73/+28)	yoeF → / ← yeeX	pseudogene, CP4‑44 putative prophage remnant;Phage or Prophage Related/UPF0265 family protein
RA	2,081,688	A→T	6.5%	I287N (ATT→AAT)	dacD ←	D‑alanyl‑D‑alanine carboxypeptidase; penicillin‑binding protein 6b
RA	2,090,122	A→G	9.4%	intergenic (+76/‑70)	hisL → / → hisG	his operon leader peptide/ATP phosphoribosyltransferase
RA	2,090,124	C→G	9.2%	intergenic (+78/‑68)	hisL → / → hisG	his operon leader peptide/ATP phosphoribosyltransferase
RA	2,090,126	C→T	9.1%	intergenic (+80/‑66)	hisL → / → hisG	his operon leader peptide/ATP phosphoribosyltransferase
RA	2,115,847	G→T	5.3%	A17E (GCG→GAG)	wcaM ←	colanic acid biosynthesis protein
RA	2,115,849	C→G	5.1%	S16S (TCG→TCC) ‡	wcaM ←	colanic acid biosynthesis protein
RA	2,115,851	A→C	5.3%	S16A (TCG→GCG) ‡	wcaM ←	colanic acid biosynthesis protein
RA	2,139,720	C→A	5.3%	intergenic (+235/+39)	yegH → / ← asmA	inner membrane protein/suppressor of OmpF assembly mutants; putative outer membrane protein assembly factor; inner membrane‑anchored periplasmic protein
RA	2,145,313	C→A	100%	S683Y (TCC→TAC)	yegE →	putative diguanylate cyclase
RA	2,165,626	T→C	6.4%	intergenic (+105/‑42)	yegP → / → yegQ	UPF0339 family protein/putative peptidase
RA	2,165,628	A→T	5.9%	intergenic (+107/‑40)	yegP → / → yegQ	UPF0339 family protein/putative peptidase
RA	2,165,630	G→A	5.4%	intergenic (+109/‑38)	yegP → / → yegQ	UPF0339 family protein/putative peptidase
RA	2,168,423	A→T	5.1%	intergenic (‑117/‑289)	yegR ← / → yegS	uncharacterized protein/phosphatidylglycerol kinase, metal‑dependent
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	6.2%	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	6.0%	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	6.0%	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	5.7%	intergenic (‑141/+167)	gatY ← / ← fbaB	D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I
RA	2,229,322	C→G	6.4%	intergenic (+257/+116)	yohP → / ← dusC	uncharacterized protein/tRNA‑dihydrouridine synthase C
RA	2,229,323	C→G	6.4%	intergenic (+258/+115)	yohP → / ← dusC	uncharacterized protein/tRNA‑dihydrouridine synthase C
RA	2,282,830	T→C	5.5%	intergenic (+29/+110)	rplY → / ← yejK	50S ribosomal subunit protein L25/spermidine nucleoid‑associated protein
RA	2,282,831	C→G	5.5%	intergenic (+30/+109)	rplY → / ← yejK	50S ribosomal subunit protein L25/spermidine nucleoid‑associated protein
RA	2,282,832	C→G	6.4%	intergenic (+31/+108)	rplY → / ← yejK	50S ribosomal subunit protein L25/spermidine nucleoid‑associated protein
RA	2,282,833	G→A	5.6%	intergenic (+32/+107)	rplY → / ← yejK	50S ribosomal subunit protein L25/spermidine nucleoid‑associated protein
RA	2,286,311	C→G	7.5%	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	7.5%	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	7.3%	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	2,311,616	C→T	6.2%	intergenic (‑82/+30)	apbE ← / ← ompC	putative thiamine‑synthetic flavin transferase lipoprotein/outer membrane porin protein C
RA	2,311,619	A→G	5.9%	intergenic (‑85/+27)	apbE ← / ← ompC	putative thiamine‑synthetic flavin transferase lipoprotein/outer membrane porin protein C
RA	2,314,800	A→C	10.4%	Q438P (CAG→CCG) ‡	rcsD →	phosphotransfer intermediate protein in two‑component regulatory system with RcsBC
RA	2,314,801	G→T	10.6%	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	2,336,763	A→C	5.3%	intergenic (‑119/+30)	yfaA ← / ← gyrA	DUF2138 family protein, putative host defense protein/DNA gyrase (type II topoisomerase), subunit A
RA	2,336,766	G→T	5.3%	intergenic (‑122/+27)	yfaA ← / ← gyrA	DUF2138 family protein, putative host defense protein/DNA gyrase (type II topoisomerase), subunit A
RA	2,375,483	A→T	5.4%	L160L (CTT→CTA) ‡	menC ←	O‑succinylbenzoyl‑CoA synthase
RA	2,375,484	A→T	5.4%	L160H (CTT→CAT) ‡	menC ←	O‑succinylbenzoyl‑CoA synthase
RA	2,383,956	A→T	17.6%	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	17.8%	intergenic (+35/+36)	elaD → / ← yfbK	protease, capable of cleaving an AMC‑ubiquitin model substrate/Von Willebrand factor domain putative lipoprotein
RA	2,390,012	Δ1 bp	8.8%	intergenic (+48/+36)	yfbP → / ← nuoN	TPR‑like repeats‑containing protein/NADH:ubiquinone oxidoreductase, membrane subunit N
RA	2,390,016:1	+C	9.2%	intergenic (+52/+32)	yfbP → / ← nuoN	TPR‑like repeats‑containing protein/NADH:ubiquinone oxidoreductase, membrane subunit N
RA	2,390,024	C→T	8.7%	intergenic (+60/+24)	yfbP → / ← nuoN	TPR‑like repeats‑containing protein/NADH:ubiquinone oxidoreductase, membrane subunit N
RA	2,391,414	C→G	5.4%	R31P (CGA→CCA)	nuoN ←	NADH:ubiquinone oxidoreductase, membrane subunit N
RA	2,391,417	C→G	5.5%	W30S (TGG→TCG)	nuoN ←	NADH:ubiquinone oxidoreductase, membrane subunit N
RA	2,414,689	C→G	8.7%	intergenic (+17/‑58)	ackA → / → pta	acetate kinase A and propionate kinase 2/phosphate acetyltransferase
RA	2,415,725	C→A	5.9%	L327M (CTG→ATG) ‡	pta →	phosphate acetyltransferase
RA	2,415,726	T→G	6.3%	L327R (CTG→CGG) ‡	pta →	phosphate acetyltransferase
RA	2,425,968	T→G	6.1%	intergenic (‑52/+38)	hisQ ← / ← hisJ	histidine ABC transporter permease/histidine ABC transporter periplasmic binding protein
RA	2,425,971	C→A	6.1%	intergenic (‑55/+35)	hisQ ← / ← hisJ	histidine ABC transporter permease/histidine ABC transporter periplasmic binding protein
RA	2,425,975	A→G	5.8%	intergenic (‑59/+31)	hisQ ← / ← hisJ	histidine ABC transporter permease/histidine ABC transporter periplasmic binding protein
RA	2,427,625	C→A	5.2%	G56V (GGT→GTT)	argT ←	lysine/arginine/ornithine transporter subunit
RA	2,428,697	A→G	5.6%	intergenic (‑71/+24)	ubiX ← / ← purF	3‑octaprenyl‑4‑hydroxybenzoate carboxy‑lyase/amidophosphoribosyltransferase
RA	2,428,699	A→T	5.5%	intergenic (‑73/+22)	ubiX ← / ← purF	3‑octaprenyl‑4‑hydroxybenzoate carboxy‑lyase/amidophosphoribosyltransferase
RA	2,428,701	C→T	5.5%	intergenic (‑75/+20)	ubiX ← / ← purF	3‑octaprenyl‑4‑hydroxybenzoate carboxy‑lyase/amidophosphoribosyltransferase
RA	2,432,985	A→G	7.2%	intergenic (‑43/+27)	folC ← / ← accD	bifunctional folylpolyglutamate synthase/ dihydrofolate synthase/acetyl‑CoA carboxylase, beta (carboxyltransferase) subunit
RA	2,432,990	G→C	7.3%	intergenic (‑48/+22)	folC ← / ← accD	bifunctional folylpolyglutamate synthase/ dihydrofolate synthase/acetyl‑CoA carboxylase, beta (carboxyltransferase) subunit
RA	2,432,995	C→T	6.3%	intergenic (‑53/+17)	folC ← / ← accD	bifunctional folylpolyglutamate synthase/ dihydrofolate synthase/acetyl‑CoA carboxylase, beta (carboxyltransferase) subunit
RA	2,462,677	A→T	5.6%	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	5.7%	intergenic (+33/‑333)	fadL → / → yfdF	long‑chain fatty acid outer membrane transporter/uncharacterized protein
RA	2,474,878	T→C	8.7%	intergenic (+22/‑106)	yfdQ → / → yfdR	CPS‑53 (KpLE1) prophage; uncharacterized protein/CPS‑53 (KpLE1) prophage; conserved protein
RA	2,474,881	G→A	9.3%	intergenic (+25/‑103)	yfdQ → / → yfdR	CPS‑53 (KpLE1) prophage; uncharacterized protein/CPS‑53 (KpLE1) prophage; conserved protein
RA	2,504,192	T→A	5.2%	A98A (GCA→GCT)	fryA ←	putative PTS enzyme: Hpr, enzyme I and IIA components
RA	2,504,197	G→A	5.2%	Q97* (CAG→TAG)	fryA ←	putative PTS enzyme: Hpr, enzyme I and IIA components
RA	2,521,344	C→T	7.3%	intergenic (+16/+249)	lysV → / ← xapR	tRNA‑Lys/transcriptional activator of xapAB
RA	2,521,346	A→T	7.5%	intergenic (+18/+247)	lysV → / ← xapR	tRNA‑Lys/transcriptional activator of xapAB
RA	2,521,348	A→G	7.3%	intergenic (+20/+245)	lysV → / ← xapR	tRNA‑Lys/transcriptional activator of xapAB
RA	2,525,907	G→A	6.0%	intergenic (+16/+23)	yfeN → / ← yfeR	putative outer membrane protein/transcriptional regulator of yefH
RA	2,525,908	C→G	5.9%	intergenic (+17/+22)	yfeN → / ← yfeR	putative outer membrane protein/transcriptional regulator of yefH
RA	2,561,205	A→T	7.1%	intergenic (+307/‑163)	yffL → / → yffM	CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein
RA	2,561,206	A→T	7.1%	intergenic (+308/‑162)	yffL → / → yffM	CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein
RA	2,581,762	G→A	6.1%	A339V (GCC→GTC)	ypfG ←	DUF1176 family protein
RA	2,581,765	T→C	6.0%	D338G (GAC→GGC)	ypfG ←	DUF1176 family protein
RA	2,589,122	G→A	9.4%	G510S (GGC→AGC)	acrD →	aminoglycoside/multidrug efflux system
RA	2,589,125	T→C	10.2%	F511L (TTT→CTT)	acrD →	aminoglycoside/multidrug efflux system
RA	2,622,348:1	+A	5.9%	coding (115/639 nt)	purN →	phosphoribosylglycinamide formyltransferase 1
RA	2,622,354	Δ1 bp	5.9%	coding (121/639 nt)	purN →	phosphoribosylglycinamide formyltransferase 1
RA	2,638,584	A→T	5.9%	F23L (TTT→TTA)	bamB ←	BamABCDE complex OM biogenesis lipoprotein
RA	2,653,367	G→A	9.4%	intergenic (+28/‑488)	sseA → / → ryfA	3‑mercaptopyruvate sulfurtransferase/novel sRNA, function unknown
RA	2,653,372	T→C	9.5%	intergenic (+33/‑483)	sseA → / → ryfA	3‑mercaptopyruvate sulfurtransferase/novel sRNA, function unknown
RA	2,655,044	A→G	5.8%	intergenic (‑111/+31)	sseB ← / ← pepB	rhodanase‑like enzyme, sulfur transfer from thiosulfate/aminopeptidase B
RA	2,655,045	A→C	5.8%	intergenic (‑112/+30)	sseB ← / ← pepB	rhodanase‑like enzyme, sulfur transfer from thiosulfate/aminopeptidase B
RA	2,655,051	T→A	5.7%	intergenic (‑118/+24)	sseB ← / ← pepB	rhodanase‑like enzyme, sulfur transfer from thiosulfate/aminopeptidase B
RA	2,655,052	T→A	5.7%	intergenic (‑119/+23)	sseB ← / ← pepB	rhodanase‑like enzyme, sulfur transfer from thiosulfate/aminopeptidase B
RA	2,655,059	C→T	5.1%	intergenic (‑126/+16)	sseB ← / ← pepB	rhodanase‑like enzyme, sulfur transfer from thiosulfate/aminopeptidase B
RA	2,679,430	Δ1 bp	6.5%	intergenic (‑63/+34)	yphF ← / ← yphG	putative sugar ABC transporter periplasmic binding protein/DUF4380 domain‑containing TPR repeat protein
RA	2,679,434:1	+C	6.5%	intergenic (‑67/+30)	yphF ← / ← yphG	putative sugar ABC transporter periplasmic binding protein/DUF4380 domain‑containing TPR repeat protein
RA	2,691,169	A→T	7.0%	noncoding (172/184 nt)	glmY ←	sRNA activator of glmS mRNA, glmZ processing antagonist
RA	2,691,171	T→A	6.7%	noncoding (170/184 nt)	glmY ←	sRNA activator of glmS mRNA, glmZ processing antagonist
RA	2,691,173	A→T	6.9%	noncoding (168/184 nt)	glmY ←	sRNA activator of glmS mRNA, glmZ processing antagonist
RA	2,704,304	A→G	6.9%	intergenic (‑241/+31)	rnc ← / ← lepB	RNase III/leader peptidase (signal peptidase I)
RA	2,704,306	A→T	7.0%	intergenic (‑243/+29)	rnc ← / ← lepB	RNase III/leader peptidase (signal peptidase I)
RA	2,704,308	C→T	6.9%	intergenic (‑245/+27)	rnc ← / ← lepB	RNase III/leader peptidase (signal peptidase I)
RA	2,707,320	A→T	7.4%	intergenic (‑196/+2)	lepA ← / ← rseC	back‑translocating elongation factor EF4, GTPase/SoxR iron‑sulfur cluster reduction factor component
RA	2,707,321	A→T	7.4%	intergenic (‑197/+1)	lepA ← / ← rseC	back‑translocating elongation factor EF4, GTPase/SoxR iron‑sulfur cluster reduction factor component
RA	2,716,030	T→G	9.1%	intergenic (+20/+36)	eamB → / ← grcA	cysteine and O‑acetylserine exporter/autonomous glycyl radical cofactor
RA	2,716,033	C→A	9.1%	intergenic (+23/+33)	eamB → / ← grcA	cysteine and O‑acetylserine exporter/autonomous glycyl radical cofactor
RA	2,729,465	G→A	5.6%	intergenic (‑21/+151)	gltW ← / ← rrsG	tRNA‑Glu/16S ribosomal RNA of rrnG operon
RA	2,729,466	T→A	6.5%	intergenic (‑22/+150)	gltW ← / ← rrsG	tRNA‑Glu/16S ribosomal RNA of rrnG operon
RA	2,729,467	T→C	6.7%	intergenic (‑23/+149)	gltW ← / ← rrsG	tRNA‑Glu/16S ribosomal RNA of rrnG operon
RA	2,737,711	G→A	5.1%	intergenic (+65/‑34)	pheL → / → pheA	pheA gene leader peptide/chorismate mutase and prephenate dehydratase, P‑protein
RA	2,753,986	A→T	5.7%	intergenic (+40/+22)	bamE → / ← ratB	lipoprotein component of BamABCDE OM biogenesis complex/UPF0125 family protein
RA	2,761,620	T→G	9.8%	K641Q (AAG→CAG)	yfjK ←	radiation resistance protein; DEAD/H helicase‑like protein; CP4‑57 putative defective prophage
RA	2,761,623	C→A	8.6%	V640L (GTA→TTA)	yfjK ←	radiation resistance protein; DEAD/H helicase‑like protein; CP4‑57 putative defective prophage
RA	2,768,609	T→C	6.2%	intergenic (+36/‑56)	yfjP → / → yfjQ	CP4‑57 prophage; 50S ribosome‑binding GTPase family protein/CP4‑57 prophage; uncharacterized protein
RA	2,768,614	A→C	5.3%	intergenic (+41/‑51)	yfjP → / → yfjQ	CP4‑57 prophage; 50S ribosome‑binding GTPase family protein/CP4‑57 prophage; uncharacterized protein
RA	2,768,615	G→T	5.3%	intergenic (+42/‑50)	yfjP → / → yfjQ	CP4‑57 prophage; 50S ribosome‑binding GTPase family protein/CP4‑57 prophage; uncharacterized protein
RA	2,768,620	G→A	5.3%	intergenic (+47/‑45)	yfjP → / → yfjQ	CP4‑57 prophage; 50S ribosome‑binding GTPase family protein/CP4‑57 prophage; uncharacterized protein
RA	2,778,123	G→T	7.6%	intergenic (+341/+23)	ypjF → / ← ypjA	CP4‑57 prophage; toxin of the YpjF‑YfjZ toxin‑antitoxin system/adhesin‑like autotransporter
RA	2,778,124	A→C	7.4%	intergenic (+342/+22)	ypjF → / ← ypjA	CP4‑57 prophage; toxin of the YpjF‑YfjZ toxin‑antitoxin system/adhesin‑like autotransporter
RA	2,801,056	A→T	7.0%	N31I (AAT→ATT)	nrdI →	NrdEF cluster assembly flavodoxin
RA	2,807,093	A→T	5.4%	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	5.5%	intergenic (+21/‑37)	proW → / → proX	glycine betaine/proline ABC transporter permease/glycine betaine/proline ABC transporter periplasmic binding protein; cold shock protein
RA	2,814,174	T→A	5.5%	intergenic (+20/+44)	emrB → / ← luxS	multidrug efflux system protein/S‑ribosylhomocysteine lyase
RA	2,814,175	T→A	5.5%	intergenic (+21/+43)	emrB → / ← luxS	multidrug efflux system protein/S‑ribosylhomocysteine lyase
RA	2,822,673	C→T	7.0%	intergenic (‑34/+35)	recX ← / ← recA	regulatory protein for RecA/DNA recombination and repair protein; ssDNA‑dependent ATPase; synaptase; ssDNA and dsDNA binding protein; ATP‑dependent homologous DNA strand exchanger; recombinase A; LexA autocleavage cofactor
RA	2,822,678	G→T	6.8%	intergenic (‑39/+30)	recX ← / ← recA	regulatory protein for RecA/DNA recombination and repair protein; ssDNA‑dependent ATPase; synaptase; ssDNA and dsDNA binding protein; ATP‑dependent homologous DNA strand exchanger; recombinase A; LexA autocleavage cofactor
RA	2,822,679	A→C	6.8%	intergenic (‑40/+29)	recX ← / ← recA	regulatory protein for RecA/DNA recombination and repair protein; ssDNA‑dependent ATPase; synaptase; ssDNA and dsDNA binding protein; ATP‑dependent homologous DNA strand exchanger; recombinase A; LexA autocleavage cofactor
RA	2,822,684	A→G	6.8%	intergenic (‑45/+24)	recX ← / ← recA	regulatory protein for RecA/DNA recombination and repair protein; ssDNA‑dependent ATPase; synaptase; ssDNA and dsDNA binding protein; ATP‑dependent homologous DNA strand exchanger; recombinase A; LexA autocleavage cofactor
RA	2,856,257	G→C	8.6%	L640L (CTG→CTC)	fhlA →	formate hydrogenlyase transcriptional activator
RA	2,856,258	G→C	8.7%	E641Q (GAG→CAG)	fhlA →	formate hydrogenlyase transcriptional activator
RA	2,866,487	G→C	7.7%	intergenic (+22/+72)	ygbN → / ← rpoS	putative transporter/RNA polymerase, sigma S (sigma 38) factor
RA	2,866,488	G→C	7.7%	intergenic (+23/+71)	ygbN → / ← rpoS	putative transporter/RNA polymerase, sigma S (sigma 38) factor
RA	2,873,915	A→G	7.5%	H26H (CAT→CAC) ‡	cysC ←	adenosine 5'‑phosphosulfate kinase
RA	2,873,917	G→C	7.7%	H26D (CAT→GAT) ‡	cysC ←	adenosine 5'‑phosphosulfate kinase
RA	2,873,919	C→T	7.7%	G25D (GGT→GAT)	cysC ←	adenosine 5'‑phosphosulfate kinase
RA	2,890,625	A→T	5.4%	L425H (CTC→CAC)	cysJ ←	sulfite reductase, alpha subunit, flavoprotein
RA	2,900,327	A→C	5.1%	intergenic (‑54/‑265)	ygcW ← / → yqcE	putative SDR family oxidoreductase/putative MFS transporter, inner membrane protein
RA	2,906,607	C→T	6.1%	intergenic (+24/+36)	ygcG → / ← eno	TPM domain protein, putative phosphatase/enolase
RA	2,906,608	G→C	6.1%	intergenic (+25/+35)	ygcG → / ← eno	TPM domain protein, putative phosphatase/enolase
RA	2,906,609	G→C	6.1%	intergenic (+26/+34)	ygcG → / ← eno	TPM domain protein, putative phosphatase/enolase
RA	2,936,359	T→A	5.6%	V259D (GTT→GAT) ‡	fucI →	L‑fucose isomerase
RA	2,936,360	T→A	5.6%	V259V (GTT→GTA) ‡	fucI →	L‑fucose isomerase
RA	2,939,331	A→G	5.2%	intergenic (+21/‑37)	fucU → / → fucR	L‑fucose mutarotase/l‑fucose operon activator
RA	2,939,333	G→C	5.2%	intergenic (+23/‑35)	fucU → / → fucR	L‑fucose mutarotase/l‑fucose operon activator
RA	2,939,335	C→T	5.3%	intergenic (+25/‑33)	fucU → / → fucR	L‑fucose mutarotase/l‑fucose operon activator
RA	2,951,471	G→A	6.5%	R331C (CGC→TGC)	recD ←	exonuclease V (RecBCD complex), alpha chain
RA	2,951,475	T→A	6.4%	L329L (CTA→CTT)	recD ←	exonuclease V (RecBCD complex), alpha chain
RA	2,951,479	T→C	5.6%	Q328R (CAG→CGG)	recD ←	exonuclease V (RecBCD complex), alpha chain
RA	2,972,652	A→T	9.9%	intergenic (+15/+17)	tas → / ← lplT	putative NADP(H)‑dependent aldo‑keto reductase/lysophospholipid transporter
RA	2,972,653	A→T	9.8%	intergenic (+16/+16)	tas → / ← lplT	putative NADP(H)‑dependent aldo‑keto reductase/lysophospholipid transporter
RA	3,007,466	T→C	9.9%	intergenic (+14/‑44)	ygeW → / → ygeX	putative carbamoyltransferase/2,3‑diaminopropionate ammonia lyase, PLP‑dependent
RA	3,007,473	G→A	7.3%	intergenic (+21/‑37)	ygeW → / → ygeX	putative carbamoyltransferase/2,3‑diaminopropionate ammonia lyase, PLP‑dependent
RA	3,020,509:1	+T	5.4%	intergenic (+20/‑31)	ssnA → / → ygfM	putative chlorohydrolase/aminohydrolase/putative oxidoreductase
RA	3,020,510	G→T	6.4%	intergenic (+21/‑30)	ssnA → / → ygfM	putative chlorohydrolase/aminohydrolase/putative oxidoreductase
RA	3,020,511	C→G	6.4%	intergenic (+22/‑29)	ssnA → / → ygfM	putative chlorohydrolase/aminohydrolase/putative oxidoreductase
RA	3,020,512	A→C	6.8%	intergenic (+23/‑28)	ssnA → / → ygfM	putative chlorohydrolase/aminohydrolase/putative oxidoreductase
RA	3,033,624	A→G	6.2%	intergenic (+11/+33)	idi → / ← lysS	isopentenyl diphosphate isomerase/lysine tRNA synthetase, constitutive
RA	3,033,627	T→A	5.8%	intergenic (+14/+30)	idi → / ← lysS	isopentenyl diphosphate isomerase/lysine tRNA synthetase, constitutive
RA	3,033,628	T→A	5.8%	intergenic (+15/+29)	idi → / ← lysS	isopentenyl diphosphate isomerase/lysine tRNA synthetase, constitutive
RA	3,033,631	C→T	5.8%	intergenic (+18/+26)	idi → / ← lysS	isopentenyl diphosphate isomerase/lysine tRNA synthetase, constitutive
RA	3,051,723	C→G	6.4%	D199H (GAT→CAT)	ubiI ←	2‑octaprenylphenol hydroxylase, FAD‑dependent
RA	3,057,145	G→C	5.0%	intergenic (+157/+33)	sibC → / ← serA	sRNA antisense regulator of toxic IbsC protein/D‑3‑phosphoglycerate dehydrogenase
RA	3,057,150	C→T	6.3%	intergenic (+162/+28)	sibC → / ← serA	sRNA antisense regulator of toxic IbsC protein/D‑3‑phosphoglycerate dehydrogenase
RA	3,066,293	T→C	6.0%	D294G (GAC→GGC)	ygfI ←	putative DNA‑binding transcriptional regulator
RA	3,066,299:1	+G	6.4%	coding (875/897 nt)	ygfI ←	putative DNA‑binding transcriptional regulator
RA	3,066,319	Δ1 bp	8.6%	coding (855/897 nt)	ygfI ←	putative DNA‑binding transcriptional regulator
RA	3,066,326	G→A	5.8%	A283V (GCC→GTC)	ygfI ←	putative DNA‑binding transcriptional regulator
RA	3,091,033	T→C	5.3%	A229A (GCT→GCC)	endA →	DNA‑specific endonuclease I
RA	3,091,036	C→G	5.1%	C230W (TGC→TGG)	endA →	DNA‑specific endonuclease I
RA	3,098,515	G→C	6.8%	intergenic (+112/+43)	yggW → / ← yggM	HemN family putative oxidoreductase/DUF1202 family putative secreted protein
RA	3,098,518	C→T	6.4%	intergenic (+115/+40)	yggW → / ← yggM	HemN family putative oxidoreductase/DUF1202 family putative secreted protein
RA	3,098,519	A→G	6.4%	intergenic (+116/+39)	yggW → / ← yggM	HemN family putative oxidoreductase/DUF1202 family putative secreted protein
RA	3,098,522	G→C	6.6%	intergenic (+119/+36)	yggW → / ← yggM	HemN family putative oxidoreductase/DUF1202 family putative secreted protein
RA	3,101,655	T→A	6.5%	intergenic (‑32/+152)	yggN ← / ← yggL	DUF2884 family putative periplasmic protein/DUF469 family protein
RA	3,101,656	T→A	6.5%	intergenic (‑33/+151)	yggN ← / ← yggL	DUF2884 family putative periplasmic protein/DUF469 family protein
RA	3,156,590	C→A	6.8%	intergenic (+72/‑33)	yqhD → / → dkgA	aldehyde reductase, NADPH‑dependent/2,5‑diketo‑D‑gluconate reductase A
RA	3,156,591	T→G	6.7%	intergenic (+73/‑32)	yqhD → / → dkgA	aldehyde reductase, NADPH‑dependent/2,5‑diketo‑D‑gluconate reductase A
RA	3,171,852	C→T	6.7%	intergenic (+19/+27)	qseC → / ← ygiZ	quorum sensing sensory histidine kinase in two‑component regulatory system with QseB/inner membrane protein
RA	3,171,857	A→T	7.0%	intergenic (+24/+22)	qseC → / ← ygiZ	quorum sensing sensory histidine kinase in two‑component regulatory system with QseB/inner membrane protein
RA	3,171,858	A→T	7.0%	intergenic (+25/+21)	qseC → / ← ygiZ	quorum sensing sensory histidine kinase in two‑component regulatory system with QseB/inner membrane protein
RA	3,171,863	A→G	7.7%	intergenic (+30/+16)	qseC → / ← ygiZ	quorum sensing sensory histidine kinase in two‑component regulatory system with QseB/inner membrane protein
RA	3,200,991	A→T	5.7%	intergenic (‑26/‑216)	ygiF ← / → ygiM	inorganic triphosphatase/SH3 domain protein
RA	3,202,685	A→G	5.2%	E265E (GAA→GAG)	cca →	fused tRNA nucleotidyl transferase/2'3'‑cyclic phosphodiesterase/2'nucleotidase and phosphatase
RA	3,202,686	C→T	5.1%	L266F (CTC→TTC)	cca →	fused tRNA nucleotidyl transferase/2'3'‑cyclic phosphodiesterase/2'nucleotidase and phosphatase
RA	3,234,506	G→A	8.2%	intergenic (‑51/+233)	higB ← / ← rlmG	mRNA interferase toxin of the HigB‑HigA toxin‑antitoxin system/23S rRNA m(2)G1835 methyltransferase, SAM‑dependent
RA	3,234,507	A→T	8.2%	intergenic (‑52/+232)	higB ← / ← rlmG	mRNA interferase toxin of the HigB‑HigA toxin‑antitoxin system/23S rRNA m(2)G1835 methyltransferase, SAM‑dependent
RA	3,234,508	T→C	8.3%	intergenic (‑53/+231)	higB ← / ← rlmG	mRNA interferase toxin of the HigB‑HigA toxin‑antitoxin system/23S rRNA m(2)G1835 methyltransferase, SAM‑dependent
RA	3,239,609	T→G	6.6%	intergenic (+64/‑335)	alx → / → sstT	putative membrane‑bound redox modulator/sodium:serine/threonine symporter
RA	3,239,610	C→G	6.1%	intergenic (+65/‑334)	alx → / → sstT	putative membrane‑bound redox modulator/sodium:serine/threonine symporter
RA	3,239,611	C→A	6.5%	intergenic (+66/‑333)	alx → / → sstT	putative membrane‑bound redox modulator/sodium:serine/threonine symporter
RA	3,253,285	T→A	9.3%	intergenic (+18/+33)	yhaI → / ← yhaJ	DUF805 family inner membrane protein/LysR family putative transcriptional regulator
RA	3,253,288	T→A	9.4%	intergenic (+21/+30)	yhaI → / ← yhaJ	DUF805 family inner membrane protein/LysR family putative transcriptional regulator
RA	3,288,032	C→A	11.9%	intergenic (+22/‑58)	yraH → / → yraI	putative fimbrial‑like adhesin protein/putative periplasmic pilin chaperone
RA	3,288,033	T→G	12.7%	intergenic (+23/‑57)	yraH → / → yraI	putative fimbrial‑like adhesin protein/putative periplasmic pilin chaperone
RA	3,291,109	A→T	5.6%	K766* (AAA→TAA) ‡	yraJ →	putative outer membrane protein
RA	3,291,110	A→T	5.6%	K766I (AAA→ATA) ‡	yraJ →	putative outer membrane protein
RA	3,309,004	C→T	7.3%	intergenic (‑80/+29)	nlpI ← / ← pnp	lipoprotein involved in osmotic sensitivity and filamentation/polynucleotide phosphorylase/polyadenylase
RA	3,309,009	C→T	6.9%	intergenic (‑85/+24)	nlpI ← / ← pnp	lipoprotein involved in osmotic sensitivity and filamentation/polynucleotide phosphorylase/polyadenylase
RA	3,309,012	A→G	7.7%	intergenic (‑88/+21)	nlpI ← / ← pnp	lipoprotein involved in osmotic sensitivity and filamentation/polynucleotide phosphorylase/polyadenylase
RA	3,313,207	G→A	5.1%	intergenic (‑29/+135)	rbfA ← / ← infB	30s ribosome binding factor/translation initiation factor IF‑2
RA	3,313,208	T→A	5.1%	intergenic (‑30/+134)	rbfA ← / ← infB	30s ribosome binding factor/translation initiation factor IF‑2
RA	3,313,209	T→C	5.1%	intergenic (‑31/+133)	rbfA ← / ← infB	30s ribosome binding factor/translation initiation factor IF‑2
RA	3,332,822	G→A	7.2%	intergenic (‑87/+40)	yhbE ← / ← rpmA	EamA family inner membrane putative transporter/50S ribosomal subunit protein L27
RA	3,332,823	T→C	7.3%	intergenic (‑88/+39)	yhbE ← / ← rpmA	EamA family inner membrane putative transporter/50S ribosomal subunit protein L27
RA	3,334,703	A→G	9.9%	intergenic (+22/‑206)	ispB → / → sfsB	octaprenyl diphosphate synthase/malPQ operon transcriptional activator
RA	3,334,704	G→C	9.9%	intergenic (+23/‑205)	ispB → / → sfsB	octaprenyl diphosphate synthase/malPQ operon transcriptional activator
RA	3,334,705	C→T	9.9%	intergenic (+24/‑204)	ispB → / → sfsB	octaprenyl diphosphate synthase/malPQ operon transcriptional activator
RA	3,405,586	C→T	5.3%	P51S (CCA→TCA)	accB →	acetyl CoA carboxylase, BCCP subunit
RA	3,405,589	A→T	5.3%	M52L (ATG→TTG)	accB →	acetyl CoA carboxylase, BCCP subunit
RA	3,405,592	A→G	5.1%	M53V (ATG→GTG)	accB →	acetyl CoA carboxylase, BCCP subunit
RA	3,439,588	G→C	11.0%	intergenic (‑79/+28)	yhdN ← / ← rplQ	DUF1992 family protein/50S ribosomal subunit protein L17
RA	3,439,589	G→C	10.9%	intergenic (‑80/+27)	yhdN ← / ← rplQ	DUF1992 family protein/50S ribosomal subunit protein L17
RA	3,471,357	C→T	5.5%	intergenic (‑28/+43)	tufA ← / ← fusA	translation elongation factor EF‑Tu 1/protein chain elongation factor EF‑G, GTP‑binding
RA	3,471,361	T→G	5.3%	intergenic (‑32/+39)	tufA ← / ← fusA	translation elongation factor EF‑Tu 1/protein chain elongation factor EF‑G, GTP‑binding
RA	3,471,362	C→A	5.7%	intergenic (‑33/+38)	tufA ← / ← fusA	translation elongation factor EF‑Tu 1/protein chain elongation factor EF‑G, GTP‑binding
RA	3,471,366	A→G	5.5%	intergenic (‑37/+34)	tufA ← / ← fusA	translation elongation factor EF‑Tu 1/protein chain elongation factor EF‑G, GTP‑binding
RA	3,477,878	T→A	8.7%	intergenic (+20/+29)	slyX → / ← slyD	phi X174 lysis protein/FKBP‑type peptidyl prolyl cis‑trans isomerase (rotamase)
RA	3,504,875	T→G	6.3%	intergenic (+92/+60)	frlR → / ← yhfS	putative DNA‑binding transcriptional regulator/FNR‑regulated pyridoxal phosphate‑dependent aminotransferase family protein
RA	3,512,306	G→C	7.5%	I13M (ATC→ATG)	yhfZ ←	putative DNA‑binding transcriptional regulator
RA	3,512,309	G→C	7.8%	V12V (GTC→GTG)	yhfZ ←	putative DNA‑binding transcriptional regulator
RA	3,522,778	C→G	5.4%	intergenic (‑27/‑93)	hofM ← / → mrcA	DNA catabolic putative pilus assembly protein/penicillin‑binding protein 1a, murein transglycosylase and transpeptidase
RA	3,522,779	T→A	5.5%	intergenic (‑28/‑92)	hofM ← / → mrcA	DNA catabolic putative pilus assembly protein/penicillin‑binding protein 1a, murein transglycosylase and transpeptidase
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	3,566,210	A→T	5.5%	G124G (GGT→GGA) ‡	glgP ←	glycogen phosphorylase
RA	3,566,212	C→G	5.6%	G124R (GGT→CGT) ‡	glgP ←	glycogen phosphorylase
RA	3,566,215	T→A	5.6%	N123Y (AAC→TAC)	glgP ←	glycogen phosphorylase
RA	3,566,218	C→G	5.5%	G122R (GGT→CGT)	glgP ←	glycogen phosphorylase
RA	3,566,220	A→T	5.4%	L121H (CTC→CAC)	glgP ←	glycogen phosphorylase
RA	3,639,165	T→C	5.3%	intergenic (+24/+220)	pitA → / ← uspB	phosphate transporter, low‑affinity; tellurite importer/universal stress (ethanol tolerance) protein B
RA	3,639,172	G→A	6.0%	intergenic (+31/+213)	pitA → / ← uspB	phosphate transporter, low‑affinity; tellurite importer/universal stress (ethanol tolerance) protein B
RA	3,642,358	T→A	7.8%	intergenic (+27/+22)	dtpB → / ← rsmJ	dipeptide and tripeptide permease B/16S rRNA m(2)G1516 methyltransferase, SAM‑dependent
RA	3,642,361	T→A	7.7%	intergenic (+30/+19)	dtpB → / ← rsmJ	dipeptide and tripeptide permease B/16S rRNA m(2)G1516 methyltransferase, SAM‑dependent
RA	3,657,599	T→A	5.2%	intergenic (+32/+387)	hdeD → / ← arrS	acid‑resistance membrane protein/antisense sRNA ArrS, function unknown
RA	3,657,601	G→C	5.2%	intergenic (+34/+385)	hdeD → / ← arrS	acid‑resistance membrane protein/antisense sRNA ArrS, function unknown
RA	3,657,603	T→A	5.4%	intergenic (+36/+383)	hdeD → / ← arrS	acid‑resistance membrane protein/antisense sRNA ArrS, function unknown
RA	3,708,595	G→A	10.0%	intergenic (‑890/+21)	dppA ← / ← proK	dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro
RA	3,708,596	T→A	9.7%	intergenic (‑891/+20)	dppA ← / ← proK	dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro
RA	3,708,597	T→C	9.7%	intergenic (‑892/+19)	dppA ← / ← proK	dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro
RA	3,740,791	G→C	5.4%	G363R (GGC→CGC)	avtA →	valine‑pyruvate aminotransferase; transaminase C; alanine‑valine transaminase
RA	3,774,207	C→T	8.5%	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	8.0%	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	8.1%	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	7.6%	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	9.4%	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	6.9%	intergenic (‑219/+20)	waaH ← / ← tdh	LPS(HepIII)‑glucuronic acid glycosyltransferase/L‑threonine 3‑dehydrogenase, NAD(P)‑binding
RA	3,790,303	A→T	6.9%	intergenic (‑222/+17)	waaH ← / ← tdh	LPS(HepIII)‑glucuronic acid glycosyltransferase/L‑threonine 3‑dehydrogenase, NAD(P)‑binding
RA	3,807,638	T→G	6.5%	E154A (GAA→GCA)	waaQ ←	lipopolysaccharide core biosynthesis protein
RA	3,814,164	G→A	5.1%	G78D (GGT→GAT)	dut →	deoxyuridinetriphosphatase
RA	3,877,558	G→C	6.9%	intergenic (‑93/+147)	yidB ← / ← gyrB	DUF937 family protein/DNA gyrase, subunit B
RA	3,878,894	T→A	7.4%	D409V (GAC→GTC)	gyrB ←	DNA gyrase, subunit B
RA	3,882,514	G→T	5.7%	P406T (CCG→ACG)	dnaA ←	chromosomal replication initiator protein DnaA, DNA‑binding transcriptional dual regulator
RA	3,882,515	A→C	5.1%	R405R (CGT→CGG)	dnaA ←	chromosomal replication initiator protein DnaA, DNA‑binding transcriptional dual regulator
RA	3,891,502	C→G	7.1%	intergenic (+19/‑113)	tnaB → / → mdtL	tryptophan transporter of low affinity/multidrug efflux system protein
RA	3,891,504	T→A	7.3%	intergenic (+21/‑111)	tnaB → / → mdtL	tryptophan transporter of low affinity/multidrug efflux system protein
RA	3,891,506	C→G	7.2%	intergenic (+23/‑109)	tnaB → / → mdtL	tryptophan transporter of low affinity/multidrug efflux system protein
RA	3,954,273	G→T	5.8%	E266* (GAA→TAA) ‡	ilvD →	dihydroxyacid dehydratase
RA	3,954,274	A→C	5.8%	E266A (GAA→GCA) ‡	ilvD →	dihydroxyacid dehydratase
RA	3,959,480	A→T	6.6%	intergenic (+35/+52)	ilvC → / ← ppiC	ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C)
RA	3,959,481	C→G	6.6%	intergenic (+36/+51)	ilvC → / ← ppiC	ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C)
RA	3,981,102	T→A	6.8%	V72V (GTT→GTA)	yifK →	putative APC family amino acid transporter
RA	3,992,624	T→G	46.2%	L491R (CTG→CGG)	cyaA →	adenylate cyclase
RA	3,993,145	C→A	57.0%	R665S (CGT→AGT)	cyaA →	adenylate cyclase
RA	4,015,333	A→T	6.3%	intergenic (+19/+21)	metE → / ← ysgA	5‑methyltetrahydropteroyltriglutamate‑ homocysteine S‑methyltransferase/putative carboxymethylenebutenolidase
RA	4,017,222	Δ1 bp	5.5%	intergenic (+30/‑111)	udp → / → rmuC	uridine phosphorylase/DNA recombination protein
RA	4,040,661	G→A	6.7%	intergenic (+25/+245)	rrfA → / ← mobB	5S ribosomal RNA of rrnA operon/molybdopterin‑guanine dinucleotide biosynthesis protein B
RA	4,041,216	T→C	10.1%	Q73R (CAG→CGG) ‡	mobB ←	molybdopterin‑guanine dinucleotide biosynthesis protein B
RA	4,041,217	G→A	10.5%	Q73* (CAG→TAG) ‡	mobB ←	molybdopterin‑guanine dinucleotide biosynthesis protein B
RA	4,041,220	T→C	10.6%	S72G (AGC→GGC)	mobB ←	molybdopterin‑guanine dinucleotide biosynthesis protein B
RA	4,041,221	G→A	10.5%	A71A (GCC→GCT)	mobB ←	molybdopterin‑guanine dinucleotide biosynthesis protein B
RA	4,049,986	G→T	9.2%	noncoding (88/109 nt)	spf →	Spot 42 sRNA antisense regulator of galK translation, Hfq‑dependent
RA	4,049,989	A→C	9.4%	noncoding (91/109 nt)	spf →	Spot 42 sRNA antisense regulator of galK translation, Hfq‑dependent
RA	4,051,259	G→T	10.7%	noncoding (224/245 nt)	csrC →	CsrC sRNA sequesters CsrA, a carbon flux regulator
RA	4,051,262	A→C	8.9%	noncoding (227/245 nt)	csrC →	CsrC sRNA sequesters CsrA, a carbon flux regulator
RA	4,060,261	G→T	11.7%	intergenic (+31/‑186)	typA → / → yihL	GTP‑binding protein/putative DNA‑binding transcriptional regulator
RA	4,060,264	A→C	11.6%	intergenic (+34/‑183)	typA → / → yihL	GTP‑binding protein/putative DNA‑binding transcriptional regulator
RA	4,070,413	T→G	5.7%	intergenic (‑12/+102)	yihR ← / ← yihS	putative sulphoquinovose mutarotase/sulphoquinovose isomerase
RA	4,088,091	G→C	6.9%	intergenic (+34/+16)	yiiG → / ← frvR	DUF3829 family lipoprotein/putative frv operon regulator; contains a PTS EIIA domain
RA	4,117,005	T→A	44.7%	D73V (GAT→GTT)	glpK ←	glycerol kinase
RA	4,117,047	G→T	61.7%	S59Y (TCC→TAC)	glpK ←	glycerol kinase
RA	4,127,251	C→T	8.1%	intergenic (+26/+35)	rpmE → / ← yiiX	50S ribosomal subunit protein L31/putative lipid binding hydrolase, DUF830 family protein
RA	4,127,252	A→G	7.8%	intergenic (+27/+34)	rpmE → / ← yiiX	50S ribosomal subunit protein L31/putative lipid binding hydrolase, DUF830 family protein
RA	4,130,005	G→A	5.2%	L57L (TTG→TTA)	metL →	Bifunctional aspartokinase/homoserine dehydrogenase 2
RA	4,130,008	T→C	5.2%	I58I (ATT→ATC)	metL →	Bifunctional aspartokinase/homoserine dehydrogenase 2
RA	4,185,907	G→T	7.4%	Q186H (CAG→CAT)	rpoC →	RNA polymerase, beta prime subunit
RA	4,185,913	G→T	6.6%	L188L (CTG→CTT)	rpoC →	RNA polymerase, beta prime subunit
RA	4,185,915	T→A	6.6%	L189Q (CTG→CAG)	rpoC →	RNA polymerase, beta prime subunit
RA	4,185,917	A→C	6.5%	K190Q (AAG→CAG)	rpoC →	RNA polymerase, beta prime subunit
RA	4,185,923	A→C	6.5%	M192L (ATG→CTG)	rpoC →	RNA polymerase, beta prime subunit
RA	4,213,131	C→T	5.0%	noncoding (92/120 nt)	rrfE →	5S ribosomal RNA of rrnE operon
RA	4,235,581	T→A	7.4%	intergenic (+174/‑325)	pgi → / → yjbE	glucosephosphate isomerase/extracellular polysaccharide production threonine‑rich protein
RA	4,245,108	T→G	5.3%	intergenic (‑33/+121)	malF ← / ← malE	maltose transporter subunit/maltose transporter subunit
RA	4,245,110	T→G	5.2%	intergenic (‑35/+119)	malF ← / ← malE	maltose transporter subunit/maltose transporter subunit
RA	4,245,111	C→A	5.4%	intergenic (‑36/+118)	malF ← / ← malE	maltose transporter subunit/maltose transporter subunit
RA	4,245,113	C→A	5.1%	intergenic (‑38/+116)	malF ← / ← malE	maltose transporter subunit/maltose transporter subunit
RA	4,274,740	G→A	6.6%	intergenic (+79/+20)	ssb → / ← yjcB	single‑stranded DNA‑binding protein/putative inner membrane protein
RA	4,274,742	T→A	7.6%	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	6.8%	M1M (GTG→ATG) †‡	nrfE →	heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfE
RA	4,291,513	T→C	6.8%	M1A (GTG→GCG) †‡	nrfE →	heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfE
RA	4,296,060	C→T	21.8%	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	4,312,074	C→T	7.5%	intergenic (‑32/+27)	alsB ← / ← alsR	D‑allose ABC transporter periplasmic binding protein/d‑allose‑inducible als operon transcriptional repressor; autorepressor; repressor of rpiR
RA	4,312,080	G→C	7.9%	intergenic (‑38/+21)	alsB ← / ← alsR	D‑allose ABC transporter periplasmic binding protein/d‑allose‑inducible als operon transcriptional repressor; autorepressor; repressor of rpiR
RA	4,312,083	G→C	8.0%	intergenic (‑41/+18)	alsB ← / ← alsR	D‑allose ABC transporter periplasmic binding protein/d‑allose‑inducible als operon transcriptional repressor; autorepressor; repressor of rpiR
RA	4,312,089	A→G	7.9%	intergenic (‑47/+12)	alsB ← / ← alsR	D‑allose ABC transporter periplasmic binding protein/d‑allose‑inducible als operon transcriptional repressor; autorepressor; repressor of rpiR
RA	4,332,868	G→T	6.4%	R135R (CGC→CGA)	basS ←	sensory histidine kinase in two‑component regulatory system with BasR
RA	4,332,871	A→C	6.4%	S134R (AGT→AGG)	basS ←	sensory histidine kinase in two‑component regulatory system with BasR
RA	4,335,654	T→A	5.7%	intergenic (‑64/+40)	eptA ← / ← adiC	lipid A phosphoethanolamine transferase/arginine:agmatine antiporter
RA	4,335,655	T→A	6.2%	intergenic (‑65/+39)	eptA ← / ← adiC	lipid A phosphoethanolamine transferase/arginine:agmatine antiporter
RA	4,336,988	A→T	5.3%	V15D (GTC→GAC)	adiC ←	arginine:agmatine antiporter
RA	4,339,802	A→G	6.0%	A240A (GCT→GCC)	adiA ←	arginine decarboxylase
RA	4,339,805	C→T	6.0%	Q239Q (CAG→CAA)	adiA ←	arginine decarboxylase
RA	4,347,285	C→G	5.3%	M14I (ATG→ATC)	fumB ←	anaerobic class I fumarate hydratase (fumarase B)
RA	4,347,288	C→G	5.0%	P13P (CCG→CCC)	fumB ←	anaerobic class I fumarate hydratase (fumarase B)
RA	4,356,445	A→T	6.0%	intergenic (‑34/+25)	dtpC ← / ← cadA	dipeptide and tripeptide permease/lysine decarboxylase, acid‑inducible
RA	4,356,446	A→T	6.0%	intergenic (‑35/+24)	dtpC ← / ← cadA	dipeptide and tripeptide permease/lysine decarboxylase, acid‑inducible
RA	4,362,528	G→A	6.5%	intergenic (‑175/+23)	yjdQ ← / ← pheU	pseudogene, P4‑like integrase remnant/tRNA‑Phe
RA	4,362,529	T→C	6.3%	intergenic (‑176/+22)	yjdQ ← / ← pheU	pseudogene, P4‑like integrase remnant/tRNA‑Phe
RA	4,366,854	T→G	11.0%	intergenic (‑81/+37)	dcuA ← / ← aspA	C4‑dicarboxylate antiporter/aspartate ammonia‑lyase
RA	4,366,855	C→A	11.0%	intergenic (‑82/+36)	dcuA ← / ← aspA	C4‑dicarboxylate antiporter/aspartate ammonia‑lyase
RA	4,392,617	C→G	5.0%	noncoding (35/76 nt)	glyY →	tRNA‑Gly
RA	4,395,454	T→C	6.4%	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	5.2%	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	4,424,465	G→T	5.3%	intergenic (+79/+51)	ulaF → / ← yjfY	L‑ribulose 5‑phosphate 4‑epimerase/YhcN family protein, periplasmic
RA	4,424,468	A→C	5.3%	intergenic (+82/+48)	ulaF → / ← yjfY	L‑ribulose 5‑phosphate 4‑epimerase/YhcN family protein, periplasmic
RA	4,447,964	T→A	5.6%	L24* (TTA→TAA)	ytfP →	GGCT‑like protein
RA	4,450,962	T→G	5.4%	intergenic (+44/‑96)	ytfQ → / → ytfR	galactofuranose ABC transporter periplasmic binding protein/putative sugar ABC transporter ATPase
RA	4,450,963	C→A	5.4%	intergenic (+45/‑95)	ytfQ → / → ytfR	galactofuranose ABC transporter periplasmic binding protein/putative sugar ABC transporter ATPase
RA	4,472,434	G→A	8.5%	R34* (CGA→TGA)	pyrL ←	pyrBI operon leader peptide
RA	4,472,437	T→C	8.0%	N33D (AAT→GAT)	pyrL ←	pyrBI operon leader peptide
RA	4,479,012	A→T	7.9%	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	8.3%	intergenic (+131/+14)	rraB → / ← yjgM	protein inhibitor of RNase E/GNAT family putative N‑acetyltransferase
RA	4,520,500	Δ1 bp	7.7%	intergenic (‑176/+171)	yjhU ← / ← yjhF	putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter
RA	4,520,504:1	+T	7.7%	intergenic (‑180/+167)	yjhU ← / ← yjhF	putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter
RA	4,537,639	T→G	5.2%	intergenic (‑45/+20)	nanS ← / ← nanM	9‑O‑acetyl N‑acetylneuraminic acid esterase/N‑acetylneuraminic acid mutarotase
RA	4,537,640	T→G	5.2%	intergenic (‑46/+19)	nanS ← / ← nanM	9‑O‑acetyl N‑acetylneuraminic acid esterase/N‑acetylneuraminic acid mutarotase
RA	4,537,643	C→A	5.3%	intergenic (‑49/+16)	nanS ← / ← nanM	9‑O‑acetyl N‑acetylneuraminic acid esterase/N‑acetylneuraminic acid mutarotase
RA	4,537,644	C→A	5.3%	intergenic (‑50/+15)	nanS ← / ← nanM	9‑O‑acetyl N‑acetylneuraminic acid esterase/N‑acetylneuraminic acid mutarotase
RA	4,549,932	T→A	5.5%	intergenic (+222/+21)	fimH → / ← gntP	minor component of type 1 fimbriae/fructuronate transporter
RA	4,551,422	T→A	5.2%	intergenic (‑126/‑214)	gntP ← / → uxuA	fructuronate transporter/mannonate hydrolase
RA	4,608,604	C→G	5.3%	I140M (ATC→ATG)	rimI →	ribosomal‑protein‑S18‑alanine N‑acetyltransferase
RA	4,608,607	C→G	5.3%	I141M (ATC→ATG)	rimI →	ribosomal‑protein‑S18‑alanine N‑acetyltransferase
RA	4,612,329	A→G	9.9%	intergenic (+40/‑82)	ytjA → / → yjjU	uncharacterized protein/putative patatin‑like family phospholipase
RA	4,612,330	G→C	9.7%	intergenic (+41/‑81)	ytjA → / → yjjU	uncharacterized protein/putative patatin‑like family phospholipase
RA	4,612,331	C→T	9.8%	intergenic (+42/‑80)	ytjA → / → yjjU	uncharacterized protein/putative patatin‑like family phospholipase
RA	4,638,690	C→T	5.7%	G171G (GGC→GGT)	creD →	inner membrane protein
RA	4,638,691	A→G	5.7%	T172A (ACC→GCC)	creD →	inner membrane protein

Unassigned missing coverage evidence
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	3423741–3424234	3424547–3424238	5–807	87 [81]	[79] 83	[rrfD]–[rrlD]	[rrfD],[rrlD]

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 16653	NA (NA)	3 (0.020)	3/248	NT	NA	noncoding (1267/1345 nt)	IS186	repeat region
	?	NC_000913	= 16691	NA (NA)					noncoding (1305/1345 nt)	IS186	repeat region
*	?	NC_000913	= 66642	141 (0.870)	9 (0.060)	8/248	NT	9.1%	noncoding (78/248 nt)	REP6 (repetitive extragenic palindromic) element; contains 6 REP sequences	REP6 (repetitive extragenic palindromic) element; contains 6 REP sequences
	?	NC_000913	2304955 =	46 (0.300)					noncoding (539/655 nt)	REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences	REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences
*	?	NC_000913	193444 =	121 (0.750)	6 (0.040)	6/242	NT	5.0%	intergenic (+15/‑77)	frr/dxr	ribosome recycling factor/1‑deoxy‑D‑xylulose 5‑phosphate reductoisomerase
	?	NC_000913	193489 =	115 (0.770)					intergenic (+60/‑32)	frr/dxr	ribosome recycling factor/1‑deoxy‑D‑xylulose 5‑phosphate reductoisomerase
*	?	NC_000913	= 224374	NA (NA)	4 (0.030)	3/248	NT	NA	noncoding (604/1542 nt)	rrsH	16S ribosomal RNA of rrnH operon
	?	NC_000913	= 224403	NA (NA)					noncoding (633/1542 nt)	rrsH	16S ribosomal RNA of rrnH operon
*	?	NC_000913	224957 =	NA (NA)	9 (0.060)	16/250	NT	NA	noncoding (1187/1542 nt)	rrsH	16S ribosomal RNA of rrnH operon
	?	NC_000913	224974 =	NA (NA)					noncoding (1204/1542 nt)	rrsH	16S ribosomal RNA of rrnH operon
*	?	NC_000913	= 227444	NA (NA)	7 (0.040)	7/252	NT	NA	noncoding (1686/2904 nt)	rrlH	23S ribosomal RNA of rrnH operon
	?	NC_000913	= 227459	NA (NA)					noncoding (1701/2904 nt)	rrlH	23S ribosomal RNA of rrnH operon
*	?	NC_000913	= 228744	109 (0.670)	63 (0.410)	23/250	NT	37.7%	intergenic (+82/‑12)	rrlH/rrfH	23S ribosomal RNA of rrnH operon/5S ribosomal RNA of rrnH 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	274347 =	NA (NA)	5 (0.030)	5/248	NT	NA	noncoding (803/1195 nt)	IS5	repeat region
	?	NC_000913	274410 =	NA (NA)					noncoding (740/1195 nt)	IS5	repeat region
*	?	NC_000913	274674 =	NA (NA)	3 (0.020)	3/252	NT	NA	noncoding (476/1195 nt)	IS5	repeat region
	?	NC_000913	274711 =	NA (NA)					noncoding (439/1195 nt)	IS5	repeat region
*	?	NC_000913	= 288413	113 (0.700)	6 (0.040)	6/244	NT	5.2%	coding (750/759 nt)	yagI	CP4‑6 prophage; putative DNA‑binding transcriptional regulator
	?	NC_000913	= 288439	113 (0.750)					coding (724/759 nt)	yagI	CP4‑6 prophage; putative DNA‑binding transcriptional regulator
*	?	NC_000913	= 381669	NA (NA)	12 (0.080)	9/248	NT	NA	noncoding (410/1331 nt)	IS2	repeat region
	?	NC_000913	= 381695	NA (NA)					noncoding (436/1331 nt)	IS2	repeat region
*	?	NC_000913	448501 =	172 (1.060)	10 (0.070)	6/246	NT	6.1%	coding (160/615 nt)	cyoC	cytochrome o ubiquinol oxidase subunit III
	?	NC_000913	448521 =	147 (0.970)					coding (140/615 nt)	cyoC	cytochrome o ubiquinol oxidase subunit III
*	?	NC_000913	= 686699	143 (0.880)	13 (0.090)	13/240	NT	8.7%	intergenic (‑30/+140)	gltJ/gltI	glutamate/aspartate ABC transporter permease/glutamate/aspartate periplasmic binding protein
	?	NC_000913	= 686705	143 (0.960)					intergenic (‑36/+134)	gltJ/gltI	glutamate/aspartate ABC transporter permease/glutamate/aspartate periplasmic binding protein
*	?	NC_000913	= 730045	NA (NA)	5 (0.030)	4/252	NT	NA	coding (463/4194 nt)	rhsC	Rhs protein with putative toxin domain; putative neighboring cell growth inhibitor
	?	NC_000913	= 730067	NA (NA)					coding (485/4194 nt)	rhsC	Rhs protein with putative toxin domain; putative neighboring cell growth inhibitor
*	?	NC_000913	= 758527	NA (NA)	8 (0.050)	5/258	NT	NA	intergenic (+122/‑179)	sdhB/sucA	succinate dehydrogenase, FeS subunit/2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding
	?	NC_000913	4618143 =	NA (NA)					noncoding (27/82 nt)	REP353 (repetitive extragenic palindromic) element; contains 2 REP sequences	REP353 (repetitive extragenic palindromic) element; contains 2 REP sequences
*	?	NC_000913	1021683 =	158 (0.980)	10 (0.060)	8/252	NT	6.1%	coding (546/630 nt)	sxy	CRP‑S‑dependent promoter expression factor
	?	NC_000913	1021709 =	154 (0.990)					coding (572/630 nt)	sxy	CRP‑S‑dependent promoter expression factor
*	?	NC_000913	1207790 =	52 (0.320)	85 (0.600)	60/230	NT	60.4%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	66 (0.460)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1207805	51 (0.310)	72 (0.510)	56/230	NT	56.5%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	66 (0.460)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1299498	0 (0.000)	149 (0.950)	98/254	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	1512410 =	164 (1.010)	8 (0.050)	7/254	NT	5.1%	coding (757/1146 nt)	ydcS	putative ABC transporter periplasmic binding protein
	?	NC_000913	1512451 =	138 (0.880)					coding (798/1146 nt)	ydcS	putative ABC transporter periplasmic binding protein
*	?	NC_000913	2340313 =	NA (NA)	7 (0.050)	6/248	NT	NA	noncoding (1/82 nt)	REP163 (repetitive extragenic palindromic) element; contains 2 REP sequences	REP163 (repetitive extragenic palindromic) element; contains 2 REP sequences
	?	NC_000913	2340346 =	NA (NA)					noncoding (34/82 nt)	REP163 (repetitive extragenic palindromic) element; contains 2 REP sequences	REP163 (repetitive extragenic palindromic) element; contains 2 REP sequences
*	?	NC_000913	2506031 =	143 (0.880)	8 (0.050)	4/248	NT	6.0%	coding (602/1086 nt)	ypdF	Xaa‑Pro aminopeptidase
	?	NC_000913	2506083 =	117 (0.760)					coding (550/1086 nt)	ypdF	Xaa‑Pro aminopeptidase
*	?	NC_000913	2728214 =	NA (NA)	17 (0.110)	8/254	NT	NA	noncoding (971/2904 nt)	rrlG	23S ribosomal RNA of rrnG operon
	?	NC_000913	2728240 =	NA (NA)					noncoding (945/2904 nt)	rrlG	23S ribosomal RNA of rrnG operon
*	?	NC_000913	2729443 =	70 (0.430)	10 (0.070)	5/242	NT	14.2%	noncoding (2/76 nt)	gltW	tRNA‑Glu
	?	NC_000913	2729485 =	56 (0.370)					intergenic (‑41/+131)	gltW/rrsG	tRNA‑Glu/16S ribosomal RNA of rrnG operon
*	?	NC_000913	= 2964996	150 (0.930)	8 (0.050)	6/250	NT	5.3%	coding (160/795 nt)	thyA	thymidylate synthetase
	?	NC_000913	= 2965032	144 (0.930)					coding (124/795 nt)	thyA	thymidylate synthetase
*	?	NC_000913	3296997 =	NA (NA)	4 (0.030)	4/252	NT	NA	intergenic (+13/+101)	yraP/yraQ	outer membrane lipoprotein/putative inner membrane permease
	?	NC_000913	3297033 =	NA (NA)					noncoding (35/84 nt)	REP240 (repetitive extragenic palindromic) element; contains 2 REP sequences	REP240 (repetitive extragenic palindromic) element; contains 2 REP sequences
*	?	NC_000913	= 3587439	159 (0.980)	10 (0.070)	8/242	NT	6.1%	coding (675/744 nt)	ugpQ	glycerophosphodiester phosphodiesterase, cytosolic
	?	NC_000913	= 3587453	162 (1.080)					coding (661/744 nt)	ugpQ	glycerophosphodiester phosphodiesterase, cytosolic
*	?	NC_000913	3721045 =	198 (1.220)	418 (2.600)	170/260	NT	70.3%	noncoding (413/1443 nt)	IS150	repeat region
	?	NC_000913	= 3839774	157 (0.980)					coding (220/819 nt)	nlpA	cytoplasmic membrane lipoprotein‑28
*	?	NC_000913	3774236 =	NA (NA)	16 (0.100)	9/248	NT	NA	noncoding (1/99 nt)	RIP271 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site	RIP271 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site
	?	NC_000913	3774261 =	NA (NA)					noncoding (26/99 nt)	RIP271 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site	RIP271 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site
*	?	NC_000913	3943467 =	NA (NA)	16 (0.100)	9/250	NT	16.3%	noncoding (33/76 nt)	gltU	tRNA‑Glu
	?	NC_000913	3943474 =	86 (0.530)					noncoding (40/76 nt)	gltU	tRNA‑Glu
*	?	NC_000913	3975245 =	152 (0.940)	13 (0.080)	11/256	NT	8.0%	coding (100/1131 nt)	wecE	TDP‑4‑oxo‑6‑deoxy‑D‑glucose transaminase
	?	NC_000913	3975274 =	152 (0.960)					coding (129/1131 nt)	wecE	TDP‑4‑oxo‑6‑deoxy‑D‑glucose transaminase
*	?	NC_000913	4037397 =	95 (0.590)	10 (0.060)	4/258	NT	7.1%	intergenic (+62/‑122)	alaT/rrlA	tRNA‑Ala/23S ribosomal RNA of rrnA operon
	?	NC_000913	4168483 =	169 (1.060)					intergenic (+36/‑158)	gltT/rrlB	tRNA‑Glu/23S ribosomal RNA of rrnB operon
*	?	NC_000913	= 4040683	105 (0.650)	37 (0.230)	6/258	NT	24.2%	intergenic (+47/+223)	rrfA/mobB	5S ribosomal RNA of rrnA operon/molybdopterin‑guanine dinucleotide biosynthesis protein B
	?	NC_000913	= 4213162	129 (0.810)					intergenic (+3/‑72)	rrfE/yjaA	5S ribosomal RNA of rrnE operon/stress‑induced protein