breseq  version 0.32.1  revision aa8f2595a244 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence	position	mutation	annotation	gene	description
RA	7,878	A→G	F28L (TTC→CTC)	yaaJ ←	putative transporter
RA	7,925	+A	coding (35/1431 nt)	yaaJ ←	putative transporter
RA	10,647	A→G	V237A (GTC→GCC)	yaaW ←	UPF0174 family protein
RA	14,301	C→T	A45V (GCG→GTG)	dnaJ →	chaperone Hsp40, DnaK co‑chaperone
RA	28,269	C→T	intergenic (+62/‑105)	rihC → / → dapB	ribonucleoside hydrolase 3/dihydrodipicolinate reductase
RA	30,616	T→C	P322P (CCT→CCC)	carA →	carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
RA	35,373	G→C	intergenic (‑2/+4)	caiE ← / ← caiD	stimulator of CaiD and CaiB enzyme activities/carnitinyl‑CoA dehydratase
RA	37,903	C→T	D405N (GAC→AAC)	caiB ←	crotonobetainyl CoA:carnitine CoA transferase
RA	47,776	G→A	*177* (TAG→TAA)  S3N (AGC→AAC)	kefF → kefC →	potassium‑efflux system ancillary protein for KefC, glutathione‑regulated, quinone oxidoreductase, FMN‑dependent potassium:proton antiporter
RA	49,765	C→T	intergenic (+134/‑58)	kefC → / → folA	potassium:proton antiporter/dihydrofolate reductase
RA	49,767	A→G	intergenic (+136/‑56)	kefC → / → folA	potassium:proton antiporter/dihydrofolate reductase
RA	66,447	T→C	E35G (GAG→GGG)	araD ←	L‑ribulose‑5‑phosphate 4‑epimerase
RA	69,078	A→G	V324A (GTG→GCG)	araB ←	L‑ribulokinase
RA	72,115	G→A	*255* (TAG→TAA)	yabI →	DedA family inner membrane protein
RA	72,229	C→T	*233* (TAG→TAA)	thiQ ←	thiamine/thiamine pyrophosphate ABC transporter ATPase
RA	75,447	A→G	C12R (TGC→CGC)	thiB ←	thiamine/thiamine pyrophosphate/thiamine monophosphate ABC transporter periplasmic binding protein
RA	96,008	G→A	*453* (TAG→TAA)  V3I (GTT→ATT)	murF → mraY →	UDP‑N‑acetylmuramoyl‑tripeptide:D‑alanyl‑D‑ alanine ligase phospho‑N‑acetylmuramoyl‑pentapeptide transferase
RA	104,352	A→G	E124G (GAG→GGG)	ftsA →	ATP‑binding cell division FtsK recruitment protein
RA	111,433	G→A	*130* (TAG→TAA)	mutT →	dGTP‑preferring nucleoside triphosphate pyrophosphohydrolase
RA	115,661	T→C	M22V (ATG→GTG)	hofC ←	assembly protein in type IV pilin biogenesis, transmembrane protein
RA	117,798	A→G	L283P (CTA→CCA)	nadC ←	quinolinate phosphoribosyltransferase
RA	122,856	G→A	*255* (TAG→TAA)	pdhR →	pyruvate dehydrogenase complex repressor, autorepressor
RA	125,227	T→C	R737R (CGT→CGC)	aceE →	pyruvate dehydrogenase, decarboxylase component E1, thiamine triphosphate‑binding
RA	150,947	T→C	T3A (ACT→GCT)	yadC ←	putative fimbrial‑like adhesin protein
RA	152,036	C→T	V66I (GTA→ATA)	yadL ←	putative fimbrial‑like adhesin protein
RA	155,935	T→C	K89K (AAA→AAG)	yadV ←	putative periplasmic pilin chaperone
RA	160,782	C→T	*235* (TAG→TAA)	sfsA ←	sugar fermentation stimulation protein A
RA	162,927	G→A	A275T (GCT→ACT)	hrpB →	putative ATP‑dependent helicase
RA	167,743	C→T	T87I (ACC→ATC)	fhuA →	ferrichrome outer membrane transporter
RA	169,645	A→G	Y721C (TAC→TGC)	fhuA →	ferrichrome outer membrane transporter
RA	177,662	C→T	*267* (TAG→TAA)	btuF ←	vitamin B12 ABC transporter periplasmic binding protein
RA	183,215	C→T	G251G (GGC→GGT)	cdaR →	carbohydrate diacid regulon transcriptional regulator, autoregulator
RA	183,607	Δ1 bp	coding (1145/1158 nt)	cdaR →	carbohydrate diacid regulon transcriptional regulator, autoregulator
RA	183,620	G→A	*386* (TAG→TAA)	cdaR →	carbohydrate diacid regulon transcriptional regulator, autoregulator
RA	184,257	C→T	*271* (TAG→TAA)	yaeI ←	phosphodiesterase with model substrate bis‑pNPP
RA	197,574	T→C	S343S (AGT→AGC)	rseP →	inner membrane zinc RIP metalloprotease, RpoE activator, by degrading RseA, cleaved signal peptide endoprotease
RA	200,214	C→T	P763S (CCA→TCA)	bamA →	BamABCDE complex OM biogenesis outer membrane pore‑forming assembly factor
RA	219,364	T→C	P77P (CCA→CCG)	tsaA ←	tRNA‑Thr(GGU) m(6)t(6)A37 methyltransferase, SAM‑dependent
RA	220,239	C→T	L230L (CTG→CTA)	metQ ←	DL‑methionine transporter subunit
RA	239,378	G→A	pseudogene (273/273 nt)	yafF →	pseudogene, H repeat‑associated protein
RA	247,461	G→A	*250* (TAG→TAA)	yafL →	putative lipoprotein and C40 family peptidase
RA	247,466	Δ1 bp	intergenic (+5/‑171)	yafL → / → rayT	putative lipoprotein and C40 family peptidase/RAYT REP element‑mobilizing transposase, TnpA(REP)
RA	253,084	A→G	T126A (ACA→GCA)	yafP →	GNAT family putative N‑acetyltransferase
RA	255,659	A→G	C20R (TGT→CGT)	pepD ←	aminoacyl‑histidine dipeptidase (peptidase D)
MC JC	257,908	Δ776 bp		[crl]	[crl]
RA	262,563	G→A	R354H (CGT→CAT)	proA →	gamma‑glutamylphosphate reductase
RA	280,024	C→T	pseudogene (94/174 nt)	insI1 →	IS30 transposase,IS, phage, Tn, Transposon‑related functions, extrachromosomal, transposon related
RA	281,662	Δ1 bp	coding (322/1155 nt)	yagA ←	CP4‑6 prophage, putative DNA‑binding transcriptional regulator
RA	283,014	T→C	L246P (CTG→CCG)	yagE →	2‑keto‑3‑deoxy gluconate (KDG) aldolase, CP4‑6 prophage
RA	284,869	C→T	P557S (CCG→TCG)	yagF →	CP4‑6 prophage, dehydratase family protein
RA	287,977	A→G	M397V (ATG→GTG)	yagH →	CP4‑6 prophage, putative xylosidase/arabinosidase
RA	291,324	C→T	C8Y (TGT→TAT)	insA ←	IS1 repressor TnpA
RA	309,358	C→T	*223* (TAG→TAA)	ecpB ←	ECP production pilus chaperone
RA	312,189	C→T	G26G (GGC→GGT)	ykgL →	uncharacterized protein
RA	315,244	G→A	intergenic (+16/‑47)	eaeH → / → insE1	pseudogene, attaching and effacing protein homology,factor, Not classified/IS3 transposase A
RA	316,453	G→A	*289* (TAG→TAA)	insF1 →	IS3 transposase B
RA	321,564	(G)7→6	intergenic (+483/‑44)	rclR → / → ykgE	reactive chlorine species (RCS)‑specific activator of the rcl genes/cysteine‑rich LutA family protein, putative electron transport chain YkgEFG component
RA	323,355	C→T	P340S (CCA→TCA)	ykgF →	ferridoxin‑like LutB family protein, putative electron transport chain YkgEFG component
RA	335,970	C→T	Q16* (CAA→TAA)	yahE →	DUF2877 family protein
RA	340,089	G→A	intergenic (+346/‑76)	yahG → / → yahI	DUF1116 family protein/carbamate kinase‑like protein
RA	344,674	T→C	Y167H (TAC→CAC)	yahL →	uncharacterized protein
RA	344,991	G→A	*272* (TAG→TAA)	yahL →	uncharacterized protein
RA	345,649	G→A	*82* (TAG→TAA)	yahM →	uncharacterized protein
RA	349,847	T→C	intergenic (+275/‑165)	prpB → / → prpC	2‑methylisocitrate lyase/2‑methylcitrate synthase
RA	354,592	G→A	*629* (TAG→TAA)	prpE →	propionate‑‑CoA ligase
RA	357,591	C→T	intergenic (+137/+200)	codA → / ← cynR	cytosine/isoguanine deaminase/transcriptional activator of cyn operon, autorepressor
RA	357,606	C→T	intergenic (+152/+185)	codA → / ← cynR	cytosine/isoguanine deaminase/transcriptional activator of cyn operon, autorepressor
RA	357,626	2 bp→TA	intergenic (+172/+164)	codA → / ← cynR	cytosine/isoguanine deaminase/transcriptional activator of cyn operon, autorepressor
RA	357,791	C→T	*300* (TAG→TAA)	cynR ←	transcriptional activator of cyn operon, autorepressor
RA	371,542	C→T	Q102* (CAA→TAA)	mhpC →	2‑hydroxy‑6‑ketonona‑2,4‑dienedioic acid hydrolase
RA	372,966	A→G	T16A (ACC→GCC)	mhpF →	acetaldehyde‑CoA dehydrogenase II, NAD‑binding
RA	375,067	A→G	intergenic (+186/‑392)	mhpE → / → mhpT	4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter
RA	375,075	G→A	intergenic (+194/‑384)	mhpE → / → mhpT	4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter
RA	375,307	C→T	intergenic (+426/‑152)	mhpE → / → mhpT	4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter
RA	379,606	C→T	*92* (TAG→TAA)	frmR ←	regulator protein that represses frmRAB operon
RA	382,579	G→A	*302* (TAG→TAA)	insD1 →	IS2 transposase TnpB
RA	383,259	C→T	R226Q (CGG→CAG)	yaiP ←	putative family 2 glycosyltransferase
RA	384,059	C→T	*186* (TAG→TAA)	yaiS ←	putative PIG‑L family deacetylase
RA	385,737	A→G	D169G (GAT→GGT)	tauA →	taurine ABC transporter periplasmic binding protein
RA	391,739	C→T	*289* (TAG→TAA)	insF1 ←	IS3 transposase B
RA	401,548	(G)5→4	coding (163/261 nt)	iraP →	anti‑RssB factor, RpoS stabilzer during Pi starvation, anti‑adapter protein
RA	411,297	C→T	*395* (TAG→TAA)	araJ ←	L‑arabinose‑inducible putative transporter, MFS family
RA	424,700	C→T	A73A (GCG→GCA)	acpH ←	acyl carrier protein (ACP) phosphodiesterase, ACP hydrolyase
RA	437,107	G→A	*173* (TAG→TAA)	pgpA →	phosphatidylglycerophosphatase A
RA	443,051	C→T	*197* (TAG→TAA)	yajL ←	oxidative‑stress‑resistance chaperone
RA	443,604	C→T	S13N (AGT→AAT)  *304* (TAG→TAA)	yajL ← panE ←	oxidative‑stress‑resistance chaperone 2‑dehydropantoate reductase, NADPH‑specific
RA	444,641	C→T	intergenic (‑126/‑42)	panE ← / → yajQ	2‑dehydropantoate reductase, NADPH‑specific/phage Phi6 host factor, ATP/GTP binding protein
RA	450,764	C→T	A283T (GCT→ACT)	cyoA ←	cytochrome o ubiquinol oxidase subunit II
RA	461,242	G→A	*785* (TAG→TAA)	lon →	DNA‑binding ATP‑dependent protease La
RA	468,510	A→G	E43G (GAG→GGG)	ybaO →	putative DNA‑binding transcriptional regulator
RA	469,429	A→G	K187E (AAG→GAG)	mdlA →	putative multidrug ABC transporter ATPase
RA	470,643	G→A	*591* (TAG→TAA)  S3N (AGT→AAT)	mdlA → mdlB →	putative multidrug ABC transporter ATPase putative multidrug ABC transporter ATPase
RA	475,667	T→C	S97P (TCA→CCA)	ybaY →	outer membrane lipoprotein
RA	477,025	G→A	*118* (TAG→TAA)	ybaA →	DUF1428 family protein
RA	477,435	T→C	T395A (ACT→GCT)	ylaB ←	putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	478,533	C→T	A29T (GCC→ACC)	ylaB ←	putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	480,334	C→T	*125* (TAG→TAA)	tomB ←	Hha toxicity attenuator, conjugation‑related protein
RA	486,641	T→C	S36P (TCA→CCA)	mscK →	mechanosensitive channel protein, intermediate conductance, K+ regulated
RA	490,285	C→T	*176* (TAG→TAA)	priC ←	primosomal replication protein N''
RA	491,776	T→C	V122A (GTT→GCT)	apt →	adenine phosphoribosyltransferase
RA	499,014	C→T	R320R (CGC→CGT)  *320* (TAG→TAA)	hemH → aes ←	ferrochelatase acetyl esterase
RA	515,808	C→T	intergenic (‑35/‑111)	qmcA ← / → fetA	PHB domain membrane‑anchored putative protease/iron export ABC transporter ATPase, peroxide resistance protein
RA	518,721	C→A	M143I (ATG→ATT)	ybbO ←	putative oxidoreductase
RA	522,463	T→C	V683A (GTG→GCG)	ybbP →	putative ABC transporter permease
RA	524,158	C→T	L300L (CTG→TTG)	rhsD →	Rhs protein with DUF4329 family putative toxin domain, putative neighboring cell growth inhibitor
RA	540,515	C→T	intergenic (+7/‑50)	allB → / → ybbY	allantoinase/putative uracil/xanthine transporter
RA	542,530	A→G	T215A (ACG→GCG)	glxK →	glycerate kinase II
RA	544,754	C→T	R180H (CGT→CAT)	allC ←	allantoate amidohydrolase
RA	551,137	G→T	T233T (ACG→ACT)	ybcF →	putative carbonate kinase
RA	551,332	G→A	*298* (TAG→TAA)	ybcF →	putative carbonate kinase
RA	568,004	G→A	*289* (TAG→TAA)	insF1 →	IS3 transposase B
RA	571,444	G→A	*184* (TAG→TAA)	ybcL →	inactive polymorphonuclear leukocyte migration suppressor, DLP12 prophage, UPF0098 family secreted protein
RA	572,454	C→T	C29C (TGC→TGT)	ylcH →	uncharacterized protein, DLP12 prophage
RA	578,568	G→A	*154* (TAG→TAA)	rzpD →	DLP12 prophage, putative murein endopeptidase
RA	582,148	Δ1 bp	intergenic (+51/+4)	tfaD → / ← ybcY	pseudogene, DLP12 prophage, tail fiber assembly protein family,Phage or Prophage Related/pseudogene, DLP12 prophage, methyltransferase homology,Phage or Prophage Related
RA	582,152	C→T	pseudogene (653/653 nt)	ybcY ←	pseudogene, DLP12 prophage, methyltransferase homology,Phage or Prophage Related
RA	586,280	T→C	N210S (AAC→AGC)	envY ←	porin thermoregulatory transcriptional activator
RA	607,988	G→A	*51* (TAG→TAA)	hokE →	toxic polypeptide, small
RA	610,746	C→T	A583A (GCG→GCA)	fepA ←	ferrienterobactin outer membrane transporter
RA	631,812	T→C	F640S (TTC→TCC)	cstA →	carbon starvation protein involved in peptide utilization, APC peptide transporter family protein
RA	634,746	2 bp→AT		[ybdL]–[ybdM]	[ybdL], [ybdM]
RA	649,372	A→G	F67S (TTC→TCC)	citF ←	citrate lyase, citrate‑ACP transferase (alpha) subunit
RA	649,648	A→G	G281G (GGT→GGC)	citE ←	citrate lyase, citryl‑ACP lyase (beta) subunit
RA	662,153	C→A	E42D (GAG→GAT)	lipB ←	octanoyltransferase, octanoyl‑[ACP]:protein N‑octanoyltransferase
RA	664,102	C→T	*363* (TAG→TAA)	rlpA ←	septal ring protein, suppressor of prc, minor lipoprotein
RA	672,947	C→A	V613F (GTT→TTT)	leuS ←	leucyl‑tRNA synthetase
RA	675,570	C→T	*326* (TAG→TAA)	ybeQ ←	Sel1 family TPR‑like repeat protein
RA	675,601	Δ1 bp	coding (947/978 nt)	ybeQ ←	Sel1 family TPR‑like repeat protein
RA	677,889	G→A	A159T (GCC→ACC)	djlB →	putative HscC co‑chaperone, uncharacterized J domain‑containing protein
RA	679,874	G→A	G123R (GGG→AGG)	ybeU →	DUF1266 family protein
RA	681,418	C→T	R403C (CGT→TGT)	djlC →	J domain‑containing HscC co‑chaperone, Hsc56
RA	696,276	G→A	*392* (TAG→TAA)	ubiF →	2‑octaprenyl‑3‑methyl‑6‑methoxy‑1,4‑benzoquinol oxygenase
RA	711,724	C→T	A59T (GCG→ACG)	ybfE ←	LexA‑regulated protein, CopB family
RA	716,388	C→T	pseudogene (210/651 nt)	ybfG ←	pseudogene
RA	723,528	(T)8→9	coding (887/2685 nt)	kdpD ←	fused sensory histidine kinase in two‑component regulatory system with KdpE: signal sensing protein
RA	738,853	G→A	*254* (TAG→TAA)	ybfD →	H repeat‑associated putative transposase
RA	746,723	C→T	H263H (CAC→CAT)  *349* (TAG→TAA)	nei → abrB ←	endonuclease VIII and 5‑formyluracil/5‑hydroxymethyluracil DNA glycosylase regulator of aidB expression, inner membrane protein
RA	746,726	G→A	*264* (TAG→TAA)  A348A (GCC→GCT)	nei → abrB ←	endonuclease VIII and 5‑formyluracil/5‑hydroxymethyluracil DNA glycosylase regulator of aidB expression, inner membrane protein
RA	753,428	C→T	A347A (GCG→GCA)	gltA ←	citrate synthase
RA	762,739	G→A	*406* (TAG→TAA)	sucB →	dihydrolipoyltranssuccinase
RA	775,120	G→A	A123A (GCG→GCA)	ybgC →	acyl‑CoA thioester hydrolase
RA	789,464	G→A	I172I (ATC→ATT)	galK ←	galactokinase
RA	812,947	G→A	*226* (TAG→TAA)	bioD →	dethiobiotin synthetase
RA	819,747	G→A	*151* (TAG→TAA)	moaE →	molybdopterin synthase, large subunit
RA	821,506	G→A	*238* (TAG→TAA)	ybhM →	BAX Inhibitor‑1 family inner membrane protein
RA	825,102	G→A	A336V (GCG→GTG)	ybhR ←	putative ABC transporter permease
RA	826,119	C→T	*378* (TAG→TAA)	ybhS ←	putative ABC transporter permease
RA	829,972	C→T	M1M (GTG→ATG) † *224* (TAG→TAA)	ybhG ← ybiH ←	putative membrane fusion protein (MFP) component of efflux pump, membrane anchor DUF1956 domain‑containing tetR family putative transcriptional regulator
RA	850,389	T→C	intergenic (‑292/‑61)	rhtA ← / → ompX	threonine and homoserine efflux system/outer membrane protein X
RA	852,869	C→T	*43* (TAG→TAA)	mntS ←	Mn(2)‑response protein, MntR‑repressed
RA	854,765	G→A	*373* (TAG→TAA)	ybiR →	putative transporter
RA	855,796	A→G	intergenic (‑52/‑167)	ldtB ← / → ybiT	L,D‑transpeptidase linking Lpp to murein/ABC‑F family putative regulatory ATPase
RA	860,638	A→G	Y657H (TAT→CAT)	ybiW ←	putative pyruvate formate lyase
RA	868,422	(C)8→7	coding (903/1872 nt)	gsiA →	glutathione ABC transporter ATPase
RA	872,801	G→A	*304* (TAG→TAA)	gsiD →	glutathione ABC transporter permease
RA	875,327	G→A	*783* (TAG→TAA)	yliE →	putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	879,857	G→A	*372* (TAG→TAA)  S208S (AGC→AGT)	yliI → gstB ←	soluble aldose sugar dehydrogenase glutathione S‑transferase
JC JC	883,665	IS1 (–) +9 bp		[mdfA]	[mdfA]
RA	887,959	G→A	*179* (TAG→TAA)	rcdA →	transcriptional regulator of csgD and ybiJI, autoregulator
RA	892,869	G→A	*301* (TAG→TAA)	rimK →	ribosomal protein S6 modification protein
RA	905,743	G→A	*277* (TAG→TAA)  R337R (CGC→CGT)	amiD → ybjS ←	1,6‑anhydro‑N‑acetylmuramyl‑L‑alanine amidase, Zn‑dependent, OM lipoprotein putative NAD(P)H‑dependent oxidoreductase
RA	909,654	C→T	V466M (GTG→ATG)	poxB ←	pyruvate dehydrogenase, thiamine triphosphate‑binding, FAD‑binding
RA	911,132	A→G	intergenic (‑83/+50)	poxB ← / ← hcr	pyruvate dehydrogenase, thiamine triphosphate‑binding, FAD‑binding/HCP oxidoreductase, NADH‑dependent
RA	913,349	G→A	L156L (CTG→TTG)	hcp ←	hybrid‑cluster [4Fe‑2S‑2O] subunit of anaerobic terminal reductases
RA	915,730	T→C	K106K (AAA→AAG)	aqpZ ←	aquaporin Z
RA	919,010	A→G	S37S (AGT→AGC)	ybjX ←	DUF535 family protein
RA	922,366	C→T	*75* (TAG→TAA)	cspD ←	inhibitor of DNA replication, cold shock protein homolog
RA	927,205	A→G	R76R (CGT→CGC)	aat ←	leucyl/phenylalanyl‑tRNA‑protein transferase
RA	932,340	(A)8→7	intergenic (‑290/‑255)	trxB ← / → lrp	thioredoxin reductase, FAD/NAD(P)‑binding/leucine‑responsive global transcriptional regulator
RA	937,983	G→A	*204* (TAG→TAA)	lolA →	lipoprotein chaperone
RA	966,584	G→A	*755* (TAG→TAA)	ycaI →	ComEC family inner membrane protein
RA	967,118	A→G	Q166Q (CAA→CAG)	msbA →	lipid ABC transporter permease/ATPase
RA	969,352	G→A	*329* (TAG→TAA)	lpxK →	lipid A 4'kinase
RA	983,623	G→A	*183* (TAG→TAA)	ycbK →	M15A protease‑related family periplasmic protein
RA	986,671	A→G	R104R (CGT→CGC)	ompF ←	outer membrane porin 1a (Ia,b,F)
RA	1,006,415	Δ1 bp	coding (464/543 nt)	zapC →	FtsZ stabilizer
RA	1,006,491	C→T	V180V (GTC→GTT)  *370* (TAG→TAA)	zapC → ycbX ←	FtsZ stabilizer 6‑N‑hydroxylaminopurine detoxification oxidoreductase
RA	1,050,350	C→A	S108S (TCC→TCA)	insB1 →	IS1 transposase B
RA	1,068,254	G→A	*58* (TAG→TAA)	ymdF →	KGG family protein
RA	1,068,276	Δ1 bp	intergenic (+22/+235)	ymdF → / ← rutG	KGG family protein/pyrimidine permease
RA	1,068,285	Δ1 bp	intergenic (+31/+226)	ymdF → / ← rutG	KGG family protein/pyrimidine permease
RA	1,072,060	G→A	L34L (CTG→TTG)	rutC ←	putative aminoacrylate deaminase, reactive intermediate detoxification, weak enamine/imine deaminase activity
RA	1,073,732	C→T	A94T (GCG→ACG)	rutA ←	pyrimidine oxygenase, FMN‑dependent
RA	1,082,060	A→G	pseudogene (601/726 nt)	efeU →	ferrous iron permease (pseudogene)
RA	1,089,570	T→C	E96E (GAA→GAG)	pgaB ←	poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine (PGA) N‑deacetylase outer membrane export lipoprotein
RA	1,094,275	C→T	*289* (TAG→TAA)	insF1 ←	IS3 transposase B
RA	1,102,221	T→C	E107E (GAA→GAG)	csgE ←	curlin secretion specificity factor
RA	1,119,307	C→T	*47* (TAG→TAA)	yceO ←	uncharacterized protein
RA	1,125,011	A→G	C106R (TGC→CGC)	mdtH ←	multidrug resistance efflux transporter conferring overexpression resistance to norfloxacin and enoxacin
RA	1,139,406	Δ1 bp	coding (1029/1644 nt)	flgK →	flagellar hook‑filament junction protein 1
RA	1,146,011	C→T	*195* (TAG→TAA)	yceF ←	m(7)GTP pyrophosphatase
RA	1,148,691	G→A	*357* (TAG→TAA)	plsX →	putative phosphate acyltransferase
RA	1,149,712	G→A	*318* (TAG→TAA)	fabH →	3‑oxoacyl‑[acyl‑carrier‑protein] synthase III
RA	1,153,047	A→G	D370G (GAT→GGT)	fabF →	3‑oxoacyl‑[acyl‑carrier‑protein] synthase II
RA	1,154,109	G→A	*270* (TAG→TAA)	pabC →	4‑amino‑4‑deoxychorismate lyase component of para‑aminobenzoate synthase multienzyme complex
RA	1,168,350	Δ1 bp	coding (483/633 nt)	ycfQ ←	repressor for bhsA(ycfR)
RA	1,200,881	G→A	A51V (GCC→GTC)	xisE ←	e14 prophage, putative excisionase
RA	1,203,224	G→A	*67* (TAG→TAA)	croE →	e14 prophage, putative DNA‑binding transcriptional regulator
RA	1,204,160	G→A	*113* (TAG→TAA)	ymfM →	e14 prophage, uncharacterized protein
RA	1,205,731	G→A	*61* (TAG→TAA)  pseudogene (1/412 nt)	ymfR → beeE →	e14 prophage, uncharacterized protein pseudogene, portal protein family, e14 prophage,Phage or Prophage Related
RA	1,208,517	C→T	P129L (CCT→CTT)  *201* (TAG→TAA)	tfaP → tfaE ←	e14 prophage, uncharacterized protein e14 prophage, putative tail fiber assembly protein
RA	1,208,534	Δ1 bp	coding (403/414 nt);coding (586/603 nt)	tfaP → tfaE ←	e14 prophage, uncharacterized protein e14 prophage, putative tail fiber assembly protein
RA	1,211,652	C→T	intergenic (+75/+28)	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	1,212,233	A→G	intergenic (‑230/+470)	iraM ← / ← ycgX	RpoS stabilzer during Mg starvation, anti‑RssB factor/DUF1398 family protein
RA	1,212,703	C→T	*135* (TAG→TAA)	ycgX ←	DUF1398 family protein
RA	1,216,996	Δ2 bp		[ymgC]	[ymgC]
RA	1,228,724	A→G	T216A (ACT→GCT)	ycgM →	putative isomerase/hydrolase
RA	1,245,600	G→A	*147* (TAG→TAA)	ycgY →	uncharacterized protein
RA	1,250,629	(C)5→6	coding (210/1071 nt)	dhaK ←	dihydroxyacetone kinase, PTS‑dependent, dihydroxyacetone‑binding subunit
RA	1,252,038	G→A	A325T (GCT→ACT)	dhaR →	dhaKLM operon transcription activator
RA	1,260,528	A→G	I92I (ATT→ATC)	dauA ←	C4‑dicarboxylic acid transporter
RA	1,264,970	G→A	*419* (TAG→TAA)	hemA →	glutamyl tRNA reductase
MC JC	1,265,001	1086 bp→GAGG		[prfA]	[prfA]
RA	1,271,455	G→A	T132I (ACC→ATC)	chaA ←	calcium/sodium:proton antiporter
RA	1,275,815	T→C	E5E (GAA→GAG)	narL ←	response regulator in two‑component regulatory system with NarX
RA	1,286,984	G→A	intergenic (+458/+82)	narI → / ← rttR	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
MC JC	1,299,499	Δ1,199 bp	intergenic (+254/‑485)	ychE → / → oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
RA	1,309,016	C→T	*418* (TAG→TAA)	kch ←	voltage‑gated potassium channel
RA	1,315,402	C→T	L123L (CTG→CTA)	yciF ←	putative rubrerythrin/ferritin‑like metal‑binding protein
RA	1,330,454	G→A	A72V (GCC→GTC)	yciN ←	DUF2498 protein YciN
RA	1,354,505	C→T	S5N (AGC→AAC)  *322* (TAG→TAA)	sapC ← sapB ←	antimicrobial peptide transport ABC transporter permease antimicrobial peptide transport ABC transporter permease
RA	1,366,935	C→T	*326* (TAG→TAA)	pspF ←	psp operon transcriptional activator
RA	1,370,044	(T)9→8	intergenic (+41/‑172)	pspE → / → ycjM	thiosulfate:cyanide sulfurtransferase (rhodanese)/alpha amylase catalytic domain family protein
RA	1,380,807	G→A	*220* (TAG→TAA)	ycjU →	beta‑phosphoglucomutase
RA	1,381,789	G→A	pseudogene (13/126 nt)	ycjV →	pseudogene, putative ATP‑binding component of a transport system
RA	1,389,242	C→T	Q105* (CAA→TAA)	ycjG →	L‑Ala‑D/L‑Glu epimerase
RA	1,389,499	C→T	C190C (TGC→TGT)	ycjG →	L‑Ala‑D/L‑Glu epimerase
RA	1,389,895	G→A	*322* (TAG→TAA)  P235L (CCT→CTT)	ycjG → mpaA ←	L‑Ala‑D/L‑Glu epimerase murein peptide amidase A
RA	1,392,890	G→A	*300* (TAG→TAA)	pgrR →	murein peptide degradation regulator
RA	1,399,985	(C)7→8	coding (252/516 nt)	ogt ←	O‑6‑alkylguanine‑DNA:cysteine‑protein methyltransferase
RA	1,403,912	C→T	V218V (GTG→GTA)	abgA ←	p‑aminobenzoyl‑glutamate hydrolase, A subunit
RA	1,412,000	C→T	*412* (TAG→TAA)	intR ←	Rac prophage, integrase
RA	1,418,386	G→A	intergenic (‑157/‑285)	kilR ← / → sieB	killing protein, Rac prophage, FtsZ inhibitor protein/phage superinfection exclusion protein, Rac prophage
RA	1,419,159	G→A	*163* (TAG→TAA)  S51S (AGC→AGT)	sieB → ydaF ←	phage superinfection exclusion protein, Rac prophage uncharacterized protein, Rac prophage
RA	1,419,344	G→A	A38V (GCT→GTT)	ydaG ←	Rac prophage, uncharacterized protein
RA	1,421,933	T→C	V272A (GTC→GCC)	ydaU →	Rac prophage, conserved protein
RA	1,425,980	G→A	pseudogene (351/453 nt)	ydaY →	pseudogene, Rac prophage,Phage or Prophage Related
RA	1,426,288	G→A	intergenic (+206/‑166)	ydaY → / → tmpR	pseudogene, Rac prophage,Phage or Prophage Related/Rac prophage, pseudogene, tail protein family,Phage or Prophage Related, putative alpha helix protein
RA	1,431,882	T→C	V945A (GTG→GCG)	stfR →	Rac prophage, putative tail fiber protein
RA	1,432,273	G→A	A1075A (GCG→GCA)	stfR →	Rac prophage, putative tail fiber protein
RA	1,441,436	T→C	N103S (AAC→AGC)	hslJ ←	heat‑inducible lipoprotein involved in novobiocin resistance
RA	1,450,392	C→T	A320T (GCA→ACA)	tynA ←	tyramine oxidase, copper‑requiring
RA	1,454,292	C→A	G122G (GGC→GGA)	paaA →	ring 1,2‑phenylacetyl‑CoA epoxidase subunit
RA	1,458,617	A→G	A118A (GCA→GCG)	paaG →	1,2‑epoxyphenylacetyl‑CoA isomerase, oxepin‑CoA‑forming
RA	1,459,052	G→A	*263* (TAG→TAA)	paaG →	1,2‑epoxyphenylacetyl‑CoA isomerase, oxepin‑CoA‑forming
RA	1,464,489	G→A	*317* (TAG→TAA)  D7N (GAC→AAC)	paaX → paaY →	transcriptional repressor of phenylacetic acid degradation paa operon, phenylacetyl‑CoA inducer thioesterase required for phenylacetic acid degradation, trimeric, phenylacetate regulatory and detoxification protein, hexapeptide repeat protein
RA	1,466,996	T→C	pseudogene (1605/2513 nt)	ydbA →	pseudogene, autotransporter homolog, interrupted by IS2 and IS30
RA	1,467,921	C→T	*302* (TAG→TAA)	insD1 ←	IS2 transposase TnpB
RA	1,491,389	A→G	K163R (AAG→AGG)	cybB →	cytochrome b561
RA	1,493,219	A→G	E250E (GAA→GAG)	trg →	methyl‑accepting chemotaxis protein III, ribose and galactose sensor receptor
RA	1,497,308	A→G	E151E (GAA→GAG)	opgD →	OPG biosynthetic periplasmic protein
RA	1,503,125	G→A	*223* (TAG→TAA)	ydcL →	lipoprotein
RA	1,513,468	T→C	S218P (TCC→CCC)	ydcT →	putative ABC transporter ATPase
RA	1,529,938	G→A	pseudogene (2037/2037 nt) R6K (AGA→AAA)	rhsE → ydcD →	pseudogene, Rhs family putative immunity protein for RhsE
RA	1,533,045	C→T	intergenic (+93/‑7)	ydcC → / → pptA	H repeat‑associated putative transposase/4‑oxalocrotonate tautomerase
RA	1,544,384	C→T	pseudogene (381/381 nt)	yddK ←	pseudogene, leucine‑rich protein, putative glycoportein
RA	1,548,360	C→T	D320D (GAC→GAT)	fdnG →	formate dehydrogenase‑N, alpha subunit, nitrate‑inducible
RA	1,557,112	C→T	*309* (TAG→TAA)	ddpF ←	D,D‑dipeptide ABC transporter ATPase
RA	1,559,680	G→A	G77G (GGC→GGT)	ddpC ←	D,D‑dipeptide ABC transporter permease
RA	1,565,758	C→T	*461* (TAG→TAA)	dosC ←	diguanylate cyclase, cold‑ and stationary phase‑induced oxygen‑dependent biofilm regulator
RA	1,571,332	G→T	I238I (ATC→ATA)	gadB ←	glutamate decarboxylase B, PLP‑dependent
RA	1,571,902	G→A	D48D (GAC→GAT)	gadB ←	glutamate decarboxylase B, PLP‑dependent
RA	1,571,917	G→A	F43F (TTC→TTT)	gadB ←	glutamate decarboxylase B, PLP‑dependent
RA	1,598,617	C→T	*531* (TAG→TAA)	lsrK ←	autoinducer‑2 (AI‑2) kinase
RA	1,614,789	C→T	intergenic (‑86/‑15)	sad ← / → yneJ	succinate semialdehyde dehydrogenase, NAD(P)+‑dependent/putative DNA‑binding transcriptional regulator
RA	1,618,218	G→A	*397* (TAG→TAA)	ydeA →	arabinose efflux transporter, arabinose‑inducible
RA	1,619,957	G→A	*128* (TAG→TAA)	marA →	multiple antibiotic resistance transcriptional regulator
RA	1,620,207	G→A	*73* (TAG→TAA)	marB →	periplasmic mar operon regulator
RA	1,621,542	G→A	D71N (GAC→AAC)	ydeE →	putative transporter
RA	1,624,357	(T)8→7	coding (141/393 nt)	ydeI ←	hydrogen peroxide resistance OB fold protein, putative periplasmic protein
RA	1,626,825	C→T	V186I (GTT→ATT)	dcp ←	dipeptidyl carboxypeptidase II
RA	1,627,124	T→C	D86G (GAT→GGT)	dcp ←	dipeptidyl carboxypeptidase II
RA	1,627,625	T→C	L37L (TTG→CTG)	ydfG →	NADP‑dependent 3‑hydroxy acid dehydrogenase, malonic semialdehyde reductase
RA	1,630,986	A→G	intergenic (‑73/+16)	ydfI ← / ← ydfJ	putative NAD‑dependent D‑mannonate oxidoreductase/pseudogene, MFS transporter family, interrupted by Qin prophage,Phage or Prophage Related, putative transport protein
RA	1,639,030	C→T	*166* (TAG→TAA)	rzpQ ←	Rz‑like protein, Qin prophage
RA	1,649,041	G→A	*73* (TAG→TAA)	ydfC →	uncharacterized protein, Qin prophage
RA	1,651,537	G→A	pseudogene (693/693 nt)	insD1 →	IS2 transposase TnpB,IS, phage, Tn, Transposon‑related functions, extrachromosomal, transposon related
RA	1,652,273	T→C	pseudogene (723/1158 nt)	intQ →	pseudogene, Qin prophage, phage integrase family,Phage or Prophage Related
RA	1,655,057	T→C	T29A (ACG→GCG)	rspA ←	bifunctional D‑altronate/D‑mannonate dehydratase
RA	1,655,347	C→T	*109* (TAG→TAA)	ynfA ←	UPF0060 family inner membrane protein
RA	1,655,360	(C)5→4	coding (314/327 nt)	ynfA ←	UPF0060 family inner membrane protein
RA	1,656,744	G→A	*187* (TAG→TAA)	speG →	spermidine N(1)‑acetyltransferase
RA	1,664,096	T→C	I163T (ATA→ACA)	ynfH →	oxidoreductase, membrane subunit
RA	1,665,120	G→A	*205* (TAG→TAA)	dmsD →	twin‑argninine leader‑binding protein for DmsA and TorA
RA	1,670,581	G→A	G295R (GGA→AGA)	ynfM →	putative arabinose efflux transporter
RA	1,672,863	A→G	L96P (CTG→CCG)	mdtI ←	multidrug efflux system transporter
RA	1,685,542	(C)6→5	coding (1047/1404 nt)	fumC ←	fumarate hydratase (fumarase C),aerobic Class II
RA	1,691,192	G→A	Q447Q (CAG→CAA)	ydgA →	DUF945 family protein
RA	1,696,452	(A)5→4	intergenic (‑381/+10)	uidA ← / ← uidR	beta‑D‑glucuronidase/transcriptional repressor
RA	1,700,201	(T)5→6	coding (847/1593 nt)	malX →	maltose and glucose‑specific PTS enzyme IIB component and IIC component
RA	1,709,163	T→C	S8P (TCC→CCC)	rsxD →	SoxR iron‑sulfur cluster reduction factor component, putative membrane protein of electron transport complex
RA	1,712,518	(C)6→7	intergenic (+360/‑251)	nth → / → dtpA	DNA glycosylase and apyrimidinic (AP) lyase (endonuclease III)/dipeptide and tripeptide permease A
RA	1,719,058	G→A	P182L (CCG→CTG)	anmK ←	anhydro‑N‑acetylmuramic acid kinase
RA	1,726,622	G→A	*200* (TAG→TAA)	nemR →	transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated
RA	1,733,703	G→A	*1539* (TAG→TAA)	lhr →	putative ATP‑dependent helicase
RA	1,735,484	T→C	V36A (GTC→GCC)	sodB →	superoxide dismutase, Fe
RA	1,742,575	G→A	intergenic (+14/+26)	cfa → / ← ribC	cyclopropane fatty acyl phospholipid synthase, SAM‑dependent/riboflavin synthase, alpha subunit
RA	1,744,740	C→T	G428G (GGC→GGT)	mdtK →	multidrug efflux system transporter
RA	1,756,152	T→C	L152P (CTG→CCG)	pykF →	pyruvate kinase I
RA	1,757,006	G→A	A437T (GCT→ACT)	pykF →	pyruvate kinase I
RA	1,757,721	C→T	*335* (TAG→TAA)	ldtE ←	murein L,D‑transpeptidase
MC JC	1,757,753	Δ5 bp	coding (969‑973/1005 nt)	ldtE ←	murein L,D‑transpeptidase
RA	1,759,680	(C)5→6	coding (844/1221 nt)	sufS ←	cysteine desulfurase, stimulated by SufE, selenocysteine lyase, PLP‑dependent
RA	1,761,518	G→A	R92C (CGT→TGT)	sufD ←	component of SufBCD Fe‑S cluster assembly scaffold
RA	1,763,987	Δ1 bp	coding (23/1488 nt)	sufB ←	component of SufBCD Fe‑S cluster assembly scaffold
RA	1,764,018	C→T	*123* (TAG→TAA)	sufA ←	Fe‑S cluster assembly protein
RA	1,765,668	T→C	V1006V (GTA→GTG)	ydiJ ←	putative FAD‑linked oxidoreductase
RA	1,766,131	T→C	N852S (AAC→AGC)	ydiJ ←	putative FAD‑linked oxidoreductase
RA	1,769,478	(G)7→8	coding (405/1113 nt)	ydiK →	UPF0118 family inner membrane protein
RA	1,781,964	C→G	G190G (GGC→GGG)	ydiS →	putative oxidoreductase
RA	1,788,278	G→A	*278* (TAG→TAA)	ppsR →	PEP synthase kinase and PEP synthase pyrophosphorylase
RA	1,789,804	G→A	*64* (TAG→TAA)	ydiE →	hemin uptake protein HemP homolog
RA	1,792,267	C→T	*155* (TAG→TAA)	nlpC ←	putative C40 clan peptidase lipoprotein
RA	1,794,172	C→T	*327* (TAG→TAA)	btuC ←	vitamin B12 ABC transporter permease
RA	1,799,883	T→C	K39K (AAA→AAG)	rpmI ←	50S ribosomal subunit protein L35
RA	1,803,567	G→A	pseudogene (50/1476 nt)	arpB →	pseudogene, ankyrin repeats
RA	1,819,569	A→G	G79G (GGT→GGC)	chbA ←	N,N'‑diacetylchitobiose‑specific enzyme IIA component of PTS
RA	1,821,867	(A)8→7	intergenic (‑248/+51)	chbB ← / ← osmE	N,N'‑diacetylchitobiose‑specific enzyme IIB component of PTS/osmotically‑inducible lipoprotein
RA	1,826,546	T→C	E126E (GAA→GAG)	astE ←	succinylglutamate desuccinylase
RA	1,834,111	G→A	*237* (TAG→TAA)	ydjX →	TVP38/TMEM64 family inner membrane protein
RA	1,841,897	G→A	*136* (TAG→TAA)  T80I (ACT→ATT)	nudG → ynjH ←	CTP pyrophosphohydrolase, also hydrolyzes 2‑hydroxy‑dATP, 8‑hydroxy‑dGTP, 5‑hydroxy‑CTP, dCTP and 5‑methyl‑dCTP DUF1496 family protein
RA	1,850,810	(C)5→4	intergenic (+117/‑50)	sppA → / → ansA	protease IV (signal peptide peptidase)/cytoplasmic L‑asparaginase 1
RA	1,862,634	A→G	intergenic (‑205/‑137)	msrB ← / → gapA	methionine sulfoxide reductase B/glyceraldehyde‑3‑phosphate dehydrogenase A
RA	1,863,004	T→C	R78R (CGT→CGC)	gapA →	glyceraldehyde‑3‑phosphate dehydrogenase A
RA	1,869,022	(T)6→5	coding (68/1284 nt)	yeaH →	UPF0229 family protein
RA	1,874,078	C→T	*35* (TAG→TAA)	yoaI ←	uncharacterized protein
RA	1,874,798	G→A	*149* (TAG→TAA)  T260I (ACT→ATT)	yeaL → yeaM ←	UPF0756 family putative inner membrane protein putative DNA‑binding transcriptional regulator
RA	1,875,056	(C)6→5	coding (521/822 nt)	yeaM ←	putative DNA‑binding transcriptional regulator
RA	1,881,463	G→A	A116V (GCG→GTG)	dmlR ←	transcriptional activator of dmlA
RA	1,886,810	G→A	*322* (TAG→TAA)	yeaX →	putative YeaWX dioxygenase beta subunit, reductase component
RA	1,892,402	A→G	S278S (AGT→AGC)	yoaA ←	putative ATP‑dependent helicase, DinG family
RA	1,905,805	G→A	G40S (GGC→AGC)	mntP →	putative Mn(2+) efflux pump, mntR‑regulated
RA	1,905,989	G→A	R101H (CGT→CAT)	mntP →	putative Mn(2+) efflux pump, mntR‑regulated
RA	1,910,474	T→C	S67P (TCC→CCC)	yebQ →	putative transporter
RA	1,920,205	(T)7→8	intergenic (+62/‑18)	yebT → / → rsmF	MCE domain protein/16S rRNA m(5)C1407 methyltransferase, SAM‑dependent
RA	1,926,096	G→A	*219* (TAG→TAA)	yobB →	C‑N hydrolase family protein
RA	1,926,782	G→A	*221* (TAG→TAA)  D686D (GAC→GAT)	exoX → ptrB ←	exodeoxyribonuclease 10, DNA exonuclease X protease II
RA	1,939,673	T→C	N174S (AAC→AGC)	lpxM ←	myristoyl‑acyl carrier protein (ACP)‑dependent acyltransferase
RA	1,942,993	G→A	G111E (GGG→GAG)	znuC →	zinc ABC transporter ATPase
RA	1,950,559	(C)5→6	intergenic (‑37/‑273)	aspS ← / → yecD	aspartyl‑tRNA synthetase/isochorismatase family protein
RA	1,952,661	G→A	*132* (TAG→TAA)	yecN →	MAPEG family inner membrane protein
RA	1,958,496	G→A	intergenic (‑364/+24)	torY ← / ← cutC	TMAO reductase III (TorYZ), cytochrome c‑type subunit/copper homeostasis protein
RA	1,964,697	G→A	L118L (CTC→CTT)	flhA ←	putative flagellar export pore protein
RA	1,971,902	T→C	T264A (ACC→GCC)	tar ←	methyl‑accepting chemotaxis protein II
RA	1,977,529	A→G	C106R (TGC→CGC)	flhC ←	flagellar class II regulon transcriptional activator, with FlhD
MC JC	1,978,503	Δ776 bp		insB1–insA	insB1, insA
RA	1,980,188	C→T	*475* (TAG→TAA)	otsA ←	trehalose‑6‑phosphate synthase
RA	1,998,494	C→T	*329* (TAG→TAA)	dcyD ←	D‑cysteine desulfhydrase, PLP‑dependent
RA	2,012,001	C→T	pseudogene (40/678 nt)	yedN ←	pseudogene, IpaH/YopM family
RA	2,012,700	C→T	*105* (TAG→TAA)	fliE ←	flagellar basal‑body component
RA	2,016,095	G→A	L76L (CTG→CTA)	fliH →	negative regulator of FliI ATPase activity
RA	2,021,501	G→A	*138* (TAG→TAA)	fliN →	flagellar motor switching and energizing component
RA	2,022,606	G→A	*246* (TAG→TAA)	fliP →	flagellar biosynthesis protein
RA	2,022,885	G→A	*90* (TAG→TAA)	fliQ →	flagellar biosynthesis protein
RA	2,029,729	(C)6→5	coding (191/921 nt)	yedA →	amino acid exporter for phenylalanine, threonine
RA	2,034,536	G→A	pseudogene (486/663 nt)	yedS →	pseudogene, outer membrane protein homology, putative outer membrane protein
RA	2,049,336	C→T	P1467S (CCG→TCG)	yeeJ →	putative adhesin
RA	2,059,964	C→T	*317* (TAG→TAA)	cbl ←	ssuEADCB/tauABCD operon transcriptional activator
RA	2,068,952	C→T	*302* (TAG→TAA)	insD1 ←	IS2 transposase TnpB
RA	2,084,773	G→A	G251G (GGC→GGT)	yeeE ←	UPF0394 family inner membrane protein
RA	2,090,046	G→A	*17* (TAG→TAA)	hisL →	his operon leader peptide
RA	2,099,237	G→A	A126V (GCG→GTG)	ugd ←	UDP‑glucose 6‑dehydrogenase
RA	2,102,890	T→C	R8G (AGA→GGA)	insH1 ←	IS5 transposase and trans‑activator
RA	2,104,494	C→T	V6I (GTC→ATC)  *197* (TAG→TAA)	wbbK ← wbbJ ←	lipopolysaccharide biosynthesis protein putative lipopolysaccharide biosynthesis O‑acetyl transferase
RA	2,114,502	C→T	*465* (TAG→TAA)	wcaM ←	colanic acid biosynthesis protein
RA	2,115,907	C→T	*407* (TAG→TAA)	wcaL ←	putative glycosyl transferase
RA	2,118,164	G→A	R81C (CGT→TGT)	wcaK ←	colanic acid biosynthesis protein
RA	2,130,853	C→T	S9N (AGC→AAC)  *406* (TAG→TAA)	wcaD ← wcaC ←	putative colanic acid polymerase putative glycosyl transferase
RA	2,131,667	T→C	D135G (GAC→GGC)	wcaC ←	putative glycosyl transferase
RA	2,139,759	C→T	*618* (TAG→TAA)	asmA ←	suppressor of OmpF assembly mutants, putative outer membrane protein assembly factor, inner membrane‑anchored periplasmic protein
RA	2,149,963	G→T	G341G (GGC→GGA)	yegI ←	protein kinase‑related putative non‑specific DNA‑binding protein
RA	2,164,998	G→A	*241* (TAG→TAA)	baeR →	response regulator in two‑component regulatory system with BaeS
RA	2,169,693	C→T	pseudogene (475/475 nt)	gatR ←	pseudogene, repressor for gat operon, interrupted by IS3, split galactitol utilization operon repressor, fragment 2, split galactitol utilization operon repressor, interrupted
RA	2,171,398	G→A	*289* (TAG→TAA)	insF1 →	IS3 transposase B
RA	2,173,363	Δ2 bp	intergenic (‑1/+1)	gatC ← / ← gatC	pseudogene, galactitol‑specific enzyme IIC component of PTS,transport, Transport of small molecules: Carbohydrates, organic acids, alcohols, PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS,transport, Transport of small molecules: Carbohydrates, organic acids, alcohols, PTS system galactitol‑specific enzyme IIC
RA	2,179,330	T→C	S170S (AGT→AGC)	yegT →	nucleoside transporter, low affinity
RA	2,182,035	C→T	L314L (CTA→TTA)  *249* (TAG→TAA)	yegV → yegW ←	putative kinase putative DNA‑binding transcriptional regulator
RA	2,182,061	G→A	*322* (TAG→TAA)  L241L (CTA→TTA)	yegV → yegW ←	putative kinase putative DNA‑binding transcriptional regulator
RA	2,185,875	(G)7→8	intergenic (‑79/‑42)	rcnR ← / → rcnA	transcriptional repressor of rcnA/membrane protein conferring nickel and cobalt resistance
RA	2,189,594	C→T	A439A (GCG→GCA)	yehB ←	putative outer membrane protein
RA	2,199,396	C→T	pseudogene (75/948 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	2,200,454	(A)8→7	coding (176/3633 nt)	yehI →	DUF4132 domain‑containing protein
RA	2,210,944	G→A	pseudogene (1845/2001 nt)	yehQ →	pseudogene
RA	2,214,339	(C)6→5	coding (306/1686 nt)	yehU ←	inner membrane putative sensory kinase in two‑component system with YehT
RA	2,218,207	C→T	A117A (GCG→GCA)	yehY ←	putative ABC transporter permease
RA	2,220,789	G→A	R401C (CGT→TGT)	bglX ←	beta‑D‑glucoside glucohydrolase, periplasmic
RA	2,225,044	C→T	*196* (TAG→TAA)	yohC ←	Yip1 family inner membrane protein
RA	2,226,509	C→T	*254* (TAG→TAA)	yohF ←	putative oxidoreductase
RA	2,233,597	G→A	*240* (TAG→TAA)	sanA →	DUF218 superfamily vancomycin high temperature exclusion protein
RA	2,240,754	(C)5→6	coding (915/1041 nt)	galS ←	galactose‑ and fucose‑inducible galactose regulon transcriptional isorepressor, mgl operon transcriptional repressor, autorepressor
RA	2,263,478	T→C	V6V (GTA→GTG)	fruB ←	fused fructose‑specific PTS enzymes: IIA component/HPr component
RA	2,266,013	T→C	R188R (CGT→CGC)	yeiP →	elongation factor P‑like protein
RA	2,274,166	A→G	K601K (AAA→AAG)	yejA →	microcin C ABC transporter periplasmic binding protein
RA	2,274,178	G→A	*605* (TAG→TAA)	yejA →	microcin C ABC transporter periplasmic binding protein
RA	2,276,298	G→A	*342* (TAG→TAA)	yejE →	microcin C ABC transporter permease
RA	2,288,561	(C)7→6	pseudogene (354/2525 nt)	yejO ←	pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system
RA	2,289,027	G→A	intergenic (‑113/+38)	yejO ← / ← insH1	pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system/IS5 transposase and trans‑activator
RA	2,291,973	T→C	G146G (GGA→GGG)	ccmH ←	heme lyase, CcmH subunit
RA	2,316,160	G→A	*891* (TAG→TAA)	rcsD →	phosphotransfer intermediate protein in two‑component regulatory system with RcsBC
RA	2,317,027	C→T	*950* (TAG→TAA)	rcsC ←	hybrid sensory kinase in two‑component regulatory system with RcsB and YojN
RA	2,318,019	G→A	R620C (CGT→TGT)	rcsC ←	hybrid sensory kinase in two‑component regulatory system with RcsB and YojN
RA	2,334,336	C→T	pseudogene (67/4605 nt) *208* (TAG→TAA)	yfaS ← yfaT ←	pseudogene, bacterial alpha2‑macroglobulin YfaS variant family, putative membrane protein DUF1175 family protein, putative host defense protein
RA	2,350,162	A→G	L284L (TTG→CTG)	glpQ ←	periplasmic glycerophosphodiester phosphodiesterase
RA	2,358,163	G→A	A228V (GCG→GTG)	rhmA ←	2‑keto‑3‑deoxy‑L‑rhamnonate aldolase
RA	2,370,019	T→C	*661R (TGA→CGA)  M1T (ATG→ACG) †	arnA → arnD →	fused UDP‑L‑Ara4N formyltransferase/UDP‑GlcA C‑4'‑decarboxylase undecaprenyl phosphate‑alpha‑L‑ara4FN deformylase
RA	2,379,348	C→T	*432* (TAG→TAA)	menF ←	isochorismate synthase 2
RA	2,414,699	T→C	intergenic (+27/‑48)	ackA → / → pta	acetate kinase A and propionate kinase 2/phosphate acetyltransferase
RA	2,416,763	2 bp→TC	coding (2017‑2018/2145 nt)	pta →	phosphate acetyltransferase
RA	2,438,548	T→C	V200A (GTG→GCG)	flk →	putative flagella assembly protein
RA	2,442,490	+G	coding (727/2007 nt)	mnmC →	fused 5‑methylaminomethyl‑2‑thiouridine‑forming enzyme methyltransferase and FAD‑dependent demodification enzyme
RA	2,449,228	C→T	*274* (TAG→TAA)	yfcO ←	DUF2544 family putative outer membrane protein
RA	2,453,265	C→T	pseudogene (1737/2646 nt)	yfcU ←	pseudogene, FimD fimbrial export usher family,putative membrane, Not classified, putative outer membrane protein
RA	2,462,889	(C)9→8	intergenic (+243/‑123)	fadL → / → yfdF	long‑chain fatty acid outer membrane transporter/uncharacterized protein
RA	2,468,106	T→C	A84A (GCT→GCC)	gtrA →	CPS‑53 (KpLE1) prophage, bactoprenol‑linked glucose translocase/flippase
RA	2,471,105	G→A	pseudogene (291/291 nt) P138L (CCT→CTT)	tfaS → yfdK ←	pseudogene, CPS‑53 (KpLE1) prophage, tail fiber assembly protein fragment,Phage or Prophage Related CPS‑53 (KpLE1) prophage, conserved protein
RA	2,478,092	A→G	V82V (GTA→GTG)	dsdX →	D‑serine transporter
RA	2,484,897	(C)6→7	coding (524/3594 nt)	evgS →	hybrid sensory histidine kinase in two‑component regulatory system with EvgA
RA	2,494,950	T→C	Y85H (TAT→CAT)	ypdI →	putative lipoprotein involved in colanic acid biosynthesis
RA	2,494,973	G→A	*92* (TAG→TAA)	ypdI →	putative lipoprotein involved in colanic acid biosynthesis
RA	2,495,050	C→T	*81* (TAG→TAA)	yfdY ←	DUF2545 family putative inner membrane protein
RA	2,504,391	T→C	E32G (GAA→GGA)	fryA ←	putative PTS enzyme: Hpr, enzyme I and IIA components
RA	2,510,886	G→A	*419* (TAG→TAA)	yfeO →	putative ion channel protein
RA	2,511,468	C→T	*413* (TAG→TAA)	mntH ←	manganese/divalent cation transporter
RA	2,521,593	C→T	*295* (TAG→TAA)	xapR ←	transcriptional activator of xapAB
RA	2,521,852	T→C	D209G (GAT→GGT)	xapR ←	transcriptional activator of xapAB
MC JC	2,525,917	Δ9 bp	intergenic (+26/+5)	yfeN → / ← yfeR	putative outer membrane protein/transcriptional regulator of yefH
RA	2,525,930	C→T	*309* (TAG→TAA)	yfeR ←	transcriptional regulator of yefH
RA	2,534,031	T→C	intergenic (+10/‑35)	ptsH → / → ptsI	phosphohistidinoprotein‑hexose phosphotransferase component of PTS system (Hpr)/PEP‑protein phosphotransferase of PTS system (enzyme I)
RA	2,552,094	G→A	I15I (ATC→ATT)	ypeA ←	GNAT family putative N‑acetyltransferase
RA	2,574,135	G→A	D57D (GAC→GAT)	eutT ←	cobalamin adenosyltransferase involved in ethanolamine utilization
RA	2,589,535	C→T	I647I (ATC→ATT)	acrD →	aminoglycoside/multidrug efflux system
RA	2,591,603	G→A	*119* (TAG→TAA)	yffB →	putative ArsC family reductase
RA	2,595,227	T→C	Q211Q (CAA→CAG)	tmcA ←	elongator methionine tRNA (ac4C34) acetyltransferase
RA	2,597,904	G→A	P321L (CCG→CTG)	bamC ←	BamABCDE complex OM biogenesis lipoprotein
RA	2,600,609	(C)5→6	coding (132/471 nt)	bcp →	peroxiredoxin, thiol peroxidase, thioredoxin‑dependent
MC JC	2,614,614	Δ3 bp	coding (681‑683/849 nt)	focB →	putative formate transporter
RA	2,618,075	C→T	*234* (TAG→TAA)	hda ←	ATPase regulatory factor involved in DnaA inactivation
RA	2,621,307	A→G	E37E (GAA→GAG)	purM →	phosphoribosylaminoimidazole synthetase
RA	2,629,481	G→A	*64* (TAG→TAA)	yfgG →	uncharacterized protein
RA	2,637,295	C→T	R21H (CGT→CAT)	der ←	GTPase, multicopy suppressor of ftsJ
RA	2,645,013	C→T	*771* (TAG→TAA)	pbpC ←	penicillin‑insensitive murein repair transglycosylase, inactive transpeptidase domain protein
RA	2,654,538	G→A	S132S (AGC→AGT)	sseB ←	rhodanase‑like enzyme, sulfur transfer from thiosulfate
RA	2,655,767	T→C	T198A (ACT→GCT)	pepB ←	aminopeptidase B
RA	2,673,768	G→A	*141* (TAG→TAA)	yphA →	DoxX family inner membrane protein
RA	2,684,971	G→A	G179G (GGC→GGT)	glyA ←	serine hydroxymethyltransferase
RA	2,685,561	T→C	intergenic (‑54/‑274)	glyA ← / → hmp	serine hydroxymethyltransferase/fused nitric oxide dioxygenase/dihydropteridine reductase 2
RA	2,685,910	G→A	A26T (GCC→ACC)	hmp →	fused nitric oxide dioxygenase/dihydropteridine reductase 2
RA	2,697,915	C→T	*212* (TAG→TAA)	pgpC ←	phosphatidylglycerophosphatase C, membrane bound
RA	2,713,568	T→C	W225R (TGG→CGG)	srmB →	ATP‑dependent RNA helicase
RA	2,717,821	(C)5→4	coding (708/1038 nt)	yfiF ←	putative methyltransferase
RA	2,723,065	G→A	A113A (GCG→GCA)	pssA →	phosphatidylserine synthase, CDP‑diacylglycerol‑serine O‑phosphatidyltransferase
RA	2,724,448	C→T	H107H (CAC→CAT)  *433* (TAG→TAA)	yfiM → kgtP ←	putative lipoprotein alpha‑ketoglutarate transporter
RA	2,737,495	G→A	*114* (TAG→TAA)	raiA →	cold shock protein associated with 30S ribosomal subunit
RA	2,742,962	G→A	D194N (GAT→AAT)	yfiN →	putative membrane‑anchored diguanylate cyclase
RA	2,764,608	T→C	I182M (ATA→ATG)	yfjL ←	CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein
RA	2,765,829	(C)5→4	intergenic (‑53/‑89)	yfjM ← / → rnlA	CP4‑57 prophage, uncharacterized protein/CP4‑57 prophage, RNase LS
RA	2,767,445	(C)7→8	intergenic (+90/‑265)	rnlB → / → yfjP	CP4‑57 prophage, uncharacterized protein/CP4‑57 prophage, 50S ribosome‑binding GTPase family protein
RA	2,769,486	G→A	*274* (TAG→TAA)	yfjQ →	CP4‑57 prophage, uncharacterized protein
RA	2,769,648	(C)6→5	intergenic (+162/‑55)	yfjQ → / → yfjR	CP4‑57 prophage, uncharacterized protein/CP4‑57 prophage, putative DNA‑binding transcriptional regulator
RA	2,770,404	G→A	*234* (TAG→TAA)	yfjR →	CP4‑57 prophage, putative DNA‑binding transcriptional regulator
RA	2,781,132	T→C	D532G (GAC→GGC)	ypjA ←	adhesin‑like autotransporter
RA	2,782,393	(C)5→4	coding (334/4581 nt)	ypjA ←	adhesin‑like autotransporter
RA	2,784,529	C→T	pseudogene (483/1374 nt)	ypjC ←	pseudogene
RA	2,786,729	G→A	pseudogene (333/2253 nt)	ygaQ →	uncharacterized protein, putative enzyme
RA	2,786,746	Δ1 bp	pseudogene (350/2253 nt)	ygaQ →	uncharacterized protein, putative enzyme
RA	2,787,434	G→A	pseudogene (1038/2253 nt)	ygaQ →	uncharacterized protein, putative enzyme
RA	2,788,238	G→A	pseudogene (1842/2253 nt)	ygaQ →	uncharacterized protein, putative enzyme
RA	2,794,015	G→A	*427* (TAG→TAA)	gabT →	4‑aminobutyrate aminotransferase, PLP‑dependent
RA	2,796,146	C→T	A158V (GCG→GTG)	csiR →	transcriptional repressor of csiD
RA	2,796,337	C→T	*150* (TAG→TAA)	ygaU ←	uncharacterized protein
RA	2,796,916	T→C	Y38C (TAT→TGT)	yqaE ←	cyaR sRNA‑regulated protein
RA	2,800,475	G→A	*110* (TAG→TAA)	ygaM →	putative membrane‑anchored DUF883 family ribosome‑binding protein
RA	2,814,218	C→T	*172* (TAG→TAA)	luxS ←	S‑ribosylhomocysteine lyase
RA	2,824,491	C→T	*362* (TAG→TAA)	mltB ←	membrane‑bound lytic murein transglycosylase B
RA	2,824,496	Δ1 bp	coding (1081/1086 nt)	mltB ←	membrane‑bound lytic murein transglycosylase B
RA	2,827,351	G→A	*320* (TAG→TAA)	srlE →	glucitol/sorbitol‑specific enzyme IIB component of PTS
RA	2,835,045	G→A	*378* (TAG→TAA)	norW →	NADH:flavorubredoxin oxidoreductase
RA	2,839,384	T→A	intergenic (‑120/‑140)	ascG ← / → ascF	asc operon transcriptional repressor, prpBC operon repressor/cellobiose/arbutin/salicin‑specific PTS enzymes, IIB and IC components
RA	2,842,414	G→A	*475* (TAG→TAA)	ascB →	cryptic 6‑phospho‑beta‑glucosidase
RA	2,842,573	C→T	*157* (TAG→TAA)	hycI ←	protease involved in processing C‑terminal end of HycE
RA	2,851,873	G→A	*291* (TAG→TAA)  G4S (GGC→AGC)	hypB → hypC →	GTP hydrolase involved in nickel liganding into hydrogenases hydrogenase maturation protein
RA	2,856,453	C→T	*118* (TAG→TAA)	ygbA ←	uncharacterized protein
RA	2,859,538	C→T	L816L (CTG→TTG)	mutS →	methyl‑directed mismatch repair protein
RA	2,860,416	G→A	*219* (TAG→TAA)	pphB →	serine/threonine‑specific protein phosphatase 2
RA	2,860,426	Δ1 bp	intergenic (+10/+41)	pphB → / ← ygbI	serine/threonine‑specific protein phosphatase 2/DeoR family putative transcriptional regulator
RA	2,871,264	G→A	P14L (CCG→CTG)	truD ←	tRNA(Glu) pseudouridine(13) synthase
RA	2,876,944	G→A	A122T (GCC→ACC)	iap →	aminopeptidase in alkaline phosphatase isozyme conversion
RA	2,893,928	G→A	*424* (TAG→TAA)  A4T (GCC→ACC)	ygcN → ygcO →	putative oxidoreductase putative 4Fe‑4S cluster‑containing protein
MC JC	2,893,961	Δ3 bp	coding (43‑45/261 nt)	ygcO →	putative 4Fe‑4S cluster‑containing protein
RA	2,902,543	G→A	G216G (GGG→GGA)	ygcE →	putative kinase
RA	2,905,532	T→C	intergenic (‑114/‑25)	queE ← / → yqcG	7‑carboxy‑7‑deazaguanine synthase, queosine biosynthesis/membrane stress resistance protein
RA	2,910,756	C→T	*112* (TAG→TAA)	mazF ←	mRNA interferase toxin, antitoxin is MazE
RA	2,911,417	C→T	*745* (TAG→TAA)	relA ←	(p)ppGpp synthetase I/GTP pyrophosphokinase
RA	2,913,699	C→T	*434* (TAG→TAA)	rlmD ←	23S rRNA m(5)U1939 methyltransferase, SAM‑dependent
RA	2,915,105	C→T	P17S (CCG→TCG)	barA →	hybrid sensory histidine kinase, in two‑component regulatory system with UvrY
RA	2,935,917	G→A	G112S (GGC→AGC)	fucI →	L‑fucose isomerase
RA	2,936,931	T→C	F450L (TTC→CTC)	fucI →	L‑fucose isomerase
RA	2,937,802	A→G	D112G (GAC→GGC)	fucK →	L‑fuculokinase
RA	2,962,441	C→T	*108* (TAG→TAA)	ppdC ←	putative prepilin peptidase‑dependent protein
RA	2,966,188	C→T	*749* (TAG→TAA)	ptsP ←	PEP‑protein phosphotransferase enzyme I, GAF domain containing protein
RA	2,970,351	G→A	*230* (TAG→TAA)	mutH →	methyl‑directed mismatch repair protein
RA	2,979,943	C→T	A308V (GCT→GTT)  *231* (TAG→TAA)	lysR → ygeA ←	transcriptional activator of lysA, autorepressor Asp/Glu_racemase family protein
RA	2,983,288	C→T	*279* (TAG→TAA)	kduI ←	hexuronate isomerase
RA	2,984,411	C→T	*394* (TAG→TAA)	yqeF ←	short chain acyltransferase
RA	2,993,856	G→A	*73* (TAG→TAA)	ygeI →	uncharacterized protein
RA	2,994,415	G→A	pseudogene (34/60 nt)	pbl →	pseudogene, peptidoglycan‑binding enzyme family
RA	2,995,231	(A)7→8	intergenic (‑139/+83)	ygeK ← / ← ygeN	pseudogene, response regulator family, part of T3SS PAI ETT2 remnant, putative 2‑component transcriptional regulator/pseudogene, orgB family, part of T3SS PAI ETT2 remnant
RA	2,995,314	C→T	pseudogene (447/447 nt)	ygeN ←	pseudogene, orgB family, part of T3SS PAI ETT2 remnant
RA	2,996,372	C→T	*302* (TAG→TAA)	insD1 ←	IS2 transposase TnpB
RA	2,997,689	C→T	intergenic (‑89/+3)	insC1 ← / ← ygeQ	IS2 repressor TnpA/pseudogene, glycosyl hydrolase family 15, part of T3SS PAI ETT2 remnant
RA	3,012,553	Δ1 bp	intergenic (+160/+61)	yqeA → / ← yqeB	putative amino acid kinase/XdhC‑CoxI family protein with NAD(P)‑binding Rossman fold
RA	3,014,259	Δ1 bp	intergenic (‑20/+28)	yqeB ← / ← yqeC	XdhC‑CoxI family protein with NAD(P)‑binding Rossman fold/putative selenium‑dependent hydroxylase accessory protein
RA	3,014,287	C→T	*257* (TAG→TAA)	yqeC ←	putative selenium‑dependent hydroxylase accessory protein
RA	3,015,738	G→A	*193* (TAG→TAA)	mocA →	CTP:molybdopterin cytidylyltransferase
RA	3,032,032	G→A	S222S (TCG→TCA)	uacT →	uric acid permease
RA	3,035,546	T→C	T246A (ACG→GCG)	prfB ←	peptide chain release factor RF‑2
RA	3,036,373	C→T	*578* (TAG→TAA)	recJ ←	ssDNA exonuclease, 5' ‑‑> 3'‑specific
RA	3,050,691	G→A	intergenic (‑24/+424)	gcvT ← / ← ubiI	aminomethyltransferase, tetrahydrofolate‑dependent, subunit (T protein) of glycine cleavage complex/2‑octaprenylphenol hydroxylase, FAD‑dependent
RA	3,056,273	G→A	P11P (CCG→CCA)	fau →	5‑formyltetrahydrofolate cyclo‑ligase family protein
RA	3,059,293	T→C	G11G (GGA→GGG)	rpiA ←	ribose 5‑phosphate isomerase, constitutive
RA	3,061,202	A→G	N118S (AAC→AGC)	scpA →	methylmalonyl‑CoA mutase
RA	3,068,173	C→T	*212* (TAG→TAA)	argO ←	arginine transporter
RA	3,082,038	T→C	D42D (GAT→GAC)	loiP →	Phe‑Phe periplasmic metalloprotease, OM lipoprotein, low salt‑inducible, Era‑binding heat shock protein
RA	3,083,620	G→A	R60C (CGT→TGT)	speB ←	agmatinase
RA	3,085,461	A→G	S151P (TCC→CCC)	speA ←	biosynthetic arginine decarboxylase, PLP‑binding
RA	3,094,234	T→C	T283A (ACA→GCA)	yggR ←	putative PilT family AAA+ ATPase
RA	3,096,673	G→A	*97* (TAG→TAA)	yggU →	UPF0235 family protein
RA	3,101,039	(C)7→8	coding (585/720 nt)	yggN ←	DUF2884 family putative periplasmic protein
RA	3,104,065	G→A	*351* (TAG→TAA)	mutY →	adenine DNA glycosylase
RA	3,129,036	G→A	*255* (TAG→TAA)	glcC →	glycolate‑inducible glc operon transcriptional repressor, autorepressor
RA	3,131,341	C→T	*356* (TAG→TAA)	yghQ ←	putative inner membrane polysaccharide flippase
RA	3,134,811	Δ1 bp	coding (681/693 nt)	yghT →	putative ATP‑binding protein
RA	3,134,823	G→A	*231* (TAG→TAA)	yghT →	putative ATP‑binding protein
RA	3,140,294	T→C	S9G (AGC→GGC)	hybF ←	protein involved with the maturation of hydrogenases 1 and 2
RA	3,162,308	G→A	S121L (TCG→TTG)	ftsP ←	septal ring component that protects the divisome from stress, multicopy suppressor of ftsI(Ts)
RA	3,171,879	C→T	*111* (TAG→TAA)	ygiZ ←	inner membrane protein
RA	3,176,721	G→A	T38I (ACC→ATC)	cpdA ←	3',5' cAMP phosphodiesterase
RA	3,176,858	C→T	*141* (TAG→TAA)	yqiB ←	DUF1249 protein YqiB
RA	3,178,015	G→A	intergenic (‑105/‑100)	nudF ← / → tolC	ADP‑ribose pyrophosphatase/transport channel
RA	3,183,006	G→A	G153S (GGT→AGT)	zupT →	zinc transporter
RA	3,187,415	G→A	*302* (TAG→TAA)	insD1 →	IS2 transposase TnpB
RA	3,187,588	G→A	pseudogene (162/2439 nt)	yqiG →	pseudogene, fimbrial export usher family,putative membrane, Not classified, putative membrane protein
RA	3,191,696	G→A	*355* (TAG→TAA)	yqiI →	fimbrial protein
RA	3,199,429	T→C	A71A (GCA→GCG)	glnE ←	fused deadenylyltransferase/adenylyltransferase for glutamine synthetase
RA	3,205,324	C→T	*311* (TAG→TAA)	ttdR ←	transcriptional activator of ttdABT
RA	3,214,757	T→C	Y571H (TAC→CAC)	rpoD →	RNA polymerase, sigma 70 (sigma D) factor
RA	3,218,365	C→T	E238K (GAG→AAG)	aer ←	fused signal transducer for aerotaxis sensory component/methyl accepting chemotaxis component
RA	3,220,190	G→A	A233T (GCT→ACT)	patA →	putrescine:2‑oxoglutaric acid aminotransferase, PLP‑dependent
RA	3,238,562	(T)7→6	intergenic (+265/‑18)	ygjR → / → alx	putative NAD(P)‑dependent dehydrogenase/putative membrane‑bound redox modulator
RA	3,240,984	(G)7→9	coding (1041/1245 nt)	sstT →	sodium:serine/threonine symporter
RA	3,248,939	T→C	intergenic (+117/‑30)	mzrA → / → yqjC	modulator of EnvZ/OmpR regulon/DUF1090 family putative periplasmic protein
RA	3,255,020	G→A	*234* (TAG→TAA)	yhaK →	redox‑sensitive bicupin
RA	3,257,675	G→A	G112G (GGC→GGT)	yhaO ←	putative transporter
RA	3,266,127	C→T	*313* (TAG→TAA)	tdcA ←	tdc operon transcriptional activator
RA	3,269,012	A→G	S200G (AGT→GGT)	yhaC →	pentapetide repeats‑related protein
RA	3,269,602	G→A	*396* (TAG→TAA)	yhaC →	pentapetide repeats‑related protein
RA	3,271,932	T→C	T274A (ACG→GCG)	garR ←	tartronate semialdehyde reductase
RA	3,277,726	C→T	F130F (TTC→TTT)	yhaV →	toxin of the SohB(PrlF)‑YhaV toxin‑antitoxin system
RA	3,277,867	C→T	V267I (GTC→ATC)	agaR ←	transcriptional repressor of the aga regulon
RA	3,282,504	A→G	T177A (ACC→GCC)	agaS →	tagatose‑6‑phosphate ketose/aldose isomerase
RA	3,296,984	G→A	*192* (TAG→TAA)	yraP →	outer membrane lipoprotein
RA	3,298,035	T→C	E35G (GAA→GGA)	yraQ ←	putative inner membrane permease
RA	3,299,438	A→G	T155T (ACA→ACG)	yhbO →	stress‑resistance protein
RA	3,299,999	G→A	A12T (GCC→ACC)	yhbQ →	GIY‑YIG nuclease superfamily protein
RA	3,301,599	G→A	G39S (GGC→AGC)	yhbU →	U32 peptidase family protein
RA	3,304,455	G→A	*336* (TAG→TAA)	yhbW →	putative luciferase‑like monooxygenase
RA	3,308,040	C→T	*295* (TAG→TAA)	nlpI ←	lipoprotein involved in osmotic sensitivity and filamentation
RA	3,308,868	G→A	C19C (TGC→TGT)	nlpI ←	lipoprotein involved in osmotic sensitivity and filamentation
RA	3,309,006	(C)6→5	intergenic (‑82/+27)	nlpI ← / ← pnp	lipoprotein involved in osmotic sensitivity and filamentation/polynucleotide phosphorylase/polyadenylase
RA	3,309,007	G→A	intergenic (‑83/+26)	nlpI ← / ← pnp	lipoprotein involved in osmotic sensitivity and filamentation/polynucleotide phosphorylase/polyadenylase
RA	3,320,333	T→C	E427E (GAA→GAG)	yhbX ←	putative EptAB family phosphoethanolamine transferase, inner membrane protein
RA	3,330,357	+T	coding (1395/1434 nt)	dacB →	D‑alanyl‑D‑alanine carboxypeptidase
RA	3,330,396	G→A	*478* (TAG→TAA)	dacB →	D‑alanyl‑D‑alanine carboxypeptidase
RA	3,340,588	T→C	L105S (TTA→TCA)	yrbG →	putative calcium/sodium:proton antiporter
RA	3,343,891	A→G	D171G (GAC→GGC)	lptA →	lipopolysaccharide export ABC transporter periplasmic binding protein, Lipid A binding protein, LPS export and assembly protein
RA	3,347,069	G→A	*164* (TAG→TAA)	ptsN →	sugar‑specific enzyme IIA component of PTS
RA	3,347,945	T→C	R277R (CGT→CGC)	yhbJ →	adaptor protein for GlmZ/GlmY sRNA decay, glucosamine‑6‑phosphate‑regulated, NTPase
RA	3,353,121	C→T	*310* (TAG→TAA)	yhcC ←	putative Fe‑S oxidoreductase, Radical SAM superfamily protein
RA	3,360,769	G→A	intergenic (+153/‑407)	gltD → / → gltF	glutamate synthase, 4Fe‑4S protein, small subunit/periplasmic protein
RA	3,366,953	G→A	G10R (GGA→AGA)	yhcF →	putative transcriptional regulator
RA	3,372,254	G→A	G107G (GGC→GGT)	nanT ←	sialic acid transporter
RA	3,385,857	C→T	*91* (TAG→TAA)	yhcO ←	putative barnase inhibitor
RA	3,398,875	C→T	M1M (GTG→ATG) † *368* (TAG→TAA)	mreD ← mreC ←	cell wall structural complex MreBCD transmembrane component MreD cell wall structural complex MreBCD transmembrane component MreC
RA	3,400,773	A→G	R105R (CGT→CGC)	mreB ←	cell wall structural complex MreBCD, actin‑like component MreB
RA	3,410,230	(A)6→7	intergenic (+279/‑50)	prmA → / → dusB	methyltransferase for 50S ribosomal subunit protein L11/tRNA‑dihydrouridine synthase B
RA	3,410,406	T→C	S43P (TCT→CCT)	dusB →	tRNA‑dihydrouridine synthase B
RA	3,432,994	(C)6→7	coding (567/1125 nt)	smf ←	DNA recombination‑mediator A family protein
RA	3,434,577	G→A	A122T (GCA→ACA)	fmt →	10‑formyltetrahydrofolate:L‑methionyl‑tRNA(fMet) N‑formyltransferase
RA	3,439,141	C→T	*123* (TAG→TAA)	yhdN ←	DUF1992 family protein
RA	3,440,950	G→A	T27I (ACC→ATC)	rpoA ←	RNA polymerase, alpha subunit
RA	3,457,616	G→A	A414T (GCC→ACC)	gspD →	general secretory pathway component, cryptic
RA	3,466,313	A→G	L138P (CTT→CCT)	bfr ←	bacterioferritin, iron storage and detoxification protein
RA	3,472,033	G→A	I494I (ATC→ATT)	fusA ←	protein chain elongation factor EF‑G, GTP‑binding
RA	3,478,592	C→T	*67* (TAG→TAA)	yheV ←	DUF2387 family putative metal‑binding protein
RA	3,478,802	C→T	*602* (TAG→TAA)	kefB ←	potassium:proton antiporter
RA	3,482,967	T→C	L560P (CTG→CCG)	yheS →	ABC‑F family protein predicted regulatory ATPase
RA	3,503,952	G→A	*262* (TAG→TAA)	frlD →	fructoselysine 6‑kinase
RA	3,507,942	A→G	Y217H (TAC→CAC)	php ←	phosphotriesterase homology protein
RA	3,508,454	Δ1 bp	coding (137/879 nt)	php ←	phosphotriesterase homology protein
RA	3,511,332	T→C	T31A (ACA→GCA)	yhfY ←	PRD domain protein
RA	3,511,746	(A)8→9	coding (599/906 nt)	yhfZ ←	putative DNA‑binding transcriptional regulator
RA	3,515,726	T→C	Y63C (TAT→TGT)	dam ←	DNA adenine methyltransferase
RA	3,516,104	T→C	K401K (AAA→AAG)	damX ←	cell division protein that binds to the septal ring
RA	3,530,528	T→C	I252T (ATC→ACC)	hslO →	heat shock protein Hsp33
RA	3,531,605	T→C	T279A (ACA→GCA)	yhgE ←	DUF4153 family putative inner membrane protein
RA	3,534,656	C→T	G405R (GGG→AGG)	envZ ←	sensory histidine kinase in two‑component regulatory system with OmpR
RA	3,544,074	C→T	*257* (TAG→TAA)	bioH ←	pimeloyl‑ACP methyl ester carboxylesterase
RA	3,545,565	G→A	*228* (TAG→TAA)	gntX →	DNA catabolic protein
RA	3,547,986	C→T	*695* (TAG→TAA)	malQ ←	4‑alpha‑glucanotransferase (amylomaltase)
RA	3,556,033	A→G	Y273H (TAC→CAC)	rtcA ←	RNA 3'‑terminal phosphate cyclase
RA	3,560,455	+G	intergenic (‑2/+1)	glpR ← / ← glpR	pseudogene, DNA‑binding transcriptional repressor,regulator, Energy metabolism, carbon: Anaerobic respiration, repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor,regulator, Energy metabolism, carbon: Anaerobic respiration, repressor of the glp operon
RA	3,566,600	C→T	*478* (TAG→TAA)	glgA ←	glycogen synthase
RA	3,567,251	C→T	L261L (TTG→TTA)	glgA ←	glycogen synthase
RA	3,583,454	G→A	intergenic (+36/‑29)	yrhA → / → insA	pseudogene, interrupted by IS1E/IS1 repressor TnpA
RA	3,587,370	C→T	T143I (ACT→ATT)  *248* (TAG→TAA)	yhhA → ugpQ ←	DUF2756 family protein glycerophosphodiester phosphodiesterase, cytosolic
RA	3,589,820	T→C	S70G (AGC→GGC)	ugpE ←	sn‑glycerol‑3‑phosphate ABC transporter permease
RA	3,598,557	A→G	*368Q (TAA→CAA)	livJ ←	branched‑chain amino acid ABC transporter periplasmic binding protein
RA	3,614,092	T→C	I142I (ATT→ATC)	nikA →	nickel/heme ABC transporter periplasmic binding protein
RA	3,619,269	A→G	V26V (GTA→GTG)	rhsB →	Rhs protein with DUF4329 family putative toxin domain, putative neighboring cell growth inhibitor
RA	3,619,272	T→C	R27R (CGT→CGC)	rhsB →	Rhs protein with DUF4329 family putative toxin domain, putative neighboring cell growth inhibitor
RA	3,643,899	G→A	G428G (GGC→GGT)	prlC ←	oligopeptidase A
RA	3,652,144	G→A	intergenic (+113/+38)	yhiS → / ← insH1	pseudogene/IS5 transposase and trans‑activator
RA	3,658,893	G→A	*176* (TAG→TAA)	gadE →	gad regulon transcriptional activator
RA	3,664,363	(G)6→7	coding (256/729 nt)	gadW ←	transcriptional activator of gadA and gadBC, repressor of gadX
RA	3,664,986	C→T	*275* (TAG→TAA)	gadX ←	acid resistance regulon transcriptional activator, autoactivator
RA	3,683,630	C→T	*663* (TAG→TAA)	yhjK ←	cyclic‑di‑GMP phosphodiesterase
RA	3,694,840	G→A	H133Y (CAT→TAT)	bcsA ←	cellulose synthase, catalytic subunit
RA	3,695,997	C→T	*63* (TAG→TAA)	yhjR ←	DUF2629 family protein
RA	3,719,768	G→A	*97* (TAG→TAA)	yiaG →	HTH_CROC1 family putative transcriptional regulator
RA	3,728,118	(C)8→9	coding (1254/1455 nt)	xylB ←	xylulokinase
RA	3,731,980	G→A	G284S (GGT→AGT)	xylF →	D‑xylose transporter subunit
RA	3,732,319	G→A	G40E (GGG→GAG)	xylG →	D‑xylose ABC transporter dual domain ATPase
RA	3,736,157	G→A	*393* (TAG→TAA)	xylR →	xylose divergent operon transcriptional activator
RA	3,736,160	+A	intergenic (+3/+193)	xylR → / ← bax	xylose divergent operon transcriptional activator/putative glucosaminidase
RA	3,742,599	Δ1 bp	intergenic (‑67/‑134)	yiaJ ← / → yiaK	transcriptional repressor for the yiaKLMNO‑lyxK‑sgbHUE operon/2,3‑diketo‑L‑gulonate reductase, NADH‑dependent
RA	3,750,092	G→A	*287* (TAG→TAA)  E3K (GAG→AAG)	sgbU → sgbE →	putative L‑xylulose 5‑phosphate 3‑epimerase L‑ribulose‑5‑phosphate 4‑epimerase
RA	3,757,183	A→G	C215C (TGT→TGC)	yiaY ←	L‑threonine dehydrogenase
RA	3,761,850	C→T	A36T (GCG→ACG)	yibF ←	glutathione S‑transferase homolog
RA	3,766,316	G→A	*1378* (TAG→TAA)	rhsA →	Rhs protein with putative toxin 55 domain, putative polysaccharide synthesis/export protein, putative neighboring cell growth inhibitor
RA	3,767,179	G→A	*281* (TAG→TAA)	yibA →	putative immunity protein for polymorphic toxin RhsA, HEAT‑domain protein, lethality reduction protein
RA	3,773,602	T→C	V441A (GTT→GCT)	mtlA →	mannitol‑specific PTS enzyme: IIA, IIB and IIC components
RA	3,781,017	G→A	*397* (TAG→TAA)	lldD →	L‑lactate dehydrogenase, FMN‑linked
RA	3,781,688	G→A	*158* (TAG→TAA)	trmL →	tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent
RA	3,789,047	C→T	A316V (GCT→GTT)  *345* (TAG→TAA)	yibQ → waaH ←	putative polysaccharide deacetylase LPS(HepIII)‑glucuronic acid glycosyltransferase
RA	3,789,352	G→A	R244C (CGC→TGC)	waaH ←	LPS(HepIII)‑glucuronic acid glycosyltransferase
RA	3,789,913	C→T	A57T (GCA→ACA)	waaH ←	LPS(HepIII)‑glucuronic acid glycosyltransferase
RA	3,792,826	C→T	*286* (TAG→TAA)	yibB ←	YibB family protein, function unknown
RA	3,810,304	G→A	*160* (TAG→TAA)	coaD →	pantetheine‑phosphate adenylyltransferase
RA	3,815,863	C→T	pseudogene (19/48 nt)	rph ←	ribonuclease PH (defective),enzyme, Degradation of RNA, RNase PH
RA	3,815,883	Δ1 bp	pseudogene (667/669 nt)	rph ←	ribonuclease PH (defective),enzyme, Degradation of RNA, RNase PH
RA	3,818,584	G→A	*275* (TAG→TAA)	dinD →	DNA damage‑inducible protein
RA	3,819,488	C→T	H205H (CAC→CAT)  *561* (TAG→TAA)	yicG → ligB ←	UPF0126 family inner membrane protein DNA ligase, NAD(+)‑dependent
RA	3,838,137	G→A	*395* (TAG→TAA)	setC →	putative arabinose efflux transporter
RA	3,842,455	C→T	*445* (TAG→TAA)	adeQ ←	adenine permease, high affinity, adenine:H+ symporter
RA	3,852,890	C→T	*33* (TAG→TAA)	ivbL ←	ilvB operon leader peptide
RA	3,854,092	T→C	G57G (GGT→GGC)	emrD →	multidrug efflux system protein
RA	3,855,960	C→T	S4N (AGC→AAC)  *116* (TAG→TAA)	yidG ← yidH ←	inner membrane protein DUF202 family inner membrane protein
RA	3,862,497	C→T	pseudogene (1107/1617 nt)	glvC ←	pseudogene, arbutin specific enzyme IIC component of PTS,enzyme, Transport of small molecules: Carbohydrates, organic acids, alcohols, PTS system, arbutin‑like IIB component, PTS system, arbutin‑like IIC component
RA	3,862,518	Δ1 bp	pseudogene (1086/1617 nt)	glvC ←	pseudogene, arbutin specific enzyme IIC component of PTS,enzyme, Transport of small molecules: Carbohydrates, organic acids, alcohols, PTS system, arbutin‑like IIB component, PTS system, arbutin‑like IIC component
JC	3,862,524	Δ3 bp	pseudogene (1078‑1080/1617 nt)	glvC ←	pseudogene, arbutin specific enzyme IIC component of PTS,enzyme, Transport of small molecules: Carbohydrates, organic acids, alcohols, PTS system, arbutin‑like IIB component, PTS system, arbutin‑like IIC component
RA	3,870,441	G→A	*355* (TAG→TAA)  G430G (GGC→GGT)	cbrA → dgoT ←	colicin M resistance protein, FAD‑binding protein, putative oxidoreductase D‑galactonate transporter
RA	3,892,455	G→A	A281T (GCG→ACG)	mdtL →	multidrug efflux system protein
RA	3,897,050	+G	coding (277/666 nt)	yieH →	phosphoenolpyruvate and 6‑phosphogluconate phosphatase
RA	3,897,439	G→A	*222* (TAG→TAA)	yieH →	phosphoenolpyruvate and 6‑phosphogluconate phosphatase
RA	3,898,609	G→A	*196* (TAG→TAA)	cbrC →	UPF0167 family protein
RA	3,908,514	A→G	intergenic (‑148/+35)	pstB ← / ← pstA	phosphate ABC transporter ATPase/phosphate ABC transporter permease
RA	3,920,950	C→T	*80* (TAG→TAA)	atpE ←	F0 sector of membrane‑bound ATP synthase, subunit c
RA	3,921,515	C→T	T179T (ACG→ACA)	atpB ←	F0 sector of membrane‑bound ATP synthase, subunit a
RA	3,922,931	(A)7→8	intergenic (‑491/+126)	atpI ← / ← rsmG	ATP synthase, membrane‑bound accessory factor/16S rRNA m(7)G527 methyltransferase, SAM‑dependent, glucose‑inhibited cell‑division protein
RA	3,937,168	G→A	*297* (TAG→TAA)	rbsB →	D‑ribose ABC transporter periplasmic binding protein, ribose chemotaxis receptor
RA	3,939,219	G→A	*331* (TAG→TAA)  S465F (TCT→TTT)	rbsR → hsrA ←	transcriptional repressor of ribose metabolism putative multidrug or homocysteine efflux system
RA	3,950,420	G→A	*33* (TAG→TAA)	ilvL →	ilvG operon leader peptide
RA	3,956,875	G→A	*515* (TAG→TAA)	ilvA →	l‑threonine dehydratase, biosynthetic, also known as threonine deaminase
RA	3,963,829	C→T	R134H (CGC→CAC)	gpp ←	guanosine pentaphosphatase/exopolyphosphatase
RA	3,970,015	T→C	W329R (TGG→CGG)	wzzE →	Entobacterial Common Antigen (ECA) polysaccharide chain length modulation protein
RA	3,970,032	(G)6→7	coding (1002/1047 nt)	wzzE →	Entobacterial Common Antigen (ECA) polysaccharide chain length modulation protein
RA	3,970,077	G→A	*349* (TAG→TAA)	wzzE →	Entobacterial Common Antigen (ECA) polysaccharide chain length modulation protein
RA	3,976,605	T→C	F110L (TTT→CTT)	wzxE →	O‑antigen translocase
RA	3,980,957	(G)6→7	coding (71/1386 nt)	yifK →	putative APC family amino acid transporter
RA	3,984,193	G→A	*412* (TAG→TAA)	aslB →	putative AslA‑specific sulfatase‑maturating enzyme
RA	3,986,686	C→T	*399* (TAG→TAA)	hemY ←	putative protoheme IX synthesis protein
RA	3,992,054	C→T	P301L (CCA→CTA)	cyaA →	adenylate cyclase
RA	4,002,813	C→T	*127* (TAG→TAA)	yigG ←	PRK11371 family inner membrane protein
RA	4,007,693	G→A	*610* (TAG→TAA)	recQ →	ATP‑dependent DNA helicase
RA	4,018,760	G→A	*476* (TAG→TAA)	rmuC →	DNA recombination protein
RA	4,024,336	G→A	*261* (TAG→TAA)  L162L (CTC→CTT)	tatD → rfaH ←	quality control of Tat‑exported FeS proteins, Mg‑dependent cytoplasmic DNase transcription antitermination protein
RA	4,054,439	A→G	T280T (ACT→ACC)	glnG ←	fused DNA‑binding response regulator in two‑component regulatory system with GlnL: response regulator/sigma54 interaction protein
RA	4,061,157	G→A	*237* (TAG→TAA)	yihL →	putative DNA‑binding transcriptional regulator
RA	4,075,454	G→A	*262* (TAG→TAA)	yihW →	putative transcriptional regulator for sulphoquinovose utilization
RA	4,077,469	G→A	L7L (TTG→TTA)	yiiD →	GNAT family putative N‑acetyltransferase
RA	4,078,438	G→A	*330* (TAG→TAA)	yiiD →	GNAT family putative N‑acetyltransferase
RA	4,106,320	G→A	*167* (TAG→TAA)	cpxP →	inhibitor of the cpx response, periplasmic adaptor protein
RA	4,117,123	G→A	R34C (CGC→TGC)	glpK ←	glycerol kinase
RA	4,137,229	A→G	S143S (AGT→AGC)	yijF ←	DUF1287 family protein
RA	4,147,479	G→A	*114* (TAG→TAA)  T280I (ACT→ATT)	frwD → yijO ←	putative enzyme IIB component of PTS AraC family putative transcriptional activator
RA	4,148,681	C→T	G529S (GGC→AGC)	eptC ←	LPS heptose I phosphoethanolamine transferase
RA	4,188,124	A→G	E925E (GAA→GAG)	rpoC →	RNA polymerase, beta prime subunit
RA	4,204,645	G→A	*442* (TAG→TAA)  N429N (AAC→AAT)	zraR → purD ←	fused DNA‑binding response regulator in two‑component regulatory system with ZraS: response regulator/sigma54 interaction protein phosphoribosylglycinamide synthetase phosphoribosylamine‑glycine ligase
RA	4,213,680	C→T	*148* (TAG→TAA)	yjaB ←	GNAT‑family putative N‑acetyltransferase, acetyl coenzyme A‑binding protein
RA	4,215,740	A→G	E88G (GAA→GGA)	aceB →	malate synthase A
RA	4,218,815	A→G	T74A (ACG→GCG)	aceK →	isocitrate dehydrogenase kinase/phosphatase
RA	4,232,752	G→A	A161V (GCG→GTG)	lysC ←	lysine‑sensitive aspartokinase 3
RA	4,268,487	(T)7→8	intergenic (+180/+322)	tyrB → / ← yjbS	tyrosine aminotransferase, tyrosine‑repressible, PLP‑dependent/uncharacterized protein
RA	4,268,809	C→T	*68* (TAG→TAA)	yjbS ←	uncharacterized protein
RA	4,279,849	A→G	intergenic (+21/‑131)	ghxP → / → yjcE	guanine/hypoxanthine permease, high affinity, guanine/hypoxanthine:H+ symporter/putative cation/proton antiporter
RA	4,296,381	+GC	intergenic (+587/+55)	gltP → / ← yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA	4,297,668	C→T	D567N (GAC→AAC)	fdhF ←	formate dehydrogenase‑H, selenopolypeptide subunit
RA	4,302,240	A→G	I280T (ATC→ACC)	mdtO ←	membrane translocase (MDR) of MdtNOP efflux pump, PET family
RA	4,317,409	C→T	G163S (GGC→AGC)	phnL ←	ribophosphonate triphosphate synthase subunit, putative ABC transporter‑related ATPase
RA	4,324,876	A→G	L97P (CTG→CCG)	phnC ←	phosphonate ABC transporter ATPase
RA	4,325,152	A→G	I5T (ATC→ACC)	phnC ←	phosphonate ABC transporter ATPase
RA	4,328,224	G→A	E364K (GAA→AAA)	crfC →	clamp‑binding sister replication fork colocalization protein, dynamin‑related
RA	4,331,634	C→T	A378V (GCG→GTG)	proP →	proline/glycine betaine transporter
RA	4,336,405	A→G	S209S (AGT→AGC)	adiC ←	arginine:agmatine antiporter
RA	4,346,086	A→G	I414T (ATC→ACC)	fumB ←	anaerobic class I fumarate hydratase (fumarase B)
RA	4,352,880	G→A	*99* (TAG→TAA)	ghoS →	antitoxin of GhoTS toxin‑antitoxin pair, endonuclease for ghoT mRNA
RA	4,353,081	G→A	*58* (TAG→TAA)	ghoT →	toxin of GhoTS toxin‑antitoxin pair, membrane‑lytic protein, stimulator of persister cell formation
RA	4,373,635	G→C	Y200* (TAC→TAG)	yjeJ ←	uncharacterized protein
RA	4,377,189	C→T	H105H (CAC→CAT)  *178* (TAG→TAA)	sugE → blc ←	multidrug efflux system protein outer membrane lipoprotein cell division and growth lipocalin
RA	4,386,872	C→T	A833A (GCG→GCA)	mscM ←	mechanosensitive channel protein, miniconductance
RA	4,389,934	A→G	Y143H (TAC→CAC)	psd ←	phosphatidylserine decarboxylase
RA	4,395,058	C→T	G331G (GGC→GGT)	nnr →	bifunctional NAD(P)H‑hydrate repair enzyme, C‑terminal domain ADP‑dependent (S)‑NAD(P)H‑hydrate dehydratase and N‑terminal domain NAD(P)H‑hydrate epimerase
RA	4,422,793	C→T	A203V (GCC→GTC)	ulaD →	3‑keto‑L‑gulonate 6‑phosphate decarboxylase
RA	4,424,386	G→A	*229* (TAG→TAA)	ulaF →	L‑ribulose 5‑phosphate 4‑epimerase
RA	4,424,516	C→T	*92* (TAG→TAA)	yjfY ←	YhcN family protein, periplasmic
RA	4,424,543	Δ1 bp	coding (249/276 nt)	yjfY ←	YhcN family protein, periplasmic
RA	4,425,834	G→A	*105* (TAG→TAA)	priB →	primosomal protein N
RA	4,428,079	C→T	pseudogene (386/402 nt) *213* (TAG→TAA)	ytfA → ytfB ←	pseudogene, related to transcriptional regulators OapA family protein
RA	4,433,164	C→T	*287* (TAG→TAA)	qorB ←	NAD(P)H:quinone oxidoreductase
RA	4,441,538	C→T	*213* (TAG→TAA)	msrA ←	methionine sulfoxide reductase A
RA	4,442,007	T→C	E57G (GAG→GGG)	msrA ←	methionine sulfoxide reductase A
RA	4,447,869	Δ1 bp	coding (3758/3780 nt)	tamB →	translocation and assembly module for autotransporter export, inner membrane subunit
RA	4,447,891	G→A	*1260* (TAG→TAA)	tamB →	translocation and assembly module for autotransporter export, inner membrane subunit
RA	4,474,138	(A)6→7	coding (15/594 nt)	bdcR →	transcriptional repressor for divergent bdcA
RA	4,474,391	G→A	G90S (GGC→AGC)	bdcR →	transcriptional repressor for divergent bdcA
RA	4,475,562	(G)6→7	coding (126/1815 nt)	yjgL →	SopA‑central‑domain‑like hexapeptide repeat protein
RA	4,488,579	(C)7→8	coding (1485/1503 nt)	yjgR ←	DUF853 family protein with NTPase fold
MC JC	4,490,116	Δ11 bp	intergenic (‑53/+15)	yjgR ← / ← idnR	DUF853 family protein with NTPase fold/transcriptional repressor, 5‑gluconate‑binding
RA	4,490,141	C→T	*333* (TAG→TAA)	idnR ←	transcriptional repressor, 5‑gluconate‑binding
RA	4,490,375	C→T	A255A (GCG→GCA)	idnR ←	transcriptional repressor, 5‑gluconate‑binding
RA	4,499,500	G→A	*302* (TAG→TAA)	insD1 →	IS2 transposase TnpB
RA	4,500,043	C→T	pseudogene (492/942 nt)	yjgX ←	pseudogene fragment
RA	4,500,060	C→T	pseudogene (475/942 nt)	yjgX ←	pseudogene fragment
RA	4,504,006	G→A	intergenic (‑575/‑52)	insG ← / → yjhB	IS4 transposase/putative MFS transporter, membrane protein
RA	4,507,463	G→A	intergenic (+12/+3)	insO → / ← insI1	pseudogene, IS911 transposase B,IS, phage, Tn, Transposon‑related functions, extrachromosomal, transposon related/IS30 transposase
RA	4,510,188	A→G	intergenic (+55/+502)	yjhV → / ← fecE	pseudogene, KpLE2 phage‑like element/ferric citrate ABC transporter ATPase
RA	4,510,690	C→T	*256* (TAG→TAA)	fecE ←	ferric citrate ABC transporter ATPase
RA	4,511,146	C→T	W104* (TGG→TGA)	fecE ←	ferric citrate ABC transporter ATPase
RA	4,515,284	C→T	G465D (GGC→GAC)	fecA ←	TonB‑dependent outer membrane ferric citrate transporter and signal transducer, ferric citrate extracelluar receptor, FecR‑interacting protein
RA	4,519,014	G→A	pseudogene (294/504 nt)	insB1 →	IS1 transposase B,IS, phage, Tn, Transposon‑related functions, extrachromosomal, transposon related
RA	4,535,441	C→T	pseudogene (439/1029 nt)	yjhR →	pseudogene, helicase family, putative frameshift suppressor
RA	4,538,785	C→T	*239* (TAG→TAA)	nanC ←	N‑acetylnuraminic acid outer membrane channel protein
RA	4,541,559	G→A	*201* (TAG→TAA)	fimB →	tyrosine recombinase/inversion of on/off regulator of fimA
RA	4,565,464	C→A	L129F (TTG→TTT)	yjiM ←	putative 2‑hydroxyglutaryl‑CoA dehydratase
RA	4,565,966	C→T	*427* (TAG→TAA)	yjiN ←	zinc‑type alcohol dehydrogenase‑like protein
RA	4,569,309	G→A	pseudogene (312/921 nt)	yjiP →	pseudogene, transposase_31 family protein
RA	4,577,958	C→T	M1M (GTG→ATG) † *460* (TAG→TAA)	mcrC ← mcrB ←	5‑methylcytosine‑specific restriction enzyme McrBC, subunit McrC 5‑methylcytosine‑specific restriction enzyme McrBC, subunit McrB
RA	4,581,621	G→A	A476A (GCC→GCT)	hsdM ←	DNA methyltransferase M
RA	4,604,202	G→A	*242* (TAG→TAA)  E15K (GAA→AAA)	yjjQ → bglJ →	putative transcriptional regulator bgl operon transcriptional activator
RA	4,606,094	(G)8→7	noncoding (72/87 nt)	leuV ←	tRNA‑Leu
RA	4,606,239	A→G	noncoding (48/87 nt)	leuP ←	tRNA‑Leu
RA	4,606,330	(G)8→9	noncoding (72/87 nt)	leuQ ←	tRNA‑Leu
RA	4,609,336	(C)7→8	intergenic (+13/‑78)	yjjG → / → prfC	dUMP phosphatase/peptide chain release factor RF‑3
RA	4,612,289	G→A	*54* (TAG→TAA)	ytjA →	uncharacterized protein
RA	4,614,260	G→A	*260* (TAG→TAA)	yjjV →	putative DNase
MC JC	4,619,478	Δ9 bp	coding (1250‑1258/1323 nt)	deoA →	thymidine phosphorylase
RA	4,619,913	A→G	E104G (GAA→GGA)	deoB →	phosphopentomutase
RA	4,623,101	C→T	*339* (TAG→TAA)	lplA ←	lipoate‑protein ligase A
RA	4,634,532	T→C	D260G (GAT→GGT)	rob ←	right oriC‑binding transcriptional activator, AraC family
RA	4,638,120	G→A	*475* (TAG→TAA)	creC →	sensory histidine kinase in two‑component regulatory system with CreB or PhoB

Unassigned missing coverage evidence
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	66611	66733	123	13 [11]	[0] 14	araD/araA	L‑ribulose‑5‑phosphate 4‑epimerase/L‑arabinose isomerase
*	*	÷	NC_000913	225834–226298	226870–226606	309–1037	13 [11]	[10] 12	rrlH	23S ribosomal RNA of rrnH operon
*	*	÷	NC_000913	789974	789980	7	13 [11]	[0] 39	[galK]	[galK]
*	*	÷	NC_000913	807329	810360	3032	12 [9]	[10] 12	ybhB–[bioB]	ybhB, bioA, [bioB]
*	*	÷	NC_000913	1286766–1286773	1286869	97–104	12 [11]	[11] 13	narI/rttR	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
*	*	÷	NC_000913	1427873–1427957	1428189–1428098	142–317	12 [10]	[11] 15	insH1	IS5 transposase and trans‑activator
*	*	÷	NC_000913	1432750–1433198	1433991–1433668	471–1242	14 [10]	[8] 13	[tfaR]–[ynaE]	[tfaR], pinR, [ynaE]
*	*	÷	NC_000913	2033825	2033941	117	13 [11]	[11] 14	rseX/yedS	sRNA antisense regulator of ompA and ompC translation, Hfq‑dependent/pseudogene, outer membrane protein homology, putative outer membrane protein
*	*	÷	NC_000913	3423765–3424234	3424559–3424243	10–795	13 [11]	[11] 13	[rrfD]–[rrlD]	[rrfD], [rrlD]
*	*	÷	NC_000913	3944039–3944058	3945812–3945569	1512–1774	13 [10]	[11] 12	rrlC	23S ribosomal RNA of rrnC operon
*	*	÷	NC_000913	4037949–4038687	4039277–4038731	45–1329	12 [10]	[10] 13	rrlA	23S ribosomal RNA of rrnA operon

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 788831	1 (0.020)	36 (0.690)	29/214	0.6	98.7%	coding (7/1041 nt) coding (1149/1149 nt)	galM galK	aldose 1‑epimerase, type‑1 mutarotase, galactose mutarotase galactokinase
	?	NC_000913	789981 =	0 (0.000)					intergenic (‑2/+2)	galK/galT	galactokinase/galactose‑1‑phosphate uridylyltransferase
*	?	NC_000913	788831 =	0 (0.000)	92 (1.730)	50/218	0.1	93.9%	coding (7/1041 nt) coding (1149/1149 nt)	galM galK	aldose 1‑epimerase, type‑1 mutarotase, galactose mutarotase galactokinase
	?	NC_000913	3742633 =	12 (0.230)					intergenic (‑101/‑100)	yiaJ/yiaK	transcriptional repressor for the yiaKLMNO‑lyxK‑sgbHUE operon/2,3‑diketo‑L‑gulonate reductase, NADH‑dependent
*	?	NC_000913	1207790 =	3 (0.060)	58 (1.280)	42/186	0.1	97.0%	coding (290/630 nt)	stfP	e14 prophage, uncharacterized protein
	?	NC_000913	1209619 =	1 (0.020)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related
*	?	NC_000913	= 1207805	3 (0.060)	27 (0.600)	20/186	1.0	93.8%	coding (305/630 nt)	stfP	e14 prophage, uncharacterized protein
	?	NC_000913	= 1209602	1 (0.020)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related
*	?	NC_000913	= 3709555	57 (1.140)	64 (1.240) +CCC	41/200	0.1	52.9%	coding (921/1692 nt)	eptB	KDO phosphoethanolamine transferase, Ca(2+)‑inducible
	?	NC_000913	3709556 =	57 (1.070)					coding (920/1692 nt)	eptB	KDO phosphoethanolamine transferase, Ca(2+)‑inducible