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	5.0%	intergenic (+14/+21)	mog → / ← satP	molybdochelatase incorporating molybdenum into molybdopterin/succinate‑acetate transporter
RA	9,908	G→T	5.2%	intergenic (+15/+20)	mog → / ← satP	molybdochelatase incorporating molybdenum into molybdopterin/succinate‑acetate transporter
RA	53,376	G→A	7.4%	P14L (CCC→CTC)	pdxA ←	4‑hydroxy‑L‑threonine phosphate dehydrogenase, NAD‑dependent
RA	53,379	T→C	8.1%	E13G (GAG→GGG)	pdxA ←	4‑hydroxy‑L‑threonine phosphate dehydrogenase, NAD‑dependent
RA	78,830	T→A	5.6%	intergenic (+31/+18)	setA → / ← leuD	broad specificity sugar efflux system/3‑isopropylmalate dehydratase small subunit
RA	78,831	T→A	5.4%	intergenic (+32/+17)	setA → / ← leuD	broad specificity sugar efflux system/3‑isopropylmalate dehydratase small subunit
RA	85,337	G→T	5.7%	intergenic (+25/‑293)	leuO → / → ilvI	global transcription factor/acetolactate synthase 3 large subunit
RA	85,338	A→C	6.4%	intergenic (+26/‑292)	leuO → / → ilvI	global transcription factor/acetolactate synthase 3 large subunit
RA	106,831	T→A	7.4%	I92N (ATT→AAT)	lpxC →	UDP‑3‑O‑acyl N‑acetylglucosamine deacetylase
RA	110,876	C→T	5.4%	A866A (GCC→GCT)	secA →	preprotein translocase subunit, ATPase
RA	110,879	A→G	6.5%	A867A (GCA→GCG)	secA →	preprotein translocase subunit, ATPase
RA	164,620	C→T	9.9%	intergenic (+86/‑110)	hrpB → / → mrcB	putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase
RA	164,621	A→G	11.0%	intergenic (+87/‑109)	hrpB → / → mrcB	putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase
RA	167,291	G→A	17.9%	intergenic (+27/‑193)	mrcB → / → fhuA	fused glycosyl transferase and transpeptidase/ferrichrome outer membrane transporter
RA	167,293	G→C	18.0%	intergenic (+29/‑191)	mrcB → / → fhuA	fused glycosyl transferase and transpeptidase/ferrichrome outer membrane transporter
RA	167,295	T→C	20.8%	intergenic (+31/‑189)	mrcB → / → fhuA	fused glycosyl transferase and transpeptidase/ferrichrome outer membrane transporter
RA	201,032	G→A	8.5%	G21D (GGC→GAC)	lpxD →	UDP‑3‑O‑(3‑hydroxymyristoyl)‑glucosamine N‑acyltransferase
RA	208,552	T→A	5.1%	L1143I (TTA→ATA)	dnaE →	DNA polymerase III alpha subunit
RA	254,228	A→T	5.2%	intergenic (+26/+31)	prfH → / ← pepD	pseudogene, RF‑1 domain family; probable peptide chain release factor/aminoacyl‑histidine dipeptidase (peptidase D)
RA	256,449	T→C	6.4%	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	6.6%	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	6.5%	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	285,882	T→G	14.3%	I163S (ATC→AGC)	yagG →	CP4‑6 prophage; putative sugar transporter
RA	285,887	C→A	14.8%	L165M (CTG→ATG)	yagG →	CP4‑6 prophage; putative sugar transporter
RA	292,302	C→G	10.3%	intergenic (+71/+20)	yagJ → / ← yagK	CP4‑6 prophage; uncharacterized protein;Phage or Prophage Related/CP4‑6 prophage; conserved protein
RA	314,255	T→C	7.1%	intergenic (‑450/‑102)	ykgP ← / → eaeH	pseudogene, oxidoreductase family/pseudogene, attaching and effacing protein homology;factor; Not classified
RA	314,258	G→A	7.0%	intergenic (‑453/‑99)	ykgP ← / → eaeH	pseudogene, oxidoreductase family/pseudogene, attaching and effacing protein homology;factor; Not classified
RA	317,566	G→A	7.5%	pseudogene (128/129 nt)	ykgQ →	pseudogene, putative dehydrogenase
RA	317,571	T→C	7.0%	intergenic (+4/+155)	ykgQ → / ← rclC	pseudogene, putative dehydrogenase/reactive chlorine species (RCS) stress resistance inner membrane protein
RA	328,375	A→C	8.2%	I120S (ATC→AGC)	betB ←	betaine aldehyde dehydrogenase, NAD‑dependent
RA	328,377	C→G	8.0%	L119L (CTG→CTC) ‡	betB ←	betaine aldehyde dehydrogenase, NAD‑dependent
RA	328,379	G→T	7.9%	L119M (CTG→ATG) ‡	betB ←	betaine aldehyde dehydrogenase, NAD‑dependent
RA	336,866	G→C	5.0%	G30A (GGC→GCC)	yahF →	putative NAD(P)‑binding succinyl‑CoA synthase
RA	339,756	T→C	6.3%	intergenic (+13/‑409)	yahG → / → yahI	DUF1116 family protein/carbamate kinase‑like protein
RA	339,761	G→C	6.3%	intergenic (+18/‑404)	yahG → / → yahI	DUF1116 family protein/carbamate kinase‑like protein
RA	339,764	G→C	5.7%	intergenic (+21/‑401)	yahG → / → yahI	DUF1116 family protein/carbamate kinase‑like protein
RA	339,769	G→A	6.3%	intergenic (+26/‑396)	yahG → / → yahI	DUF1116 family protein/carbamate kinase‑like protein
RA	344,704	A→T	5.2%	K177* (AAA→TAA) ‡	yahL →	uncharacterized protein
RA	344,705	A→T	5.3%	K177I (AAA→ATA) ‡	yahL →	uncharacterized protein
RA	374,682	C→T	5.4%	P272L (CCG→CTG) ‡	mhpE →	4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I
RA	374,683	G→C	5.3%	P272P (CCG→CCC) ‡	mhpE →	4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I
RA	374,688	G→C	5.3%	R274P (CGA→CCA) ‡	mhpE →	4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I
RA	374,689	A→G	6.1%	R274R (CGA→CGG) ‡	mhpE →	4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I
RA	443,022	G→A	14.4%	intergenic (+25/+29)	thiI → / ← yajL	tRNA s(4)U8 sulfurtransferase/oxidative‑stress‑resistance chaperone
RA	443,023	T→C	12.9%	intergenic (+26/+28)	thiI → / ← yajL	tRNA s(4)U8 sulfurtransferase/oxidative‑stress‑resistance chaperone
RA	457,649	A→C	5.5%	D75A (GAC→GCC)	clpX →	ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease
RA	457,659	T→A	5.4%	V78V (GTT→GTA)	clpX →	ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease
RA	475,971	C→G	13.4%	intergenic (+20/+11)	ybaY → / ← ybaZ	outer membrane lipoprotein/excision repair protein, alkyltransferase‑like protein ATL
RA	475,972	C→G	13.3%	intergenic (+21/+10)	ybaY → / ← ybaZ	outer membrane lipoprotein/excision repair protein, alkyltransferase‑like protein ATL
RA	480,236	C→G	6.6%	E25Q (GAG→CAG)	hha ←	modulator of gene expression, with H‑NS
RA	480,237	C→G	7.1%	L24L (CTG→CTC)	hha ←	modulator of gene expression, with H‑NS
RA	501,463	C→A	5.3%	intergenic (+34/+99)	gsk → / ← ybaL	inosine/guanosine kinase/inner membrane putative NAD(P)‑binding transporter
RA	512,212	T→G	6.3%	V191G (GTG→GGG)	glsA →	glutaminase 1
RA	512,219	C→A	7.5%	T193T (ACC→ACA)	glsA →	glutaminase 1
RA	522,935	T→C	6.4%	intergenic (+105/‑326)	ybbP → / → rhsD	putative ABC transporter permease/Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
RA	533,846	T→C	8.6%	intergenic (+20/‑70)	allR → / → gcl	glyoxylate‑inducible transcriptional repressor of all and gcl operons/glyoxylate carboligase
RA	533,849	G→A	8.9%	intergenic (+23/‑67)	allR → / → gcl	glyoxylate‑inducible transcriptional repressor of all and gcl operons/glyoxylate carboligase
RA	543,207	A→T	5.1%	intergenic (+174/+54)	glxK → / ← allE	glycerate kinase II/S‑ureidoglycine aminohydrolase
RA	543,748	G→C	5.3%	T100R (ACA→AGA)	allE ←	S‑ureidoglycine aminohydrolase
RA	569,160	G→T	6.1%	D87Y (GAC→TAC) ‡	ybcK →	DLP12 prophage; putative recombinase
RA	569,161	A→C	6.1%	D87A (GAC→GCC) ‡	ybcK →	DLP12 prophage; putative recombinase
RA	574,504	Δ1 bp	5.6%	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	12.9%	intergenic (‑20/‑404)	ompT ← / → pauD	DLP12 prophage; outer membrane protease VII; outer membrane protein 3b/tRNA‑OTHER
RA	585,656	T→A	13.6%	intergenic (‑23/‑401)	ompT ← / → pauD	DLP12 prophage; outer membrane protease VII; outer membrane protein 3b/tRNA‑OTHER
RA	585,657	T→A	13.6%	intergenic (‑24/‑400)	ompT ← / → pauD	DLP12 prophage; outer membrane protease VII; outer membrane protein 3b/tRNA‑OTHER
RA	585,660	T→C	14.5%	intergenic (‑27/‑397)	ompT ← / → pauD	DLP12 prophage; outer membrane protease VII; outer membrane protein 3b/tRNA‑OTHER
RA	585,863	T→C	12.6%	intergenic (‑230/‑194)	ompT ← / → pauD	DLP12 prophage; outer membrane protease VII; outer membrane protein 3b/tRNA‑OTHER
RA	585,866	G→A	11.8%	intergenic (‑233/‑191)	ompT ← / → pauD	DLP12 prophage; outer membrane protease VII; outer membrane protein 3b/tRNA‑OTHER
RA	603,391	C→G	10.5%	intergenic (+56/+25)	pheP → / ← ybdG	phenylalanine transporter/mechanosensitive channel protein, miniconductance
RA	603,393	T→A	10.2%	intergenic (+58/+23)	pheP → / ← ybdG	phenylalanine transporter/mechanosensitive channel protein, miniconductance
RA	603,395	C→G	10.3%	intergenic (+60/+21)	pheP → / ← ybdG	phenylalanine transporter/mechanosensitive channel protein, miniconductance
RA	623,054	A→T	5.8%	N252I (AAC→ATC)	entS →	enterobactin exporter, iron‑regulated
RA	632,126	A→G	6.1%	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	6.2%	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	6.9%	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	6.6%	intergenic (+135/‑48)	cstA → / → ybdD	carbon starvation protein involved in peptide utilization; APC peptide transporter family protein/DUF466 family protein
RA	657,531	T→G	8.0%	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	7.3%	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	8.0%	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	5.1%	P33A (CCT→GCT)	rlpA ←	septal ring protein, suppressor of prc, minor lipoprotein
RA	678,688	A→C	5.9%	N425T (AAT→ACT)	djlB →	putative HscC co‑chaperone, uncharacterized J domain‑containing protein
RA	681,694	A→G	7.4%	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	7.6%	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	8.3%	intergenic (+37/+23)	djlC → / ← hscC	J domain‑containing HscC co‑chaperone; Hsc56/Hsp70 family chaperone Hsc62; RpoD‑binding transcription inhibitor
RA	696,325	G→T	5.6%	intergenic (+49/+105)	ubiF → / ← glnX	2‑octaprenyl‑3‑methyl‑6‑methoxy‑1,4‑benzoquinol oxygenase/tRNA‑Gln
RA	696,328	A→C	6.1%	intergenic (+52/+102)	ubiF → / ← glnX	2‑octaprenyl‑3‑methyl‑6‑methoxy‑1,4‑benzoquinol oxygenase/tRNA‑Gln
RA	699,556	C→T	12.5%	intergenic (‑379/+18)	asnB ← / ← umpH	asparagine synthetase B/UMP phosphatase
RA	699,559	A→G	11.8%	intergenic (‑382/+15)	asnB ← / ← umpH	asparagine synthetase B/UMP phosphatase
RA	710,170	C→T	7.1%	intergenic (+54/+30)	chiQ → / ← fur	chitosugar‑induced verified lipoprotein/ferric iron uptake regulon transcriptional repressor; autorepressor
RA	710,173	A→G	7.6%	intergenic (+57/+27)	chiQ → / ← fur	chitosugar‑induced verified lipoprotein/ferric iron uptake regulon transcriptional repressor; autorepressor
RA	747,895	C→G	5.5%	intergenic (‑126/+26)	abrB ← / ← ybgO	regulator of aidB expression; inner membrane protein/putative fimbrial protein
RA	747,897	G→C	5.6%	intergenic (‑128/+24)	abrB ← / ← ybgO	regulator of aidB expression; inner membrane protein/putative fimbrial protein
RA	747,900	G→C	5.6%	intergenic (‑131/+21)	abrB ← / ← ybgO	regulator of aidB expression; inner membrane protein/putative fimbrial protein
RA	747,902	C→G	5.7%	intergenic (‑133/+19)	abrB ← / ← ybgO	regulator of aidB expression; inner membrane protein/putative fimbrial protein
RA	765,132	G→A	12.5%	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	13.5%	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	5.2%	G33S (GGC→AGC)	cydB →	cytochrome d terminal oxidase, subunit II
RA	773,145	T→C	5.4%	L35P (CTC→CCC)	cydB →	cytochrome d terminal oxidase, subunit II
RA	788,385	G→T	5.2%	T151T (ACC→ACA) ‡	galM ←	aldose 1‑epimerase; type‑1 mutarotase; galactose mutarotase
RA	788,387	T→A	5.2%	T151S (ACC→TCC) ‡	galM ←	aldose 1‑epimerase; type‑1 mutarotase; galactose mutarotase
RA	788,389	A→C	5.2%	L150R (CTG→CGG)	galM ←	aldose 1‑epimerase; type‑1 mutarotase; galactose mutarotase
RA	847,214	T→A	5.4%	intergenic (‑95/+44)	glnP ← / ← glnH	glutamine transporter subunit/glutamine transporter subunit
RA	857,576	T→C	11.1%	intergenic (+21/+220)	ybiT → / ← ybiU	ABC‑F family putative regulatory ATPase/DUF1479 family protein
RA	857,578	C→G	10.7%	intergenic (+23/+218)	ybiT → / ← ybiU	ABC‑F family putative regulatory ATPase/DUF1479 family protein
RA	857,580	G→A	10.8%	intergenic (+25/+216)	ybiT → / ← ybiU	ABC‑F family putative regulatory ATPase/DUF1479 family protein
RA	860,154	A→T	7.5%	intergenic (‑126/+20)	ybiV ← / ← ybiW	sugar phosphatase; fructose‑1‑P/ribose‑5‑P/glucose‑6‑P phosphatase/putative pyruvate formate lyase
RA	867,717	G→C	5.0%	L66F (TTG→TTC)	gsiA →	glutathione ABC transporter ATPase
RA	867,718	G→C	5.1%	E67Q (GAA→CAA)	gsiA →	glutathione ABC transporter ATPase
RA	870,890	A→T	5.0%	T494S (ACC→TCC)	gsiB →	glutathione ABC transporter periplasmic binding protein
RA	892,441	G→A	5.3%	A159T (GCG→ACG) ‡	rimK →	ribosomal protein S6 modification protein
RA	892,443	G→C	6.1%	A159A (GCG→GCC) ‡	rimK →	ribosomal protein S6 modification protein
RA	892,455	G→C	14.1%	V163V (GTG→GTC)	rimK →	ribosomal protein S6 modification protein
RA	892,457	T→A	14.3%	I164N (ATT→AAT)	rimK →	ribosomal protein S6 modification protein
RA	892,459	G→C	13.9%	D165H (GAC→CAC)	rimK →	ribosomal protein S6 modification protein
RA	915,080	G→C	6.4%	intergenic (‑223/+272)	ybjE ← / ← aqpZ	putative transporter/aquaporin Z
RA	915,081	G→C	6.4%	intergenic (‑224/+271)	ybjE ← / ← aqpZ	putative transporter/aquaporin Z
RA	926,168	C→T	9.4%	intergenic (‑197/+57)	serW ← / ← infA	tRNA‑Ser/translation initiation factor IF‑1
RA	926,174	A→T	11.9%	intergenic (‑203/+51)	serW ← / ← infA	tRNA‑Ser/translation initiation factor IF‑1
RA	926,180	A→G	11.1%	intergenic (‑209/+45)	serW ← / ← infA	tRNA‑Ser/translation initiation factor IF‑1
RA	958,769	C→G	5.9%	intergenic (+28/‑43)	serC → / → aroA	3‑phosphoserine/phosphohydroxythreonine aminotransferase/5‑enolpyruvylshikimate‑3‑phosphate synthetase
RA	958,771	A→T	5.8%	intergenic (+30/‑41)	serC → / → aroA	3‑phosphoserine/phosphohydroxythreonine aminotransferase/5‑enolpyruvylshikimate‑3‑phosphate synthetase
RA	958,773	C→G	5.7%	intergenic (+32/‑39)	serC → / → aroA	3‑phosphoserine/phosphohydroxythreonine aminotransferase/5‑enolpyruvylshikimate‑3‑phosphate synthetase
RA	986,410	A→C	5.3%	S191S (TCT→TCG) ‡	ompF ←	outer membrane porin 1a (Ia;b;F)
RA	986,411	G→T	5.3%	S191Y (TCT→TAT) ‡	ompF ←	outer membrane porin 1a (Ia;b;F)
RA	1,020,958	A→T	5.6%	intergenic (‑39/‑180)	sulA ← / → sxy	SOS cell division inhibitor/CRP‑S‑dependent promoter expression factor
RA	1,041,937	T→G	9.3%	intergenic (+22/+93)	appA → / ← etk	phosphoanhydride phosphorylase/tyrosine‑protein kinase, role in O‑antigen capsule formation
RA	1,041,940	C→A	8.8%	intergenic (+25/+90)	appA → / ← etk	phosphoanhydride phosphorylase/tyrosine‑protein kinase, role in O‑antigen capsule formation
RA	1,100,125	C→T	5.4%	T162T (ACC→ACT)	ycdY →	redox enzyme maturation protein (REMP) chaperone for YcdX
RA	1,113,544	G→A	9.8%	intergenic (+138/‑35)	opgH → / → yceK	OPG biosynthetic ACP‑dependent transmembrane UDP‑glucose beta‑1,2 glycosyltransferase; nutrient‑dependent cell size regulator, FtsZ assembly antagonist/outer membrane integrity lipoprotein
RA	1,113,546	T→A	9.7%	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	9.9%	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	5.1%	K16N (AAA→AAC)	yceA →	putative rhodanese‑related sulfurtransferase
RA	1,147,980	G→T	7.7%	K120N (AAG→AAT)	plsX →	putative phosphate acyltransferase
RA	1,147,986	G→C	7.5%	L122L (CTG→CTC)	plsX →	putative phosphate acyltransferase
RA	1,147,987	G→C	7.6%	E123Q (GAG→CAG)	plsX →	putative phosphate acyltransferase
RA	1,147,993	A→C	7.5%	I125L (ATT→CTT)	plsX →	putative phosphate acyltransferase
RA	1,158,139	A→T	6.1%	K91* (AAA→TAA) ‡	ptsG →	fused glucose‑specific PTS enzymes: IIB component/IIC component
RA	1,158,140	A→T	5.2%	K91I (AAA→ATA) ‡	ptsG →	fused glucose‑specific PTS enzymes: IIB component/IIC component
RA	1,159,335	G→T	5.0%	intergenic (+33/+27)	ptsG → / ← fhuE	fused glucose‑specific PTS enzymes: IIB component/IIC component/ferric‑rhodotorulic acid outer membrane transporter
RA	1,170,272	G→C	10.3%	P35A (CCA→GCA)	ldtC ←	L,D‑transpeptidase linking Lpp to murein
RA	1,170,275	G→C	10.3%	P34A (CCG→GCG)	ldtC ←	L,D‑transpeptidase linking Lpp to murein
RA	1,170,282	C→G	11.8%	W31C (TGG→TGC)	ldtC ←	L,D‑transpeptidase linking Lpp to murein
RA	1,174,077	G→A	7.9%	intergenic (‑113/+15)	mfd ← / ← ycfT	transcription‑repair coupling factor/inner membrane protein
RA	1,174,080	T→C	8.0%	intergenic (‑116/+12)	mfd ← / ← ycfT	transcription‑repair coupling factor/inner membrane protein
RA	1,182,771	G→C	6.2%	A20G (GCC→GGC)	potD ←	spermidine/putrescine ABC transporter periplasmic binding protein
RA	1,187,091	T→A	5.3%	intergenic (+21/+28)	pepT → / ← roxA	peptidase T/50S ribosomal protein L16 arginine hydroxylase; 2‑oxoglutarate oxygenase
RA	1,224,239	A→T	5.7%	intergenic (+332/+40)	ycgI → / ← minE	pseudogene/cell division topological specificity factor
RA	1,224,242	A→T	5.5%	intergenic (+335/+37)	ycgI → / ← minE	pseudogene/cell division topological specificity factor
RA	1,226,114	C→G	6.1%	intergenic (‑34/‑486)	minC ← / → ycgJ	inhibitor of FtsZ ring polymerization/uncharacterized protein
RA	1,226,115	A→C	6.0%	intergenic (‑35/‑485)	minC ← / → ycgJ	inhibitor of FtsZ ring polymerization/uncharacterized protein
RA	1,226,118	G→T	6.0%	intergenic (‑38/‑482)	minC ← / → ycgJ	inhibitor of FtsZ ring polymerization/uncharacterized protein
RA	1,226,119	C→G	6.1%	intergenic (‑39/‑481)	minC ← / → ycgJ	inhibitor of FtsZ ring polymerization/uncharacterized protein
RA	1,227,051	G→C	8.2%	intergenic (+83/+20)	ycgJ → / ← pliG	uncharacterized protein/periplasmic inhibitor of g‑type lysozyme
RA	1,227,052	A→T	8.2%	intergenic (+84/+19)	ycgJ → / ← pliG	uncharacterized protein/periplasmic inhibitor of g‑type lysozyme
RA	1,227,053	G→C	8.2%	intergenic (+85/+18)	ycgJ → / ← pliG	uncharacterized protein/periplasmic inhibitor of g‑type lysozyme
RA	1,260,901	C→T	7.2%	intergenic (‑98/+27)	dauA ← / ← prs	C4‑dicarboxylic acid transporter/phosphoribosylpyrophosphate synthase
RA	1,260,904	A→G	7.6%	intergenic (‑101/+24)	dauA ← / ← prs	C4‑dicarboxylic acid transporter/phosphoribosylpyrophosphate synthase
RA	1,285,190	T→A	8.7%	L18I (TTA→ATA)	narJ →	molybdenum‑cofactor‑assembly chaperone delta subunit of nitrate reductase 1
RA	1,285,193	T→A	9.8%	W19R (TGG→AGG)	narJ →	molybdenum‑cofactor‑assembly chaperone delta subunit of nitrate reductase 1
RA	1,285,261	Δ1 bp	5.2%	coding (123/711 nt)	narJ →	molybdenum‑cofactor‑assembly chaperone delta subunit of nitrate reductase 1
RA	1,285,265:1	+A	5.4%	coding (127/711 nt)	narJ →	molybdenum‑cofactor‑assembly chaperone delta subunit of nitrate reductase 1
RA	1,304,474	T→A	7.3%	I214N (ATT→AAT)	oppC →	oligopeptide ABC transporter permease
RA	1,304,479	C→G	7.1%	P216A (CCG→GCG)	oppC →	oligopeptide ABC transporter permease
RA	1,324,837	A→C	7.7%	Y31S (TAT→TCT) ‡	yciQ →	enhancer of membrane protein expression; putative inner membrane protein
RA	1,324,838	T→A	8.1%	Y31* (TAT→TAA) ‡	yciQ →	enhancer of membrane protein expression; putative inner membrane protein
RA	1,324,839	G→T	8.9%	E32* (GAA→TAA)	yciQ →	enhancer of membrane protein expression; putative inner membrane protein
RA	1,327,216	A→G	6.0%	D122G (GAT→GGT)	rluB →	23S rRNA pseudouridine(2605) synthase
RA	1,344,033	A→G	6.2%	L105P (CTG→CCG)	yciT ←	global regulator of transcription; DeoR family
RA	1,344,036	G→C	6.3%	T104S (ACT→AGT)	yciT ←	global regulator of transcription; DeoR family
RA	1,344,039	C→T	5.8%	R103Q (CGG→CAG)	yciT ←	global regulator of transcription; DeoR family
RA	1,346,770	G→C	5.3%	intergenic (‑28/‑26)	gmr ← / → ymiB	cyclic‑di‑GMP phosphodiesterase; csgD regulator; modulator of RNase II stability/uncharacterized protein
RA	1,375,064	C→T	7.6%	G34G (GGC→GGT)	ycjQ →	putative Zn‑dependent NAD(P)‑binding oxidoreductase
RA	1,375,067	A→G	6.6%	A35A (GCA→GCG)	ycjQ →	putative Zn‑dependent NAD(P)‑binding oxidoreductase
RA	1,386,750	C→G	5.5%	L11V (CTC→GTC)	tyrR →	aromatic amino acid biosynthesis and transport regulon transcriptional regulator; autorepressor; ATPase; phosphatase
RA	1,388,283	C→T	5.4%	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	5.5%	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	5.5%	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	5.1%	I39V (ATC→GTC)	smrA →	DNA endonuclease
RA	1,406,098	C→T	5.8%	D40D (GAC→GAT)	smrA →	DNA endonuclease
RA	1,426,178	A→T	6.5%	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	1,451,537	A→T	5.2%	intergenic (‑188/+60)	tynA ← / ← paaZ	tyramine oxidase, copper‑requiring/oxepin‑CoA hydrolase and 3‑oxo‑5,6‑dehydrosuberyl‑CoA semialdehyde dehydrogenase
RA	1,463,480	Δ1 bp	6.6%	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	6.7%	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	6.6%	intergenic (+44/‑57)	paaK → / → paaX	phenylacetyl‑CoA ligase/transcriptional repressor of phenylacetic acid degradation paa operon, phenylacetyl‑CoA inducer
RA	1,507,500	G→T	5.1%	K240N (AAG→AAT)	ydcP →	putative peptidase
RA	1,507,501	A→C	5.3%	I241L (ATT→CTT)	ydcP →	putative peptidase
RA	1,517,481	C→G	6.3%	R31R (CGC→CGG)	ydcX →	DUF2566 family protein
RA	1,517,484	C→G	6.0%	I32M (ATC→ATG)	ydcX →	DUF2566 family protein
RA	1,541,077	G→C	6.7%	A505G (GCC→GGC)	narZ ←	nitrate reductase 2 (NRZ), alpha subunit
RA	1,572,928	C→G	5.9%	A759P (GCA→CCA)	pqqL ←	putative periplasmic M16 family zinc metalloendopeptidase
RA	1,585,149	Δ1 bp	5.8%	coding (1338/2280 nt)	ydeP ←	putative oxidoreductase
RA	1,585,156:1	+C	5.2%	coding (1331/2280 nt)	ydeP ←	putative oxidoreductase
RA	1,620,224	C→G	5.7%	intergenic (+17/+14)	marB → / ← eamA	periplasmic mar operon regulator/cysteine and O‑acetyl‑L‑serine efflux system
RA	1,620,227	C→G	6.3%	intergenic (+20/+11)	marB → / ← eamA	periplasmic mar operon regulator/cysteine and O‑acetyl‑L‑serine efflux system
RA	1,666,466	T→G	5.4%	Y384* (TAT→TAG)	clcB →	H(+)/Cl(‑) exchange transporter
RA	1,666,468	A→T	5.4%	Q385L (CAG→CTG)	clcB →	H(+)/Cl(‑) exchange transporter
RA	1,666,470	C→A	5.1%	L386I (CTA→ATA)	clcB →	H(+)/Cl(‑) exchange transporter
RA	1,684,016	A→G	5.9%	S379G (AGC→GGC)	rstB →	sensory histidine kinase of RstAB two‑component system
RA	1,684,019	C→T	5.5%	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	9.1%	intergenic (+66/‑35)	manA → / → ydgA	mannose‑6‑phosphate isomerase/DUF945 family protein
RA	1,689,819	A→T	9.1%	intergenic (+68/‑33)	manA → / → ydgA	mannose‑6‑phosphate isomerase/DUF945 family protein
RA	1,689,821	T→G	9.1%	intergenic (+70/‑31)	manA → / → ydgA	mannose‑6‑phosphate isomerase/DUF945 family protein
RA	1,736,097	T→A	5.4%	intergenic (+138/+24)	sodB → / ← ydhP	superoxide dismutase, Fe/putative MFS transporter, inner membrane protein
RA	1,736,100	T→A	5.4%	intergenic (+141/+21)	sodB → / ← ydhP	superoxide dismutase, Fe/putative MFS transporter, inner membrane protein
RA	1,743,155	C→G	6.2%	D30H (GAC→CAC)	ribC ←	riboflavin synthase, alpha subunit
RA	1,743,157	G→A	6.4%	P29L (CCC→CTC)	ribC ←	riboflavin synthase, alpha subunit
RA	1,743,160	A→T	6.5%	L28* (TTA→TAA)	ribC ←	riboflavin synthase, alpha subunit
RA	1,743,163	T→C	6.3%	E27G (GAG→GGG)	ribC ←	riboflavin synthase, alpha subunit
RA	1,743,165	C→G	6.5%	V26V (GTG→GTC)	ribC ←	riboflavin synthase, alpha subunit
RA	1,778,364	C→T	8.5%	intergenic (+17/+26)	ydiO → / ← ydiP	putative acyl‑CoA dehydrogenase/putative DNA‑binding transcriptional regulator
RA	1,778,367	C→G	6.8%	intergenic (+20/+23)	ydiO → / ← ydiP	putative acyl‑CoA dehydrogenase/putative DNA‑binding transcriptional regulator
RA	1,778,372	C→G	7.4%	intergenic (+25/+18)	ydiO → / ← ydiP	putative acyl‑CoA dehydrogenase/putative DNA‑binding transcriptional regulator
RA	1,778,375	A→G	7.2%	intergenic (+28/+15)	ydiO → / ← ydiP	putative acyl‑CoA dehydrogenase/putative DNA‑binding transcriptional regulator
RA	1,789,082	G→T	5.3%	Q216H (CAG→CAT)	aroH →	3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, tryptophan repressible
RA	1,789,083	A→C	5.5%	M217L (ATG→CTG)	aroH →	3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, tryptophan repressible
RA	1,797,388	G→T	8.0%	P186Q (CCG→CAG)	pheT ←	phenylalanine tRNA synthetase, beta subunit
RA	1,797,391	A→C	5.3%	L185R (CTG→CGG)	pheT ←	phenylalanine tRNA synthetase, beta subunit
RA	1,827,811	T→G	5.5%	K150T (AAA→ACA)	astB ←	succinylarginine dihydrolase
RA	1,827,816	C→A	5.3%	L148L (CTG→CTT)	astB ←	succinylarginine dihydrolase
RA	1,836,136	G→C	5.6%	D22H (GAC→CAC)	ynjB →	putative ABC transporter periplasmic binding protein
RA	1,856,333	T→G	7.4%	E199A (GAG→GCG) ‡	ydjH ←	putative kinase
RA	1,856,334	C→A	7.3%	E199* (GAG→TAG) ‡	ydjH ←	putative kinase
RA	1,864,758	G→A	9.9%	intergenic (+24/+24)	yeaD → / ← yeaE	D‑hexose‑6‑phosphate epimerase‑like protein/aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent
RA	1,864,763	A→T	13.8%	intergenic (+29/+19)	yeaD → / ← yeaE	D‑hexose‑6‑phosphate epimerase‑like protein/aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent
RA	1,864,768	T→C	15.5%	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	10.9%	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	8.7%	intergenic (+17/‑96)	yeaG → / → yeaH	protein kinase, endogenous substrate unidentified; autokinase/UPF0229 family protein
RA	1,868,865:1	+G	5.7%	intergenic (+23/‑90)	yeaG → / → yeaH	protein kinase, endogenous substrate unidentified; autokinase/UPF0229 family protein
RA	1,891,841	A→G	9.2%	G465G (GGT→GGC) ‡	yoaA ←	putative ATP‑dependent helicase, DinG family
RA	1,891,842	C→T	8.9%	G465D (GGT→GAT) ‡	yoaA ←	putative ATP‑dependent helicase, DinG family
RA	1,926,888	C→A	6.4%	G651V (GGC→GTC)	ptrB ←	protease II
RA	1,926,891	G→C	6.7%	S650* (TCA→TGA)	ptrB ←	protease II
RA	1,926,894	T→G	5.2%	D649A (GAC→GCC)	ptrB ←	protease II
RA	1,926,900	T→G	7.7%	D647A (GAC→GCC)	ptrB ←	protease II
RA	1,928,799	A→C	6.0%	L14R (CTT→CGT)	ptrB ←	protease II
RA	1,928,802	G→T	5.3%	T13K (ACG→AAG)	ptrB ←	protease II
MC JC	1,978,503	Δ776 bp	100%		insB1–insA	insB1, insA
RA	1,985,112	C→G	7.6%	intergenic (‑43/+27)	araG ← / ← araF	L‑arabinose ABC transporter ATPase/L‑arabinose ABC transporter periplasmic binding protein
RA	1,987,442	Δ1 bp	5.9%	intergenic (+14/+65)	ftnB → / ← yecJ	ferritin B, putative ferrous iron reservoir/DUF2766 family protein
RA	2,028,158	G→C	6.9%	intergenic (‑141/+30)	yedQ ← / ← yodC	putative membrane‑anchored diguanylate cyclase/uncharacterized protein
RA	2,028,159	T→A	6.8%	intergenic (‑142/+29)	yedQ ← / ← yodC	putative membrane‑anchored diguanylate cyclase/uncharacterized protein
RA	2,028,160	G→C	7.1%	intergenic (‑143/+28)	yedQ ← / ← yodC	putative membrane‑anchored diguanylate cyclase/uncharacterized protein
RA	2,041,159	G→A	5.8%	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	5.8%	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	6.5%	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	7.0%	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	5.7%	intergenic (+13/+25)	asnU → / ← cbl	tRNA‑Asn/ssuEADCB/tauABCD operon transcriptional activator
RA	2,059,946	T→A	5.7%	intergenic (+20/+18)	asnU → / ← cbl	tRNA‑Asn/ssuEADCB/tauABCD operon transcriptional activator
RA	2,059,948	T→A	6.0%	intergenic (+22/+16)	asnU → / ← cbl	tRNA‑Asn/ssuEADCB/tauABCD operon transcriptional activator
RA	2,059,950	T→A	6.0%	intergenic (+24/+14)	asnU → / ← cbl	tRNA‑Asn/ssuEADCB/tauABCD operon transcriptional activator
RA	2,074,691	C→G	8.3%	intergenic (+33/‑88)	flu → / → yeeR	CP4‑44 prophage; antigen 43 (Ag43) phase‑variable biofilm formation autotransporter/CP4‑44 prophage; putative membrane protein
RA	2,081,688	A→T	10.5%	I287N (ATT→AAT)	dacD ←	D‑alanyl‑D‑alanine carboxypeptidase; penicillin‑binding protein 6b
RA	2,089,854	A→T	10.0%	intergenic (‑141/‑142)	yefM ← / → hisL	antitoxin of the YoeB‑YefM toxin‑antitoxin system/his operon leader peptide
RA	2,090,122	A→G	14.9%	intergenic (+76/‑70)	hisL → / → hisG	his operon leader peptide/ATP phosphoribosyltransferase
RA	2,090,124	C→G	15.3%	intergenic (+78/‑68)	hisL → / → hisG	his operon leader peptide/ATP phosphoribosyltransferase
RA	2,090,126	C→T	15.6%	intergenic (+80/‑66)	hisL → / → hisG	his operon leader peptide/ATP phosphoribosyltransferase
RA	2,139,726	T→G	5.2%	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	5.1%	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	2,173,361	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	2,187,314	C→G	5.1%	intergenic (+16/+66)	rcnB → / ← yehA	periplasmic modulator of Ni and Co efflux/putative fimbrial‑like adhesin protein
RA	2,229,322	C→G	16.5%	intergenic (+257/+116)	yohP → / ← dusC	uncharacterized protein/tRNA‑dihydrouridine synthase C
RA	2,229,323	C→G	16.0%	intergenic (+258/+115)	yohP → / ← dusC	uncharacterized protein/tRNA‑dihydrouridine synthase C
RA	2,255,991	A→T	6.4%	K213* (AAA→TAA) ‡	yeiL →	putative transcriptional regulator
RA	2,255,992	A→T	6.3%	K213I (AAA→ATA) ‡	yeiL →	putative transcriptional regulator
RA	2,286,139	A→T	5.4%	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	5.6%	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	5.5%	intergenic (+9/‑66)	yejM → / → proL	essential inner membrane DUF3413 domain‑containing protein; lipid A production and membrane permeability factor/tRNA‑Pro
RA	2,304,762	T→C	7.0%	intergenic (+369/+346)	eco → / ← mqo	ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
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	5.2%	T395K (ACG→AAG)	rcsC ←	hybrid sensory kinase in two‑component regulatory system with RcsB and YojN
RA	2,375,483	A→T	5.2%	L160L (CTT→CTA) ‡	menC ←	O‑succinylbenzoyl‑CoA synthase
RA	2,375,484	A→T	5.2%	L160H (CTT→CAT) ‡	menC ←	O‑succinylbenzoyl‑CoA synthase
RA	2,383,956	A→T	12.8%	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	16.3%	intergenic (+35/+36)	elaD → / ← yfbK	protease, capable of cleaving an AMC‑ubiquitin model substrate/Von Willebrand factor domain putative lipoprotein
RA	2,391,414	C→G	5.7%	R31P (CGA→CCA)	nuoN ←	NADH:ubiquinone oxidoreductase, membrane subunit N
RA	2,391,417	C→G	5.1%	W30S (TGG→TCG)	nuoN ←	NADH:ubiquinone oxidoreductase, membrane subunit N
RA	2,457,128	T→A	5.2%	M678L (ATG→TTG)	fadJ ←	enoyl‑CoA hydratase/epimerase and isomerase/3‑hydroxyacyl‑CoA dehydrogenase
RA	2,474,878	T→C	11.2%	intergenic (+22/‑106)	yfdQ → / → yfdR	CPS‑53 (KpLE1) prophage; uncharacterized protein/CPS‑53 (KpLE1) prophage; conserved protein
RA	2,474,881	G→A	11.8%	intergenic (+25/‑103)	yfdQ → / → yfdR	CPS‑53 (KpLE1) prophage; uncharacterized protein/CPS‑53 (KpLE1) prophage; conserved protein
RA	2,519,222	T→G	6.4%	intergenic (+17/+35)	yfeD → / ← gltX	DUF1323 family putative DNA‑binding protein/glutamyl‑tRNA synthetase
RA	2,519,225	T→A	5.8%	intergenic (+20/+32)	yfeD → / ← gltX	DUF1323 family putative DNA‑binding protein/glutamyl‑tRNA synthetase
RA	2,519,228	C→A	5.9%	intergenic (+23/+29)	yfeD → / ← gltX	DUF1323 family putative DNA‑binding protein/glutamyl‑tRNA synthetase
RA	2,560,317	A→C	17.2%	N21H (AAT→CAT)	yffL →	CPZ‑55 prophage; uncharacterized protein
RA	2,560,321	C→T	17.6%	A22V (GCT→GTT)	yffL →	CPZ‑55 prophage; uncharacterized protein
RA	2,560,326	A→G	15.6%	T24A (ACA→GCA)	yffL →	CPZ‑55 prophage; uncharacterized protein
RA	2,560,330	G→T	16.1%	C25F (TGC→TTC)	yffL →	CPZ‑55 prophage; uncharacterized protein
RA	2,566,266	C→A	7.0%	G207C (GGC→TGC)	eutA ←	reactivating factor for ethanolamine ammonia lyase
RA	2,566,267	T→G	7.2%	A206A (GCA→GCC)	eutA ←	reactivating factor for ethanolamine ammonia lyase
RA	2,581,762	G→A	5.9%	A339V (GCC→GTC)	ypfG ←	DUF1176 family protein
RA	2,581,765	T→C	6.0%	D338G (GAC→GGC)	ypfG ←	DUF1176 family protein
RA	2,592,989	A→G	5.8%	intergenic (+27/+83)	ypfN → / ← ypfH	putative membrane protein, UPF0370 family/palmitoyl‑CoA esterase activity, uncertain physiological substrate
RA	2,592,990	A→C	6.0%	intergenic (+28/+82)	ypfN → / ← ypfH	putative membrane protein, UPF0370 family/palmitoyl‑CoA esterase activity, uncertain physiological substrate
RA	2,612,973	C→G	7.1%	L358L (CTC→CTG)	hyfR →	hydrogenase‑4 transcriptional activator
RA	2,612,974	C→G	7.0%	Q359E (CAG→GAG)	hyfR →	hydrogenase‑4 transcriptional activator
RA	2,637,433	C→T	6.4%	intergenic (‑77/+41)	der ← / ← bamB	GTPase; multicopy suppressor of ftsJ/BamABCDE complex OM biogenesis lipoprotein
RA	2,637,438	T→G	6.5%	intergenic (‑82/+36)	der ← / ← bamB	GTPase; multicopy suppressor of ftsJ/BamABCDE complex OM biogenesis lipoprotein
RA	2,637,439	C→A	6.4%	intergenic (‑83/+35)	der ← / ← bamB	GTPase; multicopy suppressor of ftsJ/BamABCDE complex OM biogenesis lipoprotein
RA	2,637,444	A→G	7.4%	intergenic (‑88/+30)	der ← / ← bamB	GTPase; multicopy suppressor of ftsJ/BamABCDE complex OM biogenesis lipoprotein
RA	2,638,584	A→T	6.5%	F23L (TTT→TTA)	bamB ←	BamABCDE complex OM biogenesis lipoprotein
RA	2,653,104	G→C	8.8%	W204S (TGG→TCG) ‡	sseA →	3‑mercaptopyruvate sulfurtransferase
RA	2,653,105	G→C	8.5%	W204C (TGG→TGC) ‡	sseA →	3‑mercaptopyruvate sulfurtransferase
RA	2,653,367	G→A	15.6%	intergenic (+28/‑488)	sseA → / → ryfA	3‑mercaptopyruvate sulfurtransferase/novel sRNA, function unknown
RA	2,653,372	T→C	16.0%	intergenic (+33/‑483)	sseA → / → ryfA	3‑mercaptopyruvate sulfurtransferase/novel sRNA, function unknown
RA	2,673,790	G→T	5.3%	intergenic (+22/+26)	yphA → / ← yphB	DoxX family inner membrane protein/mutarotase superfamily protein, YphB family
RA	2,673,791	A→C	5.0%	intergenic (+23/+25)	yphA → / ← yphB	DoxX family inner membrane protein/mutarotase superfamily protein, YphB family
RA	2,691,169	A→T	8.5%	noncoding (172/184 nt)	glmY ←	sRNA activator of glmS mRNA, glmZ processing antagonist
RA	2,691,171	T→A	8.4%	noncoding (170/184 nt)	glmY ←	sRNA activator of glmS mRNA, glmZ processing antagonist
RA	2,691,173	A→T	8.5%	noncoding (168/184 nt)	glmY ←	sRNA activator of glmS mRNA, glmZ processing antagonist
RA	2,707,320	A→T	5.5%	intergenic (‑196/+2)	lepA ← / ← rseC	back‑translocating elongation factor EF4, GTPase/SoxR iron‑sulfur cluster reduction factor component
RA	2,707,321	A→T	5.5%	intergenic (‑197/+1)	lepA ← / ← rseC	back‑translocating elongation factor EF4, GTPase/SoxR iron‑sulfur cluster reduction factor component
RA	2,716,030	T→G	9.0%	intergenic (+20/+36)	eamB → / ← grcA	cysteine and O‑acetylserine exporter/autonomous glycyl radical cofactor
RA	2,716,033	C→A	10.2%	intergenic (+23/+33)	eamB → / ← grcA	cysteine and O‑acetylserine exporter/autonomous glycyl radical cofactor
RA	2,720,209	T→C	5.4%	L86P (CTG→CCG) ‡	pka →	protein lysine acetyltransferase
RA	2,720,210	G→A	5.2%	L86L (CTG→CTA) ‡	pka →	protein lysine acetyltransferase
RA	2,750,073	G→T	5.4%	intergenic (+13/+42)	yfjD → / ← grpE	UPF0053 family inner membrane protein/heat shock protein
RA	2,750,078	T→G	5.6%	intergenic (+18/+37)	yfjD → / ← grpE	UPF0053 family inner membrane protein/heat shock protein
RA	2,750,081	C→A	6.5%	intergenic (+21/+34)	yfjD → / ← grpE	UPF0053 family inner membrane protein/heat shock protein
RA	2,761,620	T→G	5.3%	K641Q (AAG→CAG)	yfjK ←	radiation resistance protein; DEAD/H helicase‑like protein; CP4‑57 putative defective prophage
RA	2,761,623	C→A	6.6%	V640L (GTA→TTA)	yfjK ←	radiation resistance protein; DEAD/H helicase‑like protein; CP4‑57 putative defective prophage
RA	2,800,515	C→A	12.1%	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	12.0%	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	11.8%	intergenic (+44/‑204)	ygaM → / → nrdH	putative membrane‑anchored DUF883 family ribosome‑binding protein/hydrogen donor for NrdEF electron transport system; glutaredoxin‑like protein
RA	2,801,056	A→T	7.2%	N31I (AAT→ATT)	nrdI →	NrdEF cluster assembly flavodoxin
RA	2,810,872	C→T	10.3%	H35Y (CAC→TAC) ‡	mprA →	transcriptional repressor of microcin B17 synthesis and multidrug efflux
RA	2,810,873	A→G	10.2%	H35R (CAC→CGC) ‡	mprA →	transcriptional repressor of microcin B17 synthesis and multidrug efflux
RA	2,814,174	T→A	7.9%	intergenic (+20/+44)	emrB → / ← luxS	multidrug efflux system protein/S‑ribosylhomocysteine lyase
RA	2,814,175	T→A	7.9%	intergenic (+21/+43)	emrB → / ← luxS	multidrug efflux system protein/S‑ribosylhomocysteine lyase
RA	2,838,231	A→T	11.1%	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	6.9%	D167H (GAT→CAT)	ygbI ←	DeoR family putative transcriptional regulator
RA	2,860,738	A→T	7.0%	I166N (ATT→AAT)	ygbI ←	DeoR family putative transcriptional regulator
RA	2,860,740	C→G	6.2%	M165I (ATG→ATC)	ygbI ←	DeoR family putative transcriptional regulator
RA	2,866,487	G→C	8.5%	intergenic (+22/+72)	ygbN → / ← rpoS	putative transporter/RNA polymerase, sigma S (sigma 38) factor
RA	2,866,488	G→C	8.6%	intergenic (+23/+71)	ygbN → / ← rpoS	putative transporter/RNA polymerase, sigma S (sigma 38) factor
RA	2,873,915	A→G	6.1%	H26H (CAT→CAC) ‡	cysC ←	adenosine 5'‑phosphosulfate kinase
RA	2,873,917	G→C	5.8%	H26D (CAT→GAT) ‡	cysC ←	adenosine 5'‑phosphosulfate kinase
RA	2,873,919	C→T	5.2%	G25D (GGT→GAT)	cysC ←	adenosine 5'‑phosphosulfate kinase
RA	2,900,322	C→T	6.6%	intergenic (‑49/‑270)	ygcW ← / → yqcE	putative SDR family oxidoreductase/putative MFS transporter, inner membrane protein
RA	2,900,324	G→T	6.5%	intergenic (‑51/‑268)	ygcW ← / → yqcE	putative SDR family oxidoreductase/putative MFS transporter, inner membrane protein
RA	2,900,327	A→C	6.7%	intergenic (‑54/‑265)	ygcW ← / → yqcE	putative SDR family oxidoreductase/putative MFS transporter, inner membrane protein
RA	2,951,471	G→A	5.4%	R331C (CGC→TGC)	recD ←	exonuclease V (RecBCD complex), alpha chain
RA	2,971,146	T→C	8.5%	intergenic (+13/‑125)	ygdQ → / → ygdR	UPF0053 family inner membrane protein/DUF903 family verified lipoprotein
RA	2,971,151	T→C	7.7%	intergenic (+18/‑120)	ygdQ → / → ygdR	UPF0053 family inner membrane protein/DUF903 family verified lipoprotein
RA	2,971,154	G→A	7.9%	intergenic (+21/‑117)	ygdQ → / → ygdR	UPF0053 family inner membrane protein/DUF903 family verified lipoprotein
RA	2,980,742	A→G	6.2%	intergenic (‑107/+22)	ygeA ← / ← araE	Asp/Glu_racemase family protein/arabinose transporter
RA	2,980,744	A→T	6.2%	intergenic (‑109/+20)	ygeA ← / ← araE	Asp/Glu_racemase family protein/arabinose transporter
RA	2,980,746	C→T	6.3%	intergenic (‑111/+18)	ygeA ← / ← araE	Asp/Glu_racemase family protein/arabinose transporter
RA	2,997,649	T→A	5.8%	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	5.8%	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	9.8%	intergenic (+14/‑44)	ygeW → / → ygeX	putative carbamoyltransferase/2,3‑diaminopropionate ammonia lyase, PLP‑dependent
RA	3,007,473	G→A	6.7%	intergenic (+21/‑37)	ygeW → / → ygeX	putative carbamoyltransferase/2,3‑diaminopropionate ammonia lyase, PLP‑dependent
RA	3,024,038	G→C	5.1%	G908A (GGC→GCC)	xdhD →	putative hypoxanthine oxidase, molybdopterin‑binding/Fe‑S binding
RA	3,031,221	T→A	9.8%	intergenic (‑290/‑146)	ygfT ← / → uacT	putative oxidoreductase, Fe‑S subunit/nucleotide‑binding subunit/uric acid permease
RA	3,045,124	T→C	7.9%	intergenic (+23/+34)	bglA → / ← ygfF	6‑phospho‑beta‑glucosidase A/putative NAD(P)‑dependent oxidoreductase
RA	3,045,126	C→A	7.0%	intergenic (+25/+32)	bglA → / ← ygfF	6‑phospho‑beta‑glucosidase A/putative NAD(P)‑dependent oxidoreductase
RA	3,045,127	T→G	7.5%	intergenic (+26/+31)	bglA → / ← ygfF	6‑phospho‑beta‑glucosidase A/putative NAD(P)‑dependent oxidoreductase
RA	3,045,129	G→A	8.1%	intergenic (+28/+29)	bglA → / ← ygfF	6‑phospho‑beta‑glucosidase A/putative NAD(P)‑dependent oxidoreductase
RA	3,057,140	A→G	5.6%	intergenic (+152/+38)	sibC → / ← serA	sRNA antisense regulator of toxic IbsC protein/D‑3‑phosphoglycerate dehydrogenase
RA	3,057,145	G→C	6.0%	intergenic (+157/+33)	sibC → / ← serA	sRNA antisense regulator of toxic IbsC protein/D‑3‑phosphoglycerate dehydrogenase
RA	3,057,150	C→T	6.1%	intergenic (+162/+28)	sibC → / ← serA	sRNA antisense regulator of toxic IbsC protein/D‑3‑phosphoglycerate dehydrogenase
RA	3,061,817	G→C	8.7%	W323S (TGG→TCG) ‡	scpA →	methylmalonyl‑CoA mutase
RA	3,061,818	G→C	8.8%	W323C (TGG→TGC) ‡	scpA →	methylmalonyl‑CoA mutase
RA	3,082,709	C→A	5.1%	intergenic (+38/+168)	loiP → / ← speB	Phe‑Phe periplasmic metalloprotease, OM lipoprotein; low salt‑inducible; Era‑binding heat shock protein/agmatinase
RA	3,131,524	A→G	10.3%	S295S (AGT→AGC) ‡	yghQ ←	putative inner membrane polysaccharide flippase
RA	3,131,525	C→T	10.3%	S295N (AGT→AAT) ‡	yghQ ←	putative inner membrane polysaccharide flippase
RA	3,139,682	T→G	5.2%	intergenic (+89/+34)	yghU → / ← hybG	putative S‑transferase/hydrogenase 2 accessory protein
RA	3,139,685	C→A	5.1%	intergenic (+92/+31)	yghU → / ← hybG	putative S‑transferase/hydrogenase 2 accessory protein
RA	3,156,590	C→A	5.8%	intergenic (+72/‑33)	yqhD → / → dkgA	aldehyde reductase, NADPH‑dependent/2,5‑diketo‑D‑gluconate reductase A
RA	3,156,591	T→G	6.0%	intergenic (+73/‑32)	yqhD → / → dkgA	aldehyde reductase, NADPH‑dependent/2,5‑diketo‑D‑gluconate reductase A
RA	3,171,852	C→T	11.9%	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	12.1%	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	12.3%	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	12.9%	intergenic (+30/+16)	qseC → / ← ygiZ	quorum sensing sensory histidine kinase in two‑component regulatory system with QseB/inner membrane protein
RA	3,180,497	Δ1 bp	6.9%	coding (77/1161 nt)	ygiC →	ATP‑Grasp family ATPase
RA	3,180,505	G→T	9.0%	E29* (GAG→TAG) ‡	ygiC →	ATP‑Grasp family ATPase
RA	3,180,506	A→C	8.5%	E29A (GAG→GCG) ‡	ygiC →	ATP‑Grasp family ATPase
RA	3,186,137	A→T	9.5%	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	9.5%	intergenic (+48/‑49)	yqiG → / → insC1	pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein/IS2 repressor TnpA
RA	3,202,003	G→C	6.3%	G38A (GGC→GCC)	cca →	fused tRNA nucleotidyl transferase/2'3'‑cyclic phosphodiesterase/2'nucleotidase and phosphatase
RA	3,202,009	A→T	6.0%	Q40L (CAG→CTG)	cca →	fused tRNA nucleotidyl transferase/2'3'‑cyclic phosphodiesterase/2'nucleotidase and phosphatase
RA	3,202,012	A→T	6.3%	Q41L (CAG→CTG)	cca →	fused tRNA nucleotidyl transferase/2'3'‑cyclic phosphodiesterase/2'nucleotidase and phosphatase
RA	3,202,678	C→G	5.0%	P263R (CCG→CGG)	cca →	fused tRNA nucleotidyl transferase/2'3'‑cyclic phosphodiesterase/2'nucleotidase and phosphatase
RA	3,202,685	A→G	7.8%	E265E (GAA→GAG)	cca →	fused tRNA nucleotidyl transferase/2'3'‑cyclic phosphodiesterase/2'nucleotidase and phosphatase
RA	3,202,686	C→T	8.0%	L266F (CTC→TTC)	cca →	fused tRNA nucleotidyl transferase/2'3'‑cyclic phosphodiesterase/2'nucleotidase and phosphatase
RA	3,231,473	T→G	5.8%	intergenic (+234/‑192)	ygjK → / → fadH	alpha‑glucosidase/2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked
RA	3,234,506	G→A	5.6%	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	5.0%	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	5.3%	intergenic (‑53/+231)	higB ← / ← rlmG	mRNA interferase toxin of the HigB‑HigA toxin‑antitoxin system/23S rRNA m(2)G1835 methyltransferase, SAM‑dependent
RA	3,239,609	T→G	8.5%	intergenic (+64/‑335)	alx → / → sstT	putative membrane‑bound redox modulator/sodium:serine/threonine symporter
RA	3,239,610	C→G	8.9%	intergenic (+65/‑334)	alx → / → sstT	putative membrane‑bound redox modulator/sodium:serine/threonine symporter
RA	3,239,611	C→A	9.0%	intergenic (+66/‑333)	alx → / → sstT	putative membrane‑bound redox modulator/sodium:serine/threonine symporter
RA	3,250,991	A→T	5.5%	intergenic (+37/‑33)	yqjF → / → yqjG	putative quinol oxidase subunit/putative S‑transferase
RA	3,276,886	C→A	6.8%	intergenic (+33/‑116)	garD → / → prlF	D‑galactarate dehydrogenase/antitoxin of the SohA(PrlF)‑YhaV toxin‑antitoxin system
RA	3,276,887	T→C	6.5%	intergenic (+34/‑115)	garD → / → prlF	D‑galactarate dehydrogenase/antitoxin of the SohA(PrlF)‑YhaV toxin‑antitoxin system
RA	3,276,890	G→A	6.3%	intergenic (+37/‑112)	garD → / → prlF	D‑galactarate dehydrogenase/antitoxin of the SohA(PrlF)‑YhaV toxin‑antitoxin system
RA	3,276,891	T→G	6.8%	intergenic (+38/‑111)	garD → / → prlF	D‑galactarate dehydrogenase/antitoxin of the SohA(PrlF)‑YhaV toxin‑antitoxin system
RA	3,288,032	C→A	14.3%	intergenic (+22/‑58)	yraH → / → yraI	putative fimbrial‑like adhesin protein/putative periplasmic pilin chaperone
RA	3,288,033	T→G	14.6%	intergenic (+23/‑57)	yraH → / → yraI	putative fimbrial‑like adhesin protein/putative periplasmic pilin chaperone
RA	3,291,109	A→T	5.4%	K766* (AAA→TAA) ‡	yraJ →	putative outer membrane protein
RA	3,291,110	A→T	5.7%	K766I (AAA→ATA) ‡	yraJ →	putative outer membrane protein
RA	3,309,012	A→G	6.6%	intergenic (‑88/+21)	nlpI ← / ← pnp	lipoprotein involved in osmotic sensitivity and filamentation/polynucleotide phosphorylase/polyadenylase
RA	3,322,698	A→G	5.5%	intergenic (‑193/+35)	secG ← / ← glmM	preprotein translocase membrane subunit/phosphoglucosamine mutase
RA	3,322,700	A→G	5.2%	intergenic (‑195/+33)	secG ← / ← glmM	preprotein translocase membrane subunit/phosphoglucosamine mutase
RA	3,330,415	Δ1 bp	14.3%	intergenic (+19/+167)	dacB → / ← obgE	D‑alanyl‑D‑alanine carboxypeptidase/GTPase involved in cell partioning and DNA repair
RA	3,330,419:1	+T	14.3%	intergenic (+23/+163)	dacB → / ← obgE	D‑alanyl‑D‑alanine carboxypeptidase/GTPase involved in cell partioning and DNA repair
RA	3,354,537	C→G	15.2%	intergenic (‑487/‑188)	yhcC ← / → gltB	putative Fe‑S oxidoreductase, Radical SAM superfamily protein/glutamate synthase, large subunit
RA	3,360,643	T→A	8.9%	intergenic (+27/‑533)	gltD → / → gltF	glutamate synthase, 4Fe‑4S protein, small subunit/periplasmic protein
RA	3,360,644	G→C	8.9%	intergenic (+28/‑532)	gltD → / → gltF	glutamate synthase, 4Fe‑4S protein, small subunit/periplasmic protein
RA	3,360,645	T→A	8.9%	intergenic (+29/‑531)	gltD → / → gltF	glutamate synthase, 4Fe‑4S protein, small subunit/periplasmic protein
RA	3,368,134	A→G	5.7%	H103R (CAC→CGC)	yhcG →	DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily
RA	3,368,142	A→T	5.6%	M106L (ATG→TTG)	yhcG →	DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily
RA	3,380,434	A→G	5.2%	S82G (AGC→GGC)	yhcB →	DUF1043 family inner membrane‑anchored protein
RA	3,418,845	A→C	5.1%	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	5.1%	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	5.5%	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	8.3%	intergenic (+189/+40)	yhdZ → / ← rrfF	putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon
RA	3,423,620	A→G	6.2%	noncoding (36/76 nt)	thrV ←	tRNA‑Thr
RA	3,423,621	C→G	6.2%	noncoding (35/76 nt)	thrV ←	tRNA‑Thr
RA	3,423,622	C→T	6.6%	noncoding (34/76 nt)	thrV ←	tRNA‑Thr
RA	3,439,588	G→C	6.2%	intergenic (‑79/+28)	yhdN ← / ← rplQ	DUF1992 family protein/50S ribosomal subunit protein L17
RA	3,439,589	G→C	6.1%	intergenic (‑80/+27)	yhdN ← / ← rplQ	DUF1992 family protein/50S ribosomal subunit protein L17
RA	3,458,416	T→A	6.2%	I26I (ATT→ATA)	gspE →	general secretory pathway component, cryptic
RA	3,458,418	T→A	6.3%	I27N (ATT→AAT)	gspE →	general secretory pathway component, cryptic
RA	3,458,420	T→A	6.3%	Y28N (TAT→AAT)	gspE →	general secretory pathway component, cryptic
RA	3,471,357	C→T	5.5%	intergenic (‑28/+43)	tufA ← / ← fusA	translation elongation factor EF‑Tu 1/protein chain elongation factor EF‑G, GTP‑binding
RA	3,471,361	T→G	5.3%	intergenic (‑32/+39)	tufA ← / ← fusA	translation elongation factor EF‑Tu 1/protein chain elongation factor EF‑G, GTP‑binding
RA	3,471,362	C→A	5.5%	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	7.7%	intergenic (+20/+29)	slyX → / ← slyD	phi X174 lysis protein/FKBP‑type peptidyl prolyl cis‑trans isomerase (rotamase)
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	5.5%	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	5.4%	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	6.6%	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	7.6%	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	6.9%	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	5.7%	intergenic (+172/+97)	glpD → / ← yzgL	sn‑glycerol‑3‑phosphate dehydrogenase, aerobic, FAD/NAD(P)‑binding/pseudogene, periplasmic solute binding protein homology
RA	3,577,657	A→G	9.6%	intergenic (‑65/+74)	gntK ← / ← gntR	gluconate kinase 2/d‑gluconate inducible gluconate regulon transcriptional repressor
RA	3,577,660	C→T	9.1%	intergenic (‑68/+71)	gntK ← / ← gntR	gluconate kinase 2/d‑gluconate inducible gluconate regulon transcriptional repressor
RA	3,620,644	T→A	15.7%	L485M (TTG→ATG) ‡	rhsB →	Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
RA	3,620,646	G→A	16.0%	L485L (TTG→TTA) ‡	rhsB →	Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
RA	3,620,666	T→G	15.9%	L492W (TTG→TGG)	rhsB →	Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
RA	3,630,661	A→T	9.1%	intergenic (‑59/+307)	yhiI ← / ← yhiJ	putative membrane fusion protein (MFP) of efflux pump/DUF4049 family protein
RA	3,630,667	A→G	10.4%	intergenic (‑65/+301)	yhiI ← / ← yhiJ	putative membrane fusion protein (MFP) of efflux pump/DUF4049 family protein
RA	3,657,599	T→A	14.8%	intergenic (+32/+387)	hdeD → / ← arrS	acid‑resistance membrane protein/antisense sRNA ArrS, function unknown
RA	3,657,601	G→C	14.6%	intergenic (+34/+385)	hdeD → / ← arrS	acid‑resistance membrane protein/antisense sRNA ArrS, function unknown
RA	3,657,603	T→A	18.3%	intergenic (+36/+383)	hdeD → / ← arrS	acid‑resistance membrane protein/antisense sRNA ArrS, function unknown
RA	3,774,207	C→T	5.1%	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	5.4%	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	5.5%	intergenic (+21/‑209)	mtlA → / → mtlD	mannitol‑specific PTS enzyme: IIA, IIB and IIC components/mannitol‑1‑phosphate dehydrogenase, NAD‑dependent
RA	3,778,876	G→A	5.3%	G493D (GGC→GAC)	lldP →	L‑lactate permease
RA	3,778,879	T→C	5.5%	V494A (GTC→GCC)	lldP →	L‑lactate permease
RA	3,781,051	C→G	12.8%	intergenic (+34/‑164)	lldD → / → trmL	L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent
RA	3,790,300	A→T	5.9%	intergenic (‑219/+20)	waaH ← / ← tdh	LPS(HepIII)‑glucuronic acid glycosyltransferase/L‑threonine 3‑dehydrogenase, NAD(P)‑binding
RA	3,790,303	A→T	6.1%	intergenic (‑222/+17)	waaH ← / ← tdh	LPS(HepIII)‑glucuronic acid glycosyltransferase/L‑threonine 3‑dehydrogenase, NAD(P)‑binding
RA	3,798,234	A→T	20.5%	intergenic (+27/+5)	waaL → / ← waaU	O‑antigen ligase/lipopolysaccharide core biosynthesis
RA	3,798,235	A→T	20.9%	intergenic (+28/+4)	waaL → / ← waaU	O‑antigen ligase/lipopolysaccharide core biosynthesis
RA	3,817,948	G→T	5.4%	E63D (GAG→GAT)	dinD →	DNA damage‑inducible protein
RA	3,817,949	A→C	5.5%	I64L (ATC→CTC)	dinD →	DNA damage‑inducible protein
RA	3,832,188	A→T	6.8%	intergenic (+22/+31)	yicH → / ← yicI	putative inner membrane‑anchored periplasmic AsmA family protein/putative alpha‑glucosidase
RA	3,832,191	C→G	6.0%	intergenic (+25/+28)	yicH → / ← yicI	putative inner membrane‑anchored periplasmic AsmA family protein/putative alpha‑glucosidase
RA	3,832,194	A→T	5.6%	intergenic (+28/+25)	yicH → / ← yicI	putative inner membrane‑anchored periplasmic AsmA family protein/putative alpha‑glucosidase
RA	3,844,348	G→T	5.0%	A129S (GCC→TCC)	adeD →	cryptic adenine deaminase
RA	3,844,353	A→C	5.8%	G130G (GGA→GGC)	adeD →	cryptic adenine deaminase
RA	3,853,603	A→G	6.2%	A17A (GCA→GCG)	tisB →	toxic membrane persister formation peptide, LexA‑regulated
RA	3,900,542	A→T	6.7%	I12I (ATT→ATA)	yieL ←	putative xylanase
RA	3,900,545	A→T	7.1%	A11A (GCT→GCA)	yieL ←	putative xylanase
RA	3,920,796	T→C	9.0%	A31A (GCA→GCG)	atpF ←	F0 sector of membrane‑bound ATP synthase, subunit b
RA	3,920,809	G→A	5.4%	P27L (CCG→CTG)	atpF ←	F0 sector of membrane‑bound ATP synthase, subunit b
RA	3,959,515	T→A	5.1%	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	6.7%	intergenic (‑111/+88)	ppiC ← / ← yifN	peptidyl‑prolyl cis‑trans isomerase C (rotamase C)/PemK toxin family pseudogene
RA	3,959,925	A→T	6.7%	intergenic (‑112/+87)	ppiC ← / ← yifN	peptidyl‑prolyl cis‑trans isomerase C (rotamase C)/PemK toxin family pseudogene
RA	3,959,926	A→T	6.7%	intergenic (‑113/+86)	ppiC ← / ← yifN	peptidyl‑prolyl cis‑trans isomerase C (rotamase C)/PemK toxin family pseudogene
RA	3,963,415	A→C	7.7%	L272R (CTG→CGG) ‡	gpp ←	guanosine pentaphosphatase/exopolyphosphatase
RA	3,963,416	G→T	7.7%	L272M (CTG→ATG) ‡	gpp ←	guanosine pentaphosphatase/exopolyphosphatase
RA	3,970,813	Δ1 bp	5.2%	coding (681/1131 nt)	wecB →	UDP‑N‑acetyl glucosamine‑2‑epimerase
RA	3,970,817:1	+G	5.1%	coding (685/1131 nt)	wecB →	UDP‑N‑acetyl glucosamine‑2‑epimerase
RA	3,980,726	G→A	15.4%	intergenic (+30/‑161)	wecG → / → yifK	UDP‑N‑acetyl‑D‑mannosaminuronic acid transferase/putative APC family amino acid transporter
RA	3,980,727	T→C	14.1%	intergenic (+31/‑160)	wecG → / → yifK	UDP‑N‑acetyl‑D‑mannosaminuronic acid transferase/putative APC family amino acid transporter
RA	3,981,102	T→A	6.7%	V72V (GTT→GTA)	yifK →	putative APC family amino acid transporter
RA	3,991,334	T→A	11.2%	I61N (ATT→AAT) ‡	cyaA →	adenylate cyclase
RA	3,991,335	T→A	11.1%	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	8.9%	W31R (TGG→CGG)	yigF ←	DUF2628 family putative inner membrane protein
RA	4,049,986	G→T	6.1%	noncoding (88/109 nt)	spf →	Spot 42 sRNA antisense regulator of galK translation, Hfq‑dependent
RA	4,070,410	C→A	9.1%	intergenic (‑9/+105)	yihR ← / ← yihS	putative sulphoquinovose mutarotase/sulphoquinovose isomerase
RA	4,070,413	T→G	8.7%	intergenic (‑12/+102)	yihR ← / ← yihS	putative sulphoquinovose mutarotase/sulphoquinovose isomerase
RA	4,080,616	C→A	5.6%	G205C (GGC→TGC)	fdhE ←	formate dehydrogenase formation protein
RA	4,080,621	T→G	5.9%	Q203P (CAA→CCA)	fdhE ←	formate dehydrogenase formation protein
RA	4,117,005	T→A	100%	D73V (GAT→GTT)	glpK ←	glycerol kinase
RA	4,121,959	T→G	7.5%	N110T (AAC→ACC)	hslV ←	peptidase component of the HslUV protease
RA	4,121,962	C→A	6.6%	G109V (GGT→GTT)	hslV ←	peptidase component of the HslUV protease
RA	4,185,907	G→T	5.9%	Q186H (CAG→CAT)	rpoC →	RNA polymerase, beta prime subunit
RA	4,213,156	G→A	5.1%	noncoding (117/120 nt)	rrfE →	5S ribosomal RNA of rrnE operon
RA	4,223,854	T→C	5.4%	R9R (CGT→CGC)	metH →	homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent
RA	4,223,855	G→A	5.4%	A10T (GCG→ACG)	metH →	homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent
RA	4,227,550	G→A	12.9%	intergenic (+39/‑181)	metH → / → yjbB	homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent/putative Na+/Pi‑cotransporter
RA	4,227,555	A→T	12.2%	intergenic (+44/‑176)	metH → / → yjbB	homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent/putative Na+/Pi‑cotransporter
RA	4,227,560	T→C	12.5%	intergenic (+49/‑171)	metH → / → yjbB	homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent/putative Na+/Pi‑cotransporter
RA	4,235,469	G→A	6.3%	intergenic (+62/‑437)	pgi → / → yjbE	glucosephosphate isomerase/extracellular polysaccharide production threonine‑rich protein
RA	4,235,470	C→A	6.5%	intergenic (+63/‑436)	pgi → / → yjbE	glucosephosphate isomerase/extracellular polysaccharide production threonine‑rich protein
RA	4,235,477	G→A	11.3%	intergenic (+70/‑429)	pgi → / → yjbE	glucosephosphate isomerase/extracellular polysaccharide production threonine‑rich protein
RA	4,235,478	T→C	11.8%	intergenic (+71/‑428)	pgi → / → yjbE	glucosephosphate isomerase/extracellular polysaccharide production threonine‑rich protein
RA	4,235,485	T→G	11.7%	intergenic (+78/‑421)	pgi → / → yjbE	glucosephosphate isomerase/extracellular polysaccharide production threonine‑rich protein
RA	4,235,486	T→C	10.8%	intergenic (+79/‑420)	pgi → / → yjbE	glucosephosphate isomerase/extracellular polysaccharide production threonine‑rich protein
RA	4,261,358	T→A	16.0%	intergenic (+52/‑311)	yjbM → / → dusA	uncharacterized protein/tRNA‑dihydrouridine synthase A
RA	4,261,359	T→A	15.4%	intergenic (+53/‑310)	yjbM → / → dusA	uncharacterized protein/tRNA‑dihydrouridine synthase A
RA	4,262,250	G→C	10.2%	G194G (GGG→GGC)	dusA →	tRNA‑dihydrouridine synthase A
RA	4,262,255	G→C	10.1%	S196T (AGC→ACC)	dusA →	tRNA‑dihydrouridine synthase A
RA	4,296,060	C→T	18.8%	intergenic (+266/+376)	gltP → / ← yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA	4,296,268	T→C	23.2%	intergenic (+474/+168)	gltP → / ← yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA	4,296,380:1	+CG	100%	intergenic (+586/+56)	gltP → / ← yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA	4,307,294	A→T	15.6%	L169Q (CTG→CAG)	alsK ←	D‑allose kinase
RA	4,307,298	G→A	17.2%	P168S (CCC→TCC)	alsK ←	D‑allose kinase
RA	4,314,233	A→T	6.1%	intergenic (+36/+111)	yjdP → / ← phnP	putative periplasmic protein/5‑phospho‑alpha‑D‑ribosyl 1,2‑cyclic phosphate phosphodiesterase
RA	4,323,312	G→C	7.0%	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	6.9%	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	6.0%	intergenic (‑64/+40)	eptA ← / ← adiC	lipid A phosphoethanolamine transferase/arginine:agmatine antiporter
RA	4,335,655	T→A	6.0%	intergenic (‑65/+39)	eptA ← / ← adiC	lipid A phosphoethanolamine transferase/arginine:agmatine antiporter
RA	4,336,974	A→T	8.3%	S20T (TCG→ACG)	adiC ←	arginine:agmatine antiporter
RA	4,336,979	A→C	8.0%	M18R (ATG→AGG)	adiC ←	arginine:agmatine antiporter
RA	4,336,981	C→G	7.3%	L17L (CTG→CTC) ‡	adiC ←	arginine:agmatine antiporter
RA	4,336,983	G→T	7.4%	L17M (CTG→ATG) ‡	adiC ←	arginine:agmatine antiporter
RA	4,336,988	A→T	7.5%	V15D (GTC→GAC)	adiC ←	arginine:agmatine antiporter
RA	4,339,802	A→G	5.1%	A240A (GCT→GCC)	adiA ←	arginine decarboxylase
RA	4,339,805	C→T	5.1%	Q239Q (CAG→CAA)	adiA ←	arginine decarboxylase
RA	4,356,445	A→T	5.1%	intergenic (‑34/+25)	dtpC ← / ← cadA	dipeptide and tripeptide permease/lysine decarboxylase, acid‑inducible
RA	4,356,446	A→T	5.1%	intergenic (‑35/+24)	dtpC ← / ← cadA	dipeptide and tripeptide permease/lysine decarboxylase, acid‑inducible
RA	4,376,280	G→A	5.5%	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	8.1%	intergenic (+26/‑26)	efp → / → ecnA	polyproline‑specific translation elongation factor EF‑P/entericidin A membrane lipoprotein, antidote entericidin B
RA	4,388,496	T→A	7.8%	Q292L (CAG→CTG)	mscM ←	mechanosensitive channel protein, miniconductance
RA	4,388,502	G→C	7.5%	A290G (GCC→GGC)	mscM ←	mechanosensitive channel protein, miniconductance
RA	4,388,508	T→A	5.4%	Q288L (CAG→CTG)	mscM ←	mechanosensitive channel protein, miniconductance
RA	4,392,617	C→G	7.2%	noncoding (35/76 nt)	glyY →	tRNA‑Gly
RA	4,392,757	C→G	10.5%	intergenic (+99/‑135)	glyY → / → yjeV	tRNA‑Gly/uncharacterized protein
RA	4,395,454	T→C	7.0%	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	7.0%	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	5.2%	intergenic (+65/‑115)	rnr → / → rlmB	exoribonuclease R, RNase R/23S rRNA mG2251 2'‑O‑ribose methyltransferase, SAM‑dependent
RA	4,409,161	C→A	5.1%	intergenic (+66/‑114)	rnr → / → rlmB	exoribonuclease R, RNase R/23S rRNA mG2251 2'‑O‑ribose methyltransferase, SAM‑dependent
RA	4,409,167	G→T	5.1%	intergenic (+72/‑108)	rnr → / → rlmB	exoribonuclease R, RNase R/23S rRNA mG2251 2'‑O‑ribose methyltransferase, SAM‑dependent
RA	4,409,168	A→C	5.3%	intergenic (+73/‑107)	rnr → / → rlmB	exoribonuclease R, RNase R/23S rRNA mG2251 2'‑O‑ribose methyltransferase, SAM‑dependent
RA	4,447,844	T→C	7.2%	S1245P (TCT→CCT)	tamB →	translocation and assembly module for autotransporter export, inner membrane subunit
RA	4,447,850	G→C	7.0%	V1247L (GTA→CTA)	tamB →	translocation and assembly module for autotransporter export, inner membrane subunit
RA	4,447,853	G→C	6.5%	D1248H (GAC→CAC)	tamB →	translocation and assembly module for autotransporter export, inner membrane subunit
RA	4,470,951	A→C	8.6%	intergenic (‑38/+35)	ridA ← / ← pyrI	enamine/imine deaminase, reaction intermediate detoxification/aspartate carbamoyltransferase, regulatory subunit
RA	4,470,952	T→C	8.3%	intergenic (‑39/+34)	ridA ← / ← pyrI	enamine/imine deaminase, reaction intermediate detoxification/aspartate carbamoyltransferase, regulatory subunit
RA	4,470,957	G→A	7.2%	intergenic (‑44/+29)	ridA ← / ← pyrI	enamine/imine deaminase, reaction intermediate detoxification/aspartate carbamoyltransferase, regulatory subunit
RA	4,470,958	G→T	6.5%	intergenic (‑45/+28)	ridA ← / ← pyrI	enamine/imine deaminase, reaction intermediate detoxification/aspartate carbamoyltransferase, regulatory subunit
RA	4,479,012	A→T	8.9%	intergenic (+123/+22)	rraB → / ← yjgM	protein inhibitor of RNase E/GNAT family putative N‑acetyltransferase
RA	4,479,016	G→C	9.2%	intergenic (+127/+18)	rraB → / ← yjgM	protein inhibitor of RNase E/GNAT family putative N‑acetyltransferase
RA	4,479,020	A→T	9.7%	intergenic (+131/+14)	rraB → / ← yjgM	protein inhibitor of RNase E/GNAT family putative N‑acetyltransferase
RA	4,496,511	A→G	5.7%	intergenic (+22/‑164)	leuX → / → intB	tRNA‑Leu/pseudogene, integrase homology;IS, phage, Tn; Phage‑related functions and prophages; KpLE2 phage‑like element; P4‑like integrase
RA	4,496,512	C→T	5.9%	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	5.1%	coding (65/957 nt)	fecD ←	ferric citrate ABC transporter permease
RA	4,520,500	Δ1 bp	14.3%	intergenic (‑176/+171)	yjhU ← / ← yjhF	putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter
RA	4,520,504:1	+T	10.6%	intergenic (‑180/+167)	yjhU ← / ← yjhF	putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter
RA	4,548,914	G→C	7.6%	G36A (GGT→GCT)	fimH →	minor component of type 1 fimbriae
RA	4,548,917	G→C	7.6%	G37A (GGC→GCC)	fimH →	minor component of type 1 fimbriae
RA	4,548,920	G→C	6.8%	S38T (AGC→ACC)	fimH →	minor component of type 1 fimbriae
RA	4,606,417	A→T	5.0%	intergenic (‑16/+252)	leuQ ← / ← rsmC	tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase, SAM‑dependent
RA	4,606,419	A→T	5.0%	intergenic (‑18/+250)	leuQ ← / ← rsmC	tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase, SAM‑dependent
RA	4,612,329	A→G	7.0%	intergenic (+40/‑82)	ytjA → / → yjjU	uncharacterized protein/putative patatin‑like family phospholipase
RA	4,612,330	G→C	7.8%	intergenic (+41/‑81)	ytjA → / → yjjU	uncharacterized protein/putative patatin‑like family phospholipase
RA	4,612,331	C→T	7.1%	intergenic (+42/‑80)	ytjA → / → yjjU	uncharacterized protein/putative patatin‑like family phospholipase
RA	4,621,622	G→A	5.2%	intergenic (+20/‑147)	deoD → / → yjjJ	purine nucleoside phosphorylase 1; nicotinamide 1‑beta‑D‑riboside phosphorylase/putative protein kinase
RA	4,621,625	T→C	5.5%	intergenic (+23/‑144)	deoD → / → yjjJ	purine nucleoside phosphorylase 1; nicotinamide 1‑beta‑D‑riboside phosphorylase/putative protein kinase
RA	4,638,690	C→T	7.0%	G171G (GGC→GGT)	creD →	inner membrane protein
RA	4,638,691	A→G	7.0%	T172A (ACC→GCC)	creD →	inner membrane protein

Unassigned missing coverage evidence
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	583427	583846	420	48 [46]	[46] 50	[appY]	[appY]
*	*	÷	NC_000913	1197509	1197852	344	48 [46]	[43] 49	[ymfD]–[ymfE]	[ymfD],[ymfE]
*	*	÷	NC_000913	1640958	1641071	114	49 [45]	[41] 47	essQ/cspB	Qin prophage; putative S lysis protein/Qin prophage; cold shock protein
*	*	÷	NC_000913	2056625	2056800	176	47 [45]	[43] 47	amn/yeeN	AMP nucleosidase/UPF0082 family protein
*	*	÷	NC_000913	2470090	2470512	423	47 [45]	[46] 48	[gtrS]	[gtrS]
*	*	÷	NC_000913	3423768–3424533	3424533	1–766	47 [46]	[45] 47	[rrfD]–[rrlD]	[rrfD],[rrlD]
*	*	÷	NC_000913	4235530	4235800	271	53 [44]	[45] 49	pgi/yjbE	glucosephosphate isomerase/extracellular polysaccharide production threonine‑rich protein

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	74873 =	113 (0.720)	7 (0.050)	5/258	NT	6.0%	coding (608/984 nt)	thiB	thiamine/thiamine pyrophosphate/thiamine monophosphate ABC transporter periplasmic binding protein
	?	NC_000913	74897 =	111 (0.720)					coding (584/984 nt)	thiB	thiamine/thiamine pyrophosphate/thiamine monophosphate ABC transporter periplasmic binding protein
*	?	NC_000913	= 93541	135 (0.850)	13 (0.080)	11/260	NT	8.8%	coding (376/1488 nt)	murE	UDP‑N‑acetylmuramoyl‑L‑alanyl‑D‑glutamate:meso‑ diaminopimelate ligase
	?	NC_000913	= 93563	137 (0.890)					coding (398/1488 nt)	murE	UDP‑N‑acetylmuramoyl‑L‑alanyl‑D‑glutamate:meso‑ diaminopimelate ligase
*	?	NC_000913	111593 =	87 (0.550)	8 (0.050)	8/252	NT	8.7%	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 =	86 (0.570)					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	= 183661	103 (0.650)	13 (0.090)	10/246	NT	11.3%	intergenic (+41/+48)	cdaR/yaeH	carbohydrate diacid regulon transcriptional regulator; autoregulator/UPF0325 family protein
	?	NC_000913	= 183674	109 (0.750)					intergenic (+54/+35)	cdaR/yaeH	carbohydrate diacid regulon transcriptional regulator; autoregulator/UPF0325 family protein
*	?	NC_000913	= 224065	NA (NA)	23 (0.150)	11/252	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 (0.050)	7/252	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	131 (0.830)	8 (0.050)	7/260	NT	5.9%	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 (0.040)	4/256	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 (0.170)	16/258	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	231071 =	136 (0.860)	17 (0.110)	13/254	NT	12.0%	intergenic (‑190/‑51)	yafC/yafD	LysR family putative transcriptional regulator/endo/exonuclease/phosphatase family protein
	?	NC_000913	231095 =	119 (0.790)					intergenic (‑214/‑27)	yafC/yafD	LysR family putative transcriptional regulator/endo/exonuclease/phosphatase family protein
*	?	NC_000913	274620 =	NA (NA)	11 (0.070)	11/248	NT	NA	noncoding (530/1195 nt)	IS5	repeat region
	?	NC_000913	274663 =	NA (NA)					noncoding (487/1195 nt)	IS5	repeat region
*	?	NC_000913	284258 =	115 (0.730)	6 (0.040)	6/254	NT	5.4%	coding (1058/1968 nt)	yagF	CP4‑6 prophage; dehydratase family protein
	?	NC_000913	284307 =	102 (0.680)					coding (1107/1968 nt)	yagF	CP4‑6 prophage; dehydratase family protein
*	?	NC_000913	= 284691	111 (0.700)	6 (0.040)	6/258	NT	5.2%	coding (1491/1968 nt)	yagF	CP4‑6 prophage; dehydratase family protein
	?	NC_000913	= 284723	109 (0.710)					coding (1523/1968 nt)	yagF	CP4‑6 prophage; dehydratase family protein
*	?	NC_000913	340035 =	114 (0.720)	8 (0.050)	6/250	NT	7.0%	noncoding (279/358 nt)	REP23 (repetitive extragenic palindromic) element; contains 8 REP sequences	REP23 (repetitive extragenic palindromic) element; contains 8 REP sequences
	?	NC_000913	2673807 =	NA (NA)					noncoding (32/34 nt)	REP185 (repetitive extragenic palindromic) element; contains 1 REP sequences	REP185 (repetitive extragenic palindromic) element; contains 1 REP sequences
*	?	NC_000913	= 341335	139 (0.880)	10 (0.070)	7/256	NT	7.0%	coding (211/1383 nt)	yahJ	putative metallo‑dependent hydrolase domain deaminase
	?	NC_000913	= 341358	132 (0.870)					coding (234/1383 nt)	yahJ	putative metallo‑dependent hydrolase domain deaminase
*	?	NC_000913	= 349852	75 (0.470)	10 (0.070)	6/252	NT	11.5%	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	83 (0.550)					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 (0.040)	5/252	NT	NA	noncoding (404/1331 nt)	IS2	repeat region
	?	NC_000913	381703 =	NA (NA)					noncoding (444/1331 nt)	IS2	repeat region
*	?	NC_000913	= 403626	69 (0.440)	5 (0.030)	5/248	NT	7.3%	intergenic (+25/‑77)	psiF/yaiC	PsiF family protein/diguanylate cyclase, cellulose regualtor
	?	NC_000913	= 403636	62 (0.420)					intergenic (+35/‑67)	psiF/yaiC	PsiF family protein/diguanylate cyclase, cellulose regualtor
*	?	NC_000913	= 427762	129 (0.820)	8 (0.050)	7/252	NT	6.3%	coding (116/1848 nt)	secD	SecYEG protein translocase auxillary subunit
	?	NC_000913	= 427779	116 (0.780)					coding (133/1848 nt)	secD	SecYEG protein translocase auxillary subunit
*	?	NC_000913	= 456464	131 (0.830)	10 (0.060)	9/260	NT	7.2%	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	128 (0.830)					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	27 (0.170)	4 (0.030)	4/250	NT	13.3%	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	27 (0.180)					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	644022 =	133 (0.840)	12 (0.080)	12/250	NT	8.7%	intergenic (‑55/+175)	rnk/rna	regulator of nucleoside diphosphate kinase/ribonuclease I
	?	NC_000913	644051 =	128 (0.860)					intergenic (‑84/+146)	rnk/rna	regulator of nucleoside diphosphate kinase/ribonuclease I
*	?	NC_000913	= 668251	150 (0.950)	8 (0.050)	7/248	NT	5.2%	coding (465/468 nt)	rlmH	23S rRNA m(3)Psi1915 pseudouridine methyltransferase, SAM‑dependent
	?	NC_000913	= 668256	150 (1.020)					coding (460/468 nt)	rlmH	23S rRNA m(3)Psi1915 pseudouridine methyltransferase, SAM‑dependent
*	?	NC_000913	745824 =	102 (0.650)	6 (0.040)	6/256	NT	5.7%	coding (660/735 nt)	ybgL	UPF0271 family protein
	?	NC_000913	745854 =	99 (0.650)					coding (690/735 nt)	ybgL	UPF0271 family protein
*	?	NC_000913	766061 =	139 (0.880)	16 (0.100)	7/260	NT	10.0%	coding (78/1977 nt)	mngA	fused 2‑O‑a‑mannosyl‑D‑glycerate specific PTS enzymes: IIA component/IIB component/IIC component
	?	NC_000913	766084 =	151 (0.980)					coding (101/1977 nt)	mngA	fused 2‑O‑a‑mannosyl‑D‑glycerate specific PTS enzymes: IIA component/IIB component/IIC component
*	?	NC_000913	= 820612	71 (0.450)	12 (0.080)	9/254	NT	14.6%	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	73 (0.480)					intergenic (+33/‑172)	ybhL/ybhM	putative acetate transporter; BAX Inhibitor‑1 family inner membrane protein/BAX Inhibitor‑1 family inner membrane protein
*	?	NC_000913	832289 =	NA (NA)	5 (0.030)	4/252	NT	NA	noncoding (1/98 nt)	RIP75 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site	RIP75 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site
	?	NC_000913	= 845704	NA (NA)					noncoding (74/99 nt)	RIP78 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site	RIP78 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site
*	?	NC_000913	884909 =	81 (0.510)	7 (0.050)	6/248	NT	8.3%	intergenic (+4/+37)	mdfA/ybjH	multidrug efflux system protein/uncharacterized protein
	?	NC_000913	884940 =	79 (0.540)					intergenic (+35/+6)	mdfA/ybjH	multidrug efflux system protein/uncharacterized protein
*	?	NC_000913	= 902202	103 (0.650)	6 (0.040)	5/256	NT	5.5%	coding (49/717 nt)	artQ	arginine ABC transporter permease
	?	NC_000913	= 902224	106 (0.700)					coding (27/717 nt)	artQ	arginine ABC transporter permease
*	?	NC_000913	= 931034	70 (0.440)	4 (0.030)	4/250	NT	5.6%	intergenic (‑72/+51)	cydD/trxB	glutathione/cysteine ABC transporter export permease/ATPase/thioredoxin reductase, FAD/NAD(P)‑binding
	?	NC_000913	= 931049	69 (0.460)					intergenic (‑87/+36)	cydD/trxB	glutathione/cysteine ABC transporter export permease/ATPase/thioredoxin reductase, FAD/NAD(P)‑binding
*	?	NC_000913	985196 =	162 (1.030)	10 (0.070)	10/250	NT	6.6%	coding (514/1191 nt)	aspC	aspartate aminotransferase, PLP‑dependent
	?	NC_000913	985219 =	129 (0.870)					coding (491/1191 nt)	aspC	aspartate aminotransferase, PLP‑dependent
*	?	NC_000913	1100121 =	196 (1.240)	18 (0.120)	16/258	NT	9.4%	coding (482/555 nt)	ycdY	redox enzyme maturation protein (REMP) chaperone for YcdX
	?	NC_000913	1100158 =	157 (1.020)					coding (519/555 nt)	ycdY	redox enzyme maturation protein (REMP) chaperone for YcdX
*	?	NC_000913	1207790 =	81 (0.510)	113 (0.810)	81/234	NT	63.6%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	58 (0.420)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1207805	84 (0.530)	85 (0.610)	66/234	NT	56.3%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	58 (0.420)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	1213722 =	140 (0.890)	8 (0.050)	7/252	NT	5.8%	coding (338/732 nt)	bluR	repressor of blue light‑responsive genes
	?	NC_000913	1213743 =	129 (0.860)					coding (317/732 nt)	bluR	repressor of blue light‑responsive genes
*	?	NC_000913	1269276 =	60 (0.380)	6 (0.040)	4/250	NT	8.0%	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 =	81 (0.550)					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	1 (0.010)	53 (0.350)	43/258	NT	99.1%	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	1405665 =	61 (0.390)	8 (0.050)	8/248	NT	13.9%	noncoding (87/96 nt)	mcaS	motility and biofilm regulator sRNA
	?	NC_000913	1405694 =	42 (0.290)					noncoding (58/96 nt)	mcaS	motility and biofilm regulator sRNA
*	?	NC_000913	1451561 =	123 (0.780)	6 (0.040)	6/248	NT	5.0%	intergenic (‑212/+36)	tynA/paaZ	tyramine oxidase, copper‑requiring/oxepin‑CoA hydrolase and 3‑oxo‑5,6‑dehydrosuberyl‑CoA semialdehyde dehydrogenase
	?	NC_000913	1451587 =	112 (0.760)					intergenic (‑238/+10)	tynA/paaZ	tyramine oxidase, copper‑requiring/oxepin‑CoA hydrolase and 3‑oxo‑5,6‑dehydrosuberyl‑CoA semialdehyde dehydrogenase
*	?	NC_000913	= 1463445	110 (0.700)	13 (0.090)	12/252	NT	10.7%	intergenic (+7/‑94)	paaK/paaX	phenylacetyl‑CoA ligase/transcriptional repressor of phenylacetic acid degradation paa operon, phenylacetyl‑CoA inducer
	?	NC_000913	= 1463482	113 (0.760)					intergenic (+44/‑57)	paaK/paaX	phenylacetyl‑CoA ligase/transcriptional repressor of phenylacetic acid degradation paa operon, phenylacetyl‑CoA inducer
*	?	NC_000913	1672789 =	63 (0.400)	6 (0.040)	5/246	NT	10.0%	intergenic (+8/+31)	ydgD/mdtI	putative peptidase/multidrug efflux system transporter
	?	NC_000913	1672815 =	50 (0.340)					intergenic (+34/+5)	ydgD/mdtI	putative peptidase/multidrug efflux system transporter
*	?	NC_000913	= 1682065	113 (0.720)	8 (0.050)	6/252	NT	6.8%	intergenic (‑35/‑94)	ydgC/rstA	GlpM family inner membrane protein/response regulator of RstAB two‑component system
	?	NC_000913	= 1682073	113 (0.760)					intergenic (‑43/‑86)	ydgC/rstA	GlpM family inner membrane protein/response regulator of RstAB two‑component system
*	?	NC_000913	1745893 =	144 (0.910)	8 (0.050)	8/248	NT	5.9%	coding (235/1257 nt)	ydhQ	autotransporter adhesin‑related protein
	?	NC_000913	1745928 =	123 (0.840)					coding (200/1257 nt)	ydhQ	autotransporter adhesin‑related protein
*	?	NC_000913	= 1886825	61 (0.390)	8 (0.060)	8/244	NT	13.0%	intergenic (+15/+39)	yeaX/rnd	putative YeaWX dioxygenase beta subunit, reductase component/ribonuclease D
	?	NC_000913	= 1886846	51 (0.350)					intergenic (+36/+18)	yeaX/rnd	putative YeaWX dioxygenase beta subunit, reductase component/ribonuclease D
*	?	NC_000913	= 2042125	100 (0.630)	12 (0.080)	8/246	NT	11.0%	intergenic (+100/‑243)	zinT/yodB	zinc and cadmium binding protein, periplasmic/cytochrome b561 homolog
	?	NC_000913	= 2042138	101 (0.690)					intergenic (+113/‑230)	zinT/yodB	zinc and cadmium binding protein, periplasmic/cytochrome b561 homolog
*	?	NC_000913	= 2197774	123 (0.780)	20 (0.140)	16/244	NT	14.1%	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	130 (0.900)					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 =	69 (0.440)	6 (0.040)	5/250	NT	7.6%	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 =	81 (0.550)					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	2304400 =	NA (NA)	6 (0.040) +AGCGGTGTAG	6/246	NT	NA	intergenic (+7/+708)	eco/mqo	ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
	?	NC_000913	= 2347327	NA (NA)					noncoding (168/203 nt)	REP164 (repetitive extragenic palindromic) element; contains 5 REP sequences	REP164 (repetitive extragenic palindromic) element; contains 5 REP sequences
*	?	NC_000913	2304722 =	23 (0.150)	12 (0.080)	7/252	NT	18.5%	noncoding (306/655 nt)	REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences	REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences
	?	NC_000913	3042447 =	84 (0.560)					noncoding (127/155 nt)	REP210 (repetitive extragenic palindromic) element; contains 3 REP sequences	REP210 (repetitive extragenic palindromic) element; contains 3 REP sequences
*	?	NC_000913	2327300 =	84 (0.530)	10 (0.070)	7/240	NT	12.3%	intergenic (+7/+67)	atoB/yfaP	acetyl‑CoA acetyltransferase/DUF2135 family protein, putative host defense protein
	?	NC_000913	2327334 =	67 (0.470)					intergenic (+41/+33)	atoB/yfaP	acetyl‑CoA acetyltransferase/DUF2135 family protein, putative host defense protein
*	?	NC_000913	2456281 =	72 (0.460)	7 (0.050)	8/236	NT	10.6%	intergenic (‑635/+46)	yfcV/sixA	putative fimbrial‑like adhesin protein/phosphohistidine phosphatase
	?	NC_000913	2456318 =	54 (0.390)					intergenic (‑672/+9)	yfcV/sixA	putative fimbrial‑like adhesin protein/phosphohistidine phosphatase
*	?	NC_000913	= 2533705	143 (0.910)	8 (0.050)	7/250	NT	5.5%	intergenic (+325/‑59)	cysK/ptsH	cysteine synthase A, O‑acetylserine sulfhydrolase A subunit/phosphohistidinoprotein‑hexose phosphotransferase component of PTS system (Hpr)
	?	NC_000913	= 2533719	140 (0.940)					intergenic (+339/‑45)	cysK/ptsH	cysteine synthase A, O‑acetylserine sulfhydrolase A subunit/phosphohistidinoprotein‑hexose phosphotransferase component of PTS system (Hpr)
*	?	NC_000913	= 2586491	146 (0.920)	10 (0.070)	9/252	NT	6.5%	coding (761/1701 nt)	narQ	sensory histidine kinase in two‑component regulatory system with NarP
	?	NC_000913	= 2586500	149 (1.000)					coding (770/1701 nt)	narQ	sensory histidine kinase in two‑component regulatory system with NarP
*	?	NC_000913	2642131 =	117 (0.740)	6 (0.040)	6/252	NT	5.4%	coding (714/1014 nt)	rodZ	MreB assembly cytoskeletal protein
	?	NC_000913	2642169 =	101 (0.680)					coding (676/1014 nt)	rodZ	MreB assembly cytoskeletal protein
*	?	NC_000913	= 2708671	203 (1.280)	10 (0.070)	9/252	NT	5.3%	coding (84/957 nt)	rseB	anti‑sigma E factor, binds RseA
	?	NC_000913	= 2708691	164 (1.100)					coding (64/957 nt)	rseB	anti‑sigma E factor, binds RseA
*	?	NC_000913	2726200 =	NA (NA)	47 (0.310)	15/254	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 (0.320)	25/254	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 =	63 (0.400)	12 (0.080)	8/246	NT	14.7%	noncoding (2/76 nt)	gltW	tRNA‑Glu
	?	NC_000913	= 4168331	81 (0.550)					intergenic (+131/‑41)	rrsB/gltT	16S ribosomal RNA of rrnB operon/tRNA‑Glu
*	?	NC_000913	= 2925373	151 (0.960)	8 (0.050)	7/254	NT	5.0%	coding (26/849 nt)	queF	7‑cyano‑7‑deazaguanine reductase (NADPH‑dependent)
	?	NC_000913	= 2925381	158 (1.050)					coding (34/849 nt)	queF	7‑cyano‑7‑deazaguanine reductase (NADPH‑dependent)
*	?	NC_000913	= 2949337	161 (1.020)	11 (0.070)	7/250	NT	6.5%	coding (96/1332 nt)	argA	amino acid N‑acetyltransferase and inactive acetylglutamate kinase
	?	NC_000913	= 2949352	167 (1.130)					coding (111/1332 nt)	argA	amino acid N‑acetyltransferase and inactive acetylglutamate kinase
*	?	NC_000913	= 2950597	NA (NA)	4 (0.030)	4/246	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	= 3056971	127 (0.800)	13 (0.090)	11/250	NT	9.2%	noncoding (123/140 nt)	sibC	sRNA antisense regulator of toxic IbsC protein
	?	NC_000913	= 3056979	138 (0.930)					noncoding (131/140 nt)	sibC	sRNA antisense regulator of toxic IbsC protein
*	?	NC_000913	3063139 =	159 (1.010)	11 (0.070)	8/252	NT	7.1%	coding (153/996 nt)	argK	membrane ATPase/protein kinase
	?	NC_000913	3063168 =	138 (0.920)					coding (182/996 nt)	argK	membrane ATPase/protein kinase
*	?	NC_000913	= 3082836	NA (NA)	24 (0.160)	14/252	NT	7.4%	noncoding (147/147 nt)	REP214 (repetitive extragenic palindromic) element; contains 3 REP sequences	REP214 (repetitive extragenic palindromic) element; contains 3 REP sequences
	?	NC_000913	3736234 =	299 (2.000)					noncoding (81/171 nt)	REP268 (repetitive extragenic palindromic) element; contains 4 REP sequences	REP268 (repetitive extragenic palindromic) element; contains 4 REP sequences
*	?	NC_000913	= 3102653	119 (0.750)	11 (0.070)	10/256	NT	8.5%	coding (200/720 nt)	trmI	tRNA m(7)G46 methyltransferase, SAM‑dependent
	?	NC_000913	= 3102660	122 (0.800)					coding (193/720 nt)	trmI	tRNA m(7)G46 methyltransferase, SAM‑dependent
*	?	NC_000913	3217434 =	NA (NA)	5 (0.030)	4/252	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 =	142 (0.900)	8 (0.050)	6/256	NT	5.7%	coding (532/1434 nt)	ygjI	putative transporter
	?	NC_000913	3226786 =	127 (0.840)					coding (553/1434 nt)	ygjI	putative transporter
*	?	NC_000913	3250977 =	100 (0.630)	5 (0.030)	5/242	NT	5.5%	intergenic (+23/‑47)	yqjF/yqjG	putative quinol oxidase subunit/putative S‑transferase
	?	NC_000913	3251005 =	82 (0.570)					intergenic (+51/‑19)	yqjF/yqjG	putative quinol oxidase subunit/putative S‑transferase
*	?	NC_000913	3280885 =	79 (0.500)	8 (0.050)	7/256	NT	9.2%	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 =	82 (0.540)					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 =	193 (1.220)	10 (0.070)	8/256	NT	5.5%	coding (349/630 nt)	rlmE	23S rRNA U2552 2'‑O‑ribose methyltransferase, SAM‑dependent
	?	NC_000913	3327340 =	156 (1.030)					coding (325/630 nt)	rlmE	23S rRNA U2552 2'‑O‑ribose methyltransferase, SAM‑dependent
*	?	NC_000913	= 3330557	NA (NA)	6 (0.040) +AATT	4/258	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 =	125 (0.790)	13 (0.090)	9/246	NT	10.2%	coding (276/1434 nt)	rpoN	RNA polymerase, sigma 54 (sigma N) factor
	?	NC_000913	3345024 =	114 (0.780)					coding (308/1434 nt)	rpoN	RNA polymerase, sigma 54 (sigma N) factor
*	?	NC_000913	3423376 =	66 (0.420)	11 (0.070)	5/262	NT	14.4%	intergenic (+182/+47)	yhdZ/rrfF	putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon
	?	NC_000913	= 4213162	66 (0.420)					intergenic (+3/‑72)	rrfE/yjaA	5S ribosomal RNA of rrnE operon/stress‑induced protein
*	?	NC_000913	3468344 =	151 (0.960)	7 (0.050)	7/258	NT	5.1%	coding (1510/2694 nt)	chiA	periplasmic endochitinase
	?	NC_000913	3468379 =	116 (0.760)					coding (1475/2694 nt)	chiA	periplasmic endochitinase
*	?	NC_000913	3520371 =	139 (0.880)	7 (0.050)	7/252	NT	5.1%	coding (333/1239 nt)	hofQ	DNA catabolic putative fimbrial transporter
	?	NC_000913	3520402 =	131 (0.880)					coding (302/1239 nt)	hofQ	DNA catabolic putative fimbrial transporter
*	?	NC_000913	3570872 =	141 (0.890)	10 (0.070)	8/254	NT	6.9%	coding (448/1974 nt)	glgX	glycogen debranching enzyme
	?	NC_000913	3570898 =	137 (0.910)					coding (422/1974 nt)	glgX	glycogen debranching enzyme
*	?	NC_000913	3620621 =	NA (NA)	10 (0.070)	5/254	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	3680367 =	NA (NA)	4 (0.030)	4/250	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 =	189 (1.200)	471 (3.000)	206/264	NT	71.7%	noncoding (413/1443 nt)	IS150	repeat region
	?	NC_000913	= 3839774	185 (1.180)					coding (220/819 nt)	nlpA	cytoplasmic membrane lipoprotein‑28
*	?	NC_000913	3727884 =	65 (0.410)	16 (0.110)	13/250	NT	15.9%	intergenic (‑136/+33)	yiaB/xylB	YiaAB family inner membrane protein/xylulokinase
	?	NC_000913	3727914 =	108 (0.730)					intergenic (‑166/+3)	yiaB/xylB	YiaAB family inner membrane protein/xylulokinase
*	?	NC_000913	3738815 =	376 (2.380)	25 (0.170)	16/250	NT	7.0%	coding (1319/2031 nt)	malS	alpha‑amylase
	?	NC_000913	3738835 =	314 (2.120)					coding (1339/2031 nt)	malS	alpha‑amylase
*	?	NC_000913	= 3867979	151 (0.960)	8 (0.050)	7/258	NT	5.4%	coding (252/333 nt)	yidQ	DUF1375 family outer membrane protein
	?	NC_000913	= 3868017	134 (0.870)					coding (290/333 nt)	yidQ	DUF1375 family outer membrane protein
*	?	NC_000913	= 3943631	66 (0.420)	9 (0.060)	6/252	NT	8.6%	intergenic (+121/‑73)	gltU/rrlC	tRNA‑Glu/23S ribosomal RNA of rrnC operon
	?	NC_000913	= 4209974	129 (0.860)					intergenic (+125/‑69)	gltV/rrlE	tRNA‑Glu/23S ribosomal RNA of rrnE operon
*	?	NC_000913	3998038 =	68 (0.430)	5 (0.030)	4/252	NT	7.3%	coding (56/2163 nt)	uvrD	DNA‑dependent ATPase I and helicase II
	?	NC_000913	3998077 =	62 (0.410)					coding (95/2163 nt)	uvrD	DNA‑dependent ATPase I and helicase II
*	?	NC_000913	3999947 =	90 (0.570)	5 (0.030)	5/256	NT	5.4%	coding (1965/2163 nt)	uvrD	DNA‑dependent ATPase I and helicase II
	?	NC_000913	3999973 =	90 (0.590)					coding (1991/2163 nt)	uvrD	DNA‑dependent ATPase I and helicase II
*	?	NC_000913	= 4037439	NA (NA)	10 (0.070)	8/252	NT	7.3%	intergenic (+104/‑80)	alaT/rrlA	tRNA‑Ala/23S ribosomal RNA of rrnA operon
	?	NC_000913	= 4209981	134 (0.850)					intergenic (+132/‑62)	gltV/rrlE	tRNA‑Glu/23S ribosomal RNA of rrnE operon
*	?	NC_000913	4094379 =	50 (0.320)	4 (0.030)	4/254	NT	8.1%	noncoding (64/402 nt)	REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences	REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences
	?	NC_000913	4094514 =	43 (0.290)					noncoding (199/402 nt)	REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences	REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences
*	?	NC_000913	4142066 =	112 (0.710)	8 (0.050)	8/248	NT	7.3%	coding (156/2502 nt)	frwA	putative PTS enzyme: Hpr, enzyme I and II components
	?	NC_000913	4142096 =	100 (0.680)					coding (126/2502 nt)	frwA	putative PTS enzyme: Hpr, enzyme I and II components
*	?	NC_000913	= 4171473	32 (0.200)	7 (0.050)	5/256	NT	18.5%	noncoding (2833/2904 nt)	rrlB	23S ribosomal RNA of rrnB operon
	?	NC_000913	= 4212854	NA (NA)					noncoding (2812/2904 nt)	rrlE	23S ribosomal RNA of rrnE operon
*	?	NC_000913	= 4171761	79 (0.500)	8 (0.050) +TAG	8/260	NT	9.7%	intergenic (+5/‑296)	rrfB/murB	5S ribosomal RNA of rrnB operon/UDP‑N‑acetylenolpyruvoylglucosamine reductase, FAD‑binding
	?	NC_000913	= 4213198	73 (0.460)					intergenic (+39/‑36)	rrfE/yjaA	5S ribosomal RNA of rrnE operon/stress‑induced protein
*	?	NC_000913	= 4190599	107 (0.680)	6 (0.040)	5/246	NT	5.5%	intergenic (‑112/+136)	sroH/thiH	novel sRNA, function unknown/tyrosine lyase, involved in thiamine‑thiazole moiety synthesis
	?	NC_000913	= 4190612	107 (0.730)					intergenic (‑125/+123)	sroH/thiH	novel sRNA, function unknown/tyrosine lyase, involved in thiamine‑thiazole moiety synthesis
*	?	NC_000913	= 4583170	116 (0.730)	8 (0.050)	8/254	NT	6.3%	intergenic (‑122/+79)	hsdM/hsdR	DNA methyltransferase M/endonuclease R Type I restriction enzyme
	?	NC_000913	= 4583190	129 (0.860)					intergenic (‑142/+59)	hsdM/hsdR	DNA methyltransferase M/endonuclease R Type I restriction enzyme
*	?	NC_000913	= 4593334	NA (NA)	6 (0.040)	6/244	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	= 4633095	86 (0.540)	6 (0.040)	4/250	NT	6.6%	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	89 (0.600)					noncoding (73/140 nt)	REP355 (repetitive extragenic palindromic) element; contains 3 REP sequences	REP355 (repetitive extragenic palindromic) element; contains 3 REP sequences