breseq  version 0.35.4  revision f352f80f4bc9 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence	position	mutation	freq	annotation	gene	description
RA	235	A→T	5.9%	T16S (ACA→TCA) ‡	thrL →	thr operon leader peptide
RA	236	C→G	6.6%	T16R (ACA→AGA) ‡	thrL →	thr operon leader peptide
RA	237	A→T	5.9%	T16T (ACA→ACT) ‡	thrL →	thr operon leader peptide
RA	243	C→T	5.6%	N18N (AAC→AAT)	thrL →	thr operon leader peptide
RA	15,318	G→A	5.0%	intergenic (+20/‑127)	dnaJ → / → insL1	chaperone Hsp40, DnaK co‑chaperone/IS186 transposase
RA	15,319	T→C	5.0%	intergenic (+21/‑126)	dnaJ → / → insL1	chaperone Hsp40, DnaK co‑chaperone/IS186 transposase
RA	53,376	G→A	6.2%	P14L (CCC→CTC)	pdxA ←	4‑hydroxy‑L‑threonine phosphate dehydrogenase, NAD‑dependent
RA	53,379	T→C	6.2%	E13G (GAG→GGG)	pdxA ←	4‑hydroxy‑L‑threonine phosphate dehydrogenase, NAD‑dependent
RA	83,587	A→C	7.3%	intergenic (‑58/+35)	leuA ← / ← leuL	2‑isopropylmalate synthase/leu operon leader peptide
RA	83,590	G→T	8.6%	intergenic (‑61/+32)	leuA ← / ← leuL	2‑isopropylmalate synthase/leu operon leader peptide
RA	87,881	A→G	5.1%	intergenic (+33/‑147)	ilvH → / → cra	acetolactate synthase 3, small subunit, valine‑sensitive/transcriptional repressor‑activator for carbon metabolism
RA	111,013	G→A	8.4%	intergenic (+29/‑31)	secA → / → mutT	preprotein translocase subunit, ATPase/dGTP‑preferring nucleoside triphosphate pyrophosphohydrolase
RA	111,016	T→C	8.2%	intergenic (+32/‑28)	secA → / → mutT	preprotein translocase subunit, ATPase/dGTP‑preferring nucleoside triphosphate pyrophosphohydrolase
RA	114,506	G→T	5.3%	intergenic (+19/+16)	guaC → / ← hofC	GMP reductase/assembly protein in type IV pilin biogenesis, transmembrane protein
RA	126,126	G→A	6.8%	K144K (AAG→AAA)	aceF →	pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2
RA	143,533	T→C	5.5%	L252P (CTG→CCG) ‡	yadG →	putative ABC transporter ATPase
RA	143,534	G→A	5.4%	L252L (CTG→CTA) ‡	yadG →	putative ABC transporter ATPase
RA	151,519	A→C	7.8%	I27M (ATT→ATG)	yadK ←	putative fimbrial‑like adhesin protein
RA	151,522	G→T	8.2%	A26A (GCC→GCA)	yadK ←	putative fimbrial‑like adhesin protein
RA	169,748	T→A	5.5%	intergenic (+21/‑30)	fhuA → / → fhuC	ferrichrome outer membrane transporter/iron(3+)‑hydroxamate import ABC transporter ATPase
RA	169,749	T→A	5.1%	intergenic (+22/‑29)	fhuA → / → fhuC	ferrichrome outer membrane transporter/iron(3+)‑hydroxamate import ABC transporter ATPase
RA	173,567	A→C	5.9%	intergenic (+123/+35)	fhuB → / ← hemL	iron(3+)‑hydroxamate import ABC transporter permease/glutamate‑1‑semialdehyde aminotransferase (aminomutase)
RA	175,144	Δ1 bp	6.9%	coding (38/1422 nt)	clcA →	H(+)/Cl(‑) exchange transporter
RA	175,149:1	+G	7.0%	coding (43/1422 nt)	clcA →	H(+)/Cl(‑) exchange transporter
RA	191,720	G→A	5.2%	intergenic (+12/‑135)	tsf → / → pyrH	translation elongation factor EF‑Ts/uridylate kinase
RA	191,728	T→C	5.5%	intergenic (+20/‑127)	tsf → / → pyrH	translation elongation factor EF‑Ts/uridylate kinase
RA	191,729	G→T	5.3%	intergenic (+21/‑126)	tsf → / → pyrH	translation elongation factor EF‑Ts/uridylate kinase
RA	191,730	A→C	5.1%	intergenic (+22/‑125)	tsf → / → pyrH	translation elongation factor EF‑Ts/uridylate kinase
RA	191,731	G→A	5.5%	intergenic (+23/‑124)	tsf → / → pyrH	translation elongation factor EF‑Ts/uridylate kinase
RA	191,739	T→C	5.6%	intergenic (+31/‑116)	tsf → / → pyrH	translation elongation factor EF‑Ts/uridylate kinase
RA	212,728	G→C	5.5%	G133A (GGC→GCC)	tilS →	tRNA(Ile)‑lysidine synthetase
RA	242,344	C→G	5.5%	P320P (CCG→CCC)	fadE ←	acyl coenzyme A dehydrogenase
RA	254,223	A→T	5.4%	intergenic (+21/+36)	prfH → / ← pepD	pseudogene, RF‑1 domain family; probable peptide chain release factor/aminoacyl‑histidine dipeptidase (peptidase D)
RA	254,233	A→T	5.7%	intergenic (+31/+26)	prfH → / ← pepD	pseudogene, RF‑1 domain family; probable peptide chain release factor/aminoacyl‑histidine dipeptidase (peptidase D)
RA	254,238	A→T	5.5%	intergenic (+36/+21)	prfH → / ← pepD	pseudogene, RF‑1 domain family; probable peptide chain release factor/aminoacyl‑histidine dipeptidase (peptidase D)
RA	256,449	T→C	7.8%	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	7.8%	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	7.9%	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	282,513	T→C	7.0%	L79P (CTG→CCG)	yagE →	2‑keto‑3‑deoxy gluconate (KDG) aldolase; CP4‑6 prophage
RA	282,518	G→A	6.9%	G81S (GGC→AGC)	yagE →	2‑keto‑3‑deoxy gluconate (KDG) aldolase; CP4‑6 prophage
RA	298,304	T→G	5.3%	K141N (AAA→AAC)	paoD ←	moco insertion factor for PaoABC aldehyde oxidoreductase
RA	318,649	T→C	5.3%	intergenic (‑82/+27)	rclB ← / ← rclA	reactive chlorine species (RCS) stress resistance periplasmic protein/reactive chlorine stress species (RCS) resistance protein; pyridine nucleotide‑dependent disulfide oxidoreductase family
RA	318,651	T→A	6.0%	intergenic (‑84/+25)	rclB ← / ← rclA	reactive chlorine species (RCS) stress resistance periplasmic protein/reactive chlorine stress species (RCS) resistance protein; pyridine nucleotide‑dependent disulfide oxidoreductase family
RA	318,652	T→A	5.7%	intergenic (‑85/+24)	rclB ← / ← rclA	reactive chlorine species (RCS) stress resistance periplasmic protein/reactive chlorine stress species (RCS) resistance protein; pyridine nucleotide‑dependent disulfide oxidoreductase family
RA	318,654	G→A	6.1%	intergenic (‑87/+22)	rclB ← / ← rclA	reactive chlorine species (RCS) stress resistance periplasmic protein/reactive chlorine stress species (RCS) resistance protein; pyridine nucleotide‑dependent disulfide oxidoreductase family
RA	357,778	C→T	7.1%	intergenic (+324/+13)	codA → / ← cynR	cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor
RA	394,632	G→A	5.7%	D43N (GAT→AAT) ‡	yaiV →	putative transcriptional regulator
RA	394,633	A→G	5.7%	D43G (GAT→GGT) ‡	yaiV →	putative transcriptional regulator
RA	394,636	C→T	5.6%	T44I (ACT→ATT) ‡	yaiV →	putative transcriptional regulator
RA	394,637	T→C	5.7%	T44T (ACT→ACC) ‡	yaiV →	putative transcriptional regulator
RA	399,806	G→T	5.2%	intergenic (+1/+23)	yaiZ → / ← ddlA	DUF2754 family putative inner membrane protein/D‑alanine‑D‑alanine ligase A
RA	399,808	A→T	5.7%	intergenic (+3/+21)	yaiZ → / ← ddlA	DUF2754 family putative inner membrane protein/D‑alanine‑D‑alanine ligase A
RA	399,810	A→C	5.4%	intergenic (+5/+19)	yaiZ → / ← ddlA	DUF2754 family putative inner membrane protein/D‑alanine‑D‑alanine ligase A
RA	399,815	C→T	5.1%	intergenic (+10/+14)	yaiZ → / ← ddlA	DUF2754 family putative inner membrane protein/D‑alanine‑D‑alanine ligase A
RA	429,554	A→T	5.4%	Y17F (TAT→TTT)	secF →	SecYEG protein translocase auxillary subunit
RA	448,363	A→T	5.7%	S100T (TCC→ACC)	cyoC ←	cytochrome o ubiquinol oxidase subunit III
RA	448,368	A→T	5.3%	V98D (GTT→GAT)	cyoC ←	cytochrome o ubiquinol oxidase subunit III
RA	481,225	T→G	8.2%	intergenic (‑517/+29)	tomB ← / ← acrB	Hha toxicity attenuator; conjugation‑related protein/multidrug efflux system protein
RA	481,228	C→A	7.2%	intergenic (‑520/+26)	tomB ← / ← acrB	Hha toxicity attenuator; conjugation‑related protein/multidrug efflux system protein
RA	492,232	T→G	5.9%	R47R (CGT→CGG)	dnaX →	DNA polymerase III/DNA elongation factor III, tau and gamma subunits
RA	494,032	A→T	6.0%	intergenic (+9/‑44)	dnaX → / → ybaB	DNA polymerase III/DNA elongation factor III, tau and gamma subunits/DNA‑binding protein, putative nucleoid‑associated protein
RA	494,033	C→G	5.3%	intergenic (+10/‑43)	dnaX → / → ybaB	DNA polymerase III/DNA elongation factor III, tau and gamma subunits/DNA‑binding protein, putative nucleoid‑associated protein
RA	494,034	A→T	5.8%	intergenic (+11/‑42)	dnaX → / → ybaB	DNA polymerase III/DNA elongation factor III, tau and gamma subunits/DNA‑binding protein, putative nucleoid‑associated protein
RA	556,019	T→A	5.3%	intergenic (+23/+13)	cysS → / ← ybcI	cysteinyl‑tRNA synthetase/DUF457 family inner membrane protein
RA	603,393	T→A	6.2%	intergenic (+58/+23)	pheP → / ← ybdG	phenylalanine transporter/mechanosensitive channel protein, miniconductance
RA	632,126	A→G	6.9%	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	9.1%	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	7.3%	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	5.8%	intergenic (+135/‑48)	cstA → / → ybdD	carbon starvation protein involved in peptide utilization; APC peptide transporter family protein/DUF466 family protein
RA	632,140	G→T	7.8%	intergenic (+141/‑42)	cstA → / → ybdD	carbon starvation protein involved in peptide utilization; APC peptide transporter family protein/DUF466 family protein
RA	632,141	C→T	6.9%	intergenic (+142/‑41)	cstA → / → ybdD	carbon starvation protein involved in peptide utilization; APC peptide transporter family protein/DUF466 family protein
RA	645,070	G→A	5.0%	intergenic (‑67/+47)	rna ← / ← citT	ribonuclease I/citrate/succinate antiporter; citrate carrier
RA	672,245	C→A	5.1%	V847L (GTG→TTG)	leuS ←	leucyl‑tRNA synthetase
RA	710,170	C→T	7.5%	intergenic (+54/+30)	chiQ → / ← fur	chitosugar‑induced verified lipoprotein/ferric iron uptake regulon transcriptional repressor; autorepressor
RA	710,173	A→G	7.4%	intergenic (+57/+27)	chiQ → / ← fur	chitosugar‑induced verified lipoprotein/ferric iron uptake regulon transcriptional repressor; autorepressor
RA	729,376	G→T	6.6%	intergenic (+36/‑207)	ybfA → / → rhsC	DUF2517 family protein/Rhs protein with putative toxin domain; putative neighboring cell growth inhibitor
RA	729,377	A→T	6.4%	intergenic (+37/‑206)	ybfA → / → rhsC	DUF2517 family protein/Rhs protein with putative toxin domain; putative neighboring cell growth inhibitor
RA	729,378	A→T	6.4%	intergenic (+38/‑205)	ybfA → / → rhsC	DUF2517 family protein/Rhs protein with putative toxin domain; putative neighboring cell growth inhibitor
RA	729,379	A→C	5.2%	intergenic (+39/‑204)	ybfA → / → rhsC	DUF2517 family protein/Rhs protein with putative toxin domain; putative neighboring cell growth inhibitor
RA	747,895	C→G	7.5%	intergenic (‑126/+26)	abrB ← / ← ybgO	regulator of aidB expression; inner membrane protein/putative fimbrial protein
RA	747,897	G→C	7.1%	intergenic (‑128/+24)	abrB ← / ← ybgO	regulator of aidB expression; inner membrane protein/putative fimbrial protein
RA	747,900	G→C	7.1%	intergenic (‑131/+21)	abrB ← / ← ybgO	regulator of aidB expression; inner membrane protein/putative fimbrial protein
RA	747,902	C→G	7.6%	intergenic (‑133/+19)	abrB ← / ← ybgO	regulator of aidB expression; inner membrane protein/putative fimbrial protein
RA	752,065	G→C	5.9%	D35E (GAC→GAG) ‡	ybgQ ←	putative outer membrane protein
RA	752,066	T→G	6.3%	D35A (GAC→GCC) ‡	ybgQ ←	putative outer membrane protein
RA	752,067	C→A	5.0%	D35Y (GAC→TAC) ‡	ybgQ ←	putative outer membrane protein
RA	752,068	G→C	6.3%	R34R (CGC→CGG)	ybgQ ←	putative outer membrane protein
RA	770,679	G→T	5.5%	intergenic (+68/‑779)	mngB → / → cydA	alpha‑mannosidase/cytochrome d terminal oxidase, subunit I
RA	794,943	T→G	5.5%	intergenic (+21/‑146)	acrZ → / → modA	AcrAB‑TolC efflux pump accessory protein, membrane‑associated/molybdate ABC transporter periplasmic binding protein; chlorate resistance protein
RA	832,364	A→G	6.1%	intergenic (+128/+104)	rhlE → / ← ybiA	ATP‑dependent RNA helicase/DUF1768 family protein
RA	832,365	A→C	6.1%	intergenic (+129/+103)	rhlE → / ← ybiA	ATP‑dependent RNA helicase/DUF1768 family protein
RA	832,371	T→A	5.9%	intergenic (+135/+97)	rhlE → / ← ybiA	ATP‑dependent RNA helicase/DUF1768 family protein
RA	832,372	T→A	5.9%	intergenic (+136/+96)	rhlE → / ← ybiA	ATP‑dependent RNA helicase/DUF1768 family protein
RA	832,378	G→T	6.5%	intergenic (+142/+90)	rhlE → / ← ybiA	ATP‑dependent RNA helicase/DUF1768 family protein
RA	832,379	C→T	6.2%	intergenic (+143/+89)	rhlE → / ← ybiA	ATP‑dependent RNA helicase/DUF1768 family protein
RA	857,578	C→G	5.4%	intergenic (+23/+218)	ybiT → / ← ybiU	ABC‑F family putative regulatory ATPase/DUF1479 family protein
RA	858,665	A→C	6.7%	S133A (TCA→GCA)	ybiU ←	DUF1479 family protein
RA	860,151	A→G	5.7%	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	5.7%	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	5.5%	intergenic (‑129/+17)	ybiV ← / ← ybiW	sugar phosphatase; fructose‑1‑P/ribose‑5‑P/glucose‑6‑P phosphatase/putative pyruvate formate lyase
RA	887,392	T→A	5.1%	intergenic (‑53/‑31)	ybjJ ← / → rcdA	putative drug efflux MFS transporter, inner membrane protein/transcriptional regulator of csgD and ybiJI; autoregulator
RA	922,314:1	+C	5.8%	intergenic (+21/+52)	macB → / ← cspD	macrolide ABC transporter peremase/ATPase/inhibitor of DNA replication, cold shock protein homolog
RA	975,700	G→T	5.5%	D27Y (GAC→TAC) ‡	mukE →	chromosome condensin MukBEF, MukE localization factor
RA	975,701	A→C	6.5%	D27A (GAC→GCC) ‡	mukE →	chromosome condensin MukBEF, MukE localization factor
RA	980,800	G→T	5.7%	intergenic (+14/‑247)	mukB → / → ldtD	chromosome condensin MukBEF, ATPase and DNA‑binding subunit/murein L,D‑transpeptidase
RA	980,802	A→G	5.1%	intergenic (+16/‑245)	mukB → / → ldtD	chromosome condensin MukBEF, ATPase and DNA‑binding subunit/murein L,D‑transpeptidase
RA	987,418	A→T	6.6%	intergenic (‑436/+167)	ompF ← / ← asnS	outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
RA	987,420	A→C	7.0%	intergenic (‑438/+165)	ompF ← / ← asnS	outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
RA	987,421	A→T	6.7%	intergenic (‑439/+164)	ompF ← / ← asnS	outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
RA	987,422	G→T	6.8%	intergenic (‑440/+163)	ompF ← / ← asnS	outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
RA	987,560	G→C	5.7%	intergenic (‑578/+25)	ompF ← / ← asnS	outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
RA	987,561	G→C	5.7%	intergenic (‑579/+24)	ompF ← / ← asnS	outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
RA	998,448	T→A	5.9%	intergenic (+41/‑42)	elfA → / → elfD	laminin‑binding fimbrin subunit/putative periplasmic pilin chaperone
RA	998,449	G→A	5.9%	intergenic (+42/‑41)	elfA → / → elfD	laminin‑binding fimbrin subunit/putative periplasmic pilin chaperone
RA	998,450	T→C	5.9%	intergenic (+43/‑40)	elfA → / → elfD	laminin‑binding fimbrin subunit/putative periplasmic pilin chaperone
RA	998,451	T→A	5.5%	intergenic (+44/‑39)	elfA → / → elfD	laminin‑binding fimbrin subunit/putative periplasmic pilin chaperone
RA	1,004,142	A→C	10.8%	T66P (ACG→CCG)	ycbF →	putative periplasmic pilin chaperone
RA	1,052,260	T→C	5.4%	intergenic (+20/+29)	gnsA → / ← yccM	putative phosphatidylethanolamine synthesis regulator/putative 4Fe‑4S membrane protein
RA	1,129,394	G→C	5.2%	intergenic (+20/+20)	murJ → / ← flgN	putative lipid II flippase/export chaperone for FlgK and FlgL
RA	1,146,741	A→T	5.4%	noncoding (153/169 nt)	psrD →	novel Novel sRNA, function unknown
RA	1,159,335	G→T	7.2%	intergenic (+33/+27)	ptsG → / ← fhuE	fused glucose‑specific PTS enzymes: IIB component/IIC component/ferric‑rhodotorulic acid outer membrane transporter
RA	1,159,336	A→C	7.0%	intergenic (+34/+26)	ptsG → / ← fhuE	fused glucose‑specific PTS enzymes: IIB component/IIC component/ferric‑rhodotorulic acid outer membrane transporter
RA	1,211,610	A→G	6.4%	intergenic (+33/+70)	icdC → / ← iraM	pseudogene, isocitrate dehydrogenase C‑terminal gene fragment; idcC' is a 54 codon 3' gene fragment created during e14 prophage insertion/RpoS stabilzer during Mg starvation, anti‑RssB factor
RA	1,211,612	A→T	7.2%	intergenic (+35/+68)	icdC → / ← iraM	pseudogene, isocitrate dehydrogenase C‑terminal gene fragment; idcC' is a 54 codon 3' gene fragment created during e14 prophage insertion/RpoS stabilzer during Mg starvation, anti‑RssB factor
RA	1,211,614	C→T	7.2%	intergenic (+37/+66)	icdC → / ← iraM	pseudogene, isocitrate dehydrogenase C‑terminal gene fragment; idcC' is a 54 codon 3' gene fragment created during e14 prophage insertion/RpoS stabilzer during Mg starvation, anti‑RssB factor
RA	1,232,481	C→T	6.6%	intergenic (+27/+19)	umuC → / ← dsbB	translesion error‑prone DNA polymerase V subunit; DNA polymerase activity/oxidoreductase that catalyzes reoxidation of DsbA protein disulfide isomerase I
RA	1,232,484	A→G	6.3%	intergenic (+30/+16)	umuC → / ← dsbB	translesion error‑prone DNA polymerase V subunit; DNA polymerase activity/oxidoreductase that catalyzes reoxidation of DsbA protein disulfide isomerase I
RA	1,260,901	C→T	5.7%	intergenic (‑98/+27)	dauA ← / ← prs	C4‑dicarboxylic acid transporter/phosphoribosylpyrophosphate synthase
RA	1,260,904	A→G	5.6%	intergenic (‑101/+24)	dauA ← / ← prs	C4‑dicarboxylic acid transporter/phosphoribosylpyrophosphate synthase
RA	1,286,793	A→G	9.6%	intergenic (+267/+273)	narI → / ← rttR	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
RA	1,287,161	G→A	9.0%	noncoding (76/171 nt) Q6* (CAA→TAA)	rttR ← tpr ←	rtT sRNA, processed from tyrT transcript protamine‑like protein
JC JC	1,292,993	IS5 (–) +4 bp	67.9%	intergenic (‑71/‑531)	hns ← / → tdk	global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
JC JC	1,292,997	IS2 (–) +5 bp	40.0%	intergenic (‑75/‑526)	hns ← / → tdk	global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
JC JC	1,293,015	IS1 (–) +10 bp	46.5%	intergenic (‑93/‑503)	hns ← / → tdk	global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
JC JC	1,293,091	IS5 (+) +4 bp	7.1%	intergenic (‑169/‑433)	hns ← / → tdk	global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
RA	1,299,267:1	+A	5.2%	intergenic (+22/‑1915)	ychE → / → oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
RA	1,299,270	C→G	5.1%	intergenic (+25/‑1912)	ychE → / → oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
RA	1,311,285	A→C	9.2%	E66A (GAG→GCG)	tonB →	membrane spanning protein in TonB‑ExbB‑ExbD transport complex
RA	1,315,796	A→G	5.5%	intergenic (‑26/+60)	yciF ← / ← yciG	putative rubrerythrin/ferritin‑like metal‑binding protein/KGG family protein
RA	1,315,800	A→G	5.6%	intergenic (‑30/+56)	yciF ← / ← yciG	putative rubrerythrin/ferritin‑like metal‑binding protein/KGG family protein
RA	1,315,803	C→T	5.7%	intergenic (‑33/+53)	yciF ← / ← yciG	putative rubrerythrin/ferritin‑like metal‑binding protein/KGG family protein
RA	1,315,807	C→T	5.8%	intergenic (‑37/+49)	yciF ← / ← yciG	putative rubrerythrin/ferritin‑like metal‑binding protein/KGG family protein
RA	1,330,396:1	+T	7.0%	intergenic (+15/+21)	sohB → / ← yciN	inner membrane protein, S49 peptidase family protein/DUF2498 protein YciN
RA	1,330,399	A→T	7.4%	intergenic (+18/+18)	sohB → / ← yciN	inner membrane protein, S49 peptidase family protein/DUF2498 protein YciN
RA	1,330,402	Δ1 bp	6.8%	intergenic (+21/+15)	sohB → / ← yciN	inner membrane protein, S49 peptidase family protein/DUF2498 protein YciN
RA	1,410,986	A→G	5.5%	intergenic (+102/+27)	dbpA → / ← ttcA	ATP‑dependent RNA helicase, specific for 23S rRNA/tRNA s(2)C32 thioltransferase, iron sulfur cluster protein
RA	1,410,990	T→A	5.8%	intergenic (+106/+23)	dbpA → / ← ttcA	ATP‑dependent RNA helicase, specific for 23S rRNA/tRNA s(2)C32 thioltransferase, iron sulfur cluster protein
RA	1,410,991	T→A	5.8%	intergenic (+107/+22)	dbpA → / ← ttcA	ATP‑dependent RNA helicase, specific for 23S rRNA/tRNA s(2)C32 thioltransferase, iron sulfur cluster protein
RA	1,410,995	C→T	5.6%	intergenic (+111/+18)	dbpA → / ← ttcA	ATP‑dependent RNA helicase, specific for 23S rRNA/tRNA s(2)C32 thioltransferase, iron sulfur cluster protein
RA	1,426,417	T→C	6.5%	intergenic (+335/‑37)	ydaY → / → tmpR	pseudogene, Rac prophage;Phage or Prophage Related/Rac prophage; pseudogene, tail protein family;Phage or Prophage Related; putative alpha helix protein
RA	1,426,418	T→G	6.2%	intergenic (+336/‑36)	ydaY → / → tmpR	pseudogene, Rac prophage;Phage or Prophage Related/Rac prophage; pseudogene, tail protein family;Phage or Prophage Related; putative alpha helix protein
RA	1,426,421	C→A	5.8%	intergenic (+339/‑33)	ydaY → / → tmpR	pseudogene, Rac prophage;Phage or Prophage Related/Rac prophage; pseudogene, tail protein family;Phage or Prophage Related; putative alpha helix protein
RA	1,426,422	G→A	6.2%	intergenic (+340/‑32)	ydaY → / → tmpR	pseudogene, Rac prophage;Phage or Prophage Related/Rac prophage; pseudogene, tail protein family;Phage or Prophage Related; putative alpha helix protein
RA	1,449,799	C→G	5.8%	T517T (ACG→ACC)	tynA ←	tyramine oxidase, copper‑requiring
RA	1,449,802	A→G	5.9%	A516A (GCT→GCC) ‡	tynA ←	tyramine oxidase, copper‑requiring
RA	1,449,803	G→C	5.8%	A516G (GCT→GGT) ‡	tynA ←	tyramine oxidase, copper‑requiring
RA	1,449,804	C→T	6.0%	A516T (GCT→ACT) ‡	tynA ←	tyramine oxidase, copper‑requiring
RA	1,449,807	C→G	5.9%	G515R (GGT→CGT)	tynA ←	tyramine oxidase, copper‑requiring
RA	1,457,976	A→T	5.8%	G160G (GGA→GGT)	paaF →	2,3‑dehydroadipyl‑CoA hydratase
RA	1,457,979	A→T	6.9%	E161D (GAA→GAT)	paaF →	2,3‑dehydroadipyl‑CoA hydratase
RA	1,457,981	G→C	6.9%	S162T (AGT→ACT)	paaF →	2,3‑dehydroadipyl‑CoA hydratase
RA	1,457,983	A→T	6.3%	I163F (ATC→TTC)	paaF →	2,3‑dehydroadipyl‑CoA hydratase
RA	1,457,986	A→T	6.6%	T164S (ACC→TCC)	paaF →	2,3‑dehydroadipyl‑CoA hydratase
RA	1,461,488	G→C	5.0%	G199A (GGC→GCC)	paaJ →	3‑oxoadipyl‑CoA/3‑oxo‑5,6‑dehydrosuberyl‑CoA thiolase
RA	1,461,492	T→A	7.0%	I200I (ATT→ATA)	paaJ →	3‑oxoadipyl‑CoA/3‑oxo‑5,6‑dehydrosuberyl‑CoA thiolase
RA	1,461,493	C→A	5.2%	L201M (CTG→ATG)	paaJ →	3‑oxoadipyl‑CoA/3‑oxo‑5,6‑dehydrosuberyl‑CoA thiolase
RA	1,461,496	G→C	5.7%	A202P (GCT→CCT)	paaJ →	3‑oxoadipyl‑CoA/3‑oxo‑5,6‑dehydrosuberyl‑CoA thiolase
RA	1,466,336	C→G	9.8%	pseudogene (945/2513 nt)	ydbA →	pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA	1,488,050	T→C	7.7%	intergenic (+15/‑182)	ydcF → / → aldA	DUF218 superfamily protein, SAM‑binding/aldehyde dehydrogenase A, NAD‑linked
RA	1,488,051	G→A	7.6%	intergenic (+16/‑181)	ydcF → / → aldA	DUF218 superfamily protein, SAM‑binding/aldehyde dehydrogenase A, NAD‑linked
RA	1,488,055	C→A	8.6%	intergenic (+20/‑177)	ydcF → / → aldA	DUF218 superfamily protein, SAM‑binding/aldehyde dehydrogenase A, NAD‑linked
RA	1,488,057	C→G	7.5%	intergenic (+22/‑175)	ydcF → / → aldA	DUF218 superfamily protein, SAM‑binding/aldehyde dehydrogenase A, NAD‑linked
RA	1,488,059	T→G	7.2%	intergenic (+24/‑173)	ydcF → / → aldA	DUF218 superfamily protein, SAM‑binding/aldehyde dehydrogenase A, NAD‑linked
RA	1,488,063	T→C	7.5%	intergenic (+28/‑169)	ydcF → / → aldA	DUF218 superfamily protein, SAM‑binding/aldehyde dehydrogenase A, NAD‑linked
RA	1,488,064	G→A	7.5%	intergenic (+29/‑168)	ydcF → / → aldA	DUF218 superfamily protein, SAM‑binding/aldehyde dehydrogenase A, NAD‑linked
RA	1,491,906	A→T	5.0%	intergenic (+56/+16)	ydcA → / ← hokB	putative periplasmic protein/toxic polypeptide, small
RA	1,517,484	C→G	5.5%	I32M (ATC→ATG)	ydcX →	DUF2566 family protein
RA	1,537,972	G→T	7.7%	R294R (CGC→CGA)	narY ←	nitrate reductase 2 (NRZ), beta subunit
RA	1,552,191	C→A	11.8%	intergenic (+200/+207)	fdnI → / ← yddM	formate dehydrogenase‑N, cytochrome B556 (gamma) subunit, nitrate‑inducible/putative DNA‑binding transcriptional regulator
RA	1,555,781	G→C	5.1%	intergenic (‑112/+45)	maeA ← / ← sra	malate dehydrogenase, decarboxylating, NAD‑requiring; malic enzyme/stationary‑phase‑induced ribosome‑associated protein
RA	1,555,782	C→T	5.1%	intergenic (‑113/+44)	maeA ← / ← sra	malate dehydrogenase, decarboxylating, NAD‑requiring; malic enzyme/stationary‑phase‑induced ribosome‑associated protein
RA	1,555,784	G→C	5.0%	intergenic (‑115/+42)	maeA ← / ← sra	malate dehydrogenase, decarboxylating, NAD‑requiring; malic enzyme/stationary‑phase‑induced ribosome‑associated protein
RA	1,613,276	G→T	6.3%	intergenic (‑25/+39)	glsB ← / ← sad	glutaminase 2/succinate semialdehyde dehydrogenase, NAD(P)+‑dependent
RA	1,613,277	A→T	6.2%	intergenic (‑26/+38)	glsB ← / ← sad	glutaminase 2/succinate semialdehyde dehydrogenase, NAD(P)+‑dependent
RA	1,613,278	A→T	5.9%	intergenic (‑27/+37)	glsB ← / ← sad	glutaminase 2/succinate semialdehyde dehydrogenase, NAD(P)+‑dependent
RA	1,613,279	A→C	5.9%	intergenic (‑28/+36)	glsB ← / ← sad	glutaminase 2/succinate semialdehyde dehydrogenase, NAD(P)+‑dependent
RA	1,629,435	G→A	10.1%	intergenic (+17/+18)	ydfZ → / ← ydfI	selenoprotein, function unknown/putative NAD‑dependent D‑mannonate oxidoreductase
RA	1,629,436	A→T	9.4%	intergenic (+18/+17)	ydfZ → / ← ydfI	selenoprotein, function unknown/putative NAD‑dependent D‑mannonate oxidoreductase
RA	1,629,437	T→C	9.7%	intergenic (+19/+16)	ydfZ → / ← ydfI	selenoprotein, function unknown/putative NAD‑dependent D‑mannonate oxidoreductase
RA	1,657,895	A→T	5.2%	intergenic (+25/‑174)	ynfD → / → ynfE	DUF1161 family periplasmic protein/putative selenate reductase, periplasmic
RA	1,661,935	G→T	7.2%	L460L (CTG→CTT)	ynfF →	S‑ and N‑oxide reductase, A subunit, periplasmic
RA	1,661,940	T→G	6.2%	V462G (GTC→GGC) ‡	ynfF →	S‑ and N‑oxide reductase, A subunit, periplasmic
RA	1,661,941	C→G	6.3%	V462V (GTC→GTG) ‡	ynfF →	S‑ and N‑oxide reductase, A subunit, periplasmic
RA	1,661,942	C→G	7.1%	P463A (CCC→GCC) ‡	ynfF →	S‑ and N‑oxide reductase, A subunit, periplasmic
RA	1,661,943	C→A	6.2%	P463H (CCC→CAC) ‡	ynfF →	S‑ and N‑oxide reductase, A subunit, periplasmic
RA	1,661,948	A→C	5.3%	K465Q (AAG→CAG)	ynfF →	S‑ and N‑oxide reductase, A subunit, periplasmic
RA	1,684,016	A→G	8.2%	S379G (AGC→GGC)	rstB →	sensory histidine kinase of RstAB two‑component system
RA	1,684,019	C→T	8.0%	R380W (CGG→TGG)	rstB →	sensory histidine kinase of RstAB two‑component system
RA	1,689,817	C→A	5.9%	intergenic (+66/‑35)	manA → / → ydgA	mannose‑6‑phosphate isomerase/DUF945 family protein
RA	1,693,416	A→G	5.6%	L283P (CTG→CCG) ‡	uidB ←	glucuronide transporter
RA	1,693,417	G→C	5.9%	L283V (CTG→GTG) ‡	uidB ←	glucuronide transporter
RA	1,707,028	T→G	8.3%	V37G (GTA→GGA) ‡	rsxC →	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA	1,707,029	A→G	7.2%	V37V (GTA→GTG) ‡	rsxC →	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA	1,707,030	C→T	6.9%	P38S (CCC→TCC) ‡	rsxC →	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA	1,707,031	C→A	7.3%	P38H (CCC→CAC) ‡	rsxC →	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA	1,708,652	G→C	6.6%	A578A (GCG→GCC)	rsxC →	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA	1,747,155	G→T	8.2%	A9S (GCC→TCC)	ydhS →	putative oxidoreductase
RA	1,757,688	T→A	5.1%	intergenic (+31/+33)	lpp → / ← ldtE	murein lipoprotein/murein L,D‑transpeptidase
RA	1,770,387	C→T	5.3%	noncoding (16/106 nt)	rprA →	sRNA antisense activator for RpoS translation, Hfq‑dependent
RA	1,770,390	A→G	5.4%	noncoding (19/106 nt)	rprA →	sRNA antisense activator for RpoS translation, Hfq‑dependent
RA	1,799,370	Δ1 bp	6.0%	intergenic (‑100/+23)	pheM ← / ← rplT	phenylalanyl‑tRNA synthetase operon leader peptide/50S ribosomal subunit protein L20
RA	1,799,374:1	+T	5.8%	intergenic (‑104/+19)	pheM ← / ← rplT	phenylalanyl‑tRNA synthetase operon leader peptide/50S ribosomal subunit protein L20
RA	1,807,317	C→T	5.1%	intergenic (+18/‑83)	pfkB → / → ydiZ	6‑phosphofructokinase II/uncharacterized protein
RA	1,807,318	A→G	5.0%	intergenic (+19/‑82)	pfkB → / → ydiZ	6‑phosphofructokinase II/uncharacterized protein
RA	1,807,319	T→C	5.1%	intergenic (+20/‑81)	pfkB → / → ydiZ	6‑phosphofructokinase II/uncharacterized protein
RA	1,808,680	T→A	5.2%	intergenic (+24/+17)	yniA → / ← yniB	fructosamine kinase family protein/putative inner membrane protein
RA	1,808,682	C→G	5.4%	intergenic (+26/+15)	yniA → / ← yniB	fructosamine kinase family protein/putative inner membrane protein
RA	1,808,684	T→A	5.4%	intergenic (+28/+13)	yniA → / ← yniB	fructosamine kinase family protein/putative inner membrane protein
RA	1,810,062	T→C	8.1%	intergenic (+14/‑149)	yniC → / → ydjM	2‑deoxyglucose‑6‑P phosphatase/inner membrane protein regulated by LexA
RA	1,810,065	T→G	7.3%	intergenic (+17/‑146)	yniC → / → ydjM	2‑deoxyglucose‑6‑P phosphatase/inner membrane protein regulated by LexA
RA	1,810,066	C→A	7.8%	intergenic (+18/‑145)	yniC → / → ydjM	2‑deoxyglucose‑6‑P phosphatase/inner membrane protein regulated by LexA
RA	1,810,069	G→A	7.2%	intergenic (+21/‑142)	yniC → / → ydjM	2‑deoxyglucose‑6‑P phosphatase/inner membrane protein regulated by LexA
RA	1,825,936	T→A	6.3%	intergenic (‑311/+19)	spy ← / ← astE	periplasmic ATP‑independent protein refolding chaperone, stress‑induced/succinylglutamate desuccinylase
RA	1,825,937	G→T	5.7%	intergenic (‑312/+18)	spy ← / ← astE	periplasmic ATP‑independent protein refolding chaperone, stress‑induced/succinylglutamate desuccinylase
RA	1,825,938	A→C	5.8%	intergenic (‑313/+17)	spy ← / ← astE	periplasmic ATP‑independent protein refolding chaperone, stress‑induced/succinylglutamate desuccinylase
RA	1,825,939	T→A	5.7%	intergenic (‑314/+16)	spy ← / ← astE	periplasmic ATP‑independent protein refolding chaperone, stress‑induced/succinylglutamate desuccinylase
RA	1,829,322	A→C	6.7%	L138R (CTG→CGG)	astD ←	succinylglutamic semialdehyde dehydrogenase
RA	1,829,328	C→G	6.2%	G136A (GGC→GCC)	astD ←	succinylglutamic semialdehyde dehydrogenase
RA	1,829,334	G→T	6.2%	P134Q (CCG→CAG)	astD ←	succinylglutamic semialdehyde dehydrogenase
RA	1,851,204	A→C	5.6%	T115T (ACA→ACC)	ansA →	cytoplasmic L‑asparaginase 1
RA	1,851,205	G→C	6.6%	G116R (GGG→CGG) ‡	ansA →	cytoplasmic L‑asparaginase 1
RA	1,851,206	G→T	6.1%	G116V (GGG→GTG) ‡	ansA →	cytoplasmic L‑asparaginase 1
RA	1,854,021	A→G	5.5%	intergenic (‑42/+75)	ydjE ← / ← ydjF	putative MFS sugar transporter, membrane protein/putative DNA‑binding transcriptional regulator
RA	1,854,023	T→G	5.6%	intergenic (‑44/+73)	ydjE ← / ← ydjF	putative MFS sugar transporter, membrane protein/putative DNA‑binding transcriptional regulator
RA	1,854,024	C→A	6.0%	intergenic (‑45/+72)	ydjE ← / ← ydjF	putative MFS sugar transporter, membrane protein/putative DNA‑binding transcriptional regulator
RA	1,854,026	C→T	5.6%	intergenic (‑47/+70)	ydjE ← / ← ydjF	putative MFS sugar transporter, membrane protein/putative DNA‑binding transcriptional regulator
RA	1,856,334	C→A	5.6%	E199* (GAG→TAG)	ydjH ←	putative kinase
RA	1,864,763	A→T	5.0%	intergenic (+29/+19)	yeaD → / ← yeaE	D‑hexose‑6‑phosphate epimerase‑like protein/aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent
RA	1,868,865:1	+G	5.5%	intergenic (+23/‑90)	yeaG → / → yeaH	protein kinase, endogenous substrate unidentified; autokinase/UPF0229 family protein
RA	1,888,030	A→T	5.3%	intergenic (‑39/+31)	rnd ← / ← fadD	ribonuclease D/acyl‑CoA synthetase (long‑chain‑fatty‑acid‑‑CoA ligase)
RA	1,888,032	T→A	5.4%	intergenic (‑41/+29)	rnd ← / ← fadD	ribonuclease D/acyl‑CoA synthetase (long‑chain‑fatty‑acid‑‑CoA ligase)
RA	1,888,034	A→T	5.4%	intergenic (‑43/+27)	rnd ← / ← fadD	ribonuclease D/acyl‑CoA synthetase (long‑chain‑fatty‑acid‑‑CoA ligase)
RA	1,889,915	A→C	7.0%	intergenic (‑169/+36)	fadD ← / ← yeaY	acyl‑CoA synthetase (long‑chain‑fatty‑acid‑‑CoA ligase)/Slp family lipoprotein, RpoE‑regulated
RA	1,889,916	C→T	5.7%	intergenic (‑170/+35)	fadD ← / ← yeaY	acyl‑CoA synthetase (long‑chain‑fatty‑acid‑‑CoA ligase)/Slp family lipoprotein, RpoE‑regulated
RA	1,889,917	C→G	5.8%	intergenic (‑171/+34)	fadD ← / ← yeaY	acyl‑CoA synthetase (long‑chain‑fatty‑acid‑‑CoA ligase)/Slp family lipoprotein, RpoE‑regulated
RA	1,889,918	A→G	5.8%	intergenic (‑172/+33)	fadD ← / ← yeaY	acyl‑CoA synthetase (long‑chain‑fatty‑acid‑‑CoA ligase)/Slp family lipoprotein, RpoE‑regulated
RA	1,889,919	G→T	5.9%	intergenic (‑173/+32)	fadD ← / ← yeaY	acyl‑CoA synthetase (long‑chain‑fatty‑acid‑‑CoA ligase)/Slp family lipoprotein, RpoE‑regulated
RA	1,895,059	G→C	5.2%	Q85H (CAG→CAC)	pabB →	aminodeoxychorismate synthase, subunit I
RA	1,926,894	T→G	5.1%	D649A (GAC→GCC)	ptrB ←	protease II
RA	1,926,900	T→G	5.1%	D647A (GAC→GCC)	ptrB ←	protease II
RA	1,932,094	C→G	5.9%	intergenic (+35/+21)	purT → / ← eda	phosphoribosylglycinamide formyltransferase 2/KHG/KDPG aldolase; 2‑dehydro‑3‑deoxy‑phosphogluconate/4‑hydroxy‑2‑ oxoglutarate aldolase
RA	1,932,096	C→G	5.1%	intergenic (+37/+19)	purT → / ← eda	phosphoribosylglycinamide formyltransferase 2/KHG/KDPG aldolase; 2‑dehydro‑3‑deoxy‑phosphogluconate/4‑hydroxy‑2‑ oxoglutarate aldolase
MC JC	1,978,503	Δ776 bp	100%		insB1–insA	insB1, insA
JC JC	1,979,486	IS5 (+) +4 bp	100%	intergenic (‑271/‑264)	insA ← / → uspC	IS1 repressor TnpA/universal stress protein
RA	1,990,922	C→T	8.6%	intergenic (+30/+32)	tyrP → / ← yecA	tyrosine transporter/UPF0149 family protein
RA	1,990,926	A→C	8.1%	intergenic (+34/+28)	tyrP → / ← yecA	tyrosine transporter/UPF0149 family protein
RA	1,990,927	A→G	8.6%	intergenic (+35/+27)	tyrP → / ← yecA	tyrosine transporter/UPF0149 family protein
RA	1,990,932	C→T	8.5%	intergenic (+40/+22)	tyrP → / ← yecA	tyrosine transporter/UPF0149 family protein
RA	1,990,933	G→T	8.5%	intergenic (+41/+21)	tyrP → / ← yecA	tyrosine transporter/UPF0149 family protein
RA	1,990,937	A→G	8.8%	intergenic (+45/+17)	tyrP → / ← yecA	tyrosine transporter/UPF0149 family protein
RA	1,992,083	G→C	5.9%	noncoding (35/76 nt)	glyW ←	tRNA‑Gly
RA	1,996,068	T→A	7.0%	intergenic (+26/+42)	yecF → / ← sdiA	DUF2594 family protein/quorum‑sensing transcriptional activator
RA	2,032,336	G→C	6.7%	intergenic (‑19/+48)	dcm ← / ← yedJ	DNA cytosine methyltransferase/putative HD superfamily phosphohydrolase
RA	2,081,057	A→G	6.6%	V69A (GTG→GCG) ‡	sbmC ←	DNA gyrase inhibitor
RA	2,081,058	C→T	6.6%	V69M (GTG→ATG) ‡	sbmC ←	DNA gyrase inhibitor
RA	2,090,122	A→G	5.1%	intergenic (+76/‑70)	hisL → / → hisG	his operon leader peptide/ATP phosphoribosyltransferase
RA	2,090,124	C→G	5.4%	intergenic (+78/‑68)	hisL → / → hisG	his operon leader peptide/ATP phosphoribosyltransferase
RA	2,090,126	C→T	5.3%	intergenic (+80/‑66)	hisL → / → hisG	his operon leader peptide/ATP phosphoribosyltransferase
RA	2,115,849	C→G	5.1%	S16S (TCG→TCC) ‡	wcaM ←	colanic acid biosynthesis protein
RA	2,115,851	A→C	6.8%	S16A (TCG→GCG) ‡	wcaM ←	colanic acid biosynthesis protein
RA	2,121,583	Δ1 bp	5.3%	intergenic (‑29/+26)	wcaJ ← / ← cpsG	colanic biosynthesis UDP‑glucose lipid carrier transferase/phosphomannomutase
RA	2,121,586	G→C	5.9%	intergenic (‑32/+23)	wcaJ ← / ← cpsG	colanic biosynthesis UDP‑glucose lipid carrier transferase/phosphomannomutase
RA	2,121,588:1	+C	5.6%	intergenic (‑34/+21)	wcaJ ← / ← cpsG	colanic biosynthesis UDP‑glucose lipid carrier transferase/phosphomannomutase
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	2,199,607	A→G	8.6%	pseudogene (286/948 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
RA	2,199,608	A→T	8.3%	pseudogene (287/948 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
RA	2,199,609	C→T	8.3%	pseudogene (288/948 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
RA	2,259,549	A→T	5.7%	intergenic (‑253/+170)	psuK ← / ← fruA	pseudouridine kinase/fused fructose‑specific PTS enzymes: IIBcomponent/IIC components
RA	2,259,550	A→T	5.9%	intergenic (‑254/+169)	psuK ← / ← fruA	pseudouridine kinase/fused fructose‑specific PTS enzymes: IIBcomponent/IIC components
RA	2,259,553	A→T	6.0%	intergenic (‑257/+166)	psuK ← / ← fruA	pseudouridine kinase/fused fructose‑specific PTS enzymes: IIBcomponent/IIC components
RA	2,259,554	A→T	6.0%	intergenic (‑258/+165)	psuK ← / ← fruA	pseudouridine kinase/fused fructose‑specific PTS enzymes: IIBcomponent/IIC components
RA	2,266,047	T→C	5.2%	intergenic (+25/‑198)	yeiP → / → yeiQ	elongation factor P‑like protein/putative NAD‑dependent D‑mannonate oxidoreductase
RA	2,266,051	T→C	5.1%	intergenic (+29/‑194)	yeiP → / → yeiQ	elongation factor P‑like protein/putative NAD‑dependent D‑mannonate oxidoreductase
RA	2,266,052	C→T	5.7%	intergenic (+30/‑193)	yeiP → / → yeiQ	elongation factor P‑like protein/putative NAD‑dependent D‑mannonate oxidoreductase
RA	2,266,053	A→G	5.1%	intergenic (+31/‑192)	yeiP → / → yeiQ	elongation factor P‑like protein/putative NAD‑dependent D‑mannonate oxidoreductase
RA	2,266,054	G→A	5.1%	intergenic (+32/‑191)	yeiP → / → yeiQ	elongation factor P‑like protein/putative NAD‑dependent D‑mannonate oxidoreductase
RA	2,266,058	G→A	5.0%	intergenic (+36/‑187)	yeiP → / → yeiQ	elongation factor P‑like protein/putative NAD‑dependent D‑mannonate oxidoreductase
RA	2,270,602	T→C	5.0%	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	2,282,898	A→G	5.4%	intergenic (+97/+42)	rplY → / ← yejK	50S ribosomal subunit protein L25/spermidine nucleoid‑associated protein
RA	2,282,899	A→C	5.4%	intergenic (+98/+41)	rplY → / ← yejK	50S ribosomal subunit protein L25/spermidine nucleoid‑associated protein
RA	2,282,905	T→G	6.4%	intergenic (+104/+35)	rplY → / ← yejK	50S ribosomal subunit protein L25/spermidine nucleoid‑associated protein
RA	2,282,906	C→A	7.2%	intergenic (+105/+34)	rplY → / ← yejK	50S ribosomal subunit protein L25/spermidine nucleoid‑associated protein
RA	2,282,912	G→T	5.5%	intergenic (+111/+28)	rplY → / ← yejK	50S ribosomal subunit protein L25/spermidine nucleoid‑associated protein
RA	2,282,913	C→T	6.6%	intergenic (+112/+27)	rplY → / ← yejK	50S ribosomal subunit protein L25/spermidine nucleoid‑associated protein
RA	2,286,311	C→G	7.1%	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	6.8%	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	6.6%	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	2,290,448	A→G	5.3%	intergenic (‑268/‑52)	yejO ← / → narP	pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system/response regulator in two‑component regulatory system with NarQ
RA	2,290,449	C→G	5.4%	intergenic (‑269/‑51)	yejO ← / → narP	pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system/response regulator in two‑component regulatory system with NarQ
RA	2,290,450	C→T	5.4%	intergenic (‑270/‑50)	yejO ← / → narP	pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system/response regulator in two‑component regulatory system with NarQ
RA	2,361,189	G→C	5.3%	Q76E (CAG→GAG)	rhmD ←	L‑rhamnonate dehydratase
RA	2,407,898	A→C	5.5%	Q113P (CAG→CCG) ‡	alaA →	glutamate‑pyruvate aminotransferase; glutamic‑pyruvic transaminase (GPT); alanine transaminase
RA	2,407,899	G→T	6.0%	Q113H (CAG→CAT) ‡	alaA →	glutamate‑pyruvate aminotransferase; glutamic‑pyruvic transaminase (GPT); alanine transaminase
RA	2,411,413	A→T	5.6%	intergenic (‑61/+26)	yfbS ← / ← yfbT	putative transporter/sugar phosphatas
RA	2,430,144	G→C	5.5%	A32G (GCC→GGC)	purF ←	amidophosphoribosyltransferase
RA	2,438,869	A→C	5.6%	Q307P (CAA→CCA)	flk →	putative flagella assembly protein
RA	2,438,871	A→T	6.3%	N308Y (AAT→TAT)	flk →	putative flagella assembly protein
RA	2,438,874	A→T	5.3%	M309L (ATG→TTG) ‡	flk →	putative flagella assembly protein
RA	2,438,876	G→T	6.5%	M309I (ATG→ATT) ‡	flk →	putative flagella assembly protein
RA	2,462,678	T→A	5.4%	intergenic (+32/‑334)	fadL → / → yfdF	long‑chain fatty acid outer membrane transporter/uncharacterized protein
RA	2,474,878	T→C	6.9%	intergenic (+22/‑106)	yfdQ → / → yfdR	CPS‑53 (KpLE1) prophage; uncharacterized protein/CPS‑53 (KpLE1) prophage; conserved protein
RA	2,474,881	G→A	7.5%	intergenic (+25/‑103)	yfdQ → / → yfdR	CPS‑53 (KpLE1) prophage; uncharacterized protein/CPS‑53 (KpLE1) prophage; conserved protein
RA	2,477,014	C→A	6.8%	A206S (GCA→TCA)	dsdC ←	dsd operon activator; autorepressor
RA	2,477,022	T→G	7.4%	D203A (GAC→GCC)	dsdC ←	dsd operon activator; autorepressor
RA	2,512,728	C→A	5.8%	intergenic (‑22/‑314)	mntH ← / → nupC	manganese/divalent cation transporter/nucleoside (except guanosine) transporter
RA	2,512,729	T→A	6.7%	intergenic (‑23/‑313)	mntH ← / → nupC	manganese/divalent cation transporter/nucleoside (except guanosine) transporter
RA	2,512,730	T→A	6.1%	intergenic (‑24/‑312)	mntH ← / → nupC	manganese/divalent cation transporter/nucleoside (except guanosine) transporter
RA	2,512,731	T→G	5.6%	intergenic (‑25/‑311)	mntH ← / → nupC	manganese/divalent cation transporter/nucleoside (except guanosine) transporter
RA	2,519,222	T→G	6.3%	intergenic (+17/+35)	yfeD → / ← gltX	DUF1323 family putative DNA‑binding protein/glutamyl‑tRNA synthetase
RA	2,519,225	T→A	6.1%	intergenic (+20/+32)	yfeD → / ← gltX	DUF1323 family putative DNA‑binding protein/glutamyl‑tRNA synthetase
RA	2,519,228	C→A	6.8%	intergenic (+23/+29)	yfeD → / ← gltX	DUF1323 family putative DNA‑binding protein/glutamyl‑tRNA synthetase
RA	2,521,344	C→T	6.9%	intergenic (+16/+249)	lysV → / ← xapR	tRNA‑Lys/transcriptional activator of xapAB
RA	2,521,346	A→T	5.6%	intergenic (+18/+247)	lysV → / ← xapR	tRNA‑Lys/transcriptional activator of xapAB
RA	2,521,348	A→G	5.6%	intergenic (+20/+245)	lysV → / ← xapR	tRNA‑Lys/transcriptional activator of xapAB
RA	2,550,574	C→G	5.6%	intergenic (‑29/+67)	yfeX ← / ← yfeY	porphyrinogen oxidase, cytoplasmic/RpoE‑regulated lipoprotein
RA	2,550,576	A→T	5.5%	intergenic (‑31/+65)	yfeX ← / ← yfeY	porphyrinogen oxidase, cytoplasmic/RpoE‑regulated lipoprotein
RA	2,550,578	C→G	6.1%	intergenic (‑33/+63)	yfeX ← / ← yfeY	porphyrinogen oxidase, cytoplasmic/RpoE‑regulated lipoprotein
RA	2,566,490	C→T	5.7%	G132D (GGT→GAT)	eutA ←	reactivating factor for ethanolamine ammonia lyase
RA	2,566,493	G→C	5.4%	A131G (GCC→GGC)	eutA ←	reactivating factor for ethanolamine ammonia lyase
RA	2,566,496	A→G	5.3%	I130T (ATC→ACC)	eutA ←	reactivating factor for ethanolamine ammonia lyase
RA	2,638,584	A→T	5.7%	F23L (TTT→TTA)	bamB ←	BamABCDE complex OM biogenesis lipoprotein
RA	2,653,367	G→A	5.2%	intergenic (+28/‑488)	sseA → / → ryfA	3‑mercaptopyruvate sulfurtransferase/novel sRNA, function unknown
RA	2,653,372	T→C	5.2%	intergenic (+33/‑483)	sseA → / → ryfA	3‑mercaptopyruvate sulfurtransferase/novel sRNA, function unknown
RA	2,661,487	C→G	5.2%	V15V (GTG→GTC)	iscS ←	cysteine desulfurase (tRNA sulfurtransferase), PLP‑dependent
RA	2,673,790	G→T	5.4%	intergenic (+22/+26)	yphA → / ← yphB	DoxX family inner membrane protein/mutarotase superfamily protein, YphB family
RA	2,673,797	T→G	5.6%	intergenic (+29/+19)	yphA → / ← yphB	DoxX family inner membrane protein/mutarotase superfamily protein, YphB family
RA	2,684,199	T→G	5.3%	intergenic (+143/+55)	yphH → / ← glyA	putative DNA‑binding transcriptional regulator/serine hydroxymethyltransferase
RA	2,684,206	G→T	5.6%	intergenic (+150/+48)	yphH → / ← glyA	putative DNA‑binding transcriptional regulator/serine hydroxymethyltransferase
RA	2,684,207	C→T	5.0%	intergenic (+151/+47)	yphH → / ← glyA	putative DNA‑binding transcriptional regulator/serine hydroxymethyltransferase
RA	2,739,791	T→G	5.5%	T93T (ACA→ACC)	tyrA ←	fused chorismate mutase T/prephenate dehydrogenase
RA	2,761,620	T→G	8.6%	K641Q (AAG→CAG)	yfjK ←	radiation resistance protein; DEAD/H helicase‑like protein; CP4‑57 putative defective prophage
RA	2,761,623	C→A	9.0%	V640L (GTA→TTA)	yfjK ←	radiation resistance protein; DEAD/H helicase‑like protein; CP4‑57 putative defective prophage
RA	2,770,319	C→G	6.2%	P206R (CCG→CGG)	yfjR →	CP4‑57 prophage; putative DNA‑binding transcriptional regulator
RA	2,775,502	T→C	5.0%	intergenic (+481/‑43)	yfjW → / → ypjI	CP4‑57 prophage; putative inner membrane protein/pseudogene, CP4‑57 putative prophage remnant;Phage or Prophage Related
RA	2,775,503	C→T	5.7%	intergenic (+482/‑42)	yfjW → / → ypjI	CP4‑57 prophage; putative inner membrane protein/pseudogene, CP4‑57 putative prophage remnant;Phage or Prophage Related
RA	2,775,504	A→G	5.7%	intergenic (+483/‑41)	yfjW → / → ypjI	CP4‑57 prophage; putative inner membrane protein/pseudogene, CP4‑57 putative prophage remnant;Phage or Prophage Related
RA	2,775,505	G→A	5.1%	intergenic (+484/‑40)	yfjW → / → ypjI	CP4‑57 prophage; putative inner membrane protein/pseudogene, CP4‑57 putative prophage remnant;Phage or Prophage Related
RA	2,800,519	T→G	5.5%	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	6.0%	N31I (AAT→ATT)	nrdI →	NrdEF cluster assembly flavodoxin
RA	2,807,091	T→C	6.6%	intergenic (+17/‑41)	proW → / → proX	glycine betaine/proline ABC transporter permease/glycine betaine/proline ABC transporter periplasmic binding protein; cold shock protein
RA	2,807,093	A→T	6.9%	intergenic (+19/‑39)	proW → / → proX	glycine betaine/proline ABC transporter permease/glycine betaine/proline ABC transporter periplasmic binding protein; cold shock protein
RA	2,807,095	G→A	6.2%	intergenic (+21/‑37)	proW → / → proX	glycine betaine/proline ABC transporter permease/glycine betaine/proline ABC transporter periplasmic binding protein; cold shock protein
RA	2,814,860	A→G	5.5%	noncoding (59/78 nt)	micA →	sRNA antisense regulator of ompA, lamB, ompX, and phoP; Hfq‑dependent
RA	2,814,861	C→T	5.5%	noncoding (60/78 nt)	micA →	sRNA antisense regulator of ompA, lamB, ompX, and phoP; Hfq‑dependent
RA	2,818,324	G→A	8.3%	intergenic (‑50/+149)	argY ← / ← argV	tRNA‑Arg/tRNA‑Arg
RA	2,818,331	G→T	6.1%	intergenic (‑57/+142)	argY ← / ← argV	tRNA‑Arg/tRNA‑Arg
RA	2,822,673	C→T	6.6%	intergenic (‑34/+35)	recX ← / ← recA	regulatory protein for RecA/DNA recombination and repair protein; ssDNA‑dependent ATPase; synaptase; ssDNA and dsDNA binding protein; ATP‑dependent homologous DNA strand exchanger; recombinase A; LexA autocleavage cofactor
RA	2,822,678	G→T	6.9%	intergenic (‑39/+30)	recX ← / ← recA	regulatory protein for RecA/DNA recombination and repair protein; ssDNA‑dependent ATPase; synaptase; ssDNA and dsDNA binding protein; ATP‑dependent homologous DNA strand exchanger; recombinase A; LexA autocleavage cofactor
RA	2,822,679	A→C	8.6%	intergenic (‑40/+29)	recX ← / ← recA	regulatory protein for RecA/DNA recombination and repair protein; ssDNA‑dependent ATPase; synaptase; ssDNA and dsDNA binding protein; ATP‑dependent homologous DNA strand exchanger; recombinase A; LexA autocleavage cofactor
RA	2,822,684	A→G	6.6%	intergenic (‑45/+24)	recX ← / ← recA	regulatory protein for RecA/DNA recombination and repair protein; ssDNA‑dependent ATPase; synaptase; ssDNA and dsDNA binding protein; ATP‑dependent homologous DNA strand exchanger; recombinase A; LexA autocleavage cofactor
RA	2,856,257	G→C	6.1%	L640L (CTG→CTC)	fhlA →	formate hydrogenlyase transcriptional activator
RA	2,856,258	G→C	7.1%	E641Q (GAG→CAG)	fhlA →	formate hydrogenlyase transcriptional activator
RA	2,870,870	T→A	7.0%	E145D (GAA→GAT) ‡	truD ←	tRNA(Glu) pseudouridine(13) synthase
RA	2,870,871	T→A	6.4%	E145V (GAA→GTA) ‡	truD ←	tRNA(Glu) pseudouridine(13) synthase
RA	2,884,578	C→A	5.1%	R881I (AGA→ATA)	ygcB ←	Cascade complex anti‑viral R‑loop helicase‑annealase Cas3
RA	2,890,613	A→T	5.7%	V429E (GTG→GAG)	cysJ ←	sulfite reductase, alpha subunit, flavoprotein
RA	2,890,617	G→T	5.7%	R428S (CGC→AGC)	cysJ ←	sulfite reductase, alpha subunit, flavoprotein
RA	2,890,619	T→A	5.2%	D427V (GAC→GTC)	cysJ ←	sulfite reductase, alpha subunit, flavoprotein
RA	2,890,621	A→C	5.5%	A426A (GCT→GCG)	cysJ ←	sulfite reductase, alpha subunit, flavoprotein
RA	2,890,625	A→T	5.4%	L425H (CTC→CAC)	cysJ ←	sulfite reductase, alpha subunit, flavoprotein
RA	2,900,322	C→T	6.2%	intergenic (‑49/‑270)	ygcW ← / → yqcE	putative SDR family oxidoreductase/putative MFS transporter, inner membrane protein
RA	2,900,324	G→T	6.1%	intergenic (‑51/‑268)	ygcW ← / → yqcE	putative SDR family oxidoreductase/putative MFS transporter, inner membrane protein
RA	2,900,327	A→C	6.5%	intergenic (‑54/‑265)	ygcW ← / → yqcE	putative SDR family oxidoreductase/putative MFS transporter, inner membrane protein
RA	2,902,495	A→C	5.5%	G200G (GGA→GGC)	ygcE →	putative kinase
RA	2,906,609	G→C	5.0%	intergenic (+26/+34)	ygcG → / ← eno	TPM domain protein, putative phosphatase/enolase
RA	2,931,836	T→G	6.0%	intergenic (+26/+29)	ygdG → / ← fucO	Ssb‑binding protein, misidentified as ExoIX/L‑1,2‑propanediol oxidoreductase
RA	2,960,926	G→C	5.7%	G501G (GGC→GGG) ‡	recC ←	exonuclease V (RecBCD complex), gamma chain
RA	2,960,928	C→G	5.2%	G501R (GGC→CGC) ‡	recC ←	exonuclease V (RecBCD complex), gamma chain
RA	2,960,930	G→C	5.2%	S500C (TCC→TGC)	recC ←	exonuclease V (RecBCD complex), gamma chain
RA	2,962,561	G→A	5.3%	N68N (AAC→AAT) ‡	ppdC ←	putative prepilin peptidase‑dependent protein
RA	2,962,562	T→C	5.3%	N68S (AAC→AGC) ‡	ppdC ←	putative prepilin peptidase‑dependent protein
RA	2,971,146	T→C	5.8%	intergenic (+13/‑125)	ygdQ → / → ygdR	UPF0053 family inner membrane protein/DUF903 family verified lipoprotein
RA	2,971,151	T→C	5.8%	intergenic (+18/‑120)	ygdQ → / → ygdR	UPF0053 family inner membrane protein/DUF903 family verified lipoprotein
RA	2,971,154	G→A	5.7%	intergenic (+21/‑117)	ygdQ → / → ygdR	UPF0053 family inner membrane protein/DUF903 family verified lipoprotein
RA	2,971,159	G→A	5.8%	intergenic (+26/‑112)	ygdQ → / → ygdR	UPF0053 family inner membrane protein/DUF903 family verified lipoprotein
RA	2,976,320	T→G	5.6%	noncoding (66/82 nt)	omrB ←	sRNA antisense regulator downregulates OM proteins and curli; positively regulated by OmpR/EnvZ, Hfq‑dependent
RA	2,987,103	C→T	5.9%	intergenic (+27/‑433)	yqeG → / → yqeH	putative transporter/putative LuxR family transcriptional regulator
RA	2,987,104	T→A	5.9%	intergenic (+28/‑432)	yqeG → / → yqeH	putative transporter/putative LuxR family transcriptional regulator
RA	2,987,105	A→G	5.9%	intergenic (+29/‑431)	yqeG → / → yqeH	putative transporter/putative LuxR family transcriptional regulator
RA	2,991,805:1	+T	5.0%	intergenic (+46/‑289)	ygeG → / → ygeH	SycD‑like chaperone family TPR‑repeat‑containing protein/putative transcriptional regulator
RA	2,991,805:2	+G	5.0%	intergenic (+46/‑289)	ygeG → / → ygeH	SycD‑like chaperone family TPR‑repeat‑containing protein/putative transcriptional regulator
RA	2,993,889	T→A	7.1%	intergenic (+33/‑50)	ygeI → / → pbl	uncharacterized protein/pseudogene, peptidoglycan‑binding enzyme family
RA	2,993,896	T→A	7.3%	intergenic (+40/‑43)	ygeI → / → pbl	uncharacterized protein/pseudogene, peptidoglycan‑binding enzyme family
RA	3,020,512	A→C	5.1%	intergenic (+23/‑28)	ssnA → / → ygfM	putative chlorohydrolase/aminohydrolase/putative oxidoreductase
RA	3,033,624	A→G	5.2%	intergenic (+11/+33)	idi → / ← lysS	isopentenyl diphosphate isomerase/lysine tRNA synthetase, constitutive
RA	3,033,627	T→A	5.9%	intergenic (+14/+30)	idi → / ← lysS	isopentenyl diphosphate isomerase/lysine tRNA synthetase, constitutive
RA	3,033,628	T→A	5.2%	intergenic (+15/+29)	idi → / ← lysS	isopentenyl diphosphate isomerase/lysine tRNA synthetase, constitutive
RA	3,033,631	C→T	5.2%	intergenic (+18/+26)	idi → / ← lysS	isopentenyl diphosphate isomerase/lysine tRNA synthetase, constitutive
RA	3,045,124	T→C	5.9%	intergenic (+23/+34)	bglA → / ← ygfF	6‑phospho‑beta‑glucosidase A/putative NAD(P)‑dependent oxidoreductase
RA	3,045,126	C→A	6.1%	intergenic (+25/+32)	bglA → / ← ygfF	6‑phospho‑beta‑glucosidase A/putative NAD(P)‑dependent oxidoreductase
RA	3,045,127	T→G	5.8%	intergenic (+26/+31)	bglA → / ← ygfF	6‑phospho‑beta‑glucosidase A/putative NAD(P)‑dependent oxidoreductase
RA	3,045,129	G→A	5.9%	intergenic (+28/+29)	bglA → / ← ygfF	6‑phospho‑beta‑glucosidase A/putative NAD(P)‑dependent oxidoreductase
RA	3,050,713	A→T	5.4%	intergenic (‑46/+402)	gcvT ← / ← ubiI	aminomethyltransferase, tetrahydrofolate‑dependent, subunit (T protein) of glycine cleavage complex/2‑octaprenylphenol hydroxylase, FAD‑dependent
RA	3,050,715	T→A	6.5%	intergenic (‑48/+400)	gcvT ← / ← ubiI	aminomethyltransferase, tetrahydrofolate‑dependent, subunit (T protein) of glycine cleavage complex/2‑octaprenylphenol hydroxylase, FAD‑dependent
RA	3,050,717	A→T	5.1%	intergenic (‑50/+398)	gcvT ← / ← ubiI	aminomethyltransferase, tetrahydrofolate‑dependent, subunit (T protein) of glycine cleavage complex/2‑octaprenylphenol hydroxylase, FAD‑dependent
RA	3,066,309	T→A	5.5%	I289F (ATT→TTT)	ygfI ←	putative DNA‑binding transcriptional regulator
RA	3,066,310	A→T	5.2%	H288Q (CAT→CAA)	ygfI ←	putative DNA‑binding transcriptional regulator
RA	3,096,861	A→C	7.7%	T61P (ACC→CCC)	rdgB →	dITP/XTP pyrophosphatase
RA	3,101,656	T→A	5.0%	intergenic (‑33/+151)	yggN ← / ← yggL	DUF2884 family putative periplasmic protein/DUF469 family protein
RA	3,105,536	G→C	5.2%	intergenic (+24/‑178)	mltC → / → nupG	membrane‑bound lytic murein transglycosylase C/nucleoside transporter
RA	3,110,399	G→T	5.5%	noncoding (34/76 nt)	pheV →	tRNA‑Phe
RA	3,110,400	A→T	5.5%	noncoding (35/76 nt)	pheV →	tRNA‑Phe
RA	3,110,401	A→C	5.5%	noncoding (36/76 nt)	pheV →	tRNA‑Phe
RA	3,125,409	T→A	5.0%	E17D (GAA→GAT)	glcF ←	glycolate oxidase 4Fe‑4S iron‑sulfur cluster subunit
RA	3,135,356	T→C	5.2%	Q339R (CAG→CGG) ‡	pitB ←	phosphate transporter
RA	3,135,357	G→A	5.2%	Q339* (CAG→TAG) ‡	pitB ←	phosphate transporter
RA	3,140,859	T→G	7.4%	E143A (GAG→GCG)	hybD ←	maturation protease for hydrogenase 2
RA	3,140,861	A→T	7.8%	L142L (CTT→CTA) ‡	hybD ←	maturation protease for hydrogenase 2
RA	3,140,862	A→T	7.8%	L142H (CTT→CAT) ‡	hybD ←	maturation protease for hydrogenase 2
RA	3,140,864	C→A	7.5%	A141A (GCG→GCT)	hybD ←	maturation protease for hydrogenase 2
RA	3,155,227	C→A	6.2%	intergenic (‑9/‑128)	yqhC ← / → yqhD	transcriptional activator of yqhD/aldehyde reductase, NADPH‑dependent
RA	3,155,228	A→G	5.8%	intergenic (‑10/‑127)	yqhC ← / → yqhD	transcriptional activator of yqhD/aldehyde reductase, NADPH‑dependent
RA	3,155,229	C→T	6.0%	intergenic (‑11/‑126)	yqhC ← / → yqhD	transcriptional activator of yqhD/aldehyde reductase, NADPH‑dependent
RA	3,155,230	T→G	6.0%	intergenic (‑12/‑125)	yqhC ← / → yqhD	transcriptional activator of yqhD/aldehyde reductase, NADPH‑dependent
RA	3,179,613	T→G	5.4%	intergenic (+17/‑131)	tolC → / → ygiB	transport channel/DUF1190 family protein
RA	3,183,345:1	+T	7.0%	intergenic (+22/+468)	zupT → / ← ribB	zinc transporter/3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase
RA	3,183,350	Δ1 bp	7.5%	intergenic (+27/+463)	zupT → / ← ribB	zinc transporter/3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase
RA	3,233,153	A→T	5.8%	K497* (AAA→TAA) ‡	fadH →	2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked
RA	3,233,154	A→T	5.2%	K497I (AAA→ATA) ‡	fadH →	2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked
RA	3,233,155	A→T	5.0%	K497N (AAA→AAT) ‡	fadH →	2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked
RA	3,241,788	T→A	5.4%	intergenic (‑44/+39)	ygjV ← / ← uxaA	Imp‑YgjV family inner membrane protein/altronate hydrolase
RA	3,269,956	T→C	14.7%	intergenic (+354/+260)	yhaC → / ← rnpB	pentapetide repeats‑related protein/RNase P, M1 RNA component
RA	3,288,032	C→A	9.2%	intergenic (+22/‑58)	yraH → / → yraI	putative fimbrial‑like adhesin protein/putative periplasmic pilin chaperone
RA	3,288,033	T→G	8.8%	intergenic (+23/‑57)	yraH → / → yraI	putative fimbrial‑like adhesin protein/putative periplasmic pilin chaperone
RA	3,307,094	T→G	10.3%	N256T (AAC→ACC)	deaD ←	ATP‑dependent RNA helicase
RA	3,313,207	G→A	5.6%	intergenic (‑29/+135)	rbfA ← / ← infB	30s ribosome binding factor/translation initiation factor IF‑2
RA	3,313,208	T→A	5.8%	intergenic (‑30/+134)	rbfA ← / ← infB	30s ribosome binding factor/translation initiation factor IF‑2
RA	3,313,209	T→C	5.6%	intergenic (‑31/+133)	rbfA ← / ← infB	30s ribosome binding factor/translation initiation factor IF‑2
RA	3,322,049	T→A	5.2%	intergenic (‑436/+23)	yhbX ← / ← leuU	putative EptAB family phosphoethanolamine transferase, inner membrane protein/tRNA‑Leu
RA	3,322,698	A→G	5.7%	intergenic (‑193/+35)	secG ← / ← glmM	preprotein translocase membrane subunit/phosphoglucosamine mutase
RA	3,322,700	A→G	5.7%	intergenic (‑195/+33)	secG ← / ← glmM	preprotein translocase membrane subunit/phosphoglucosamine mutase
RA	3,322,703	C→T	6.0%	intergenic (‑198/+30)	secG ← / ← glmM	preprotein translocase membrane subunit/phosphoglucosamine mutase
RA	3,322,705	C→T	6.0%	intergenic (‑200/+28)	secG ← / ← glmM	preprotein translocase membrane subunit/phosphoglucosamine mutase
RA	3,332,822	G→A	6.0%	intergenic (‑87/+40)	yhbE ← / ← rpmA	EamA family inner membrane putative transporter/50S ribosomal subunit protein L27
RA	3,332,823	T→C	6.1%	intergenic (‑88/+39)	yhbE ← / ← rpmA	EamA family inner membrane putative transporter/50S ribosomal subunit protein L27
RA	3,360,643	T→A	5.1%	intergenic (+27/‑533)	gltD → / → gltF	glutamate synthase, 4Fe‑4S protein, small subunit/periplasmic protein
RA	3,377,768	C→T	5.1%	intergenic (‑348/+47)	sspA ← / ← rpsI	stringent starvation protein A, phage P1 late gene activator, RNAP‑associated acid‑resistance protein, inactive glutathione S‑transferase homolog/30S ribosomal subunit protein S9
RA	3,382,133	T→G	5.4%	intergenic (+23/‑67)	degQ → / → degS	serine endoprotease, periplasmic/serine endoprotease, periplasmic
RA	3,382,136	C→A	5.5%	intergenic (+26/‑64)	degQ → / → degS	serine endoprotease, periplasmic/serine endoprotease, periplasmic
RA	3,382,138	T→C	5.1%	intergenic (+28/‑62)	degQ → / → degS	serine endoprotease, periplasmic/serine endoprotease, periplasmic
RA	3,382,139	G→C	5.1%	intergenic (+29/‑61)	degQ → / → degS	serine endoprotease, periplasmic/serine endoprotease, periplasmic
RA	3,382,145	T→C	5.1%	intergenic (+35/‑55)	degQ → / → degS	serine endoprotease, periplasmic/serine endoprotease, periplasmic
RA	3,388,284	A→T	5.3%	A281A (GCT→GCA)	aaeA ←	p‑hydroxybenzoic acid efflux system component
RA	3,439,588	G→C	5.9%	intergenic (‑79/+28)	yhdN ← / ← rplQ	DUF1992 family protein/50S ribosomal subunit protein L17
RA	3,439,589	G→C	6.7%	intergenic (‑80/+27)	yhdN ← / ← rplQ	DUF1992 family protein/50S ribosomal subunit protein L17
RA	3,441,060	T→C	6.4%	K206E (AAG→GAG)	rpsD ←	30S ribosomal subunit protein S4
RA	3,441,061	G→C	6.6%	S205S (TCC→TCG) ‡	rpsD ←	30S ribosomal subunit protein S4
RA	3,441,062	G→A	6.6%	S205F (TCC→TTC) ‡	rpsD ←	30S ribosomal subunit protein S4
RA	3,448,275	T→G	5.3%	intergenic (‑126/+39)	rplN ← / ← rpsQ	50S ribosomal subunit protein L14/30S ribosomal subunit protein S17
RA	3,448,276	T→A	6.0%	intergenic (‑127/+38)	rplN ← / ← rpsQ	50S ribosomal subunit protein L14/30S ribosomal subunit protein S17
RA	3,448,278	C→A	6.7%	intergenic (‑129/+36)	rplN ← / ← rpsQ	50S ribosomal subunit protein L14/30S ribosomal subunit protein S17
RA	3,458,110	C→A	100%	T578T (ACC→ACA)	gspD →	general secretory pathway component, cryptic
RA	3,458,416	T→A	5.3%	I26I (ATT→ATA)	gspE →	general secretory pathway component, cryptic
RA	3,482,325	G→A	100%	R346H (CGC→CAC)	yheS →	ABC‑F family protein predicted regulatory ATPase
RA	3,491,704	G→T	12.3%	intergenic (‑84/+21)	yhfG ← / ← ppiA	putative antitoxin for Fic/peptidyl‑prolyl cis‑trans isomerase A (rotamase A)
RA	3,491,705	A→C	14.2%	intergenic (‑85/+20)	yhfG ← / ← ppiA	putative antitoxin for Fic/peptidyl‑prolyl cis‑trans isomerase A (rotamase A)
RA	3,515,785	G→T	5.6%	L43L (CTC→CTA)	dam ←	DNA adenine methyltransferase
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	3,599,755	C→A	6.3%	intergenic (‑97/+174)	livJ ← / ← rpoH	branched‑chain amino acid ABC transporter periplasmic binding protein/RNA polymerase, sigma 32 (sigma H) factor
RA	3,600,993	A→G	5.1%	intergenic (‑210/+35)	rpoH ← / ← ftsX	RNA polymerase, sigma 32 (sigma H) factor/putative ABC transporter permease
RA	3,600,995	C→T	5.0%	intergenic (‑212/+33)	rpoH ← / ← ftsX	RNA polymerase, sigma 32 (sigma H) factor/putative ABC transporter permease
RA	3,601,000	T→A	5.5%	intergenic (‑217/+28)	rpoH ← / ← ftsX	RNA polymerase, sigma 32 (sigma H) factor/putative ABC transporter permease
RA	3,601,505	A→C	8.1%	R194R (CGT→CGG) ‡	ftsX ←	putative ABC transporter permease
RA	3,601,506	C→G	7.4%	R194P (CGT→CCT) ‡	ftsX ←	putative ABC transporter permease
RA	3,601,507	G→T	7.1%	R194S (CGT→AGT) ‡	ftsX ←	putative ABC transporter permease
RA	3,648,128	G→T	6.4%	noncoding (66/84 nt)	agrA →	inactive antisense sRNA
RA	3,648,129	C→T	5.8%	noncoding (67/84 nt)	agrA →	inactive antisense sRNA
RA	3,648,130	A→T	5.5%	noncoding (68/84 nt)	agrA →	inactive antisense sRNA
RA	3,648,131	A→G	5.5%	noncoding (69/84 nt)	agrA →	inactive antisense sRNA
RA	3,648,132	A→C	5.6%	noncoding (70/84 nt)	agrA →	inactive antisense sRNA
RA	3,648,319	C→T	5.2%	noncoding (26/84 nt)	agrB →	antisense sRNA antitoxin for the DinQ toxin
RA	3,663,547	T→C	5.4%	intergenic (+20/+343)	mdtF → / ← gadW	anaerobic multidrug efflux transporter, ArcA‑regulated/transcriptional activator of gadA and gadBC; repressor of gadX
RA	3,663,553	A→C	5.3%	intergenic (+26/+337)	mdtF → / ← gadW	anaerobic multidrug efflux transporter, ArcA‑regulated/transcriptional activator of gadA and gadBC; repressor of gadX
RA	3,663,555	G→T	5.4%	intergenic (+28/+335)	mdtF → / ← gadW	anaerobic multidrug efflux transporter, ArcA‑regulated/transcriptional activator of gadA and gadBC; repressor of gadX
RA	3,663,558	G→T	5.8%	intergenic (+31/+332)	mdtF → / ← gadW	anaerobic multidrug efflux transporter, ArcA‑regulated/transcriptional activator of gadA and gadBC; repressor of gadX
RA	3,663,564	G→A	5.3%	intergenic (+37/+326)	mdtF → / ← gadW	anaerobic multidrug efflux transporter, ArcA‑regulated/transcriptional activator of gadA and gadBC; repressor of gadX
RA	3,701,840	A→G	6.3%	intergenic (+6/+24)	yhjV → / ← dppF	putative transporter/dipeptide/heme ABC transporter ATPas
RA	3,701,843	Δ1 bp	6.3%	intergenic (+9/+21)	yhjV → / ← dppF	putative transporter/dipeptide/heme ABC transporter ATPas
RA	3,701,847:1	+C	6.3%	intergenic (+13/+17)	yhjV → / ← dppF	putative transporter/dipeptide/heme ABC transporter ATPas
RA	3,701,850	C→T	6.1%	intergenic (+16/+14)	yhjV → / ← dppF	putative transporter/dipeptide/heme ABC transporter ATPas
RA	3,720,793	G→T	6.1%	Q38H (CAG→CAT)	insJ →	IS150 transposase A
RA	3,720,797	A→C	6.1%	R40R (AGG→CGG) ‡	insJ →	IS150 transposase A
RA	3,720,798	G→T	6.1%	R40M (AGG→ATG) ‡	insJ →	IS150 transposase A
RA	3,720,802	A→C	6.6%	T41T (ACA→ACC)	insJ →	IS150 transposase A
RA	3,732,136	A→C	7.7%	intergenic (+13/‑65)	xylF → / → xylG	D‑xylose transporter subunit/D‑xylose ABC transporter dual domain ATPase
RA	3,732,139	G→T	7.0%	intergenic (+16/‑62)	xylF → / → xylG	D‑xylose transporter subunit/D‑xylose ABC transporter dual domain ATPase
RA	3,732,141	G→C	7.4%	intergenic (+18/‑60)	xylF → / → xylG	D‑xylose transporter subunit/D‑xylose ABC transporter dual domain ATPase
RA	3,732,143	A→C	9.0%	intergenic (+20/‑58)	xylF → / → xylG	D‑xylose transporter subunit/D‑xylose ABC transporter dual domain ATPase
RA	3,732,146	G→T	7.2%	intergenic (+23/‑55)	xylF → / → xylG	D‑xylose transporter subunit/D‑xylose ABC transporter dual domain ATPase
RA	3,748,108	T→A	5.0%	F342Y (TTC→TAC)	lyxK →	L‑xylulose kinase
RA	3,757,942	C→A	5.3%	intergenic (‑115/+75)	yiaY ← / ← selB	L‑threonine dehydrogenase/selenocysteinyl‑tRNA‑specific translation factor
RA	3,777,135	T→C	6.4%	intergenic (+108/‑264)	yibL → / → lldP	ribosome‑associated DUF2810 family protein/L‑lactate permease
RA	3,777,139	T→A	6.6%	intergenic (+112/‑260)	yibL → / → lldP	ribosome‑associated DUF2810 family protein/L‑lactate permease
RA	3,777,140	G→T	7.1%	intergenic (+113/‑259)	yibL → / → lldP	ribosome‑associated DUF2810 family protein/L‑lactate permease
RA	3,777,141	A→C	6.0%	intergenic (+114/‑258)	yibL → / → lldP	ribosome‑associated DUF2810 family protein/L‑lactate permease
RA	3,777,142	T→A	6.8%	intergenic (+115/‑257)	yibL → / → lldP	ribosome‑associated DUF2810 family protein/L‑lactate permease
RA	3,777,146	G→A	5.9%	intergenic (+119/‑253)	yibL → / → lldP	ribosome‑associated DUF2810 family protein/L‑lactate permease
RA	3,790,300	A→T	5.3%	intergenic (‑219/+20)	waaH ← / ← tdh	LPS(HepIII)‑glucuronic acid glycosyltransferase/L‑threonine 3‑dehydrogenase, NAD(P)‑binding
RA	3,790,303	A→T	6.0%	intergenic (‑222/+17)	waaH ← / ← tdh	LPS(HepIII)‑glucuronic acid glycosyltransferase/L‑threonine 3‑dehydrogenase, NAD(P)‑binding
RA	3,811,216	C→T	6.0%	intergenic (‑64/+34)	mutM ← / ← rpmG	formamidopyrimidine/5‑formyluracil/ 5‑hydroxymethyluracil DNA glycosylase/50S ribosomal subunit protein L33
RA	3,811,217	G→C	5.3%	intergenic (‑65/+33)	mutM ← / ← rpmG	formamidopyrimidine/5‑formyluracil/ 5‑hydroxymethyluracil DNA glycosylase/50S ribosomal subunit protein L33
RA	3,811,218	G→C	5.8%	intergenic (‑66/+32)	mutM ← / ← rpmG	formamidopyrimidine/5‑formyluracil/ 5‑hydroxymethyluracil DNA glycosylase/50S ribosomal subunit protein L33
RA	3,811,219	A→G	5.3%	intergenic (‑67/+31)	mutM ← / ← rpmG	formamidopyrimidine/5‑formyluracil/ 5‑hydroxymethyluracil DNA glycosylase/50S ribosomal subunit protein L33
RA	3,811,223	A→G	5.1%	intergenic (‑71/+27)	mutM ← / ← rpmG	formamidopyrimidine/5‑formyluracil/ 5‑hydroxymethyluracil DNA glycosylase/50S ribosomal subunit protein L33
RA	3,815,816	C→G	5.6%	intergenic (‑48/+18)	pyrE ← / ← rph	orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH
RA	3,815,819	C→G	5.6%	intergenic (‑51/+15)	pyrE ← / ← rph	orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH
MC JC	3,815,859	Δ82 bp	100%		[rph]–[rph]	[rph], [rph]
RA	3,853,674	G→T	5.4%	intergenic (+32/‑248)	tisB → / → emrD	toxic membrane persister formation peptide, LexA‑regulated/multidrug efflux system protein
RA	3,906,826	T→C	5.3%	intergenic (‑259/+27)	bglG ← / ← phoU	transcriptional antiterminator of the bgl operon/negative regulator of PhoR/PhoB two‑component regulator
RA	3,906,828	A→T	5.6%	intergenic (‑261/+25)	bglG ← / ← phoU	transcriptional antiterminator of the bgl operon/negative regulator of PhoR/PhoB two‑component regulator
RA	3,906,830	G→A	5.2%	intergenic (‑263/+23)	bglG ← / ← phoU	transcriptional antiterminator of the bgl operon/negative regulator of PhoR/PhoB two‑component regulator
RA	3,908,500	G→T	5.3%	intergenic (‑134/+49)	pstB ← / ← pstA	phosphate ABC transporter ATPase/phosphate ABC transporter permease
RA	3,908,506	C→G	6.6%	intergenic (‑140/+43)	pstB ← / ← pstA	phosphate ABC transporter ATPase/phosphate ABC transporter permease
RA	3,908,507	T→A	6.2%	intergenic (‑141/+42)	pstB ← / ← pstA	phosphate ABC transporter ATPase/phosphate ABC transporter permease
RA	3,908,512	A→C	6.1%	intergenic (‑146/+37)	pstB ← / ← pstA	phosphate ABC transporter ATPase/phosphate ABC transporter permease
RA	3,920,796	T→C	5.2%	A31A (GCA→GCG)	atpF ←	F0 sector of membrane‑bound ATP synthase, subunit b
RA	3,920,809	G→A	5.5%	P27L (CCG→CTG)	atpF ←	F0 sector of membrane‑bound ATP synthase, subunit b
RA	3,923,717	G→A	5.5%	intergenic (‑37/+27)	rsmG ← / ← mnmG	16S rRNA m(7)G527 methyltransferase, SAM‑dependent; glucose‑inhibited cell‑division protein/5‑methylaminomethyl‑2‑thiouridine modification at tRNA U34
RA	3,923,718	G→C	5.3%	intergenic (‑38/+26)	rsmG ← / ← mnmG	16S rRNA m(7)G527 methyltransferase, SAM‑dependent; glucose‑inhibited cell‑division protein/5‑methylaminomethyl‑2‑thiouridine modification at tRNA U34
RA	3,923,719	G→C	5.5%	intergenic (‑39/+25)	rsmG ← / ← mnmG	16S rRNA m(7)G527 methyltransferase, SAM‑dependent; glucose‑inhibited cell‑division protein/5‑methylaminomethyl‑2‑thiouridine modification at tRNA U34
RA	3,923,720	T→C	5.5%	intergenic (‑40/+24)	rsmG ← / ← mnmG	16S rRNA m(7)G527 methyltransferase, SAM‑dependent; glucose‑inhibited cell‑division protein/5‑methylaminomethyl‑2‑thiouridine modification at tRNA U34
RA	3,959,515	T→A	7.0%	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	9.3%	intergenic (‑111/+88)	ppiC ← / ← yifN	peptidyl‑prolyl cis‑trans isomerase C (rotamase C)/PemK toxin family pseudogene
RA	3,959,925	A→T	8.1%	intergenic (‑112/+87)	ppiC ← / ← yifN	peptidyl‑prolyl cis‑trans isomerase C (rotamase C)/PemK toxin family pseudogene
RA	3,959,926	A→T	7.8%	intergenic (‑113/+86)	ppiC ← / ← yifN	peptidyl‑prolyl cis‑trans isomerase C (rotamase C)/PemK toxin family pseudogene
RA	4,008,409	A→C	6.4%	intergenic (+32/+30)	rhtC → / ← rhtB	threonine efflux pump/homoserine, homoserine lactone and S‑methyl‑methionine efflux pump
RA	4,008,422	G→T	5.3%	intergenic (+45/+17)	rhtC → / ← rhtB	threonine efflux pump/homoserine, homoserine lactone and S‑methyl‑methionine efflux pump
RA	4,063,571	A→G	5.9%	intergenic (+59/+32)	yihN → / ← ompL	MFS transporter family protein/outer membrane porin L; putative sulpholipid porin
RA	4,063,572	A→C	6.1%	intergenic (+60/+31)	yihN → / ← ompL	MFS transporter family protein/outer membrane porin L; putative sulpholipid porin
RA	4,063,578	T→A	6.0%	intergenic (+66/+25)	yihN → / ← ompL	MFS transporter family protein/outer membrane porin L; putative sulpholipid porin
RA	4,094,581	A→G	5.3%	intergenic (‑309/+142)	rhaD ← / ← rhaA	rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase
RA	4,097,357	G→C	5.5%	T31R (ACG→AGG)	rhaB ←	rhamnulokinase
RA	4,097,359	C→G	5.5%	L30L (CTG→CTC) ‡	rhaB ←	rhamnulokinase
RA	4,097,361	G→C	5.7%	L30V (CTG→GTG) ‡	rhaB ←	rhamnulokinase
RA	4,118,831	C→A	5.1%	intergenic (+71/+14)	zapB → / ← rraA	FtsZ stabilizer, septal ring assembly factor, cell division stimulator/ribonuclease E (RNase E) inhibitor protein
RA	4,153,472	C→A	11.5%	intergenic (‑374/+224)	ppc ← / ← argE	phosphoenolpyruvate carboxylase/acetylornithine deacetylase
RA	4,176,408	T→C	15.3%	R155R (CGT→CGC)	tufB →	translation elongation factor EF‑Tu 2
RA	4,177,171	T→A	9.1%	intergenic (+43/‑187)	tufB → / → secE	translation elongation factor EF‑Tu 2/preprotein translocase membrane subunit
RA	4,177,172	T→A	8.8%	intergenic (+44/‑186)	tufB → / → secE	translation elongation factor EF‑Tu 2/preprotein translocase membrane subunit
RA	4,207,576	A→G	5.6%	intergenic (‑44/‑571)	purH ← / → rrsE	IMP cyclohydrolase and phosphoribosylaminoimidazolecarboxamide formyltransferase/16S ribosomal RNA of rrnE operon
RA	4,213,179	Δ1 bp	6.8%	intergenic (+20/‑55)	rrfE → / → yjaA	5S ribosomal RNA of rrnE operon/stress‑induced protein
RA	4,213,182	A→T	6.1%	intergenic (+23/‑52)	rrfE → / → yjaA	5S ribosomal RNA of rrnE operon/stress‑induced protein
RA	4,213,185	A→T	6.4%	intergenic (+26/‑49)	rrfE → / → yjaA	5S ribosomal RNA of rrnE operon/stress‑induced protein
RA	4,213,187:1	+A	6.8%	intergenic (+28/‑47)	rrfE → / → yjaA	5S ribosomal RNA of rrnE operon/stress‑induced protein
RA	4,274,740	G→A	5.1%	intergenic (+79/+20)	ssb → / ← yjcB	single‑stranded DNA‑binding protein/putative inner membrane protein
RA	4,275,154	T→A	5.0%	intergenic (‑113/‑317)	yjcB ← / → yjcC	putative inner membrane protein/putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	4,280,219	A→C	8.1%	E80D (GAA→GAC)	yjcE →	putative cation/proton antiporter
RA	4,280,224	G→T	7.2%	G82V (GGT→GTT)	yjcE →	putative cation/proton antiporter
RA	4,283,231	G→T	5.0%	intergenic (‑156/+22)	yjcF ← / ← actP	pentapeptide repeats protein/acetate transporter
RA	4,283,232	A→C	5.7%	intergenic (‑157/+21)	yjcF ← / ← actP	pentapeptide repeats protein/acetate transporter
RA	4,296,060	C→T	40.3%	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	4,312,080	G→C	5.2%	intergenic (‑38/+21)	alsB ← / ← alsR	D‑allose ABC transporter periplasmic binding protein/d‑allose‑inducible als operon transcriptional repressor; autorepressor; repressor of rpiR
RA	4,312,083	G→C	6.0%	intergenic (‑41/+18)	alsB ← / ← alsR	D‑allose ABC transporter periplasmic binding protein/d‑allose‑inducible als operon transcriptional repressor; autorepressor; repressor of rpiR
RA	4,312,089	A→G	5.6%	intergenic (‑47/+12)	alsB ← / ← alsR	D‑allose ABC transporter periplasmic binding protein/d‑allose‑inducible als operon transcriptional repressor; autorepressor; repressor of rpiR
RA	4,323,257	A→G	5.2%	intergenic (‑27/+79)	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	4,332,868	G→T	5.5%	R135R (CGC→CGA)	basS ←	sensory histidine kinase in two‑component regulatory system with BasR
RA	4,356,445	A→T	5.6%	intergenic (‑34/+25)	dtpC ← / ← cadA	dipeptide and tripeptide permease/lysine decarboxylase, acid‑inducible
RA	4,356,446	A→T	5.2%	intergenic (‑35/+24)	dtpC ← / ← cadA	dipeptide and tripeptide permease/lysine decarboxylase, acid‑inducible
RA	4,365,132	T→G	6.0%	A75A (GCA→GCC) ‡	cutA ←	divalent‑cation tolerance protein, copper sensitivity
RA	4,365,133	G→C	6.1%	A75G (GCA→GGA) ‡	cutA ←	divalent‑cation tolerance protein, copper sensitivity
RA	4,365,134	C→A	5.9%	A75S (GCA→TCA) ‡	cutA ←	divalent‑cation tolerance protein, copper sensitivity
RA	4,378,857	G→A	6.7%	R30C (CGC→TGC)	ampC ←	penicillin‑binding protein; beta‑lactamase, intrinsically weak
RA	4,378,858	A→T	7.2%	H29Q (CAT→CAA) ‡	ampC ←	penicillin‑binding protein; beta‑lactamase, intrinsically weak
RA	4,378,859	T→C	6.7%	H29R (CAT→CGT) ‡	ampC ←	penicillin‑binding protein; beta‑lactamase, intrinsically weak
RA	4,390,401	C→A	5.5%	intergenic (‑41/+56)	psd ← / ← rsgA	phosphatidylserine decarboxylase/ribosome small subunit‑dependent GTPase A
RA	4,390,403	A→G	5.7%	intergenic (‑43/+54)	psd ← / ← rsgA	phosphatidylserine decarboxylase/ribosome small subunit‑dependent GTPase A
RA	4,390,404	C→T	5.6%	intergenic (‑44/+53)	psd ← / ← rsgA	phosphatidylserine decarboxylase/ribosome small subunit‑dependent GTPase A
RA	4,390,406	T→G	5.2%	intergenic (‑46/+51)	psd ← / ← rsgA	phosphatidylserine decarboxylase/ribosome small subunit‑dependent GTPase A
RA	4,392,506	C→G	16.0%	noncoding (35/76 nt)	glyX →	tRNA‑Gly
RA	4,410,034	G→A	5.1%	intergenic (+28/‑99)	rlmB → / → yjfI	23S rRNA mG2251 2'‑O‑ribose methyltransferase, SAM‑dependent/DUF2170 family protein
RA	4,434,081	T→A	5.3%	intergenic (‑57/‑32)	qorB ← / → ytfH	NAD(P)H:quinone oxidoreductase/DUF24 family HxlR‑type putative transcriptional regulator
RA	4,470,951	A→C	7.7%	intergenic (‑38/+35)	ridA ← / ← pyrI	enamine/imine deaminase, reaction intermediate detoxification/aspartate carbamoyltransferase, regulatory subunit
RA	4,470,952	T→C	6.6%	intergenic (‑39/+34)	ridA ← / ← pyrI	enamine/imine deaminase, reaction intermediate detoxification/aspartate carbamoyltransferase, regulatory subunit
RA	4,470,957	G→A	6.9%	intergenic (‑44/+29)	ridA ← / ← pyrI	enamine/imine deaminase, reaction intermediate detoxification/aspartate carbamoyltransferase, regulatory subunit
RA	4,470,958	G→T	7.0%	intergenic (‑45/+28)	ridA ← / ← pyrI	enamine/imine deaminase, reaction intermediate detoxification/aspartate carbamoyltransferase, regulatory subunit
RA	4,473,927	C→A	100%	A43S (GCC→TCC)	bdcA ←	c‑di‑GMP‑binding biofilm dispersal mediator protein
RA	4,484,461	A→C	5.3%	A497A (GCT→GCG)	pepA ←	multifunctional aminopeptidase A: a cyteinylglycinase, transcription regulator and site‑specific recombination factor
RA	4,502,107	G→T	5.3%	A442D (GCT→GAT)	insG ←	IS4 transposase
RA	4,519,311	A→G	5.4%	intergenic (+87/+27)	insB1 → / ← yjhU	IS1 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related/putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element
RA	4,519,313	C→A	5.4%	intergenic (+89/+25)	insB1 → / ← yjhU	IS1 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related/putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element
RA	4,519,314	T→G	5.4%	intergenic (+90/+24)	insB1 → / ← yjhU	IS1 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related/putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element
RA	4,519,316	C→T	5.5%	intergenic (+92/+22)	insB1 → / ← yjhU	IS1 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related/putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element
RA	4,520,500	Δ1 bp	8.1%	intergenic (‑176/+171)	yjhU ← / ← yjhF	putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter
RA	4,520,504:1	+T	8.3%	intergenic (‑180/+167)	yjhU ← / ← yjhF	putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter
RA	4,537,639	T→G	5.2%	intergenic (‑45/+20)	nanS ← / ← nanM	9‑O‑acetyl N‑acetylneuraminic acid esterase/N‑acetylneuraminic acid mutarotase
RA	4,537,640	T→G	5.2%	intergenic (‑46/+19)	nanS ← / ← nanM	9‑O‑acetyl N‑acetylneuraminic acid esterase/N‑acetylneuraminic acid mutarotase
RA	4,537,643	C→A	5.3%	intergenic (‑49/+16)	nanS ← / ← nanM	9‑O‑acetyl N‑acetylneuraminic acid esterase/N‑acetylneuraminic acid mutarotase
RA	4,537,644	C→A	5.4%	intergenic (‑50/+15)	nanS ← / ← nanM	9‑O‑acetyl N‑acetylneuraminic acid esterase/N‑acetylneuraminic acid mutarotase
RA	4,549,932	T→A	6.0%	intergenic (+222/+21)	fimH → / ← gntP	minor component of type 1 fimbriae/fructuronate transporter
RA	4,551,422	T→A	5.1%	intergenic (‑126/‑214)	gntP ← / → uxuA	fructuronate transporter/mannonate hydrolase
RA	4,554,524	C→A	5.1%	intergenic (+163/‑52)	uxuB → / → uxuR	D‑mannonate oxidoreductase, NAD‑dependent/fructuronate‑inducible hexuronate regulon transcriptional repressor; autorepressor
RA	4,554,531	C→T	5.2%	intergenic (+170/‑45)	uxuB → / → uxuR	D‑mannonate oxidoreductase, NAD‑dependent/fructuronate‑inducible hexuronate regulon transcriptional repressor; autorepressor
RA	4,593,430	G→T	5.2%	V431V (GTC→GTA) ‡	lgoT ←	putative L‑galactonate:H+ symporter
RA	4,593,431	A→G	5.2%	V431A (GTC→GCC) ‡	lgoT ←	putative L‑galactonate:H+ symporter
RA	4,593,435	A→C	5.5%	C430G (TGC→GGC)	lgoT ←	putative L‑galactonate:H+ symporter
RA	4,618,053	T→G	5.5%	L244R (CTG→CGG)	deoC →	2‑deoxyribose‑5‑phosphate aldolase, NAD(P)‑linked
RA	4,624,359	A→G	5.0%	L144P (CTG→CCG)	ytjB ←	SMP_2 family putative membrane‑anchored periplasmic protein
RA	4,631,638	C→T	5.8%	R302R (CGC→CGT)	slt →	lytic murein transglycosylase, soluble
RA	4,631,639	G→C	5.8%	D303H (GAT→CAT)	slt →	lytic murein transglycosylase, soluble
RA	4,631,642	G→C	5.6%	D304H (GAC→CAC) ‡	slt →	lytic murein transglycosylase, soluble
RA	4,631,643	A→G	5.5%	D304G (GAC→GGC) ‡	slt →	lytic murein transglycosylase, soluble

Unassigned missing coverage evidence
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	448615	450715	2101	68 [67]	[66] 69	[cyoC]–[cyoA]	[cyoC],cyoB,[cyoA]
*	*	÷	NC_000913	2403912	2404689	778	68 [67]	[67] 68	nuoB–[nuoA]	nuoB,[nuoA]

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 16653	NA (NA)	6 (0.050)	3/264	NT	NA	noncoding (1267/1345 nt)	IS186	repeat region
	?	NC_000913	= 16691	NA (NA)					noncoding (1305/1345 nt)	IS186	repeat region
*	?	NC_000913	= 93199	119 (1.010)	7 (0.060)	5/268	NT	5.7%	coding (34/1488 nt)	murE	UDP‑N‑acetylmuramoyl‑L‑alanyl‑D‑glutamate:meso‑ diaminopimelate ligase
	?	NC_000913	= 93223	116 (1.020)					coding (58/1488 nt)	murE	UDP‑N‑acetylmuramoyl‑L‑alanyl‑D‑glutamate:meso‑ diaminopimelate ligase
*	?	NC_000913	= 224374	NA (NA)	4 (0.040)	3/264	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	274384 =	NA (NA)	4 (0.030)	4/272	NT	NA	noncoding (766/1195 nt)	IS5	repeat region
	?	NC_000913	274422 =	NA (NA)					noncoding (728/1195 nt)	IS5	repeat region
*	?	NC_000913	274525 =	NA (NA)	5 (0.040)	3/264	NT	NA	noncoding (625/1195 nt)	IS5	repeat region
	?	NC_000913	274559 =	NA (NA)					noncoding (591/1195 nt)	IS5	repeat region
*	?	NC_000913	274620 =	NA (NA)	10 (0.090)	5/260	NT	NA	noncoding (530/1195 nt)	IS5	repeat region
	?	NC_000913	274663 =	NA (NA)					noncoding (487/1195 nt)	IS5	repeat region
*	?	NC_000913	= 274695	NA (NA)	4 (0.030)	4/270	NT	NA	noncoding (455/1195 nt)	IS5	repeat region
	?	NC_000913	= 274727	NA (NA)					noncoding (423/1195 nt)	IS5	repeat region
*	?	NC_000913	= 291401	NA (NA)	4 (0.030)	4/278	NT	17.4%	noncoding (1/768 nt)	IS1	repeat region
	?	NC_000913	= 1293005	19 (0.160)					intergenic (‑83/‑522)	hns/tdk	global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
*	?	NC_000913	= 315520	NA (NA)	4 (0.040)	3/264	NT	NA	noncoding (292/1255 nt)	IS3	repeat region
	?	NC_000913	= 315537	NA (NA)					noncoding (309/1255 nt)	IS3	repeat region
*	?	NC_000913	315563 =	NA (NA)	6 (0.050)	3/258	NT	NA	noncoding (335/1255 nt)	IS3	repeat region
	?	NC_000913	315599 =	NA (NA)					noncoding (371/1255 nt)	IS3	repeat region
*	?	NC_000913	= 315572	NA (NA)	10 (0.090)	5/258	NT	NA	noncoding (344/1255 nt)	IS3	repeat region
	?	NC_000913	= 315588	NA (NA)					noncoding (360/1255 nt)	IS3	repeat region
*	?	NC_000913	= 315646	NA (NA)	9 (0.080)	6/268	NT	NA	noncoding (418/1255 nt)	IS3	repeat region
	?	NC_000913	= 315665	NA (NA)					noncoding (437/1255 nt)	IS3	repeat region
*	?	NC_000913	= 316201	NA (NA)	5 (0.050)	3/260	NT	NA	noncoding (973/1255 nt)	IS3	repeat region
	?	NC_000913	= 316220	NA (NA)					noncoding (992/1255 nt)	IS3	repeat region
*	?	NC_000913	= 381494	NA (NA)	3 (0.030)	3/268	NT	NA	noncoding (235/1331 nt)	IS2	repeat region
	?	NC_000913	= 381540	NA (NA)					noncoding (281/1331 nt)	IS2	repeat region
*	?	NC_000913	381663 =	NA (NA)	6 (0.050)	5/264	NT	NA	noncoding (404/1331 nt)	IS2	repeat region
	?	NC_000913	381703 =	NA (NA)					noncoding (444/1331 nt)	IS2	repeat region
*	?	NC_000913	= 381669	NA (NA)	10 (0.090)	9/264	NT	NA	noncoding (410/1331 nt)	IS2	repeat region
	?	NC_000913	= 381695	NA (NA)					noncoding (436/1331 nt)	IS2	repeat region
*	?	NC_000913	382237 =	NA (NA)	3 (0.030)	3/266	NT	NA	noncoding (978/1331 nt)	IS2	repeat region
	?	NC_000913	382267 =	NA (NA)					noncoding (1008/1331 nt)	IS2	repeat region
*	?	NC_000913	= 382242	NA (NA)	5 (0.040)	5/266	NT	NA	noncoding (983/1331 nt)	IS2	repeat region
	?	NC_000913	= 382260	NA (NA)					noncoding (1001/1331 nt)	IS2	repeat region
*	?	NC_000913	382282 =	NA (NA)	7 (0.060)	6/266	NT	NA	noncoding (1023/1331 nt)	IS2	repeat region
	?	NC_000913	382313 =	NA (NA)					noncoding (1054/1331 nt)	IS2	repeat region
*	?	NC_000913	493387 =	143 (1.210)	7 (0.060)	5/266	NT	5.1%	coding (1296/1932 nt)	dnaX	DNA polymerase III/DNA elongation factor III, tau and gamma subunits
	?	NC_000913	493417 =	122 (1.080)					coding (1326/1932 nt)	dnaX	DNA polymerase III/DNA elongation factor III, tau and gamma subunits
*	?	NC_000913	= 521828	115 (0.980)	7 (0.060)	5/260	NT	6.0%	coding (1413/2415 nt)	ybbP	putative ABC transporter permease
	?	NC_000913	= 521858	113 (1.030)					coding (1443/2415 nt)	ybbP	putative ABC transporter permease
*	?	NC_000913	526459 =	NA (NA)	4 (0.040)	3/268	NT	100%	coding (3199/4281 nt)	rhsD	Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
	?	NC_000913	526482 =	0 (0.000)					coding (3222/4281 nt)	rhsD	Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
*	?	NC_000913	781369 =	62 (0.530)	13 (0.110) +GAG	7/272	NT	22.0%	noncoding (1/76 nt)	lysZ	tRNA‑Lys
	?	NC_000913	= 2521006	32 (0.270)					noncoding (76/76 nt)	valU	tRNA‑Val
*	?	NC_000913	781577 =	75 (0.640)	42 (0.360) +G	7/276	NT	48.2%	noncoding (1/76 nt)	lysQ	tRNA‑Lys
	?	NC_000913	= 2521129	16 (0.140)					intergenic (+3/‑44)	valX/valY	tRNA‑Val/tRNA‑Val
*	?	NC_000913	= 1050545	NA (NA)	3 (0.030)	3/276	NT	6.4%	noncoding (768/768 nt)	IS1	repeat region
	?	NC_000913	1293068 =	44 (0.380)					intergenic (‑146/‑459)	hns/tdk	global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
*	?	NC_000913	= 1050986	94 (0.800)	5 (0.050)	5/262	NT	5.3%	coding (190/213 nt)	cspH	stress protein, member of the CspA‑family
	?	NC_000913	= 1051010	89 (0.800)					coding (166/213 nt)	cspH	stress protein, member of the CspA‑family
*	?	NC_000913	1207790 =	51 (0.430)	41 (0.390)	36/246	NT	49.1%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	40 (0.380)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1207805	51 (0.430)	65 (0.620)	54/246	NT	60.4%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	40 (0.380)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1286906	33 (0.280)	4 (0.040)	4/238	NT	6.7%	intergenic (+380/+160)	narI/rttR	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
	?	NC_000913	1287557 =	83 (0.820)					noncoding (66/85 nt)	tyrT	tRNA‑Tyr
*	?	NC_000913	1293017 =	23 (0.200)	15 (0.130)	14/278	NT	39.5%	intergenic (‑95/‑510)	hns/tdk	global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
	?	NC_000913	= 1979270	NA (NA)					noncoding (1/768 nt)	IS1	repeat region
*	?	NC_000913	= 1299498	1 (0.010)	106 (0.930)	79/270	NT	99.5%	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	1396537 =	NA (NA)	14 (0.120)	9/266	NT	11.7%	noncoding (494/1195 nt)	IS5	repeat region
	?	NC_000913	= 1428270	110 (0.930)					noncoding (525/1196 nt)	IS5	repeat region
*	?	NC_000913	= 1406554	94 (0.800)	5 (0.040)	5/266	NT	5.2%	intergenic (+12/+9)	smrA/ydaM	DNA endonuclease/diguanylate cyclase, csgD regulator
	?	NC_000913	= 1406582	91 (0.810)					coding (1214/1233 nt)	ydaM	diguanylate cyclase, csgD regulator
*	?	NC_000913	1486986 =	97 (0.820)	5 (0.050)	5/256	NT	5.3%	intergenic (+23/‑249)	hrpA/ydcF	putative ATP‑dependent helicase/DUF218 superfamily protein, SAM‑binding
	?	NC_000913	1487021 =	88 (0.810)					intergenic (+58/‑214)	hrpA/ydcF	putative ATP‑dependent helicase/DUF218 superfamily protein, SAM‑binding
*	?	NC_000913	1897271 =	111 (0.940)	6 (0.050)	3/260	NT	5.5%	coding (340/1365 nt)	sdaA	L‑serine dehydratase 1
	?	NC_000913	1897308 =	102 (0.930)					coding (377/1365 nt)	sdaA	L‑serine dehydratase 1
*	?	NC_000913	= 2440342	NA (NA)	3 (0.030)	3/266	NT	NA	intergenic (‑222/+43)	yfcJ/fabB	putative arabinose efflux transporter/3‑oxoacyl‑[acyl‑carrier‑protein] synthase I
	?	NC_000913	= 2440374	NA (NA)					noncoding (32/36 nt)	REP170 (repetitive extragenic palindromic) element; contains 1 REP sequences	REP170 (repetitive extragenic palindromic) element; contains 1 REP sequences
*	?	NC_000913	= 2811356	114 (0.970)	6 (0.050)	5/260	NT	5.2%	intergenic (+56/‑71)	mprA/emrA	transcriptional repressor of microcin B17 synthesis and multidrug efflux/multidrug efflux system
	?	NC_000913	= 2811362	114 (1.040)					intergenic (+62/‑65)	mprA/emrA	transcriptional repressor of microcin B17 synthesis and multidrug efflux/multidrug efflux system
*	?	NC_000913	= 2854465	129 (1.090)	7 (0.060)	6/262	NT	5.4%	coding (128/2079 nt)	fhlA	formate hydrogenlyase transcriptional activator
	?	NC_000913	= 2854495	125 (1.130)					coding (158/2079 nt)	fhlA	formate hydrogenlyase transcriptional activator
*	?	NC_000913	= 2947467	19 (0.160)	3 (0.040) +40 bp	3/198	NT	5.9%	intergenic (+4/‑30)	metZ/metW	tRNA‑Met/tRNA‑Met
	?	NC_000913	= 2947757	116 (0.980)					coding (1254/1254 nt)	amiC	N‑acetylmuramoyl‑L‑alanine amidase
*	?	NC_000913	= 2949337	125 (1.060)	7 (0.060)	6/262	NT	5.4%	coding (96/1332 nt)	argA	amino acid N‑acetyltransferase and inactive acetylglutamate kinase
	?	NC_000913	= 2949352	126 (1.140)					coding (111/1332 nt)	argA	amino acid N‑acetyltransferase and inactive acetylglutamate kinase
*	?	NC_000913	3277819 =	NA (NA)	6 (0.050)	6/262	NT	NA	noncoding (1/29 nt)	REP238 (repetitive extragenic palindromic) element; contains 1 REP sequences	REP238 (repetitive extragenic palindromic) element; contains 1 REP sequences
	?	NC_000913	3277844 =	NA (NA)					noncoding (26/29 nt)	REP238 (repetitive extragenic palindromic) element; contains 1 REP sequences	REP238 (repetitive extragenic palindromic) element; contains 1 REP sequences
*	?	NC_000913	= 3620220	NA (NA)	3 (0.030)	3/266	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	= 3620350	NA (NA)	4 (0.040)	3/266	NT	100%	coding (1159/4236 nt)	rhsB	Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
	?	NC_000913	= 3620425	0 (0.000)					coding (1234/4236 nt)	rhsB	Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
*	?	NC_000913	= 3621534	NA (NA)	5 (0.050)	4/262	NT	100%	coding (2343/4236 nt)	rhsB	Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
	?	NC_000913	= 3621592	0 (0.000)					coding (2401/4236 nt)	rhsB	Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
*	?	NC_000913	4344813 =	NA (NA)	4 (0.040)	3/260	NT	NA	intergenic (+23/+116)	melB/yjdF	melibiose:sodium symporter/DUF2238 family inner membrane protein
	?	NC_000913	4344842 =	NA (NA)					noncoding (28/95 nt)	RIP327 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site	RIP327 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site
*	?	NC_000913	4369146 =	96 (0.810)	5 (0.050)	4/258	NT	5.3%	intergenic (+6/+10)	fxsA/yjeH	suppressor of F exclusion of phage T7/putative transporter
	?	NC_000913	4369185 =	90 (0.820)					coding (1228/1257 nt)	yjeH	putative transporter
*	?	NC_000913	= 4401757	143 (1.210)	7 (0.060)	6/270	NT	5.0%	coding (1086/1281 nt)	hflX	GTPase, stimulated by 50S subunit binding; Mn(2+) homeostasis regulator
	?	NC_000913	= 4401795	125 (1.090)					coding (1124/1281 nt)	hflX	GTPase, stimulated by 50S subunit binding; Mn(2+) homeostasis regulator
*	?	NC_000913	= 4549784	NA (NA)	3 (0.030)	3/266	NT	NA	noncoding (2/36 nt)	REP345 (repetitive extragenic palindromic) element; contains 1 REP sequences	REP345 (repetitive extragenic palindromic) element; contains 1 REP sequences
	?	NC_000913	= 4549822	NA (NA)					intergenic (+112/+131)	fimH/gntP	minor component of type 1 fimbriae/fructuronate transporter