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

Predicted mutations
evidence	position	mutation	freq	annotation	gene	description
RA	287	Δ1 bp	6.4%	intergenic (+32/‑50)	thrL → / → thrA	thr operon leader peptide/Bifunctional aspartokinase/homoserine dehydrogenase 1
RA	291	A→T	6.2%	intergenic (+36/‑46)	thrL → / → thrA	thr operon leader peptide/Bifunctional aspartokinase/homoserine dehydrogenase 1
RA	293:1	+G	6.3%	intergenic (+38/‑44)	thrL → / → thrA	thr operon leader peptide/Bifunctional aspartokinase/homoserine dehydrogenase 1
RA	9,907	A→C	8.3%	intergenic (+14/+21)	mog → / ← satP	molybdochelatase incorporating molybdenum into molybdopterin/succinate‑acetate transporter
RA	9,908	G→T	8.3%	intergenic (+15/+20)	mog → / ← satP	molybdochelatase incorporating molybdenum into molybdopterin/succinate‑acetate transporter
RA	15,318	G→A	8.4%	intergenic (+20/‑127)	dnaJ → / → insL1	chaperone Hsp40, DnaK co‑chaperone/IS186 transposase
RA	15,319	T→C	8.4%	intergenic (+21/‑126)	dnaJ → / → insL1	chaperone Hsp40, DnaK co‑chaperone/IS186 transposase
RA	16,926	C→A	5.1%	R12L (CGT→CTT)	mokC ←	regulatory protein for HokC, overlaps CDS of hokC
RA	17,527	G→C	7.9%	S13S (TCG→TCC)	nhaA →	sodium‑proton antiporter
RA	17,528	G→C	7.9%	G14R (GGA→CGA)	nhaA →	sodium‑proton antiporter
RA	53,376	G→A	16.4%	P14L (CCC→CTC)	pdxA ←	4‑hydroxy‑L‑threonine phosphate dehydrogenase, NAD‑dependent
RA	53,379	T→C	15.2%	E13G (GAG→GGG)	pdxA ←	4‑hydroxy‑L‑threonine phosphate dehydrogenase, NAD‑dependent
RA	83,587	A→C	10.0%	intergenic (‑58/+35)	leuA ← / ← leuL	2‑isopropylmalate synthase/leu operon leader peptide
RA	83,590	G→T	10.0%	intergenic (‑61/+32)	leuA ← / ← leuL	2‑isopropylmalate synthase/leu operon leader peptide
RA	85,337	G→T	5.3%	intergenic (+25/‑293)	leuO → / → ilvI	global transcription factor/acetolactate synthase 3 large subunit
RA	85,338	A→C	6.1%	intergenic (+26/‑292)	leuO → / → ilvI	global transcription factor/acetolactate synthase 3 large subunit
RA	87,881	A→G	7.8%	intergenic (+33/‑147)	ilvH → / → cra	acetolactate synthase 3, small subunit, valine‑sensitive/transcriptional repressor‑activator for carbon metabolism
RA	87,884	T→A	8.0%	intergenic (+36/‑144)	ilvH → / → cra	acetolactate synthase 3, small subunit, valine‑sensitive/transcriptional repressor‑activator for carbon metabolism
RA	87,887	C→T	9.7%	intergenic (+39/‑141)	ilvH → / → cra	acetolactate synthase 3, small subunit, valine‑sensitive/transcriptional repressor‑activator for carbon metabolism
RA	95,070	G→A	5.2%	V141I (GTA→ATA) ‡	murF →	UDP‑N‑acetylmuramoyl‑tripeptide:D‑alanyl‑D‑ alanine ligase
RA	95,071	T→C	5.1%	V141A (GTA→GCA) ‡	murF →	UDP‑N‑acetylmuramoyl‑tripeptide:D‑alanyl‑D‑ alanine ligase
RA	120,154	Δ1 bp	8.3%	intergenic (+19/+24)	ampE → / ← aroP	ampicillin resistance inner membrane protein; putative signaling protein in beta‑lactamase regulation/aromatic amino acid transporter
RA	120,158:1	+A	8.7%	intergenic (+23/+20)	ampE → / ← aroP	ampicillin resistance inner membrane protein; putative signaling protein in beta‑lactamase regulation/aromatic amino acid transporter
RA	124,344	C→G	5.9%	P443R (CCG→CGG)	aceE →	pyruvate dehydrogenase, decarboxylase component E1, thiamine triphosphate‑binding
RA	151,519	A→C	5.1%	I27M (ATT→ATG)	yadK ←	putative fimbrial‑like adhesin protein
RA	164,620	C→T	7.4%	intergenic (+86/‑110)	hrpB → / → mrcB	putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase
RA	164,621	A→G	7.5%	intergenic (+87/‑109)	hrpB → / → mrcB	putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase
RA	217,030	C→T	5.1%	intergenic (‑27/+27)	yaeF ← / ← proS	putative lipoprotein/prolyl‑tRNA synthetase
RA	256,449	T→C	7.0%	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	7.0%	intergenic (+19/‑73)	gpt → / → frsA	xanthine phosphoribosyltransferase; xanthine‑guanine phosphoribosyltransferase/fermentation‑respiration switch protein; PTS Enzyme IIA(Glc)‑binding protein; pNP‑butyrate esterase activity
RA	256,459	G→A	7.7%	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	272,330:1	+G	5.2%	intergenic (+141/‑250)	insN → / → eyeA	pseudogene, IS911 transposase A;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related/novel sRNA, function unknown, CP4‑6 propahge
RA	282,513	T→C	6.3%	L79P (CTG→CCG)	yagE →	2‑keto‑3‑deoxy gluconate (KDG) aldolase; CP4‑6 prophage
RA	282,518	G→A	5.5%	G81S (GGC→AGC)	yagE →	2‑keto‑3‑deoxy gluconate (KDG) aldolase; CP4‑6 prophage
RA	285,882	T→G	6.9%	I163S (ATC→AGC)	yagG →	CP4‑6 prophage; putative sugar transporter
RA	285,887	C→A	6.2%	L165M (CTG→ATG)	yagG →	CP4‑6 prophage; putative sugar transporter
RA	289,256	G→C	5.2%	intergenic (‑94/+45)	yagI ← / ← argF	CP4‑6 prophage; putative DNA‑binding transcriptional regulator/ornithine carbamoyltransferase 2, chain F; CP4‑6 prophage
RA	289,257	T→A	5.1%	intergenic (‑95/+44)	yagI ← / ← argF	CP4‑6 prophage; putative DNA‑binding transcriptional regulator/ornithine carbamoyltransferase 2, chain F; CP4‑6 prophage
RA	314,255	T→C	5.0%	intergenic (‑450/‑102)	ykgP ← / → eaeH	pseudogene, oxidoreductase family/pseudogene, attaching and effacing protein homology;factor; Not classified
RA	314,258	G→A	5.8%	intergenic (‑453/‑99)	ykgP ← / → eaeH	pseudogene, oxidoreductase family/pseudogene, attaching and effacing protein homology;factor; Not classified
RA	317,566	G→A	5.5%	pseudogene (128/129 nt)	ykgQ →	pseudogene, putative dehydrogenase
RA	361,901	T→G	5.1%	intergenic (‑41/+25)	lacA ← / ← lacY	thiogalactoside acetyltransferase/lactose permease
RA	420,941	T→A	6.1%	intergenic (+31/‑45)	brnQ → / → proY	branched‑chain amino acid transport system 2 carrier protein; LIV‑II transport system for Ile, Leu, and Val/proline‑specific permease
RA	420,942	G→T	6.8%	intergenic (+32/‑44)	brnQ → / → proY	branched‑chain amino acid transport system 2 carrier protein; LIV‑II transport system for Ile, Leu, and Val/proline‑specific permease
RA	420,945	A→C	6.0%	intergenic (+35/‑41)	brnQ → / → proY	branched‑chain amino acid transport system 2 carrier protein; LIV‑II transport system for Ile, Leu, and Val/proline‑specific permease
RA	420,946	T→A	6.0%	intergenic (+36/‑40)	brnQ → / → proY	branched‑chain amino acid transport system 2 carrier protein; LIV‑II transport system for Ile, Leu, and Val/proline‑specific permease
RA	443,022	G→A	7.6%	intergenic (+25/+29)	thiI → / ← yajL	tRNA s(4)U8 sulfurtransferase/oxidative‑stress‑resistance chaperone
RA	443,023	T→C	7.5%	intergenic (+26/+28)	thiI → / ← yajL	tRNA s(4)U8 sulfurtransferase/oxidative‑stress‑resistance chaperone
RA	448,363	A→T	5.6%	S100T (TCC→ACC)	cyoC ←	cytochrome o ubiquinol oxidase subunit III
RA	448,364	G→T	5.1%	I99I (ATC→ATA)	cyoC ←	cytochrome o ubiquinol oxidase subunit III
RA	448,367	A→C	5.2%	V98V (GTT→GTG) ‡	cyoC ←	cytochrome o ubiquinol oxidase subunit III
RA	448,368	A→T	5.4%	V98D (GTT→GAT) ‡	cyoC ←	cytochrome o ubiquinol oxidase subunit III
RA	448,965	G→A	7.3%	H559H (CAC→CAT) ‡	cyoB ←	cytochrome o ubiquinol oxidase subunit I
RA	448,966	T→C	7.4%	H559R (CAC→CGC) ‡	cyoB ←	cytochrome o ubiquinol oxidase subunit I
RA	464,354	C→A	6.0%	intergenic (+46/‑48)	ybaV → / → fadM	putative competence‑suppressing periplasmic helix‑hairpin‑helix DNA‑binding protein/long‑chain acyl‑CoA thioesterase III
RA	464,356	A→T	5.9%	intergenic (+48/‑46)	ybaV → / → fadM	putative competence‑suppressing periplasmic helix‑hairpin‑helix DNA‑binding protein/long‑chain acyl‑CoA thioesterase III
RA	464,358	T→G	6.5%	intergenic (+50/‑44)	ybaV → / → fadM	putative competence‑suppressing periplasmic helix‑hairpin‑helix DNA‑binding protein/long‑chain acyl‑CoA thioesterase III
RA	475,971	C→G	11.1%	intergenic (+20/+11)	ybaY → / ← ybaZ	outer membrane lipoprotein/excision repair protein, alkyltransferase‑like protein ATL
RA	475,972	C→G	11.0%	intergenic (+21/+10)	ybaY → / ← ybaZ	outer membrane lipoprotein/excision repair protein, alkyltransferase‑like protein ATL
RA	481,225	T→G	14.7%	intergenic (‑517/+29)	tomB ← / ← acrB	Hha toxicity attenuator; conjugation‑related protein/multidrug efflux system protein
RA	481,228	C→A	13.8%	intergenic (‑520/+26)	tomB ← / ← acrB	Hha toxicity attenuator; conjugation‑related protein/multidrug efflux system protein
RA	499,459	A→C	5.4%	L172R (CTC→CGC) ‡	aes ←	acetyl esterase
RA	499,460	G→T	5.3%	L172I (CTC→ATC) ‡	aes ←	acetyl esterase
RA	533,846	T→C	6.7%	intergenic (+20/‑70)	allR → / → gcl	glyoxylate‑inducible transcriptional repressor of all and gcl operons/glyoxylate carboligase
RA	533,849	G→A	7.0%	intergenic (+23/‑67)	allR → / → gcl	glyoxylate‑inducible transcriptional repressor of all and gcl operons/glyoxylate carboligase
RA	543,091	G→C	5.2%	intergenic (+58/+170)	glxK → / ← allE	glycerate kinase II/S‑ureidoglycine aminohydrolase
RA	543,094	G→C	5.2%	intergenic (+61/+167)	glxK → / ← allE	glycerate kinase II/S‑ureidoglycine aminohydrolase
RA	569,160	G→T	7.1%	D87Y (GAC→TAC) ‡	ybcK →	DLP12 prophage; putative recombinase
RA	569,161	A→C	6.4%	D87A (GAC→GCC) ‡	ybcK →	DLP12 prophage; putative recombinase
RA	594,946	C→A	8.8%	Q166H (CAG→CAT) ‡	cusR ←	response regulator in two‑component regulatory system with CusS
RA	594,948	G→C	8.8%	Q166E (CAG→GAG) ‡	cusR ←	response regulator in two‑component regulatory system with CusS
RA	594,950	T→G	8.9%	H165P (CAT→CCT)	cusR ←	response regulator in two‑component regulatory system with CusS
RA	595,519	T→A	6.4%	intergenic (‑76/‑81)	cusR ← / → cusC	response regulator in two‑component regulatory system with CusS/copper/silver efflux system, outer membrane component
RA	595,520	T→A	5.7%	intergenic (‑77/‑80)	cusR ← / → cusC	response regulator in two‑component regulatory system with CusS/copper/silver efflux system, outer membrane component
RA	603,391	C→G	7.0%	intergenic (+56/+25)	pheP → / ← ybdG	phenylalanine transporter/mechanosensitive channel protein, miniconductance
RA	603,393	T→A	7.2%	intergenic (+58/+23)	pheP → / ← ybdG	phenylalanine transporter/mechanosensitive channel protein, miniconductance
RA	603,395	C→G	6.8%	intergenic (+60/+21)	pheP → / ← ybdG	phenylalanine transporter/mechanosensitive channel protein, miniconductance
RA	604,752	G→T	10.0%	intergenic (‑89/+19)	ybdG ← / ← nfsB	mechanosensitive channel protein, miniconductance/dihydropteridine reductase, NAD(P)H‑dependent, oxygen‑insensitive
RA	604,753	A→C	10.0%	intergenic (‑90/+18)	ybdG ← / ← nfsB	mechanosensitive channel protein, miniconductance/dihydropteridine reductase, NAD(P)H‑dependent, oxygen‑insensitive
RA	639,654	T→C	6.5%	intergenic (+146/‑99)	ahpC → / → ahpF	alkyl hydroperoxide reductase, C22 subunit/alkyl hydroperoxide reductase, F52a subunit, FAD/NAD(P)‑binding
RA	639,657	G→A	6.2%	intergenic (+149/‑96)	ahpC → / → ahpF	alkyl hydroperoxide reductase, C22 subunit/alkyl hydroperoxide reductase, F52a subunit, FAD/NAD(P)‑binding
RA	672,110	G→A	5.6%	T26I (ACC→ATC)	lptE ←	LPS assembly OM complex LptDE, lipoprotein component
RA	672,113	T→C	5.7%	D25G (GAT→GGT)	lptE ←	LPS assembly OM complex LptDE, lipoprotein component
RA	699,556	C→T	13.5%	intergenic (‑379/+18)	asnB ← / ← umpH	asparagine synthetase B/UMP phosphatase
RA	699,559	A→G	13.4%	intergenic (‑382/+15)	asnB ← / ← umpH	asparagine synthetase B/UMP phosphatase
RA	710,170	C→T	8.6%	intergenic (+54/+30)	chiQ → / ← fur	chitosugar‑induced verified lipoprotein/ferric iron uptake regulon transcriptional repressor; autorepressor
RA	710,173	A→G	8.7%	intergenic (+57/+27)	chiQ → / ← fur	chitosugar‑induced verified lipoprotein/ferric iron uptake regulon transcriptional repressor; autorepressor
RA	729,642	C→T	5.3%	V20V (GTC→GTT)	rhsC →	Rhs protein with putative toxin domain; putative neighboring cell growth inhibitor
RA	770,679	G→T	5.7%	intergenic (+68/‑779)	mngB → / → cydA	alpha‑mannosidase/cytochrome d terminal oxidase, subunit I
RA	770,682	A→C	5.7%	intergenic (+71/‑776)	mngB → / → cydA	alpha‑mannosidase/cytochrome d terminal oxidase, subunit I
RA	773,554	G→A	5.1%	L171L (CTG→CTA)	cydB →	cytochrome d terminal oxidase, subunit II
RA	805,312	G→T	7.8%	E604* (GAG→TAG) ‡	ybhJ →	aconitase family protein
RA	805,313	A→C	7.7%	E604A (GAG→GCG) ‡	ybhJ →	aconitase family protein
RA	811,698	C→G	5.9%	H59Q (CAC→CAG)	bioC →	malonyl‑ACP O‑methyltransferase, SAM‑dependent
RA	815,666	T→G	6.2%	intergenic (+119/+73)	uvrB → / ← ybhK	exision nuclease of nucleotide excision repair, DNA damage recognition component/putative CofD superfamily transferase
RA	815,667	C→A	6.0%	intergenic (+120/+72)	uvrB → / ← ybhK	exision nuclease of nucleotide excision repair, DNA damage recognition component/putative CofD superfamily transferase
RA	847,213	A→T	8.1%	intergenic (‑94/+45)	glnP ← / ← glnH	glutamine transporter subunit/glutamine transporter subunit
RA	847,214	T→A	8.1%	intergenic (‑95/+44)	glnP ← / ← glnH	glutamine transporter subunit/glutamine transporter subunit
RA	847,215	A→T	8.0%	intergenic (‑96/+43)	glnP ← / ← glnH	glutamine transporter subunit/glutamine transporter subunit
RA	850,993	T→C	6.7%	intergenic (+28/+21)	ompX → / ← opgE	outer membrane protein X/OPG biosynthetic transmembrane phosphoethanolamine transferase
RA	850,995	T→G	6.7%	intergenic (+30/+19)	ompX → / ← opgE	outer membrane protein X/OPG biosynthetic transmembrane phosphoethanolamine transferase
RA	850,996	C→A	6.6%	intergenic (+31/+18)	ompX → / ← opgE	outer membrane protein X/OPG biosynthetic transmembrane phosphoethanolamine transferase
RA	850,998	G→A	6.6%	intergenic (+33/+16)	ompX → / ← opgE	outer membrane protein X/OPG biosynthetic transmembrane phosphoethanolamine transferase
RA	857,576	T→C	14.3%	intergenic (+21/+220)	ybiT → / ← ybiU	ABC‑F family putative regulatory ATPase/DUF1479 family protein
RA	857,578	C→G	14.3%	intergenic (+23/+218)	ybiT → / ← ybiU	ABC‑F family putative regulatory ATPase/DUF1479 family protein
RA	857,580	G→A	14.3%	intergenic (+25/+216)	ybiT → / ← ybiU	ABC‑F family putative regulatory ATPase/DUF1479 family protein
RA	858,924	T→G	5.4%	R46R (CGA→CGC)	ybiU ←	DUF1479 family protein
RA	858,927	C→A	5.3%	T45T (ACG→ACT)	ybiU ←	DUF1479 family protein
RA	860,151	A→G	6.5%	intergenic (‑123/+23)	ybiV ← / ← ybiW	sugar phosphatase; fructose‑1‑P/ribose‑5‑P/glucose‑6‑P phosphatase/putative pyruvate formate lyase
RA	860,154	A→T	6.3%	intergenic (‑126/+20)	ybiV ← / ← ybiW	sugar phosphatase; fructose‑1‑P/ribose‑5‑P/glucose‑6‑P phosphatase/putative pyruvate formate lyase
RA	860,157	C→T	5.7%	intergenic (‑129/+17)	ybiV ← / ← ybiW	sugar phosphatase; fructose‑1‑P/ribose‑5‑P/glucose‑6‑P phosphatase/putative pyruvate formate lyase
RA	926,168	C→T	6.2%	intergenic (‑197/+57)	serW ← / ← infA	tRNA‑Ser/translation initiation factor IF‑1
RA	926,174	A→T	6.0%	intergenic (‑203/+51)	serW ← / ← infA	tRNA‑Ser/translation initiation factor IF‑1
RA	926,180	A→G	5.4%	intergenic (‑209/+45)	serW ← / ← infA	tRNA‑Ser/translation initiation factor IF‑1
RA	983,117	G→A	13.6%	G15S (GGT→AGT)	ycbK →	M15A protease‑related family periplasmic protein
RA	987,560	G→C	16.6%	intergenic (‑578/+25)	ompF ← / ← asnS	outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
RA	987,561	G→C	16.5%	intergenic (‑579/+24)	ompF ← / ← asnS	outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
RA	1,015,912	T→A	7.1%	intergenic (+30/+40)	rmf → / ← fabA	ribosome modulation factor/beta‑hydroxydecanoyl thioester dehydrase
RA	1,018,983	A→T	13.4%	intergenic (+46/+30)	matP → / ← ompA	Ter macrodomain organizer matS‑binding protein/outer membrane protein A (3a;II*;G;d)
RA	1,018,986	A→T	13.2%	intergenic (+49/+27)	matP → / ← ompA	Ter macrodomain organizer matS‑binding protein/outer membrane protein A (3a;II*;G;d)
RA	1,100,789	G→T	5.9%	intergenic (+2/+62)	ycdZ → / ← csgG	DUF1097 family inner membrane protein/curli production assembly/transport outer membrane lipoprotein
RA	1,100,791	G→C	5.1%	intergenic (+4/+60)	ycdZ → / ← csgG	DUF1097 family inner membrane protein/curli production assembly/transport outer membrane lipoprotein
RA	1,100,793	A→C	5.1%	intergenic (+6/+58)	ycdZ → / ← csgG	DUF1097 family inner membrane protein/curli production assembly/transport outer membrane lipoprotein
RA	1,113,544	G→A	8.2%	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	8.2%	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	7.9%	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	1,129,394	G→C	6.8%	intergenic (+20/+20)	murJ → / ← flgN	putative lipid II flippase/export chaperone for FlgK and FlgL
RA	1,136,026	G→T	5.5%	V155L (GTA→TTA) ‡	flgH →	flagellar protein of basal‑body outer‑membrane L ring
RA	1,136,027	T→A	5.2%	V155E (GTA→GAA) ‡	flgH →	flagellar protein of basal‑body outer‑membrane L ring
RA	1,136,028	A→C	5.4%	V155V (GTA→GTC) ‡	flgH →	flagellar protein of basal‑body outer‑membrane L ring
RA	1,147,980	G→T	5.6%	K120N (AAG→AAT)	plsX →	putative phosphate acyltransferase
RA	1,147,986	G→C	5.6%	L122L (CTG→CTC)	plsX →	putative phosphate acyltransferase
RA	1,147,987	G→C	5.6%	E123Q (GAG→CAG)	plsX →	putative phosphate acyltransferase
RA	1,147,993	A→C	5.2%	I125L (ATT→CTT)	plsX →	putative phosphate acyltransferase
RA	1,149,985	A→C	5.3%	A86A (GCA→GCC)	fabD →	malonyl‑CoA‑[acyl‑carrier‑protein] transacylase
RA	1,149,988	G→C	5.3%	M87I (ATG→ATC)	fabD →	malonyl‑CoA‑[acyl‑carrier‑protein] transacylase
RA	1,149,991	G→T	5.3%	M88I (ATG→ATT)	fabD →	malonyl‑CoA‑[acyl‑carrier‑protein] transacylase
RA	1,153,208	T→C	6.7%	intergenic (+28/‑92)	fabF → / → pabC	3‑oxoacyl‑[acyl‑carrier‑protein] synthase II/4‑amino‑4‑deoxychorismate lyase component of para‑aminobenzoate synthase multienzyme complex
RA	1,153,213	T→A	7.0%	intergenic (+33/‑87)	fabF → / → pabC	3‑oxoacyl‑[acyl‑carrier‑protein] synthase II/4‑amino‑4‑deoxychorismate lyase component of para‑aminobenzoate synthase multienzyme complex
RA	1,153,214	T→A	6.9%	intergenic (+34/‑86)	fabF → / → pabC	3‑oxoacyl‑[acyl‑carrier‑protein] synthase II/4‑amino‑4‑deoxychorismate lyase component of para‑aminobenzoate synthase multienzyme complex
RA	1,153,219	G→A	7.6%	intergenic (+39/‑81)	fabF → / → pabC	3‑oxoacyl‑[acyl‑carrier‑protein] synthase II/4‑amino‑4‑deoxychorismate lyase component of para‑aminobenzoate synthase multienzyme complex
RA	1,155,440	A→G	6.4%	Q106R (CAG→CGG)	tmk →	thymidylate kinase
RA	1,159,335	G→T	6.3%	intergenic (+33/+27)	ptsG → / ← fhuE	fused glucose‑specific PTS enzymes: IIB component/IIC component/ferric‑rhodotorulic acid outer membrane transporter
RA	1,159,336	A→C	6.7%	intergenic (+34/+26)	ptsG → / ← fhuE	fused glucose‑specific PTS enzymes: IIB component/IIC component/ferric‑rhodotorulic acid outer membrane transporter
RA	1,174,077	G→A	9.5%	intergenic (‑113/+15)	mfd ← / ← ycfT	transcription‑repair coupling factor/inner membrane protein
RA	1,174,080	T→C	9.3%	intergenic (‑116/+12)	mfd ← / ← ycfT	transcription‑repair coupling factor/inner membrane protein
RA	1,233,154	T→A	5.2%	intergenic (‑124/+22)	dsbB ← / ← nhaB	oxidoreductase that catalyzes reoxidation of DsbA protein disulfide isomerase I/sodium:proton antiporter
RA	1,233,157	T→A	5.3%	intergenic (‑127/+19)	dsbB ← / ← nhaB	oxidoreductase that catalyzes reoxidation of DsbA protein disulfide isomerase I/sodium:proton antiporter
RA	1,253,830	C→G	5.3%	S708T (AGT→ACT)	ycgV ←	putative adhesin
RA	1,260,901	C→T	11.7%	intergenic (‑98/+27)	dauA ← / ← prs	C4‑dicarboxylic acid transporter/phosphoribosylpyrophosphate synthase
RA	1,260,904	A→G	11.2%	intergenic (‑101/+24)	dauA ← / ← prs	C4‑dicarboxylic acid transporter/phosphoribosylpyrophosphate synthase
RA	1,292,472	G→A	8.6%	intergenic (+107/+37)	galU → / ← hns	glucose‑1‑phosphate uridylyltransferase/global DNA‑binding transcriptional dual regulator H‑NS
RA	1,292,473	C→G	9.6%	intergenic (+108/+36)	galU → / ← hns	glucose‑1‑phosphate uridylyltransferase/global DNA‑binding transcriptional dual regulator H‑NS
RA	1,292,474	T→C	8.0%	intergenic (+109/+35)	galU → / ← hns	glucose‑1‑phosphate uridylyltransferase/global DNA‑binding transcriptional dual regulator H‑NS
JC JC	1,293,015	IS1 (+) +8 bp	44.6%	intergenic (‑93/‑505)	hns ← / → tdk	global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
MC JC	1,299,499	Δ1,199 bp	100%	intergenic (+254/‑485)	ychE → / → oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
RA	1,306,787	G→A	6.4%	intergenic (+19/+34)	oppF → / ← yciU	oligopeptide ABC transporter ATPase/UPF0263 family protein
RA	1,306,788	T→C	6.4%	intergenic (+20/+33)	oppF → / ← yciU	oligopeptide ABC transporter ATPase/UPF0263 family protein
RA	1,311,830	A→G	11.9%	intergenic (+22/+18)	tonB → / ← yciA	membrane spanning protein in TonB‑ExbB‑ExbD transport complex/acyl‑CoA esterase
RA	1,311,831	C→T	11.9%	intergenic (+23/+17)	tonB → / ← yciA	membrane spanning protein in TonB‑ExbB‑ExbD transport complex/acyl‑CoA esterase
RA	1,314,682	A→T	5.8%	intergenic (+24/+36)	ompW → / ← yciE	outer membrane protein W/putative rubrerythrin/ferritin‑like metal‑binding protein
RA	1,314,683	T→A	5.6%	intergenic (+25/+35)	ompW → / ← yciE	outer membrane protein W/putative rubrerythrin/ferritin‑like metal‑binding protein
RA	1,314,684	A→T	5.7%	intergenic (+26/+34)	ompW → / ← yciE	outer membrane protein W/putative rubrerythrin/ferritin‑like metal‑binding protein
RA	1,324,837	A→C	9.2%	Y31S (TAT→TCT) ‡	yciQ →	enhancer of membrane protein expression; putative inner membrane protein
RA	1,324,838	T→A	9.3%	Y31* (TAT→TAA) ‡	yciQ →	enhancer of membrane protein expression; putative inner membrane protein
RA	1,324,839	G→T	10.4%	E32* (GAA→TAA)	yciQ →	enhancer of membrane protein expression; putative inner membrane protein
RA	1,344,033	A→G	7.1%	L105P (CTG→CCG)	yciT ←	global regulator of transcription; DeoR family
RA	1,344,036	G→C	7.1%	T104S (ACT→AGT)	yciT ←	global regulator of transcription; DeoR family
RA	1,344,039	C→T	7.1%	R103Q (CGG→CAG)	yciT ←	global regulator of transcription; DeoR family
RA	1,355,187	A→G	6.1%	V95A (GTG→GCG) ‡	sapB ←	antimicrobial peptide transport ABC transporter permease
RA	1,355,188	C→T	6.1%	V95M (GTG→ATG) ‡	sapB ←	antimicrobial peptide transport ABC transporter permease
RA	1,370,026	T→A	7.4%	intergenic (+23/‑190)	pspE → / → ycjM	thiosulfate:cyanide sulfurtransferase (rhodanese)/alpha amylase catalytic domain family protein
RA	1,370,029	T→A	7.4%	intergenic (+26/‑187)	pspE → / → ycjM	thiosulfate:cyanide sulfurtransferase (rhodanese)/alpha amylase catalytic domain family protein
RA	1,382,000	C→T	6.4%	C18C (TGC→TGT)	ompG →	outer membrane porin G
RA	1,382,003	A→G	6.3%	A19A (GCA→GCG)	ompG →	outer membrane porin G
RA	1,426,178	A→T	5.4%	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	1,446,357:1	+T	5.3%	intergenic (+151/+21)	ydbL → / ← feaR	DUF1318 family protein/transcriptional activator for tynA and feaB
RA	1,446,362	Δ1 bp	5.3%	intergenic (+156/+16)	ydbL → / ← feaR	DUF1318 family protein/transcriptional activator for tynA and feaB
RA	1,504,884	T→C	5.2%	intergenic (+19/+21)	insQ → / ← ydcO	IS609 transposase B/BenE family inner membrane putative transporter
RA	1,504,888	T→G	5.4%	intergenic (+23/+17)	insQ → / ← ydcO	IS609 transposase B/BenE family inner membrane putative transporter
RA	1,504,889	C→A	5.3%	intergenic (+24/+16)	insQ → / ← ydcO	IS609 transposase B/BenE family inner membrane putative transporter
RA	1,504,893	G→A	5.3%	intergenic (+28/+12)	insQ → / ← ydcO	IS609 transposase B/BenE family inner membrane putative transporter
RA	1,597,272	T→A	8.0%	pseudogene (716/3861 nt)	yneO ←	pseudogene, AidA homolog
RA	1,613,461	C→T	12.5%	G415S (GGT→AGT)	sad ←	succinate semialdehyde dehydrogenase, NAD(P)+‑dependent
RA	1,620,227	C→G	5.0%	intergenic (+20/+11)	marB → / ← eamA	periplasmic mar operon regulator/cysteine and O‑acetyl‑L‑serine efflux system
RA	1,631,023	C→T	7.8%	pseudogene (1263/1284 nt)	ydfJ ←	pseudogene, MFS transporter family; interrupted by Qin prophage;Phage or Prophage Related; putative transport protein
RA	1,642,370	C→G	6.9%	intergenic (+303/+119)	cspF → / ← quuQ	Qin prophage; cold shock protein/Qin prophage; putative antitermination protein Q
RA	1,642,373	C→G	6.9%	intergenic (+306/+116)	cspF → / ← quuQ	Qin prophage; cold shock protein/Qin prophage; putative antitermination protein Q
RA	1,679,398	T→A	6.6%	intergenic (+27/‑159)	ydgH → / → ydgI	DUF1471 family periplasmic protein/putative arginine/ornithine antiporter transporter
RA	1,679,400	G→C	7.8%	intergenic (+29/‑157)	ydgH → / → ydgI	DUF1471 family periplasmic protein/putative arginine/ornithine antiporter transporter
RA	1,679,402	T→A	6.5%	intergenic (+31/‑155)	ydgH → / → ydgI	DUF1471 family periplasmic protein/putative arginine/ornithine antiporter transporter
RA	1,684,016	A→G	10.0%	S379G (AGC→GGC)	rstB →	sensory histidine kinase of RstAB two‑component system
RA	1,684,019	C→T	9.9%	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	5.1%	intergenic (+66/‑35)	manA → / → ydgA	mannose‑6‑phosphate isomerase/DUF945 family protein
RA	1,698,585	T→G	6.5%	E199A (GAA→GCA)	malI ←	transcriptional repressor of Mal regulon
RA	1,698,587	T→A	6.7%	A198A (GCA→GCT) ‡	malI ←	transcriptional repressor of Mal regulon
RA	1,698,589	C→A	6.8%	A198S (GCA→TCA) ‡	malI ←	transcriptional repressor of Mal regulon
RA	1,703,251	A→T	5.6%	intergenic (+17/+17)	add → / ← ydgJ	adenosine deaminase/putative oxidoreductase
RA	1,703,252	A→T	5.6%	intergenic (+18/+16)	add → / ← ydgJ	adenosine deaminase/putative oxidoreductase
RA	1,736,097	T→A	7.8%	intergenic (+138/+24)	sodB → / ← ydhP	superoxide dismutase, Fe/putative MFS transporter, inner membrane protein
RA	1,736,100	T→A	7.8%	intergenic (+141/+21)	sodB → / ← ydhP	superoxide dismutase, Fe/putative MFS transporter, inner membrane protein
RA	1,763,450	A→G	7.7%	V187A (GTG→GCG) ‡	sufB ←	component of SufBCD Fe‑S cluster assembly scaffold
RA	1,763,451	C→T	7.8%	V187M (GTG→ATG) ‡	sufB ←	component of SufBCD Fe‑S cluster assembly scaffold
RA	1,795,227	A→T	7.4%	intergenic (‑75/+26)	btuC ← / ← ihfA	vitamin B12 ABC transporter permease/integration host factor (IHF), DNA‑binding protein, alpha subunit
RA	1,795,228	G→C	7.5%	intergenic (‑76/+25)	btuC ← / ← ihfA	vitamin B12 ABC transporter permease/integration host factor (IHF), DNA‑binding protein, alpha subunit
RA	1,795,229	A→T	7.4%	intergenic (‑77/+24)	btuC ← / ← ihfA	vitamin B12 ABC transporter permease/integration host factor (IHF), DNA‑binding protein, alpha subunit
RA	1,797,388	G→T	6.9%	P186Q (CCG→CAG)	pheT ←	phenylalanine tRNA synthetase, beta subunit
RA	1,797,391	A→C	6.9%	L185R (CTG→CGG)	pheT ←	phenylalanine tRNA synthetase, beta subunit
RA	1,810,062	T→C	7.4%	intergenic (+14/‑149)	yniC → / → ydjM	2‑deoxyglucose‑6‑P phosphatase/inner membrane protein regulated by LexA
RA	1,810,065	T→G	8.2%	intergenic (+17/‑146)	yniC → / → ydjM	2‑deoxyglucose‑6‑P phosphatase/inner membrane protein regulated by LexA
RA	1,810,066	C→A	7.8%	intergenic (+18/‑145)	yniC → / → ydjM	2‑deoxyglucose‑6‑P phosphatase/inner membrane protein regulated by LexA
RA	1,810,069	G→A	7.8%	intergenic (+21/‑142)	yniC → / → ydjM	2‑deoxyglucose‑6‑P phosphatase/inner membrane protein regulated by LexA
RA	1,823,335	G→C	6.7%	intergenic (+50/‑180)	nadE → / → cho	NAD synthetase, NH3/glutamine‑dependent/endonuclease of nucleotide excision repair
RA	1,823,338	G→C	7.4%	intergenic (+53/‑177)	nadE → / → cho	NAD synthetase, NH3/glutamine‑dependent/endonuclease of nucleotide excision repair
RA	1,836,905	G→C	5.6%	S278T (AGC→ACC)	ynjB →	putative ABC transporter periplasmic binding protein
RA	1,864,763	A→T	12.0%	intergenic (+29/+19)	yeaD → / ← yeaE	D‑hexose‑6‑phosphate epimerase‑like protein/aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent
RA	1,864,768	T→C	11.1%	intergenic (+34/+14)	yeaD → / ← yeaE	D‑hexose‑6‑phosphate epimerase‑like protein/aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent
RA	1,865,682	G→C	8.2%	intergenic (‑46/+44)	yeaE ← / ← mipA	aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent/scaffolding protein for murein synthesizing machinery
RA	1,883,027	C→G	5.9%	intergenic (+30/‑161)	dmlA → / → yeaV	D‑malate oxidase, NAD‑dependent; putative tartrate dehydrogenase/putative transporter
RA	1,901,029	Δ1 bp	6.7%	coding (557/1557 nt)	yoaE ←	putative membrane protein/conserved protein
RA	1,901,034	C→G	6.6%	T184T (ACG→ACC)	yoaE ←	putative membrane protein/conserved protein
RA	1,901,038:1	+T	6.9%	coding (548/1557 nt)	yoaE ←	putative membrane protein/conserved protein
RA	1,954,256	T→A	7.2%	I272N (ATT→AAT)	cmoB →	tRNA (cmo5U34)‑carboxymethyltransferase, carboxy‑SAM‑dependent
MC JC	1,978,503	Δ776 bp	100%		insB1–insA	insB1, insA
RA	1,985,112	C→G	8.3%	intergenic (‑43/+27)	araG ← / ← araF	L‑arabinose ABC transporter ATPase/L‑arabinose ABC transporter periplasmic binding protein
RA	1,986,356	A→T	5.6%	intergenic (‑228/‑569)	araF ← / → ftnB	L‑arabinose ABC transporter periplasmic binding protein/ferritin B, putative ferrous iron reservoir
RA	2,009,731	A→G	7.6%	intergenic (+19/‑90)	yedF → / → yedK	putative TusA family sulfurtransferase/DUF159 family protein
RA	2,009,732	C→G	7.7%	intergenic (+20/‑89)	yedF → / → yedK	putative TusA family sulfurtransferase/DUF159 family protein
RA	2,009,733	C→T	7.7%	intergenic (+21/‑88)	yedF → / → yedK	putative TusA family sulfurtransferase/DUF159 family protein
RA	2,079,004	G→C	9.8%	intergenic (+73/+28)	yoeF → / ← yeeX	pseudogene, CP4‑44 putative prophage remnant;Phage or Prophage Related/UPF0265 family protein
RA	2,081,688	A→T	6.0%	I287N (ATT→AAT)	dacD ←	D‑alanyl‑D‑alanine carboxypeptidase; penicillin‑binding protein 6b
RA	2,090,122	A→G	7.9%	intergenic (+76/‑70)	hisL → / → hisG	his operon leader peptide/ATP phosphoribosyltransferase
RA	2,090,124	C→G	8.0%	intergenic (+78/‑68)	hisL → / → hisG	his operon leader peptide/ATP phosphoribosyltransferase
RA	2,090,126	C→T	8.1%	intergenic (+80/‑66)	hisL → / → hisG	his operon leader peptide/ATP phosphoribosyltransferase
RA	2,118,532	A→G	5.9%	intergenic (‑128/+148)	wcaK ← / ← wzxC	colanic acid biosynthesis protein/putative colanic acid exporter
RA	2,118,533	A→C	5.1%	intergenic (‑129/+147)	wcaK ← / ← wzxC	colanic acid biosynthesis protein/putative colanic acid exporter
RA	2,118,539	T→G	5.5%	intergenic (‑135/+141)	wcaK ← / ← wzxC	colanic acid biosynthesis protein/putative colanic acid exporter
RA	2,118,540	C→A	5.5%	intergenic (‑136/+140)	wcaK ← / ← wzxC	colanic acid biosynthesis protein/putative colanic acid exporter
RA	2,121,583	Δ1 bp	6.4%	intergenic (‑29/+26)	wcaJ ← / ← cpsG	colanic biosynthesis UDP‑glucose lipid carrier transferase/phosphomannomutase
RA	2,121,586	G→C	6.3%	intergenic (‑32/+23)	wcaJ ← / ← cpsG	colanic biosynthesis UDP‑glucose lipid carrier transferase/phosphomannomutase
RA	2,121,588:1	+C	6.7%	intergenic (‑34/+21)	wcaJ ← / ← cpsG	colanic biosynthesis UDP‑glucose lipid carrier transferase/phosphomannomutase
RA	2,145,313	C→A	100%	S683Y (TCC→TAC)	yegE →	putative diguanylate cyclase
RA	2,173,361	Δ2 bp	100%	pseudogene (1‑2/442 nt)	gatC ←	pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC
RA	2,177,332	C→T	6.5%	intergenic (‑128/+180)	gatY ← / ← fbaB	D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I
RA	2,177,337	G→T	5.3%	intergenic (‑133/+175)	gatY ← / ← fbaB	D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I
RA	2,177,340	A→C	6.2%	intergenic (‑136/+172)	gatY ← / ← fbaB	D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I
RA	2,177,345	A→G	6.4%	intergenic (‑141/+167)	gatY ← / ← fbaB	D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I
RA	2,270,602	T→C	8.6%	intergenic (+57/‑124)	mepS → / → rtn	murein DD‑endopeptidase, space‑maker hydrolase, mutational suppressor of prc thermosensitivity, outer membrane lipoprotein, weak murein LD‑carboxypeptidase/resistance protein for phages lambda and N4, putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	2,270,605	G→A	8.9%	intergenic (+60/‑121)	mepS → / → rtn	murein DD‑endopeptidase, space‑maker hydrolase, mutational suppressor of prc thermosensitivity, outer membrane lipoprotein, weak murein LD‑carboxypeptidase/resistance protein for phages lambda and N4, putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	2,282,832	C→G	7.1%	intergenic (+31/+108)	rplY → / ← yejK	50S ribosomal subunit protein L25/spermidine nucleoid‑associated protein
RA	2,286,311	C→G	6.1%	intergenic (+24/+79)	proL → / ← yejO	tRNA‑Pro/pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system
RA	2,286,313	T→A	6.9%	intergenic (+26/+77)	proL → / ← yejO	tRNA‑Pro/pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system
RA	2,286,315	C→G	6.8%	intergenic (+28/+75)	proL → / ← yejO	tRNA‑Pro/pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system
RA	2,305,085	A→G	18.5%	intergenic (+692/+23)	eco → / ← mqo	ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA	2,305,086	C→G	18.5%	intergenic (+693/+22)	eco → / ← mqo	ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA	2,305,087	C→T	18.5%	intergenic (+694/+21)	eco → / ← mqo	ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA	2,305,209	G→A	19.1%	L516L (CTG→TTG)	mqo ←	malate dehydrogenase, FAD/NAD(P)‑binding domain
RA	2,311,616	C→T	9.2%	intergenic (‑82/+30)	apbE ← / ← ompC	putative thiamine‑synthetic flavin transferase lipoprotein/outer membrane porin protein C
RA	2,311,619	A→G	8.4%	intergenic (‑85/+27)	apbE ← / ← ompC	putative thiamine‑synthetic flavin transferase lipoprotein/outer membrane porin protein C
RA	2,314,800	A→C	8.0%	Q438P (CAG→CCG) ‡	rcsD →	phosphotransfer intermediate protein in two‑component regulatory system with RcsBC
RA	2,314,801	G→T	8.0%	Q438H (CAG→CAT) ‡	rcsD →	phosphotransfer intermediate protein in two‑component regulatory system with RcsBC
RA	2,318,095	C→G	100%	L594F (TTG→TTC)	rcsC ←	hybrid sensory kinase in two‑component regulatory system with RcsB and YojN
RA	2,329,708	A→G	5.5%	G30G (GGT→GGC) ‡	yfaQ ←	tandem DUF2300 domain protein, putative host defense protein
RA	2,329,709	C→G	5.5%	G30A (GGT→GCT) ‡	yfaQ ←	tandem DUF2300 domain protein, putative host defense protein
RA	2,329,710	C→T	5.4%	G30S (GGT→AGT) ‡	yfaQ ←	tandem DUF2300 domain protein, putative host defense protein
RA	2,375,483	A→T	6.9%	L160L (CTT→CTA) ‡	menC ←	O‑succinylbenzoyl‑CoA synthase
RA	2,375,484	A→T	6.9%	L160H (CTT→CAT) ‡	menC ←	O‑succinylbenzoyl‑CoA synthase
RA	2,391,414	C→G	12.5%	R31P (CGA→CCA)	nuoN ←	NADH:ubiquinone oxidoreductase, membrane subunit N
RA	2,391,417	C→G	12.8%	W30S (TGG→TCG)	nuoN ←	NADH:ubiquinone oxidoreductase, membrane subunit N
RA	2,415,725	C→A	5.2%	L327M (CTG→ATG)	pta →	phosphate acetyltransferase
RA	2,425,968	T→G	7.0%	intergenic (‑52/+38)	hisQ ← / ← hisJ	histidine ABC transporter permease/histidine ABC transporter periplasmic binding protein
RA	2,425,971	C→A	7.0%	intergenic (‑55/+35)	hisQ ← / ← hisJ	histidine ABC transporter permease/histidine ABC transporter periplasmic binding protein
RA	2,425,975	A→G	5.8%	intergenic (‑59/+31)	hisQ ← / ← hisJ	histidine ABC transporter permease/histidine ABC transporter periplasmic binding protein
RA	2,430,144	G→C	7.7%	A32G (GCC→GGC)	purF ←	amidophosphoribosyltransferase
RA	2,440,295	A→T	5.1%	intergenic (‑175/+90)	yfcJ ← / ← fabB	putative arabinose efflux transporter/3‑oxoacyl‑[acyl‑carrier‑protein] synthase I
RA	2,440,298	A→T	5.7%	intergenic (‑178/+87)	yfcJ ← / ← fabB	putative arabinose efflux transporter/3‑oxoacyl‑[acyl‑carrier‑protein] synthase I
RA	2,440,865	C→T	5.2%	L247L (CTG→CTA) ‡	fabB ←	3‑oxoacyl‑[acyl‑carrier‑protein] synthase I
RA	2,440,866	A→G	5.2%	L247P (CTG→CCG) ‡	fabB ←	3‑oxoacyl‑[acyl‑carrier‑protein] synthase I
RA	2,493,562	T→A	8.2%	intergenic (‑308/+205)	frc ← / ← yfdX	formyl‑CoA transferase, NAD(P)‑binding/uncharacterized protein
RA	2,493,563	T→A	8.2%	intergenic (‑309/+204)	frc ← / ← yfdX	formyl‑CoA transferase, NAD(P)‑binding/uncharacterized protein
RA	2,497,023	A→T	6.3%	intergenic (+31/+34)	ypdK → / ← alaC	inner membrane protein/glutamate‑pyruvate aminotransferase; glutamic‑pyruvic transaminase (GPT); alanine transaminase
RA	2,497,024	T→G	6.3%	intergenic (+32/+33)	ypdK → / ← alaC	inner membrane protein/glutamate‑pyruvate aminotransferase; glutamic‑pyruvic transaminase (GPT); alanine transaminase
RA	2,497,025	C→A	6.3%	intergenic (+33/+32)	ypdK → / ← alaC	inner membrane protein/glutamate‑pyruvate aminotransferase; glutamic‑pyruvic transaminase (GPT); alanine transaminase
RA	2,497,026	A→T	6.4%	intergenic (+34/+31)	ypdK → / ← alaC	inner membrane protein/glutamate‑pyruvate aminotransferase; glutamic‑pyruvic transaminase (GPT); alanine transaminase
RA	2,518,082	C→G	9.3%	noncoding (35/76 nt)	alaX ←	tRNA‑Ala
RA	2,518,197	C→G	7.9%	noncoding (35/76 nt)	alaW ←	tRNA‑Ala
RA	2,525,907	G→A	9.3%	intergenic (+16/+23)	yfeN → / ← yfeR	putative outer membrane protein/transcriptional regulator of yefH
RA	2,525,908	C→G	9.3%	intergenic (+17/+22)	yfeN → / ← yfeR	putative outer membrane protein/transcriptional regulator of yefH
RA	2,532,268	T→C	8.1%	intergenic (+44/‑141)	cysZ → / → cysK	sulfate transporter, sulfite inhibited/cysteine synthase A, O‑acetylserine sulfhydrolase A subunit
RA	2,532,272	T→A	8.5%	intergenic (+48/‑137)	cysZ → / → cysK	sulfate transporter, sulfite inhibited/cysteine synthase A, O‑acetylserine sulfhydrolase A subunit
RA	2,532,275	T→A	8.3%	intergenic (+51/‑134)	cysZ → / → cysK	sulfate transporter, sulfite inhibited/cysteine synthase A, O‑acetylserine sulfhydrolase A subunit
RA	2,532,279	G→A	7.7%	intergenic (+55/‑130)	cysZ → / → cysK	sulfate transporter, sulfite inhibited/cysteine synthase A, O‑acetylserine sulfhydrolase A subunit
RA	2,560,317	A→C	7.7%	N21H (AAT→CAT)	yffL →	CPZ‑55 prophage; uncharacterized protein
RA	2,560,321	C→T	7.8%	A22V (GCT→GTT)	yffL →	CPZ‑55 prophage; uncharacterized protein
RA	2,560,326	A→G	8.3%	T24A (ACA→GCA)	yffL →	CPZ‑55 prophage; uncharacterized protein
RA	2,560,330	G→T	7.3%	C25F (TGC→TTC)	yffL →	CPZ‑55 prophage; uncharacterized protein
RA	2,572,483	G→T	5.4%	intergenic (‑33/+6)	eutM ← / ← eutD	ethanolamine utilization protein, putative carboxysome structural protein/phosphate acetyltransferase
RA	2,572,484	A→C	5.3%	intergenic (‑34/+5)	eutM ← / ← eutD	ethanolamine utilization protein, putative carboxysome structural protein/phosphate acetyltransferase
RA	2,575,647	C→G	7.7%	M53I (ATG→ATC)	eutS ←	putative ethanol utilization carboxysome structural protein
RA	2,581,762	G→A	6.1%	A339V (GCC→GTC)	ypfG ←	DUF1176 family protein
RA	2,581,765	T→C	5.3%	D338G (GAC→GGC)	ypfG ←	DUF1176 family protein
RA	2,636,286	G→T	5.6%	H357Q (CAC→CAA)	der ←	GTPase; multicopy suppressor of ftsJ
RA	2,636,291	A→C	5.4%	L356V (TTG→GTG)	der ←	GTPase; multicopy suppressor of ftsJ
RA	2,637,433	C→T	5.9%	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	5.7%	intergenic (‑83/+35)	der ← / ← bamB	GTPase; multicopy suppressor of ftsJ/BamABCDE complex OM biogenesis lipoprotein
RA	2,637,444	A→G	5.8%	intergenic (‑88/+30)	der ← / ← bamB	GTPase; multicopy suppressor of ftsJ/BamABCDE complex OM biogenesis lipoprotein
RA	2,640,666	A→C	6.6%	intergenic (‑91/+20)	hisS ← / ← ispG	histidyl tRNA synthetase/1‑hydroxy‑2‑methyl‑2‑(E)‑butenyl 4‑diphosphate synthase
RA	2,640,667	G→C	6.7%	intergenic (‑92/+19)	hisS ← / ← ispG	histidyl tRNA synthetase/1‑hydroxy‑2‑methyl‑2‑(E)‑butenyl 4‑diphosphate synthase
RA	2,640,668	G→T	7.0%	intergenic (‑93/+18)	hisS ← / ← ispG	histidyl tRNA synthetase/1‑hydroxy‑2‑methyl‑2‑(E)‑butenyl 4‑diphosphate synthase
RA	2,652,131	G→T	5.6%	P53T (CCG→ACG)	yfhM ←	bacterial alpha2‑macroglobulin colonization factor ECAM; anti‑host protease defense factor; periplasmic inner membrane‑anchored lipoprotein
RA	2,652,132	C→G	5.6%	V52V (GTG→GTC) ‡	yfhM ←	bacterial alpha2‑macroglobulin colonization factor ECAM; anti‑host protease defense factor; periplasmic inner membrane‑anchored lipoprotein
RA	2,652,133	A→C	5.7%	V52G (GTG→GGG) ‡	yfhM ←	bacterial alpha2‑macroglobulin colonization factor ECAM; anti‑host protease defense factor; periplasmic inner membrane‑anchored lipoprotein
RA	2,653,104	G→C	7.5%	W204S (TGG→TCG) ‡	sseA →	3‑mercaptopyruvate sulfurtransferase
RA	2,653,105	G→C	7.5%	W204C (TGG→TGC) ‡	sseA →	3‑mercaptopyruvate sulfurtransferase
RA	2,653,367	G→A	11.2%	intergenic (+28/‑488)	sseA → / → ryfA	3‑mercaptopyruvate sulfurtransferase/novel sRNA, function unknown
RA	2,653,372	T→C	12.8%	intergenic (+33/‑483)	sseA → / → ryfA	3‑mercaptopyruvate sulfurtransferase/novel sRNA, function unknown
RA	2,672,639	A→C	5.8%	Q198P (CAG→CCG) ‡	hcaD →	phenylpropionate dioxygenase, ferredoxin reductase subunit
RA	2,672,640	G→T	5.8%	Q198H (CAG→CAT) ‡	hcaD →	phenylpropionate dioxygenase, ferredoxin reductase subunit
RA	2,673,783	G→A	7.6%	intergenic (+15/+33)	yphA → / ← yphB	DoxX family inner membrane protein/mutarotase superfamily protein, YphB family
RA	2,673,784	C→A	7.3%	intergenic (+16/+32)	yphA → / ← yphB	DoxX family inner membrane protein/mutarotase superfamily protein, YphB family
RA	2,673,790	G→T	8.7%	intergenic (+22/+26)	yphA → / ← yphB	DoxX family inner membrane protein/mutarotase superfamily protein, YphB family
RA	2,673,791	A→C	8.9%	intergenic (+23/+25)	yphA → / ← yphB	DoxX family inner membrane protein/mutarotase superfamily protein, YphB family
RA	2,673,797	T→G	9.7%	intergenic (+29/+19)	yphA → / ← yphB	DoxX family inner membrane protein/mutarotase superfamily protein, YphB family
RA	2,673,798	T→C	8.6%	intergenic (+30/+18)	yphA → / ← yphB	DoxX family inner membrane protein/mutarotase superfamily protein, YphB family
RA	2,684,192	A→G	5.7%	intergenic (+136/+62)	yphH → / ← glyA	putative DNA‑binding transcriptional regulator/serine hydroxymethyltransferase
RA	2,684,193	A→C	5.7%	intergenic (+137/+61)	yphH → / ← glyA	putative DNA‑binding transcriptional regulator/serine hydroxymethyltransferase
RA	2,684,199	T→G	5.8%	intergenic (+143/+55)	yphH → / ← glyA	putative DNA‑binding transcriptional regulator/serine hydroxymethyltransferase
RA	2,684,200	C→A	5.8%	intergenic (+144/+54)	yphH → / ← glyA	putative DNA‑binding transcriptional regulator/serine hydroxymethyltransferase
RA	2,684,206	G→T	5.9%	intergenic (+150/+48)	yphH → / ← glyA	putative DNA‑binding transcriptional regulator/serine hydroxymethyltransferase
RA	2,684,207	C→T	5.9%	intergenic (+151/+47)	yphH → / ← glyA	putative DNA‑binding transcriptional regulator/serine hydroxymethyltransferase
RA	2,716,030	T→G	10.0%	intergenic (+20/+36)	eamB → / ← grcA	cysteine and O‑acetylserine exporter/autonomous glycyl radical cofactor
RA	2,716,033	C→A	8.6%	intergenic (+23/+33)	eamB → / ← grcA	cysteine and O‑acetylserine exporter/autonomous glycyl radical cofactor
RA	2,724,095	C→A	9.7%	intergenic (+13/‑33)	pssA → / → yfiM	phosphatidylserine synthase; CDP‑diacylglycerol‑serine O‑phosphatidyltransferase/putative lipoprotein
RA	2,724,097	T→A	8.7%	intergenic (+15/‑31)	pssA → / → yfiM	phosphatidylserine synthase; CDP‑diacylglycerol‑serine O‑phosphatidyltransferase/putative lipoprotein
RA	2,724,099	T→G	8.6%	intergenic (+17/‑29)	pssA → / → yfiM	phosphatidylserine synthase; CDP‑diacylglycerol‑serine O‑phosphatidyltransferase/putative lipoprotein
RA	2,724,412	A→T	8.6%	A95A (GCA→GCT)	yfiM →	putative lipoprotein
RA	2,724,413	A→T	8.6%	S96C (AGC→TGC)	yfiM →	putative lipoprotein
RA	2,729,465	G→A	8.0%	intergenic (‑21/+151)	gltW ← / ← rrsG	tRNA‑Glu/16S ribosomal RNA of rrnG operon
RA	2,729,466	T→A	7.8%	intergenic (‑22/+150)	gltW ← / ← rrsG	tRNA‑Glu/16S ribosomal RNA of rrnG operon
RA	2,729,467	T→C	7.8%	intergenic (‑23/+149)	gltW ← / ← rrsG	tRNA‑Glu/16S ribosomal RNA of rrnG operon
RA	2,731,580	C→T	5.8%	intergenic (‑423/+20)	rrsG ← / ← clpB	16S ribosomal RNA of rrnG operon/protein disaggregation chaperone
RA	2,731,581	G→T	5.3%	intergenic (‑424/+19)	rrsG ← / ← clpB	16S ribosomal RNA of rrnG operon/protein disaggregation chaperone
RA	2,731,582	A→C	5.3%	intergenic (‑425/+18)	rrsG ← / ← clpB	16S ribosomal RNA of rrnG operon/protein disaggregation chaperone
RA	2,731,583	A→G	5.3%	intergenic (‑426/+17)	rrsG ← / ← clpB	16S ribosomal RNA of rrnG operon/protein disaggregation chaperone
RA	2,737,707	C→T	5.1%	intergenic (+61/‑38)	pheL → / → pheA	pheA gene leader peptide/chorismate mutase and prephenate dehydratase, P‑protein
RA	2,750,073	G→T	8.0%	intergenic (+13/+42)	yfjD → / ← grpE	UPF0053 family inner membrane protein/heat shock protein
RA	2,750,078	T→G	9.9%	intergenic (+18/+37)	yfjD → / ← grpE	UPF0053 family inner membrane protein/heat shock protein
RA	2,750,081	C→A	9.6%	intergenic (+21/+34)	yfjD → / ← grpE	UPF0053 family inner membrane protein/heat shock protein
RA	2,750,086	A→C	7.4%	intergenic (+26/+29)	yfjD → / ← grpE	UPF0053 family inner membrane protein/heat shock protein
RA	2,753,986	A→T	7.4%	intergenic (+40/+22)	bamE → / ← ratB	lipoprotein component of BamABCDE OM biogenesis complex/UPF0125 family protein
RA	2,796,375	T→A	6.7%	I138F (ATT→TTT)	ygaU ←	uncharacterized protein
RA	2,800,515	C→A	10.1%	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	10.1%	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	10.2%	intergenic (+44/‑204)	ygaM → / → nrdH	putative membrane‑anchored DUF883 family ribosome‑binding protein/hydrogen donor for NrdEF electron transport system; glutaredoxin‑like protein
RA	2,801,056	A→T	5.7%	N31I (AAT→ATT)	nrdI →	NrdEF cluster assembly flavodoxin
RA	2,810,872	C→T	5.4%	H35Y (CAC→TAC) ‡	mprA →	transcriptional repressor of microcin B17 synthesis and multidrug efflux
RA	2,810,873	A→G	5.4%	H35R (CAC→CGC) ‡	mprA →	transcriptional repressor of microcin B17 synthesis and multidrug efflux
RA	2,814,860	A→G	7.0%	noncoding (59/78 nt)	micA →	sRNA antisense regulator of ompA, lamB, ompX, and phoP; Hfq‑dependent
RA	2,814,861	C→T	6.7%	noncoding (60/78 nt)	micA →	sRNA antisense regulator of ompA, lamB, ompX, and phoP; Hfq‑dependent
RA	2,817,977	A→T	8.1%	intergenic (‑117/+82)	argQ ← / ← argZ	tRNA‑Arg/tRNA‑Arg
RA	2,817,978	A→T	8.8%	intergenic (‑118/+81)	argQ ← / ← argZ	tRNA‑Arg/tRNA‑Arg
RA	2,860,736	C→G	5.4%	D167H (GAT→CAT)	ygbI ←	DeoR family putative transcriptional regulator
RA	2,860,738	A→T	5.5%	I166N (ATT→AAT)	ygbI ←	DeoR family putative transcriptional regulator
RA	2,860,740	C→G	5.7%	M165I (ATG→ATC)	ygbI ←	DeoR family putative transcriptional regulator
RA	2,866,487	G→C	9.7%	intergenic (+22/+72)	ygbN → / ← rpoS	putative transporter/RNA polymerase, sigma S (sigma 38) factor
RA	2,866,488	G→C	9.6%	intergenic (+23/+71)	ygbN → / ← rpoS	putative transporter/RNA polymerase, sigma S (sigma 38) factor
RA	2,873,915	A→G	9.4%	H26H (CAT→CAC) ‡	cysC ←	adenosine 5'‑phosphosulfate kinase
RA	2,873,917	G→C	9.4%	H26D (CAT→GAT) ‡	cysC ←	adenosine 5'‑phosphosulfate kinase
RA	2,873,919	C→T	9.7%	G25D (GGT→GAT)	cysC ←	adenosine 5'‑phosphosulfate kinase
RA	2,893,400	G→A	9.2%	L248L (CTG→CTA)	ygcN →	putative oxidoreductase
RA	2,900,322	C→T	5.4%	intergenic (‑49/‑270)	ygcW ← / → yqcE	putative SDR family oxidoreductase/putative MFS transporter, inner membrane protein
RA	2,900,324	G→T	5.6%	intergenic (‑51/‑268)	ygcW ← / → yqcE	putative SDR family oxidoreductase/putative MFS transporter, inner membrane protein
RA	2,900,327	A→C	6.1%	intergenic (‑54/‑265)	ygcW ← / → yqcE	putative SDR family oxidoreductase/putative MFS transporter, inner membrane protein
RA	2,971,146	T→C	5.4%	intergenic (+13/‑125)	ygdQ → / → ygdR	UPF0053 family inner membrane protein/DUF903 family verified lipoprotein
RA	2,971,154	G→A	5.0%	intergenic (+21/‑117)	ygdQ → / → ygdR	UPF0053 family inner membrane protein/DUF903 family verified lipoprotein
RA	2,971,159	G→A	5.2%	intergenic (+26/‑112)	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	5.4%	intergenic (‑109/+20)	ygeA ← / ← araE	Asp/Glu_racemase family protein/arabinose transporter
RA	2,980,746	C→T	6.4%	intergenic (‑111/+18)	ygeA ← / ← araE	Asp/Glu_racemase family protein/arabinose transporter
RA	2,987,103	C→T	5.5%	intergenic (+27/‑433)	yqeG → / → yqeH	putative transporter/putative LuxR family transcriptional regulator
RA	2,987,104	T→A	5.5%	intergenic (+28/‑432)	yqeG → / → yqeH	putative transporter/putative LuxR family transcriptional regulator
RA	2,987,105	A→G	5.3%	intergenic (+29/‑431)	yqeG → / → yqeH	putative transporter/putative LuxR family transcriptional regulator
RA	3,020,510	G→T	8.0%	intergenic (+21/‑30)	ssnA → / → ygfM	putative chlorohydrolase/aminohydrolase/putative oxidoreductase
RA	3,020,511	C→G	8.1%	intergenic (+22/‑29)	ssnA → / → ygfM	putative chlorohydrolase/aminohydrolase/putative oxidoreductase
RA	3,020,512	A→C	8.4%	intergenic (+23/‑28)	ssnA → / → ygfM	putative chlorohydrolase/aminohydrolase/putative oxidoreductase
RA	3,035,479	G→A	5.5%	T268I (ACC→ATC) ‡	prfB ←	peptide chain release factor RF‑2
RA	3,035,480	T→C	5.5%	T268A (ACC→GCC) ‡	prfB ←	peptide chain release factor RF‑2
RA	3,042,403	A→T	9.0%	intergenic (+110/+86)	ygfZ → / ← yqfA	iron‑sulfur cluster repair protein, plumbagin resistance/hemolysin III family HylIII inner membrane protein
RA	3,042,404	A→C	9.0%	intergenic (+111/+85)	ygfZ → / ← yqfA	iron‑sulfur cluster repair protein, plumbagin resistance/hemolysin III family HylIII inner membrane protein
RA	3,042,410	T→G	9.1%	intergenic (+117/+79)	ygfZ → / ← yqfA	iron‑sulfur cluster repair protein, plumbagin resistance/hemolysin III family HylIII inner membrane protein
RA	3,042,411	C→A	8.9%	intergenic (+118/+78)	ygfZ → / ← yqfA	iron‑sulfur cluster repair protein, plumbagin resistance/hemolysin III family HylIII inner membrane protein
RA	3,057,140	A→G	7.7%	intergenic (+152/+38)	sibC → / ← serA	sRNA antisense regulator of toxic IbsC protein/D‑3‑phosphoglycerate dehydrogenase
RA	3,057,145	G→C	8.3%	intergenic (+157/+33)	sibC → / ← serA	sRNA antisense regulator of toxic IbsC protein/D‑3‑phosphoglycerate dehydrogenase
RA	3,057,150	C→T	8.5%	intergenic (+162/+28)	sibC → / ← serA	sRNA antisense regulator of toxic IbsC protein/D‑3‑phosphoglycerate dehydrogenase
RA	3,059,703	A→T	5.0%	intergenic (‑2/‑50)	yqfE ← / → argP	pseudogene, LysR family/transcriptional regulator for arginine transport and DNA replication genes; replication initiation inhibitor
RA	3,059,704	A→T	5.0%	intergenic (‑3/‑49)	yqfE ← / → argP	pseudogene, LysR family/transcriptional regulator for arginine transport and DNA replication genes; replication initiation inhibitor
RA	3,061,036	C→A	6.2%	P63T (CCG→ACG)	scpA →	methylmalonyl‑CoA mutase
RA	3,061,041	T→G	6.7%	R64R (CGT→CGG)	scpA →	methylmalonyl‑CoA mutase
RA	3,061,817	G→C	9.5%	W323S (TGG→TCG) ‡	scpA →	methylmalonyl‑CoA mutase
RA	3,061,818	G→C	9.5%	W323C (TGG→TGC) ‡	scpA →	methylmalonyl‑CoA mutase
RA	3,079,615	C→T	5.2%	intergenic (‑285/+29)	cmtB ← / ← tktA	putative mannitol‑specific enzyme IIA component of PTS/transketolase 1, thiamine triphosphate‑binding
RA	3,090,226	T→C	5.2%	C158R (TGC→CGC)	yggI →	Zn‑dependent metalloprotease‑related protein
RA	3,090,229	G→A	6.1%	G159S (GGT→AGT)	yggI →	Zn‑dependent metalloprotease‑related protein
RA	3,098,515	G→C	7.6%	intergenic (+112/+43)	yggW → / ← yggM	HemN family putative oxidoreductase/DUF1202 family putative secreted protein
RA	3,098,518	C→T	7.6%	intergenic (+115/+40)	yggW → / ← yggM	HemN family putative oxidoreductase/DUF1202 family putative secreted protein
RA	3,098,519	A→G	7.5%	intergenic (+116/+39)	yggW → / ← yggM	HemN family putative oxidoreductase/DUF1202 family putative secreted protein
RA	3,098,522	G→C	7.7%	intergenic (+119/+36)	yggW → / ← yggM	HemN family putative oxidoreductase/DUF1202 family putative secreted protein
RA	3,156,590	C→A	7.5%	intergenic (+72/‑33)	yqhD → / → dkgA	aldehyde reductase, NADPH‑dependent/2,5‑diketo‑D‑gluconate reductase A
RA	3,156,591	T→G	7.4%	intergenic (+73/‑32)	yqhD → / → dkgA	aldehyde reductase, NADPH‑dependent/2,5‑diketo‑D‑gluconate reductase A
RA	3,180,505	G→T	7.1%	E29* (GAG→TAG) ‡	ygiC →	ATP‑Grasp family ATPase
RA	3,180,506	A→C	7.2%	E29A (GAG→GCG) ‡	ygiC →	ATP‑Grasp family ATPase
RA	3,183,345:1	+T	9.4%	intergenic (+22/+468)	zupT → / ← ribB	zinc transporter/3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase
RA	3,183,350	Δ1 bp	9.2%	intergenic (+27/+463)	zupT → / ← ribB	zinc transporter/3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase
RA	3,234,508	T→C	5.1%	intergenic (‑53/+231)	higB ← / ← rlmG	mRNA interferase toxin of the HigB‑HigA toxin‑antitoxin system/23S rRNA m(2)G1835 methyltransferase, SAM‑dependent
RA	3,239,609	T→G	7.9%	intergenic (+64/‑335)	alx → / → sstT	putative membrane‑bound redox modulator/sodium:serine/threonine symporter
RA	3,239,610	C→G	7.7%	intergenic (+65/‑334)	alx → / → sstT	putative membrane‑bound redox modulator/sodium:serine/threonine symporter
RA	3,239,611	C→A	7.7%	intergenic (+66/‑333)	alx → / → sstT	putative membrane‑bound redox modulator/sodium:serine/threonine symporter
RA	3,256,434	A→G	6.5%	M73T (ATG→ACG)	yhaM ←	putative L‑serine dehydratase alpha chain
RA	3,256,441	T→G	8.2%	T71P (ACG→CCG)	yhaM ←	putative L‑serine dehydratase alpha chain
RA	3,256,442	G→C	7.5%	G70G (GGC→GGG) ‡	yhaM ←	putative L‑serine dehydratase alpha chain
RA	3,256,443	C→A	8.2%	G70V (GGC→GTC) ‡	yhaM ←	putative L‑serine dehydratase alpha chain
RA	3,256,450	C→T	7.1%	V68I (GTT→ATT)	yhaM ←	putative L‑serine dehydratase alpha chain
RA	3,276,890	G→A	5.2%	intergenic (+37/‑112)	garD → / → prlF	D‑galactarate dehydrogenase/antitoxin of the SohA(PrlF)‑YhaV toxin‑antitoxin system
RA	3,282,927	A→G	5.7%	I318V (ATC→GTC) ‡	agaS →	tagatose‑6‑phosphate ketose/aldose isomerase
RA	3,282,928	T→A	5.7%	I318N (ATC→AAC) ‡	agaS →	tagatose‑6‑phosphate ketose/aldose isomerase
RA	3,282,929	C→T	5.7%	I318I (ATC→ATT) ‡	agaS →	tagatose‑6‑phosphate ketose/aldose isomerase
RA	3,288,032	C→A	6.5%	intergenic (+22/‑58)	yraH → / → yraI	putative fimbrial‑like adhesin protein/putative periplasmic pilin chaperone
RA	3,288,033	T→G	6.7%	intergenic (+23/‑57)	yraH → / → yraI	putative fimbrial‑like adhesin protein/putative periplasmic pilin chaperone
RA	3,309,004	C→T	5.5%	intergenic (‑80/+29)	nlpI ← / ← pnp	lipoprotein involved in osmotic sensitivity and filamentation/polynucleotide phosphorylase/polyadenylase
RA	3,309,009	C→T	5.4%	intergenic (‑85/+24)	nlpI ← / ← pnp	lipoprotein involved in osmotic sensitivity and filamentation/polynucleotide phosphorylase/polyadenylase
RA	3,309,012	A→G	6.3%	intergenic (‑88/+21)	nlpI ← / ← pnp	lipoprotein involved in osmotic sensitivity and filamentation/polynucleotide phosphorylase/polyadenylase
RA	3,313,207	G→A	6.9%	intergenic (‑29/+135)	rbfA ← / ← infB	30s ribosome binding factor/translation initiation factor IF‑2
RA	3,313,208	T→A	6.7%	intergenic (‑30/+134)	rbfA ← / ← infB	30s ribosome binding factor/translation initiation factor IF‑2
RA	3,313,209	T→C	6.7%	intergenic (‑31/+133)	rbfA ← / ← infB	30s ribosome binding factor/translation initiation factor IF‑2
RA	3,324,952	A→G	5.8%	intergenic (‑41/+49)	folP ← / ← ftsH	7,8‑dihydropteroate synthase/protease, ATP‑dependent zinc‑metallo
RA	3,324,955	A→G	5.6%	intergenic (‑44/+46)	folP ← / ← ftsH	7,8‑dihydropteroate synthase/protease, ATP‑dependent zinc‑metallo
RA	3,324,956	C→T	5.5%	intergenic (‑45/+45)	folP ← / ← ftsH	7,8‑dihydropteroate synthase/protease, ATP‑dependent zinc‑metallo
RA	3,324,959	C→T	5.9%	intergenic (‑48/+42)	folP ← / ← ftsH	7,8‑dihydropteroate synthase/protease, ATP‑dependent zinc‑metallo
RA	3,328,182	A→T	7.7%	intergenic (+99/+57)	yhbY → / ← greA	RNA binding protein associated with pre‑50S ribosomal subunits/transcript cleavage factor
RA	3,328,183	T→A	7.7%	intergenic (+100/+56)	yhbY → / ← greA	RNA binding protein associated with pre‑50S ribosomal subunits/transcript cleavage factor
RA	3,328,184	A→T	7.8%	intergenic (+101/+55)	yhbY → / ← greA	RNA binding protein associated with pre‑50S ribosomal subunits/transcript cleavage factor
RA	3,331,979	T→C	8.2%	T253A (ACG→GCG)	yhbE ←	EamA family inner membrane putative transporter
RA	3,331,983	G→C	8.2%	I251M (ATC→ATG)	yhbE ←	EamA family inner membrane putative transporter
RA	3,331,987	G→A	8.6%	A250V (GCG→GTG)	yhbE ←	EamA family inner membrane putative transporter
RA	3,332,822	G→A	11.9%	intergenic (‑87/+40)	yhbE ← / ← rpmA	EamA family inner membrane putative transporter/50S ribosomal subunit protein L27
RA	3,332,823	T→C	11.9%	intergenic (‑88/+39)	yhbE ← / ← rpmA	EamA family inner membrane putative transporter/50S ribosomal subunit protein L27
RA	3,333,050	T→A	5.6%	K24* (AAG→TAG)	rpmA ←	50S ribosomal subunit protein L27
RA	3,333,057	C→T	9.6%	L21L (CTG→CTA) ‡	rpmA ←	50S ribosomal subunit protein L27
RA	3,333,058	A→G	8.2%	L21P (CTG→CCG) ‡	rpmA ←	50S ribosomal subunit protein L27
RA	3,334,703	A→G	10.8%	intergenic (+22/‑206)	ispB → / → sfsB	octaprenyl diphosphate synthase/malPQ operon transcriptional activator
RA	3,334,704	G→C	11.0%	intergenic (+23/‑205)	ispB → / → sfsB	octaprenyl diphosphate synthase/malPQ operon transcriptional activator
RA	3,334,705	C→T	11.8%	intergenic (+24/‑204)	ispB → / → sfsB	octaprenyl diphosphate synthase/malPQ operon transcriptional activator
RA	3,339,813	T→C	7.8%	K85E (AAA→GAA)	mlaF ←	ABC transporter maintaining OM lipid asymmetry, ATP‑binding protein
RA	3,339,818	Δ1 bp	6.7%	coding (248/810 nt)	mlaF ←	ABC transporter maintaining OM lipid asymmetry, ATP‑binding protein
RA	3,339,828:1	+T	8.0%	coding (238/810 nt)	mlaF ←	ABC transporter maintaining OM lipid asymmetry, ATP‑binding protein
RA	3,339,833	G→A	5.3%	S78L (TCG→TTG)	mlaF ←	ABC transporter maintaining OM lipid asymmetry, ATP‑binding protein
RA	3,354,537	C→G	8.9%	intergenic (‑487/‑188)	yhcC ← / → gltB	putative Fe‑S oxidoreductase, Radical SAM superfamily protein/glutamate synthase, large subunit
RA	3,360,643	T→A	11.0%	intergenic (+27/‑533)	gltD → / → gltF	glutamate synthase, 4Fe‑4S protein, small subunit/periplasmic protein
RA	3,360,644	G→C	11.2%	intergenic (+28/‑532)	gltD → / → gltF	glutamate synthase, 4Fe‑4S protein, small subunit/periplasmic protein
RA	3,360,645	T→A	11.0%	intergenic (+29/‑531)	gltD → / → gltF	glutamate synthase, 4Fe‑4S protein, small subunit/periplasmic protein
RA	3,368,982	G→C	5.6%	intergenic (+28/+32)	yhcG → / ← yhcH	DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily/DUF386 family protein, cupin superfamily
RA	3,418,628	G→A	5.5%	intergenic (+17/‑414)	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	3,418,629	T→C	5.6%	intergenic (+18/‑413)	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	3,439,588	G→C	7.6%	intergenic (‑79/+28)	yhdN ← / ← rplQ	DUF1992 family protein/50S ribosomal subunit protein L17
RA	3,439,589	G→C	7.5%	intergenic (‑80/+27)	yhdN ← / ← rplQ	DUF1992 family protein/50S ribosomal subunit protein L17
RA	3,453,174	C→T	5.2%	G33S (GGT→AGT)	rpsJ ←	30S ribosomal subunit protein S10
RA	3,453,175	A→G	5.2%	T32T (ACT→ACC)	rpsJ ←	30S ribosomal subunit protein S10
RA	3,458,416	T→A	5.4%	I26I (ATT→ATA)	gspE →	general secretory pathway component, cryptic
RA	3,458,418	T→A	5.5%	I27N (ATT→AAT)	gspE →	general secretory pathway component, cryptic
RA	3,458,420	T→A	5.4%	Y28N (TAT→AAT)	gspE →	general secretory pathway component, cryptic
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	3,476,585	G→A	7.5%	intergenic (‑145/+22)	yheO ← / ← fkpA	putative PAS domain‑containing DNA‑binding transcriptional regulator/FKBP‑type peptidyl‑prolyl cis‑trans isomerase (rotamase)
RA	3,476,586	T→C	7.8%	intergenic (‑146/+21)	yheO ← / ← fkpA	putative PAS domain‑containing DNA‑binding transcriptional regulator/FKBP‑type peptidyl‑prolyl cis‑trans isomerase (rotamase)
RA	3,477,878	T→A	6.6%	intergenic (+20/+29)	slyX → / ← slyD	phi X174 lysis protein/FKBP‑type peptidyl prolyl cis‑trans isomerase (rotamase)
RA	3,480,662	T→A	5.7%	H167L (CAC→CTC)	kefG ←	potassium‑efflux system ancillary protein for KefB, glutathione‑regulated
RA	3,480,664	G→C	5.6%	S166R (AGC→AGG) ‡	kefG ←	potassium‑efflux system ancillary protein for KefB, glutathione‑regulated
RA	3,480,666	T→A	5.6%	S166C (AGC→TGC) ‡	kefG ←	potassium‑efflux system ancillary protein for KefB, glutathione‑regulated
RA	3,486,771	T→C	5.8%	intergenic (+19/‑20)	crp → / → yhfK	cAMP‑activated global transcription factor, mediator of catabolite repression/putative transporter, FUSC superfamily inner membrane protein
RA	3,486,776	T→A	7.1%	intergenic (+24/‑15)	crp → / → yhfK	cAMP‑activated global transcription factor, mediator of catabolite repression/putative transporter, FUSC superfamily inner membrane protein
RA	3,504,875	T→G	5.7%	intergenic (+92/+60)	frlR → / ← yhfS	putative DNA‑binding transcriptional regulator/FNR‑regulated pyridoxal phosphate‑dependent aminotransferase family protein
RA	3,504,880	A→T	7.6%	intergenic (+97/+55)	frlR → / ← yhfS	putative DNA‑binding transcriptional regulator/FNR‑regulated pyridoxal phosphate‑dependent aminotransferase family protein
RA	3,504,881	A→T	7.7%	intergenic (+98/+54)	frlR → / ← yhfS	putative DNA‑binding transcriptional regulator/FNR‑regulated pyridoxal phosphate‑dependent aminotransferase family protein
RA	3,504,882	A→T	7.7%	intergenic (+99/+53)	frlR → / ← yhfS	putative DNA‑binding transcriptional regulator/FNR‑regulated pyridoxal phosphate‑dependent aminotransferase family protein
RA	3,504,887	C→A	7.5%	intergenic (+104/+48)	frlR → / ← yhfS	putative DNA‑binding transcriptional regulator/FNR‑regulated pyridoxal phosphate‑dependent aminotransferase family protein
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	3,563,539	T→C	6.9%	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	7.5%	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	7.5%	intergenic (+29/+240)	glpD → / ← yzgL	sn‑glycerol‑3‑phosphate dehydrogenase, aerobic, FAD/NAD(P)‑binding/pseudogene, periplasmic solute binding protein homology
RA	3,577,657	A→G	5.2%	intergenic (‑65/+74)	gntK ← / ← gntR	gluconate kinase 2/d‑gluconate inducible gluconate regulon transcriptional repressor
RA	3,577,660	C→T	5.2%	intergenic (‑68/+71)	gntK ← / ← gntR	gluconate kinase 2/d‑gluconate inducible gluconate regulon transcriptional repressor
RA	3,648,273	C→G	7.2%	intergenic (+127/‑21)	agrA → / → agrB	inactive antisense sRNA/antisense sRNA antitoxin for the DinQ toxin
RA	3,657,599	T→A	12.4%	intergenic (+32/+387)	hdeD → / ← arrS	acid‑resistance membrane protein/antisense sRNA ArrS, function unknown
RA	3,657,601	G→C	12.0%	intergenic (+34/+385)	hdeD → / ← arrS	acid‑resistance membrane protein/antisense sRNA ArrS, function unknown
RA	3,657,603	T→A	13.1%	intergenic (+36/+383)	hdeD → / ← arrS	acid‑resistance membrane protein/antisense sRNA ArrS, function unknown
RA	3,676,271	A→T	6.3%	intergenic (+163/+19)	yhjE → / ← yhjG	putative MFS transporter; membrane protein/putative inner membrane‑anchored periplasmic AsmA family protein
RA	3,693,752	A→T	5.1%	I495I (ATT→ATA)	bcsA ←	cellulose synthase, catalytic subunit
RA	3,693,755	A→T	5.2%	R494R (CGT→CGA)	bcsA ←	cellulose synthase, catalytic subunit
RA	3,697,969	C→G	5.5%	H504Q (CAC→CAG)	bcsE →	cellulose production protein
RA	3,702,835	G→A	5.3%	L12L (CTG→TTG)	dppF ←	dipeptide/heme ABC transporter ATPas
RA	3,702,837	G→C	5.5%	P11R (CCG→CGG)	dppF ←	dipeptide/heme ABC transporter ATPas
RA	3,702,839	T→C	5.8%	Q10Q (CAA→CAG)	dppF ←	dipeptide/heme ABC transporter ATPas
RA	3,708,595	G→A	5.6%	intergenic (‑890/+21)	dppA ← / ← proK	dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro
RA	3,708,596	T→A	5.5%	intergenic (‑891/+20)	dppA ← / ← proK	dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro
RA	3,708,597	T→C	5.5%	intergenic (‑892/+19)	dppA ← / ← proK	dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro
RA	3,714,163:1	+T	7.2%	coding (2232/2334 nt)	bisC ←	biotin sulfoxide reductase
RA	3,714,168	Δ1 bp	6.7%	coding (2227/2334 nt)	bisC ←	biotin sulfoxide reductase
RA	3,720,300	T→A	5.1%	intergenic (+39/+148)	cspA → / ← hokA	RNA chaperone and antiterminator, cold‑inducible/toxic polypeptide, small
RA	3,722,300	G→T	5.2%	intergenic (+195/+28)	sokA → / ← glyS	pseudogene, sRNA antisense regulator blocking mokA/hokA translation/glycine tRNA synthetase, beta subunit
RA	3,722,301	A→C	5.2%	intergenic (+196/+27)	sokA → / ← glyS	pseudogene, sRNA antisense regulator blocking mokA/hokA translation/glycine tRNA synthetase, beta subunit
RA	3,774,207	C→T	6.5%	intergenic (+13/‑217)	mtlA → / → mtlD	mannitol‑specific PTS enzyme: IIA, IIB and IIC components/mannitol‑1‑phosphate dehydrogenase, NAD‑dependent
RA	3,774,214	C→T	6.6%	intergenic (+20/‑210)	mtlA → / → mtlD	mannitol‑specific PTS enzyme: IIA, IIB and IIC components/mannitol‑1‑phosphate dehydrogenase, NAD‑dependent
RA	3,774,215	A→G	6.7%	intergenic (+21/‑209)	mtlA → / → mtlD	mannitol‑specific PTS enzyme: IIA, IIB and IIC components/mannitol‑1‑phosphate dehydrogenase, NAD‑dependent
RA	3,774,222	A→G	6.8%	intergenic (+28/‑202)	mtlA → / → mtlD	mannitol‑specific PTS enzyme: IIA, IIB and IIC components/mannitol‑1‑phosphate dehydrogenase, NAD‑dependent
RA	3,781,051	C→G	8.7%	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	7.1%	intergenic (‑219/+20)	waaH ← / ← tdh	LPS(HepIII)‑glucuronic acid glycosyltransferase/L‑threonine 3‑dehydrogenase, NAD(P)‑binding
RA	3,790,303	A→T	7.1%	intergenic (‑222/+17)	waaH ← / ← tdh	LPS(HepIII)‑glucuronic acid glycosyltransferase/L‑threonine 3‑dehydrogenase, NAD(P)‑binding
RA	3,814,164	G→A	5.2%	G78D (GGT→GAT)	dut →	deoxyuridinetriphosphatase
RA	3,832,797	T→G	5.0%	N581H (AAC→CAC)	yicI ←	putative alpha‑glucosidase
RA	3,832,800	C→A	5.0%	A580S (GCG→TCG)	yicI ←	putative alpha‑glucosidase
RA	3,878,894	T→A	5.2%	D409V (GAC→GTC)	gyrB ←	DNA gyrase, subunit B
RA	3,891,502	C→G	5.7%	intergenic (+19/‑113)	tnaB → / → mdtL	tryptophan transporter of low affinity/multidrug efflux system protein
RA	3,891,504	T→A	5.5%	intergenic (+21/‑111)	tnaB → / → mdtL	tryptophan transporter of low affinity/multidrug efflux system protein
RA	3,891,506	C→G	5.6%	intergenic (+23/‑109)	tnaB → / → mdtL	tryptophan transporter of low affinity/multidrug efflux system protein
RA	3,947,332	A→T	5.9%	A212A (GCT→GCA)	hdfR ←	flhDC operon transcriptional repressor
RA	3,947,335	A→T	5.9%	S211S (TCT→TCA)	hdfR ←	flhDC operon transcriptional repressor
RA	3,959,515	T→A	11.5%	intergenic (+70/+17)	ilvC → / ← ppiC	ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C)
RA	3,963,415	A→C	6.9%	L272R (CTG→CGG) ‡	gpp ←	guanosine pentaphosphatase/exopolyphosphatase
RA	3,963,416	G→T	7.0%	L272M (CTG→ATG) ‡	gpp ←	guanosine pentaphosphatase/exopolyphosphatase
RA	3,970,813	Δ1 bp	5.7%	coding (681/1131 nt)	wecB →	UDP‑N‑acetyl glucosamine‑2‑epimerase
RA	3,970,817:1	+G	5.7%	coding (685/1131 nt)	wecB →	UDP‑N‑acetyl glucosamine‑2‑epimerase
RA	3,972,673	A→C	5.5%	E51A (GAG→GCG) ‡	rffG →	dTDP‑glucose 4,6‑dehydratase
RA	3,972,674	G→T	5.0%	E51D (GAG→GAT) ‡	rffG →	dTDP‑glucose 4,6‑dehydratase
RA	3,981,102	T→A	7.3%	V72V (GTT→GTA)	yifK →	putative APC family amino acid transporter
RA	3,991,334	T→A	5.1%	I61N (ATT→AAT)	cyaA →	adenylate cyclase
RA	3,991,459	A→G	8.4%	S103G (AGC→GGC)	cyaA →	adenylate cyclase
RA	3,991,844	A→T	81.8%	D231V (GAT→GTT)	cyaA →	adenylate cyclase
RA	4,000,230	A→G	5.8%	intergenic (+85/+62)	uvrD → / ← yigE	DNA‑dependent ATPase I and helicase II/DUF2233 family protein
RA	4,000,231	G→C	6.1%	intergenic (+86/+61)	uvrD → / ← yigE	DNA‑dependent ATPase I and helicase II/DUF2233 family protein
RA	4,000,237	T→A	5.9%	intergenic (+92/+55)	uvrD → / ← yigE	DNA‑dependent ATPase I and helicase II/DUF2233 family protein
RA	4,000,238	T→A	5.9%	intergenic (+93/+54)	uvrD → / ← yigE	DNA‑dependent ATPase I and helicase II/DUF2233 family protein
RA	4,000,244	G→C	6.2%	intergenic (+99/+48)	uvrD → / ← yigE	DNA‑dependent ATPase I and helicase II/DUF2233 family protein
RA	4,000,245	C→T	6.2%	intergenic (+100/+47)	uvrD → / ← yigE	DNA‑dependent ATPase I and helicase II/DUF2233 family protein
RA	4,015,333	A→T	5.6%	intergenic (+19/+21)	metE → / ← ysgA	5‑methyltetrahydropteroyltriglutamate‑ homocysteine S‑methyltransferase/putative carboxymethylenebutenolidase
RA	4,056,038	T→G	6.4%	D101A (GAC→GCC) ‡	glnL ←	sensory histidine kinase in two‑component regulatory system with GlnG
RA	4,056,039	C→A	6.4%	D101Y (GAC→TAC) ‡	glnL ←	sensory histidine kinase in two‑component regulatory system with GlnG
RA	4,060,261	G→T	12.1%	intergenic (+31/‑186)	typA → / → yihL	GTP‑binding protein/putative DNA‑binding transcriptional regulator
RA	4,060,264	A→C	11.2%	intergenic (+34/‑183)	typA → / → yihL	GTP‑binding protein/putative DNA‑binding transcriptional regulator
RA	4,080,006	T→C	5.6%	intergenic (+37/+293)	yiiF → / ← fdhE	putative thymol sensitivity protein, CopG family putative transcriptional regulator/formate dehydrogenase formation protein
RA	4,080,009	G→A	5.8%	intergenic (+40/+290)	yiiF → / ← fdhE	putative thymol sensitivity protein, CopG family putative transcriptional regulator/formate dehydrogenase formation protein
RA	4,082,696	G→C	9.3%	Q22E (CAG→GAG)	fdoH ←	formate dehydrogenase‑O, Fe‑S subunit
RA	4,106,369	T→G	5.9%	intergenic (+49/‑100)	cpxP → / → fieF	inhibitor of the cpx response; periplasmic adaptor protein/ferrous iron and zinc transporter
RA	4,106,370	G→C	5.8%	intergenic (+50/‑99)	cpxP → / → fieF	inhibitor of the cpx response; periplasmic adaptor protein/ferrous iron and zinc transporter
RA	4,106,371	C→A	6.3%	intergenic (+51/‑98)	cpxP → / → fieF	inhibitor of the cpx response; periplasmic adaptor protein/ferrous iron and zinc transporter
RA	4,116,937	T→G	78.0%	K96Q (AAG→CAG)	glpK ←	glycerol kinase
RA	4,117,050	C→T	10.9%	S58N (AGC→AAC)	glpK ←	glycerol kinase
RA	4,117,168	C→T	5.2%	A19T (GCG→ACG)	glpK ←	glycerol kinase
RA	4,168,349	A→G	9.5%	intergenic (+149/‑23)	rrsB → / → gltT	16S ribosomal RNA of rrnB operon/tRNA‑Glu
RA	4,168,350	A→T	9.5%	intergenic (+150/‑22)	rrsB → / → gltT	16S ribosomal RNA of rrnB operon/tRNA‑Glu
RA	4,168,351	C→T	9.2%	intergenic (+151/‑21)	rrsB → / → gltT	16S ribosomal RNA of rrnB operon/tRNA‑Glu
RA	4,227,550	G→A	6.5%	intergenic (+39/‑181)	metH → / → yjbB	homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent/putative Na+/Pi‑cotransporter
RA	4,227,555	A→T	6.4%	intergenic (+44/‑176)	metH → / → yjbB	homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent/putative Na+/Pi‑cotransporter
RA	4,227,560	T→C	6.4%	intergenic (+49/‑171)	metH → / → yjbB	homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent/putative Na+/Pi‑cotransporter
RA	4,235,579	G→A	7.3%	intergenic (+172/‑327)	pgi → / → yjbE	glucosephosphate isomerase/extracellular polysaccharide production threonine‑rich protein
RA	4,235,581	T→A	7.4%	intergenic (+174/‑325)	pgi → / → yjbE	glucosephosphate isomerase/extracellular polysaccharide production threonine‑rich protein
RA	4,235,583	T→C	7.3%	intergenic (+176/‑323)	pgi → / → yjbE	glucosephosphate isomerase/extracellular polysaccharide production threonine‑rich protein
RA	4,261,358	T→A	5.9%	intergenic (+52/‑311)	yjbM → / → dusA	uncharacterized protein/tRNA‑dihydrouridine synthase A
RA	4,261,359	T→A	5.9%	intergenic (+53/‑310)	yjbM → / → dusA	uncharacterized protein/tRNA‑dihydrouridine synthase A
RA	4,262,250	G→C	6.3%	G194G (GGG→GGC)	dusA →	tRNA‑dihydrouridine synthase A
RA	4,262,255	G→C	6.4%	S196T (AGC→ACC)	dusA →	tRNA‑dihydrouridine synthase A
RA	4,270,142	G→A	5.7%	intergenic (+15/‑96)	aphA → / → yjbQ	acid phosphatase/phosphotransferase, class B, non‑specific/thiamine phosphate synthase
RA	4,270,144	G→C	5.7%	intergenic (+17/‑94)	aphA → / → yjbQ	acid phosphatase/phosphotransferase, class B, non‑specific/thiamine phosphate synthase
RA	4,270,146	T→C	5.9%	intergenic (+19/‑92)	aphA → / → yjbQ	acid phosphatase/phosphotransferase, class B, non‑specific/thiamine phosphate synthase
RA	4,273,361	T→A	8.6%	S171C (AGC→TGC)	uvrA ←	ATPase and DNA damage recognition protein of nucleotide excision repair excinuclease UvrABC
RA	4,273,362	T→A	8.6%	A170A (GCA→GCT)	uvrA ←	ATPase and DNA damage recognition protein of nucleotide excision repair excinuclease UvrABC
RA	4,295,809:1	+T	7.0%	intergenic (+15/+627)	gltP → / ← yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA	4,295,817	Δ1 bp	7.1%	intergenic (+23/+619)	gltP → / ← yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA	4,296,060	C→T	19.3%	intergenic (+266/+376)	gltP → / ← yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA	4,296,380:1	+CG	100%	intergenic (+586/+56)	gltP → / ← yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA	4,307,294	A→T	12.2%	L169Q (CTG→CAG)	alsK ←	D‑allose kinase
RA	4,307,298	G→A	12.7%	P168S (CCC→TCC)	alsK ←	D‑allose kinase
RA	4,314,233	A→T	5.2%	intergenic (+36/+111)	yjdP → / ← phnP	putative periplasmic protein/5‑phospho‑alpha‑D‑ribosyl 1,2‑cyclic phosphate phosphodiesterase
RA	4,315,437	A→T	5.3%	F34L (TTT→TTA) ‡	phnO ←	aminoalkylphosphonate N‑acetyltransferase
RA	4,315,438	A→T	5.3%	F34Y (TTT→TAT) ‡	phnO ←	aminoalkylphosphonate N‑acetyltransferase
RA	4,315,439	A→T	5.2%	F34I (TTT→ATT) ‡	phnO ←	aminoalkylphosphonate N‑acetyltransferase
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	6.1%	intergenic (‑65/+39)	eptA ← / ← adiC	lipid A phosphoethanolamine transferase/arginine:agmatine antiporter
RA	4,339,802	A→G	5.2%	A240A (GCT→GCC)	adiA ←	arginine decarboxylase
RA	4,347,285	C→G	5.3%	M14I (ATG→ATC)	fumB ←	anaerobic class I fumarate hydratase (fumarase B)
RA	4,353,171	C→G	5.5%	intergenic (+90/+29)	ghoT → / ← lysU	toxin of GhoTS toxin‑antitoxin pair; membrane‑lytic protein; stimulator of persister cell formation/lysine tRNA synthetase, inducible
RA	4,353,173	T→C	5.3%	intergenic (+92/+27)	ghoT → / ← lysU	toxin of GhoTS toxin‑antitoxin pair; membrane‑lytic protein; stimulator of persister cell formation/lysine tRNA synthetase, inducible
RA	4,356,445	A→T	9.4%	intergenic (‑34/+25)	dtpC ← / ← cadA	dipeptide and tripeptide permease/lysine decarboxylase, acid‑inducible
RA	4,356,446	A→T	9.4%	intergenic (‑35/+24)	dtpC ← / ← cadA	dipeptide and tripeptide permease/lysine decarboxylase, acid‑inducible
RA	4,362,528	G→A	6.6%	intergenic (‑175/+23)	yjdQ ← / ← pheU	pseudogene, P4‑like integrase remnant/tRNA‑Phe
RA	4,362,529	T→C	6.8%	intergenic (‑176/+22)	yjdQ ← / ← pheU	pseudogene, P4‑like integrase remnant/tRNA‑Phe
RA	4,366,854	T→G	7.5%	intergenic (‑81/+37)	dcuA ← / ← aspA	C4‑dicarboxylate antiporter/aspartate ammonia‑lyase
RA	4,366,855	C→A	7.6%	intergenic (‑82/+36)	dcuA ← / ← aspA	C4‑dicarboxylate antiporter/aspartate ammonia‑lyase
RA	4,371,931	G→T	6.9%	E303* (GAA→TAA) ‡	groL →	Cpn60 chaperonin GroEL, large subunit of GroESL
RA	4,371,932	A→C	7.3%	E303A (GAA→GCA) ‡	groL →	Cpn60 chaperonin GroEL, large subunit of GroESL
RA	4,376,280	G→A	5.8%	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	7.1%	intergenic (+26/‑26)	efp → / → ecnA	polyproline‑specific translation elongation factor EF‑P/entericidin A membrane lipoprotein, antidote entericidin B
RA	4,378,976	A→T	5.1%	intergenic (‑32/+31)	ampC ← / ← frdD	penicillin‑binding protein; beta‑lactamase, intrinsically weak/fumarate reductase (anaerobic), membrane anchor subunit
RA	4,381,389	G→T	5.0%	G310G (GGC→GGA)	frdA ←	anaerobic fumarate reductase catalytic and NAD/flavoprotein subunit
RA	4,381,396	G→C	5.7%	P308R (CCG→CGG)	frdA ←	anaerobic fumarate reductase catalytic and NAD/flavoprotein subunit
RA	4,392,617	C→G	10.6%	noncoding (35/76 nt)	glyY →	tRNA‑Gly
RA	4,398,580	G→A	11.5%	W390* (TGG→TAG)	mutL →	methyl‑directed mismatch repair protein
RA	4,410,034	G→A	5.4%	intergenic (+28/‑99)	rlmB → / → yjfI	23S rRNA mG2251 2'‑O‑ribose methyltransferase, SAM‑dependent/DUF2170 family protein
RA	4,418,263	G→C	5.6%	P64R (CCG→CGG) ‡	ulaR ←	transcriptional repressor for the L‑ascorbate utilization divergent operon
RA	4,418,264	G→C	5.4%	P64A (CCG→GCG) ‡	ulaR ←	transcriptional repressor for the L‑ascorbate utilization divergent operon
RA	4,422,895	C→G	7.3%	A17G (GCC→GGC)	ulaE →	L‑xylulose 5‑phosphate 3‑epimerase
RA	4,422,903	T→C	6.5%	C20R (TGC→CGC)	ulaE →	L‑xylulose 5‑phosphate 3‑epimerase
RA	4,470,951	A→C	9.2%	intergenic (‑38/+35)	ridA ← / ← pyrI	enamine/imine deaminase, reaction intermediate detoxification/aspartate carbamoyltransferase, regulatory subunit
RA	4,470,952	T→C	9.4%	intergenic (‑39/+34)	ridA ← / ← pyrI	enamine/imine deaminase, reaction intermediate detoxification/aspartate carbamoyltransferase, regulatory subunit
RA	4,470,957	G→A	9.2%	intergenic (‑44/+29)	ridA ← / ← pyrI	enamine/imine deaminase, reaction intermediate detoxification/aspartate carbamoyltransferase, regulatory subunit
RA	4,470,958	G→T	9.9%	intergenic (‑45/+28)	ridA ← / ← pyrI	enamine/imine deaminase, reaction intermediate detoxification/aspartate carbamoyltransferase, regulatory subunit
RA	4,472,434	G→A	5.5%	R34* (CGA→TGA)	pyrL ←	pyrBI operon leader peptide
RA	4,472,437	T→C	5.7%	N33D (AAT→GAT)	pyrL ←	pyrBI operon leader peptide
RA	4,479,012	A→T	7.4%	intergenic (+123/+22)	rraB → / ← yjgM	protein inhibitor of RNase E/GNAT family putative N‑acetyltransferase
RA	4,479,016	G→C	7.6%	intergenic (+127/+18)	rraB → / ← yjgM	protein inhibitor of RNase E/GNAT family putative N‑acetyltransferase
RA	4,479,020	A→T	7.7%	intergenic (+131/+14)	rraB → / ← yjgM	protein inhibitor of RNase E/GNAT family putative N‑acetyltransferase
RA	4,496,511	A→G	6.8%	intergenic (+22/‑164)	leuX → / → intB	tRNA‑Leu/pseudogene, integrase homology;IS, phage, Tn; Phage‑related functions and prophages; KpLE2 phage‑like element; P4‑like integrase
RA	4,496,512	C→T	6.7%	intergenic (+23/‑163)	leuX → / → intB	tRNA‑Leu/pseudogene, integrase homology;IS, phage, Tn; Phage‑related functions and prophages; KpLE2 phage‑like element; P4‑like integrase
RA	4,514,335	A→T	5.1%	intergenic (‑27/+18)	fecB ← / ← fecA	ferric citrate ABC transporter periplasmic binding protein/TonB‑dependent outer membrane ferric citrate transporter and signal transducer; ferric citrate extracelluar receptor; FecR‑interacting protein
RA	4,514,336	A→T	5.6%	intergenic (‑28/+17)	fecB ← / ← fecA	ferric citrate ABC transporter periplasmic binding protein/TonB‑dependent outer membrane ferric citrate transporter and signal transducer; ferric citrate extracelluar receptor; FecR‑interacting protein
RA	4,520,500	Δ1 bp	11.2%	intergenic (‑176/+171)	yjhU ← / ← yjhF	putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter
RA	4,520,504:1	+T	10.7%	intergenic (‑180/+167)	yjhU ← / ← yjhF	putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter
RA	4,532,534	G→C	6.4%	A217G (GCC→GGC)	yjhP ←	putative methyltransferase
RA	4,532,537	G→C	6.4%	A216G (GCC→GGC)	yjhP ←	putative methyltransferase
RA	4,638,690	C→T	8.2%	G171G (GGC→GGT)	creD →	inner membrane protein
RA	4,638,691	A→G	9.1%	T172A (ACC→GCC)	creD →	inner membrane protein

Unassigned missing coverage evidence
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	3423751–3424234	3424546–3424238	5–796	53 [50]	[49] 52	[rrfD]–[rrlD]	[rrfD],[rrlD]

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	193444 =	81 (0.690)	4 (0.040)	4/240	NT	5.1%	intergenic (+15/‑77)	frr/dxr	ribosome recycling factor/1‑deoxy‑D‑xylulose 5‑phosphate reductoisomerase
	?	NC_000913	193489 =	73 (0.680)					intergenic (+60/‑32)	frr/dxr	ribosome recycling factor/1‑deoxy‑D‑xylulose 5‑phosphate reductoisomerase
*	?	NC_000913	265229 =	111 (0.950)	6 (0.050)	5/244	NT	5.4%	intergenic (‑23/+75)	yafX/ykfF	CP4‑6 prophage; uncharacterized protein/CP4‑6 prophage; uncharacterized protein
	?	NC_000913	265252 =	105 (0.960)					intergenic (‑46/+52)	yafX/ykfF	CP4‑6 prophage; uncharacterized protein/CP4‑6 prophage; uncharacterized protein
*	?	NC_000913	274674 =	NA (NA)	6 (0.050)	5/250	NT	NA	noncoding (476/1195 nt)	IS5	repeat region
	?	NC_000913	274711 =	NA (NA)					noncoding (439/1195 nt)	IS5	repeat region
*	?	NC_000913	= 284691	68 (0.580)	4 (0.040)	4/252	NT	5.7%	coding (1491/1968 nt)	yagF	CP4‑6 prophage; dehydratase family protein
	?	NC_000913	= 284723	67 (0.590)					coding (1523/1968 nt)	yagF	CP4‑6 prophage; dehydratase family protein
*	?	NC_000913	497914 =	NA (NA)	4 (0.040)	4/248	NT	NA	intergenic (+95/‑141)	adk/hemH	adenylate kinase/ferrochelatase
	?	NC_000913	497936 =	NA (NA)					intergenic (+117/‑119)	adk/hemH	adenylate kinase/ferrochelatase
*	?	NC_000913	= 709171	87 (0.750)	7 (0.060)	5/246	NT	7.6%	coding (838/1407 nt)	chiP	chitoporin, uptake of chitosugars
	?	NC_000913	= 709178	87 (0.790)					coding (845/1407 nt)	chiP	chitoporin, uptake of chitosugars
*	?	NC_000913	765068 =	79 (0.680)	4 (0.040)	3/248	NT	5.4%	intergenic (+19/+85)	sucD/mngR	succinyl‑CoA synthetase, NAD(P)‑binding, alpha subunit/transcriptional repressor for the mannosyl‑D‑glycerate catabolic operon
	?	NC_000913	765107 =	66 (0.590)					intergenic (+58/+46)	sucD/mngR	succinyl‑CoA synthetase, NAD(P)‑binding, alpha subunit/transcriptional repressor for the mannosyl‑D‑glycerate catabolic operon
*	?	NC_000913	1207790 =	38 (0.330)	61 (0.600)	49/228	NT	62.8%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	39 (0.380)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1207805	40 (0.340)	61 (0.600)	49/228	NT	62.2%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	39 (0.380)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	1286928 =	67 (0.570)	4 (0.040)	4/250	NT	5.2%	intergenic (+402/+138)	narI/rttR	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
	?	NC_000913	1287082 =	80 (0.710)					noncoding (155/171 nt)	rttR	rtT sRNA, processed from tyrT transcript
*	?	NC_000913	1396531 =	NA (NA)	4 (0.040)	4/248	NT	NA	noncoding (488/1195 nt)	IS5	repeat region
	?	NC_000913	= 1428264	NA (NA)					noncoding (531/1196 nt)	IS5	repeat region
*	?	NC_000913	= 1815291	89 (0.760)	6 (0.050)	6/246	NT	7.0%	coding (1425/2262 nt)	katE	catalase HPII, heme d‑containing
	?	NC_000913	= 1815302	76 (0.690)					coding (1436/2262 nt)	katE	catalase HPII, heme d‑containing
*	?	NC_000913	1886815 =	63 (0.540)	4 (0.040)	5/238	NT	7.1%	intergenic (+5/+49)	yeaX/rnd	putative YeaWX dioxygenase beta subunit, reductase component/ribonuclease D
	?	NC_000913	1886858 =	47 (0.440)					intergenic (+48/+6)	yeaX/rnd	putative YeaWX dioxygenase beta subunit, reductase component/ribonuclease D
*	?	NC_000913	= 2290113	NA (NA)	8 (0.070)	8/258	NT	6.8%	noncoding (1/1195 nt)	IS5	repeat region
	?	NC_000913	= 3992708	109 (0.940)					coding (1556/2547 nt)	cyaA	adenylate cyclase
*	?	NC_000913	= 2644346	89 (0.760)	5 (0.040)	4/248	NT	5.9%	intergenic (‑63/+87)	rlmN/ndk	dual specificity 23S rRNA m(2)A2503, tRNA m(2)A37 methyltransferase, SAM‑dependent/multifunctional nucleoside diphosphate kinase and apyrimidinic endonuclease and 3'‑phosphodiesterase
	?	NC_000913	= 2644366	74 (0.670)					intergenic (‑83/+67)	rlmN/ndk	dual specificity 23S rRNA m(2)A2503, tRNA m(2)A37 methyltransferase, SAM‑dependent/multifunctional nucleoside diphosphate kinase and apyrimidinic endonuclease and 3'‑phosphodiesterase
*	?	NC_000913	2726200 =	NA (NA)	39 (0.350)	15/248	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	3423376 =	83 (0.710)	17 (0.150)	8/256	NT	17.2%	intergenic (+182/+47)	yhdZ/rrfF	putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon
	?	NC_000913	= 4213162	NA (NA)					intergenic (+3/‑72)	rrfE/yjaA	5S ribosomal RNA of rrnE operon/stress‑induced protein
*	?	NC_000913	= 3620220	NA (NA)	3 (0.030)	3/248	NT	100%	coding (1029/4236 nt)	rhsB	Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
	?	NC_000913	= 3620255	0 (0.000)					coding (1064/4236 nt)	rhsB	Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
*	?	NC_000913	3721045 =	130 (1.110)	374 (3.230)	181/258	NT	75.1%	noncoding (413/1443 nt)	IS150	repeat region
	?	NC_000913	= 3839774	119 (1.030)					coding (220/819 nt)	nlpA	cytoplasmic membrane lipoprotein‑28
*	?	NC_000913	= 3962703	NA (NA)	7 (0.060)	7/248	NT	NA	noncoding (4/36 nt)	REP286 (repetitive extragenic palindromic) element; contains 1 REP sequences	REP286 (repetitive extragenic palindromic) element; contains 1 REP sequences
	?	NC_000913	= 3962735	NA (NA)					noncoding (36/36 nt)	REP286 (repetitive extragenic palindromic) element; contains 1 REP sequences	REP286 (repetitive extragenic palindromic) element; contains 1 REP sequences
*	?	NC_000913	4272636 =	99 (0.850)	7 (0.060)	7/250	NT	6.4%	coding (1236/2823 nt)	uvrA	ATPase and DNA damage recognition protein of nucleotide excision repair excinuclease UvrABC
	?	NC_000913	4272663 =	108 (0.960)					coding (1209/2823 nt)	uvrA	ATPase and DNA damage recognition protein of nucleotide excision repair excinuclease UvrABC
*	?	NC_000913	4295974 =	83 (0.710)	7 (0.060)	4/246	NT	8.2%	noncoding (140/600 nt)	RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites	RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites
	?	NC_000913	4296068 =	NA (NA)					noncoding (234/600 nt)	RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites	RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites
*	?	NC_000913	4369146 =	72 (0.620)	4 (0.040)	4/240	NT	5.7%	intergenic (+6/+10)	fxsA/yjeH	suppressor of F exclusion of phage T7/putative transporter
	?	NC_000913	4369185 =	65 (0.600)					coding (1228/1257 nt)	yjeH	putative transporter
*	?	NC_000913	= 4542690	92 (0.790)	6 (0.060)	6/242	NT	6.4%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	89 (0.820)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)