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	10.9%	intergenic (+14/+21)	mog → / ← satP	molybdochelatase incorporating molybdenum into molybdopterin/succinate‑acetate transporter
RA	9,908	G→T	10.9%	intergenic (+15/+20)	mog → / ← satP	molybdochelatase incorporating molybdenum into molybdopterin/succinate‑acetate transporter
RA	17,527	G→C	7.3%	S13S (TCG→TCC)	nhaA →	sodium‑proton antiporter
RA	17,528	G→C	7.5%	G14R (GGA→CGA)	nhaA →	sodium‑proton antiporter
RA	22,773	A→T	10.3%	E128V (GAA→GTA)	ileS →	isoleucyl‑tRNA synthetase
RA	22,776	A→T	11.3%	Y129F (TAC→TTC)	ileS →	isoleucyl‑tRNA synthetase
RA	30,052	G→C	5.3%	A134A (GCG→GCC)	carA →	carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
RA	30,053	G→C	5.1%	G135R (GGC→CGC)	carA →	carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
RA	53,376	G→A	10.8%	P14L (CCC→CTC)	pdxA ←	4‑hydroxy‑L‑threonine phosphate dehydrogenase, NAD‑dependent
RA	53,379	T→C	10.5%	E13G (GAG→GGG)	pdxA ←	4‑hydroxy‑L‑threonine phosphate dehydrogenase, NAD‑dependent
RA	60,254	A→G	6.3%	G31G (GGT→GGC)	rluA ←	dual specificity 23S rRNA pseudouridine(746), tRNA pseudouridine(32) synthase, SAM‑dependent
RA	60,258	C→A	5.2%	S30I (AGC→ATC)	rluA ←	dual specificity 23S rRNA pseudouridine(746), tRNA pseudouridine(32) synthase, SAM‑dependent
RA	60,263	C→T	5.1%	K28K (AAG→AAA)	rluA ←	dual specificity 23S rRNA pseudouridine(746), tRNA pseudouridine(32) synthase, SAM‑dependent
RA	65,812	T→C	9.3%	intergenic (‑32/+43)	polB ← / ← araD	DNA polymerase II/L‑ribulose‑5‑phosphate 4‑epimerase
RA	75,708	A→G	5.8%	L531P (CTG→CCG)	sgrR ←	transcriptional DNA‑binding transcriptional activator of sgrS sRNA
RA	75,710	G→C	5.7%	G530G (GGC→GGG) ‡	sgrR ←	transcriptional DNA‑binding transcriptional activator of sgrS sRNA
RA	75,712	C→T	5.7%	G530S (GGC→AGC) ‡	sgrR ←	transcriptional DNA‑binding transcriptional activator of sgrS sRNA
RA	78,830	T→A	20.8%	intergenic (+31/+18)	setA → / ← leuD	broad specificity sugar efflux system/3‑isopropylmalate dehydratase small subunit
RA	78,831	T→A	20.7%	intergenic (+32/+17)	setA → / ← leuD	broad specificity sugar efflux system/3‑isopropylmalate dehydratase small subunit
RA	85,337	G→T	7.5%	intergenic (+25/‑293)	leuO → / → ilvI	global transcription factor/acetolactate synthase 3 large subunit
RA	85,338	A→C	8.5%	intergenic (+26/‑292)	leuO → / → ilvI	global transcription factor/acetolactate synthase 3 large subunit
RA	87,881	A→G	9.1%	intergenic (+33/‑147)	ilvH → / → cra	acetolactate synthase 3, small subunit, valine‑sensitive/transcriptional repressor‑activator for carbon metabolism
RA	87,884	T→A	8.7%	intergenic (+36/‑144)	ilvH → / → cra	acetolactate synthase 3, small subunit, valine‑sensitive/transcriptional repressor‑activator for carbon metabolism
RA	87,887	C→T	8.3%	intergenic (+39/‑141)	ilvH → / → cra	acetolactate synthase 3, small subunit, valine‑sensitive/transcriptional repressor‑activator for carbon metabolism
RA	90,573	T→G	8.5%	F160L (TTT→TTG)	rsmH →	16S rRNA m(4)C1402 methyltransferase, SAM‑dependent
RA	90,576	C→A	8.3%	A161A (GCC→GCA)	rsmH →	16S rRNA m(4)C1402 methyltransferase, SAM‑dependent
RA	93,867	C→T	5.5%	C234C (TGC→TGT)	murE →	UDP‑N‑acetylmuramoyl‑L‑alanyl‑D‑glutamate:meso‑ diaminopimelate ligase
RA	100,158	C→T	6.7%	P172L (CCG→CTG)	murG →	N‑acetylglucosaminyl transferase
RA	100,161	A→G	6.8%	Q173R (CAG→CGG)	murG →	N‑acetylglucosaminyl transferase
RA	105,046	A→C	5.8%	Q355H (CAA→CAC)	ftsA →	ATP‑binding cell division FtsK recruitment protein
RA	105,047	G→T	6.1%	V356L (GTG→TTG)	ftsA →	ATP‑binding cell division FtsK recruitment protein
RA	106,831	T→A	10.5%	I92N (ATT→AAT)	lpxC →	UDP‑3‑O‑acyl N‑acetylglucosamine deacetylase
RA	110,876	C→T	10.3%	A866A (GCC→GCT)	secA →	preprotein translocase subunit, ATPase
RA	110,879	A→G	10.3%	A867A (GCA→GCG)	secA →	preprotein translocase subunit, ATPase
RA	125,226	G→T	9.3%	R737L (CGT→CTT)	aceE →	pyruvate dehydrogenase, decarboxylase component E1, thiamine triphosphate‑binding
RA	125,232	T→G	8.8%	V739G (GTC→GGC) ‡	aceE →	pyruvate dehydrogenase, decarboxylase component E1, thiamine triphosphate‑binding
RA	125,233	C→A	8.7%	V739V (GTC→GTA) ‡	aceE →	pyruvate dehydrogenase, decarboxylase component E1, thiamine triphosphate‑binding
RA	138,792	C→G	6.6%	intergenic (+159/+43)	cueO → / ← gcd	multicopper oxidase (laccase)/glucose dehydrogenase
RA	138,797	A→G	6.4%	intergenic (+164/+38)	cueO → / ← gcd	multicopper oxidase (laccase)/glucose dehydrogenase
RA	138,807	C→T	7.1%	intergenic (+174/+28)	cueO → / ← gcd	multicopper oxidase (laccase)/glucose dehydrogenase
RA	138,810	A→G	7.1%	intergenic (+177/+25)	cueO → / ← gcd	multicopper oxidase (laccase)/glucose dehydrogenase
RA	144,806	C→A	5.6%	S77* (TCA→TAA)	yadI →	putative PTS Enzyme IIA
RA	144,809	T→A	5.7%	L78* (TTA→TAA)	yadI →	putative PTS Enzyme IIA
RA	144,812	T→G	5.8%	L79* (TTA→TGA)	yadI →	putative PTS Enzyme IIA
RA	151,519	A→C	9.1%	I27M (ATT→ATG)	yadK ←	putative fimbrial‑like adhesin protein
RA	151,522	G→T	6.1%	A26A (GCC→GCA)	yadK ←	putative fimbrial‑like adhesin protein
RA	164,098	T→A	9.0%	L665Q (CTG→CAG)	hrpB →	putative ATP‑dependent helicase
RA	164,101	T→A	9.0%	L666Q (CTG→CAG)	hrpB →	putative ATP‑dependent helicase
RA	164,620	C→T	21.0%	intergenic (+86/‑110)	hrpB → / → mrcB	putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase
RA	164,621	A→G	26.6%	intergenic (+87/‑109)	hrpB → / → mrcB	putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase
RA	167,291	G→A	37.9%	intergenic (+27/‑193)	mrcB → / → fhuA	fused glycosyl transferase and transpeptidase/ferrichrome outer membrane transporter
RA	167,293	G→C	37.9%	intergenic (+29/‑191)	mrcB → / → fhuA	fused glycosyl transferase and transpeptidase/ferrichrome outer membrane transporter
RA	167,295	T→C	52.5%	intergenic (+31/‑189)	mrcB → / → fhuA	fused glycosyl transferase and transpeptidase/ferrichrome outer membrane transporter
RA	167,917	A→C	7.6%	Q145P (CAG→CCG) ‡	fhuA →	ferrichrome outer membrane transporter
RA	167,918	G→C	8.3%	Q145H (CAG→CAC) ‡	fhuA →	ferrichrome outer membrane transporter
RA	167,919	G→T	8.1%	G146C (GGC→TGC)	fhuA →	ferrichrome outer membrane transporter
RA	195,908	C→T	6.4%	R78* (CGA→TGA)	cdsA →	CDP‑diglyceride synthase
RA	201,032	G→A	12.5%	G21D (GGC→GAC)	lpxD →	UDP‑3‑O‑(3‑hydroxymyristoyl)‑glucosamine N‑acyltransferase
RA	208,552	T→A	8.4%	L1143I (TTA→ATA)	dnaE →	DNA polymerase III alpha subunit
RA	234,579	C→A	6.1%	K68N (AAG→AAT) ‡	gloB ←	hydroxyacylglutathione hydrolase
RA	234,580	T→G	6.7%	K68T (AAG→ACG) ‡	gloB ←	hydroxyacylglutathione hydrolase
RA	248,868	C→G	8.3%	pseudogene (1203/1713 nt)	lfhA ←	pseudogene, flagellar system protein, promoterless fragment; flagellar biosynthesis
RA	254,223	A→T	10.0%	intergenic (+21/+36)	prfH → / ← pepD	pseudogene, RF‑1 domain family; probable peptide chain release factor/aminoacyl‑histidine dipeptidase (peptidase D)
RA	254,228	A→T	15.4%	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	10.5%	intergenic (+31/+26)	prfH → / ← pepD	pseudogene, RF‑1 domain family; probable peptide chain release factor/aminoacyl‑histidine dipeptidase (peptidase D)
RA	256,449	T→C	21.4%	intergenic (+14/‑78)	gpt → / → frsA	xanthine phosphoribosyltransferase; xanthine‑guanine phosphoribosyltransferase/fermentation‑respiration switch protein; PTS Enzyme IIA(Glc)‑binding protein; pNP‑butyrate esterase activity
RA	256,454	C→G	24.0%	intergenic (+19/‑73)	gpt → / → frsA	xanthine phosphoribosyltransferase; xanthine‑guanine phosphoribosyltransferase/fermentation‑respiration switch protein; PTS Enzyme IIA(Glc)‑binding protein; pNP‑butyrate esterase activity
RA	256,459	G→A	24.0%	intergenic (+24/‑68)	gpt → / → frsA	xanthine phosphoribosyltransferase; xanthine‑guanine phosphoribosyltransferase/fermentation‑respiration switch protein; PTS Enzyme IIA(Glc)‑binding protein; pNP‑butyrate esterase activity
MC JC	257,908	Δ776 bp	100%		[crl]	[crl]
RA	266,465	G→A	5.5%	A30V (GCC→GTC)	yafY ←	lipoprotein, inner membrane; degP regulator; CP4‑6 prophage
RA	276,935	C→A	6.1%	T74K (ACG→AAG)	mmuM →	CP4‑6 prophage; S‑methylmethionine:homocysteine methyltransferase
RA	276,939	G→C	7.3%	P75P (CCG→CCC)	mmuM →	CP4‑6 prophage; S‑methylmethionine:homocysteine methyltransferase
RA	276,942	G→C	7.3%	A76A (GCG→GCC)	mmuM →	CP4‑6 prophage; S‑methylmethionine:homocysteine methyltransferase
RA	276,946	T→G	7.1%	F78V (TTC→GTC)	mmuM →	CP4‑6 prophage; S‑methylmethionine:homocysteine methyltransferase
RA	282,513	T→C	9.3%	L79P (CTG→CCG)	yagE →	2‑keto‑3‑deoxy gluconate (KDG) aldolase; CP4‑6 prophage
RA	282,518	G→A	7.4%	G81S (GGC→AGC)	yagE →	2‑keto‑3‑deoxy gluconate (KDG) aldolase; CP4‑6 prophage
RA	285,882	T→G	27.7%	I163S (ATC→AGC)	yagG →	CP4‑6 prophage; putative sugar transporter
RA	285,887	C→A	28.9%	L165M (CTG→ATG)	yagG →	CP4‑6 prophage; putative sugar transporter
RA	285,896	G→A	9.3%	V168M (GTG→ATG)	yagG →	CP4‑6 prophage; putative sugar transporter
RA	292,302	C→G	21.1%	intergenic (+71/+20)	yagJ → / ← yagK	CP4‑6 prophage; uncharacterized protein;Phage or Prophage Related/CP4‑6 prophage; conserved protein
RA	299,050	C→G	5.6%	A629P (GCA→CCA)	paoC ←	PaoABC aldehyde oxidoreductase, Moco‑containing subunit
RA	299,051	G→C	5.6%	G628G (GGC→GGG) ‡	paoC ←	PaoABC aldehyde oxidoreductase, Moco‑containing subunit
RA	299,052	C→G	5.4%	G628A (GGC→GCC) ‡	paoC ←	PaoABC aldehyde oxidoreductase, Moco‑containing subunit
RA	304,085	A→C	5.7%	I33S (ATT→AGT)	ykgJ ←	UPF0153 cysteine cluster protein
RA	304,088	G→T	6.2%	T32N (ACT→AAT)	ykgJ ←	UPF0153 cysteine cluster protein
RA	304,090	A→C	6.6%	G31G (GGT→GGG)	ykgJ ←	UPF0153 cysteine cluster protein
RA	314,255	T→C	21.4%	intergenic (‑450/‑102)	ykgP ← / → eaeH	pseudogene, oxidoreductase family/pseudogene, attaching and effacing protein homology;factor; Not classified
RA	314,258	G→A	21.4%	intergenic (‑453/‑99)	ykgP ← / → eaeH	pseudogene, oxidoreductase family/pseudogene, attaching and effacing protein homology;factor; Not classified
RA	317,566	G→A	9.7%	pseudogene (128/129 nt)	ykgQ →	pseudogene, putative dehydrogenase
RA	317,571	T→C	8.8%	intergenic (+4/+155)	ykgQ → / ← rclC	pseudogene, putative dehydrogenase/reactive chlorine species (RCS) stress resistance inner membrane protein
RA	321,483	C→A	9.4%	intergenic (+402/‑125)	rclR → / → ykgE	reactive chlorine species (RCS)‑specific activator of the rcl genes/cysteine‑rich LutA family protein; putative electron transport chain YkgEFG component
RA	321,484	A→T	9.4%	intergenic (+403/‑124)	rclR → / → ykgE	reactive chlorine species (RCS)‑specific activator of the rcl genes/cysteine‑rich LutA family protein; putative electron transport chain YkgEFG component
RA	321,485	T→G	9.4%	intergenic (+404/‑123)	rclR → / → ykgE	reactive chlorine species (RCS)‑specific activator of the rcl genes/cysteine‑rich LutA family protein; putative electron transport chain YkgEFG component
RA	324,575	T→C	8.3%	intergenic (+122/+121)	ykgG → / ← ykgH	LutC family protein; putative electron transport chain YkgEFG component/putative inner membrane protein
RA	324,579	A→G	6.5%	intergenic (+126/+117)	ykgG → / ← ykgH	LutC family protein; putative electron transport chain YkgEFG component/putative inner membrane protein
RA	324,580	C→G	6.9%	intergenic (+127/+116)	ykgG → / ← ykgH	LutC family protein; putative electron transport chain YkgEFG component/putative inner membrane protein
RA	324,581	C→T	6.9%	intergenic (+128/+115)	ykgG → / ← ykgH	LutC family protein; putative electron transport chain YkgEFG component/putative inner membrane protein
RA	324,585	G→A	6.4%	intergenic (+132/+111)	ykgG → / ← ykgH	LutC family protein; putative electron transport chain YkgEFG component/putative inner membrane protein
RA	328,375	A→C	12.0%	I120S (ATC→AGC)	betB ←	betaine aldehyde dehydrogenase, NAD‑dependent
RA	328,377	C→G	12.3%	L119L (CTG→CTC) ‡	betB ←	betaine aldehyde dehydrogenase, NAD‑dependent
RA	328,379	G→T	12.0%	L119M (CTG→ATG) ‡	betB ←	betaine aldehyde dehydrogenase, NAD‑dependent
RA	335,166	T→A	8.9%	intergenic (‑144/‑114)	yahC ← / → yahD	putative inner membrane protein/ankyrin repeat protein
RA	336,866	G→C	7.6%	G30A (GGC→GCC)	yahF →	putative NAD(P)‑binding succinyl‑CoA synthase
RA	339,756	T→C	13.4%	intergenic (+13/‑409)	yahG → / → yahI	DUF1116 family protein/carbamate kinase‑like protein
RA	339,761	G→C	13.8%	intergenic (+18/‑404)	yahG → / → yahI	DUF1116 family protein/carbamate kinase‑like protein
RA	339,764	G→C	14.9%	intergenic (+21/‑401)	yahG → / → yahI	DUF1116 family protein/carbamate kinase‑like protein
RA	339,769	G→A	14.9%	intergenic (+26/‑396)	yahG → / → yahI	DUF1116 family protein/carbamate kinase‑like protein
RA	344,704	A→T	10.3%	K177* (AAA→TAA) ‡	yahL →	uncharacterized protein
RA	344,705	A→T	10.5%	K177I (AAA→ATA) ‡	yahL →	uncharacterized protein
RA	361,894	A→G	5.8%	intergenic (‑34/+32)	lacA ← / ← lacY	thiogalactoside acetyltransferase/lactose permease
RA	361,895	A→C	5.8%	intergenic (‑35/+31)	lacA ← / ← lacY	thiogalactoside acetyltransferase/lactose permease
RA	361,901	T→G	5.7%	intergenic (‑41/+25)	lacA ← / ← lacY	thiogalactoside acetyltransferase/lactose permease
RA	361,902	C→A	5.9%	intergenic (‑42/+24)	lacA ← / ← lacY	thiogalactoside acetyltransferase/lactose permease
RA	374,682	C→T	8.1%	P272L (CCG→CTG) ‡	mhpE →	4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I
RA	374,683	G→C	7.9%	P272P (CCG→CCC) ‡	mhpE →	4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I
RA	374,688	G→C	8.0%	R274P (CGA→CCA) ‡	mhpE →	4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I
RA	374,689	A→G	7.8%	R274R (CGA→CGG) ‡	mhpE →	4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I
RA	397,273	C→T	5.3%	A212V (GCC→GTC)	sbmA →	peptide antibiotic transporter
RA	397,277	C→G	5.4%	I213M (ATC→ATG)	sbmA →	peptide antibiotic transporter
RA	397,281	A→G	5.1%	T215A (ACG→GCG)	sbmA →	peptide antibiotic transporter
RA	414,832	G→T	6.4%	H308N (CAT→AAT)	sbcC ←	exonuclease, dsDNA, ATP‑dependent
RA	436,696	T→C	5.3%	V36V (GTT→GTC)	pgpA →	phosphatidylglycerophosphatase A
RA	436,699	T→A	5.4%	P37P (CCT→CCA)	pgpA →	phosphatidylglycerophosphatase A
RA	436,702	G→A	5.5%	G38G (GGG→GGA)	pgpA →	phosphatidylglycerophosphatase A
RA	443,022	G→A	36.4%	intergenic (+25/+29)	thiI → / ← yajL	tRNA s(4)U8 sulfurtransferase/oxidative‑stress‑resistance chaperone
RA	443,023	T→C	36.4%	intergenic (+26/+28)	thiI → / ← yajL	tRNA s(4)U8 sulfurtransferase/oxidative‑stress‑resistance chaperone
RA	448,965	G→A	6.3%	H559H (CAC→CAT) ‡	cyoB ←	cytochrome o ubiquinol oxidase subunit I
RA	448,966	T→C	6.3%	H559R (CAC→CGC) ‡	cyoB ←	cytochrome o ubiquinol oxidase subunit I
RA	454,853	T→C	22.2%	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	22.2%	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	455,632	A→G	5.5%	D167G (GAC→GGC)	tig →	peptidyl‑prolyl cis/trans isomerase (trigger factor)
RA	456,490	T→C	10.1%	intergenic (+59/‑187)	tig → / → clpP	peptidyl‑prolyl cis/trans isomerase (trigger factor)/proteolytic subunit of ClpA‑ClpP and ClpX‑ClpP ATP‑dependent serine proteases
RA	457,649	A→C	7.8%	D75A (GAC→GCC)	clpX →	ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease
RA	457,654	T→A	8.1%	Y77N (TAC→AAC)	clpX →	ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease
RA	457,659	T→A	9.0%	V78V (GTT→GTA)	clpX →	ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease
RA	457,664	G→T	5.6%	G80V (GGC→GTC)	clpX →	ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease
RA	475,971	C→G	27.4%	intergenic (+20/+11)	ybaY → / ← ybaZ	outer membrane lipoprotein/excision repair protein, alkyltransferase‑like protein ATL
RA	475,972	C→G	27.4%	intergenic (+21/+10)	ybaY → / ← ybaZ	outer membrane lipoprotein/excision repair protein, alkyltransferase‑like protein ATL
RA	478,750	C→T	5.5%	intergenic (‑133/+31)	ylaB ← / ← ylaC	putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase/DUF1449 family inner membrane protein
RA	478,752	G→A	6.1%	intergenic (‑135/+29)	ylaB ← / ← ylaC	putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase/DUF1449 family inner membrane protein
RA	478,757	T→C	6.0%	intergenic (‑140/+24)	ylaB ← / ← ylaC	putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase/DUF1449 family inner membrane protein
RA	478,759	A→G	5.7%	intergenic (‑142/+22)	ylaB ← / ← ylaC	putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase/DUF1449 family inner membrane protein
RA	480,236	C→G	14.6%	E25Q (GAG→CAG)	hha ←	modulator of gene expression, with H‑NS
RA	480,237	C→G	14.6%	L24L (CTG→CTC)	hha ←	modulator of gene expression, with H‑NS
RA	501,455	A→G	12.2%	intergenic (+26/+107)	gsk → / ← ybaL	inosine/guanosine kinase/inner membrane putative NAD(P)‑binding transporter
RA	501,456	A→C	12.2%	intergenic (+27/+106)	gsk → / ← ybaL	inosine/guanosine kinase/inner membrane putative NAD(P)‑binding transporter
RA	501,462	T→G	14.7%	intergenic (+33/+100)	gsk → / ← ybaL	inosine/guanosine kinase/inner membrane putative NAD(P)‑binding transporter
RA	501,463	C→A	15.1%	intergenic (+34/+99)	gsk → / ← ybaL	inosine/guanosine kinase/inner membrane putative NAD(P)‑binding transporter
RA	504,822	G→C	5.3%	intergenic (‑126/‑92)	fsr ← / → ushA	putative fosmidomycin efflux system protein/bifunctional UDP‑sugar hydrolase/5'‑nucleotidase
RA	512,212	T→G	8.3%	V191G (GTG→GGG)	glsA →	glutaminase 1
RA	512,219	C→A	9.7%	T193T (ACC→ACA)	glsA →	glutaminase 1
RA	513,464	C→A	5.5%	L297M (CTG→ATG) ‡	ybaT →	putative amino acid transporter
RA	513,465	T→G	5.5%	L297R (CTG→CGG) ‡	ybaT →	putative amino acid transporter
RA	514,599	A→G	5.9%	S87S (AGT→AGC)	ybbJ ←	inner membrane protein; stimulator of the QmcA suppressor of ftsH‑htpX
RA	521,941	T→G	5.3%	L509R (CTC→CGC)	ybbP →	putative ABC transporter permease
RA	521,944	C→A	5.5%	A510E (GCG→GAG)	ybbP →	putative ABC transporter permease
RA	532,335	A→G	6.7%	intergenic (‑114/‑116)	allS ← / → allA	allD operon transcriptional activator/ureidoglycolate lyase, releasing urea
RA	533,846	T→C	14.3%	intergenic (+20/‑70)	allR → / → gcl	glyoxylate‑inducible transcriptional repressor of all and gcl operons/glyoxylate carboligase
RA	533,849	G→A	14.9%	intergenic (+23/‑67)	allR → / → gcl	glyoxylate‑inducible transcriptional repressor of all and gcl operons/glyoxylate carboligase
RA	542,153	A→G	6.1%	E89G (GAG→GGG)	glxK →	glycerate kinase II
RA	543,091	G→C	23.5%	intergenic (+58/+170)	glxK → / ← allE	glycerate kinase II/S‑ureidoglycine aminohydrolase
RA	543,094	G→C	23.5%	intergenic (+61/+167)	glxK → / ← allE	glycerate kinase II/S‑ureidoglycine aminohydrolase
RA	543,207	A→T	50.0%	intergenic (+174/+54)	glxK → / ← allE	glycerate kinase II/S‑ureidoglycine aminohydrolase
RA	543,210	A→T	50.0%	intergenic (+177/+51)	glxK → / ← allE	glycerate kinase II/S‑ureidoglycine aminohydrolase
RA	543,747	T→A	8.3%	T100T (ACA→ACT) ‡	allE ←	S‑ureidoglycine aminohydrolase
RA	543,748	G→C	8.3%	T100R (ACA→AGA) ‡	allE ←	S‑ureidoglycine aminohydrolase
RA	543,749	T→A	8.7%	T100S (ACA→TCA) ‡	allE ←	S‑ureidoglycine aminohydrolase
RA	543,956	G→A	6.4%	P31S (CCG→TCG)	allE ←	S‑ureidoglycine aminohydrolase
RA	553,473	C→A	7.4%	M156I (ATG→ATT)	lpxH ←	UDP‑2,3‑diacylglucosamine pyrophosphohydrolase
RA	558,654	C→T	5.9%	T148I (ACC→ATC)	sfmA →	FimA homolog, function unknown
RA	569,160	G→T	11.6%	D87Y (GAC→TAC) ‡	ybcK →	DLP12 prophage; putative recombinase
RA	569,161	A→C	11.4%	D87A (GAC→GCC) ‡	ybcK →	DLP12 prophage; putative recombinase
RA	574,504	Δ1 bp	9.5%	intergenic (+165/+25)	quuD → / ← nmpC	DLP12 prophage; putative antitermination protein/DLP12 prophage; truncated outer membrane porin (pseudogene);IS, phage, Tn; Phage or Prophage Related; outer membrane porin protein; locus of qsr prophage
RA	585,653	G→A	14.3%	intergenic (‑20/‑404)	ompT ← / → pauD	DLP12 prophage; outer membrane protease VII; outer membrane protein 3b/tRNA‑OTHER
RA	585,656	T→A	15.3%	intergenic (‑23/‑401)	ompT ← / → pauD	DLP12 prophage; outer membrane protease VII; outer membrane protein 3b/tRNA‑OTHER
RA	585,657	T→A	15.3%	intergenic (‑24/‑400)	ompT ← / → pauD	DLP12 prophage; outer membrane protease VII; outer membrane protein 3b/tRNA‑OTHER
RA	585,660	T→C	16.4%	intergenic (‑27/‑397)	ompT ← / → pauD	DLP12 prophage; outer membrane protease VII; outer membrane protein 3b/tRNA‑OTHER
RA	585,863	T→C	16.7%	intergenic (‑230/‑194)	ompT ← / → pauD	DLP12 prophage; outer membrane protease VII; outer membrane protein 3b/tRNA‑OTHER
RA	585,866	G→A	15.5%	intergenic (‑233/‑191)	ompT ← / → pauD	DLP12 prophage; outer membrane protease VII; outer membrane protein 3b/tRNA‑OTHER
RA	595,519	T→A	8.3%	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	8.3%	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	29.5%	intergenic (+56/+25)	pheP → / ← ybdG	phenylalanine transporter/mechanosensitive channel protein, miniconductance
RA	603,393	T→A	28.3%	intergenic (+58/+23)	pheP → / ← ybdG	phenylalanine transporter/mechanosensitive channel protein, miniconductance
RA	603,395	C→G	28.3%	intergenic (+60/+21)	pheP → / ← ybdG	phenylalanine transporter/mechanosensitive channel protein, miniconductance
RA	605,022	C→G	5.6%	D135H (GAT→CAT)	nfsB ←	dihydropteridine reductase, NAD(P)H‑dependent, oxygen‑insensitive
RA	605,025	C→G	5.6%	D134H (GAT→CAT)	nfsB ←	dihydropteridine reductase, NAD(P)H‑dependent, oxygen‑insensitive
RA	622,455	G→C	6.1%	W52C (TGG→TGC)	entS →	enterobactin exporter, iron‑regulated
RA	622,531	C→T	5.0%	R78C (CGC→TGC)	entS →	enterobactin exporter, iron‑regulated
RA	623,054	A→T	11.4%	N252I (AAC→ATC)	entS →	enterobactin exporter, iron‑regulated
RA	623,058	G→C	8.2%	W253C (TGG→TGC)	entS →	enterobactin exporter, iron‑regulated
RA	623,062	A→T	8.6%	M255L (ATG→TTG)	entS →	enterobactin exporter, iron‑regulated
RA	632,126	A→G	12.4%	intergenic (+127/‑56)	cstA → / → ybdD	carbon starvation protein involved in peptide utilization; APC peptide transporter family protein/DUF466 family protein
RA	632,127	A→C	12.5%	intergenic (+128/‑55)	cstA → / → ybdD	carbon starvation protein involved in peptide utilization; APC peptide transporter family protein/DUF466 family protein
RA	632,133	T→G	12.7%	intergenic (+134/‑49)	cstA → / → ybdD	carbon starvation protein involved in peptide utilization; APC peptide transporter family protein/DUF466 family protein
RA	632,134	C→A	12.7%	intergenic (+135/‑48)	cstA → / → ybdD	carbon starvation protein involved in peptide utilization; APC peptide transporter family protein/DUF466 family protein
RA	642,862	G→C	5.5%	D259H (GAT→CAT)	ybdR →	putative Zn‑dependent NAD(P)‑binding oxidoreductase
RA	650,529	G→A	7.9%	R85R (CGC→CGT)	citD ←	citrate lyase, acyl carrier (gamma) subunit
RA	650,532	T→C	7.5%	A84A (GCA→GCG)	citD ←	citrate lyase, acyl carrier (gamma) subunit
RA	657,531	T→G	25.9%	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	25.9%	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	28.0%	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	665,094	G→C	9.1%	P33A (CCT→GCT)	rlpA ←	septal ring protein, suppressor of prc, minor lipoprotein
RA	672,110	G→A	6.5%	T26I (ACC→ATC)	lptE ←	LPS assembly OM complex LptDE, lipoprotein component
RA	672,113	T→C	6.5%	D25G (GAT→GGT)	lptE ←	LPS assembly OM complex LptDE, lipoprotein component
RA	678,688	A→C	9.8%	N425T (AAT→ACT)	djlB →	putative HscC co‑chaperone, uncharacterized J domain‑containing protein
RA	681,694	A→G	37.5%	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	42.9%	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	42.9%	intergenic (+37/+23)	djlC → / ← hscC	J domain‑containing HscC co‑chaperone; Hsc56/Hsp70 family chaperone Hsc62; RpoD‑binding transcription inhibitor
RA	691,390	G→C	7.7%	A132G (GCC→GGC)	ybeX ←	putative ion transport
RA	693,030	C→A	8.0%	V117L (GTA→TTA)	ybeZ ←	heat shock protein, putative NTPase; PhoH‑like protein
RA	696,325	G→T	12.8%	intergenic (+49/+105)	ubiF → / ← glnX	2‑octaprenyl‑3‑methyl‑6‑methoxy‑1,4‑benzoquinol oxygenase/tRNA‑Gln
RA	696,328	A→C	13.3%	intergenic (+52/+102)	ubiF → / ← glnX	2‑octaprenyl‑3‑methyl‑6‑methoxy‑1,4‑benzoquinol oxygenase/tRNA‑Gln
RA	699,556	C→T	22.2%	intergenic (‑379/+18)	asnB ← / ← umpH	asparagine synthetase B/UMP phosphatase
RA	699,559	A→G	21.6%	intergenic (‑382/+15)	asnB ← / ← umpH	asparagine synthetase B/UMP phosphatase
RA	710,170	C→T	24.1%	intergenic (+54/+30)	chiQ → / ← fur	chitosugar‑induced verified lipoprotein/ferric iron uptake regulon transcriptional repressor; autorepressor
RA	710,173	A→G	24.9%	intergenic (+57/+27)	chiQ → / ← fur	chitosugar‑induced verified lipoprotein/ferric iron uptake regulon transcriptional repressor; autorepressor
RA	715,755	A→C	7.8%	Q115P (CAG→CCG) ‡	ybfP →	lipoprotein
RA	715,756	G→T	7.7%	Q115H (CAG→CAT) ‡	ybfP →	lipoprotein
RA	715,762	G→A	7.4%	K117K (AAG→AAA)	ybfP →	lipoprotein
RA	725,276	G→A	6.2%	Y587Y (TAC→TAT)	kdpB ←	potassium translocating ATPase, subunit B
RA	725,279	T→C	6.1%	K586K (AAA→AAG)	kdpB ←	potassium translocating ATPase, subunit B
RA	732,503	G→A	5.8%	R974Q (CGG→CAG)	rhsC →	Rhs protein with putative toxin domain; putative neighboring cell growth inhibitor
RA	732,506	T→C	5.5%	L975P (CTG→CCG)	rhsC →	Rhs protein with putative toxin domain; putative neighboring cell growth inhibitor
RA	747,895	C→G	12.3%	intergenic (‑126/+26)	abrB ← / ← ybgO	regulator of aidB expression; inner membrane protein/putative fimbrial protein
RA	747,897	G→C	12.7%	intergenic (‑128/+24)	abrB ← / ← ybgO	regulator of aidB expression; inner membrane protein/putative fimbrial protein
RA	747,900	G→C	12.7%	intergenic (‑131/+21)	abrB ← / ← ybgO	regulator of aidB expression; inner membrane protein/putative fimbrial protein
RA	747,902	C→G	12.7%	intergenic (‑133/+19)	abrB ← / ← ybgO	regulator of aidB expression; inner membrane protein/putative fimbrial protein
RA	761,664	A→C	5.1%	E48A (GAA→GCA)	sucB →	dihydrolipoyltranssuccinase
RA	762,869	A→T	9.0%	intergenic (+130/‑145)	sucB → / → sucC	dihydrolipoyltranssuccinase/succinyl‑CoA synthetase, beta subunit
RA	762,870	A→T	9.1%	intergenic (+131/‑144)	sucB → / → sucC	dihydrolipoyltranssuccinase/succinyl‑CoA synthetase, beta subunit
RA	764,078	A→G	5.3%	E355E (GAA→GAG)	sucC →	succinyl‑CoA synthetase, beta subunit
RA	764,079	C→T	5.3%	L356F (CTC→TTC)	sucC →	succinyl‑CoA synthetase, beta subunit
RA	765,132	G→A	23.8%	intergenic (+83/+21)	sucD → / ← mngR	succinyl‑CoA synthetase, NAD(P)‑binding, alpha subunit/transcriptional repressor for the mannosyl‑D‑glycerate catabolic operon
RA	765,135	T→C	29.4%	intergenic (+86/+18)	sucD → / ← mngR	succinyl‑CoA synthetase, NAD(P)‑binding, alpha subunit/transcriptional repressor for the mannosyl‑D‑glycerate catabolic operon
RA	773,138	G→A	7.5%	G33S (GGC→AGC)	cydB →	cytochrome d terminal oxidase, subunit II
RA	773,145	T→C	7.2%	L35P (CTC→CCC)	cydB →	cytochrome d terminal oxidase, subunit II
RA	784,012	T→A	6.1%	Q271L (CAG→CTG)	zitB ←	zinc efflux system
RA	788,385	G→T	8.4%	T151T (ACC→ACA) ‡	galM ←	aldose 1‑epimerase; type‑1 mutarotase; galactose mutarotase
RA	788,387	T→A	8.3%	T151S (ACC→TCC) ‡	galM ←	aldose 1‑epimerase; type‑1 mutarotase; galactose mutarotase
RA	788,389	A→C	8.0%	L150R (CTG→CGG)	galM ←	aldose 1‑epimerase; type‑1 mutarotase; galactose mutarotase
RA	813,570:1	+T	6.0%	coding (45/2022 nt)	uvrB →	exision nuclease of nucleotide excision repair, DNA damage recognition component
RA	813,575	Δ1 bp	5.7%	coding (50/2022 nt)	uvrB →	exision nuclease of nucleotide excision repair, DNA damage recognition component
RA	828,746	T→C	5.6%	H79R (CAC→CGC)	ybhF ←	putative ABC transporter ATPase
RA	828,749	A→T	5.5%	L78Q (CTG→CAG)	ybhF ←	putative ABC transporter ATPase
RA	828,752	G→A	5.5%	A77V (GCG→GTG)	ybhF ←	putative ABC transporter ATPase
RA	832,934	T→C	6.3%	Q6R (CAA→CGA)	ybiA ←	DUF1768 family protein
RA	847,213	A→T	9.1%	intergenic (‑94/+45)	glnP ← / ← glnH	glutamine transporter subunit/glutamine transporter subunit
RA	847,214	T→A	9.3%	intergenic (‑95/+44)	glnP ← / ← glnH	glutamine transporter subunit/glutamine transporter subunit
RA	847,215	A→T	9.6%	intergenic (‑96/+43)	glnP ← / ← glnH	glutamine transporter subunit/glutamine transporter subunit
RA	848,350	C→T	6.2%	intergenic (‑346/+58)	glnH ← / ← dps	glutamine transporter subunit/Fe‑binding and storage protein; stress‑inducible DNA‑binding protein
RA	848,356	T→A	6.2%	intergenic (‑352/+52)	glnH ← / ← dps	glutamine transporter subunit/Fe‑binding and storage protein; stress‑inducible DNA‑binding protein
RA	848,362	A→G	6.0%	intergenic (‑358/+46)	glnH ← / ← dps	glutamine transporter subunit/Fe‑binding and storage protein; stress‑inducible DNA‑binding protein
RA	848,367	C→T	6.0%	intergenic (‑363/+41)	glnH ← / ← dps	glutamine transporter subunit/Fe‑binding and storage protein; stress‑inducible DNA‑binding protein
RA	857,576	T→C	31.2%	intergenic (+21/+220)	ybiT → / ← ybiU	ABC‑F family putative regulatory ATPase/DUF1479 family protein
RA	857,578	C→G	31.2%	intergenic (+23/+218)	ybiT → / ← ybiU	ABC‑F family putative regulatory ATPase/DUF1479 family protein
RA	857,580	G→A	31.2%	intergenic (+25/+216)	ybiT → / ← ybiU	ABC‑F family putative regulatory ATPase/DUF1479 family protein
RA	858,924	T→G	5.3%	R46R (CGA→CGC)	ybiU ←	DUF1479 family protein
RA	858,927	C→A	5.3%	T45T (ACG→ACT)	ybiU ←	DUF1479 family protein
RA	860,154	A→T	30.0%	intergenic (‑126/+20)	ybiV ← / ← ybiW	sugar phosphatase; fructose‑1‑P/ribose‑5‑P/glucose‑6‑P phosphatase/putative pyruvate formate lyase
RA	860,157	C→T	20.0%	intergenic (‑129/+17)	ybiV ← / ← ybiW	sugar phosphatase; fructose‑1‑P/ribose‑5‑P/glucose‑6‑P phosphatase/putative pyruvate formate lyase
RA	867,717	G→C	9.1%	L66F (TTG→TTC)	gsiA →	glutathione ABC transporter ATPase
RA	867,718	G→C	9.1%	E67Q (GAA→CAA)	gsiA →	glutathione ABC transporter ATPase
RA	870,888	T→G	6.9%	L493R (CTG→CGG)	gsiB →	glutathione ABC transporter periplasmic binding protein
RA	870,890	A→T	8.4%	T494S (ACC→TCC) ‡	gsiB →	glutathione ABC transporter periplasmic binding protein
RA	870,892	C→A	7.1%	T494T (ACC→ACA) ‡	gsiB →	glutathione ABC transporter periplasmic binding protein
RA	884,868	T→A	7.0%	L399* (TTA→TAA)	mdfA →	multidrug efflux system protein
RA	887,392	T→A	5.5%	intergenic (‑53/‑31)	ybjJ ← / → rcdA	putative drug efflux MFS transporter, inner membrane protein/transcriptional regulator of csgD and ybiJI; autoregulator
RA	887,393	T→A	5.5%	intergenic (‑54/‑30)	ybjJ ← / → rcdA	putative drug efflux MFS transporter, inner membrane protein/transcriptional regulator of csgD and ybiJI; autoregulator
RA	892,441	G→A	9.3%	A159T (GCG→ACG) ‡	rimK →	ribosomal protein S6 modification protein
RA	892,443	G→C	9.3%	A159A (GCG→GCC) ‡	rimK →	ribosomal protein S6 modification protein
RA	892,455	G→C	24.4%	V163V (GTG→GTC)	rimK →	ribosomal protein S6 modification protein
RA	892,457	T→A	25.7%	I164N (ATT→AAT)	rimK →	ribosomal protein S6 modification protein
RA	892,459	G→C	23.8%	D165H (GAC→CAC)	rimK →	ribosomal protein S6 modification protein
RA	894,952	T→A	5.6%	intergenic (+56/‑39)	potF → / → potG	putrescine ABC transporter periplasmic binding protein/putrescine ABC transporter ATPase
RA	915,080	G→C	16.0%	intergenic (‑223/+272)	ybjE ← / ← aqpZ	putative transporter/aquaporin Z
RA	915,081	G→C	16.0%	intergenic (‑224/+271)	ybjE ← / ← aqpZ	putative transporter/aquaporin Z
RA	926,168	C→T	18.2%	intergenic (‑197/+57)	serW ← / ← infA	tRNA‑Ser/translation initiation factor IF‑1
RA	926,174	A→T	22.4%	intergenic (‑203/+51)	serW ← / ← infA	tRNA‑Ser/translation initiation factor IF‑1
RA	926,180	A→G	19.4%	intergenic (‑209/+45)	serW ← / ← infA	tRNA‑Ser/translation initiation factor IF‑1
RA	958,769	C→G	12.9%	intergenic (+28/‑43)	serC → / → aroA	3‑phosphoserine/phosphohydroxythreonine aminotransferase/5‑enolpyruvylshikimate‑3‑phosphate synthetase
RA	958,771	A→T	12.9%	intergenic (+30/‑41)	serC → / → aroA	3‑phosphoserine/phosphohydroxythreonine aminotransferase/5‑enolpyruvylshikimate‑3‑phosphate synthetase
RA	958,773	C→G	12.8%	intergenic (+32/‑39)	serC → / → aroA	3‑phosphoserine/phosphohydroxythreonine aminotransferase/5‑enolpyruvylshikimate‑3‑phosphate synthetase
RA	964,938	T→A	5.2%	S207T (TCC→ACC)	ycaI →	ComEC family inner membrane protein
RA	986,410	A→C	7.8%	S191S (TCT→TCG) ‡	ompF ←	outer membrane porin 1a (Ia;b;F)
RA	986,411	G→T	7.9%	S191Y (TCT→TAT) ‡	ompF ←	outer membrane porin 1a (Ia;b;F)
RA	989,879:1	+C	6.3%	coding (478/1203 nt)	pncB ←	nicotinate phosphoribosyltransferase
RA	996,662	C→A	6.7%	G95W (GGG→TGG)	ssuA ←	aliphatic sulfonate ABC transporter periplasmic binding protein
RA	996,666	A→T	5.9%	A93A (GCT→GCA)	ssuA ←	aliphatic sulfonate ABC transporter periplasmic binding protein
RA	996,670	T→G	5.9%	Q92P (CAG→CCG)	ssuA ←	aliphatic sulfonate ABC transporter periplasmic binding protein
RA	998,996	G→T	7.2%	T169T (ACG→ACT)	elfD →	putative periplasmic pilin chaperone
RA	998,998	T→A	7.2%	V170D (GTC→GAC)	elfD →	putative periplasmic pilin chaperone
RA	999,000	A→C	7.2%	S171R (AGT→CGT)	elfD →	putative periplasmic pilin chaperone
RA	1,010,823	C→G	7.5%	A287G (GCC→GGC)	uup →	replication regulatory ABC‑F family DNA‑binding ATPase
RA	1,020,958	A→T	7.3%	intergenic (‑39/‑180)	sulA ← / → sxy	SOS cell division inhibitor/CRP‑S‑dependent promoter expression factor
RA	1,037,339	G→C	5.0%	E197D (GAG→GAC)	hyaF →	hydrogenase‑1 protein nickel incorporation factor
RA	1,038,117	C→G	5.8%	H126Q (CAC→CAG)	cbdA →	cytochrome bd‑II oxidase, subunit I
RA	1,038,118	C→G	6.2%	L127V (CTG→GTG)	cbdA →	cytochrome bd‑II oxidase, subunit I
RA	1,039,479	G→A	8.4%	V62I (GTC→ATC) ‡	cbdB →	cytochrome bd‑II oxidase, subunit II
RA	1,039,480	T→C	8.5%	V62A (GTC→GCC) ‡	cbdB →	cytochrome bd‑II oxidase, subunit II
RA	1,041,937	T→G	27.3%	intergenic (+22/+93)	appA → / ← etk	phosphoanhydride phosphorylase/tyrosine‑protein kinase, role in O‑antigen capsule formation
RA	1,041,940	C→A	30.0%	intergenic (+25/+90)	appA → / ← etk	phosphoanhydride phosphorylase/tyrosine‑protein kinase, role in O‑antigen capsule formation
RA	1,048,701	T→C	7.0%	K211R (AAA→AGA)	gfcB ←	O‑antigen capsule production lipoprotein
RA	1,052,257	C→T	9.1%	intergenic (+17/+32)	gnsA → / ← yccM	putative phosphatidylethanolamine synthesis regulator/putative 4Fe‑4S membrane protein
RA	1,052,260	T→C	9.4%	intergenic (+20/+29)	gnsA → / ← yccM	putative phosphatidylethanolamine synthesis regulator/putative 4Fe‑4S membrane protein
RA	1,052,261	G→A	9.4%	intergenic (+21/+28)	gnsA → / ← yccM	putative phosphatidylethanolamine synthesis regulator/putative 4Fe‑4S membrane protein
RA	1,052,264	A→G	8.7%	intergenic (+24/+25)	gnsA → / ← yccM	putative phosphatidylethanolamine synthesis regulator/putative 4Fe‑4S membrane protein
RA	1,064,160	T→C	7.3%	L42P (CTG→CCG) ‡	yccE →	uncharacterized protein
RA	1,064,161	G→A	7.6%	L42L (CTG→CTA) ‡	yccE →	uncharacterized protein
RA	1,075,515	G→T	5.1%	A1123E (GCG→GAG)	putA ←	fused DNA‑binding transcriptional regulator/proline dehydrogenase/pyrroline‑5‑carboxylate dehydrogenase
RA	1,082,499	T→A	7.3%	F86Y (TTT→TAT) ‡	efeO →	inactive ferrous ion transporter EfeUOB
RA	1,082,500	T→A	7.2%	F86L (TTT→TTA) ‡	efeO →	inactive ferrous ion transporter EfeUOB
RA	1,087,568	Δ1 bp	5.3%	coding (279/1326 nt)	pgaC ←	biofilm PGA synthase PgaCD, catalytic subunit; poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine synthase
RA	1,100,125	C→T	7.0%	T162T (ACC→ACT)	ycdY →	redox enzyme maturation protein (REMP) chaperone for YcdX
RA	1,100,126:1	+A	5.9%	coding (487/555 nt)	ycdY →	redox enzyme maturation protein (REMP) chaperone for YcdX
RA	1,113,544	G→A	50.0%	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	50.0%	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	50.0%	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	1,116,854	A→C	8.3%	K16N (AAA→AAC)	yceA →	putative rhodanese‑related sulfurtransferase
RA	1,116,857	G→T	5.5%	M17I (ATG→ATT)	yceA →	putative rhodanese‑related sulfurtransferase
RA	1,133,157	A→T	7.0%	D195V (GAC→GTC)	flgE →	flagellar hook protein
RA	1,134,661	A→G	7.5%	intergenic (+104/‑68)	flgF → / → flgG	flagellar component of cell‑proximal portion of basal‑body rod/flagellar component of cell‑distal portion of basal‑body rod
RA	1,134,662	A→C	7.5%	intergenic (+105/‑67)	flgF → / → flgG	flagellar component of cell‑proximal portion of basal‑body rod/flagellar component of cell‑distal portion of basal‑body rod
RA	1,134,668	T→A	8.0%	intergenic (+111/‑61)	flgF → / → flgG	flagellar component of cell‑proximal portion of basal‑body rod/flagellar component of cell‑distal portion of basal‑body rod
RA	1,134,669	T→A	8.0%	intergenic (+112/‑60)	flgF → / → flgG	flagellar component of cell‑proximal portion of basal‑body rod/flagellar component of cell‑distal portion of basal‑body rod
RA	1,136,026	G→T	7.5%	V155L (GTA→TTA) ‡	flgH →	flagellar protein of basal‑body outer‑membrane L ring
RA	1,136,027	T→A	7.1%	V155E (GTA→GAA) ‡	flgH →	flagellar protein of basal‑body outer‑membrane L ring
RA	1,136,028	A→C	7.2%	V155V (GTA→GTC) ‡	flgH →	flagellar protein of basal‑body outer‑membrane L ring
RA	1,138,936	A→T	6.9%	T187S (ACA→TCA)	flgK →	flagellar hook‑filament junction protein 1
RA	1,139,790	T→A	5.9%	A471A (GCT→GCA)	flgK →	flagellar hook‑filament junction protein 1
RA	1,139,793	T→A	6.1%	Y472* (TAT→TAA)	flgK →	flagellar hook‑filament junction protein 1
RA	1,139,796	C→G	6.1%	A473A (GCC→GCG)	flgK →	flagellar hook‑filament junction protein 1
RA	1,147,980	G→T	14.0%	K120N (AAG→AAT)	plsX →	putative phosphate acyltransferase
RA	1,147,986	G→C	13.2%	L122L (CTG→CTC)	plsX →	putative phosphate acyltransferase
RA	1,147,987	G→C	13.2%	E123Q (GAG→CAG)	plsX →	putative phosphate acyltransferase
RA	1,147,993	A→C	10.8%	I125L (ATT→CTT)	plsX →	putative phosphate acyltransferase
RA	1,158,139	A→T	8.2%	K91* (AAA→TAA) ‡	ptsG →	fused glucose‑specific PTS enzymes: IIB component/IIC component
RA	1,158,140	A→T	8.2%	K91I (AAA→ATA) ‡	ptsG →	fused glucose‑specific PTS enzymes: IIB component/IIC component
RA	1,159,335	G→T	18.5%	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	20.0%	intergenic (+34/+26)	ptsG → / ← fhuE	fused glucose‑specific PTS enzymes: IIB component/IIC component/ferric‑rhodotorulic acid outer membrane transporter
RA	1,170,272	G→C	22.2%	P35A (CCA→GCA)	ldtC ←	L,D‑transpeptidase linking Lpp to murein
RA	1,170,275	G→C	22.2%	P34A (CCG→GCG)	ldtC ←	L,D‑transpeptidase linking Lpp to murein
RA	1,170,282	C→G	22.2%	W31C (TGG→TGC)	ldtC ←	L,D‑transpeptidase linking Lpp to murein
RA	1,174,077	G→A	14.3%	intergenic (‑113/+15)	mfd ← / ← ycfT	transcription‑repair coupling factor/inner membrane protein
RA	1,174,080	T→C	14.7%	intergenic (‑116/+12)	mfd ← / ← ycfT	transcription‑repair coupling factor/inner membrane protein
RA	1,177,646	T→G	5.5%	N109K (AAT→AAG)	lolE →	lipoprotein‑releasing system transmembrane protein
RA	1,177,647	C→A	5.6%	L110I (CTT→ATT)	lolE →	lipoprotein‑releasing system transmembrane protein
RA	1,181,764	C→T	16.5%	intergenic (‑39/+19)	ymfA ← / ← potD	DUF3592 family inner membrane protein/spermidine/putrescine ABC transporter periplasmic binding protein
RA	1,182,764	G→A	7.6%	H22H (CAC→CAT)	potD ←	spermidine/putrescine ABC transporter periplasmic binding protein
RA	1,182,771	G→C	11.4%	A20G (GCC→GGC)	potD ←	spermidine/putrescine ABC transporter periplasmic binding protein
RA	1,182,778	T→C	5.8%	M18V (ATG→GTG)	potD ←	spermidine/putrescine ABC transporter periplasmic binding protein
RA	1,214,599	T→A	9.9%	K293* (AAA→TAA)	bluF ←	anti‑repressor for YcgE, blue light‑responsive; FAD‑binding; inactive c‑di‑GMP phosphodiesterase‑like EAL domain protein
RA	1,224,239	A→T	15.0%	intergenic (+332/+40)	ycgI → / ← minE	pseudogene/cell division topological specificity factor
RA	1,224,242	A→T	15.0%	intergenic (+335/+37)	ycgI → / ← minE	pseudogene/cell division topological specificity factor
RA	1,226,114	C→G	11.4%	intergenic (‑34/‑486)	minC ← / → ycgJ	inhibitor of FtsZ ring polymerization/uncharacterized protein
RA	1,226,115	A→C	11.1%	intergenic (‑35/‑485)	minC ← / → ycgJ	inhibitor of FtsZ ring polymerization/uncharacterized protein
RA	1,226,118	G→T	11.3%	intergenic (‑38/‑482)	minC ← / → ycgJ	inhibitor of FtsZ ring polymerization/uncharacterized protein
RA	1,226,119	C→G	11.4%	intergenic (‑39/‑481)	minC ← / → ycgJ	inhibitor of FtsZ ring polymerization/uncharacterized protein
RA	1,227,051	G→C	13.2%	intergenic (+83/+20)	ycgJ → / ← pliG	uncharacterized protein/periplasmic inhibitor of g‑type lysozyme
RA	1,227,052	A→T	13.2%	intergenic (+84/+19)	ycgJ → / ← pliG	uncharacterized protein/periplasmic inhibitor of g‑type lysozyme
RA	1,227,053	G→C	13.1%	intergenic (+85/+18)	ycgJ → / ← pliG	uncharacterized protein/periplasmic inhibitor of g‑type lysozyme
RA	1,231,963	T→A	6.1%	Y260N (TAT→AAT)	umuC →	translesion error‑prone DNA polymerase V subunit; DNA polymerase activity
RA	1,247,626	G→A	8.3%	intergenic (‑250/+70)	treA ← / ← dhaM	periplasmic trehalase/putative dihydroxyacetone‑specific PTS enzymes: HPr, EI components
RA	1,248,064	T→A	7.7%	K351* (AAA→TAA)	dhaM ←	putative dihydroxyacetone‑specific PTS enzymes: HPr, EI components
RA	1,250,962	T→C	5.7%	intergenic (‑124/‑104)	dhaK ← / → dhaR	dihydroxyacetone kinase, PTS‑dependent, dihydroxyacetone‑binding subunit/dhaKLM operon transcription activator
RA	1,250,963	A→T	5.7%	intergenic (‑125/‑103)	dhaK ← / → dhaR	dihydroxyacetone kinase, PTS‑dependent, dihydroxyacetone‑binding subunit/dhaKLM operon transcription activator
RA	1,250,964	G→A	5.7%	intergenic (‑126/‑102)	dhaK ← / → dhaR	dihydroxyacetone kinase, PTS‑dependent, dihydroxyacetone‑binding subunit/dhaKLM operon transcription activator
RA	1,260,901	C→T	15.1%	intergenic (‑98/+27)	dauA ← / ← prs	C4‑dicarboxylic acid transporter/phosphoribosylpyrophosphate synthase
RA	1,260,904	A→G	13.8%	intergenic (‑101/+24)	dauA ← / ← prs	C4‑dicarboxylic acid transporter/phosphoribosylpyrophosphate synthase
RA	1,268,694	T→A	7.1%	L177Q (CTG→CAG)	kdsA →	3‑deoxy‑D‑manno‑octulosonate 8‑phosphate synthase
RA	1,285,190	T→A	19.1%	L18I (TTA→ATA)	narJ →	molybdenum‑cofactor‑assembly chaperone delta subunit of nitrate reductase 1
RA	1,285,193	T→A	20.9%	W19R (TGG→AGG)	narJ →	molybdenum‑cofactor‑assembly chaperone delta subunit of nitrate reductase 1
RA	1,285,261	Δ1 bp	10.3%	coding (123/711 nt)	narJ →	molybdenum‑cofactor‑assembly chaperone delta subunit of nitrate reductase 1
RA	1,285,265:1	+A	10.5%	coding (127/711 nt)	narJ →	molybdenum‑cofactor‑assembly chaperone delta subunit of nitrate reductase 1
RA	1,302,827	G→A	7.1%	intergenic (+14/‑72)	oppA → / → oppB	oligopeptide ABC transporter periplasmic binding protein/oligopeptide ABC transporter permease
RA	1,302,834	G→C	8.6%	intergenic (+21/‑65)	oppA → / → oppB	oligopeptide ABC transporter periplasmic binding protein/oligopeptide ABC transporter permease
RA	1,302,835	T→A	8.6%	intergenic (+22/‑64)	oppA → / → oppB	oligopeptide ABC transporter periplasmic binding protein/oligopeptide ABC transporter permease
RA	1,302,836	G→C	8.6%	intergenic (+23/‑63)	oppA → / → oppB	oligopeptide ABC transporter periplasmic binding protein/oligopeptide ABC transporter permease
RA	1,303,657	T→A	6.4%	I253I (ATT→ATA)	oppB →	oligopeptide ABC transporter permease
RA	1,303,658	T→A	6.1%	Y254N (TAT→AAT)	oppB →	oligopeptide ABC transporter permease
RA	1,304,469	C→G	7.3%	R212R (CGC→CGG)	oppC →	oligopeptide ABC transporter permease
RA	1,304,474	T→A	10.1%	I214N (ATT→AAT)	oppC →	oligopeptide ABC transporter permease
RA	1,304,479	C→G	10.5%	P216A (CCG→GCG)	oppC →	oligopeptide ABC transporter permease
RA	1,324,837	A→C	16.1%	Y31S (TAT→TCT) ‡	yciQ →	enhancer of membrane protein expression; putative inner membrane protein
RA	1,324,838	T→A	17.1%	Y31* (TAT→TAA) ‡	yciQ →	enhancer of membrane protein expression; putative inner membrane protein
RA	1,324,839	G→T	20.4%	E32* (GAA→TAA)	yciQ →	enhancer of membrane protein expression; putative inner membrane protein
RA	1,327,213	C→T	6.2%	T121I (ACC→ATC)	rluB →	23S rRNA pseudouridine(2605) synthase
RA	1,327,216	A→G	7.6%	D122G (GAT→GGT)	rluB →	23S rRNA pseudouridine(2605) synthase
RA	1,335,681	T→C	8.0%	intergenic (+223/‑150)	yciX → / → acnA	uncharacterized protein/aconitate hydratase 1; aconitase A
RA	1,344,033	A→G	11.3%	L105P (CTG→CCG)	yciT ←	global regulator of transcription; DeoR family
RA	1,344,036	G→C	11.3%	T104S (ACT→AGT)	yciT ←	global regulator of transcription; DeoR family
RA	1,344,039	C→T	10.4%	R103Q (CGG→CAG)	yciT ←	global regulator of transcription; DeoR family
RA	1,346,770	G→C	6.1%	intergenic (‑28/‑26)	gmr ← / → ymiB	cyclic‑di‑GMP phosphodiesterase; csgD regulator; modulator of RNase II stability/uncharacterized protein
RA	1,357,224	G→A	5.6%	intergenic (‑114/+199)	sapA ← / ← ymjA	antimicrobial peptide transport ABC transporter periplasmic binding protein/DUF2543 family protein
RA	1,357,227	A→G	5.7%	intergenic (‑117/+196)	sapA ← / ← ymjA	antimicrobial peptide transport ABC transporter periplasmic binding protein/DUF2543 family protein
RA	1,357,230	T→A	5.5%	intergenic (‑120/+193)	sapA ← / ← ymjA	antimicrobial peptide transport ABC transporter periplasmic binding protein/DUF2543 family protein
RA	1,357,233	C→T	5.6%	intergenic (‑123/+190)	sapA ← / ← ymjA	antimicrobial peptide transport ABC transporter periplasmic binding protein/DUF2543 family protein
RA	1,357,236	T→C	5.5%	intergenic (‑126/+187)	sapA ← / ← ymjA	antimicrobial peptide transport ABC transporter periplasmic binding protein/DUF2543 family protein
RA	1,359,877	C→A	13.0%	Q344H (CAG→CAT) ‡	puuA ←	glutamate‑‑putrescine ligase
RA	1,359,878	T→G	12.8%	Q344P (CAG→CCG) ‡	puuA ←	glutamate‑‑putrescine ligase
RA	1,375,064	C→T	11.2%	G34G (GGC→GGT)	ycjQ →	putative Zn‑dependent NAD(P)‑binding oxidoreductase
RA	1,375,067	A→G	10.8%	A35A (GCA→GCG)	ycjQ →	putative Zn‑dependent NAD(P)‑binding oxidoreductase
RA	1,381,915	G→T	6.3%	intergenic (+13/‑32)	ycjV → / → ompG	pseudogene; putative ATP‑binding component of a transport system/outer membrane porin G
RA	1,381,918	A→C	6.5%	intergenic (+16/‑29)	ycjV → / → ompG	pseudogene; putative ATP‑binding component of a transport system/outer membrane porin G
RA	1,385,650	A→G	5.1%	E47G (GAA→GGA)	ycjF →	UPF0283 family inner membrane protein
RA	1,386,750	C→G	7.3%	L11V (CTC→GTC)	tyrR →	aromatic amino acid biosynthesis and transport regulon transcriptional regulator; autorepressor; ATPase; phosphatase
RA	1,388,283	C→T	17.9%	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	20.0%	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	20.8%	intergenic (+24/+20)	tyrR → / ← tpx	aromatic amino acid biosynthesis and transport regulon transcriptional regulator; autorepressor; ATPase; phosphatase/lipid hydroperoxide peroxidase
RA	1,406,093	A→G	7.5%	I39V (ATC→GTC)	smrA →	DNA endonuclease
RA	1,406,098	C→T	8.6%	D40D (GAC→GAT)	smrA →	DNA endonuclease
RA	1,426,178	A→T	10.3%	intergenic (+96/‑276)	ydaY → / → tmpR	pseudogene, Rac prophage;Phage or Prophage Related/Rac prophage; pseudogene, tail protein family;Phage or Prophage Related; putative alpha helix protein
RA	1,441,833	G→C	10.0%	intergenic (‑90/+21)	hslJ ← / ← ldhA	heat‑inducible lipoprotein involved in novobiocin resistance/fermentative D‑lactate dehydrogenase, NAD‑dependent
RA	1,441,835	A→T	9.8%	intergenic (‑92/+19)	hslJ ← / ← ldhA	heat‑inducible lipoprotein involved in novobiocin resistance/fermentative D‑lactate dehydrogenase, NAD‑dependent
RA	1,441,837	G→C	9.8%	intergenic (‑94/+17)	hslJ ← / ← ldhA	heat‑inducible lipoprotein involved in novobiocin resistance/fermentative D‑lactate dehydrogenase, NAD‑dependent
RA	1,451,536	A→G	9.1%	intergenic (‑187/+61)	tynA ← / ← paaZ	tyramine oxidase, copper‑requiring/oxepin‑CoA hydrolase and 3‑oxo‑5,6‑dehydrosuberyl‑CoA semialdehyde dehydrogenase
RA	1,451,537	A→T	9.0%	intergenic (‑188/+60)	tynA ← / ← paaZ	tyramine oxidase, copper‑requiring/oxepin‑CoA hydrolase and 3‑oxo‑5,6‑dehydrosuberyl‑CoA semialdehyde dehydrogenase
RA	1,451,538	C→T	8.6%	intergenic (‑189/+59)	tynA ← / ← paaZ	tyramine oxidase, copper‑requiring/oxepin‑CoA hydrolase and 3‑oxo‑5,6‑dehydrosuberyl‑CoA semialdehyde dehydrogenase
RA	1,456,819	T→A	6.4%	I130I (ATT→ATA)	paaE →	ring 1,2‑phenylacetyl‑CoA epoxidase, NAD(P)H oxidoreductase component
RA	1,462,028	G→A	6.8%	G379D (GGT→GAT) ‡	paaJ →	3‑oxoadipyl‑CoA/3‑oxo‑5,6‑dehydrosuberyl‑CoA thiolase
RA	1,462,029	T→C	6.7%	G379G (GGT→GGC) ‡	paaJ →	3‑oxoadipyl‑CoA/3‑oxo‑5,6‑dehydrosuberyl‑CoA thiolase
RA	1,463,480	Δ1 bp	13.4%	intergenic (+42/‑59)	paaK → / → paaX	phenylacetyl‑CoA ligase/transcriptional repressor of phenylacetic acid degradation paa operon, phenylacetyl‑CoA inducer
RA	1,463,481	Δ1 bp	13.8%	intergenic (+43/‑58)	paaK → / → paaX	phenylacetyl‑CoA ligase/transcriptional repressor of phenylacetic acid degradation paa operon, phenylacetyl‑CoA inducer
RA	1,463,482	Δ1 bp	13.4%	intergenic (+44/‑57)	paaK → / → paaX	phenylacetyl‑CoA ligase/transcriptional repressor of phenylacetic acid degradation paa operon, phenylacetyl‑CoA inducer
RA	1,488,492	T→C	5.8%	S87S (AGT→AGC)	aldA →	aldehyde dehydrogenase A, NAD‑linked
RA	1,488,495	G→A	6.2%	A88A (GCG→GCA)	aldA →	aldehyde dehydrogenase A, NAD‑linked
RA	1,499,361	A→G	5.6%	N142D (AAC→GAC)	rimL →	ribosomal‑protein‑L7/L12‑serine acetyltransferase
RA	1,499,365	A→T	5.5%	Q143L (CAG→CTG)	rimL →	ribosomal‑protein‑L7/L12‑serine acetyltransferase
RA	1,499,369	C→T	5.5%	V144V (GTC→GTT)	rimL →	ribosomal‑protein‑L7/L12‑serine acetyltransferase
RA	1,507,492	Δ1 bp	6.3%	coding (712/1962 nt)	ydcP →	putative peptidase
RA	1,507,500	G→T	7.8%	K240N (AAG→AAT)	ydcP →	putative peptidase
RA	1,507,501	A→C	7.8%	I241L (ATT→CTT)	ydcP →	putative peptidase
RA	1,509,243	C→T	8.2%	intergenic (‑179/‑43)	yncJ ← / → hicA	uncharacterized protein/mRNA interferase toxin of the HicAB toxin‑antitoxin system
RA	1,509,246	A→G	7.7%	intergenic (‑182/‑40)	yncJ ← / → hicA	uncharacterized protein/mRNA interferase toxin of the HicAB toxin‑antitoxin system
RA	1,517,481	C→G	17.4%	R31R (CGC→CGG)	ydcX →	DUF2566 family protein
RA	1,517,484	C→G	16.7%	I32M (ATC→ATG)	ydcX →	DUF2566 family protein
RA	1,541,077	G→C	11.5%	A505G (GCC→GGC)	narZ ←	nitrate reductase 2 (NRZ), alpha subunit
RA	1,572,928	C→G	10.0%	A759P (GCA→CCA)	pqqL ←	putative periplasmic M16 family zinc metalloendopeptidase
RA	1,579,563	G→T	6.9%	intergenic (‑221/+70)	yddA ← / ← ydeM	putative multidrug ABC transporter permease/ATPase/putative YdeN‑specific sulfatase‑maturating enzyme
RA	1,579,564	G→A	6.9%	intergenic (‑222/+69)	yddA ← / ← ydeM	putative multidrug ABC transporter permease/ATPase/putative YdeN‑specific sulfatase‑maturating enzyme
RA	1,579,569	T→C	6.2%	intergenic (‑227/+64)	yddA ← / ← ydeM	putative multidrug ABC transporter permease/ATPase/putative YdeN‑specific sulfatase‑maturating enzyme
RA	1,579,570	A→C	6.3%	intergenic (‑228/+63)	yddA ← / ← ydeM	putative multidrug ABC transporter permease/ATPase/putative YdeN‑specific sulfatase‑maturating enzyme
RA	1,585,149	Δ1 bp	11.0%	coding (1338/2280 nt)	ydeP ←	putative oxidoreductase
RA	1,585,156:1	+C	9.2%	coding (1331/2280 nt)	ydeP ←	putative oxidoreductase
RA	1,609,555	Δ1 bp	5.4%	coding (1126/1452 nt)	uxaB ←	altronate oxidoreductase, NAD‑dependent
RA	1,609,561:1	+C	6.5%	coding (1120/1452 nt)	uxaB ←	altronate oxidoreductase, NAD‑dependent
RA	1,620,224	C→G	10.0%	intergenic (+17/+14)	marB → / ← eamA	periplasmic mar operon regulator/cysteine and O‑acetyl‑L‑serine efflux system
RA	1,620,227	C→G	11.1%	intergenic (+20/+11)	marB → / ← eamA	periplasmic mar operon regulator/cysteine and O‑acetyl‑L‑serine efflux system
RA	1,642,370	C→G	15.4%	intergenic (+303/+119)	cspF → / ← quuQ	Qin prophage; cold shock protein/Qin prophage; putative antitermination protein Q
RA	1,642,373	C→G	15.4%	intergenic (+306/+116)	cspF → / ← quuQ	Qin prophage; cold shock protein/Qin prophage; putative antitermination protein Q
RA	1,643,773	C→G	5.7%	A178P (GCA→CCA)	ydfU ←	Qin prophage; uncharacterized protein
RA	1,643,776	C→G	5.4%	D177H (GAT→CAT)	ydfU ←	Qin prophage; uncharacterized protein
RA	1,643,780	C→T	5.2%	V175V (GTG→GTA)	ydfU ←	Qin prophage; uncharacterized protein
RA	1,660,438	A→G	8.3%	S790S (TCA→TCG)	ynfE →	putative selenate reductase, periplasmic
RA	1,660,442	C→G	8.6%	L792V (CTG→GTG)	ynfE →	putative selenate reductase, periplasmic
RA	1,660,446	C→T	8.9%	A793V (GCG→GTG)	ynfE →	putative selenate reductase, periplasmic
RA	1,666,466	T→G	16.7%	Y384* (TAT→TAG)	clcB →	H(+)/Cl(‑) exchange transporter
RA	1,666,468	A→T	17.8%	Q385L (CAG→CTG)	clcB →	H(+)/Cl(‑) exchange transporter
RA	1,666,470	C→A	15.5%	L386I (CTA→ATA)	clcB →	H(+)/Cl(‑) exchange transporter
RA	1,681,622	T→A	5.6%	L216Q (CTG→CAG)	folM →	dihydromonapterin reductase, NADPH‑dependent; dihydrofolate reductase isozyme
RA	1,684,016	A→G	8.5%	S379G (AGC→GGC)	rstB →	sensory histidine kinase of RstAB two‑component system
RA	1,684,019	C→T	8.5%	R380W (CGG→TGG)	rstB →	sensory histidine kinase of RstAB two‑component system
RA	1,685,527	A→G	100%	G354G (GGT→GGC)	fumC ←	fumarate hydratase (fumarase C),aerobic Class II
RA	1,689,817	C→A	23.5%	intergenic (+66/‑35)	manA → / → ydgA	mannose‑6‑phosphate isomerase/DUF945 family protein
RA	1,689,819	A→T	23.5%	intergenic (+68/‑33)	manA → / → ydgA	mannose‑6‑phosphate isomerase/DUF945 family protein
RA	1,689,821	T→G	23.5%	intergenic (+70/‑31)	manA → / → ydgA	mannose‑6‑phosphate isomerase/DUF945 family protein
RA	1,698,585	T→G	8.3%	E199A (GAA→GCA)	malI ←	transcriptional repressor of Mal regulon
RA	1,698,587	T→A	8.3%	A198A (GCA→GCT) ‡	malI ←	transcriptional repressor of Mal regulon
RA	1,698,589	C→A	8.3%	A198S (GCA→TCA) ‡	malI ←	transcriptional repressor of Mal regulon
RA	1,702,500	C→G	6.3%	H90D (CAC→GAC)	add →	adenosine deaminase
RA	1,702,505	C→G	6.5%	G91G (GGC→GGG)	add →	adenosine deaminase
RA	1,706,742	T→A	5.7%	I132N (ATC→AAC)	rsxB →	SoxR iron‑sulfur cluster reduction factor component; putative iron‑sulfur protein
RA	1,706,745	T→A	5.8%	V133D (GTT→GAT)	rsxB →	SoxR iron‑sulfur cluster reduction factor component; putative iron‑sulfur protein
RA	1,706,750:1	+T	5.3%	coding (403/579 nt)	rsxB →	SoxR iron‑sulfur cluster reduction factor component; putative iron‑sulfur protein
RA	1,712,337	A→T	8.7%	intergenic (+179/‑432)	nth → / → dtpA	DNA glycosylase and apyrimidinic (AP) lyase (endonuclease III)/dipeptide and tripeptide permease A
RA	1,712,338	A→T	8.7%	intergenic (+180/‑431)	nth → / → dtpA	DNA glycosylase and apyrimidinic (AP) lyase (endonuclease III)/dipeptide and tripeptide permease A
RA	1,718,588	A→T	9.1%	W339R (TGG→AGG)	anmK ←	anhydro‑N‑acetylmuramic acid kinase
RA	1,718,592	A→T	8.5%	L337L (CTT→CTA) ‡	anmK ←	anhydro‑N‑acetylmuramic acid kinase
RA	1,718,593	A→T	8.5%	L337H (CTT→CAT) ‡	anmK ←	anhydro‑N‑acetylmuramic acid kinase
RA	1,718,597	A→T	10.4%	W336R (TGG→AGG)	anmK ←	anhydro‑N‑acetylmuramic acid kinase
RA	1,721,507	A→C	6.9%	I82L (ATC→CTC)	ydhJ →	putative membrane fusion protein (MFP) of YdhJK efflux pump
RA	1,721,511	C→G	6.7%	A83G (GCC→GGC)	ydhJ →	putative membrane fusion protein (MFP) of YdhJK efflux pump
RA	1,721,515	G→T	6.2%	E84D (GAG→GAT)	ydhJ →	putative membrane fusion protein (MFP) of YdhJK efflux pump
RA	1,736,097	T→A	11.1%	intergenic (+138/+24)	sodB → / ← ydhP	superoxide dismutase, Fe/putative MFS transporter, inner membrane protein
RA	1,736,100	T→A	11.3%	intergenic (+141/+21)	sodB → / ← ydhP	superoxide dismutase, Fe/putative MFS transporter, inner membrane protein
RA	1,743,155	C→G	10.2%	D30H (GAC→CAC)	ribC ←	riboflavin synthase, alpha subunit
RA	1,743,157	G→A	11.4%	P29L (CCC→CTC)	ribC ←	riboflavin synthase, alpha subunit
RA	1,743,160	A→T	10.9%	L28* (TTA→TAA)	ribC ←	riboflavin synthase, alpha subunit
RA	1,743,163	T→C	10.6%	E27G (GAG→GGG)	ribC ←	riboflavin synthase, alpha subunit
RA	1,743,165	C→G	12.1%	V26V (GTG→GTC)	ribC ←	riboflavin synthase, alpha subunit
RA	1,766,262	A→T	5.6%	F808L (TTT→TTA)	ydiJ ←	putative FAD‑linked oxidoreductase
RA	1,772,475	C→T	6.1%	intergenic (+190/‑37)	ydiM → / → ydiN	putative MFS transporter, membrane protein/putative MFS transporter, membrane protein
RA	1,778,372	C→G	46.2%	intergenic (+25/+18)	ydiO → / ← ydiP	putative acyl‑CoA dehydrogenase/putative DNA‑binding transcriptional regulator
RA	1,778,375	A→G	42.8%	intergenic (+28/+15)	ydiO → / ← ydiP	putative acyl‑CoA dehydrogenase/putative DNA‑binding transcriptional regulator
RA	1,789,082	G→T	7.9%	Q216H (CAG→CAT)	aroH →	3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, tryptophan repressible
RA	1,789,083	A→C	8.3%	M217L (ATG→CTG)	aroH →	3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, tryptophan repressible
RA	1,793,667	T→G	12.5%	E148A (GAA→GCA) ‡	btuE ←	glutathione peroxidase
RA	1,793,668	C→A	11.4%	E148* (GAA→TAA) ‡	btuE ←	glutathione peroxidase
RA	1,797,388	G→T	12.7%	P186Q (CCG→CAG)	pheT ←	phenylalanine tRNA synthetase, beta subunit
RA	1,797,391	A→C	9.1%	L185R (CTG→CGG)	pheT ←	phenylalanine tRNA synthetase, beta subunit
RA	1,799,370	Δ1 bp	8.7%	intergenic (‑100/+23)	pheM ← / ← rplT	phenylalanyl‑tRNA synthetase operon leader peptide/50S ribosomal subunit protein L20
RA	1,801,371	A→G	7.2%	C400C (TGT→TGC) ‡	thrS ←	threonyl‑tRNA synthetase
RA	1,801,372	C→T	7.1%	C400Y (TGT→TAT) ‡	thrS ←	threonyl‑tRNA synthetase
RA	1,810,062	T→C	14.3%	intergenic (+14/‑149)	yniC → / → ydjM	2‑deoxyglucose‑6‑P phosphatase/inner membrane protein regulated by LexA
RA	1,810,065	T→G	14.3%	intergenic (+17/‑146)	yniC → / → ydjM	2‑deoxyglucose‑6‑P phosphatase/inner membrane protein regulated by LexA
RA	1,810,066	C→A	14.2%	intergenic (+18/‑145)	yniC → / → ydjM	2‑deoxyglucose‑6‑P phosphatase/inner membrane protein regulated by LexA
RA	1,810,069	G→A	13.3%	intergenic (+21/‑142)	yniC → / → ydjM	2‑deoxyglucose‑6‑P phosphatase/inner membrane protein regulated by LexA
RA	1,827,811	T→G	9.4%	K150T (AAA→ACA)	astB ←	succinylarginine dihydrolase
RA	1,827,816	C→A	8.6%	L148L (CTG→CTT)	astB ←	succinylarginine dihydrolase
RA	1,835,582	A→G	7.7%	H23R (CAT→CGT)	ynjA →	carboxymuconolactone decarboxylase family protein
RA	1,835,584	T→A	7.7%	Y24N (TAC→AAC) ‡	ynjA →	carboxymuconolactone decarboxylase family protein
RA	1,835,586	C→T	7.7%	Y24Y (TAC→TAT) ‡	ynjA →	carboxymuconolactone decarboxylase family protein
RA	1,836,136	G→C	10.0%	D22H (GAC→CAC)	ynjB →	putative ABC transporter periplasmic binding protein
RA	1,843,965	G→T	7.0%	R303S (CGC→AGC)	ynjI ←	inner membrane protein
RA	1,844,375	T→G	5.7%	E166A (GAG→GCG)	ynjI ←	inner membrane protein
RA	1,844,378	C→A	5.7%	R165L (CGC→CTC)	ynjI ←	inner membrane protein
RA	1,856,333	T→G	13.9%	E199A (GAG→GCG) ‡	ydjH ←	putative kinase
RA	1,856,334	C→A	13.9%	E199* (GAG→TAG) ‡	ydjH ←	putative kinase
RA	1,861,425	A→C	5.6%	intergenic (‑93/+277)	ydjL ← / ← yeaC	putative Zn‑dependent NAD(P)‑binding oxidoreductase/DUF1315 family protein
RA	1,861,428	G→T	5.7%	intergenic (‑96/+274)	ydjL ← / ← yeaC	putative Zn‑dependent NAD(P)‑binding oxidoreductase/DUF1315 family protein
RA	1,863,257	A→G	5.5%	N163D (AAC→GAC) ‡	gapA →	glyceraldehyde‑3‑phosphate dehydrogenase A
RA	1,863,258	A→T	5.5%	N163I (AAC→ATC) ‡	gapA →	glyceraldehyde‑3‑phosphate dehydrogenase A
RA	1,863,259	C→T	5.4%	N163N (AAC→AAT) ‡	gapA →	glyceraldehyde‑3‑phosphate dehydrogenase A
RA	1,864,758	G→A	36.0%	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	48.0%	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	50.0%	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	25.0%	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	17.8%	intergenic (+17/‑96)	yeaG → / → yeaH	protein kinase, endogenous substrate unidentified; autokinase/UPF0229 family protein
RA	1,868,865:1	+G	10.3%	intergenic (+23/‑90)	yeaG → / → yeaH	protein kinase, endogenous substrate unidentified; autokinase/UPF0229 family protein
RA	1,880,851	T→A	9.5%	intergenic (‑92/+35)	leuE ← / ← dmlR	leucine efflux protein/transcriptional activator of dmlA
RA	1,880,852	T→A	9.4%	intergenic (‑93/+34)	leuE ← / ← dmlR	leucine efflux protein/transcriptional activator of dmlA
RA	1,891,841	A→G	15.2%	G465G (GGT→GGC) ‡	yoaA ←	putative ATP‑dependent helicase, DinG family
RA	1,891,842	C→T	15.7%	G465D (GGT→GAT) ‡	yoaA ←	putative ATP‑dependent helicase, DinG family
RA	1,898,075	G→A	5.1%	D382N (GAC→AAC)	sdaA →	L‑serine dehydratase 1
RA	1,926,888	C→A	17.0%	G651V (GGC→GTC)	ptrB ←	protease II
RA	1,926,891	G→C	18.4%	S650* (TCA→TGA)	ptrB ←	protease II
RA	1,926,894	T→G	15.5%	D649A (GAC→GCC)	ptrB ←	protease II
RA	1,926,900	T→G	20.0%	D647A (GAC→GCC)	ptrB ←	protease II
RA	1,928,799	A→C	10.4%	L14R (CTT→CGT)	ptrB ←	protease II
RA	1,928,802	G→T	9.5%	T13K (ACG→AAG)	ptrB ←	protease II
RA	1,948,179	T→A	6.8%	intergenic (‑28/+1)	yebC ← / ← nudB	UPF0082 family protein/dihydroneopterin triphosphate pyrophosphatase
RA	1,948,180	T→A	6.7%	*151C (TGA→TGT)	nudB ←	dihydroneopterin triphosphate pyrophosphatase
RA	1,950,292	C→G	7.2%	A77A (GCG→GCC)	aspS ←	aspartyl‑tRNA synthetase
RA	1,950,295:1	+C	7.3%	coding (228/1773 nt)	aspS ←	aspartyl‑tRNA synthetase
RA	1,950,301	Δ1 bp	7.5%	coding (222/1773 nt)	aspS ←	aspartyl‑tRNA synthetase
RA	1,950,306	C→G	7.5%	G73R (GGC→CGC)	aspS ←	aspartyl‑tRNA synthetase
RA	1,954,256	T→A	6.6%	I272N (ATT→AAT)	cmoB →	tRNA (cmo5U34)‑carboxymethyltransferase, carboxy‑SAM‑dependent
RA	1,960,127	G→C	5.9%	A22A (GCG→GCC)	argS →	arginyl‑tRNA synthetase
RA	1,968,073	T→C	5.0%	A143A (GCA→GCG) ‡	cheB ←	fused chemotaxis regulator: protein‑glutamate methylesterase in two‑component regulatory system with CheA
RA	1,968,074	G→A	5.1%	A143V (GCA→GTA) ‡	cheB ←	fused chemotaxis regulator: protein‑glutamate methylesterase in two‑component regulatory system with CheA
MC JC	1,978,503	Δ776 bp	100%		insB1–insA	insB1, insA
RA	1,985,112	C→G	17.9%	intergenic (‑43/+27)	araG ← / ← araF	L‑arabinose ABC transporter ATPase/L‑arabinose ABC transporter periplasmic binding protein
RA	1,986,176	A→T	8.5%	intergenic (‑48/‑749)	araF ← / → ftnB	L‑arabinose ABC transporter periplasmic binding protein/ferritin B, putative ferrous iron reservoir
RA	1,987,442	Δ1 bp	14.3%	intergenic (+14/+65)	ftnB → / ← yecJ	ferritin B, putative ferrous iron reservoir/DUF2766 family protein
RA	1,991,866	T→A	8.0%	noncoding (36/87 nt)	leuZ ←	tRNA‑Leu
RA	2,008,406	G→A	6.5%	E44K (GAA→AAA)	yedE →	UPF0394 family sulphur transport domain‑containing inner membrane protein
RA	2,020,838	T→C	5.5%	V251A (GTG→GCG)	fliM →	flagellar motor switching and energizing component
RA	2,020,841	G→A	5.5%	R252H (CGC→CAC)	fliM →	flagellar motor switching and energizing component
RA	2,028,158	G→C	20.6%	intergenic (‑141/+30)	yedQ ← / ← yodC	putative membrane‑anchored diguanylate cyclase/uncharacterized protein
RA	2,028,159	T→A	20.0%	intergenic (‑142/+29)	yedQ ← / ← yodC	putative membrane‑anchored diguanylate cyclase/uncharacterized protein
RA	2,028,160	G→C	20.0%	intergenic (‑143/+28)	yedQ ← / ← yodC	putative membrane‑anchored diguanylate cyclase/uncharacterized protein
RA	2,028,171	A→G	11.4%	intergenic (‑154/+17)	yedQ ← / ← yodC	putative membrane‑anchored diguanylate cyclase/uncharacterized protein
RA	2,035,593	G→A	6.4%	intergenic (+350/‑242)	yedS → / → hchA	pseudogene, outer membrane protein homology; putative outer membrane protein/glyoxalase III and Hsp31 molecular chaperone
RA	2,041,159	G→A	8.0%	intergenic (+41/‑216)	yedZ → / → zinT	inner membrane heme subunit for periplasmic YedYZ reductase/zinc and cadmium binding protein, periplasmic
RA	2,041,160	T→G	8.0%	intergenic (+42/‑215)	yedZ → / → zinT	inner membrane heme subunit for periplasmic YedYZ reductase/zinc and cadmium binding protein, periplasmic
RA	2,041,166	G→T	9.1%	intergenic (+48/‑209)	yedZ → / → zinT	inner membrane heme subunit for periplasmic YedYZ reductase/zinc and cadmium binding protein, periplasmic
RA	2,041,167	A→C	10.0%	intergenic (+49/‑208)	yedZ → / → zinT	inner membrane heme subunit for periplasmic YedYZ reductase/zinc and cadmium binding protein, periplasmic
RA	2,059,939	G→T	12.3%	intergenic (+13/+25)	asnU → / ← cbl	tRNA‑Asn/ssuEADCB/tauABCD operon transcriptional activator
RA	2,059,946	T→A	11.9%	intergenic (+20/+18)	asnU → / ← cbl	tRNA‑Asn/ssuEADCB/tauABCD operon transcriptional activator
RA	2,059,948	T→A	13.2%	intergenic (+22/+16)	asnU → / ← cbl	tRNA‑Asn/ssuEADCB/tauABCD operon transcriptional activator
RA	2,059,950	T→A	13.2%	intergenic (+24/+14)	asnU → / ← cbl	tRNA‑Asn/ssuEADCB/tauABCD operon transcriptional activator
RA	2,065,864	G→A	6.1%	intergenic (‑100/+204)	cobU ← / ← yeeH	cobinamide kinase and cobinamide phosphate guanylyltransferase/pseudogene
RA	2,074,691	C→G	23.5%	intergenic (+33/‑88)	flu → / → yeeR	CP4‑44 prophage; antigen 43 (Ag43) phase‑variable biofilm formation autotransporter/CP4‑44 prophage; putative membrane protein
RA	2,074,810	Δ1 bp	8.7%	coding (32/1533 nt)	yeeR →	CP4‑44 prophage; putative membrane protein
RA	2,074,814:1	+A	8.3%	coding (36/1533 nt)	yeeR →	CP4‑44 prophage; putative membrane protein
RA	2,079,004	G→C	19.0%	intergenic (+73/+28)	yoeF → / ← yeeX	pseudogene, CP4‑44 putative prophage remnant;Phage or Prophage Related/UPF0265 family protein
RA	2,081,688	A→T	23.8%	I287N (ATT→AAT)	dacD ←	D‑alanyl‑D‑alanine carboxypeptidase; penicillin‑binding protein 6b
RA	2,089,854	A→T	15.4%	intergenic (‑141/‑142)	yefM ← / → hisL	antitoxin of the YoeB‑YefM toxin‑antitoxin system/his operon leader peptide
RA	2,090,122	A→G	60.9%	intergenic (+76/‑70)	hisL → / → hisG	his operon leader peptide/ATP phosphoribosyltransferase
RA	2,090,124	C→G	63.7%	intergenic (+78/‑68)	hisL → / → hisG	his operon leader peptide/ATP phosphoribosyltransferase
RA	2,090,126	C→T	73.7%	intergenic (+80/‑66)	hisL → / → hisG	his operon leader peptide/ATP phosphoribosyltransferase
RA	2,115,847	G→T	11.9%	A17E (GCG→GAG)	wcaM ←	colanic acid biosynthesis protein
RA	2,115,849	C→G	11.9%	S16S (TCG→TCC) ‡	wcaM ←	colanic acid biosynthesis protein
RA	2,115,851	A→C	11.9%	S16A (TCG→GCG) ‡	wcaM ←	colanic acid biosynthesis protein
RA	2,123,257	C→T	5.1%	D422N (GAT→AAT)	cpsB ←	mannose‑1‑phosphate guanyltransferase
RA	2,123,258	A→G	5.2%	I421I (ATT→ATC)	cpsB ←	mannose‑1‑phosphate guanyltransferase
RA	2,130,803	G→T	5.1%	Q26K (CAG→AAG)	wcaD ←	putative colanic acid polymerase
RA	2,139,709	G→A	7.1%	intergenic (+224/+50)	yegH → / ← asmA	inner membrane protein/suppressor of OmpF assembly mutants; putative outer membrane protein assembly factor; inner membrane‑anchored periplasmic protein
RA	2,139,710	C→A	7.1%	intergenic (+225/+49)	yegH → / ← asmA	inner membrane protein/suppressor of OmpF assembly mutants; putative outer membrane protein assembly factor; inner membrane‑anchored periplasmic protein
RA	2,139,716	T→G	7.4%	intergenic (+231/+43)	yegH → / ← asmA	inner membrane protein/suppressor of OmpF assembly mutants; putative outer membrane protein assembly factor; inner membrane‑anchored periplasmic protein
RA	2,139,718	T→A	7.4%	intergenic (+233/+41)	yegH → / ← asmA	inner membrane protein/suppressor of OmpF assembly mutants; putative outer membrane protein assembly factor; inner membrane‑anchored periplasmic protein
RA	2,139,720	C→A	8.9%	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	2,139,726	T→G	9.1%	intergenic (+241/+33)	yegH → / ← asmA	inner membrane protein/suppressor of OmpF assembly mutants; putative outer membrane protein assembly factor; inner membrane‑anchored periplasmic protein
RA	2,139,727	T→C	9.1%	intergenic (+242/+32)	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	2,160,692	C→T	5.7%	I769I (ATC→ATT)	mdtC →	multidrug efflux system, subunit C
RA	2,165,626	T→C	7.7%	intergenic (+105/‑42)	yegP → / → yegQ	UPF0339 family protein/putative peptidase
RA	2,165,628	A→T	7.5%	intergenic (+107/‑40)	yegP → / → yegQ	UPF0339 family protein/putative peptidase
RA	2,165,630	G→A	8.2%	intergenic (+109/‑38)	yegP → / → yegQ	UPF0339 family protein/putative peptidase
RA	2,169,075	A→G	5.3%	I122V (ATT→GTT)	yegS →	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	2,177,427	T→G	5.5%	intergenic (‑223/+85)	gatY ← / ← fbaB	D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I
RA	2,177,428	C→A	5.3%	intergenic (‑224/+84)	gatY ← / ← fbaB	D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I
RA	2,187,314	C→G	22.2%	intergenic (+16/+66)	rcnB → / ← yehA	periplasmic modulator of Ni and Co efflux/putative fimbrial‑like adhesin protein
RA	2,211,186	G→C	5.3%	intergenic (+86/‑39)	yehQ → / → yehR	pseudogene/lipoprotein, DUF1307 family
RA	2,211,187	A→T	5.3%	intergenic (+87/‑38)	yehQ → / → yehR	pseudogene/lipoprotein, DUF1307 family
RA	2,211,188	G→C	5.2%	intergenic (+88/‑37)	yehQ → / → yehR	pseudogene/lipoprotein, DUF1307 family
RA	2,220,357	G→C	6.3%	L545V (CTG→GTG)	bglX ←	beta‑D‑glucoside glucohydrolase, periplasmic
RA	2,229,322	C→G	48.0%	intergenic (+257/+116)	yohP → / ← dusC	uncharacterized protein/tRNA‑dihydrouridine synthase C
RA	2,229,323	C→G	48.0%	intergenic (+258/+115)	yohP → / ← dusC	uncharacterized protein/tRNA‑dihydrouridine synthase C
RA	2,255,991	A→T	12.5%	K213* (AAA→TAA) ‡	yeiL →	putative transcriptional regulator
RA	2,255,992	A→T	12.5%	K213I (AAA→ATA) ‡	yeiL →	putative transcriptional regulator
RA	2,258,165	A→T	5.6%	I68N (ATT→AAT)	psuG ←	pseudouridine 5'‑phosphate glycosidase
RA	2,258,168	A→T	5.6%	I67N (ATT→AAT)	psuG ←	pseudouridine 5'‑phosphate glycosidase
RA	2,279,708	A→T	9.4%	L18Q (CTG→CAG)	bcr ←	bicyclomycin/cysteine/sulfonamide efflux transporter
RA	2,279,711	A→T	9.5%	L17Q (CTG→CAG)	bcr ←	bicyclomycin/cysteine/sulfonamide efflux transporter
RA	2,286,139	A→T	11.4%	intergenic (+3/‑72)	yejM → / → proL	essential inner membrane DUF3413 domain‑containing protein; lipid A production and membrane permeability factor/tRNA‑Pro
RA	2,286,142	T→A	12.1%	intergenic (+6/‑69)	yejM → / → proL	essential inner membrane DUF3413 domain‑containing protein; lipid A production and membrane permeability factor/tRNA‑Pro
RA	2,286,145	A→T	12.1%	intergenic (+9/‑66)	yejM → / → proL	essential inner membrane DUF3413 domain‑containing protein; lipid A production and membrane permeability factor/tRNA‑Pro
RA	2,297,451	T→A	6.2%	Q65L (CAG→CTG)	ccmA ←	heme export ABC transporter ATPase
RA	2,302,452	A→C	7.3%	L101R (CTG→CGG)	napA ←	nitrate reductase, periplasmic, large subunit
RA	2,302,455	G→T	7.3%	P100Q (CCG→CAG)	napA ←	nitrate reductase, periplasmic, large subunit
RA	2,304,762	T→C	11.4%	intergenic (+369/+346)	eco → / ← mqo	ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA	2,312,170	G→C	11.4%	L194V (CTG→GTG)	ompC ←	outer membrane porin protein C
RA	2,314,800	A→C	5.6%	Q438P (CAG→CCG) ‡	rcsD →	phosphotransfer intermediate protein in two‑component regulatory system with RcsBC
RA	2,314,801	G→T	5.6%	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	2,318,693	G→T	7.5%	T395K (ACG→AAG)	rcsC ←	hybrid sensory kinase in two‑component regulatory system with RcsB and YojN
RA	2,318,696	A→C	8.0%	L394R (CTT→CGT)	rcsC ←	hybrid sensory kinase in two‑component regulatory system with RcsB and YojN
RA	2,322,146	Δ1 bp	5.9%	coding (281/1386 nt)	atoC →	fused response regulator of ato operon, in two‑component system with AtoS: response regulator/sigma54 interaction protein
RA	2,322,150	A→C	5.3%	L95L (CTA→CTC)	atoC →	fused response regulator of ato operon, in two‑component system with AtoS: response regulator/sigma54 interaction protein
RA	2,322,158	G→T	5.2%	G98V (GGA→GTA)	atoC →	fused response regulator of ato operon, in two‑component system with AtoS: response regulator/sigma54 interaction protein
RA	2,348,795	T→A	5.4%	intergenic (+27/+27)	yfaE → / ← inaA	ferredoxin involved with ribonucleotide reductase diferric‑tyrosyl radical (Y*) cofactor maintenance/acid‑inducible Kdo/WaaP family putative kinase
RA	2,348,798	T→A	6.0%	intergenic (+30/+24)	yfaE → / ← inaA	ferredoxin involved with ribonucleotide reductase diferric‑tyrosyl radical (Y*) cofactor maintenance/acid‑inducible Kdo/WaaP family putative kinase
RA	2,348,803	C→T	6.1%	intergenic (+35/+19)	yfaE → / ← inaA	ferredoxin involved with ribonucleotide reductase diferric‑tyrosyl radical (Y*) cofactor maintenance/acid‑inducible Kdo/WaaP family putative kinase
RA	2,348,804	T→G	5.9%	intergenic (+36/+18)	yfaE → / ← inaA	ferredoxin involved with ribonucleotide reductase diferric‑tyrosyl radical (Y*) cofactor maintenance/acid‑inducible Kdo/WaaP family putative kinase
RA	2,364,995	T→G	9.8%	intergenic (+16/+23)	nudI → / ← ais	nucleoside triphosphatase/putative LPS core heptose(II)‑phosphate phosphatase
RA	2,367,637	T→G	6.1%	N189K (AAT→AAG)	arnC →	undecaprenyl phosphate‑L‑Ara4FN transferase
RA	2,367,640	C→A	6.1%	I190I (ATC→ATA)	arnC →	undecaprenyl phosphate‑L‑Ara4FN transferase
RA	2,375,483	A→T	9.5%	L160L (CTT→CTA) ‡	menC ←	O‑succinylbenzoyl‑CoA synthase
RA	2,375,484	A→T	9.5%	L160H (CTT→CAT) ‡	menC ←	O‑succinylbenzoyl‑CoA synthase
RA	2,383,956	A→T	21.8%	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	27.0%	intergenic (+35/+36)	elaD → / ← yfbK	protease, capable of cleaving an AMC‑ubiquitin model substrate/Von Willebrand factor domain putative lipoprotein
RA	2,387,587	T→A	5.6%	intergenic (+150/+123)	yfbM → / ← yfbN	DUF1877 family protein/uncharacterized protein
RA	2,391,414	C→G	9.3%	R31P (CGA→CCA)	nuoN ←	NADH:ubiquinone oxidoreductase, membrane subunit N
RA	2,391,417	C→G	9.2%	W30S (TGG→TCG)	nuoN ←	NADH:ubiquinone oxidoreductase, membrane subunit N
RA	2,400,684	T→A	5.4%	Q291L (CAG→CTG)	nuoF ←	NADH:ubiquinone oxidoreductase, chain F
RA	2,407,890	Δ1 bp	6.4%	coding (330/1218 nt)	alaA →	glutamate‑pyruvate aminotransferase; glutamic‑pyruvic transaminase (GPT); alanine transaminase
RA	2,407,898	A→C	5.6%	Q113P (CAG→CCG) ‡	alaA →	glutamate‑pyruvate aminotransferase; glutamic‑pyruvic transaminase (GPT); alanine transaminase
RA	2,407,899	G→T	5.7%	Q113H (CAG→CAT) ‡	alaA →	glutamate‑pyruvate aminotransferase; glutamic‑pyruvic transaminase (GPT); alanine transaminase
RA	2,411,963	T→C	6.3%	I43V (ATT→GTT)	yfbT ←	sugar phosphatas
RA	2,412,639	T→A	5.6%	intergenic (‑45/+38)	yfbU ← / ← yfbV	UPF0304 family protein/UPF0208 family inner membrane protein
RA	2,412,640	G→T	5.4%	intergenic (‑46/+37)	yfbU ← / ← yfbV	UPF0304 family protein/UPF0208 family inner membrane protein
RA	2,412,642	G→C	5.7%	intergenic (‑48/+35)	yfbU ← / ← yfbV	UPF0304 family protein/UPF0208 family inner membrane protein
RA	2,412,644	A→C	5.8%	intergenic (‑50/+33)	yfbU ← / ← yfbV	UPF0304 family protein/UPF0208 family inner membrane protein
RA	2,412,645	T→A	5.9%	intergenic (‑51/+32)	yfbU ← / ← yfbV	UPF0304 family protein/UPF0208 family inner membrane protein
RA	2,415,725	C→A	7.0%	L327M (CTG→ATG) ‡	pta →	phosphate acetyltransferase
RA	2,415,726	T→G	7.0%	L327R (CTG→CGG) ‡	pta →	phosphate acetyltransferase
RA	2,421,856	G→C	5.9%	G50A (GGG→GCG) ‡	yfcH →	putative NAD‑dependent nucleotide‑sugar epimerase
RA	2,421,857	G→C	6.6%	G50G (GGG→GGC) ‡	yfcH →	putative NAD‑dependent nucleotide‑sugar epimerase
RA	2,425,968	T→G	5.1%	intergenic (‑52/+38)	hisQ ← / ← hisJ	histidine ABC transporter permease/histidine ABC transporter periplasmic binding protein
RA	2,430,144	G→C	6.5%	A32G (GCC→GGC)	purF ←	amidophosphoribosyltransferase
RA	2,440,865	C→T	6.1%	L247L (CTG→CTA) ‡	fabB ←	3‑oxoacyl‑[acyl‑carrier‑protein] synthase I
RA	2,440,866	A→G	6.1%	L247P (CTG→CCG) ‡	fabB ←	3‑oxoacyl‑[acyl‑carrier‑protein] synthase I
RA	2,449,607:1	+G	8.0%	coding (443/822 nt)	yfcO ←	DUF2544 family putative outer membrane protein
RA	2,449,615	C→G	8.2%	G145G (GGG→GGC) ‡	yfcO ←	DUF2544 family putative outer membrane protein
RA	2,449,616	C→G	8.2%	G145A (GGG→GCG) ‡	yfcO ←	DUF2544 family putative outer membrane protein
RA	2,457,128	T→A	7.6%	M678L (ATG→TTG)	fadJ ←	enoyl‑CoA hydratase/epimerase and isomerase/3‑hydroxyacyl‑CoA dehydrogenase
RA	2,457,131	T→A	7.7%	I677L (ATA→TTA)	fadJ ←	enoyl‑CoA hydratase/epimerase and isomerase/3‑hydroxyacyl‑CoA dehydrogenase
RA	2,474,878	T→C	24.2%	intergenic (+22/‑106)	yfdQ → / → yfdR	CPS‑53 (KpLE1) prophage; uncharacterized protein/CPS‑53 (KpLE1) prophage; conserved protein
RA	2,474,881	G→A	30.8%	intergenic (+25/‑103)	yfdQ → / → yfdR	CPS‑53 (KpLE1) prophage; uncharacterized protein/CPS‑53 (KpLE1) prophage; conserved protein
RA	2,491,264	T→A	6.2%	E229D (GAA→GAT) ‡	oxc ←	oxalyl CoA decarboxylase, ThDP‑dependent
RA	2,491,266	C→G	7.1%	E229Q (GAA→CAA) ‡	oxc ←	oxalyl CoA decarboxylase, ThDP‑dependent
RA	2,491,268	T→A	7.0%	D228V (GAT→GTT)	oxc ←	oxalyl CoA decarboxylase, ThDP‑dependent
RA	2,516,076	T→C	5.4%	Q586R (CAA→CGA)	yfeA ←	putative diguanylate cyclase
RA	2,518,082	C→G	6.1%	noncoding (35/76 nt)	alaX ←	tRNA‑Ala
RA	2,518,197	C→G	6.7%	noncoding (35/76 nt)	alaW ←	tRNA‑Ala
RA	2,519,222	T→G	15.4%	intergenic (+17/+35)	yfeD → / ← gltX	DUF1323 family putative DNA‑binding protein/glutamyl‑tRNA synthetase
RA	2,519,225	T→A	12.5%	intergenic (+20/+32)	yfeD → / ← gltX	DUF1323 family putative DNA‑binding protein/glutamyl‑tRNA synthetase
RA	2,519,228	C→A	13.0%	intergenic (+23/+29)	yfeD → / ← gltX	DUF1323 family putative DNA‑binding protein/glutamyl‑tRNA synthetase
RA	2,549,556	C→G	10.1%	intergenic (+150/+90)	yfeW → / ← yfeX	penicillin binding protein PBP4B; weak DD‑carboxypeptidase activity/porphyrinogen oxidase, cytoplasmic
RA	2,549,559	C→G	10.5%	intergenic (+153/+87)	yfeW → / ← yfeX	penicillin binding protein PBP4B; weak DD‑carboxypeptidase activity/porphyrinogen oxidase, cytoplasmic
RA	2,560,317	A→C	33.3%	N21H (AAT→CAT)	yffL →	CPZ‑55 prophage; uncharacterized protein
RA	2,560,321	C→T	33.3%	A22V (GCT→GTT)	yffL →	CPZ‑55 prophage; uncharacterized protein
RA	2,560,326	A→G	31.2%	T24A (ACA→GCA)	yffL →	CPZ‑55 prophage; uncharacterized protein
RA	2,560,330	G→T	30.2%	C25F (TGC→TTC)	yffL →	CPZ‑55 prophage; uncharacterized protein
RA	2,561,205	A→T	7.7%	intergenic (+307/‑163)	yffL → / → yffM	CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein
RA	2,561,206	A→T	7.7%	intergenic (+308/‑162)	yffL → / → yffM	CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein
RA	2,566,266	C→A	10.6%	G207C (GGC→TGC)	eutA ←	reactivating factor for ethanolamine ammonia lyase
RA	2,566,267	T→G	10.6%	A206A (GCA→GCC)	eutA ←	reactivating factor for ethanolamine ammonia lyase
RA	2,566,490	C→T	8.1%	G132D (GGT→GAT)	eutA ←	reactivating factor for ethanolamine ammonia lyase
RA	2,566,493	G→C	8.1%	A131G (GCC→GGC)	eutA ←	reactivating factor for ethanolamine ammonia lyase
RA	2,566,496	A→G	8.2%	I130T (ATC→ACC)	eutA ←	reactivating factor for ethanolamine ammonia lyase
RA	2,581,762	G→A	16.7%	A339V (GCC→GTC)	ypfG ←	DUF1176 family protein
RA	2,581,765	T→C	15.4%	D338G (GAC→GGC)	ypfG ←	DUF1176 family protein
RA	2,589,186	C→A	7.7%	A531E (GCG→GAG)	acrD →	aminoglycoside/multidrug efflux system
RA	2,592,989	A→G	13.0%	intergenic (+27/+83)	ypfN → / ← ypfH	putative membrane protein, UPF0370 family/palmitoyl‑CoA esterase activity, uncertain physiological substrate
RA	2,592,990	A→C	13.0%	intergenic (+28/+82)	ypfN → / ← ypfH	putative membrane protein, UPF0370 family/palmitoyl‑CoA esterase activity, uncertain physiological substrate
RA	2,596,016	T→C	5.3%	D241G (GAC→GGC)	ypfJ ←	putative neutral zinc metallopeptidase
RA	2,612,973	C→G	11.9%	L358L (CTC→CTG)	hyfR →	hydrogenase‑4 transcriptional activator
RA	2,612,974	C→G	11.4%	Q359E (CAG→GAG)	hyfR →	hydrogenase‑4 transcriptional activator
RA	2,620,623	T→C	5.5%	M84V (ATG→GTG)	upp ←	uracil phosphoribosyltransferase
RA	2,632,029	A→T	9.1%	A169A (GCT→GCA)	guaA ←	GMP synthetase (glutamine aminotransferase)
RA	2,632,035	A→T	8.3%	I167I (ATT→ATA)	guaA ←	GMP synthetase (glutamine aminotransferase)
RA	2,637,433	C→T	33.3%	intergenic (‑77/+41)	der ← / ← bamB	GTPase; multicopy suppressor of ftsJ/BamABCDE complex OM biogenesis lipoprotein
RA	2,637,438	T→G	28.6%	intergenic (‑82/+36)	der ← / ← bamB	GTPase; multicopy suppressor of ftsJ/BamABCDE complex OM biogenesis lipoprotein
RA	2,637,439	C→A	28.6%	intergenic (‑83/+35)	der ← / ← bamB	GTPase; multicopy suppressor of ftsJ/BamABCDE complex OM biogenesis lipoprotein
RA	2,637,444	A→G	28.6%	intergenic (‑88/+30)	der ← / ← bamB	GTPase; multicopy suppressor of ftsJ/BamABCDE complex OM biogenesis lipoprotein
RA	2,638,584	A→T	11.8%	F23L (TTT→TTA)	bamB ←	BamABCDE complex OM biogenesis lipoprotein
RA	2,653,104	G→C	14.9%	W204S (TGG→TCG) ‡	sseA →	3‑mercaptopyruvate sulfurtransferase
RA	2,653,105	G→C	14.9%	W204C (TGG→TGC) ‡	sseA →	3‑mercaptopyruvate sulfurtransferase
RA	2,653,367	G→A	36.8%	intergenic (+28/‑488)	sseA → / → ryfA	3‑mercaptopyruvate sulfurtransferase/novel sRNA, function unknown
RA	2,653,372	T→C	36.4%	intergenic (+33/‑483)	sseA → / → ryfA	3‑mercaptopyruvate sulfurtransferase/novel sRNA, function unknown
RA	2,661,482	G→C	6.2%	P17R (CCG→CGG)	iscS ←	cysteine desulfurase (tRNA sulfurtransferase), PLP‑dependent
RA	2,661,486	C→G	6.0%	D16H (GAC→CAC)	iscS ←	cysteine desulfurase (tRNA sulfurtransferase), PLP‑dependent
RA	2,661,487	C→G	5.9%	V15V (GTG→GTC)	iscS ←	cysteine desulfurase (tRNA sulfurtransferase), PLP‑dependent
RA	2,661,491	G→C	6.2%	P14R (CCG→CGG)	iscS ←	cysteine desulfurase (tRNA sulfurtransferase), PLP‑dependent
RA	2,672,631:1	+A	6.5%	coding (585/1203 nt)	hcaD →	phenylpropionate dioxygenase, ferredoxin reductase subunit
RA	2,672,639	A→C	7.4%	Q198P (CAG→CCG) ‡	hcaD →	phenylpropionate dioxygenase, ferredoxin reductase subunit
RA	2,672,640	G→T	7.3%	Q198H (CAG→CAT) ‡	hcaD →	phenylpropionate dioxygenase, ferredoxin reductase subunit
RA	2,680,639	T→C	5.1%	S703G (AGC→GGC)	yphG ←	DUF4380 domain‑containing TPR repeat protein
RA	2,680,640	G→A	5.1%	A702A (GCC→GCT)	yphG ←	DUF4380 domain‑containing TPR repeat protein
RA	2,681,967	T→C	5.1%	Y260C (TAC→TGC)	yphG ←	DUF4380 domain‑containing TPR repeat protein
RA	2,681,969	C→G	5.2%	Q259H (CAG→CAC) ‡	yphG ←	DUF4380 domain‑containing TPR repeat protein
RA	2,681,971	G→A	5.4%	Q259* (CAG→TAG) ‡	yphG ←	DUF4380 domain‑containing TPR repeat protein
RA	2,684,210	C→G	5.4%	intergenic (+154/+44)	yphH → / ← glyA	putative DNA‑binding transcriptional regulator/serine hydroxymethyltransferase
RA	2,691,169	A→T	21.9%	noncoding (172/184 nt)	glmY ←	sRNA activator of glmS mRNA, glmZ processing antagonist
RA	2,691,171	T→A	20.9%	noncoding (170/184 nt)	glmY ←	sRNA activator of glmS mRNA, glmZ processing antagonist
RA	2,691,173	A→T	21.9%	noncoding (168/184 nt)	glmY ←	sRNA activator of glmS mRNA, glmZ processing antagonist
RA	2,703,331	A→T	6.0%	V19D (GTT→GAT)	era ←	membrane‑associated, 16S rRNA‑binding GTPase
RA	2,703,334	Δ1 bp	6.0%	coding (53/906 nt)	era ←	membrane‑associated, 16S rRNA‑binding GTPase
RA	2,707,320	A→T	9.9%	intergenic (‑196/+2)	lepA ← / ← rseC	back‑translocating elongation factor EF4, GTPase/SoxR iron‑sulfur cluster reduction factor component
RA	2,707,321	A→T	9.9%	intergenic (‑197/+1)	lepA ← / ← rseC	back‑translocating elongation factor EF4, GTPase/SoxR iron‑sulfur cluster reduction factor component
RA	2,716,030	T→G	29.4%	intergenic (+20/+36)	eamB → / ← grcA	cysteine and O‑acetylserine exporter/autonomous glycyl radical cofactor
RA	2,716,033	C→A	29.4%	intergenic (+23/+33)	eamB → / ← grcA	cysteine and O‑acetylserine exporter/autonomous glycyl radical cofactor
RA	2,720,209	T→C	11.8%	L86P (CTG→CCG) ‡	pka →	protein lysine acetyltransferase
RA	2,720,210	G→A	11.3%	L86L (CTG→CTA) ‡	pka →	protein lysine acetyltransferase
RA	2,724,230	T→G	6.5%	S35A (TCG→GCG) ‡	yfiM →	putative lipoprotein
RA	2,724,231	C→A	6.5%	S35* (TCG→TAG) ‡	yfiM →	putative lipoprotein
RA	2,744,135	C→T	5.9%	intergenic (+28/+48)	yfiB → / ← rplS	OM lipoprotein putative positive effector of YfiN activity/50S ribosomal subunit protein L19
RA	2,744,136	A→G	5.9%	intergenic (+29/+47)	yfiB → / ← rplS	OM lipoprotein putative positive effector of YfiN activity/50S ribosomal subunit protein L19
RA	2,744,147	C→T	8.4%	intergenic (+40/+36)	yfiB → / ← rplS	OM lipoprotein putative positive effector of YfiN activity/50S ribosomal subunit protein L19
RA	2,744,148	A→G	6.0%	intergenic (+41/+35)	yfiB → / ← rplS	OM lipoprotein putative positive effector of YfiN activity/50S ribosomal subunit protein L19
RA	2,750,073	G→T	20.0%	intergenic (+13/+42)	yfjD → / ← grpE	UPF0053 family inner membrane protein/heat shock protein
RA	2,750,078	T→G	20.0%	intergenic (+18/+37)	yfjD → / ← grpE	UPF0053 family inner membrane protein/heat shock protein
RA	2,750,081	C→A	22.1%	intergenic (+21/+34)	yfjD → / ← grpE	UPF0053 family inner membrane protein/heat shock protein
RA	2,760,584	T→G	5.2%	L13R (CTA→CGA)	yfjJ →	CP4‑57 prophage; uncharacterized protein
RA	2,760,589	C→A	5.2%	R15R (CGG→AGG)	yfjJ →	CP4‑57 prophage; uncharacterized protein
RA	2,761,620	T→G	10.8%	K641Q (AAG→CAG)	yfjK ←	radiation resistance protein; DEAD/H helicase‑like protein; CP4‑57 putative defective prophage
RA	2,761,623	C→A	12.4%	V640L (GTA→TTA)	yfjK ←	radiation resistance protein; DEAD/H helicase‑like protein; CP4‑57 putative defective prophage
RA	2,767,006	A→G	5.5%	N8S (AAC→AGC)	rnlB →	CP4‑57 prophage; uncharacterized protein
RA	2,770,319	C→G	5.8%	P206R (CCG→CGG)	yfjR →	CP4‑57 prophage; putative DNA‑binding transcriptional regulator
RA	2,777,571	A→G	5.8%	D40G (GAC→GGC)	ypjF →	CP4‑57 prophage; toxin of the YpjF‑YfjZ toxin‑antitoxin system
RA	2,777,573	A→G	5.9%	T41A (ACG→GCG) ‡	ypjF →	CP4‑57 prophage; toxin of the YpjF‑YfjZ toxin‑antitoxin system
RA	2,777,574	C→T	5.9%	T41M (ACG→ATG) ‡	ypjF →	CP4‑57 prophage; toxin of the YpjF‑YfjZ toxin‑antitoxin system
RA	2,777,576	C→T	5.8%	P42S (CCG→TCG)	ypjF →	CP4‑57 prophage; toxin of the YpjF‑YfjZ toxin‑antitoxin system
RA	2,780,505	C→T	5.5%	S741N (AGT→AAT)	ypjA ←	adhesin‑like autotransporter
RA	2,796,375	T→A	9.8%	I138F (ATT→TTT)	ygaU ←	uncharacterized protein
RA	2,800,515	C→A	47.4%	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	47.4%	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	36.0%	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	13.1%	N31I (AAT→ATT)	nrdI →	NrdEF cluster assembly flavodoxin
RA	2,807,091	T→C	8.9%	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	8.9%	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	8.6%	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	16.1%	H35Y (CAC→TAC) ‡	mprA →	transcriptional repressor of microcin B17 synthesis and multidrug efflux
RA	2,810,873	A→G	16.1%	H35R (CAC→CGC) ‡	mprA →	transcriptional repressor of microcin B17 synthesis and multidrug efflux
RA	2,814,174	T→A	20.6%	intergenic (+20/+44)	emrB → / ← luxS	multidrug efflux system protein/S‑ribosylhomocysteine lyase
RA	2,814,175	T→A	20.6%	intergenic (+21/+43)	emrB → / ← luxS	multidrug efflux system protein/S‑ribosylhomocysteine lyase
RA	2,823,838	C→A	5.4%	intergenic (‑69/+11)	recA ← / ← pncC	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/nicotinamide‑nucleotide amidohydrolase; NMN amidohydrolase
RA	2,823,839	T→G	5.5%	intergenic (‑70/+10)	recA ← / ← pncC	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/nicotinamide‑nucleotide amidohydrolase; NMN amidohydrolase
RA	2,835,126	A→G	7.4%	intergenic (+81/+47)	norW → / ← hypF	NADH:flavorubredoxin oxidoreductase/carbamoyl phosphate phosphatase and [NiFe] hydrogenase maturation protein
RA	2,835,127	A→C	7.4%	intergenic (+82/+46)	norW → / ← hypF	NADH:flavorubredoxin oxidoreductase/carbamoyl phosphate phosphatase and [NiFe] hydrogenase maturation protein
RA	2,835,133	T→A	7.0%	intergenic (+88/+40)	norW → / ← hypF	NADH:flavorubredoxin oxidoreductase/carbamoyl phosphate phosphatase and [NiFe] hydrogenase maturation protein
RA	2,835,134	T→A	7.0%	intergenic (+89/+39)	norW → / ← hypF	NADH:flavorubredoxin oxidoreductase/carbamoyl phosphate phosphatase and [NiFe] hydrogenase maturation protein
RA	2,838,231	A→T	14.8%	intergenic (‑126/+23)	hydN ← / ← ascG	formate dehydrogenase‑H, [4Fe‑4S] ferredoxin subunit/asc operon transcriptional repressor; prpBC operon repressor
RA	2,860,736	C→G	12.1%	D167H (GAT→CAT)	ygbI ←	DeoR family putative transcriptional regulator
RA	2,860,738	A→T	12.5%	I166N (ATT→AAT)	ygbI ←	DeoR family putative transcriptional regulator
RA	2,860,740	C→G	11.1%	M165I (ATG→ATC)	ygbI ←	DeoR family putative transcriptional regulator
RA	2,866,487	G→C	44.4%	intergenic (+22/+72)	ygbN → / ← rpoS	putative transporter/RNA polymerase, sigma S (sigma 38) factor
RA	2,866,488	G→C	44.4%	intergenic (+23/+71)	ygbN → / ← rpoS	putative transporter/RNA polymerase, sigma S (sigma 38) factor
RA	2,866,940	C→A	5.3%	K204N (AAG→AAT) ‡	rpoS ←	RNA polymerase, sigma S (sigma 38) factor
RA	2,866,942	T→A	5.5%	K204* (AAG→TAG) ‡	rpoS ←	RNA polymerase, sigma S (sigma 38) factor
RA	2,866,944	T→G	5.5%	D203A (GAT→GCT)	rpoS ←	RNA polymerase, sigma S (sigma 38) factor
RA	2,868,883	T→C	5.5%	intergenic (‑130/+10)	nlpD ← / ← pcm	activator of AmiC murein hydrolase activity, lipoprotein/L‑isoaspartate protein carboxylmethyltransferase type II
RA	2,870,870	T→A	6.3%	E145D (GAA→GAT) ‡	truD ←	tRNA(Glu) pseudouridine(13) synthase
RA	2,870,871	T→A	6.3%	E145V (GAA→GTA) ‡	truD ←	tRNA(Glu) pseudouridine(13) synthase
RA	2,873,915	A→G	12.5%	H26H (CAT→CAC) ‡	cysC ←	adenosine 5'‑phosphosulfate kinase
RA	2,873,917	G→C	11.7%	H26D (CAT→GAT) ‡	cysC ←	adenosine 5'‑phosphosulfate kinase
RA	2,873,919	C→T	10.9%	G25D (GGT→GAT)	cysC ←	adenosine 5'‑phosphosulfate kinase
RA	2,900,322	C→T	42.9%	intergenic (‑49/‑270)	ygcW ← / → yqcE	putative SDR family oxidoreductase/putative MFS transporter, inner membrane protein
RA	2,900,324	G→T	33.3%	intergenic (‑51/‑268)	ygcW ← / → yqcE	putative SDR family oxidoreductase/putative MFS transporter, inner membrane protein
RA	2,900,327	A→C	28.6%	intergenic (‑54/‑265)	ygcW ← / → yqcE	putative SDR family oxidoreductase/putative MFS transporter, inner membrane protein
RA	2,907,998	A→T	16.7%	intergenic (‑57/+31)	eno ← / ← pyrG	enolase/CTP synthetase
RA	2,926,036	A→C	5.6%	E230A (GAA→GCA)	queF →	7‑cyano‑7‑deazaguanine reductase (NADPH‑dependent)
RA	2,926,039	A→T	5.5%	Q231L (CAG→CTG)	queF →	7‑cyano‑7‑deazaguanine reductase (NADPH‑dependent)
RA	2,926,042	G→T	6.0%	C232F (TGC→TTC)	queF →	7‑cyano‑7‑deazaguanine reductase (NADPH‑dependent)
RA	2,945,970	A→G	8.0%	intergenic (‑128/+111)	tcdA ← / ← mltA	tRNA threonylcarbamoyladenosine dehydratase; sulfur acceptor for CsdA/membrane‑bound lytic murein transglycosylase A
RA	2,945,971	A→C	8.0%	intergenic (‑129/+110)	tcdA ← / ← mltA	tRNA threonylcarbamoyladenosine dehydratase; sulfur acceptor for CsdA/membrane‑bound lytic murein transglycosylase A
RA	2,945,977	T→G	8.9%	intergenic (‑135/+104)	tcdA ← / ← mltA	tRNA threonylcarbamoyladenosine dehydratase; sulfur acceptor for CsdA/membrane‑bound lytic murein transglycosylase A
RA	2,945,978	C→A	8.9%	intergenic (‑136/+103)	tcdA ← / ← mltA	tRNA threonylcarbamoyladenosine dehydratase; sulfur acceptor for CsdA/membrane‑bound lytic murein transglycosylase A
RA	2,945,984	G→T	9.4%	intergenic (‑142/+97)	tcdA ← / ← mltA	tRNA threonylcarbamoyladenosine dehydratase; sulfur acceptor for CsdA/membrane‑bound lytic murein transglycosylase A
RA	2,945,985	C→T	9.4%	intergenic (‑143/+96)	tcdA ← / ← mltA	tRNA threonylcarbamoyladenosine dehydratase; sulfur acceptor for CsdA/membrane‑bound lytic murein transglycosylase A
RA	2,951,471	G→A	8.2%	R331C (CGC→TGC)	recD ←	exonuclease V (RecBCD complex), alpha chain
RA	2,951,475	T→A	7.9%	L329L (CTA→CTT)	recD ←	exonuclease V (RecBCD complex), alpha chain
RA	2,951,479	T→C	6.3%	Q328R (CAG→CGG)	recD ←	exonuclease V (RecBCD complex), alpha chain
RA	2,960,926	G→C	5.8%	G501G (GGC→GGG) ‡	recC ←	exonuclease V (RecBCD complex), gamma chain
RA	2,960,928	C→G	6.0%	G501R (GGC→CGC) ‡	recC ←	exonuclease V (RecBCD complex), gamma chain
RA	2,960,930	G→C	6.1%	S500C (TCC→TGC)	recC ←	exonuclease V (RecBCD complex), gamma chain
RA	2,961,248	A→T	6.9%	L394Q (CTG→CAG)	recC ←	exonuclease V (RecBCD complex), gamma chain
RA	2,961,251	A→T	6.9%	L393Q (CTG→CAG)	recC ←	exonuclease V (RecBCD complex), gamma chain
RA	2,962,561	G→A	6.0%	N68N (AAC→AAT) ‡	ppdC ←	putative prepilin peptidase‑dependent protein
RA	2,962,562	T→C	6.3%	N68S (AAC→AGC) ‡	ppdC ←	putative prepilin peptidase‑dependent protein
RA	2,971,146	T→C	13.4%	intergenic (+13/‑125)	ygdQ → / → ygdR	UPF0053 family inner membrane protein/DUF903 family verified lipoprotein
RA	2,971,151	T→C	13.3%	intergenic (+18/‑120)	ygdQ → / → ygdR	UPF0053 family inner membrane protein/DUF903 family verified lipoprotein
RA	2,971,154	G→A	13.2%	intergenic (+21/‑117)	ygdQ → / → ygdR	UPF0053 family inner membrane protein/DUF903 family verified lipoprotein
RA	2,971,159	G→A	8.1%	intergenic (+26/‑112)	ygdQ → / → ygdR	UPF0053 family inner membrane protein/DUF903 family verified lipoprotein
RA	2,976,320	T→G	9.2%	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	9.2%	noncoding (65/82 nt)	omrB ←	sRNA antisense regulator downregulates OM proteins and curli; positively regulated by OmpR/EnvZ, Hfq‑dependent
RA	2,977,936	Δ1 bp	6.4%	coding (964/1263 nt)	lysA ←	diaminopimelate decarboxylase, PLP‑binding
RA	2,977,941	A→C	6.3%	L320R (CTG→CGG) ‡	lysA ←	diaminopimelate decarboxylase, PLP‑binding
RA	2,977,942	G→T	6.3%	L320M (CTG→ATG) ‡	lysA ←	diaminopimelate decarboxylase, PLP‑binding
RA	2,977,946:1	+G	6.5%	coding (954/1263 nt)	lysA ←	diaminopimelate decarboxylase, PLP‑binding
RA	2,980,742	A→G	23.1%	intergenic (‑107/+22)	ygeA ← / ← araE	Asp/Glu_racemase family protein/arabinose transporter
RA	2,980,744	A→T	23.1%	intergenic (‑109/+20)	ygeA ← / ← araE	Asp/Glu_racemase family protein/arabinose transporter
RA	2,980,746	C→T	23.1%	intergenic (‑111/+18)	ygeA ← / ← araE	Asp/Glu_racemase family protein/arabinose transporter
RA	2,993,276	A→C	6.2%	I395L (ATA→CTA)	ygeH →	putative transcriptional regulator
RA	2,993,279	G→T	5.9%	D396Y (GAC→TAC)	ygeH →	putative transcriptional regulator
RA	2,997,649	T→A	7.3%	intergenic (‑49/+43)	insC1 ← / ← ygeQ	IS2 repressor TnpA/pseudogene, glycosyl hydrolase family 15, part of T3SS PAI ETT2 remnant
RA	2,997,650	T→A	7.3%	intergenic (‑50/+42)	insC1 ← / ← ygeQ	IS2 repressor TnpA/pseudogene, glycosyl hydrolase family 15, part of T3SS PAI ETT2 remnant
RA	3,007,466	T→C	18.0%	intergenic (+14/‑44)	ygeW → / → ygeX	putative carbamoyltransferase/2,3‑diaminopropionate ammonia lyase, PLP‑dependent
RA	3,007,473	G→A	15.8%	intergenic (+21/‑37)	ygeW → / → ygeX	putative carbamoyltransferase/2,3‑diaminopropionate ammonia lyase, PLP‑dependent
RA	3,012,599	T→C	7.5%	intergenic (+206/+15)	yqeA → / ← yqeB	putative amino acid kinase/XdhC‑CoxI family protein with NAD(P)‑binding Rossman fold
RA	3,024,038	G→C	7.2%	G908A (GGC→GCC)	xdhD →	putative hypoxanthine oxidase, molybdopterin‑binding/Fe‑S binding
RA	3,024,043	T→A	6.5%	F910I (TTC→ATC) ‡	xdhD →	putative hypoxanthine oxidase, molybdopterin‑binding/Fe‑S binding
RA	3,024,044	T→A	6.5%	F910Y (TTC→TAC) ‡	xdhD →	putative hypoxanthine oxidase, molybdopterin‑binding/Fe‑S binding
RA	3,024,049	G→C	7.0%	A912P (GCG→CCG)	xdhD →	putative hypoxanthine oxidase, molybdopterin‑binding/Fe‑S binding
RA	3,031,221	T→A	13.1%	intergenic (‑290/‑146)	ygfT ← / → uacT	putative oxidoreductase, Fe‑S subunit/nucleotide‑binding subunit/uric acid permease
RA	3,032,708	C→G	5.5%	H448D (CAT→GAT)	uacT →	uric acid permease
RA	3,033,624	A→G	13.0%	intergenic (+11/+33)	idi → / ← lysS	isopentenyl diphosphate isomerase/lysine tRNA synthetase, constitutive
RA	3,033,627	T→A	11.5%	intergenic (+14/+30)	idi → / ← lysS	isopentenyl diphosphate isomerase/lysine tRNA synthetase, constitutive
RA	3,033,628	T→A	11.5%	intergenic (+15/+29)	idi → / ← lysS	isopentenyl diphosphate isomerase/lysine tRNA synthetase, constitutive
RA	3,033,631	C→T	12.0%	intergenic (+18/+26)	idi → / ← lysS	isopentenyl diphosphate isomerase/lysine tRNA synthetase, constitutive
RA	3,045,124	T→C	12.6%	intergenic (+23/+34)	bglA → / ← ygfF	6‑phospho‑beta‑glucosidase A/putative NAD(P)‑dependent oxidoreductase
RA	3,045,126	C→A	11.1%	intergenic (+25/+32)	bglA → / ← ygfF	6‑phospho‑beta‑glucosidase A/putative NAD(P)‑dependent oxidoreductase
RA	3,045,127	T→G	13.8%	intergenic (+26/+31)	bglA → / ← ygfF	6‑phospho‑beta‑glucosidase A/putative NAD(P)‑dependent oxidoreductase
RA	3,045,129	G→A	13.8%	intergenic (+28/+29)	bglA → / ← ygfF	6‑phospho‑beta‑glucosidase A/putative NAD(P)‑dependent oxidoreductase
RA	3,057,140	A→G	8.7%	intergenic (+152/+38)	sibC → / ← serA	sRNA antisense regulator of toxic IbsC protein/D‑3‑phosphoglycerate dehydrogenase
RA	3,057,145	G→C	8.7%	intergenic (+157/+33)	sibC → / ← serA	sRNA antisense regulator of toxic IbsC protein/D‑3‑phosphoglycerate dehydrogenase
RA	3,057,150	C→T	9.9%	intergenic (+162/+28)	sibC → / ← serA	sRNA antisense regulator of toxic IbsC protein/D‑3‑phosphoglycerate dehydrogenase
RA	3,059,703	A→T	6.7%	intergenic (‑2/‑50)	yqfE ← / → argP	pseudogene, LysR family/transcriptional regulator for arginine transport and DNA replication genes; replication initiation inhibitor
RA	3,059,704	A→T	6.7%	intergenic (‑3/‑49)	yqfE ← / → argP	pseudogene, LysR family/transcriptional regulator for arginine transport and DNA replication genes; replication initiation inhibitor
RA	3,061,041	T→G	5.1%	R64R (CGT→CGG)	scpA →	methylmalonyl‑CoA mutase
RA	3,061,817	G→C	14.8%	W323S (TGG→TCG) ‡	scpA →	methylmalonyl‑CoA mutase
RA	3,061,818	G→C	14.8%	W323C (TGG→TGC) ‡	scpA →	methylmalonyl‑CoA mutase
RA	3,066,299:1	+G	6.0%	coding (875/897 nt)	ygfI ←	putative DNA‑binding transcriptional regulator
RA	3,066,308	A→T	7.0%	I289N (ATT→AAT) ‡	ygfI ←	putative DNA‑binding transcriptional regulator
RA	3,066,309	T→A	5.6%	I289F (ATT→TTT) ‡	ygfI ←	putative DNA‑binding transcriptional regulator
RA	3,066,310	A→T	5.6%	H288Q (CAT→CAA)	ygfI ←	putative DNA‑binding transcriptional regulator
RA	3,081,664	A→G	6.8%	intergenic (‑29/‑249)	tktA ← / → loiP	transketolase 1, thiamine triphosphate‑binding/Phe‑Phe periplasmic metalloprotease, OM lipoprotein; low salt‑inducible; Era‑binding heat shock protein
RA	3,081,665	C→T	6.8%	intergenic (‑30/‑248)	tktA ← / → loiP	transketolase 1, thiamine triphosphate‑binding/Phe‑Phe periplasmic metalloprotease, OM lipoprotein; low salt‑inducible; Era‑binding heat shock protein
RA	3,082,701	A→G	9.1%	intergenic (+30/+176)	loiP → / ← speB	Phe‑Phe periplasmic metalloprotease, OM lipoprotein; low salt‑inducible; Era‑binding heat shock protein/agmatinase
RA	3,082,702	A→C	9.1%	intergenic (+31/+175)	loiP → / ← speB	Phe‑Phe periplasmic metalloprotease, OM lipoprotein; low salt‑inducible; Era‑binding heat shock protein/agmatinase
RA	3,082,708	T→G	9.7%	intergenic (+37/+169)	loiP → / ← speB	Phe‑Phe periplasmic metalloprotease, OM lipoprotein; low salt‑inducible; Era‑binding heat shock protein/agmatinase
RA	3,082,709	C→A	9.4%	intergenic (+38/+168)	loiP → / ← speB	Phe‑Phe periplasmic metalloprotease, OM lipoprotein; low salt‑inducible; Era‑binding heat shock protein/agmatinase
RA	3,082,814	A→G	14.8%	intergenic (+143/+63)	loiP → / ← speB	Phe‑Phe periplasmic metalloprotease, OM lipoprotein; low salt‑inducible; Era‑binding heat shock protein/agmatinase
RA	3,082,815	A→C	14.8%	intergenic (+144/+62)	loiP → / ← speB	Phe‑Phe periplasmic metalloprotease, OM lipoprotein; low salt‑inducible; Era‑binding heat shock protein/agmatinase
RA	3,082,821	T→G	12.9%	intergenic (+150/+56)	loiP → / ← speB	Phe‑Phe periplasmic metalloprotease, OM lipoprotein; low salt‑inducible; Era‑binding heat shock protein/agmatinase
RA	3,082,822	C→A	10.8%	intergenic (+151/+55)	loiP → / ← speB	Phe‑Phe periplasmic metalloprotease, OM lipoprotein; low salt‑inducible; Era‑binding heat shock protein/agmatinase
RA	3,090,226	T→C	5.3%	C158R (TGC→CGC)	yggI →	Zn‑dependent metalloprotease‑related protein
RA	3,090,229	G→A	5.5%	G159S (GGT→AGT)	yggI →	Zn‑dependent metalloprotease‑related protein
RA	3,092,774:1	+A	5.5%	coding (897/951 nt)	gshB →	glutathione synthetase
RA	3,092,779	Δ1 bp	5.2%	coding (902/951 nt)	gshB →	glutathione synthetase
RA	3,131,457	C→A	5.4%	G318C (GGT→TGT)	yghQ ←	putative inner membrane polysaccharide flippase
RA	3,131,524	A→G	18.6%	S295S (AGT→AGC) ‡	yghQ ←	putative inner membrane polysaccharide flippase
RA	3,131,525	C→T	18.6%	S295N (AGT→AAT) ‡	yghQ ←	putative inner membrane polysaccharide flippase
RA	3,135,356	T→C	7.8%	Q339R (CAG→CGG) ‡	pitB ←	phosphate transporter
RA	3,135,357	G→A	7.8%	Q339* (CAG→TAG) ‡	pitB ←	phosphate transporter
RA	3,139,639	T→G	8.0%	intergenic (+46/+77)	yghU → / ← hybG	putative S‑transferase/hydrogenase 2 accessory protein
RA	3,139,640	C→A	8.3%	intergenic (+47/+76)	yghU → / ← hybG	putative S‑transferase/hydrogenase 2 accessory protein
RA	3,139,682	T→G	15.1%	intergenic (+89/+34)	yghU → / ← hybG	putative S‑transferase/hydrogenase 2 accessory protein
RA	3,139,685	C→A	13.9%	intergenic (+92/+31)	yghU → / ← hybG	putative S‑transferase/hydrogenase 2 accessory protein
RA	3,139,691	T→G	12.2%	intergenic (+98/+25)	yghU → / ← hybG	putative S‑transferase/hydrogenase 2 accessory protein
RA	3,139,692	T→C	12.1%	intergenic (+99/+24)	yghU → / ← hybG	putative S‑transferase/hydrogenase 2 accessory protein
RA	3,139,919	T→G	5.2%	I16L (ATT→CTT)	hybG ←	hydrogenase 2 accessory protein
RA	3,139,922	C→A	5.0%	D15Y (GAT→TAT)	hybG ←	hydrogenase 2 accessory protein
RA	3,156,590	C→A	17.1%	intergenic (+72/‑33)	yqhD → / → dkgA	aldehyde reductase, NADPH‑dependent/2,5‑diketo‑D‑gluconate reductase A
RA	3,156,591	T→G	17.1%	intergenic (+73/‑32)	yqhD → / → dkgA	aldehyde reductase, NADPH‑dependent/2,5‑diketo‑D‑gluconate reductase A
RA	3,165,154	T→A	7.0%	M274L (ATG→TTG)	parC ←	DNA topoisomerase IV, subunit A
RA	3,165,155	T→A	7.0%	Q273H (CAA→CAT)	parC ←	DNA topoisomerase IV, subunit A
RA	3,171,852	C→T	16.1%	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	17.4%	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	17.7%	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	17.8%	intergenic (+30/+16)	qseC → / ← ygiZ	quorum sensing sensory histidine kinase in two‑component regulatory system with QseB/inner membrane protein
RA	3,172,436	T→G	7.4%	intergenic (‑225/‑94)	ygiZ ← / → mdaB	inner membrane protein/NADPH quinone reductase
RA	3,172,439	A→T	7.7%	intergenic (‑228/‑91)	ygiZ ← / → mdaB	inner membrane protein/NADPH quinone reductase
RA	3,172,442	C→A	7.7%	intergenic (‑231/‑88)	ygiZ ← / → mdaB	inner membrane protein/NADPH quinone reductase
RA	3,180,497	Δ1 bp	13.2%	coding (77/1161 nt)	ygiC →	ATP‑Grasp family ATPase
RA	3,180,505	G→T	14.9%	E29* (GAG→TAG) ‡	ygiC →	ATP‑Grasp family ATPase
RA	3,180,506	A→C	15.3%	E29A (GAG→GCG) ‡	ygiC →	ATP‑Grasp family ATPase
RA	3,180,685	T→C	7.6%	S89P (TCA→CCA)	ygiC →	ATP‑Grasp family ATPase
RA	3,180,690	G→A	8.9%	W90* (TGG→TGA)	ygiC →	ATP‑Grasp family ATPase
RA	3,180,694	A→G	9.5%	T92A (ACG→GCG)	ygiC →	ATP‑Grasp family ATPase
RA	3,186,137	A→T	11.8%	intergenic (+47/‑50)	yqiG → / → insC1	pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein/IS2 repressor TnpA
RA	3,186,138	A→T	11.8%	intergenic (+48/‑49)	yqiG → / → insC1	pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein/IS2 repressor TnpA
RA	3,187,991	T→A	6.7%	pseudogene (565/2439 nt)	yqiG →	pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein
RA	3,187,993	C→T	6.8%	pseudogene (567/2439 nt)	yqiG →	pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein
RA	3,200,991	A→T	5.9%	intergenic (‑26/‑216)	ygiF ← / → ygiM	inorganic triphosphatase/SH3 domain protein
RA	3,202,003	G→C	14.0%	G38A (GGC→GCC)	cca →	fused tRNA nucleotidyl transferase/2'3'‑cyclic phosphodiesterase/2'nucleotidase and phosphatase
RA	3,202,009	A→T	14.9%	Q40L (CAG→CTG)	cca →	fused tRNA nucleotidyl transferase/2'3'‑cyclic phosphodiesterase/2'nucleotidase and phosphatase
RA	3,202,012	A→T	14.9%	Q41L (CAG→CTG)	cca →	fused tRNA nucleotidyl transferase/2'3'‑cyclic phosphodiesterase/2'nucleotidase and phosphatase
RA	3,202,678	C→G	10.6%	P263R (CCG→CGG)	cca →	fused tRNA nucleotidyl transferase/2'3'‑cyclic phosphodiesterase/2'nucleotidase and phosphatase
RA	3,202,685	A→G	15.8%	E265E (GAA→GAG)	cca →	fused tRNA nucleotidyl transferase/2'3'‑cyclic phosphodiesterase/2'nucleotidase and phosphatase
RA	3,202,686	C→T	16.6%	L266F (CTC→TTC)	cca →	fused tRNA nucleotidyl transferase/2'3'‑cyclic phosphodiesterase/2'nucleotidase and phosphatase
RA	3,202,693	C→G	8.8%	P268R (CCG→CGG)	cca →	fused tRNA nucleotidyl transferase/2'3'‑cyclic phosphodiesterase/2'nucleotidase and phosphatase
RA	3,206,172	T→C	9.2%	T29A (ACG→GCG)	ttdR ←	transcriptional activator of ttdABT
RA	3,206,176	C→A	9.3%	A27A (GCG→GCT)	ttdR ←	transcriptional activator of ttdABT
RA	3,206,179	T→G	9.3%	A26A (GCA→GCC)	ttdR ←	transcriptional activator of ttdABT
RA	3,217,246	G→A	7.7%	A156A (GCG→GCA)	yqjI →	PadR family putative transcriptional regulator
RA	3,217,251	T→C	7.7%	L158P (CTG→CCG)	yqjI →	PadR family putative transcriptional regulator
RA	3,221,150	A→T	5.8%	I33N (ATC→AAC) ‡	ygjH ←	putative tRNA binding protein; putative tRNA corner chaperone
RA	3,221,151	T→C	5.8%	I33V (ATC→GTC) ‡	ygjH ←	putative tRNA binding protein; putative tRNA corner chaperone
RA	3,234,506	G→A	18.2%	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	18.2%	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	23.1%	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	12.8%	intergenic (+64/‑335)	alx → / → sstT	putative membrane‑bound redox modulator/sodium:serine/threonine symporter
RA	3,239,610	C→G	13.9%	intergenic (+65/‑334)	alx → / → sstT	putative membrane‑bound redox modulator/sodium:serine/threonine symporter
RA	3,239,611	C→A	14.0%	intergenic (+66/‑333)	alx → / → sstT	putative membrane‑bound redox modulator/sodium:serine/threonine symporter
RA	3,250,989	G→C	13.8%	intergenic (+35/‑35)	yqjF → / → yqjG	putative quinol oxidase subunit/putative S‑transferase
RA	3,250,991	A→T	13.9%	intergenic (+37/‑33)	yqjF → / → yqjG	putative quinol oxidase subunit/putative S‑transferase
RA	3,250,992	G→C	13.5%	intergenic (+38/‑32)	yqjF → / → yqjG	putative quinol oxidase subunit/putative S‑transferase
RA	3,256,434	A→G	6.3%	M73T (ATG→ACG)	yhaM ←	putative L‑serine dehydratase alpha chain
RA	3,256,450	C→T	7.4%	V68I (GTT→ATT)	yhaM ←	putative L‑serine dehydratase alpha chain
RA	3,271,825	T→A	11.6%	intergenic (‑55/+42)	garK ← / ← garR	glycerate kinase I/tartronate semialdehyde reductase
RA	3,276,886	C→A	15.8%	intergenic (+33/‑116)	garD → / → prlF	D‑galactarate dehydrogenase/antitoxin of the SohA(PrlF)‑YhaV toxin‑antitoxin system
RA	3,276,887	T→C	14.6%	intergenic (+34/‑115)	garD → / → prlF	D‑galactarate dehydrogenase/antitoxin of the SohA(PrlF)‑YhaV toxin‑antitoxin system
RA	3,276,890	G→A	14.0%	intergenic (+37/‑112)	garD → / → prlF	D‑galactarate dehydrogenase/antitoxin of the SohA(PrlF)‑YhaV toxin‑antitoxin system
RA	3,276,891	T→G	14.0%	intergenic (+38/‑111)	garD → / → prlF	D‑galactarate dehydrogenase/antitoxin of the SohA(PrlF)‑YhaV toxin‑antitoxin system
RA	3,288,017	A→G	5.8%	intergenic (+7/‑73)	yraH → / → yraI	putative fimbrial‑like adhesin protein/putative periplasmic pilin chaperone
RA	3,288,032	C→A	36.5%	intergenic (+22/‑58)	yraH → / → yraI	putative fimbrial‑like adhesin protein/putative periplasmic pilin chaperone
RA	3,288,033	T→G	32.7%	intergenic (+23/‑57)	yraH → / → yraI	putative fimbrial‑like adhesin protein/putative periplasmic pilin chaperone
RA	3,291,109	A→T	9.7%	K766* (AAA→TAA) ‡	yraJ →	putative outer membrane protein
RA	3,291,110	A→T	9.7%	K766I (AAA→ATA) ‡	yraJ →	putative outer membrane protein
RA	3,309,004	C→T	7.7%	intergenic (‑80/+29)	nlpI ← / ← pnp	lipoprotein involved in osmotic sensitivity and filamentation/polynucleotide phosphorylase/polyadenylase
RA	3,309,009	C→T	8.5%	intergenic (‑85/+24)	nlpI ← / ← pnp	lipoprotein involved in osmotic sensitivity and filamentation/polynucleotide phosphorylase/polyadenylase
RA	3,309,012	A→G	10.5%	intergenic (‑88/+21)	nlpI ← / ← pnp	lipoprotein involved in osmotic sensitivity and filamentation/polynucleotide phosphorylase/polyadenylase
RA	3,322,698	A→G	13.0%	intergenic (‑193/+35)	secG ← / ← glmM	preprotein translocase membrane subunit/phosphoglucosamine mutase
RA	3,322,700	A→G	11.5%	intergenic (‑195/+33)	secG ← / ← glmM	preprotein translocase membrane subunit/phosphoglucosamine mutase
RA	3,322,703	C→T	10.0%	intergenic (‑198/+30)	secG ← / ← glmM	preprotein translocase membrane subunit/phosphoglucosamine mutase
RA	3,322,705	C→T	10.1%	intergenic (‑200/+28)	secG ← / ← glmM	preprotein translocase membrane subunit/phosphoglucosamine mutase
RA	3,329,295	A→T	7.1%	L111F (TTA→TTT)	dacB →	D‑alanyl‑D‑alanine carboxypeptidase
RA	3,329,296	A→T	7.1%	K112* (AAA→TAA)	dacB →	D‑alanyl‑D‑alanine carboxypeptidase
RA	3,330,415	Δ1 bp	42.9%	intergenic (+19/+167)	dacB → / ← obgE	D‑alanyl‑D‑alanine carboxypeptidase/GTPase involved in cell partioning and DNA repair
RA	3,330,419:1	+T	42.9%	intergenic (+23/+163)	dacB → / ← obgE	D‑alanyl‑D‑alanine carboxypeptidase/GTPase involved in cell partioning and DNA repair
RA	3,354,537	C→G	19.3%	intergenic (‑487/‑188)	yhcC ← / → gltB	putative Fe‑S oxidoreductase, Radical SAM superfamily protein/glutamate synthase, large subunit
RA	3,360,643	T→A	15.4%	intergenic (+27/‑533)	gltD → / → gltF	glutamate synthase, 4Fe‑4S protein, small subunit/periplasmic protein
RA	3,360,644	G→C	15.4%	intergenic (+28/‑532)	gltD → / → gltF	glutamate synthase, 4Fe‑4S protein, small subunit/periplasmic protein
RA	3,360,645	T→A	15.4%	intergenic (+29/‑531)	gltD → / → gltF	glutamate synthase, 4Fe‑4S protein, small subunit/periplasmic protein
RA	3,368,134	A→G	11.8%	H103R (CAC→CGC)	yhcG →	DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily
RA	3,368,142	A→T	12.8%	M106L (ATG→TTG)	yhcG →	DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily
RA	3,368,150	C→T	9.1%	G108G (GGC→GGT)	yhcG →	DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily
RA	3,380,434	A→G	7.8%	S82G (AGC→GGC)	yhcB →	DUF1043 family inner membrane‑anchored protein
RA	3,380,440	C→A	6.9%	L84M (CTG→ATG) ‡	yhcB →	DUF1043 family inner membrane‑anchored protein
RA	3,380,441	T→G	6.9%	L84R (CTG→CGG) ‡	yhcB →	DUF1043 family inner membrane‑anchored protein
RA	3,380,447	C→T	7.0%	P86L (CCG→CTG)	yhcB →	DUF1043 family inner membrane‑anchored protein
RA	3,400,846	A→T	8.3%	I81N (ATC→AAC)	mreB ←	cell wall structural complex MreBCD, actin‑like component MreB
RA	3,400,849	A→T	8.3%	V80D (GTT→GAT)	mreB ←	cell wall structural complex MreBCD, actin‑like component MreB
RA	3,418,845	A→C	11.8%	intergenic (+234/‑197)	yhdV → / → yhdW	putative outer membrane protein/pseudogene, ABC transporter periplasmic binding protein family;putative transport; Not classified; putative periplasmic binding transport protein; periplasmic‑binding component of ABC superfamily
RA	3,418,847	A→T	11.8%	intergenic (+236/‑195)	yhdV → / → yhdW	putative outer membrane protein/pseudogene, ABC transporter periplasmic binding protein family;putative transport; Not classified; putative periplasmic binding transport protein; periplasmic‑binding component of ABC superfamily
RA	3,418,849	G→T	14.3%	intergenic (+238/‑193)	yhdV → / → yhdW	putative outer membrane protein/pseudogene, ABC transporter periplasmic binding protein family;putative transport; Not classified; putative periplasmic binding transport protein; periplasmic‑binding component of ABC superfamily
RA	3,423,383	A→G	22.2%	intergenic (+189/+40)	yhdZ → / ← rrfF	putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon
RA	3,423,620	A→G	8.4%	noncoding (36/76 nt)	thrV ←	tRNA‑Thr
RA	3,423,621	C→G	8.4%	noncoding (35/76 nt)	thrV ←	tRNA‑Thr
RA	3,423,622	C→T	8.4%	noncoding (34/76 nt)	thrV ←	tRNA‑Thr
RA	3,439,588	G→C	50.0%	intergenic (‑79/+28)	yhdN ← / ← rplQ	DUF1992 family protein/50S ribosomal subunit protein L17
RA	3,439,589	G→C	50.0%	intergenic (‑80/+27)	yhdN ← / ← rplQ	DUF1992 family protein/50S ribosomal subunit protein L17
RA	3,451,410	T→A	8.3%	N92I (AAT→ATT)	rplW ←	50S ribosomal subunit protein L23
RA	3,451,416	C→A	8.1%	G90V (GGC→GTC)	rplW ←	50S ribosomal subunit protein L23
RA	3,458,416	T→A	13.5%	I26I (ATT→ATA)	gspE →	general secretory pathway component, cryptic
RA	3,458,418	T→A	13.5%	I27N (ATT→AAT)	gspE →	general secretory pathway component, cryptic
RA	3,458,420	T→A	13.5%	Y28N (TAT→AAT)	gspE →	general secretory pathway component, cryptic
RA	3,471,357	C→T	15.5%	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	12.8%	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	13.9%	intergenic (‑33/+38)	tufA ← / ← fusA	translation elongation factor EF‑Tu 1/protein chain elongation factor EF‑G, GTP‑binding
RA	3,477,878	T→A	33.3%	intergenic (+20/+29)	slyX → / ← slyD	phi X174 lysis protein/FKBP‑type peptidyl prolyl cis‑trans isomerase (rotamase)
RA	3,483,242	G→C	6.8%	S14T (AGC→ACC) ‡	yheT →	UPF0017 family putative hydrolase
RA	3,483,243	C→T	6.8%	S14S (AGC→AGT) ‡	yheT →	UPF0017 family putative hydrolase
RA	3,483,244	A→G	8.3%	S15G (AGT→GGT) ‡	yheT →	UPF0017 family putative hydrolase
RA	3,483,245	G→C	6.8%	S15T (AGT→ACT) ‡	yheT →	UPF0017 family putative hydrolase
RA	3,488,989	G→T	5.3%	H398N (CAC→AAC)	argD ←	bifunctional acetylornithine aminotransferase and succinyldiaminopimelate aminotransferase
RA	3,498,176	A→G	8.0%	I117V (ATT→GTT)	cysG →	fused siroheme synthase 1,3‑dimethyluroporphyriongen III dehydrogenase and siroheme ferrochelatase/uroporphyrinogen methyltransferase
RA	3,512,601	A→G	9.5%	intergenic (‑257/+33)	yhfZ ← / ← trpS	putative DNA‑binding transcriptional regulator/tryptophanyl‑tRNA synthetase
RA	3,523,934	C→G	5.1%	T355S (ACC→AGC)	mrcA →	penicillin‑binding protein 1a, murein transglycosylase and transpeptidase
RA	3,533,037	C→A	5.9%	R74S (CGT→AGT) ‡	pck →	phosphoenolpyruvate carboxykinase [ATP]
RA	3,533,038	G→C	5.8%	R74P (CGT→CCT) ‡	pck →	phosphoenolpyruvate carboxykinase [ATP]
RA	3,533,039	T→G	5.8%	R74R (CGT→CGG) ‡	pck →	phosphoenolpyruvate carboxykinase [ATP]
RA	3,548,178	A→T	6.0%	A631A (GCT→GCA)	malQ ←	4‑alpha‑glucanotransferase (amylomaltase)
RA	3,548,181	A→T	5.8%	S630R (AGT→AGA)	malQ ←	4‑alpha‑glucanotransferase (amylomaltase)
RA	3,556,245	C→A	5.8%	R202L (CGC→CTC)	rtcA ←	RNA 3'‑terminal phosphate cyclase
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	3,561,969	A→T	7.1%	intergenic (‑146/‑44)	glpE ← / → glpD	thiosulfate:cyanide sulfurtransferase (rhodanese)/sn‑glycerol‑3‑phosphate dehydrogenase, aerobic, FAD/NAD(P)‑binding
RA	3,561,972	A→T	7.1%	intergenic (‑149/‑41)	glpE ← / → glpD	thiosulfate:cyanide sulfurtransferase (rhodanese)/sn‑glycerol‑3‑phosphate dehydrogenase, aerobic, FAD/NAD(P)‑binding
RA	3,563,539	T→C	11.6%	intergenic (+21/+248)	glpD → / ← yzgL	sn‑glycerol‑3‑phosphate dehydrogenase, aerobic, FAD/NAD(P)‑binding/pseudogene, periplasmic solute binding protein homology
RA	3,563,546	T→G	11.6%	intergenic (+28/+241)	glpD → / ← yzgL	sn‑glycerol‑3‑phosphate dehydrogenase, aerobic, FAD/NAD(P)‑binding/pseudogene, periplasmic solute binding protein homology
RA	3,563,547	C→A	11.9%	intergenic (+29/+240)	glpD → / ← yzgL	sn‑glycerol‑3‑phosphate dehydrogenase, aerobic, FAD/NAD(P)‑binding/pseudogene, periplasmic solute binding protein homology
RA	3,563,690	C→T	8.8%	intergenic (+172/+97)	glpD → / ← yzgL	sn‑glycerol‑3‑phosphate dehydrogenase, aerobic, FAD/NAD(P)‑binding/pseudogene, periplasmic solute binding protein homology
RA	3,563,693	A→G	8.6%	intergenic (+175/+94)	glpD → / ← yzgL	sn‑glycerol‑3‑phosphate dehydrogenase, aerobic, FAD/NAD(P)‑binding/pseudogene, periplasmic solute binding protein homology
RA	3,569,431	A→G	6.4%	I630T (ATT→ACT)	glgX ←	glycogen debranching enzyme
RA	3,569,437	T→C	5.1%	H628R (CAC→CGC)	glgX ←	glycogen debranching enzyme
RA	3,569,442	C→T	6.4%	E626E (GAG→GAA)	glgX ←	glycogen debranching enzyme
RA	3,577,657	A→G	13.2%	intergenic (‑65/+74)	gntK ← / ← gntR	gluconate kinase 2/d‑gluconate inducible gluconate regulon transcriptional repressor
RA	3,577,660	C→T	13.0%	intergenic (‑68/+71)	gntK ← / ← gntR	gluconate kinase 2/d‑gluconate inducible gluconate regulon transcriptional repressor
RA	3,601,824	G→C	7.7%	P88R (CCC→CGC) ‡	ftsX ←	putative ABC transporter permease
RA	3,601,825	G→C	7.7%	P88A (CCC→GCC) ‡	ftsX ←	putative ABC transporter permease
RA	3,620,644	T→A	17.1%	L485M (TTG→ATG) ‡	rhsB →	Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
RA	3,620,646	G→A	17.4%	L485L (TTG→TTA) ‡	rhsB →	Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
RA	3,620,666	T→G	17.3%	L492W (TTG→TGG)	rhsB →	Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
RA	3,630,661	A→T	13.6%	intergenic (‑59/+307)	yhiI ← / ← yhiJ	putative membrane fusion protein (MFP) of efflux pump/DUF4049 family protein
RA	3,630,667	A→G	15.2%	intergenic (‑65/+301)	yhiI ← / ← yhiJ	putative membrane fusion protein (MFP) of efflux pump/DUF4049 family protein
RA	3,636,004	C→T	7.8%	intergenic (+111/+204)	yhiM → / ← yhiN	acid resistance protein, inner membrane/putative oxidoreductase
RA	3,636,007	A→C	7.8%	intergenic (+114/+201)	yhiM → / ← yhiN	acid resistance protein, inner membrane/putative oxidoreductase
RA	3,636,008	G→T	7.5%	intergenic (+115/+200)	yhiM → / ← yhiN	acid resistance protein, inner membrane/putative oxidoreductase
RA	3,636,011	A→G	7.5%	intergenic (+118/+197)	yhiM → / ← yhiN	acid resistance protein, inner membrane/putative oxidoreductase
RA	3,639,165	T→C	6.3%	intergenic (+24/+220)	pitA → / ← uspB	phosphate transporter, low‑affinity; tellurite importer/universal stress (ethanol tolerance) protein B
RA	3,639,208	T→C	8.6%	intergenic (+67/+177)	pitA → / ← uspB	phosphate transporter, low‑affinity; tellurite importer/universal stress (ethanol tolerance) protein B
RA	3,639,213	G→C	8.9%	intergenic (+72/+172)	pitA → / ← uspB	phosphate transporter, low‑affinity; tellurite importer/universal stress (ethanol tolerance) protein B
RA	3,657,599	T→A	26.3%	intergenic (+32/+387)	hdeD → / ← arrS	acid‑resistance membrane protein/antisense sRNA ArrS, function unknown
RA	3,657,601	G→C	25.0%	intergenic (+34/+385)	hdeD → / ← arrS	acid‑resistance membrane protein/antisense sRNA ArrS, function unknown
RA	3,657,603	T→A	34.1%	intergenic (+36/+383)	hdeD → / ← arrS	acid‑resistance membrane protein/antisense sRNA ArrS, function unknown
RA	3,676,271	A→T	11.8%	intergenic (+163/+19)	yhjE → / ← yhjG	putative MFS transporter; membrane protein/putative inner membrane‑anchored periplasmic AsmA family protein
RA	3,697,970	T→C	5.4%	W505R (TGG→CGG)	bcsE →	cellulose production protein
RA	3,729,405	C→G	8.3%	intergenic (‑34/+38)	xylB ← / ← xylA	xylulokinase/D‑xylose isomerase
RA	3,729,408	C→G	8.2%	intergenic (‑37/+35)	xylB ← / ← xylA	xylulokinase/D‑xylose isomerase
RA	3,729,413	Δ1 bp	6.5%	intergenic (‑42/+30)	xylB ← / ← xylA	xylulokinase/D‑xylose isomerase
RA	3,736,322	G→T	10.1%	intergenic (+165/+31)	xylR → / ← bax	xylose divergent operon transcriptional activator/putative glucosaminidase
RA	3,736,323	A→G	9.8%	intergenic (+166/+30)	xylR → / ← bax	xylose divergent operon transcriptional activator/putative glucosaminidase
RA	3,736,324	C→T	9.7%	intergenic (+167/+29)	xylR → / ← bax	xylose divergent operon transcriptional activator/putative glucosaminidase
RA	3,736,325	A→C	9.9%	intergenic (+168/+28)	xylR → / ← bax	xylose divergent operon transcriptional activator/putative glucosaminidase
RA	3,740,791	G→C	5.9%	G363R (GGC→CGC)	avtA →	valine‑pyruvate aminotransferase; transaminase C; alanine‑valine transaminase
RA	3,747,168:1	+C	8.8%	coding (85/1497 nt)	lyxK →	L‑xylulose kinase
RA	3,747,173	Δ1 bp	9.2%	coding (90/1497 nt)	lyxK →	L‑xylulose kinase
RA	3,749,465	T→A	5.7%	R78R (CGT→CGA)	sgbU →	putative L‑xylulose 5‑phosphate 3‑epimerase
RA	3,756,563	A→G	5.8%	intergenic (‑52/+113)	aldB ← / ← yiaY	aldehyde dehydrogenase B/L‑threonine dehydrogenase
RA	3,756,564	T→A	5.1%	intergenic (‑53/+112)	aldB ← / ← yiaY	aldehyde dehydrogenase B/L‑threonine dehydrogenase
RA	3,756,565	C→T	5.1%	intergenic (‑54/+111)	aldB ← / ← yiaY	aldehyde dehydrogenase B/L‑threonine dehydrogenase
RA	3,774,207	C→T	9.0%	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	9.3%	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	9.3%	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	8.4%	intergenic (+28/‑202)	mtlA → / → mtlD	mannitol‑specific PTS enzyme: IIA, IIB and IIC components/mannitol‑1‑phosphate dehydrogenase, NAD‑dependent
RA	3,776,125	C→T	7.6%	S185F (TCC→TTC) ‡	mtlR →	mannitol operon repressor
RA	3,776,126	C→G	7.7%	S185S (TCC→TCG) ‡	mtlR →	mannitol operon repressor
RA	3,776,127	A→G	7.5%	K186E (AAA→GAA)	mtlR →	mannitol operon repressor
RA	3,778,876	G→A	8.6%	G493D (GGC→GAC)	lldP →	L‑lactate permease
RA	3,778,879	T→C	8.6%	V494A (GTC→GCC)	lldP →	L‑lactate permease
RA	3,781,051	C→G	23.9%	intergenic (+34/‑164)	lldD → / → trmL	L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent
RA	3,781,138	A→C	6.9%	intergenic (+121/‑77)	lldD → / → trmL	L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent
RA	3,787,619	Δ1 bp	7.3%	coding (782/1260 nt)	envC →	activator of AmiB,C murein hydrolases, septal ring factor
RA	3,787,624:1	+A	6.0%	coding (787/1260 nt)	envC →	activator of AmiB,C murein hydrolases, septal ring factor
RA	3,790,300	A→T	10.7%	intergenic (‑219/+20)	waaH ← / ← tdh	LPS(HepIII)‑glucuronic acid glycosyltransferase/L‑threonine 3‑dehydrogenase, NAD(P)‑binding
RA	3,790,303	A→T	10.0%	intergenic (‑222/+17)	waaH ← / ← tdh	LPS(HepIII)‑glucuronic acid glycosyltransferase/L‑threonine 3‑dehydrogenase, NAD(P)‑binding
RA	3,792,765	C→T	14.9%	intergenic (‑214/+61)	kbl ← / ← yibB	glycine C‑acetyltransferase/YibB family protein, function unknown
RA	3,792,766	A→T	17.9%	intergenic (‑215/+60)	kbl ← / ← yibB	glycine C‑acetyltransferase/YibB family protein, function unknown
RA	3,792,767	A→T	18.0%	intergenic (‑216/+59)	kbl ← / ← yibB	glycine C‑acetyltransferase/YibB family protein, function unknown
RA	3,792,768	A→G	18.0%	intergenic (‑217/+58)	kbl ← / ← yibB	glycine C‑acetyltransferase/YibB family protein, function unknown
RA	3,798,234	A→T	22.9%	intergenic (+27/+5)	waaL → / ← waaU	O‑antigen ligase/lipopolysaccharide core biosynthesis
RA	3,798,235	A→T	23.3%	intergenic (+28/+4)	waaL → / ← waaU	O‑antigen ligase/lipopolysaccharide core biosynthesis
RA	3,809,681	T→A	6.6%	V381D (GTT→GAT) ‡	waaA →	3‑deoxy‑D‑manno‑octulosonic‑acid transferase (KDO transferase)
RA	3,809,682	T→A	6.6%	V381V (GTT→GTA) ‡	waaA →	3‑deoxy‑D‑manno‑octulosonic‑acid transferase (KDO transferase)
RA	3,809,683	T→A	6.6%	S382T (TCC→ACC)	waaA →	3‑deoxy‑D‑manno‑octulosonic‑acid transferase (KDO transferase)
RA	3,814,164	G→A	5.8%	G78D (GGT→GAT)	dut →	deoxyuridinetriphosphatase
RA	3,814,167	T→C	5.6%	I79T (ATC→ACC)	dut →	deoxyuridinetriphosphatase
RA	3,815,816	C→G	20.0%	intergenic (‑48/+18)	pyrE ← / ← rph	orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH
RA	3,815,819	C→G	19.9%	intergenic (‑51/+15)	pyrE ← / ← rph	orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH
RA	3,817,940	T→A	5.5%	F61I (TTC→ATC)	dinD →	DNA damage‑inducible protein
RA	3,817,948	G→T	9.8%	E63D (GAG→GAT)	dinD →	DNA damage‑inducible protein
RA	3,817,949	A→C	9.3%	I64L (ATC→CTC)	dinD →	DNA damage‑inducible protein
RA	3,817,957	T→A	6.0%	D66E (GAT→GAA)	dinD →	DNA damage‑inducible protein
RA	3,831,757	C→T	6.6%	A434V (GCC→GTC)	yicH →	putative inner membrane‑anchored periplasmic AsmA family protein
RA	3,831,761	C→G	6.6%	A435A (GCC→GCG)	yicH →	putative inner membrane‑anchored periplasmic AsmA family protein
RA	3,831,764	C→G	6.7%	A436A (GCC→GCG)	yicH →	putative inner membrane‑anchored periplasmic AsmA family protein
RA	3,831,768	A→G	6.5%	T438A (ACA→GCA)	yicH →	putative inner membrane‑anchored periplasmic AsmA family protein
RA	3,832,188	A→T	16.0%	intergenic (+22/+31)	yicH → / ← yicI	putative inner membrane‑anchored periplasmic AsmA family protein/putative alpha‑glucosidase
RA	3,832,191	C→G	13.6%	intergenic (+25/+28)	yicH → / ← yicI	putative inner membrane‑anchored periplasmic AsmA family protein/putative alpha‑glucosidase
RA	3,832,194	A→T	12.4%	intergenic (+28/+25)	yicH → / ← yicI	putative inner membrane‑anchored periplasmic AsmA family protein/putative alpha‑glucosidase
RA	3,844,348	G→T	8.3%	A129S (GCC→TCC)	adeD →	cryptic adenine deaminase
RA	3,844,353	A→C	8.2%	G130G (GGA→GGC)	adeD →	cryptic adenine deaminase
RA	3,852,558	T→A	5.3%	K76I (AAA→ATA) ‡	ilvB ←	acetolactate synthase 2 large subunit
RA	3,852,559	T→A	5.3%	K76* (AAA→TAA) ‡	ilvB ←	acetolactate synthase 2 large subunit
RA	3,852,564	T→G	5.1%	D74A (GAC→GCC)	ilvB ←	acetolactate synthase 2 large subunit
RA	3,853,602	C→T	7.3%	A17V (GCA→GTA) ‡	tisB →	toxic membrane persister formation peptide, LexA‑regulated
RA	3,853,603	A→G	8.9%	A17A (GCA→GCG) ‡	tisB →	toxic membrane persister formation peptide, LexA‑regulated
RA	3,880,440	T→A	5.1%	D261V (GAC→GTC)	recF ←	gap repair protein
RA	3,880,444	C→T	5.2%	A260T (GCC→ACC)	recF ←	gap repair protein
RA	3,894,868	G→C	5.3%	A73P (GCT→CCT)	chrR →	chromate reductase, Class I, flavoprotein
RA	3,900,410	A→T	7.6%	P56P (CCT→CCA)	yieL ←	putative xylanase
RA	3,900,542	A→T	13.5%	I12I (ATT→ATA)	yieL ←	putative xylanase
RA	3,900,545	A→T	14.9%	A11A (GCT→GCA)	yieL ←	putative xylanase
RA	3,917,686	A→C	5.1%	S194A (TCA→GCA)	atpG ←	F1 sector of membrane‑bound ATP synthase, gamma subunit
RA	3,917,692	G→T	5.1%	P192T (CCG→ACG)	atpG ←	F1 sector of membrane‑bound ATP synthase, gamma subunit
RA	3,918,296	C→T	7.1%	intergenic (‑31/+20)	atpG ← / ← atpA	F1 sector of membrane‑bound ATP synthase, gamma subunit/F1 sector of membrane‑bound ATP synthase, alpha subunit
RA	3,918,299	A→G	6.4%	intergenic (‑34/+17)	atpG ← / ← atpA	F1 sector of membrane‑bound ATP synthase, gamma subunit/F1 sector of membrane‑bound ATP synthase, alpha subunit
RA	3,918,304	A→G	5.7%	intergenic (‑39/+12)	atpG ← / ← atpA	F1 sector of membrane‑bound ATP synthase, gamma subunit/F1 sector of membrane‑bound ATP synthase, alpha subunit
RA	3,920,796	T→C	17.5%	A31A (GCA→GCG)	atpF ←	F0 sector of membrane‑bound ATP synthase, subunit b
RA	3,920,809	G→A	10.3%	P27L (CCG→CTG)	atpF ←	F0 sector of membrane‑bound ATP synthase, subunit b
RA	3,935,454	A→C	5.4%	N56T (AAC→ACC)	rbsC →	D‑ribose ABC transporter permease
RA	3,959,480	A→T	8.2%	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	8.0%	intergenic (+36/+51)	ilvC → / ← ppiC	ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C)
RA	3,959,515	T→A	16.7%	intergenic (+70/+17)	ilvC → / ← ppiC	ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C)
RA	3,959,924	A→T	15.1%	intergenic (‑111/+88)	ppiC ← / ← yifN	peptidyl‑prolyl cis‑trans isomerase C (rotamase C)/PemK toxin family pseudogene
RA	3,959,925	A→T	15.2%	intergenic (‑112/+87)	ppiC ← / ← yifN	peptidyl‑prolyl cis‑trans isomerase C (rotamase C)/PemK toxin family pseudogene
RA	3,959,926	A→T	15.2%	intergenic (‑113/+86)	ppiC ← / ← yifN	peptidyl‑prolyl cis‑trans isomerase C (rotamase C)/PemK toxin family pseudogene
RA	3,963,415	A→C	15.3%	L272R (CTG→CGG) ‡	gpp ←	guanosine pentaphosphatase/exopolyphosphatase
RA	3,963,416	G→T	15.3%	L272M (CTG→ATG) ‡	gpp ←	guanosine pentaphosphatase/exopolyphosphatase
RA	3,965,396	C→T	6.2%	D79N (GAT→AAT)	rhlB ←	ATP‑dependent RNA helicase
RA	3,965,398	G→C	5.9%	A78G (GCC→GGC)	rhlB ←	ATP‑dependent RNA helicase
RA	3,965,400	A→G	5.9%	I77I (ATT→ATC)	rhlB ←	ATP‑dependent RNA helicase
RA	3,966,768	G→T	8.1%	E118* (GAA→TAA) ‡	rho →	transcription termination factor
RA	3,966,769	A→T	9.1%	E118V (GAA→GTA) ‡	rho →	transcription termination factor
RA	3,966,770	A→C	9.1%	E118D (GAA→GAC) ‡	rho →	transcription termination factor
RA	3,970,813	Δ1 bp	8.2%	coding (681/1131 nt)	wecB →	UDP‑N‑acetyl glucosamine‑2‑epimerase
RA	3,970,817:1	+G	7.9%	coding (685/1131 nt)	wecB →	UDP‑N‑acetyl glucosamine‑2‑epimerase
RA	3,971,996	T→A	6.0%	L246Q (CTG→CAG)	wecC →	UDP‑N‑acetyl‑D‑mannosaminuronic acid dehydrogenase
RA	3,977,701	T→A	6.3%	P59P (CCT→CCA)	wecF →	TDP‑Fuc4NAc:lipidIIFuc4NAc transferase
RA	3,981,102	T→A	9.8%	V72V (GTT→GTA)	yifK →	putative APC family amino acid transporter
RA	3,981,376	A→G	5.4%	M164V (ATG→GTG)	yifK →	putative APC family amino acid transporter
RA	3,991,334	T→A	14.7%	I61N (ATT→AAT) ‡	cyaA →	adenylate cyclase
RA	3,991,335	T→A	14.6%	I61I (ATT→ATA) ‡	cyaA →	adenylate cyclase
RA	3,992,624	T→G	100%	L491R (CTG→CGG)	cyaA →	adenylate cyclase
RA	4,002,709	A→G	11.1%	W31R (TGG→CGG)	yigF ←	DUF2628 family putative inner membrane protein
RA	4,015,333	A→T	19.8%	intergenic (+19/+21)	metE → / ← ysgA	5‑methyltetrahydropteroyltriglutamate‑ homocysteine S‑methyltransferase/putative carboxymethylenebutenolidase
RA	4,017,216:1	+A	7.4%	intergenic (+24/‑117)	udp → / → rmuC	uridine phosphorylase/DNA recombination protein
RA	4,017,222	Δ1 bp	7.3%	intergenic (+30/‑111)	udp → / → rmuC	uridine phosphorylase/DNA recombination protein
RA	4,022,007	C→T	7.6%	G21G (GGC→GGT)	tatA →	TatABCE protein translocation system subunit
RA	4,022,008	A→G	7.6%	T22A (ACC→GCC)	tatA →	TatABCE protein translocation system subunit
RA	4,041,216	T→C	8.3%	Q73R (CAG→CGG) ‡	mobB ←	molybdopterin‑guanine dinucleotide biosynthesis protein B
RA	4,041,217	G→A	6.0%	Q73* (CAG→TAG) ‡	mobB ←	molybdopterin‑guanine dinucleotide biosynthesis protein B
RA	4,041,220	T→C	6.0%	S72G (AGC→GGC)	mobB ←	molybdopterin‑guanine dinucleotide biosynthesis protein B
RA	4,041,221	G→A	6.0%	A71A (GCC→GCT)	mobB ←	molybdopterin‑guanine dinucleotide biosynthesis protein B
RA	4,049,986	G→T	30.7%	noncoding (88/109 nt)	spf →	Spot 42 sRNA antisense regulator of galK translation, Hfq‑dependent
RA	4,051,951	G→C	5.3%	intergenic (+95/‑94)	yihI → / → hemN	activator of Der GTPase/coproporphyrinogen III oxidase, SAM and NAD(P)H dependent, oxygen‑independent
RA	4,061,993	T→C	5.4%	Y277H (TAT→CAT)	yihM →	putative sugar phosphate isomerase
RA	4,062,371	A→T	14.0%	N42I (AAT→ATT)	yihN →	MFS transporter family protein
RA	4,070,410	C→A	14.5%	intergenic (‑9/+105)	yihR ← / ← yihS	putative sulphoquinovose mutarotase/sulphoquinovose isomerase
RA	4,070,413	T→G	13.6%	intergenic (‑12/+102)	yihR ← / ← yihS	putative sulphoquinovose mutarotase/sulphoquinovose isomerase
RA	4,080,616	C→A	7.9%	G205C (GGC→TGC)	fdhE ←	formate dehydrogenase formation protein
RA	4,080,621	T→G	8.5%	Q203P (CAA→CCA)	fdhE ←	formate dehydrogenase formation protein
RA	4,093,463	A→G	5.3%	S270S (AGT→AGC)	rhaD ←	rhamnulose‑1‑phosphate aldolase
RA	4,111,939	T→G	6.3%	T92T (ACA→ACC)	yiiQ ←	DUF1454 family putative periplasmic protein
RA	4,113,473	T→C	7.4%	L61L (TTG→CTG) ‡	uspD →	stress‑induced protein
RA	4,113,474	T→A	7.3%	L61* (TTG→TAG) ‡	uspD →	stress‑induced protein
RA	4,113,475	G→A	7.4%	L61L (TTG→TTA) ‡	uspD →	stress‑induced protein
RA	4,114,536	C→T	5.5%	intergenic (‑64/+33)	fpr ← / ← glpX	ferredoxin‑NADP reductase; flavodoxin reductase/fructose 1,6‑bisphosphatase II
RA	4,114,537	G→T	5.5%	intergenic (‑65/+32)	fpr ← / ← glpX	ferredoxin‑NADP reductase; flavodoxin reductase/fructose 1,6‑bisphosphatase II
RA	4,114,538	A→C	5.2%	intergenic (‑66/+31)	fpr ← / ← glpX	ferredoxin‑NADP reductase; flavodoxin reductase/fructose 1,6‑bisphosphatase II
RA	4,114,539	A→G	5.2%	intergenic (‑67/+30)	fpr ← / ← glpX	ferredoxin‑NADP reductase; flavodoxin reductase/fructose 1,6‑bisphosphatase II
RA	4,117,005	T→A	100%	D73V (GAT→GTT)	glpK ←	glycerol kinase
RA	4,121,959	T→G	12.7%	N110T (AAC→ACC)	hslV ←	peptidase component of the HslUV protease
RA	4,121,962	C→A	11.3%	G109V (GGT→GTT)	hslV ←	peptidase component of the HslUV protease
RA	4,130,005	G→A	6.5%	L57L (TTG→TTA)	metL →	Bifunctional aspartokinase/homoserine dehydrogenase 2
RA	4,130,008	T→C	7.0%	I58I (ATT→ATC)	metL →	Bifunctional aspartokinase/homoserine dehydrogenase 2
RA	4,138,006	T→G	6.2%	T344P (ACG→CCG)	gldA ←	glycerol dehydrogenase, NAD+ dependent; 1,2‑propanediol:NAD+ oxidoreductase
RA	4,138,011	C→A	6.2%	G342V (GGC→GTC)	gldA ←	glycerol dehydrogenase, NAD+ dependent; 1,2‑propanediol:NAD+ oxidoreductase
RA	4,142,509	T→G	5.9%	intergenic (‑288/‑21)	frwA ← / → frwC	putative PTS enzyme: Hpr, enzyme I and II components/putative enzyme IIC component of PTS
RA	4,142,512	C→A	5.6%	intergenic (‑291/‑18)	frwA ← / → frwC	putative PTS enzyme: Hpr, enzyme I and II components/putative enzyme IIC component of PTS
RA	4,146,431:1	+A	7.8%	coding (174/879 nt)	pflC →	putative [formate‑C‑acetyltransferase 2]‑activating enzyme; pyruvate formate‑lyase 1‑activating enzyme
RA	4,146,436	Δ1 bp	7.5%	coding (179/879 nt)	pflC →	putative [formate‑C‑acetyltransferase 2]‑activating enzyme; pyruvate formate‑lyase 1‑activating enzyme
RA	4,148,049	C→G	6.5%	G90A (GGC→GCC)	yijO ←	AraC family putative transcriptional activator
RA	4,158,153	C→T	6.6%	A435V (GCG→GTG)	argH →	argininosuccinate lyase
RA	4,184,278	G→T	7.4%	E1012* (GAA→TAA) ‡	rpoB →	RNA polymerase, beta subunit
RA	4,184,279	A→T	7.2%	E1012V (GAA→GTA) ‡	rpoB →	RNA polymerase, beta subunit
RA	4,184,280	A→C	7.1%	E1012D (GAA→GAC) ‡	rpoB →	RNA polymerase, beta subunit
RA	4,185,306	A→T	6.3%	intergenic (+33/‑44)	rpoB → / → rpoC	RNA polymerase, beta subunit/RNA polymerase, beta prime subunit
RA	4,185,307	A→T	6.6%	intergenic (+34/‑43)	rpoB → / → rpoC	RNA polymerase, beta subunit/RNA polymerase, beta prime subunit
RA	4,185,907	G→T	8.1%	Q186H (CAG→CAT)	rpoC →	RNA polymerase, beta prime subunit
RA	4,185,913	G→T	5.7%	L188L (CTG→CTT)	rpoC →	RNA polymerase, beta prime subunit
RA	4,185,915	T→A	5.6%	L189Q (CTG→CAG)	rpoC →	RNA polymerase, beta prime subunit
RA	4,185,917	A→C	5.4%	K190Q (AAG→CAG)	rpoC →	RNA polymerase, beta prime subunit
RA	4,185,923	A→C	5.7%	M192L (ATG→CTG)	rpoC →	RNA polymerase, beta prime subunit
RA	4,189,525	C→G	6.1%	S1392R (AGC→AGG)	rpoC →	RNA polymerase, beta prime subunit
RA	4,213,156	G→A	14.3%	noncoding (117/120 nt)	rrfE →	5S ribosomal RNA of rrnE operon
RA	4,215,198	A→G	5.9%	T307A (ACG→GCG)	metA →	homoserine O‑transsuccinylase
RA	4,215,201	C→T	5.9%	L308L (CTG→TTG)	metA →	homoserine O‑transsuccinylase
RA	4,220,272	T→C	8.0%	D559D (GAT→GAC)	aceK →	isocitrate dehydrogenase kinase/phosphatase
RA	4,223,854	T→C	8.4%	R9R (CGT→CGC)	metH →	homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent
RA	4,223,855	G→A	8.4%	A10T (GCG→ACG)	metH →	homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent
RA	4,225,743	G→T	6.2%	R639L (CGC→CTC)	metH →	homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent
RA	4,227,550	G→A	23.9%	intergenic (+39/‑181)	metH → / → yjbB	homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent/putative Na+/Pi‑cotransporter
RA	4,227,555	A→T	22.4%	intergenic (+44/‑176)	metH → / → yjbB	homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent/putative Na+/Pi‑cotransporter
RA	4,227,560	T→C	22.4%	intergenic (+49/‑171)	metH → / → yjbB	homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent/putative Na+/Pi‑cotransporter
RA	4,235,469	G→A	19.0%	intergenic (+62/‑437)	pgi → / → yjbE	glucosephosphate isomerase/extracellular polysaccharide production threonine‑rich protein
RA	4,235,470	C→A	19.0%	intergenic (+63/‑436)	pgi → / → yjbE	glucosephosphate isomerase/extracellular polysaccharide production threonine‑rich protein
RA	4,235,477	G→A	31.8%	intergenic (+70/‑429)	pgi → / → yjbE	glucosephosphate isomerase/extracellular polysaccharide production threonine‑rich protein
RA	4,235,478	T→C	31.8%	intergenic (+71/‑428)	pgi → / → yjbE	glucosephosphate isomerase/extracellular polysaccharide production threonine‑rich protein
RA	4,235,485	T→G	25.0%	intergenic (+78/‑421)	pgi → / → yjbE	glucosephosphate isomerase/extracellular polysaccharide production threonine‑rich protein
RA	4,235,486	T→C	25.0%	intergenic (+79/‑420)	pgi → / → yjbE	glucosephosphate isomerase/extracellular polysaccharide production threonine‑rich protein
RA	4,258,702	G→A	6.3%	D321N (GAC→AAC)	dinF →	oxidative stress resistance protein; putative MATE family efflux pump; UV and mitomycin C inducible protein
RA	4,261,358	T→A	19.1%	intergenic (+52/‑311)	yjbM → / → dusA	uncharacterized protein/tRNA‑dihydrouridine synthase A
RA	4,261,359	T→A	19.1%	intergenic (+53/‑310)	yjbM → / → dusA	uncharacterized protein/tRNA‑dihydrouridine synthase A
RA	4,262,250	G→C	17.0%	G194G (GGG→GGC)	dusA →	tRNA‑dihydrouridine synthase A
RA	4,262,255	G→C	16.6%	S196T (AGC→ACC)	dusA →	tRNA‑dihydrouridine synthase A
RA	4,265,670	T→G	5.9%	F453V (TTT→GTT)	dnaB →	replicative DNA helicase
RA	4,270,142	G→A	7.7%	intergenic (+15/‑96)	aphA → / → yjbQ	acid phosphatase/phosphotransferase, class B, non‑specific/thiamine phosphate synthase
RA	4,270,144	G→C	8.0%	intergenic (+17/‑94)	aphA → / → yjbQ	acid phosphatase/phosphotransferase, class B, non‑specific/thiamine phosphate synthase
RA	4,270,146	T→C	7.8%	intergenic (+19/‑92)	aphA → / → yjbQ	acid phosphatase/phosphotransferase, class B, non‑specific/thiamine phosphate synthase
RA	4,296,060	C→T	25.7%	intergenic (+266/+376)	gltP → / ← yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA	4,307,294	A→T	19.1%	L169Q (CTG→CAG)	alsK ←	D‑allose kinase
RA	4,307,298	G→A	21.5%	P168S (CCC→TCC)	alsK ←	D‑allose kinase
RA	4,314,233	A→T	8.6%	intergenic (+36/+111)	yjdP → / ← phnP	putative periplasmic protein/5‑phospho‑alpha‑D‑ribosyl 1,2‑cyclic phosphate phosphodiesterase
RA	4,323,258	A→C	7.5%	intergenic (‑28/+78)	phnE ← / ← phnD	defective phosphonate ABC transporter permease;transport; Transport of small molecules: Anions; membrane channel protein component of Pn transporter; membrane component of ABC superfamily/phosphonate ABC transporter periplasmic binding protein
RA	4,323,312	G→C	14.3%	intergenic (‑82/+24)	phnE ← / ← phnD	defective phosphonate ABC transporter permease;transport; Transport of small molecules: Anions; membrane channel protein component of Pn transporter; membrane component of ABC superfamily/phosphonate ABC transporter periplasmic binding protein
RA	4,323,313	G→C	14.2%	intergenic (‑83/+23)	phnE ← / ← phnD	defective phosphonate ABC transporter permease;transport; Transport of small molecules: Anions; membrane channel protein component of Pn transporter; membrane component of ABC superfamily/phosphonate ABC transporter periplasmic binding protein
RA	4,335,654	T→A	20.0%	intergenic (‑64/+40)	eptA ← / ← adiC	lipid A phosphoethanolamine transferase/arginine:agmatine antiporter
RA	4,335,655	T→A	20.0%	intergenic (‑65/+39)	eptA ← / ← adiC	lipid A phosphoethanolamine transferase/arginine:agmatine antiporter
RA	4,336,974	A→T	14.5%	S20T (TCG→ACG)	adiC ←	arginine:agmatine antiporter
RA	4,336,979	A→C	13.3%	M18R (ATG→AGG)	adiC ←	arginine:agmatine antiporter
RA	4,336,981	C→G	13.0%	L17L (CTG→CTC) ‡	adiC ←	arginine:agmatine antiporter
RA	4,336,983	G→T	13.6%	L17M (CTG→ATG) ‡	adiC ←	arginine:agmatine antiporter
RA	4,336,988	A→T	13.9%	V15D (GTC→GAC)	adiC ←	arginine:agmatine antiporter
RA	4,339,802	A→G	8.5%	A240A (GCT→GCC)	adiA ←	arginine decarboxylase
RA	4,339,805	C→T	8.5%	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	5.3%	P13P (CCG→CCC)	fumB ←	anaerobic class I fumarate hydratase (fumarase B)
RA	4,356,445	A→T	33.4%	intergenic (‑34/+25)	dtpC ← / ← cadA	dipeptide and tripeptide permease/lysine decarboxylase, acid‑inducible
RA	4,356,446	A→T	33.3%	intergenic (‑35/+24)	dtpC ← / ← cadA	dipeptide and tripeptide permease/lysine decarboxylase, acid‑inducible
RA	4,376,280	G→A	9.0%	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	13.1%	intergenic (+26/‑26)	efp → / → ecnA	polyproline‑specific translation elongation factor EF‑P/entericidin A membrane lipoprotein, antidote entericidin B
RA	4,385,206	T→A	5.1%	P456P (CCT→CCA)	yjeM →	putative transporter
RA	4,385,207	G→C	5.2%	V457L (GTG→CTG) ‡	yjeM →	putative transporter
RA	4,385,208	T→A	5.2%	V457E (GTG→GAG) ‡	yjeM →	putative transporter
RA	4,388,496	T→A	14.3%	Q292L (CAG→CTG)	mscM ←	mechanosensitive channel protein, miniconductance
RA	4,388,502	G→C	14.3%	A290G (GCC→GGC)	mscM ←	mechanosensitive channel protein, miniconductance
RA	4,388,508	T→A	10.1%	Q288L (CAG→CTG)	mscM ←	mechanosensitive channel protein, miniconductance
RA	4,392,617	C→G	8.2%	noncoding (35/76 nt)	glyY →	tRNA‑Gly
RA	4,392,757	C→G	13.6%	intergenic (+99/‑135)	glyY → / → yjeV	tRNA‑Gly/uncharacterized protein
RA	4,395,454	T→C	14.7%	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	14.7%	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	4,409,160	G→A	11.3%	intergenic (+65/‑115)	rnr → / → rlmB	exoribonuclease R, RNase R/23S rRNA mG2251 2'‑O‑ribose methyltransferase, SAM‑dependent
RA	4,409,161	C→A	11.1%	intergenic (+66/‑114)	rnr → / → rlmB	exoribonuclease R, RNase R/23S rRNA mG2251 2'‑O‑ribose methyltransferase, SAM‑dependent
RA	4,409,167	G→T	11.1%	intergenic (+72/‑108)	rnr → / → rlmB	exoribonuclease R, RNase R/23S rRNA mG2251 2'‑O‑ribose methyltransferase, SAM‑dependent
RA	4,409,168	A→C	11.5%	intergenic (+73/‑107)	rnr → / → rlmB	exoribonuclease R, RNase R/23S rRNA mG2251 2'‑O‑ribose methyltransferase, SAM‑dependent
RA	4,409,402	Δ1 bp	9.4%	coding (128/732 nt)	rlmB →	23S rRNA mG2251 2'‑O‑ribose methyltransferase, SAM‑dependent
RA	4,409,407	T→A	9.7%	S45T (TCT→ACT)	rlmB →	23S rRNA mG2251 2'‑O‑ribose methyltransferase, SAM‑dependent
RA	4,409,410:1	+A	9.7%	coding (136/732 nt)	rlmB →	23S rRNA mG2251 2'‑O‑ribose methyltransferase, SAM‑dependent
RA	4,422,887	G→A	7.0%	A14A (GCG→GCA)	ulaE →	L‑xylulose 5‑phosphate 3‑epimerase
RA	4,422,895	C→G	9.1%	A17G (GCC→GGC)	ulaE →	L‑xylulose 5‑phosphate 3‑epimerase
RA	4,433,316	G→A	6.3%	P237S (CCC→TCC)	qorB ←	NAD(P)H:quinone oxidoreductase
RA	4,433,318	A→T	6.3%	L236Q (CTG→CAG)	qorB ←	NAD(P)H:quinone oxidoreductase
RA	4,433,320	T→C	6.3%	G235G (GGA→GGG)	qorB ←	NAD(P)H:quinone oxidoreductase
RA	4,447,844	T→C	11.8%	S1245P (TCT→CCT)	tamB →	translocation and assembly module for autotransporter export, inner membrane subunit
RA	4,447,850	G→C	11.1%	V1247L (GTA→CTA)	tamB →	translocation and assembly module for autotransporter export, inner membrane subunit
RA	4,447,853	G→C	10.2%	D1248H (GAC→CAC)	tamB →	translocation and assembly module for autotransporter export, inner membrane subunit
RA	4,447,964	T→A	6.5%	L24* (TTA→TAA)	ytfP →	GGCT‑like protein
RA	4,454,799	G→T	5.2%	R271S (CGT→AGT)	fbp ←	fructose‑1,6‑bisphosphatase I
RA	4,454,800	C→G	5.4%	L270L (CTG→CTC) ‡	fbp ←	fructose‑1,6‑bisphosphatase I
RA	4,454,801	A→C	5.6%	L270R (CTG→CGG) ‡	fbp ←	fructose‑1,6‑bisphosphatase I
RA	4,457,246	T→A	7.0%	intergenic (+88/+68)	mpl → / ← yjgA	UDP‑N‑acetylmuramate:L‑alanyl‑gamma‑D‑glutamyl‑ meso‑diaminopimelate ligase/ribosome‑associated UPF0307 family protein
RA	4,457,248	G→C	7.0%	intergenic (+90/+66)	mpl → / ← yjgA	UDP‑N‑acetylmuramate:L‑alanyl‑gamma‑D‑glutamyl‑ meso‑diaminopimelate ligase/ribosome‑associated UPF0307 family protein
RA	4,457,250	T→A	7.3%	intergenic (+92/+64)	mpl → / ← yjgA	UDP‑N‑acetylmuramate:L‑alanyl‑gamma‑D‑glutamyl‑ meso‑diaminopimelate ligase/ribosome‑associated UPF0307 family protein
RA	4,457,256	T→G	9.1%	intergenic (+98/+58)	mpl → / ← yjgA	UDP‑N‑acetylmuramate:L‑alanyl‑gamma‑D‑glutamyl‑ meso‑diaminopimelate ligase/ribosome‑associated UPF0307 family protein
RA	4,457,257	T→C	9.1%	intergenic (+99/+57)	mpl → / ← yjgA	UDP‑N‑acetylmuramate:L‑alanyl‑gamma‑D‑glutamyl‑ meso‑diaminopimelate ligase/ribosome‑associated UPF0307 family protein
RA	4,467,149	T→C	6.7%	Q33R (CAG→CGG) ‡	treR ←	trehalose 6‑phosphate‑inducible trehalose regulon transcriptional repressor
RA	4,467,150	G→A	6.8%	Q33* (CAG→TAG) ‡	treR ←	trehalose 6‑phosphate‑inducible trehalose regulon transcriptional repressor
RA	4,470,951	A→C	20.5%	intergenic (‑38/+35)	ridA ← / ← pyrI	enamine/imine deaminase, reaction intermediate detoxification/aspartate carbamoyltransferase, regulatory subunit
RA	4,470,952	T→C	22.9%	intergenic (‑39/+34)	ridA ← / ← pyrI	enamine/imine deaminase, reaction intermediate detoxification/aspartate carbamoyltransferase, regulatory subunit
RA	4,470,957	G→A	16.3%	intergenic (‑44/+29)	ridA ← / ← pyrI	enamine/imine deaminase, reaction intermediate detoxification/aspartate carbamoyltransferase, regulatory subunit
RA	4,470,958	G→T	16.2%	intergenic (‑45/+28)	ridA ← / ← pyrI	enamine/imine deaminase, reaction intermediate detoxification/aspartate carbamoyltransferase, regulatory subunit
RA	4,479,012	A→T	17.9%	intergenic (+123/+22)	rraB → / ← yjgM	protein inhibitor of RNase E/GNAT family putative N‑acetyltransferase
RA	4,479,016	G→C	19.7%	intergenic (+127/+18)	rraB → / ← yjgM	protein inhibitor of RNase E/GNAT family putative N‑acetyltransferase
RA	4,479,020	A→T	21.8%	intergenic (+131/+14)	rraB → / ← yjgM	protein inhibitor of RNase E/GNAT family putative N‑acetyltransferase
RA	4,484,395	A→C	5.3%	intergenic (‑115/+45)	holC ← / ← pepA	DNA polymerase III, chi subunit/multifunctional aminopeptidase A: a cyteinylglycinase, transcription regulator and site‑specific recombination factor
RA	4,496,511	A→G	12.3%	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	11.7%	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	7.3%	coding (65/957 nt)	fecD ←	ferric citrate ABC transporter permease
RA	4,520,500	Δ1 bp	33.3%	intergenic (‑176/+171)	yjhU ← / ← yjhF	putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter
RA	4,520,504:1	+T	19.2%	intergenic (‑180/+167)	yjhU ← / ← yjhF	putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter
RA	4,532,534	G→C	5.6%	A217G (GCC→GGC)	yjhP ←	putative methyltransferase
RA	4,532,537	G→C	5.6%	A216G (GCC→GGC)	yjhP ←	putative methyltransferase
RA	4,548,914	G→C	12.5%	G36A (GGT→GCT)	fimH →	minor component of type 1 fimbriae
RA	4,548,917	G→C	12.3%	G37A (GGC→GCC)	fimH →	minor component of type 1 fimbriae
RA	4,548,920	G→C	11.3%	S38T (AGC→ACC)	fimH →	minor component of type 1 fimbriae
RA	4,551,422	T→A	6.9%	intergenic (‑126/‑214)	gntP ← / → uxuA	fructuronate transporter/mannonate hydrolase
RA	4,565,341	A→G	11.1%	I170I (ATT→ATC)	yjiM ←	putative 2‑hydroxyglutaryl‑CoA dehydratase
RA	4,565,345	G→C	11.5%	A169G (GCC→GGC)	yjiM ←	putative 2‑hydroxyglutaryl‑CoA dehydratase
RA	4,565,349	C→T	9.7%	D168N (GAT→AAT)	yjiM ←	putative 2‑hydroxyglutaryl‑CoA dehydratase
RA	4,565,354	A→T	6.6%	L166Q (CTG→CAG)	yjiM ←	putative 2‑hydroxyglutaryl‑CoA dehydratase
RA	4,566,645	T→A	7.7%	K201I (AAA→ATA) ‡	yjiN ←	zinc‑type alcohol dehydrogenase‑like protein
RA	4,566,646	T→A	7.7%	K201* (AAA→TAA) ‡	yjiN ←	zinc‑type alcohol dehydrogenase‑like protein
RA	4,592,199	C→T	6.7%	A181A (GCC→GCT)	tsr →	methyl‑accepting chemotaxis protein I, serine sensor receptor
RA	4,592,201	T→A	6.7%	V182D (GTC→GAC)	tsr →	methyl‑accepting chemotaxis protein I, serine sensor receptor
RA	4,592,203	A→G	6.5%	S183G (AGC→GGC)	tsr →	methyl‑accepting chemotaxis protein I, serine sensor receptor
RA	4,604,753	T→A	6.6%	S198R (AGT→AGA)	bglJ →	bgl operon transcriptional activator
RA	4,604,754	T→A	6.6%	S199T (TCT→ACT)	bglJ →	bgl operon transcriptional activator
RA	4,606,417	A→T	9.1%	intergenic (‑16/+252)	leuQ ← / ← rsmC	tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase, SAM‑dependent
RA	4,606,418	A→T	9.0%	intergenic (‑17/+251)	leuQ ← / ← rsmC	tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase, SAM‑dependent
RA	4,606,419	A→T	9.1%	intergenic (‑18/+250)	leuQ ← / ← rsmC	tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase, SAM‑dependent
RA	4,610,720	T→A	5.1%	L436Q (CTG→CAG)	prfC →	peptide chain release factor RF‑3
RA	4,612,329	A→G	33.2%	intergenic (+40/‑82)	ytjA → / → yjjU	uncharacterized protein/putative patatin‑like family phospholipase
RA	4,612,330	G→C	29.4%	intergenic (+41/‑81)	ytjA → / → yjjU	uncharacterized protein/putative patatin‑like family phospholipase
RA	4,612,331	C→T	29.4%	intergenic (+42/‑80)	ytjA → / → yjjU	uncharacterized protein/putative patatin‑like family phospholipase
RA	4,621,622	G→A	7.8%	intergenic (+20/‑147)	deoD → / → yjjJ	purine nucleoside phosphorylase 1; nicotinamide 1‑beta‑D‑riboside phosphorylase/putative protein kinase
RA	4,621,625	T→C	8.4%	intergenic (+23/‑144)	deoD → / → yjjJ	purine nucleoside phosphorylase 1; nicotinamide 1‑beta‑D‑riboside phosphorylase/putative protein kinase
RA	4,638,690	C→T	11.3%	G171G (GGC→GGT)	creD →	inner membrane protein
RA	4,638,691	A→G	11.2%	T172A (ACC→GCC)	creD →	inner membrane protein

Unassigned missing coverage evidence
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	375092–375166	375292	127–201	14 [12]	[12] 16	mhpE/mhpT	4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter
*	*	÷	NC_000913	583490	583581	92	14 [8]	[12] 16	tfaX/appY	pseudogene, DLP12 prophage;Phage or Prophage Related/global transcriptional activator; DLP12 prophage
*	*	÷	NC_000913	707925	708066	142	14 [12]	[12] 14	glnS/chiP	glutamyl‑tRNA synthetase/chitoporin, uptake of chitosugars
*	*	÷	NC_000913	781665–781676	781830	155–166	14 [12]	[3] 13	lysQ/nadA	tRNA‑Lys/quinolinate synthase, subunit A
*	*	÷	NC_000913	1121130	1121229	100	16 [10]	[12] 14	bssS/dinI	biofilm regulator/DNA damage‑inducible protein I
*	*	÷	NC_000913	1197726	1197821	96	14 [12]	[10] 20	ymfE	e14 prophage; putative inner membrane protein
*	*	÷	NC_000913	1292406	1292494	89	14 [12]	[11] 13	galU/hns	glucose‑1‑phosphate uridylyltransferase/global DNA‑binding transcriptional dual regulator H‑NS
*	*	÷	NC_000913	1530052	1530168	117	14 [12]	[12] 14	ydcD	putative immunity protein for RhsE
*	*	÷	NC_000913	1640981	1641042	62	13 [9]	[10] 14	essQ/cspB	Qin prophage; putative S lysis protein/Qin prophage; cold shock protein
*	*	÷	NC_000913	1795207	1795246	40	14 [12]	[12] 16	btuC/ihfA	vitamin B12 ABC transporter permease/integration host factor (IHF), DNA‑binding protein, alpha subunit
*	*	÷	NC_000913	1816133	1816229	97	14 [12]	[12] 14	katE/chbG	catalase HPII, heme d‑containing/chito‑oligosaccharide deacetylase
*	*	÷	NC_000913	1889890	1889941	52	14 [12]	[12] 17	fadD/yeaY	acyl‑CoA synthetase (long‑chain‑fatty‑acid‑‑CoA ligase)/Slp family lipoprotein, RpoE‑regulated
*	*	÷	NC_000913	2056666	2056780	115	14 [12]	[12] 14	amn/yeeN	AMP nucleosidase/UPF0082 family protein
*	*	÷	NC_000913	2057552	2057713	162	15 [11]	[11] 13	[yeeN]	[yeeN]
*	*	÷	NC_000913	2405598	2405651	54	13 [11]	[12] 13	nuoA/lrhA	NADH:ubiquinone oxidoreductase, membrane subunit A/transcriptional repressor of flagellar, motility and chemotaxis genes
*	*	÷	NC_000913	2470176	2470288	113	14 [12]	[12] 14	gtrS	serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
*	*	÷	NC_000913	2521313–2521352	2521508	157–196	16 [12]	[12] 20	[lysV]	[lysV]
*	*	÷	NC_000913	2620193	2620250	58	13 [11]	[11] 13	[upp]	[upp]
*	*	÷	NC_000913	2788641	2788676	36	14 [12]	[12] 15	[ygaQ]	[ygaQ]
*	*	÷	NC_000913	2877899	2878111	213	13 [12]	[12] 14	iap/ygbF	aminopeptidase in alkaline phosphatase isozyme conversion/CRISPR adaptation ssRNA endonuclease
*	*	÷	NC_000913	3313168	3313245	78	14 [12]	[12] 14	[rbfA]	[rbfA]
*	*	÷	NC_000913	3377743	3377811	69	13 [11]	[12] 14	sspA/rpsI	stringent starvation protein A, phage P1 late gene activator, RNAP‑associated acid‑resistance protein, inactive glutathione S‑transferase homolog/30S ribosomal subunit protein S9
*	*	÷	NC_000913	3413576	3413646	71	16 [8]	[10] 14	acrS/acrE	acrAB operon transcriptional repressor/cytoplasmic membrane lipoprotein
*	*	÷	NC_000913	3423762–3424234	3424532–3424238	5–771	13 [11]	[11] 13	[rrfD]–[rrlD]	[rrfD],[rrlD]
*	*	÷	NC_000913	3469957	3470122	166	14 [12]	[12] 14	chiA/tufA	periplasmic endochitinase/translation elongation factor EF‑Tu 1
*	*	÷	NC_000913	4044065	4044118	54	14 [12]	[12] 14	dsbA/yihF	periplasmic protein disulfide isomerase I/DUF945 family protein
*	*	÷	NC_000913	4235678	4235767	90	14 [12]	[8] 15	pgi/yjbE	glucosephosphate isomerase/extracellular polysaccharide production threonine‑rich protein
*	*	÷	NC_000913	4304525	4304607	83	15 [12]	[12] 16	ytcA/yjcS	putative inner membrane efflux pump‑associated DUF1656 family protein/metallo‑beta‑lactamase superfamily protein
*	*	÷	NC_000913	4537627	4537673	47	13 [11]	[11] 13	[nanM]	[nanM]
*	*	÷	NC_000913	4579993	4580099	107	14 [12]	[12] 14	[hsdS]	[hsdS]

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	37863 =	66 (0.710)	6 (0.070)	6/192	NT	8.9%	intergenic (‑39/+35)	caiC/caiB	putative crotonobetaine/carnitine‑CoA ligase/crotonobetainyl CoA:carnitine CoA transferase
	?	NC_000913	37892 =	59 (0.660)					intergenic (‑68/+6)	caiC/caiB	putative crotonobetaine/carnitine‑CoA ligase/crotonobetainyl CoA:carnitine CoA transferase
*	?	NC_000913	= 39288	81 (0.870)	6 (0.070)	5/186	NT	6.9%	coding (1099/1143 nt)	caiA	crotonobetaine reductase subunit II, FAD‑binding
	?	NC_000913	= 39296	87 (1.000)					coding (1091/1143 nt)	caiA	crotonobetaine reductase subunit II, FAD‑binding
*	?	NC_000913	= 66642	14 (0.150)	12 (0.140)	7/186	NT	57.1%	noncoding (78/248 nt)	REP6 (repetitive extragenic palindromic) element; contains 6 REP sequences	REP6 (repetitive extragenic palindromic) element; contains 6 REP sequences
	?	NC_000913	2304729 =	5 (0.060)					noncoding (313/655 nt)	REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences	REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences
*	?	NC_000913	= 66727	9 (0.100)	6 (0.070) +CTACACCGCT	6/180	NT	42.6%	noncoding (163/248 nt)	REP6 (repetitive extragenic palindromic) element; contains 6 REP sequences	REP6 (repetitive extragenic palindromic) element; contains 6 REP sequences
	?	NC_000913	2304400 =	NA (NA)					intergenic (+7/+708)	eco/mqo	ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
*	?	NC_000913	= 68731	83 (0.890)	5 (0.060)	4/186	NT	6.2%	coding (1318/1701 nt)	araB	L‑ribulokinase
	?	NC_000913	= 68753	75 (0.860)					coding (1296/1701 nt)	araB	L‑ribulokinase
*	?	NC_000913	= 72220	NA (NA)	24 (0.280)	14/186	NT	15.9%	noncoding (85/85 nt)	REP7 (repetitive extragenic palindromic) element; contains 2 REP sequences	REP7 (repetitive extragenic palindromic) element; contains 2 REP sequences
	?	NC_000913	3736234 =	127 (1.460)					noncoding (81/171 nt)	REP268 (repetitive extragenic palindromic) element; contains 4 REP sequences	REP268 (repetitive extragenic palindromic) element; contains 4 REP sequences
*	?	NC_000913	74873 =	54 (0.580)	7 (0.080)	5/192	NT	11.2%	coding (608/984 nt)	thiB	thiamine/thiamine pyrophosphate/thiamine monophosphate ABC transporter periplasmic binding protein
	?	NC_000913	74897 =	59 (0.660)					coding (584/984 nt)	thiB	thiamine/thiamine pyrophosphate/thiamine monophosphate ABC transporter periplasmic binding protein
*	?	NC_000913	= 93541	90 (0.960)	13 (0.140)	11/194	NT	13.0%	coding (376/1488 nt)	murE	UDP‑N‑acetylmuramoyl‑L‑alanyl‑D‑glutamate:meso‑ diaminopimelate ligase
	?	NC_000913	= 93563	87 (0.960)					coding (398/1488 nt)	murE	UDP‑N‑acetylmuramoyl‑L‑alanyl‑D‑glutamate:meso‑ diaminopimelate ligase
*	?	NC_000913	103901 =	107 (1.150)	8 (0.090)	6/188	NT	8.3%	coding (747/831 nt)	ftsQ	divisome assembly protein, membrane anchored protein involved in growth of wall at septum
	?	NC_000913	103941 =	76 (0.870)					coding (787/831 nt)	ftsQ	divisome assembly protein, membrane anchored protein involved in growth of wall at septum
*	?	NC_000913	111593 =	35 (0.370)	8 (0.090)	8/186	NT	17.5%	noncoding (164/200 nt)	RIP8 (repetitive extragenic palindromic) element; contains 4 REP sequences and 1 IHF site	RIP8 (repetitive extragenic palindromic) element; contains 4 REP sequences and 1 IHF site
	?	NC_000913	111626 =	43 (0.500)					noncoding (197/200 nt)	RIP8 (repetitive extragenic palindromic) element; contains 4 REP sequences and 1 IHF site	RIP8 (repetitive extragenic palindromic) element; contains 4 REP sequences and 1 IHF site
*	?	NC_000913	158092 =	85 (0.910)	4 (0.050)	4/186	NT	5.7%	coding (1035/1398 nt)	pcnB	poly(A) polymerase
	?	NC_000913	158122 =	53 (0.610)					coding (1005/1398 nt)	pcnB	poly(A) polymerase
*	?	NC_000913	= 183661	44 (0.470)	13 (0.150)	10/180	NT	22.5%	intergenic (+41/+48)	cdaR/yaeH	carbohydrate diacid regulon transcriptional regulator; autoregulator/UPF0325 family protein
	?	NC_000913	= 183674	50 (0.590)					intergenic (+54/+35)	cdaR/yaeH	carbohydrate diacid regulon transcriptional regulator; autoregulator/UPF0325 family protein
*	?	NC_000913	= 224065	NA (NA)	23 (0.260)	11/186	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	= 224374	NA (NA)	8 (0.090)	7/186	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	= 225998	NA (NA)	8 (0.090)	7/194	NT	NA	noncoding (240/2904 nt)	rrlH	23S ribosomal RNA of rrnH operon
	?	NC_000913	= 226016	NA (NA)					noncoding (258/2904 nt)	rrlH	23S ribosomal RNA of rrnH operon
*	?	NC_000913	= 227444	NA (NA)	6 (0.070)	4/190	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	= 228108	NA (NA)	26 (0.290)	16/192	NT	NA	noncoding (2350/2904 nt)	rrlH	23S ribosomal RNA of rrnH operon
	?	NC_000913	= 228124	NA (NA)					noncoding (2366/2904 nt)	rrlH	23S ribosomal RNA of rrnH operon
*	?	NC_000913	= 228575	NA (NA)	7 (0.080)	5/190	NT	NA	noncoding (2817/2904 nt)	rrlH	23S ribosomal RNA of rrnH operon
	?	NC_000913	= 228586	NA (NA)					noncoding (2828/2904 nt)	rrlH	23S ribosomal RNA of rrnH operon
*	?	NC_000913	231071 =	72 (0.770)	17 (0.190)	13/188	NT	22.0%	intergenic (‑190/‑51)	yafC/yafD	LysR family putative transcriptional regulator/endo/exonuclease/phosphatase family protein
	?	NC_000913	231095 =	53 (0.600)					intergenic (‑214/‑27)	yafC/yafD	LysR family putative transcriptional regulator/endo/exonuclease/phosphatase family protein
*	?	NC_000913	= 248210	34 (0.360)	4 (0.050)	4/186	NT	12.8%	noncoding (64/188 nt)	REP19 (repetitive extragenic palindromic) element; contains 4 REP sequences	REP19 (repetitive extragenic palindromic) element; contains 4 REP sequences
	?	NC_000913	= 248226	23 (0.260)					noncoding (80/188 nt)	REP19 (repetitive extragenic palindromic) element; contains 4 REP sequences	REP19 (repetitive extragenic palindromic) element; contains 4 REP sequences
*	?	NC_000913	274620 =	NA (NA)	11 (0.130)	11/182	NT	NA	noncoding (530/1195 nt)	IS5	repeat region
	?	NC_000913	274663 =	NA (NA)					noncoding (487/1195 nt)	IS5	repeat region
*	?	NC_000913	284258 =	74 (0.790)	6 (0.070)	6/188	NT	8.7%	coding (1058/1968 nt)	yagF	CP4‑6 prophage; dehydratase family protein
	?	NC_000913	284307 =	56 (0.640)					coding (1107/1968 nt)	yagF	CP4‑6 prophage; dehydratase family protein
*	?	NC_000913	= 284691	74 (0.790)	6 (0.070)	6/192	NT	7.8%	coding (1491/1968 nt)	yagF	CP4‑6 prophage; dehydratase family protein
	?	NC_000913	= 284723	71 (0.790)					coding (1523/1968 nt)	yagF	CP4‑6 prophage; dehydratase family protein
*	?	NC_000913	291960 =	139 (1.490)	9 (0.100)	6/184	NT	6.8%	pseudogene (557/828 nt)	yagJ	CP4‑6 prophage; uncharacterized protein;Phage or Prophage Related
	?	NC_000913	291982 =	119 (1.390)					pseudogene (579/828 nt)	yagJ	CP4‑6 prophage; uncharacterized protein;Phage or Prophage Related
*	?	NC_000913	302247 =	96 (1.030)	6 (0.070)	5/190	NT	5.8%	coding (327/690 nt)	paoA	PaoABC aldehyde oxidoreductase, 2Fe‑2S subunit
	?	NC_000913	302274 =	102 (1.150)					coding (300/690 nt)	paoA	PaoABC aldehyde oxidoreductase, 2Fe‑2S subunit
*	?	NC_000913	= 341335	76 (0.810)	10 (0.110)	7/190	NT	12.5%	coding (211/1383 nt)	yahJ	putative metallo‑dependent hydrolase domain deaminase
	?	NC_000913	= 341358	68 (0.770)					coding (234/1383 nt)	yahJ	putative metallo‑dependent hydrolase domain deaminase
*	?	NC_000913	= 349852	27 (0.290)	10 (0.120)	6/186	NT	26.6%	noncoding (248/365 nt)	REP25 (repetitive extragenic palindromic) element; contains 8 REP sequences	REP25 (repetitive extragenic palindromic) element; contains 8 REP sequences
	?	NC_000913	= 349869	30 (0.350)					noncoding (265/365 nt)	REP25 (repetitive extragenic palindromic) element; contains 8 REP sequences	REP25 (repetitive extragenic palindromic) element; contains 8 REP sequences
*	?	NC_000913	381663 =	NA (NA)	6 (0.070)	5/186	NT	NA	noncoding (404/1331 nt)	IS2	repeat region
	?	NC_000913	381703 =	NA (NA)					noncoding (444/1331 nt)	IS2	repeat region
*	?	NC_000913	= 403626	28 (0.300)	5 (0.060)	5/182	NT	17.4%	intergenic (+25/‑77)	psiF/yaiC	PsiF family protein/diguanylate cyclase, cellulose regualtor
	?	NC_000913	= 403636	22 (0.260)					intergenic (+35/‑67)	psiF/yaiC	PsiF family protein/diguanylate cyclase, cellulose regualtor
*	?	NC_000913	= 427762	76 (0.810)	8 (0.090)	7/186	NT	11.2%	coding (116/1848 nt)	secD	SecYEG protein translocase auxillary subunit
	?	NC_000913	= 427779	56 (0.640)					coding (133/1848 nt)	secD	SecYEG protein translocase auxillary subunit
*	?	NC_000913	= 444575	34 (0.360)	4 (0.050)	4/164	NT	12.7%	intergenic (‑60/‑108)	panE/yajQ	2‑dehydropantoate reductase, NADPH‑specific/phage Phi6 host factor, ATP/GTP binding protein
	?	NC_000913	= 444587	27 (0.350)					intergenic (‑72/‑96)	panE/yajQ	2‑dehydropantoate reductase, NADPH‑specific/phage Phi6 host factor, ATP/GTP binding protein
*	?	NC_000913	= 456464	47 (0.500)	10 (0.110)	9/194	NT	18.1%	intergenic (+33/‑213)	tig/clpP	peptidyl‑prolyl cis/trans isomerase (trigger factor)/proteolytic subunit of ClpA‑ClpP and ClpX‑ClpP ATP‑dependent serine proteases
	?	NC_000913	= 456490	45 (0.500)					intergenic (+59/‑187)	tig/clpP	peptidyl‑prolyl cis/trans isomerase (trigger factor)/proteolytic subunit of ClpA‑ClpP and ClpX‑ClpP ATP‑dependent serine proteases
*	?	NC_000913	= 574464	12 (0.130)	4 (0.050)	4/184	NT	29.6%	intergenic (+125/+65)	quuD/nmpC	DLP12 prophage; putative antitermination protein/DLP12 prophage; truncated outer membrane porin (pseudogene);IS, phage, Tn; Phage or Prophage Related; outer membrane porin protein; locus of qsr prophage
	?	NC_000913	= 574470	8 (0.090)					intergenic (+131/+59)	quuD/nmpC	DLP12 prophage; putative antitermination protein/DLP12 prophage; truncated outer membrane porin (pseudogene);IS, phage, Tn; Phage or Prophage Related; outer membrane porin protein; locus of qsr prophage
*	?	NC_000913	= 609415	105 (1.120)	6 (0.070)	5/184	NT	6.0%	intergenic (+238/+44)	insL1/entD	IS186 transposase/phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex
	?	NC_000913	= 609431	92 (1.070)					intergenic (+254/+28)	insL1/entD	IS186 transposase/phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex
*	?	NC_000913	= 632148	NA (NA)	8 (0.090)	6/184	NT	NA	noncoding (34/34 nt)	REP55 (repetitive extragenic palindromic) element; contains 1 REP sequences	REP55 (repetitive extragenic palindromic) element; contains 1 REP sequences
	?	NC_000913	2673806 =	NA (NA)					noncoding (31/34 nt)	REP185 (repetitive extragenic palindromic) element; contains 1 REP sequences	REP185 (repetitive extragenic palindromic) element; contains 1 REP sequences
*	?	NC_000913	644022 =	45 (0.480)	12 (0.140)	12/184	NT	21.5%	intergenic (‑55/+175)	rnk/rna	regulator of nucleoside diphosphate kinase/ribonuclease I
	?	NC_000913	644051 =	46 (0.540)					intergenic (‑84/+146)	rnk/rna	regulator of nucleoside diphosphate kinase/ribonuclease I
*	?	NC_000913	= 668251	83 (0.890)	8 (0.090)	7/182	NT	9.1%	coding (465/468 nt)	rlmH	23S rRNA m(3)Psi1915 pseudouridine methyltransferase, SAM‑dependent
	?	NC_000913	= 668256	84 (0.990)					coding (460/468 nt)	rlmH	23S rRNA m(3)Psi1915 pseudouridine methyltransferase, SAM‑dependent
*	?	NC_000913	745824 =	68 (0.730)	6 (0.070)	6/190	NT	8.5%	coding (660/735 nt)	ybgL	UPF0271 family protein
	?	NC_000913	745854 =	64 (0.720)					coding (690/735 nt)	ybgL	UPF0271 family protein
*	?	NC_000913	766061 =	100 (1.070)	16 (0.180)	7/194	NT	13.7%	coding (78/1977 nt)	mngA	fused 2‑O‑a‑mannosyl‑D‑glycerate specific PTS enzymes: IIA component/IIB component/IIC component
	?	NC_000913	766084 =	104 (1.150)					coding (101/1977 nt)	mngA	fused 2‑O‑a‑mannosyl‑D‑glycerate specific PTS enzymes: IIA component/IIB component/IIC component
*	?	NC_000913	= 820612	36 (0.390)	12 (0.140)	9/188	NT	25.0%	intergenic (+24/‑181)	ybhL/ybhM	putative acetate transporter; BAX Inhibitor‑1 family inner membrane protein/BAX Inhibitor‑1 family inner membrane protein
	?	NC_000913	= 820621	38 (0.430)					intergenic (+33/‑172)	ybhL/ybhM	putative acetate transporter; BAX Inhibitor‑1 family inner membrane protein/BAX Inhibitor‑1 family inner membrane protein
*	?	NC_000913	871110 =	59 (0.630)	4 (0.050)	4/180	NT	6.6%	coding (144/921 nt)	gsiC	glutathione ABC transporter permease
	?	NC_000913	871163 =	60 (0.710)					coding (197/921 nt)	gsiC	glutathione ABC transporter permease
*	?	NC_000913	884909 =	29 (0.310)	7 (0.080)	6/182	NT	18.1%	intergenic (+4/+37)	mdfA/ybjH	multidrug efflux system protein/uncharacterized protein
	?	NC_000913	884940 =	37 (0.440)					intergenic (+35/+6)	mdfA/ybjH	multidrug efflux system protein/uncharacterized protein
*	?	NC_000913	893340 =	129 (1.380)	8 (0.090)	8/190	NT	6.6%	coding (384/477 nt)	ybjN	negative regulator of motility; multicopy suppressor of coaA(Ts)
	?	NC_000913	893369 =	105 (1.180)					coding (413/477 nt)	ybjN	negative regulator of motility; multicopy suppressor of coaA(Ts)
*	?	NC_000913	= 902202	37 (0.400)	6 (0.070)	5/190	NT	14.1%	coding (49/717 nt)	artQ	arginine ABC transporter permease
	?	NC_000913	= 902224	38 (0.430)					coding (27/717 nt)	artQ	arginine ABC transporter permease
*	?	NC_000913	914576 =	86 (0.920)	4 (0.050)	4/188	NT	5.1%	coding (282/900 nt)	ybjE	putative transporter
	?	NC_000913	914621 =	68 (0.770)					coding (237/900 nt)	ybjE	putative transporter
*	?	NC_000913	= 931034	9 (0.100)	4 (0.050)	4/184	NT	31.6%	intergenic (‑72/+51)	cydD/trxB	glutathione/cysteine ABC transporter export permease/ATPase/thioredoxin reductase, FAD/NAD(P)‑binding
	?	NC_000913	= 931049	9 (0.100)					intergenic (‑87/+36)	cydD/trxB	glutathione/cysteine ABC transporter export permease/ATPase/thioredoxin reductase, FAD/NAD(P)‑binding
*	?	NC_000913	985196 =	98 (1.050)	10 (0.120)	10/184	NT	11.4%	coding (514/1191 nt)	aspC	aspartate aminotransferase, PLP‑dependent
	?	NC_000913	985219 =	65 (0.760)					coding (491/1191 nt)	aspC	aspartate aminotransferase, PLP‑dependent
*	?	NC_000913	= 1085804	67 (0.720)	4 (0.050)	4/188	NT	5.5%	coding (813/1065 nt)	phoH	ATP‑binding protein; putative PhoH family P‑loop ATPase
	?	NC_000913	= 1085830	74 (0.840)					coding (839/1065 nt)	phoH	ATP‑binding protein; putative PhoH family P‑loop ATPase
*	?	NC_000913	1100121 =	147 (1.570)	18 (0.200)	16/192	NT	12.3%	coding (482/555 nt)	ycdY	redox enzyme maturation protein (REMP) chaperone for YcdX
	?	NC_000913	1100158 =	116 (1.290)					coding (519/555 nt)	ycdY	redox enzyme maturation protein (REMP) chaperone for YcdX
*	?	NC_000913	= 1125728	72 (0.770)	8 (0.090)	7/192	NT	12.2%	coding (167/585 nt)	rimJ	ribosomal‑protein‑S5‑alanine N‑acetyltransferase
	?	NC_000913	= 1125751	46 (0.510)					coding (190/585 nt)	rimJ	ribosomal‑protein‑S5‑alanine N‑acetyltransferase
*	?	NC_000913	= 1163332	38 (0.410)	4 (0.050)	4/190	NT	10.7%	coding (73/825 nt)	thiK	thiamine kinase
	?	NC_000913	= 1163360	31 (0.350)					coding (101/825 nt)	thiK	thiamine kinase
*	?	NC_000913	1207790 =	58 (0.620)	67 (0.850)	52/168	NT	61.0%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	37 (0.470)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1207805	61 (0.650)	46 (0.590)	33/168	NT	51.0%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	37 (0.470)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	1213722 =	73 (0.780)	8 (0.090)	7/186	NT	10.6%	coding (338/732 nt)	bluR	repressor of blue light‑responsive genes
	?	NC_000913	1213743 =	67 (0.770)					coding (317/732 nt)	bluR	repressor of blue light‑responsive genes
*	?	NC_000913	1225763 =	34 (0.360)	3 (0.030)	3/194	NT	7.5%	coding (318/696 nt)	minC	inhibitor of FtsZ ring polymerization
	?	NC_000913	1225804 =	41 (0.450)					coding (277/696 nt)	minC	inhibitor of FtsZ ring polymerization
*	?	NC_000913	1269276 =	24 (0.260)	6 (0.070)	4/184	NT	16.2%	intergenic (‑1/‑47)	ldrA/rdlA	toxic polypeptide, small/sRNA antisense regulator affects LdrA translation; proposed addiction module in LDR‑A repeat, with toxic peptide LdrA
	?	NC_000913	1269849 =	40 (0.470)					intergenic (‑39/‑9)	ldrB/rdlB	toxic polypeptide, small/sRNA antisense regulator affects LdrB translation; proposed addiction module in LDR‑B repeat, with toxic peptide LdrB
*	?	NC_000913	= 1299498	0 (0.000)	46 (0.510)	38/192	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	= 1320872	62 (0.660)	4 (0.050)	4/184	NT	5.8%	coding (513/1596 nt)	trpD	fused glutamine amidotransferase (component II) of anthranilate synthase/anthranilate phosphoribosyl transferase
	?	NC_000913	= 1320882	72 (0.840)					coding (503/1596 nt)	trpD	fused glutamine amidotransferase (component II) of anthranilate synthase/anthranilate phosphoribosyl transferase
*	?	NC_000913	1405665 =	35 (0.370)	8 (0.090)	8/182	NT	20.3%	noncoding (87/96 nt)	mcaS	motility and biofilm regulator sRNA
	?	NC_000913	1405694 =	31 (0.360)					noncoding (58/96 nt)	mcaS	motility and biofilm regulator sRNA
*	?	NC_000913	1451561 =	59 (0.630)	6 (0.070)	6/182	NT	10.0%	intergenic (‑212/+36)	tynA/paaZ	tyramine oxidase, copper‑requiring/oxepin‑CoA hydrolase and 3‑oxo‑5,6‑dehydrosuberyl‑CoA semialdehyde dehydrogenase
	?	NC_000913	1451587 =	54 (0.640)					intergenic (‑238/+10)	tynA/paaZ	tyramine oxidase, copper‑requiring/oxepin‑CoA hydrolase and 3‑oxo‑5,6‑dehydrosuberyl‑CoA semialdehyde dehydrogenase
*	?	NC_000913	= 1463445	47 (0.500)	13 (0.150)	12/186	NT	22.1%	intergenic (+7/‑94)	paaK/paaX	phenylacetyl‑CoA ligase/transcriptional repressor of phenylacetic acid degradation paa operon, phenylacetyl‑CoA inducer
	?	NC_000913	= 1463482	48 (0.550)					intergenic (+44/‑57)	paaK/paaX	phenylacetyl‑CoA ligase/transcriptional repressor of phenylacetic acid degradation paa operon, phenylacetyl‑CoA inducer
*	?	NC_000913	1484624 =	51 (0.550)	6 (0.070)	6/192	NT	9.7%	coding (1564/3903 nt)	hrpA	putative ATP‑dependent helicase
	?	NC_000913	1484660 =	63 (0.700)					coding (1600/3903 nt)	hrpA	putative ATP‑dependent helicase
*	?	NC_000913	1504210 =	75 (0.800)	6 (0.070)	6/186	NT	7.9%	noncoding (1050/1748 nt)	IS609	repeat region
	?	NC_000913	1504231 =	71 (0.820)					noncoding (1071/1748 nt)	IS609	repeat region
*	?	NC_000913	1512410 =	85 (0.910)	6 (0.070)	5/192	NT	7.7%	coding (757/1146 nt)	ydcS	putative ABC transporter periplasmic binding protein
	?	NC_000913	1512451 =	63 (0.700)					coding (798/1146 nt)	ydcS	putative ABC transporter periplasmic binding protein
*	?	NC_000913	1537117 =	116 (1.240)	6 (0.070)	4/186	NT	5.6%	coding (193/696 nt)	narW	nitrate reductase 2 (NRZ), delta subunit (assembly subunit)
	?	NC_000913	1537148 =	95 (1.090)					coding (162/696 nt)	narW	nitrate reductase 2 (NRZ), delta subunit (assembly subunit)
*	?	NC_000913	1665217 =	45 (0.480)	4 (0.050)	4/182	NT	8.3%	intergenic (+97/‑98)	dmsD/clcB	twin‑argninine leader‑binding protein for DmsA and TorA/H(+)/Cl(‑) exchange transporter
	?	NC_000913	1665246 =	47 (0.550)					intergenic (+126/‑69)	dmsD/clcB	twin‑argninine leader‑binding protein for DmsA and TorA/H(+)/Cl(‑) exchange transporter
*	?	NC_000913	= 1668051	70 (0.750)	4 (0.050)	4/188	NT	5.8%	coding (514/1221 nt)	mlc	glucosamine anaerobic growth regulon transcriptional repressor; autorepressor
	?	NC_000913	= 1668068	65 (0.740)					coding (497/1221 nt)	mlc	glucosamine anaerobic growth regulon transcriptional repressor; autorepressor
*	?	NC_000913	1672789 =	10 (0.110)	6 (0.070)	5/180	NT	41.4%	intergenic (+8/+31)	ydgD/mdtI	putative peptidase/multidrug efflux system transporter
	?	NC_000913	1672815 =	8 (0.100)					intergenic (+34/+5)	ydgD/mdtI	putative peptidase/multidrug efflux system transporter
*	?	NC_000913	= 1682065	82 (0.880)	8 (0.090)	6/186	NT	9.3%	intergenic (‑35/‑94)	ydgC/rstA	GlpM family inner membrane protein/response regulator of RstAB two‑component system
	?	NC_000913	= 1682073	79 (0.910)					intergenic (‑43/‑86)	ydgC/rstA	GlpM family inner membrane protein/response regulator of RstAB two‑component system
*	?	NC_000913	= 1685678	64 (0.690)	4 (0.050)	4/190	NT	6.3%	coding (911/1404 nt)	fumC	fumarate hydratase (fumarase C),aerobic Class II
	?	NC_000913	= 1685700	58 (0.650)					coding (889/1404 nt)	fumC	fumarate hydratase (fumarase C),aerobic Class II
*	?	NC_000913	1745893 =	90 (0.960)	8 (0.090)	8/182	NT	9.1%	coding (235/1257 nt)	ydhQ	autotransporter adhesin‑related protein
	?	NC_000913	1745928 =	77 (0.910)					coding (200/1257 nt)	ydhQ	autotransporter adhesin‑related protein
*	?	NC_000913	1877268 =	76 (0.810)	4 (0.050)	4/184	NT	5.4%	intergenic (+12/+10)	yeaO/yoaF	DUF488 family protein/DUF333 family outer membrane lipoprotein
	?	NC_000913	1877299 =	70 (0.810)					coding (234/255 nt)	yoaF	DUF333 family outer membrane lipoprotein
*	?	NC_000913	= 1886825	14 (0.150)	8 (0.100)	8/178	NT	52.5%	intergenic (+15/+39)	yeaX/rnd	putative YeaWX dioxygenase beta subunit, reductase component/ribonuclease D
	?	NC_000913	= 1886846	2 (0.020)					intergenic (+36/+18)	yeaX/rnd	putative YeaWX dioxygenase beta subunit, reductase component/ribonuclease D
*	?	NC_000913	= 1934529	91 (0.970)	8 (0.090)	7/196	NT	7.4%	coding (76/1812 nt)	edd	6‑phosphogluconate dehydratase
	?	NC_000913	= 1934556	110 (1.200)					coding (49/1812 nt)	edd	6‑phosphogluconate dehydratase
*	?	NC_000913	1974246 =	73 (0.780)	4 (0.050)	4/182	NT	5.4%	coding (1079/1965 nt)	cheA	fused chemotactic sensory histidine kinase in two‑component regulatory system with CheB and CheY: sensory histidine kinase/signal sensing protein
	?	NC_000913	1974275 =	73 (0.860)					coding (1050/1965 nt)	cheA	fused chemotactic sensory histidine kinase in two‑component regulatory system with CheB and CheY: sensory histidine kinase/signal sensing protein
*	?	NC_000913	= 2042125	75 (0.800)	12 (0.140)	8/180	NT	14.2%	intergenic (+100/‑243)	zinT/yodB	zinc and cadmium binding protein, periplasmic/cytochrome b561 homolog
	?	NC_000913	= 2042138	77 (0.920)					intergenic (+113/‑230)	zinT/yodB	zinc and cadmium binding protein, periplasmic/cytochrome b561 homolog
*	?	NC_000913	2064305 =	92 (0.990)	6 (0.070)	6/188	NT	5.8%	coding (163/1080 nt)	cobT	nicotinate‑nucleotide‑‑dimethylbenzimidazole phosphoribosyltransferase
	?	NC_000913	2064343 =	108 (1.230)					coding (125/1080 nt)	cobT	nicotinate‑nucleotide‑‑dimethylbenzimidazole phosphoribosyltransferase
*	?	NC_000913	2076358 =	65 (0.700)	4 (0.050)	4/186	NT	5.5%	coding (51/447 nt)	yeeS	CP4‑44 prophage; putative DNA repair protein
	?	NC_000913	2076435 =	78 (0.900)					coding (128/447 nt)	yeeS	CP4‑44 prophage; putative DNA repair protein
*	?	NC_000913	= 2197774	63 (0.670)	20 (0.240)	16/178	NT	24.4%	pseudogene (1301/2847 nt)	yehH	DUF4132 family pseudogene; defective yehI paralog; molybdate metabolism regulator, first fragment; molybdate metabolism regulator, second fragment 2; yehI' molR mutations have phenotypes and the N‑terminal molR fragment of yehI' may be expressed and may have retained or evolved MolR function
	?	NC_000913	= 2197784	68 (0.820)					pseudogene (1311/2847 nt)	yehH	DUF4132 family pseudogene; defective yehI paralog; molybdate metabolism regulator, first fragment; molybdate metabolism regulator, second fragment 2; yehI' molR mutations have phenotypes and the N‑terminal molR fragment of yehI' may be expressed and may have retained or evolved MolR function
*	?	NC_000913	2286347 =	34 (0.360)	6 (0.070)	5/184	NT	12.9%	intergenic (+60/+43)	proL/yejO	tRNA‑Pro/pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system
	?	NC_000913	2286381 =	50 (0.580)					intergenic (+94/+9)	proL/yejO	tRNA‑Pro/pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system
*	?	NC_000913	2327300 =	35 (0.370)	10 (0.120)	7/174	NT	28.0%	intergenic (+7/+67)	atoB/yfaP	acetyl‑CoA acetyltransferase/DUF2135 family protein, putative host defense protein
	?	NC_000913	2327334 =	21 (0.260)					intergenic (+41/+33)	atoB/yfaP	acetyl‑CoA acetyltransferase/DUF2135 family protein, putative host defense protein
*	?	NC_000913	2456281 =	39 (0.420)	7 (0.090)	8/170	NT	18.4%	intergenic (‑635/+46)	yfcV/sixA	putative fimbrial‑like adhesin protein/phosphohistidine phosphatase
	?	NC_000913	2456318 =	29 (0.370)					intergenic (‑672/+9)	yfcV/sixA	putative fimbrial‑like adhesin protein/phosphohistidine phosphatase
*	?	NC_000913	= 2505958	72 (0.770)	6 (0.070)	3/186	NT	8.3%	coding (675/1086 nt)	ypdF	Xaa‑Pro aminopeptidase
	?	NC_000913	= 2505986	66 (0.760)					coding (647/1086 nt)	ypdF	Xaa‑Pro aminopeptidase
*	?	NC_000913	= 2533705	89 (0.950)	8 (0.090)	7/184	NT	8.8%	intergenic (+325/‑59)	cysK/ptsH	cysteine synthase A, O‑acetylserine sulfhydrolase A subunit/phosphohistidinoprotein‑hexose phosphotransferase component of PTS system (Hpr)
	?	NC_000913	= 2533719	83 (0.970)					intergenic (+339/‑45)	cysK/ptsH	cysteine synthase A, O‑acetylserine sulfhydrolase A subunit/phosphohistidinoprotein‑hexose phosphotransferase component of PTS system (Hpr)
*	?	NC_000913	= 2586491	94 (1.010)	10 (0.120)	9/186	NT	9.8%	coding (761/1701 nt)	narQ	sensory histidine kinase in two‑component regulatory system with NarP
	?	NC_000913	= 2586500	97 (1.120)					coding (770/1701 nt)	narQ	sensory histidine kinase in two‑component regulatory system with NarP
*	?	NC_000913	2642131 =	46 (0.490)	6 (0.070)	6/186	NT	14.2%	coding (714/1014 nt)	rodZ	MreB assembly cytoskeletal protein
	?	NC_000913	2642169 =	30 (0.350)					coding (676/1014 nt)	rodZ	MreB assembly cytoskeletal protein
*	?	NC_000913	= 2691723	81 (0.870)	4 (0.050)	4/184	NT	5.1%	coding (3821/3888 nt)	purL	phosphoribosylformyl‑glycineamide synthetase
	?	NC_000913	= 2691746	73 (0.850)					coding (3798/3888 nt)	purL	phosphoribosylformyl‑glycineamide synthetase
*	?	NC_000913	= 2708671	131 (1.400)	10 (0.120)	9/186	NT	8.5%	coding (84/957 nt)	rseB	anti‑sigma E factor, binds RseA
	?	NC_000913	= 2708691	94 (1.080)					coding (64/957 nt)	rseB	anti‑sigma E factor, binds RseA
*	?	NC_000913	2721644 =	79 (0.850)	6 (0.070)	4/188	NT	7.4%	coding (1692/2661 nt)	pka	protein lysine acetyltransferase
	?	NC_000913	2721667 =	76 (0.870)					coding (1715/2661 nt)	pka	protein lysine acetyltransferase
*	?	NC_000913	2726200 =	NA (NA)	47 (0.540)	15/188	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	2727891 =	NA (NA)	49 (0.560)	25/188	NT	NA	noncoding (1294/2904 nt)	rrlG	23S ribosomal RNA of rrnG operon
	?	NC_000913	2727910 =	NA (NA)					noncoding (1275/2904 nt)	rrlG	23S ribosomal RNA of rrnG operon
*	?	NC_000913	2729443 =	3 (0.030)	12 (0.140)	8/180	NT	75.7%	noncoding (2/76 nt)	gltW	tRNA‑Glu
	?	NC_000913	= 4168331	5 (0.060)					intergenic (+131/‑41)	rrsB/gltT	16S ribosomal RNA of rrnB operon/tRNA‑Glu
*	?	NC_000913	2811829 =	74 (0.790)	4 (0.040)	4/192	NT	5.2%	coding (403/1173 nt)	emrA	multidrug efflux system
	?	NC_000913	2811877 =	74 (0.830)					coding (451/1173 nt)	emrA	multidrug efflux system
*	?	NC_000913	= 2820286	113 (1.210)	7 (0.080)	6/190	NT	6.1%	coding (1726/2631 nt)	alaS	alanyl‑tRNA synthetase
	?	NC_000913	= 2820304	108 (1.220)					coding (1708/2631 nt)	alaS	alanyl‑tRNA synthetase
*	?	NC_000913	= 2858336	73 (0.780)	6 (0.070)	6/190	NT	8.0%	coding (1244/2562 nt)	mutS	methyl‑directed mismatch repair protein
	?	NC_000913	= 2858358	68 (0.770)					coding (1266/2562 nt)	mutS	methyl‑directed mismatch repair protein
*	?	NC_000913	= 2925373	65 (0.700)	8 (0.090)	7/188	NT	10.9%	coding (26/849 nt)	queF	7‑cyano‑7‑deazaguanine reductase (NADPH‑dependent)
	?	NC_000913	= 2925381	70 (0.800)					coding (34/849 nt)	queF	7‑cyano‑7‑deazaguanine reductase (NADPH‑dependent)
*	?	NC_000913	= 2949337	88 (0.940)	11 (0.130)	7/184	NT	11.1%	coding (96/1332 nt)	argA	amino acid N‑acetyltransferase and inactive acetylglutamate kinase
	?	NC_000913	= 2949352	95 (1.110)					coding (111/1332 nt)	argA	amino acid N‑acetyltransferase and inactive acetylglutamate kinase
*	?	NC_000913	= 2950597	NA (NA)	4 (0.050)	4/180	NT	NA	intergenic (+24/+38)	argA/recD	amino acid N‑acetyltransferase and inactive acetylglutamate kinase/exonuclease V (RecBCD complex), alpha chain
	?	NC_000913	= 2950614	NA (NA)					noncoding (2/14 nt)	REP207 (repetitive extragenic palindromic) element; contains 1 REP sequences	REP207 (repetitive extragenic palindromic) element; contains 1 REP sequences
*	?	NC_000913	2977931 =	106 (1.140)	6 (0.070)	12/190	NT	5.9%	coding (969/1263 nt)	lysA	diaminopimelate decarboxylase, PLP‑binding
	?	NC_000913	2977952 =	92 (1.040)					coding (948/1263 nt)	lysA	diaminopimelate decarboxylase, PLP‑binding
*	?	NC_000913	= 3056971	74 (0.790)	13 (0.150)	11/184	NT	14.4%	noncoding (123/140 nt)	sibC	sRNA antisense regulator of toxic IbsC protein
	?	NC_000913	= 3056979	86 (1.000)					noncoding (131/140 nt)	sibC	sRNA antisense regulator of toxic IbsC protein
*	?	NC_000913	3063139 =	99 (1.060)	11 (0.130)	8/186	NT	11.3%	coding (153/996 nt)	argK	membrane ATPase/protein kinase
	?	NC_000913	3063168 =	80 (0.920)					coding (182/996 nt)	argK	membrane ATPase/protein kinase
*	?	NC_000913	= 3102653	53 (0.570)	11 (0.120)	10/190	NT	17.4%	coding (200/720 nt)	trmI	tRNA m(7)G46 methyltransferase, SAM‑dependent
	?	NC_000913	= 3102660	54 (0.610)					coding (193/720 nt)	trmI	tRNA m(7)G46 methyltransferase, SAM‑dependent
*	?	NC_000913	= 3161672	133 (1.420)	7 (0.080)	5/194	NT	5.5%	coding (998/1413 nt)	ftsP	septal ring component that protects the divisome from stress; multicopy suppressor of ftsI(Ts)
	?	NC_000913	= 3161700	111 (1.230)					coding (970/1413 nt)	ftsP	septal ring component that protects the divisome from stress; multicopy suppressor of ftsI(Ts)
*	?	NC_000913	3217434 =	NA (NA)	5 (0.060)	4/186	NT	NA	noncoding (1/89 nt)	REP229 (repetitive extragenic palindromic) element; contains 2 REP sequences	REP229 (repetitive extragenic palindromic) element; contains 2 REP sequences
	?	NC_000913	3217467 =	NA (NA)					noncoding (34/89 nt)	REP229 (repetitive extragenic palindromic) element; contains 2 REP sequences	REP229 (repetitive extragenic palindromic) element; contains 2 REP sequences
*	?	NC_000913	3226765 =	66 (0.710)	8 (0.090)	6/190	NT	12.2%	coding (532/1434 nt)	ygjI	putative transporter
	?	NC_000913	3226786 =	52 (0.590)					coding (553/1434 nt)	ygjI	putative transporter
*	?	NC_000913	3250977 =	40 (0.430)	5 (0.060)	5/176	NT	15.1%	intergenic (+23/‑47)	yqjF/yqjG	putative quinol oxidase subunit/putative S‑transferase
	?	NC_000913	3251005 =	21 (0.260)					intergenic (+51/‑19)	yqjF/yqjG	putative quinol oxidase subunit/putative S‑transferase
*	?	NC_000913	3280885 =	30 (0.320)	8 (0.090)	7/190	NT	19.9%	pseudogene (185/375 nt)	agaW	pseudogene, N‑acetylgalactosamine‑specific enzyme IIC component of PTS;enzyme; Central intermediary metabolism: Amino sugars; PTS system N‑acetylgalactosameine‑specific IIC component 2
	?	NC_000913	3280913 =	36 (0.410)					pseudogene (213/375 nt)	agaW	pseudogene, N‑acetylgalactosamine‑specific enzyme IIC component of PTS;enzyme; Central intermediary metabolism: Amino sugars; PTS system N‑acetylgalactosameine‑specific IIC component 2
*	?	NC_000913	3327316 =	117 (1.250)	10 (0.110)	8/190	NT	8.9%	coding (349/630 nt)	rlmE	23S rRNA U2552 2'‑O‑ribose methyltransferase, SAM‑dependent
	?	NC_000913	3327340 =	93 (1.050)					coding (325/630 nt)	rlmE	23S rRNA U2552 2'‑O‑ribose methyltransferase, SAM‑dependent
*	?	NC_000913	= 3330557	NA (NA)	6 (0.070) +AATT	4/192	NT	NA	noncoding (98/98 nt)	RIP243 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site	RIP243 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site
	?	NC_000913	3774198 =	NA (NA)					intergenic (+4/‑226)	mtlA/mtlD	mannitol‑specific PTS enzyme: IIA, IIB and IIC components/mannitol‑1‑phosphate dehydrogenase, NAD‑dependent
*	?	NC_000913	3344992 =	64 (0.690)	13 (0.150)	9/180	NT	18.6%	coding (276/1434 nt)	rpoN	RNA polymerase, sigma 54 (sigma N) factor
	?	NC_000913	3345024 =	56 (0.670)					coding (308/1434 nt)	rpoN	RNA polymerase, sigma 54 (sigma N) factor
*	?	NC_000913	3353202 =	111 (1.190)	6 (0.070)	3/192	NT	5.8%	coding (849/930 nt)	yhcC	putative Fe‑S oxidoreductase, Radical SAM superfamily protein
	?	NC_000913	3353272 =	88 (0.980)					coding (779/930 nt)	yhcC	putative Fe‑S oxidoreductase, Radical SAM superfamily protein
*	?	NC_000913	3423376 =	16 (0.170)	11 (0.120)	5/196	NT	48.2%	intergenic (+182/+47)	yhdZ/rrfF	putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon
	?	NC_000913	= 4213162	8 (0.090)					intergenic (+3/‑72)	rrfE/yjaA	5S ribosomal RNA of rrnE operon/stress‑induced protein
*	?	NC_000913	3426836 =	NA (NA)	10 (0.120)	8/186	NT	NA	intergenic (‑53/+122)	rrlD/alaU	23S ribosomal RNA of rrnD operon/tRNA‑Ala
	?	NC_000913	3426854 =	NA (NA)					intergenic (‑71/+104)	rrlD/alaU	23S ribosomal RNA of rrnD operon/tRNA‑Ala
*	?	NC_000913	3468344 =	73 (0.780)	7 (0.080)	7/192	NT	10.4%	coding (1510/2694 nt)	chiA	periplasmic endochitinase
	?	NC_000913	3468379 =	51 (0.570)					coding (1475/2694 nt)	chiA	periplasmic endochitinase
*	?	NC_000913	3479094 =	73 (0.780)	4 (0.050)	4/190	NT	5.5%	coding (1514/1806 nt)	kefB	potassium:proton antiporter
	?	NC_000913	3479124 =	68 (0.770)					coding (1484/1806 nt)	kefB	potassium:proton antiporter
*	?	NC_000913	3520371 =	81 (0.870)	7 (0.080)	7/186	NT	8.5%	coding (333/1239 nt)	hofQ	DNA catabolic putative fimbrial transporter
	?	NC_000913	3520402 =	75 (0.860)					coding (302/1239 nt)	hofQ	DNA catabolic putative fimbrial transporter
*	?	NC_000913	= 3542317	74 (0.790)	4 (0.050)	4/188	NT	5.2%	coding (1911/2322 nt)	feoB	ferrous iron transporter protein B and GTP‑binding protein; membrane protein
	?	NC_000913	= 3542340	77 (0.880)					coding (1934/2322 nt)	feoB	ferrous iron transporter protein B and GTP‑binding protein; membrane protein
*	?	NC_000913	3562500 =	84 (0.900)	4 (0.050)	4/186	NT	5.4%	coding (488/1506 nt)	glpD	sn‑glycerol‑3‑phosphate dehydrogenase, aerobic, FAD/NAD(P)‑binding
	?	NC_000913	3562544 =	63 (0.730)					coding (532/1506 nt)	glpD	sn‑glycerol‑3‑phosphate dehydrogenase, aerobic, FAD/NAD(P)‑binding
*	?	NC_000913	3570872 =	91 (0.970)	10 (0.110)	8/188	NT	10.6%	coding (448/1974 nt)	glgX	glycogen debranching enzyme
	?	NC_000913	3570898 =	83 (0.950)					coding (422/1974 nt)	glgX	glycogen debranching enzyme
*	?	NC_000913	3620621 =	NA (NA)	10 (0.110)	5/188	NT	100%	coding (1430/4236 nt)	rhsB	Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
	?	NC_000913	3620630 =	0 (0.000)					coding (1439/4236 nt)	rhsB	Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
*	?	NC_000913	3630240 =	66 (0.710)	4 (0.050)	4/182	NT	5.5%	coding (363/1068 nt)	yhiI	putative membrane fusion protein (MFP) of efflux pump
	?	NC_000913	3630348 =	78 (0.920)					coding (255/1068 nt)	yhiI	putative membrane fusion protein (MFP) of efflux pump
*	?	NC_000913	3680367 =	NA (NA)	4 (0.050)	4/184	NT	NA	noncoding (1/76 nt)	REP265 (repetitive extragenic palindromic) element; contains 2 REP sequences	REP265 (repetitive extragenic palindromic) element; contains 2 REP sequences
	?	NC_000913	3680397 =	NA (NA)					noncoding (31/76 nt)	REP265 (repetitive extragenic palindromic) element; contains 2 REP sequences	REP265 (repetitive extragenic palindromic) element; contains 2 REP sequences
*	?	NC_000913	3721045 =	87 (0.930)	286 (3.090)	134/198	NT	73.2%	noncoding (413/1443 nt)	IS150	repeat region
	?	NC_000913	= 3839774	123 (1.330)					coding (220/819 nt)	nlpA	cytoplasmic membrane lipoprotein‑28
*	?	NC_000913	3727884 =	56 (0.600)	16 (0.190)	13/184	NT	20.4%	intergenic (‑136/+33)	yiaB/xylB	YiaAB family inner membrane protein/xylulokinase
	?	NC_000913	3727914 =	73 (0.850)					intergenic (‑166/+3)	yiaB/xylB	YiaAB family inner membrane protein/xylulokinase
*	?	NC_000913	3738815 =	213 (2.280)	25 (0.290)	16/184	NT	11.9%	coding (1319/2031 nt)	malS	alpha‑amylase
	?	NC_000913	3738835 =	174 (2.030)					coding (1339/2031 nt)	malS	alpha‑amylase
*	?	NC_000913	= 3749441	265 (2.840)	21 (0.230)	15/196	NT	7.3%	coding (210/861 nt)	sgbU	putative L‑xylulose 5‑phosphate 3‑epimerase
	?	NC_000913	= 3749465	271 (2.960)					coding (234/861 nt)	sgbU	putative L‑xylulose 5‑phosphate 3‑epimerase
*	?	NC_000913	= 3754859	76 (0.840)	4 (0.040)	4/192	NT	5.0%	intergenic (‑431/+114)	yiaW/aldB	DUF3302 family inner membrane protein/aldehyde dehydrogenase B
	?	NC_000913	= 3754941	NA (NA)					noncoding (82/82 nt)	REP270 (repetitive extragenic palindromic) element; contains 2 REP sequences	REP270 (repetitive extragenic palindromic) element; contains 2 REP sequences
*	?	NC_000913	3817574 =	169 (1.810)	11 (0.130)	8/182	NT	6.4%	intergenic (+35/‑186)	yicC/dinD	UPF0701 family protein/DNA damage‑inducible protein
	?	NC_000913	3817604 =	169 (1.990)					intergenic (+65/‑156)	yicC/dinD	UPF0701 family protein/DNA damage‑inducible protein
*	?	NC_000913	= 3831416	210 (2.250)	15 (0.170)	11/190	NT	6.7%	coding (960/1710 nt)	yicH	putative inner membrane‑anchored periplasmic AsmA family protein
	?	NC_000913	= 3831425	220 (2.480)					coding (969/1710 nt)	yicH	putative inner membrane‑anchored periplasmic AsmA family protein
*	?	NC_000913	= 3836447	315 (3.370)	20 (0.230)	15/188	NT	5.9%	pseudogene (23/132 nt)	yicT	pseudogene
	?	NC_000913	= 3836459	340 (3.870)					pseudogene (35/132 nt)	yicT	pseudogene
*	?	NC_000913	= 3867979	82 (0.880)	8 (0.090)	7/192	NT	10.0%	coding (252/333 nt)	yidQ	DUF1375 family outer membrane protein
	?	NC_000913	= 3868017	65 (0.730)					coding (290/333 nt)	yidQ	DUF1375 family outer membrane protein
*	?	NC_000913	= 3943624	NA (NA)	9 (0.100)	6/186	NT	51.8%	intergenic (+114/‑80)	gltU/rrlC	tRNA‑Glu/23S ribosomal RNA of rrnC operon
	?	NC_000913	= 4037457	9 (0.100)					intergenic (+122/‑62)	alaT/rrlA	tRNA‑Ala/23S ribosomal RNA of rrnA operon
*	?	NC_000913	= 3944991	NA (NA)	4 (0.050)	4/188	NT	6.8%	noncoding (1288/2904 nt)	rrlC	23S ribosomal RNA of rrnC operon
	?	NC_000913	= 4038798	58 (0.620)					noncoding (1280/2905 nt)	rrlA	23S ribosomal RNA of rrnA operon
*	?	NC_000913	3998038 =	16 (0.170)	5 (0.060)	4/186	NT	22.8%	coding (56/2163 nt)	uvrD	DNA‑dependent ATPase I and helicase II
	?	NC_000913	3998077 =	19 (0.220)					coding (95/2163 nt)	uvrD	DNA‑dependent ATPase I and helicase II
*	?	NC_000913	3999947 =	43 (0.460)	5 (0.060)	5/190	NT	10.4%	coding (1965/2163 nt)	uvrD	DNA‑dependent ATPase I and helicase II
	?	NC_000913	3999973 =	45 (0.510)					coding (1991/2163 nt)	uvrD	DNA‑dependent ATPase I and helicase II
*	?	NC_000913	4066701 =	112 (1.200)	6 (0.070)	6/190	NT	5.4%	coding (494/1386 nt)	yihP	putative 2,3‑dihydroxypropane‑1‑sulphonate exporter, membrane protein
	?	NC_000913	4066735 =	103 (1.160)					coding (460/1386 nt)	yihP	putative 2,3‑dihydroxypropane‑1‑sulphonate exporter, membrane protein
*	?	NC_000913	4094379 =	5 (0.050)	4 (0.050)	4/170	NT	39.5%	noncoding (64/402 nt)	REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences	REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences
	?	NC_000913	4094422 =	8 (0.100)					noncoding (107/402 nt)	REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences	REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences
*	?	NC_000913	4142066 =	67 (0.720)	8 (0.090)	8/182	NT	11.1%	coding (156/2502 nt)	frwA	putative PTS enzyme: Hpr, enzyme I and II components
	?	NC_000913	4142096 =	67 (0.790)					coding (126/2502 nt)	frwA	putative PTS enzyme: Hpr, enzyme I and II components
*	?	NC_000913	= 4171761	14 (0.150)	8 (0.090) +TAG	8/194	NT	39.8%	intergenic (+5/‑296)	rrfB/murB	5S ribosomal RNA of rrnB operon/UDP‑N‑acetylenolpyruvoylglucosamine reductase, FAD‑binding
	?	NC_000913	= 4213198	11 (0.120)					intergenic (+39/‑36)	rrfE/yjaA	5S ribosomal RNA of rrnE operon/stress‑induced protein
*	?	NC_000913	= 4190599	51 (0.550)	6 (0.070)	5/180	NT	11.2%	intergenic (‑112/+136)	sroH/thiH	novel sRNA, function unknown/tyrosine lyase, involved in thiamine‑thiazole moiety synthesis
	?	NC_000913	= 4190612	49 (0.580)					intergenic (‑125/+123)	sroH/thiH	novel sRNA, function unknown/tyrosine lyase, involved in thiamine‑thiazole moiety synthesis
*	?	NC_000913	4205219 =	80 (0.860)	4 (0.050)	4/186	NT	5.4%	coding (713/1290 nt)	purD	phosphoribosylglycinamide synthetase phosphoribosylamine‑glycine ligase
	?	NC_000913	4205254 =	67 (0.770)					coding (678/1290 nt)	purD	phosphoribosylglycinamide synthetase phosphoribosylamine‑glycine ligase
*	?	NC_000913	4326437 =	60 (0.640)	4 (0.050)	4/190	NT	7.1%	coding (298/336 nt)	yjdM	zinc‑ribbon family protein
	?	NC_000913	4326474 =	47 (0.530)					coding (261/336 nt)	yjdM	zinc‑ribbon family protein
*	?	NC_000913	= 4559488	66 (0.710)	6 (0.060)	6/198	NT	7.2%	coding (39/1173 nt)	iadA	isoaspartyl dipeptidase
	?	NC_000913	= 4559512	89 (0.960)					coding (15/1173 nt)	iadA	isoaspartyl dipeptidase
*	?	NC_000913	= 4583170	57 (0.610)	8 (0.090)	8/188	NT	11.8%	intergenic (‑122/+79)	hsdM/hsdR	DNA methyltransferase M/endonuclease R Type I restriction enzyme
	?	NC_000913	= 4583190	66 (0.750)					intergenic (‑142/+59)	hsdM/hsdR	DNA methyltransferase M/endonuclease R Type I restriction enzyme
*	?	NC_000913	= 4593334	NA (NA)	6 (0.070)	6/178	NT	NA	noncoding (9/26 nt)	REP349 (repetitive extragenic palindromic) element; contains 1 REP sequences	REP349 (repetitive extragenic palindromic) element; contains 1 REP sequences
	?	NC_000913	= 4593342	NA (NA)					noncoding (17/26 nt)	REP349 (repetitive extragenic palindromic) element; contains 1 REP sequences	REP349 (repetitive extragenic palindromic) element; contains 1 REP sequences
*	?	NC_000913	= 4614762	44 (0.470)	4 (0.040)	4/192	NT	7.4%	coding (782/864 nt)	yjjW	putative pyruvate formate lyase activating enzyme
	?	NC_000913	= 4614786	58 (0.650)					coding (758/864 nt)	yjjW	putative pyruvate formate lyase activating enzyme
*	?	NC_000913	= 4633095	26 (0.280)	6 (0.070)	4/184	NT	16.5%	noncoding (5/140 nt)	REP355 (repetitive extragenic palindromic) element; contains 3 REP sequences	REP355 (repetitive extragenic palindromic) element; contains 3 REP sequences
	?	NC_000913	= 4633163	37 (0.430)					noncoding (73/140 nt)	REP355 (repetitive extragenic palindromic) element; contains 3 REP sequences	REP355 (repetitive extragenic palindromic) element; contains 3 REP sequences