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	958	G→T	55.7%	D208Y (GAC→TAC)	thrA →	Bifunctional aspartokinase/homoserine dehydrogenase 1
RA	2,577	C→A	16.9%	G747G (GGC→GGA)	thrA →	Bifunctional aspartokinase/homoserine dehydrogenase 1
RA	3,618	C→A	18.9%	P273Q (CCG→CAG)	thrB →	homoserine kinase
RA	5,144	G→A	100%	intergenic (+124/‑90)	thrC → / → yaaX	L‑threonine synthase/DUF2502 family putative periplasmic protein
RA	10,444	G→T	100%	F17L (TTC→TTA)	satP ←	succinate‑acetate transporter
RA	12,901	G→A	100%	D247N (GAT→AAT)	dnaK →	chaperone Hsp70, with co‑chaperone DnaJ
RA	22,030	G→T	14.2%	P208P (CCG→CCT)	ribF →	bifunctional riboflavin kinase/FAD synthetase
RA	25,546	G→T	100%	D114Y (GAC→TAC)	lspA →	prolipoprotein signal peptidase (signal peptidase II)
RA	29,139	G→T	100%	G256C (GGT→TGT)	dapB →	dihydrodipicolinate reductase
RA	32,632	G→T	21.5%	V606F (GTC→TTC)	carB →	carbamoyl‑phosphate synthase large subunit
RA	41,442	G→T	7.5%	R164S (CGC→AGC)	caiT ←	putative transporter
RA	42,079	G→A	60.2%	intergenic (‑148/‑324)	caiT ← / → fixA	putative transporter/anaerobic carnitine reduction putative electron transfer flavoprotein subunit
RA	42,150	G→A	91.6%	intergenic (‑219/‑253)	caiT ← / → fixA	putative transporter/anaerobic carnitine reduction putative electron transfer flavoprotein subunit
RA	42,415	A→C	62.5%	T5P (ACT→CCT)	fixA →	anaerobic carnitine reduction putative electron transfer flavoprotein subunit
RA	49,029	A→C	9.5%	S421R (AGC→CGC)	kefC →	potassium:proton antiporter
RA	49,840	G→T	100%	A6A (GCG→GCT)	folA →	dihydrofolate reductase
RA	51,352	A→T	5.1%	G85G (GGT→GGA)	apaG ←	protein associated with Co2+ and Mg2+ efflux
RA	55,590	G→T	100%	T507K (ACG→AAG)	lptD ←	LPS assembly OM complex LptDE, beta‑barrel component
RA	56,677	G→T	100%	R145S (CGC→AGC)	lptD ←	LPS assembly OM complex LptDE, beta‑barrel component
RA	60,819	C→T	6.1%	V816M (GTG→ATG)	rapA ←	RNA polymerase remodeling/recycling factor ATPase; RNA polymerase‑associated, ATP‑dependent RNA translocase
RA	69,209	G→T	9.2%	S69* (TCA→TAA)	thiQ ←	thiamine, thiamine pyrophosphate ABC transporter ATPase; ThiBPQ thiamine, thiamine pyrophosphate importer
RA	69,367	C→A	58.9%	M16I (ATG→ATT)	thiQ ←	thiamine, thiamine pyrophosphate ABC transporter ATPase; ThiBPQ thiamine, thiamine pyrophosphate importer
RA	69,546	A→T	16.4%	F488Y (TTC→TAC)	thiP ←	thiamine, thiamine pyrophosphate ABC transporter permease; ThiBPQ thiamine, thiamine pyrophosphate importer
RA	70,465	G→T	56.5%	H182N (CAT→AAT)	thiP ←	thiamine, thiamine pyrophosphate ABC transporter permease; ThiBPQ thiamine, thiamine pyrophosphate importer
RA	76,821	G→T	70.1%	G177G (GGC→GGA)	leuC ←	3‑isopropylmalate dehydratase large subunit
RA	80,123	C→T	100%	G25S (GGC→AGC)	leuL ←	leu operon leader peptide
RA	81,562	C→A	100%	I236I (ATC→ATA)	leuO →	global transcription factor
RA	84,481	G→A	11.2%	intergenic (+146/‑34)	ilvH → / → cra	acetolactate synthase 3, small subunit, valine‑sensitive/transcriptional repressor‑activator for carbon metabolism
RA	86,729	G→T	17.8%	R50L (CGT→CTT)	rsmH →	16S rRNA m(4)C1402 methyltransferase, SAM‑dependent
RA	90,252	G→T	47.6%	A200A (GCG→GCT)	murE →	UDP‑N‑acetylmuramoyl‑L‑alanyl‑D‑glutamate:meso‑ diaminopimelate ligase
RA	92,294	C→A	5.7%	R386R (CGC→CGA)	murF →	UDP‑N‑acetylmuramoyl‑tripeptide:D‑alanyl‑D‑ alanine ligase
RA	93,391	G→T	92.2%	T301T (ACG→ACT)	mraY →	phospho‑N‑acetylmuramoyl‑pentapeptide transferase
RA	95,873	G→T	14.5%	S328S (TCG→TCT)	ftsW →	lipid II flippase; integral membrane protein involved in stabilizing FstZ ring during cell division
RA	97,521	C→A	100%	A90A (GCC→GCA)	murC →	UDP‑N‑acetylmuramate:L‑alanine ligase
RA	97,893	T→A	6.7%	F214L (TTT→TTA)	murC →	UDP‑N‑acetylmuramate:L‑alanine ligase
RA	100,187	A→T	9.5%	A182A (GCA→GCT)	ftsQ →	divisome assembly protein, membrane anchored protein involved in growth of wall at septum
RA	103,467	G→T	100%	D142Y (GAT→TAT)	lpxC →	UDP‑3‑O‑acyl N‑acetylglucosamine deacetylase
RA	104,561	G→T	100%	A124S (GCG→TCG)	secM →	regulator of secA translation
RA	107,298	C→A	36.3%	R845S (CGT→AGT)	secA →	preprotein translocase subunit, ATPase
RA	108,648	Δ1 bp	100%	coding (439/744 nt)	zapD ←	FtsZ stabilizer
RA	110,883	A→T	12.5%	Y318F (TAC→TTC)	guaC →	GMP reductase
RA	112,729	G→T	59.5%	D286E (GAC→GAA)	hofB ←	T2SE secretion family protein; P‑loop ATPase superfamily protein
RA	114,825	G→A	14.6%	S103F (TCC→TTC)	nadC ←	quinolinate phosphoribosyltransferase
RA	116,052	G→T	13.5%	L95L (CTG→CTT)	ampE →	ampicillin resistance inner membrane protein; putative signaling protein in beta‑lactamase regulation
RA	118,526	C→T	10.3%	intergenic (‑488/‑53)	aroP ← / → pdhR	aromatic amino acid transporter/pyruvate dehydrogenase complex repressor; autorepressor
RA	118,873	G→T	100%	D99Y (GAC→TAC)	pdhR →	pyruvate dehydrogenase complex repressor; autorepressor
RA	119,467	G→T	19.3%	intergenic (+124/‑37)	pdhR → / → aceE	pyruvate dehydrogenase complex repressor; autorepressor/pyruvate dehydrogenase, decarboxylase component E1, thiamine triphosphate‑binding
RA	120,313	C→A	60.4%	T270T (ACC→ACA)	aceE →	pyruvate dehydrogenase, decarboxylase component E1, thiamine triphosphate‑binding
RA	122,150	A→T	8.9%	N883Y (AAC→TAC)	aceE →	pyruvate dehydrogenase, decarboxylase component E1, thiamine triphosphate‑binding
RA	122,790	G→T	51.2%	A203A (GCG→GCT)	aceF →	pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2
RA	124,371	C→A	9.9%	intergenic (+297/‑28)	aceF → / → lpd	pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2/lipoamide dehydrogenase, E3 component is part of three enzyme complexes
RA	126,667	G→T	10.6%	R361R (CGG→AGG)	yacH ←	uncharacterized protein
RA	126,784	C→A	38.7%	D322Y (GAT→TAT)	yacH ←	uncharacterized protein
RA	130,349	G→T	7.9%	E750* (GAA→TAA)	acnB →	bifunctional aconitate hydratase 2/2‑methylisocitrate dehydratase
RA	134,028	G→T	87.9%	A153A (GCG→GCT)	cueO →	multicopper oxidase (laccase)
RA	134,652	G→T	8.0%	M361I (ATG→ATT)	cueO →	multicopper oxidase (laccase)
RA	135,557	G→T	37.6%	A719E (GCG→GAG)	gcd ←	glucose dehydrogenase
RA	142,460	T→A	100%	F298Y (TTC→TAC)	yadE →	putative polysaccharide deacetylase lipoprotein
RA	144,698	C→A	35.3%	A195A (GCG→GCT)	panC ←	pantothenate synthetase
RA	146,343	G→T	15.8%	T366T (ACC→ACA)	yadC ←	putative fimbrial‑like adhesin protein
RA	149,697	G→T	21.8%	I739I (ATC→ATA)	htrE ←	putative outer membrane usher protein
RA	151,620	C→A	15.9%	K98N (AAG→AAT)	htrE ←	putative outer membrane usher protein
RA	153,472	G→T	100%	intergenic (‑102/+268)	yadN ← / ← folK	putative fimbrial‑like adhesin protein/2‑amino‑4‑hydroxy‑6‑hydroxymethyldihyropteridine pyrophosphokinase
RA	158,287	C→A	100%	D78Y (GAC→TAC)	ligT ←	2'‑5' RNA ligase
RA	159,121	A→T	15.4%	E177V (GAA→GTA)	hrpB →	putative ATP‑dependent helicase
RA	161,051	A→T	22.2%	intergenic (+30/‑166)	hrpB → / → mrcB	putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase
RA	161,068	A→C	17.4%	intergenic (+47/‑149)	hrpB → / → mrcB	putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase
RA	162,905	G→T	57.9%	V563V (GTG→GTT)	mrcB →	fused glycosyl transferase and transpeptidase
RA	163,686	C→A	20.2%	Q824K (CAG→AAG)	mrcB →	fused glycosyl transferase and transpeptidase
RA	176,783	G→T	89.4%	D354Y (GAT→TAT)	dgt →	deoxyguanosine triphosphate triphosphohydrolase
RA	176,864	C→T	6.3%	L381L (CTA→TTA)	dgt →	deoxyguanosine triphosphate triphosphohydrolase
RA	183,669	C→A	10.8%	R490L (CGC→CTC)	glnD ←	uridylyltransferase
RA	186,279	A→T	5.3%	noncoding (81/136 nt)	tff →	novel sRNA, function unknown
RA	194,124	C→A	13.9%	I364I (ATC→ATA)	rseP →	inner membrane zinc RIP metalloprotease; RpoE activator, by degrading RseA; cleaved signal peptide endoprotease
RA	199,858	G→T	41.5%	T8T (ACG→ACT)	lpxB →	tetraacyldisaccharide‑1‑P synthase
RA	201,962	A→T	100%	D117V (GAT→GTT)	dnaE →	DNA polymerase III alpha subunit
RA	212,284	G→T	38.5%	A177S (GCA→TCA)	nlpE →	lipoprotein involved with copper homeostasis and adhesion
RA	217,932	A→C	91.4%	I59M (ATT→ATG)	metI ←	DL‑methionine transporter subunit
RA	219,803	A→T	13.9%	T162S (ACG→TCG)	gmhB →	D,D‑heptose 1,7‑bisphosphate phosphatase
RA	225,620	C→A	6.3%	intergenic (+129/‑34)	aspU → / → dkgB	tRNA‑Asp/2,5‑diketo‑D‑gluconate reductase B
RA	229,707	G→T	61.2%	R246S (CGT→AGT)	mltD ←	putative membrane‑bound lytic murein transglycosylase D
RA	230,579	C→T	100%	E231K (GAA→AAA)	gloB ←	hydroxyacylglutathione hydrolase
RA	232,860	G→T	100%	D103Y (GAT→TAT)	dnaQ →	DNA polymerase III epsilon subunit
RA	236,234	A→T	92.2%	V148E (GTG→GAG)	yafV ←	putative NAD(P)‑binding C‑N hydrolase family amidase
RA	238,195	G→T	100%	V532V (GTC→GTA)	fadE ←	acyl coenzyme A dehydrogenase
RA	241,624	G→T	35.4%	V223V (GTC→GTA)	yafK ←	L,D‑transpeptidase‑related protein
RA	247,048	G→T	40.4%	pseudogene (490/756 nt)	lafU →	pseudogene, lateral flagellar motor protein fragment
RA	250,880	G→T	8.5%	P442T (CCG→ACG)	pepD ←	aminoacyl‑histidine dipeptidase (peptidase D)
RA	253,769	C→T	15.7%	V252V (GTC→GTT)	frsA →	fermentation‑respiration switch protein; PTS Enzyme IIA(Glc)‑binding protein; pNP‑butyrate esterase activity
RA	255,284	G→T	15.6%	N176K (AAC→AAA)	phoE ←	outer membrane phosphoporin protein E
RA	256,882	C→T	7.2%	L262F (CTT→TTT)	proB →	gamma‑glutamate kinase
RA	258,054	G→T	24.1%	G281C (GGC→TGC)	proA →	gamma‑glutamylphosphate reductase
RA	262,114	C→A	90.5%	D51Y (GAT→TAT)	yafY ←	lipoprotein, inner membrane; overproduction stimulates degP expression; CP4‑6 prophage
RA	263,270	C→A	58.0%	V149V (GTG→GTT)	yafZ ←	CP4‑6 prophage; conserved protein
RA	270,864	G→T	35.5%	intergenic (‑36/‑172)	insH1 ← / → mmuP	IS5 transposase and trans‑activator/CP4‑6 prophage; putative S‑methylmethionine transporter
RA	274,735	A→T	100%	pseudogene (138/348 nt)	afuB ←	pseudogene, CP4‑6 prophage; ABC transporter permease family;Phage or Prophage Related
RA	279,334	C→A	19.3%	I141I (ATC→ATA)	yagF →	CP4‑6 prophage; dehydratase family protein
RA	284,904	C→A	13.9%	intergenic (‑31/+108)	yagI ← / ← argF	CP4‑6 prophage; putative DNA‑binding transcriptional regulator/ornithine carbamoyltransferase 2, chain F; CP4‑6 prophage
RA	285,869	G→T	8.7%	L50I (CTC→ATC)	argF ←	ornithine carbamoyltransferase 2, chain F; CP4‑6 prophage
RA	290,073	G→T	29.4%	F146L (TTC→TTA)	yagM ←	CP4‑6 prophage; uncharacterized protein
RA	291,453	A→T	9.2%	L452* (TTA→TAA)	intF ←	CP4‑6 prophage; putative phage integrase
RA	296,308	G→T	18.4%	A113E (GCG→GAG)	paoC ←	PaoABC aldehyde oxidoreductase, Moco‑containing subunit
RA	299,623	C→A	13.5%	G91* (GGA→TGA)	ykgJ ←	UPF0153 cysteine cluster protein
RA	302,428	G→T	24.3%	P34Q (CCG→CAG)	ecpD ←	polymerized tip adhesin of ECP fibers
RA	309,541	C→A	39.9%	intergenic (‑25/‑527)	ykgP ← / → eaeH	pseudogene, oxidoreductase family/pseudogene, attaching and effacing protein homology;factor; Not classified
RA	312,532	G→A	93.8%	pseudogene (349/684 nt)	ykgA ←	pseudogene, AraC family;putative regulator; Not classified; putative ARAC‑type regulatory protein
RA	314,408	A→G	9.8%	D435D (GAT→GAC)	rclA ←	reactive chlorine stress species (RCS) resistance protein; pyridine nucleotide‑dependent disulfide oxidoreductase family
RA	317,205	G→A	91.8%	intergenic (+413/‑114)	rclR → / → ykgE	reactive chlorine species (RCS)‑specific activator of the rcl genes/cysteine‑rich LutA family protein; putative electron transport chain YkgEFG component
RA	319,825	G→T	9.7%	E119D (GAG→GAT)	ykgG →	LutC family protein; putative electron transport chain YkgEFG component
RA	319,890	C→A	44.4%	S141* (TCG→TAG)	ykgG →	LutC family protein; putative electron transport chain YkgEFG component
RA	320,920	G→A	100%	S52S (AGC→AGT)	ykgH ←	putative inner membrane protein
RA	321,223	C→A	100%	intergenic (‑148/+65)	ykgH ← / ← betA	putative inner membrane protein/choline dehydrogenase, a flavoprotein
RA	326,385	G→T	8.6%	P404P (CCG→CCT)	betT →	choline transporter of high affinity
RA	328,436	A→T	7.6%	N119Y (AAC→TAC)	yahA →	c‑di‑GMP‑specific phosphodiesterase
RA	344,800	G→T	100%	E136D (GAG→GAT)	prpB →	2‑methylisocitrate lyase
RA	345,384	G→C	8.0%	intergenic (+101/‑339)	prpB → / → prpC	2‑methylisocitrate lyase/2‑methylcitrate synthase
RA	345,451	C→A	5.6%	intergenic (+168/‑272)	prpB → / → prpC	2‑methylisocitrate lyase/2‑methylcitrate synthase
RA	347,382	G→T	6.1%	E153* (GAA→TAA)	prpD →	2‑methylcitrate dehydratase
RA	360,317	C→A	21.5%	intergenic (‑251/+344)	lacZ ← / ← lacI	pseudogene, truncated/DNA‑binding transcriptional repressor
RA	360,680	C→A	16.2%	R355L (CGA→CTA)	lacI ←	DNA‑binding transcriptional repressor
RA	360,714	C→A	6.2%	D344Y (GAT→TAT)	lacI ←	DNA‑binding transcriptional repressor
RA	360,752	A→G	100%	V331A (GTG→GCG)	lacI ←	DNA‑binding transcriptional repressor
JC	361,139	+GCCA	9.7%	coding (605/1083 nt)	lacI ←	DNA‑binding transcriptional repressor
RA	361,667	T→A	10.0%	Q26L (CAG→CTG)	lacI ←	DNA‑binding transcriptional repressor
RA	361,692	G→T	6.8%	Q18K (CAG→AAG)	lacI ←	DNA‑binding transcriptional repressor
RA	361,806	G→A	100%	intergenic (‑63/+14)	lacI ← / ← mhpR	DNA‑binding transcriptional repressor/mhp operon transcriptional activator
RA	362,159	G→T	100%	I165I (ATC→ATA)	mhpR ←	mhp operon transcriptional activator
RA	380,236	C→A	55.7%	intergenic (‑164/‑452)	yaiS ← / → tauA	putative PIG‑L family deacetylase/taurine transporter subunit
RA	385,485	C→T	54.0%	intergenic (‑302/‑222)	hemB ← / → yaiT	5‑aminolevulinate dehydratase (porphobilinogen synthase)/pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein
RA	385,815	G→T	89.9%	pseudogene (109/1458 nt)	yaiT →	pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein
RA	395,884	G→T	27.7%	R166S (CGT→AGT)	ddlA ←	D‑alanine‑D‑alanine ligase A
RA	395,951	G→T	17.6%	V143V (GTC→GTA)	ddlA ←	D‑alanine‑D‑alanine ligase A
RA	396,272	G→T	35.1%	F36L (TTC→TTA)	ddlA ←	D‑alanine‑D‑alanine ligase A
RA	396,883	A→G	94.7%	Q14Q (CAA→CAG)	iraP →	anti‑RssB factor, RpoS stabilzer during Pi starvation; anti‑adapter protein
RA	397,959	G→A	87.0%	A253T (GCG→ACG)	phoA →	bacterial alkaline phosphatase
RA	399,531	G→T	13.8%	A125S (GCG→TCG)	yaiC →	diguanylate cyclase, cellulose regualtor
RA	402,340	G→T	100%	V160V (GTG→GTT)	aroL →	shikimate kinase II
RA	405,970	C→A	16.0%	T124K (ACG→AAG)	mak →	manno(fructo)kinase
RA	406,002	G→T	14.9%	G135C (GGC→TGC)	mak →	manno(fructo)kinase
RA	406,075	C→A	100%	P159Q (CCG→CAG)	mak →	manno(fructo)kinase
RA	409,063	A→T	9.7%	L716* (TTG→TAG)	sbcC ←	exonuclease, dsDNA, ATP‑dependent
RA	411,027	G→T	100%	L61L (CTC→CTA)	sbcC ←	exonuclease, dsDNA, ATP‑dependent
RA	421,799	C→A	92.2%	I69I (ATC→ATA)	tgt →	tRNA‑guanine transglycosylase
RA	425,143	G→T	90.1%	T61T (ACG→ACT)	secF →	SecYEG protein translocase auxillary subunit
RA	427,603	C→T	7.3%	intergenic (‑134/+165)	tsx ← / ← yajI	nucleoside channel, receptor of phage T6 and colicin K/putative lipoprotein
RA	432,092	G→A	14.0%	K16K (AAG→AAA)	pgpA →	phosphatidylglycerophosphatase A
RA	433,551	G→T	100%	S14Y (TCC→TAC)	yajO ←	2‑carboxybenzaldehyde reductase
RA	433,738	A→C	13.4%	intergenic (‑147/+33)	yajO ← / ← dxs	2‑carboxybenzaldehyde reductase/1‑deoxyxylulose‑5‑phosphate synthase, thiamine triphosphate‑binding, FAD‑requiring
RA	434,663	A→C	100%	I324S (ATC→AGC)	dxs ←	1‑deoxyxylulose‑5‑phosphate synthase, thiamine triphosphate‑binding, FAD‑requiring
RA	435,336	G→T	100%	Q100K (CAG→AAG)	dxs ←	1‑deoxyxylulose‑5‑phosphate synthase, thiamine triphosphate‑binding, FAD‑requiring
RA	437,371	G→T	11.8%	D123Y (GAT→TAT)	thiI →	tRNA s(4)U8 sulfurtransferase
RA	437,672	T→A	100%	V223E (GTG→GAG)	thiI →	tRNA s(4)U8 sulfurtransferase
RA	444,489	G→A	100%	R537C (CGT→TGT)	cyoB ←	cytochrome o ubiquinol oxidase subunit I
RA	446,369	T→G	87.2%	Q233P (CAG→CCG)	cyoA ←	cytochrome o ubiquinol oxidase subunit II
RA	450,290	G→A	100%	intergenic (+45/‑299)	bolA → / → tig	stationary‑phase morphogene, transcriptional repressor for mreB; also regulator for dacA, dacC, and ampC/peptidyl‑prolyl cis/trans isomerase (trigger factor)
RA	451,853	C→A	5.9%	T422N (ACC→AAC)	tig →	peptidyl‑prolyl cis/trans isomerase (trigger factor)
RA	456,298	T→A	100%	L652Q (CTG→CAG)	lon →	DNA‑binding ATP‑dependent protease La
RA	456,588	G→T	100%	D749Y (GAC→TAC)	lon →	DNA‑binding ATP‑dependent protease La
RA	458,644	C→A	19.1%	P425Q (CCG→CAG)	ppiD →	periplasmic folding chaperone, has an inactive PPIase domain
RA	458,681	C→A	47.9%	I437I (ATC→ATA)	ppiD →	periplasmic folding chaperone, has an inactive PPIase domain
RA	463,131	G→T	38.1%	A88A (GCG→GCT)	cof →	thiamine pyrimidine pyrophosphate hydrolase; HMP‑PP phosphatase
RA	465,341	A→C	6.2%	I339L (ATT→CTT)	mdlA →	putative multidrug transporter subunit of ABC superfamily, ATP‑binding component
RA	466,184	G→T	16.5%	M31I (ATG→ATT)	mdlB →	putative multidrug transporter subunit of ABC superfamily, ATP‑binding component
RA	474,138	G→T	94.8%	intergenic (‑65/+99)	ylaB ← / ← ylaC	putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase/DUF1449 family inner membrane protein
RA	475,494	G→A	7.0%	intergenic (‑120/+52)	maa ← / ← hha	maltose O‑acetyltransferase/modulator of gene expression, with H‑NS
RA	475,805	C→A	100%	A120A (GCG→GCT)	tomB ←	Hha toxicity attenuator; conjugation‑related protein
RA	479,122	G→T	54.1%	F246L (TTC→TTA)	acrB ←	multidrug efflux system protein
RA	479,244	C→A	100%	A206S (GCC→TCC)	acrB ←	multidrug efflux system protein
RA	480,820	C→T	100%	D86N (GAC→AAC)	acrA ←	multidrug efflux system
RA	481,667	G→A	100%	A151T (GCG→ACG)	acrR →	transcriptional repressor
RA	487,486	G→T	8.1%	intergenic (+67/‑62)	apt → / → dnaX	adenine phosphoribosyltransferase/DNA polymerase III/DNA elongation factor III, tau and gamma subunits
RA	498,579	G→T	19.0%	A39E (GCG→GAG)	ybaL ←	inner membrane putative NAD(P)‑binding transporter
RA	500,178	G→T	13.2%	intergenic (‑26/‑192)	fsr ← / → ushA	putative fosmidomycin efflux system protein/bifunctional UDP‑sugar hydrolase/5'‑nucleotidase
RA	500,613	G→T	12.1%	G82C (GGT→TGT)	ushA →	bifunctional UDP‑sugar hydrolase/5'‑nucleotidase
RA	503,214	G→T	32.0%	S108Y (TCT→TAT)	ybaP ←	TraB family protein
RA	509,737	G→A	93.3%	E97K (GAG→AAG)	cueR →	copper‑responsive regulon transcriptional regulator
RA	512,167	G→T	40.4%	A43A (GCG→GCT)	fetB →	iron exporter permease subunit, ABC transporter FetAB; peroxide resistance protein
RA	512,872	A→T	35.3%	intergenic (+54/+9)	fetB → / ← ybbN	iron exporter permease subunit, ABC transporter FetAB; peroxide resistance protein/DnaK co‑chaperone, thioredoxin‑like protein
RA	512,883	A→T	5.3%	*285R (TGA→AGA)	ybbN ←	DnaK co‑chaperone, thioredoxin‑like protein
RA	515,004	G→T	35.2%	S73* (TCG→TAG)	tesA ←	multifunctional acyl‑CoA thioesterase 1; protease I; lysophospholipase L1
RA	520,873	A→T	14.2%	A719A (GCA→GCT)	rhsD →	Rhs family putative polymorphic toxin
RA	521,011	G→T	57.0%	E765D (GAG→GAT)	rhsD →	Rhs family putative polymorphic toxin
RA	522,859	T→G	12.7%	S1381R (AGT→AGG)	rhsD →	Rhs family putative polymorphic toxin
RA	523,413	G→T	11.9%	pseudogene (6/708 nt)	rhsH →	pseudogene, Rhs familly protein
RA	524,334:1	+T	100%	pseudogene (239/491 nt)	ybbD →	pseudogene
RA	530,466	C→A	100%	F365L (TTC→TTA)	gcl →	glyoxylate carboligase
RA	531,155	G→A	36.9%	intergenic (+2/‑11)	gcl → / → hyi	glyoxylate carboligase/hydroxypyruvate isomerase
RA	531,226	T→A	6.3%	F21I (TTT→ATT)	hyi →	hydroxypyruvate isomerase
RA	538,153	A→C	14.9%	E270D (GAA→GAC)	glxK →	glycerate kinase II
RA	538,400	G→T	19.0%	E353* (GAA→TAA)	glxK →	glycerate kinase II
RA	542,200	Δ1 bp	100%	coding (65/1668 nt)	fdrA →	putative NAD(P)‑binding acyl‑CoA synthetase
RA	544,142	G→T	13.9%	P110P (CCG→CCT)	ylbE →	NO‑induced DUF1116 protein
RA	545,542	G→T	39.9%	D154Y (GAC→TAC)	ylbF →	putative anaerobic allantoin catabolic oxamate carbamoyltransferase; DUF2877 family protein
RA	546,491	G→T	100%	V199V (GTG→GTT)	ybcF →	putative carbonate kinase
RA	549,397	G→T	100%	intergenic (‑1/+2)	lpxH ← / ← ppiB	UDP‑2,3‑diacylglucosamine pyrophosphohydrolase/peptidyl‑prolyl cis‑trans isomerase B (rotamase B)
RA	552,831	A→T	6.8%	F123I (TTC→ATC)	folD ←	bifunctional 5,10‑methylene‑tetrahydrofolate dehydrogenase/ 5,10‑methylene‑tetrahydrofolate cyclohydrolase
RA	554,715	G→T	5.0%	G96C (GGT→TGT)	sfmC →	putative periplasmic pilus chaperone
RA	557,592	G→T	89.2%	D814Y (GAC→TAC)	sfmD →	putative outer membrane export usher protein
RA	557,784	G→T	58.0%	intergenic (+28/‑8)	sfmD → / → sfmH	putative outer membrane export usher protein/FimA homolog
RA	565,131	G→A	46.4%	G258G (GGG→GGA)	ybcK →	DLP12 prophage; putative recombinase
RA	566,710	G→T	17.2%	G121V (GGC→GTC)	ybcL →	inactive polymorphonuclear leukocyte migration suppressor; DLP12 prophage; secreted protein, UPF0098 family
RA	569,775	G→A	43.1%	V122I (GTT→ATT)	quuD →	DLP12 prophage; putative antitermination protein
RA	571,745	G→T	19.2%	pseudogene (537/1040 nt)	nmpC ←	DLP12 prophage; truncated outer membrane porin (pseudogene);IS, phage, Tn; Phage or Prophage Related; outer membrane porin protein; locus of qsr prophage
RA	572,129	T→G	12.4%	pseudogene (153/1040 nt)	nmpC ←	DLP12 prophage; truncated outer membrane porin (pseudogene);IS, phage, Tn; Phage or Prophage Related; outer membrane porin protein; locus of qsr prophage
RA	576,653	G→T	9.8%	A122S (GCA→TCA)	nohD →	DLP12 prophage; DNA packaging protein
RA	576,998	G→T	100%	pseudogene (189/309 nt)	aaaD →	pseudogene; DLP12 prophage; tail fiber assembly protein family;Phage or Prophage Related
RA	579,853	C→A	35.9%	G239G (GGC→GGA)	appY →	global transcriptional activator; DLP12 prophage
RA	580,102	G→T	13.7%	intergenic (+216/+34)	appY → / ← ompT	global transcriptional activator; DLP12 prophage/DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
RA	580,558	C→A	6.8%	D178Y (GAT→TAT)	ompT ←	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
RA	581,203	A→T	94.6%	intergenic (‑114/‑310)	ompT ← / → pauD	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)/tRNA‑OTHER
RA	583,341	T→G	100%	S33R (AGT→CGT)	ybcH ←	PRK09936 family protein
RA	596,812	G→T	15.6%	M881I (ATG→ATT)	cusA →	copper/silver efflux system, membrane component
RA	598,618	G→T	5.3%	E402* (GAA→TAA)	pheP →	phenylalanine transporter
RA	602,195	C→A	10.6%	T215T (ACG→ACT)	ybdK ←	weak gamma‑glutamyl:cysteine ligase
RA	603,207	G→T	55.7%	noncoding (18/59 nt)	sokE →	sRNA at remnant mokE/hokE locus
RA	604,929	A→T	18.6%	C203S (TGC→AGC)	entD ←	phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex
RA	607,931	G→A	100%	S7F (TCC→TTC)	fepA ←	iron‑enterobactin outer membrane transporter
RA	613,755	G→T	32.0%	D16Y (GAT→TAT)	fepE →	regulator of length of O‑antigen component of lipopolysaccharide chains
RA	614,511	G→T	19.5%	D268Y (GAT→TAT)	fepE →	regulator of length of O‑antigen component of lipopolysaccharide chains
RA	615,143	C→A	10.9%	T171T (ACG→ACT)	fepC ←	iron‑enterobactin transporter subunit
RA	619,048	C→A	93.0%	A307S (GCC→TCC)	fepB ←	iron‑enterobactin transporter subunit
RA	623,812	G→T	13.2%	V221V (GTG→GTT)	entB →	isochorismatase
RA	625,364	G→T	100%	G5G (GGG→GGT)	cstA →	carbon starvation protein involved in peptide utilization; APC peptide transporter family protein
RA	627,152	G→T	33.2%	A601A (GCG→GCT)	cstA →	carbon starvation protein involved in peptide utilization; APC peptide transporter family protein
RA	629,276	A→T	54.9%	K79* (AAA→TAA)	ybdL →	methionine aminotransferase, PLP‑dependent
RA	630,742	C→A	17.3%	E31* (GAA→TAA)	ybdM ←	Spo0J family protein, ParB‑like nuclease domain
RA	632,286	C→A	19.6%	E263D (GAG→GAT)	ybdO ←	putative DNA‑binding transcriptional regulator
RA	638,587	G→T	5.2%	E348D (GAG→GAT)	ybdR →	putative Zn‑dependent NAD(P)‑binding oxidoreductase
RA	639,231	G→A	100%	L65F (CTT→TTT)	rnk ←	regulator of nucleoside diphosphate kinase
RA	647,234	C→T	94.2%	E27K (GAA→AAA)	citC ←	[citrate [pro‑3S]‑lyase] ligase
RA	647,422	G→T	100%	intergenic (‑110/‑269)	citC ← / → citA	[citrate [pro‑3S]‑lyase] ligase/sensory histidine kinase in two‑component regulatory system with CitB
RA	647,509	T→C	100%	intergenic (‑197/‑182)	citC ← / → citA	[citrate [pro‑3S]‑lyase] ligase/sensory histidine kinase in two‑component regulatory system with CitB
RA	647,882	T→G	7.9%	I64M (ATT→ATG)	citA →	sensory histidine kinase in two‑component regulatory system with CitB
RA	648,056	C→A	100%	F122L (TTC→TTA)	citA →	sensory histidine kinase in two‑component regulatory system with CitB
RA	652,442	T→A	15.6%	Y144N (TAC→AAC)	pagP →	phospholipid:lipid A palmitoyltransferase
RA	652,597	C→T	100%	intergenic (+24/‑151)	pagP → / → cspE	phospholipid:lipid A palmitoyltransferase/constitutive cold shock family transcription antitermination protein; negative regulator of cspA transcription; RNA melting protein; ssDNA‑binding protein
RA	652,865	Δ1 bp	91.5%	coding (118/210 nt)	cspE →	constitutive cold shock family transcription antitermination protein; negative regulator of cspA transcription; RNA melting protein; ssDNA‑binding protein
RA	659,689	G→T	5.1%	R320S (CGC→AGC)	rlpA ←	septal ring protein, suppressor of prc, minor lipoprotein
RA	662,108	A→T	100%	V522V (GTT→GTA)	mrdA ←	transpeptidase involved in peptidoglycan synthesis (penicillin‑binding protein 2)
RA	662,631	C→A	100%	R348L (CGC→CTC)	mrdA ←	transpeptidase involved in peptidoglycan synthesis (penicillin‑binding protein 2)
RA	666,998	G→T	5.9%	L22I (CTT→ATT)	holA ←	DNA polymerase III, delta subunit
RA	667,348	G→T	91.1%	Q99K (CAG→AAG)	lptE ←	LPS assembly OM complex LptDE, lipoprotein component
RA	667,397	G→T	18.4%	I82I (ATC→ATA)	lptE ←	LPS assembly OM complex LptDE, lipoprotein component
RA	672,142	T→A	93.1%	intergenic (‑139/‑25)	ybeQ ← / → ybeR	Sel1 family TPR‑like repeat protein/uncharacterized protein
RA	678,325	G→T	16.7%	G175G (GGC→GGA)	hscC ←	Hsp70 family chaperone Hsc62, binds to RpoD and inhibits transcription
RA	679,765	G→T	12.4%	S35Y (TCT→TAT)	rihA ←	ribonucleoside hydrolase 1
RA	693,739	G→T	89.6%	H299N (CAC→AAC)	asnB ←	asparagine synthetase B
RA	702,869	G→T	13.1%	D441Y (GAT→TAT)	glnS →	glutamyl‑tRNA synthetase
RA	705,588	C→A	100%	intergenic (+16/+68)	chiQ → / ← fur	chitosugar‑induced verified lipoprotein/ferric iron uptake regulon transcriptional repressor; autorepressor
RA	706,097	A→C	92.3%	T2T (ACT→ACG)  *29G (TGA→GGA)	fur ← uof ←	ferric iron uptake regulon transcriptional repressor; autorepressor ryhB‑regulated fur leader peptide
RA	706,479	C→A	57.4%	R148L (CGT→CTT)	fldA ←	flavodoxin 1
RA	709,827	G→T	12.1%	D272Y (GAT→TAT)	pgm →	phosphoglucomutase
RA	720,173	G→T	13.9%	A88E (GCG→GAG)	kdpC ←	potassium translocating ATPase, subunit C
RA	721,412	T→A	21.7%	N361Y (AAC→TAC)	kdpB ←	potassium translocating ATPase, subunit B
RA	724,813	A→T	100%	intergenic (+17/‑226)	ybfA → / → rhsC	DUF2517 family protein/Rhs family putative polymorphic toxin
RA	725,650	G→T	7.7%	P204P (CCG→CCT)	rhsC →	Rhs family putative polymorphic toxin
RA	729,456	G→A	87.7%	R75R (AGG→AGA)	ybfB →	putative membrane protein
RA	732,349	G→T	47.4%	pseudogene (69/1137 nt)	ybfL →	pseudogene, DDE domain transposase family;putative factor; Not classified; putative receptor protein
RA	732,416	G→A	44.0%	pseudogene (136/1137 nt)	ybfL →	pseudogene, DDE domain transposase family;putative factor; Not classified; putative receptor protein
RA	732,494	G→T	86.8%	pseudogene (214/1137 nt)	ybfL →	pseudogene, DDE domain transposase family;putative factor; Not classified; putative receptor protein
RA	732,752	C→T	21.1%	pseudogene (472/1137 nt)	ybfL →	pseudogene, DDE domain transposase family;putative factor; Not classified; putative receptor protein
RA	733,541	G→A	14.9%	intergenic (+124/‑7)	ybfL → / → ybfD	pseudogene, DDE domain transposase family;putative factor; Not classified; putative receptor protein/H repeat‑associated putative transposase
RA	735,817	G→T	7.3%	L285L (CTG→CTT)	phr →	deoxyribodipyrimidine photolyase, FAD‑binding
RA	738,124:1	+T	12.8%	intergenic (‑112/‑159)	dtpD ← / → ybgI	dipeptide and tripeptide permease D/NIF3 family metal‑binding protein
RA	743,278	G→A	5.1%	intergenic (‑53/+99)	abrB ← / ← ybgO	regulator of aidB expression; inner membrane protein/putative fimbrial protein
RA	745,420	C→A	64.0%	G736C (GGT→TGT)	ybgQ ←	putative outer membrane protein
RA	750,112	A→T	8.6%	intergenic (‑188/‑521)	gltA ← / → sdhC	citrate synthase/succinate dehydrogenase, membrane subunit, binds cytochrome b556
RA	754,572	G→T	100%	E137D (GAG→GAT)	sucA →	2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding
RA	757,353	A→T	5.7%	N126Y (AAT→TAT)	sucB →	dihydrolipoyltranssuccinase
RA	759,000	C→A	100%	F177L (TTC→TTA)	sucC →	succinyl‑CoA synthetase, beta subunit
RA	761,420	C→T	14.4%	intergenic (‑89/‑20)	mngR ← / → mngA	Transcriptional repressor for the mannosyl‑D‑glycerate catabolic operon/fused 2‑O‑a‑mannosyl‑D‑glycerate specific PTS enzymes: IIA component/IIB component/IIC component
RA	767,694	G→A	16.6%	E261K (GAA→AAA)	cydA →	cytochrome d terminal oxidase, subunit I
RA	769,421	C→A	19.5%	I308I (ATC→ATA)	cydB →	cytochrome d terminal oxidase, subunit II
RA	772,664	A→C	10.5%	K289N (AAA→AAC)	tolA →	membrane anchored protein in TolA‑TolQ‑TolR complex
RA	776,049	C→A	16.8%	noncoding (40/76 nt)	lysT →	tRNA‑Lys
RA	784,482	G→T	12.6%	I318I (ATC→ATA)	galK ←	galactokinase
RA	788,902	G→T	100%	R115S (CGT→AGT)	modF ←	fused molybdate transporter subunits of ABC superfamily: ATP‑binding components
RA	792,078	C→A	6.9%	A23A (GCC→GCA)	modC →	molybdate transporter subunit
RA	792,957	C→A	11.6%	V316V (GTC→GTA)	modC →	molybdate transporter subunit
RA	796,821	G→T	24.3%	A203S (GCT→TCT)	ybhH →	putative PrpF family isomerase
RA	800,488	G→T	94.6%	V510V (GTG→GTT)	ybhJ →	putative hydratase
RA	800,779	G→T	100%	E607D (GAG→GAT)	ybhJ →	putative hydratase
RA	815,168	C→A	56.3%	R140R (CGG→AGG)	moaE →	molybdopterin synthase, large subunit
RA	816,292	A→T	5.2%	H15L (CAC→CTC)	ybhM →	UPF0005 family inner membrane protein
RA	818,362	G→T	14.0%	G278G (GGC→GGA)	clsB ←	cardiolipin synthase 2
RA	825,641	G→T	16.2%	A153A (GCC→GCA)	ybiH ←	DUF1956 domain‑containing tetR family putative transcriptional regulator
RA	828,374	G→T	91.8%	V11V (GTC→GTA)	ybiA ←	DUF1768 family protein
RA	832,317	C→A	6.3%	R171S (CGT→AGT)	ybiC →	putative dehydrogenase
RA	832,445	G→T	100%	P213P (CCG→CCT)	ybiC →	putative dehydrogenase
RA	834,612	G→T	29.3%	R18S (CGC→AGC)	ybiX ←	Fe(II)‑dependent oxygenase superfamily protein
RA	837,698	G→A	15.8%	intergenic (‑186/‑90)	mcbA ← / → rlmF	colanic acid mucoidy stimulation protein/23S rRNA m(6)A1618 methyltransferase, SAM‑dependent
RA	843,299	C→A	100%	W54C (TGG→TGT)	glnH ←	glutamine transporter subunit
RA	851,782	A→T	5.9%	K122* (AAA→TAA)	ybiT →	putative transporter subunit of ABC superfamily: ATP‑binding component
RA	858,992	C→T	52.3%	intergenic (‑25/‑106)	ybiY ← / → fsaA	putative pyruvate formate lyase activating enzyme/fructose‑6‑phosphate aldolase 1
RA	860,669	G→T	9.9%	I384I (ATC→ATA)	moeA ←	molybdopterin molybdenumtransferase; molybdopterin biosynthesis protein
RA	862,017	G→T	17.9%	intergenic (‑197/‑7)	moeA ← / → iaaA	molybdopterin molybdenumtransferase; molybdopterin biosynthesis protein/Isoaspartyl peptidase
RA	876,447	G→A	100%	D89N (GAT→AAT)	dacC →	D‑alanyl‑D‑alanine carboxypeptidase (penicillin‑binding protein 6a)
RA	876,738	G→T	56.6%	D186Y (GAT→TAT)	dacC →	D‑alanyl‑D‑alanine carboxypeptidase (penicillin‑binding protein 6a)
RA	879,085	G→T	100%	intergenic (‑241/‑44)	ybjG ← / → mdfA	undecaprenyl pyrophosphate phosphatase/multidrug efflux system protein
RA	884,152	G→T	5.5%	S375* (TCG→TAG)	ybjL ←	putative transporter
RA	889,044	G→T	6.2%	intergenic (+155/‑196)	ybjN → / → potF	negative regulator of motility; multicopy suppressor of coaA(Ts)/putrescine transporter subunit: periplasmic‑binding component of ABC superfamily
RA	890,555	G→T	14.2%	D37Y (GAT→TAT)	potG →	putrescine transporter subunit: ATP‑binding component of ABC superfamily
RA	896,095	C→A	39.0%	intergenic (‑64/+227)	artJ ← / ← artM	arginine binding protein, periplasmic/arginine transporter subunit
RA	898,457	G→T	15.8%	intergenic (‑13/+5)	artI ← / ← artP	arginine transporter subunit/arginine transporter subunit
RA	910,671	T→G	12.3%	intergenic (‑358/+137)	ybjE ← / ← aqpZ	putative transporter/aquaporin Z
RA	910,682	T→G	8.5%	intergenic (‑369/+126)	ybjE ← / ← aqpZ	putative transporter/aquaporin Z
RA	911,375	G→T	10.7%	F43L (TTC→TTA)	aqpZ ←	aquaporin Z
RA	912,614	G→T	14.1%	R229L (CGA→CTA)	ybjD →	putative OLD family ATP‑dependent endonuclease; DUF2813 family protein
RA	918,410	G→T	31.1%	A14A (GCG→GCT)	clpS →	regulatory protein for ClpA substrate specificity
RA	919,481	A→C	5.0%	L254F (TTA→TTC)	clpA →	ATPase and specificity subunit of ClpA‑ClpP ATP‑dependent serine protease, chaperone activity
RA	925,160	G→T	100%	S420* (TCA→TAA)	cydD ←	fused glutathione, cysteine exporter subunits of ABC superfamily: membrane component/ATP‑binding component
RA	929,510	G→T	36.2%	E277D (GAG→GAT)	ftsK →	DNA translocase at septal ring sorting daughter chromsomes
RA	943,573	G→T	100%	A297S (GCC→TCC)	ycaM →	putative transporter
RA	954,765	C→A	16.3%	G166G (GGC→GGA)	aroA →	5‑enolpyruvylshikimate‑3‑phosphate synthetase
RA	955,568	A→T	94.2%	intergenic (+17/‑152)	aroA → / → ycaL	5‑enolpyruvylshikimate‑3‑phosphate synthetase/putative peptidase‑related chaperone
RA	968,415	G→T	93.4%	S148* (TCG→TAG)	ycbC ←	DUF218 superfamily protein
RA	972,542	C→A	32.4%	S254* (TCG→TAG)	mukB →	chromosome condensin MukBEF, ATPase and DNA‑binding subunit
RA	976,873	C→A	6.6%	A124E (GCG→GAG)	ldtD →	murein L,D‑transpeptidase
RA	997,965	G→T	94.5%	D235Y (GAT→TAT)	elfG →	putative fimbrial‑like adhesin protein
RA	998,782	C→A	36.3%	A146A (GCC→GCA)	ycbU →	putative fimbriae protein
RA	1,011,409	C→A	17.3%	*173L (TGA→TTA)	fabA ←	beta‑hydroxydecanoyl thioester dehydrase
RA	1,017,626	G→T	15.9%	R572S (CGT→AGT)	yccS ←	putative transporter, FUSC superfamily inner membrane protein, tandem domains
RA	1,024,387	C→A	14.0%	D347Y (GAT→TAT)	rlmI ←	23S rRNA m(5)C1962 methyltransferase, SAM‑dependent
RA	1,024,703	G→T	92.5%	G241G (GGC→GGA)	rlmI ←	23S rRNA m(5)C1962 methyltransferase, SAM‑dependent
RA	1,037,576	G→T	16.9%	G697G (GGC→GGA)	etk ←	tyrosine‑protein kinase, role in O‑antigen capsule formation
RA	1,041,662	G→T	11.2%	F580L (TTC→TTA)	gfcD ←	putative O‑antigen capsule production periplasmic protein
RA	1,045,280	G→T	19.4%	intergenic (‑80/‑9)	gfcA ← / → insA	O‑antigen capsule production threonine‑rich inner membrane protein/IS1 repressor TnpA
RA	1,045,471	G→T	14.3%	M61I (ATG→ATT)	insA →	IS1 repressor TnpA
RA	1,048,928	C→A	100%	E903* (GAA→TAA)	torS ←	hybrid sensory histidine kinase in two‑component regulatory system with TorR
RA	1,049,407	G→T	94.8%	T743K (ACG→AAG)	torS ←	hybrid sensory histidine kinase in two‑component regulatory system with TorR
RA	1,055,070	A→T	35.8%	Q120L (CAG→CTG)	torA →	trimethylamine N‑oxide (TMAO) reductase I, catalytic subunit
RA	1,063,736	T→C	15.6%	intergenic (+26/+231)	ymdF → / ← rutG	KGG family protein/pyrimidine permease
RA	1,068,091	G→T	19.6%	Q77K (CAG→AAG)	rutB ←	ureidoacrylate amidohydrolase
RA	1,073,243	C→A	5.7%	G366C (GGT→TGT)	putA ←	fused DNA‑binding transcriptional regulator/proline dehydrogenase/pyrroline‑5‑carboxylate dehydrogenase
RA	1,073,863	G→T	9.2%	S159* (TCG→TAG)	putA ←	fused DNA‑binding transcriptional regulator/proline dehydrogenase/pyrroline‑5‑carboxylate dehydrogenase
RA	1,077,911	A→C	100%	K71N (AAA→AAC)	efeO →	inactive ferrous ion transporter EfeUOB
RA	1,079,951	G→T	31.2%	D374Y (GAT→TAT)	efeB →	deferrrochelatase, periplasmic
RA	1,080,620	A→T	14.2%	K58I (AAA→ATA)	phoH →	ATP‑binding protein; putative PhoH family P‑loop ATPase
RA	1,083,443	G→T	87.3%	S624* (TCG→TAG)	pgaB ←	poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine (PGA) N‑deacetylase outer membrane export lipoprotein
RA	1,084,103	A→T	93.9%	L404* (TTA→TAA)	pgaB ←	poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine (PGA) N‑deacetylase outer membrane export lipoprotein
RA	1,085,019	G→T	7.2%	R99R (CGA→AGA)	pgaB ←	poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine (PGA) N‑deacetylase outer membrane export lipoprotein
RA	1,087,360	G→T	13.5%	P129Q (CCG→CAG)	pgaA ←	biofilm adhesin polysaccharide PGA secretin; OM porin; poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine export protein
RA	1,088,607	C→A	31.2%	V92V (GTC→GTA)	ycdT →	diguanylate cyclase, membrane‑anchored
RA	1,088,734	G→T	38.7%	V135F (GTT→TTT)	ycdT →	diguanylate cyclase, membrane‑anchored
RA	1,089,009	G→T	35.8%	V226V (GTG→GTT)	ycdT →	diguanylate cyclase, membrane‑anchored
RA	1,099,378	A→C	61.8%	intergenic (‑726/‑29)	csgD ← / → csgB	csgBAC operon transcriptional regulator/curlin nucleator protein, minor subunit in curli complex
RA	1,105,607	G→T	10.3%	D273Y (GAC→TAC)	opgG →	osmoregulated periplasmic glucan (OPG) biosynthesis periplasmic protein
RA	1,107,069	T→G	38.9%	C251G (TGT→GGT)	opgH →	membrane glycosyltransferase; nutrient‑dependent cell size regulator, FtsZ assembly antagonist
RA	1,116,601	T→A	6.2%	intergenic (‑190/+97)	bssS ← / ← dinI	biofilm regulator/DNA damage‑inducible protein I
RA	1,116,964	A→G	100%	intergenic (‑21/+53)	dinI ← / ← pyrC	DNA damage‑inducible protein I/dihydro‑orotase
RA	1,118,841	A→T	10.8%	intergenic (‑112/+22)	yceB ← / ← grxB	lipoprotein, DUF1439 family/glutaredoxin 2 (Grx2)
RA	1,120,612	A→T	16.2%	F57L (TTT→TTA)	mdtH ←	multidrug resistance efflux transporter conferring overexpression resistance to norfloxacin and enoxacin
RA	1,132,098	G→T	11.4%	M123I (ATG→ATT)	flgI →	putative flagellar basal body protein
RA	1,132,494	T→A	5.6%	I255I (ATT→ATA)	flgI →	putative flagellar basal body protein
RA	1,147,164	G→A	51.9%	D32N (GAC→AAC)	acpP →	acyl carrier protein (ACP)
RA	1,150,407	G→T	57.7%	P280P (CCG→CCT)	yceG →	septation protein, ampicillin sensitivity
RA	1,151,750	G→T	100%	R178L (CGC→CTC)	holB →	DNA polymerase III, delta prime subunit
RA	1,152,278	G→T	100%	E16* (GAA→TAA)	ycfH →	putative DNase
RA	1,153,110	T→A	52.7%	intergenic (+80/‑215)	ycfH → / → ptsG	putative DNase/fused glucose‑specific PTS enzymes: IIB component/IIC component
RA	1,154,905	G→T	56.3%	F701L (TTC→TTA)	fhuE ←	ferric‑rhodotorulic acid outer membrane transporter
RA	1,169,283	T→A	13.1%	A46A (GCA→GCT)	mfd ←	transcription‑repair coupling factor
RA	1,172,212	C→A	47.2%	S46S (TCC→TCA)	lolD →	outer membrane‑specific lipoprotein transporter subunit
RA	1,173,073	T→A	13.0%	F100I (TTC→ATC)	lolE →	lipoprotein‑releasing system transmembrane protein
RA	1,175,193	A→T	9.4%	E36V (GAA→GTA)	cobB →	deacetylase of acs and cheY, chemotaxis regulator
RA	1,191,676	C→T	87.4%	H366H (CAC→CAT)	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,688	C→T	86.0%	T370T (ACC→ACT)	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,701	T→C	80.5%	L375L (TTA→CTA) ‡	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,703	A→G	80.5%	L375L (TTA→TTG) ‡	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,733	C→T	69.4%	N385N (AAC→AAT)	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,736	G→C	69.4%	A386A (GCG→GCC)	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,739	A→G	67.5%	K387K (AAA→AAG)	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,748	C→T	64.2%	T390T (ACC→ACT)	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,760	G→A	42.2%	E394E (GAG→GAA)	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,193,873	G→T	100%	intergenic (‑180/‑278)	ymfE ← / → lit	e14 prophage; putative inner membrane protein/e14 prophage; cell death peptidase, inhibitor of T4 late gene expression
RA	1,204,284	C→A	50.0%	D98Y (GAT→TAT)	tfaE ←	e14 prophage; putative tail fiber assembly protein
RA	1,205,954	G→T	34.1%	L51F (TTG→TTT)	mcrA →	putative 5‑methylcytosine/5‑hydroxymethylcytosine‑specific restriction nuclease; 5‑methylcytosine DNA binding protein; e14 prophage gene
RA	1,207,379	C→T	33.0%	M27I (ATG→ATA)	iraM ←	RpoS stabilzer during Mg starvation, anti‑RssB factor
RA	1,211,169	C→A	100%	intergenic (‑238/‑76)	bluF ← / → ycgZ	anti‑repressor for YcgE, blue light‑responsive; FAD‑binding; has c‑di‑GMP phosphodiesterase‑like EAL domain, but does not degrade c‑di‑GMP/RcsB connector protein for regulation of biofilm and acid‑resistance
RA	1,215,936	G→T	19.8%	pseudogene (880/2648 nt)	ycgH →	pseudogene; putative ATP‑binding component of a transport system
RA	1,219,533	A→G	100%	intergenic (+170/+202)	ycgI → / ← minE	pseudogene/cell division topological specificity factor
RA	1,220,996	G→T	100%	R181R (CGG→AGG)	minC ←	cell division inhibitor
RA	1,224,292	G→A	100%	D8N (GAT→AAT)	ycgN →	UPF0153 family cysteine cluster protein
RA	1,225,922	C→T	17.8%	intergenic (‑72/‑301)	hlyE ← / → umuD	hemolysin E/DNA polymerase V, subunit D
RA	1,226,292	T→A	100%	C24S (TGT→AGT)	umuD →	DNA polymerase V, subunit D
RA	1,228,033	C→A	58.6%	A152S (GCT→TCT)	dsbB ←	oxidoreductase that catalyzes reoxidation of DsbA protein disulfide isomerase I
RA	1,228,591	G→T	100%	intergenic (‑105/+41)	dsbB ← / ← nhaB	oxidoreductase that catalyzes reoxidation of DsbA protein disulfide isomerase I/sodium:proton antiporter
RA	1,235,606	G→T	33.7%	intergenic (+201/+185)	dadX → / ← cvrA	alanine racemase, catabolic, PLP‑binding/putative cation/proton antiporter
RA	1,238,721	C→A	5.0%	A29E (GCG→GAG)	emtA →	lytic murein endotransglycosylase E
RA	1,240,865	A→T	9.1%	K84* (AAA→TAA)	ycgY →	uncharacterized protein
RA	1,242,574	C→A	9.2%	G87* (GGA→TGA)	treA ←	periplasmic trehalase
RA	1,246,435	T→A	48.3%	intergenic (‑141/‑87)	dhaK ← / → dhaR	dihydroxyacetone kinase, PTS‑dependent, dihydroxyacetone‑binding subunit/dhaKLM operon transcription activator
RA	1,253,739	C→A	5.3%	A77A (GCG→GCT)	pth ←	peptidyl‑tRNA hydrolase
RA	1,268,535	A→T	20.1%	S191S (TCA→TCT)	chaC →	cation transport regulator
RA	1,276,723	C→A	59.3%	T468T (ACC→ACA)	narG →	nitrate reductase 1, alpha subunit
RA	1,277,786	G→A	100%	D823N (GAC→AAC)	narG →	nitrate reductase 1, alpha subunit
RA	1,284,124	C→A	58.8%	intergenic (‑44/+6)	purU ← / ← ychJ	formyltetrahydrofolate hydrolase/UPF0225 family protein
RA	1,284,545	A→C	31.8%	L15R (CTA→CGA)	ychJ ←	UPF0225 family protein
RA	1,285,956	G→T	10.8%	A87S (GCC→TCC)	rssB →	PcnB‑degradosome interaction factor; response regulator
RA	1,287,881	C→A	11.8%	intergenic (+60/+84)	galU → / ← hns	glucose‑1‑phosphate uridylyltransferase/global DNA‑binding transcriptional dual regulator H‑NS
RA	1,288,669	A→T	88.5%	intergenic (‑291/‑314)	hns ← / → tdk	global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
RA	1,299,742	C→A	60.4%	A244A (GCC→GCA)	oppD →	oligopeptide transporter subunit
RA	1,322,140	T→A	100%	T159S (ACG→TCG)	btuR ←	cob(I)yrinic acid a,c‑diamide adenosyltransferase
RA	1,330,955	G→T	89.6%	D290Y (GAT→TAT)	acnA →	aconitate hydratase 1
RA	1,332,486	G→T	13.0%	R800L (CGA→CTA)	acnA →	aconitate hydratase 1
RA	1,333,690	G→T	20.9%	S35I (AGT→ATT)	pgpB →	phosphatidylglycerophosphatase B
RA	1,334,048	G→T	5.0%	E154D (GAG→GAT)	pgpB →	phosphatidylglycerophosphatase B
RA	1,337,533	G→T	94.8%	A18E (GCA→GAA)	osmB ←	lipoprotein
RA	1,340,820	G→T	10.1%	I60I (ATC→ATA)	gmr ←	cyclic‑di‑GMP phosphodiesterase; csgD regulator; modulator of Rnase II stability
RA	1,341,061	C→A	67.7%	Y3* (TAC→TAA)	ymiB →	uncharacterized protein
RA	1,344,412	G→A	18.5%	intergenic (‑48/+96)	yciW ← / ← fabI	putative oxidoreductase/enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent
RA	1,365,283	G→T	100%	E271* (GAG→TAG)	ycjM →	alpha amylase catalytic domain family protein
RA	1,372,069	G→T	18.6%	E327D (GAG→GAT)	ycjS →	putative NADH‑binding oxidoreductase
JC JC	1,376,043	IS5 (–) +4 bp	100%	pseudogene (10‑13/126 nt)	ycjV →	pseudogene; putative ATP‑binding component of a transport system
RA	1,377,394	C→T	100%	A275A (GCG→GCA)	ycjW ←	LacI family putative transcriptional repressor
RA	1,384,386	T→A	35.4%	H157L (CAC→CTC)	mpaA ←	murein peptide amidase A
RA	1,386,008	G→T	100%	Q35K (CAG→AAG)	ycjY ←	S9 homolog non‑peptidase family protein
RA	1,388,406	G→T	100%	R308L (CGC→CTC)	mppA →	murein tripeptide (L‑ala‑gamma‑D‑glutamyl‑meso‑DAP) transporter subunit
RA	1,388,474	G→T	14.3%	E331* (GAA→TAA)	mppA →	murein tripeptide (L‑ala‑gamma‑D‑glutamyl‑meso‑DAP) transporter subunit
RA	1,424,234	C→A	100%	S310* (TCA→TAA)	stfR →	Rac prophage; putative tail fiber protein
JC JC	1,428,894	IS2 (–) +5 bp	94.0%	intergenic (‑413/+317)	ynaE ← / ← ttcC	cold shock protein, Rac prophage/pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related
RA	1,429,517	G→T	14.5%	I120I (ATC→ATA)	uspF ←	stress‑induced protein, ATP‑binding protein
RA	1,430,751	C→A	15.3%	G134C (GGT→TGT)	ompN ←	outer membrane pore protein N, non‑specific
RA	1,434,587	G→T	30.8%	S152* (TCG→TAG)	pfo ←	pyruvate‑flavodoxin oxidoreductase
RA	1,439,518	C→A	100%	S737S (TCC→TCA)	ydbH →	putative membrane‑anchored protein, function unknown
RA	1,441,854	C→A	56.4%	R27S (CGT→AGT)	feaB →	phenylacetaldehyde dehydrogenase
RA	1,445,781	G→T	51.3%	intergenic (‑175/+73)	tynA ← / ← paaZ	tyramine oxidase, copper‑requiring/fused oxepin‑CoA hydrolase/3‑oxo‑5,6‑dehydrosuberyl‑CoA semialdehyde dehydrogenase
RA	1,448,131	G→A	61.2%	intergenic (‑232/‑53)	paaZ ← / → paaA	fused oxepin‑CoA hydrolase/3‑oxo‑5,6‑dehydrosuberyl‑CoA semialdehyde dehydrogenase/ring 1,2‑phenylacetyl‑CoA epoxidase subunit
RA	1,448,418	C→T	58.3%	L79F (CTC→TTC)	paaA →	ring 1,2‑phenylacetyl‑CoA epoxidase subunit
RA	1,448,466	C→A	11.1%	Q95K (CAA→AAA)	paaA →	ring 1,2‑phenylacetyl‑CoA epoxidase subunit
RA	1,451,422	A→T	92.8%	T246S (ACG→TCG)	paaE →	ring 1,2‑phenylacetyl‑CoA epoxidase, NAD(P)H oxidoreductase component
RA	1,454,724	G→T	94.0%	G472C (GGT→TGT)	paaH →	3‑hydroxyadipyl‑CoA dehydrogenase, NAD+‑dependent
RA	1,457,811	A→T	17.5%	T6S (ACT→TCT)	paaX →	transcriptional repressor of phenylacetic acid degradation paa operon, phenylacetyl‑CoA inducer
RA	1,460,887	G→C	5.7%	pseudogene (1239/2513 nt)	ydbA →	pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA	1,460,896	C→T	5.7%	pseudogene (1248/2513 nt)	ydbA →	pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA	1,477,570	G→A	51.1%	D85N (GAC→AAC)	hrpA →	putative ATP‑dependent helicase
RA	1,481,236	G→T	17.0%	intergenic (+16/‑256)	hrpA → / → ydcF	putative ATP‑dependent helicase/DUF218 superfamily protein, SAM‑binding
RA	1,488,630	C→A	7.0%	T233T (ACG→ACT)	ydcI ←	putative DNA‑binding transcriptional regulator
RA	1,489,197	C→T	59.9%	K44K (AAG→AAA)	ydcI ←	putative DNA‑binding transcriptional regulator
RA	1,491,823	C→A	8.0%	S237R (AGC→AGA)	opgD →	osmoregulated periplasmic glucan (OPG) biosynthesis periplasmic protein
RA	1,494,358	C→A	10.9%	D117Y (GAC→TAC)	ydcK ←	uncharacterized protein
RA	1,499,199	A→T	14.6%	V380E (GTG→GAG)	ydcO ←	BenE family inner membrane putative transporter
RA	1,499,759	G→T	62.4%	V193V (GTC→GTA)	ydcO ←	BenE family inner membrane putative transporter
RA	1,503,014	G→T	11.3%	intergenic (+15/+77)	ydcP → / ← yncJ	putative peptidase/uncharacterized protein
RA	1,503,039	C→T	6.6%	intergenic (+40/+52)	ydcP → / ← yncJ	putative peptidase/uncharacterized protein
RA	1,515,221	T→A	6.2%	*701L (TAA→TTA)	yncD ←	putative iron outer membrane transporter
RA	1,519,349	T→A	100%	K297* (AAA→TAA)	ansP ←	L‑asparagine transporter
RA	1,525,685	G→A	38.9%	pseudogene (104/315 nt)	yncI →	pseudogene
RA	1,529,506	C→T	13.4%	G204S (GGC→AGC)	yddE ←	PhzC‑PhzF family protein
RA	1,531,040	C→A	15.8%	R176L (CGC→CTC)	narW ←	nitrate reductase 2 (NRZ), delta subunit (assembly subunit)
RA	1,533,556	G→T	16.5%	H1098N (CAC→AAC)	narZ ←	nitrate reductase 2 (NRZ), alpha subunit
RA	1,536,606	G→A	33.2%	T81I (ACT→ATT)	narZ ←	nitrate reductase 2 (NRZ), alpha subunit
RA	1,538,689	C→A	10.0%	pseudogene (333/381 nt)	yddK ←	pseudogene, leucine‑rich protein; putative glycoportein
RA	1,540,526	C→A	20.0%	intergenic (‑241/+19)	yddL ← / ← yddG	putative lipoprotein;putative membrane; Not classified; putative outer membrane porin protein/aromatic amino acid exporter
RA	1,543,054	G→T	36.3%	G466V (GGT→GTT)	fdnG →	formate dehydrogenase‑N, alpha subunit, nitrate‑inducible
RA	1,548,144	G→T	100%	intergenic (‑49/+85)	adhP ← / ← maeA	ethanol‑active dehydrogenase/acetaldehyde‑active reductase/malate dehydrogenase, (decarboxylating, NAD‑requiring) (malic enzyme)
RA	1,552,629	C→A	90.2%	D216Y (GAT→TAT)	ddpD ←	D,D‑dipeptide permease system, ATP‑binding component
RA	1,554,300	G→T	11.2%	S296* (TCA→TAA)	ddpB ←	D‑ala‑D‑ala transporter subunit
RA	1,554,475	T→A	30.7%	T238S (ACC→TCC)	ddpB ←	D‑ala‑D‑ala transporter subunit
RA	1,554,588	G→T	21.5%	A200E (GCG→GAG)	ddpB ←	D‑ala‑D‑ala transporter subunit
RA	1,561,151	C→A	62.6%	D83Y (GAT→TAT)	dosC ←	diguanylate cyclase, cold‑ and stationary phase‑induced oxygen‑dependent biofilm regulator
RA	1,563,276	G→T	100%	H491N (CAC→AAC)	gadC ←	glutamate:gamma‑aminobutyric acid antiporter
RA	1,565,497	G→A	100%	S269L (TCG→TTG)	gadB ←	glutamate decarboxylase B, PLP‑dependent
RA	1,566,392	A→T	6.6%	intergenic (‑90/+272)	gadB ← / ← pqqL	glutamate decarboxylase B, PLP‑dependent/putative periplasmic M16 family zinc metalloendopeptidase
RA	1,572,192	G→T	17.7%	L470I (CTT→ATT)	yddA ←	putative multidrug transporter subunit of ABC superfamily, membrane component/ATP‑binding component
RA	1,575,339	G→T	100%	F481L (TTC→TTA)	ydeN ←	putative Ser‑type periplasmic non‑aryl sulfatase
RA	1,576,844	G→A	16.0%	intergenic (‑63/+339)	ydeN ← / ← ydeO	putative Ser‑type periplasmic non‑aryl sulfatase/UV‑inducible global regulator, EvgA‑, GadE‑dependent
RA	1,586,871	G→T	14.4%	intergenic (‑172/+51)	hipB ← / ← yneO	antitoxin of HipAB toxin‑antitoxin system/pseudogene, AidA homolog
RA	1,591,853	C→A	15.6%	pseudogene (392/5323 nt)	yneO ←	pseudogene, AidA homolog
RA	1,593,900	G→T	17.9%	N189K (AAC→AAA)	lsrK ←	autoinducer‑2 (AI‑2) kinase
RA	1,597,517	T→G	15.7%	L81* (TTA→TGA)	lsrC →	autoinducer 2 import system permease protein
RA	1,599,968	G→T	7.6%	D221Y (GAT→TAT)	lsrB →	autoinducer 2‑binding protein
RA	1,600,589	T→G	12.6%	L78R (CTG→CGG)	lsrF →	putative autoinducer‑2 (AI‑2) aldolase
RA	1,602,131	G→T	5.8%	D177Y (GAT→TAT)	tam →	trans‑aconitate methyltransferase
RA	1,603,440	G→A	100%	intergenic (‑161/+46)	yneE ← / ← uxaB	bestrophin family putative inner membrane protein/altronate oxidoreductase, NAD‑dependent
RA	1,604,237	T→A	5.1%	H234L (CAC→CTC)	uxaB ←	altronate oxidoreductase, NAD‑dependent
RA	1,604,655	C→A	16.4%	E95* (GAA→TAA)	uxaB ←	altronate oxidoreductase, NAD‑dependent
RA	1,605,105	C→T	15.5%	intergenic (‑168/+59)	uxaB ← / ← yneF	altronate oxidoreductase, NAD‑dependent/putative membrane‑bound diguanylate cyclase
RA	1,610,766	C→T	59.2%	S249S (AGC→AGT)	yneK →	uncharacterized protein
RA	1,611,158	G→T	65.4%	intergenic (+23/‑127)	yneK → / → ydeA	uncharacterized protein/arabinose efflux transporter, arabinose‑inducible
RA	1,616,682	T→G	11.0%	L365R (CTG→CGG)	ydeE →	putative transporter
RA	1,618,960	A→C	27.7%	intergenic (‑206/‑70)	ydeI ← / → ydeJ	hydrogen peroxide resistance OB fold protein; putative periplasmic protein/inactive PncC family protein
RA	1,620,961	T→G	100%	Q226P (CAA→CCA)	dcp ←	dipeptidyl carboxypeptidase II
RA	1,621,470	G→A	16.3%	N56N (AAC→AAT)	dcp ←	dipeptidyl carboxypeptidase II
RA	1,628,207	G→A	100%	G110E (GGA→GAA)	pinQ →	Qin prophage; putative site‑specific recombinase
RA	1,634,934	C→A	5.2%	intergenic (‑92/+662)	essQ ← / ← cspB	Qin prophage; putative S lysis protein/Qin prophage; cold shock protein
RA	1,646,412	A→T	56.9%	pseudogene (605/1158 nt)	intQ →	pseudogene, Qin prophage; phage integrase family;Phage or Prophage Related
RA	1,646,993	C→T	18.5%	intergenic (+28/+19)	intQ → / ← ydfJ	pseudogene, Qin prophage; phage integrase family;Phage or Prophage Related/pseudogene, MFS transporter family; interrupted by Qin prophage;Phage or Prophage Related; putative transport protein
RA	1,648,200	G→T	12.0%	T400K (ACG→AAG)	rspA ←	bifunctional D‑altronate/D‑mannonate dehydratase
RA	1,649,014	C→A	37.4%	D129Y (GAT→TAT)	rspA ←	bifunctional D‑altronate/D‑mannonate dehydratase
RA	1,656,349	G→T	56.0%	D513Y (GAT→TAT)	ynfF →	S‑ and N‑oxide reductase, A subunit, periplasmic
RA	1,661,763	C→A	100%	P353P (CCG→CCT)	mlc ←	glucosamine anaerobic growth regulon transcriptional repressor; autorepressor
RA	1,662,162	G→T	7.1%	I220I (ATC→ATA)	mlc ←	glucosamine anaerobic growth regulon transcriptional repressor; autorepressor
RA	1,667,443	T→G	13.7%	T106P (ACC→CCC)	mdtJ ←	multidrug efflux system transporter
RA	1,675,777	C→A	16.0%	S182* (TCG→TAG)	folM →	dihydromonapterin reductase, NADPH‑dependent; dihydrofolate reductase isozyme
RA	1,689,180	T→G	91.9%	E383D (GAA→GAC)	uidA ←	beta‑D‑glucuronidase
RA	1,690,981	G→T	12.6%	A110E (GCG→GAG)	uidR ←	transcriptional repressor
RA	1,692,573	C→A	89.2%	D289Y (GAT→TAT)	malI ←	transcriptional repressor of Mal regulon
RA	1,696,612	A→T	100%	E41D (GAA→GAT)	add →	adenosine deaminase
RA	1,697,123	C→A	10.7%	R212S (CGT→AGT)	add →	adenosine deaminase
RA	1,698,343	C→A	16.9%	D75Y (GAT→TAT)	ydgJ ←	putative oxidoreductase
RA	1,699,862	T→A	94.9%	L119* (TTG→TAG)	ydgK →	DUF2569 family inner membrane protein
RA	1,701,260	T→A	57.4%	S29T (TCC→ACC)	rsxC →	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA	1,702,966	T→A	6.5%	R597R (CGT→CGA)	rsxC →	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA	1,703,071	A→T	8.3%	A632A (GCA→GCT)	rsxC →	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA	1,703,101	C→G	5.4%	A642A (GCC→GCG)	rsxC →	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA	1,706,450	C→T	14.2%	intergenic (+35/‑576)	nth → / → dtpA	DNA glycosylase and apyrimidinic (AP) lyase (endonuclease III)/dipeptide and tripeptide permease A
RA	1,706,994	C→T	15.0%	intergenic (+579/‑32)	nth → / → dtpA	DNA glycosylase and apyrimidinic (AP) lyase (endonuclease III)/dipeptide and tripeptide permease A
RA	1,711,397	C→T	93.4%	R28Q (CGA→CAA)	tyrS ←	tyrosyl‑tRNA synthetase
RA	1,711,486	C→A	6.3%	intergenic (‑7/+122)	tyrS ← / ← pdxH	tyrosyl‑tRNA synthetase/pyridoxine 5'‑phosphate oxidase
RA	1,718,636	G→T	22.5%	L93I (CTT→ATT)	sodC ←	superoxide dismutase, Cu, Zn, periplasmic
RA	1,721,644	C→A	16.9%	N243K (AAC→AAA)	nemA →	chromate reductase, quinone reductase, FMN‑linked; N‑Ethylmaleimide reductase; old yellow enzyme
RA	1,722,475	G→T	43.1%	D128Y (GAC→TAC)	gloA →	glyoxalase I, Ni‑dependent
RA	1,723,809	G→T	91.4%	E156* (GAA→TAA)	lhr →	putative ATP‑dependent helicase
RA	1,724,141	C→A	34.2%	G266G (GGC→GGA)	lhr →	putative ATP‑dependent helicase
RA	1,725,272	G→T	12.7%	A643A (GCG→GCT)	lhr →	putative ATP‑dependent helicase
RA	1,727,929	C→A	37.4%	S1529* (TCA→TAA)	lhr →	putative ATP‑dependent helicase
RA	1,732,093	G→T	34.0%	intergenic (‑291/‑8)	ynhF ← / → purR	stress response membrane/transcriptional repressor, hypoxanthine‑binding
RA	1,732,758	G→T	20.9%	D220Y (GAC→TAC)	purR →	transcriptional repressor, hypoxanthine‑binding
RA	1,747,034	C→A	12.9%	D352Y (GAT→TAT)	ydhV ←	putative oxidoreductase subunit
RA	1,751,673	T→G	14.1%	intergenic (+306/‑5)	pykF → / → lpp	pyruvate kinase I/murein lipoprotein
RA	1,753,293	G→T	13.1%	V85V (GTC→GTA)	sufE ←	sulfur acceptor protein
RA	1,754,950	T→A	100%	I367F (ATT→TTT)	sufD ←	component of SufBCD Fe‑S cluster assembly scaffold
RA	1,755,736	C→A	15.2%	G105* (GGA→TGA)	sufD ←	component of SufBCD Fe‑S cluster assembly scaffold
RA	1,757,647	G→T	40.1%	T207K (ACG→AAG)	sufB ←	component of SufBCD Fe‑S cluster assembly scaffold
RA	1,763,457	A→T	9.0%	T43S (ACG→TCG)	ydiK →	UPF0118 family inner membrane protein
RA	1,764,150	G→T	89.7%	D274Y (GAT→TAT)	ydiK →	UPF0118 family inner membrane protein
RA	1,767,963	C→A	13.3%	P399T (CCT→ACT)	ydiN →	MFS transporter superfamily protein
RA	1,769,440	C→A	19.3%	A166A (GCC→GCA)	aroD →	3‑dehydroquinate dehydratase
RA	1,770,281	T→A	100%	D146E (GAT→GAA)	ydiF →	putative acetyl‑CoA:acetoacetyl‑CoA transferase: alpha subunit/beta subunit
RA	1,774,858	C→T	12.7%	Y67Y (TAC→TAT)	ydiR →	putative electron transfer flavoprotein, FAD‑binding subunit
RA	1,775,744	C→A	56.7%	V31V (GTC→GTA)	ydiS →	putative oxidoreductase
RA	1,777,451	C→A	88.1%	A55E (GCG→GAG)	fadK →	short chain acyl‑CoA synthetase, anaerobic
RA	1,778,803	T→C	14.5%	Y506H (TAT→CAT)	fadK →	short chain acyl‑CoA synthetase, anaerobic
RA	1,783,091	G→T	5.7%	E134* (GAG→TAG)	aroH →	3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, tryptophan repressible
RA	1,798,234	G→T	18.1%	pseudogene (460/1476 nt)	arpB →	pseudogene, ankyrin repeats
RA	1,799,157	G→T	34.0%	pseudogene (1383/1476 nt)	arpB →	pseudogene, ankyrin repeats
RA	1,800,416	C→T	63.0%	intergenic (‑76/‑211)	ydiY ← / → pfkB	acid‑inducible putative outer membrane protein/6‑phosphofructokinase II
RA	1,802,047	G→A	100%	intergenic (+100/‑6)	ydiZ → / → yniA	uncharacterized protein/fructosamine kinase family protein
RA	1,803,109	C→T	93.3%	A128T (GCC→ACC)	yniB ←	putative inner membrane protein
RA	1,809,895	A→T	11.9%	Y591F (TAC→TTC)	katE →	catalase HPII, heme d‑containing
RA	1,810,619	G→T	13.7%	intergenic (+234/+24)	katE → / ← chbG	catalase HPII, heme d‑containing/chito‑oligosaccharide deacetylase
RA	1,813,263	C→A	6.3%	E148* (GAG→TAG)	chbR ←	repressor of chb operon for N,N'‑diacetylchitobiose utilization
RA	1,813,578	C→A	5.7%	D43Y (GAC→TAC)	chbR ←	repressor of chb operon for N,N'‑diacetylchitobiose utilization
RA	1,819,917	C→T	18.9%	intergenic (‑35/+295)	spy ← / ← astE	periplasmic ATP‑independent protein refolding chaperone, stress‑induced/succinylglutamate desuccinylase
RA	1,820,020	C→A	18.6%	intergenic (‑138/+192)	spy ← / ← astE	periplasmic ATP‑independent protein refolding chaperone, stress‑induced/succinylglutamate desuccinylase
RA	1,821,696	A→T	89.3%	L274Q (CTG→CAG)	astB ←	succinylarginine dihydrolase
RA	1,822,975	C→A	14.7%	A339A (GCG→GCT)	astD ←	succinylglutamic semialdehyde dehydrogenase
RA	1,823,903	T→A	7.4%	Q30L (CAA→CTA)	astD ←	succinylglutamic semialdehyde dehydrogenase
RA	1,825,763	C→A	100%	A159A (GCG→GCT)	astC ←	succinylornithine transaminase, PLP‑dependent
RA	1,832,413	C→A	100%	L315L (CTC→CTA)	ynjC →	inner membrane putative ABC superfamily transporter permease
RA	1,833,730	C→A	100%	R3S (CGT→AGT)	ynjE →	molybdopterin synthase sulfurtransferase
RA	1,849,550	C→A	13.3%	G227C (GGC→TGC)	ydjG ←	alpha‑Keto reductase, NADH‑dependent; can use methylglyoxal as substrate
RA	1,850,880	C→A	59.1%	V102V (GTG→GTT)	ydjH ←	putative kinase
RA	1,862,142	C→A	23.1%	I326I (ATC→ATA)	yeaG →	protein kinase, endogenous substrate unidentified; autokinase
RA	1,864,752	C→A	16.3%	S37R (AGC→AGA)	yeaI →	putative membrane‑anchored diguanylate cyclase
RA	1,865,422	C→A	100%	R261R (CGA→AGA)	yeaI →	putative membrane‑anchored diguanylate cyclase
RA	1,866,685	T→G	37.4%	F130V (TTT→GTT)	yeaJ →	putative diguanylate cyclase
RA	1,868,749	A→C	10.6%	E47D (GAA→GAC)	yeaL →	UPF0756 family putative inner membrane protein
RA	1,872,520	G→T	94.5%	P183P (CCG→CCT)	yeaP →	diguanylate cyclase
RA	1,873,569	C→A	15.7%	intergenic (‑57/+91)	yeaQ ← / ← yoaG	UPF0410 family protein/uncharacterized protein
RA	1,874,423	C→A	20.1%	L198F (TTG→TTT)	leuE ←	leucine efflux protein
RA	1,879,386	C→A	16.1%	I155I (ATC→ATA)	yeaW →	putative YeaWX dioxygenase alpha subunit; 2Fe‑2S cluster
RA	1,880,857	G→T	16.3%	M252I (ATG→ATT)	yeaX →	putative YeaWX dioxygenase beta subunit, reductase component
RA	1,885,243	C→A	10.4%	T94T (ACG→ACT)	tsaB ←	tRNA(ANN) t(6)A37 threonylcarbamoyladenosine modification protein; binding partner and protease for TsaD
RA	1,895,069	C→T	11.3%	G258G (GGG→GGA)	yoaE ←	putative membrane protein/conserved protein
RA	1,909,342	T→A	100%	E150D (GAA→GAT)	proQ ←	RNA chaperone, putative ProP translation regulator
RA	1,937,083	A→T	18.1%	T55T (ACA→ACT)	znuC →	zinc transporter subunit: ATP‑binding component of ABC superfamily
RA	1,937,457	A→T	32.1%	D180V (GAT→GTT)	znuC →	zinc transporter subunit: ATP‑binding component of ABC superfamily
RA	1,941,921	A→T	15.3%	V163E (GTG→GAG)	yebC ←	UPF0082 family protein
RA	1,942,066	G→T	5.2%	H115N (CAT→AAT)	yebC ←	UPF0082 family protein
RA	1,943,414	C→A	14.2%	D456Y (GAT→TAT)	aspS ←	aspartyl‑tRNA synthetase
RA	1,944,177	C→A	100%	L201L (CTG→CTT)	aspS ←	aspartyl‑tRNA synthetase
RA	1,946,006	G→T	16.5%	D119Y (GAT→TAT)	yecE →	UPF0759 family protein
RA	1,948,050	C→A	5.6%	L118I (CTT→ATT)	cmoB →	tRNA (cmo5U34)‑carboxymethyltransferase, carboxy‑SAM‑dependent
RA	1,957,975	C→A	13.7%	A445S (GCT→TCT)	flhA ←	putative flagellar export pore protein
RA	1,957,991	C→A	5.0%	A439A (GCG→GCT)	flhA ←	putative flagellar export pore protein
RA	1,959,915	C→A	88.8%	P178P (CCG→CCT)	flhB ←	flagellin export apparatus, substrate specificity protein
RA	1,969,291	G→T	100%	I97I (ATC→ATA)	cheA ←	fused chemotactic sensory histidine kinase in two‑component regulatory system with CheB and CheY: sensory histidine kinase/signal sensing protein
RA	1,975,265	C→A	11.9%	D202Y (GAT→TAT)	otsB ←	trehalose‑6‑phosphate phosphatase, biosynthetic
RA	1,980,472	C→A	18.0%	L23I (CTC→ATC)	ftnB →	ferritin B, putative ferrous iron reservoir
RA	1,984,478	G→T	17.8%	P208Q (CCG→CAG)	yecA ←	UPF0149 family protein
RA	1,984,987	C→A	90.6%	T38T (ACG→ACT)	yecA ←	UPF0149 family protein
RA	1,985,366	G→T	13.2%	noncoding (17/87 nt)	leuZ ←	tRNA‑Leu
RA	1,986,289	T→A	100%	N4Y (AAT→TAT)	pgsA ←	phosphatidylglycerophosphate synthetase
RA	1,990,489	C→T	7.9%	intergenic (‑176/+54)	sdiA ← / ← yecC	quorum‑sensing transcriptional activator/putative ABC superfamily transporter ATP‑binding subunit
RA	1,991,843	G→A	13.1%	L40F (CTC→TTC)	yecS ←	ABC family putative inner membrane permease
RA	1,997,314	G→T	93.9%	intergenic (‑227/‑39)	fliC ← / → fliD	flagellar filament structural protein (flagellin)/flagellar filament capping protein
RA	1,999,632	G→T	100%	intergenic (+73/‑5)	fliT → / → amyA	putative flagellar synthesis and assembly chaperone/cytoplasmic alpha‑amylase
RA	2,000,765	G→T	34.9%	D377Y (GAT→TAT)	amyA →	cytoplasmic alpha‑amylase
RA	2,005,913	T→A	18.2%	intergenic (‑81/‑70)	yedN ← / → intG	pseudogene, IpaH/YopM family/pseudogene, phage integrase family
RA	2,015,451	T→A	16.7%	G34G (GGT→GGA)	fliP →	flagellar biosynthesis protein
RA	2,018,422	T→A	11.8%	intergenic (‑118/‑45)	dsrB ← / → yodD	uncharacterized protein/uncharacterized protein
RA	2,020,166	C→A	100%	D445Y (GAC→TAC)	yedQ ←	putative membrane‑anchored diguanylate cyclase
RA	2,021,794	C→A	13.0%	V20F (GTC→TTC)	yodC ←	uncharacterized protein
RA	2,023,279	C→A	12.3%	T87K (ACG→AAG)	yedA →	amino acid exporter for phenylalanine, threonine
RA	2,029,767	T→A	18.3%	V151D (GTT→GAT)	hchA →	glyoxalase III and Hsp31 molecular chaperone
RA	2,032,032	G→A	35.8%	D91D (GAC→GAT)	yedW ←	response regulator family protein
RA	2,035,090	C→A	100%	Q79K (CAG→AAG)	zinT →	zinc and cadmium binding protein, periplasmic
RA	2,036,546	C→A	27.4%	intergenic (+167/+403)	yodB → / ← serU	cytochrome b561 homolog/tRNA‑Ser
RA	2,039,694	C→T	48.3%	R426C (CGC→TGC)	yeeJ →	putative adhesin
RA	2,040,800	C→A	6.1%	T794T (ACC→ACA)	yeeJ →	putative adhesin
RA	2,060,661	T→A	21.2%	N48Y (AAC→TAC)	insH1 ←	IS5 transposase and trans‑activator
RA	2,070,265	A→T	31.5%	intergenic (+30/‑33)	yeeS → / → yeeT	CP4‑44 prophage; putative DNA repair protein/CP4‑44 prophage; uncharacterized protein
RA	2,074,680	A→T	100%	W22R (TGG→AGG)	sbmC ←	DNA gyrase inhibitor
RA	2,075,255	T→A	18.4%	V258V (GTA→GTT)	dacD ←	D‑alanyl‑D‑alanine carboxypeptidase (penicillin‑binding protein 6b)
RA	2,077,212	A→T	93.4%	N326Y (AAT→TAT)	sbcB →	exodeoxyribonuclease I; exonuclease I
RA	2,082,619	C→T	18.9%	intergenic (‑10/+73)	yeeZ ← / ← yoeB	putative epimerase/toxin of the YoeB‑YefM toxin‑antitoxin system
RA	2,096,801	C→T	7.4%	pseudogene (70/446 nt)	wbbL ←	lipopolysaccharide biosynthesis protein, N‑ter fragment (pseudogene)
RA	2,098,995	C→A	100%	G182* (GGA→TGA)	wbbI ←	d‑Galf:alpha‑d‑Glc beta‑1,6‑galactofuranosyltransferase
RA	2,102,786	C→T	16.6%	V94I (GTT→ATT)	wzxB ←	putative polisoprenol‑linked O‑antigen transporter
RA	2,107,658	C→A	28.4%	E51* (GAA→TAA)	wcaN ←	putative regulatory subunit for GalU
RA	2,108,199	C→T	7.0%	M393I (ATG→ATA)	wcaM ←	colanic acid biosynthesis protein
RA	2,108,219:1	+A	100%	coding (1159/1395 nt)	wcaM ←	colanic acid biosynthesis protein
RA	2,110,346	G→A	87.4%	T88I (ACC→ATC)	wcaL ←	putative glycosyl transferase
RA	2,114,414	C→A	10.1%	V208F (GTC→TTC)	wcaJ ←	colanic biosynthesis UDP‑glucose lipid carrier transferase
RA	2,114,911	A→T	100%	L42Q (CTG→CAG)	wcaJ ←	colanic biosynthesis UDP‑glucose lipid carrier transferase
RA	2,115,361	C→A	8.9%	R367L (CGC→CTC)	cpsG ←	phosphomannomutase
RA	2,121,246	G→T	10.0%	L184I (CTC→ATC)	gmd ←	GDP‑D‑mannose dehydratase, NAD(P)‑binding
RA	2,124,797	C→A	13.1%	R252L (CGT→CTT)	wcaC ←	putative glycosyl transferase
RA	2,130,684	G→T	13.8%	S14* (TCA→TAA)	wza ←	colanic acid export protein; outer membrane auxillary lipoprotein
RA	2,130,777	T→A	14.5%	intergenic (‑53/‑606)	wza ← / → yegH	colanic acid export protein; outer membrane auxillary lipoprotein/inner membrane protein
RA	2,135,016	C→A	15.0%	V26V (GTG→GTT)	asmA ←	suppressor of OmpF assembly mutants; putative outer membrane protein assembly factor; inner membrane‑anchored periplasmic protein
RA	2,137,659	C→A	15.5%	R305R (CGG→AGG)	yegE →	putative diguanylate cyclase
RA	2,137,749	C→A	12.4%	L335I (CTC→ATC)	yegE →	putative diguanylate cyclase
RA	2,139,450	G→T	20.1%	E902* (GAG→TAG)	yegE →	putative diguanylate cyclase
RA	2,139,910	G→T	100%	R1055L (CGA→CTA)	yegE →	putative diguanylate cyclase
RA	2,144,474	C→A	100%	intergenic (‑8/‑192)	yegI ← / → yegJ	protein kinase‑related putative non‑specific DNA‑binding protein/uncharacterized protein
RA	2,145,887	G→T	17.9%	Q23K (CAG→AAG)	yegK ←	ser/thr phosphatase‑related protein
RA	2,146,030	T→A	55.8%	S194C (AGT→TGT)	yegL ←	VMA domain protein
RA	2,148,615	C→A	5.2%	R373R (CGC→CGA)	mdtA →	multidrug efflux system, subunit A
RA	2,149,603	A→T	100%	E287V (GAA→GTA)	mdtB →	multidrug efflux system, subunit B
RA	2,155,768	T→C	15.5%	I275T (ATT→ACT)	mdtD →	putative arabinose efflux transporter
RA	2,157,455	C→A	9.2%	R367S (CGC→AGC)	baeS →	sensory histidine kinase in two‑component regulatory system with BaeR
RA	2,162,105	T→A	13.0%	intergenic (‑318/‑88)	yegR ← / → yegS	uncharacterized protein/phosphatidylglycerol kinase, metal‑dependent
RA	2,168,795	C→A	100%	D336Y (GAT→TAT)	gatZ ←	D‑tagatose 1,6‑bisphosphate aldolase 2, subunit
RA	2,170,401	G→T	6.1%	R95S (CGT→AGT)	gatY ←	D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit
RA	2,170,713	C→A	11.4%	intergenic (‑30/+278)	gatY ← / ← fbaB	D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I
RA	2,170,758	C→A	6.1%	intergenic (‑75/+233)	gatY ← / ← fbaB	D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I
RA	2,172,567	A→T	38.7%	T90S (ACT→TCT)	yegT →	nucleoside transporter, low affinity
RA	2,176,158	C→T	10.7%	A35T (GCC→ACC)	yegW ←	putative DNA‑binding transcriptional regulator
RA	2,177,743	C→A	10.8%	D85Y (GAT→TAT)	thiD ←	bifunctional hydroxy‑methylpyrimidine kinase/ hydroxy‑phosphomethylpyrimidine kinase
RA	2,178,987	C→A	12.8%	intergenic (‑207/+16)	thiM ← / ← rcnR	hydoxyethylthiazole kinase/transcriptional repressor of rcnA
RA	2,179,205	G→T	100%	A24E (GCG→GAG)	rcnR ←	transcriptional repressor of rcnA
RA	2,181,645	A→G	100%	N83N (AAT→AAC)	yehA ←	putative fimbrial‑like adhesin protein
RA	2,192,748	T→A	16.5%	pseudogene (2796/2847 nt)	yehH →	DUF4132 family pseudogene; defective yehI paralog; molybdate metabolism regulator, first fragment; molybdate metabolism regulator, second fragment 2; yehI' molR mutations have phenotypes and the N‑terminal molR fragment of yehI' may be expressed and may have retained or evolved MolR function
RA	2,194,695	T→A	100%	L313Q (CTA→CAA)	yehI →	DUF4132 domain‑containing protein
RA	2,195,449	A→T	100%	E564D (GAA→GAT)	yehI →	DUF4132 domain‑containing protein
RA	2,204,432	G→T	56.7%	pseudogene (1854/2001 nt)	yehQ →	pseudogene
RA	2,209,162	C→A	94.3%	I9I (ATC→ATA)	yohO →	putative membrane protein
RA	2,214,191	C→A	41.8%	V426V (GTG→GTT)	bglX ←	beta‑D‑glucoside glucohydrolase, periplasmic
RA	2,216,296	C→A	92.1%	I211I (ATC→ATA)	dld →	D‑lactate dehydrogenase, FAD‑binding, NADH independent
RA	2,221,550	G→T	23.3%	pseudogene (539/1287 nt)	mdtQ ←	pseudogene; putative channel/filament proteins
RA	2,223,247	C→T	93.3%	W206* (TGG→TGA)	dusC ←	tRNA‑dihydrouridine synthase C
RA	2,224,396	T→A	6.4%	V98V (GTT→GTA)	yohJ →	UPF0299 family inner membrane protein
RA	2,225,190	C→T	100%	G231G (GGC→GGT)	yohK →	LrgB family inner membrane protein
RA	2,232,373	C→A	6.5%	A132A (GCG→GCT)	mglA ←	fused methyl‑galactoside transporter subunits of ABC superfamily: ATP‑binding components
RA	2,233,243	T→G	5.2%	K195N (AAA→AAC)	mglB ←	methyl‑galactoside transporter subunit
RA	2,234,467	C→A	5.5%	A227A (GCG→GCT)	galS ←	galactose‑ and fucose‑inducible galactose regulon transcriptional isorepressor; mgl operon transcriptional repressor; autorepressor
RA	2,237,098	G→T	100%	H12N (CAT→AAT)	folE ←	GTP cyclohydrolase I
RA	2,244,455	C→A	12.1%	T46K (ACG→AAG)	nfo →	endonuclease IV with intrinsic 3'‑5' exonuclease activity
RA	2,246,428	C→A	10.7%	T399T (ACG→ACT)	nupX ←	nucleoside permease
RA	2,263,137	C→A	93.7%	intergenic (+91/‑321)	lpxT → / → mepS	lipid A 1‑diphosphate synthase; undecaprenyl pyrophosphate:lipid A 1‑phosphate phosphotransferase/murein DD‑endopeptidase, space‑maker hydrolase, mutational suppressor of prc thermosensitivity, outer membrane lipoprotein
RA	2,264,143	G→A	100%	intergenic (+119/‑62)	mepS → / → rtn	murein DD‑endopeptidase, space‑maker hydrolase, mutational suppressor of prc thermosensitivity, outer membrane lipoprotein/resistance protein for phages lambda and N4, putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	2,272,063	G→T	11.5%	P393T (CCG→ACG)	bcr ←	bicyclomycin/cysteine/sulfonamide efflux transporter
RA	2,281,560	T→A	17.5%	pseudogene (834/2525 nt)	yejO ←	pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system
RA	2,287,028	C→A	40.9%	T452T (ACG→ACT)	ccmF ←	heme lyase, CcmF subunit
RA	2,287,829	C→A	95.0%	S185S (TCG→TCT)	ccmF ←	heme lyase, CcmF subunit
RA	2,289,043	C→A	90.5%	W8L (TGG→TTG)	ccmD ←	cytochrome c biogenesis protein
RA	2,289,374	C→A	100%	V142V (GTG→GTT)	ccmC ←	heme exporter subunit
RA	2,291,194	C→A	20.0%	C182F (TGC→TTC)	napC ←	quinol dehydrogenase, electron source for NapAB
RA	2,298,128	C→T	10.4%	intergenic (+256/+459)	eco → / ← mqo	ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA	2,303,070	T→G	100%	Q272P (CAG→CCG)	ada ←	fused DNA‑binding transcriptional dual regulator/O6‑methylguanine‑DNA methyltransferase
RA	2,303,607	A→C	21.9%	L93R (CTG→CGG)	ada ←	fused DNA‑binding transcriptional dual regulator/O6‑methylguanine‑DNA methyltransferase
RA	2,305,116	C→A	100%	intergenic (‑103/+9)	apbE ← / ← ompC	putative thiamine‑synthetic flavin transferase lipoprotein/outer membrane porin protein C
RA	2,305,135	T→C	100%	Y365C (TAC→TGC)	ompC ←	outer membrane porin protein C
RA	2,310,213	G→T	20.9%	K186N (AAG→AAT)	rcsB →	response regulator in two‑component regulatory system with RcsC and YojN
RA	2,310,604	C→A	59.5%	G918C (GGT→TGT)	rcsC ←	hybrid sensory kinase in two‑component regulatory system with RcsB and YojN
RA	2,311,008	T→A	15.1%	H783L (CAC→CTC)	rcsC ←	hybrid sensory kinase in two‑component regulatory system with RcsB and YojN
RA	2,313,511	T→A	22.3%	intergenic (‑156/‑11)	rcsC ← / → atoS	hybrid sensory kinase in two‑component regulatory system with RcsB and YojN/sensory histidine kinase in two‑component regulatory system with AtoC
RA	2,313,924	C→A	5.8%	R135S (CGC→AGC)	atoS →	sensory histidine kinase in two‑component regulatory system with AtoC
RA	2,321,041	G→T	53.3%	F194L (TTC→TTA)	yfaP ←	DUF2135 family protein, putative host defense protein
RA	2,329,729	G→T	54.9%	A132E (GCG→GAG)	yfaA ←	DUF2138 family protein, putative host defense protein
RA	2,330,502	C→A	100%	D800Y (GAT→TAT)	gyrA ←	DNA gyrase (type II topoisomerase), subunit A
RA	2,338,302	G→T	6.9%	intergenic (‑654/‑42)	yfaL ← / → nrdA	adhesin/ribonucleoside‑diphosphate reductase 1, alpha subunit
RA	2,348,894	T→A	88.3%	V384E (GTG→GAG)	glpB →	sn‑glycerol‑3‑phosphate dehydrogenase (anaerobic), membrane anchor subunit
RA	2,352,082	C→A	42.4%	P81P (CCG→CCT)	rhmA ←	2‑keto‑3‑deoxy‑L‑rhamnonate aldolase
RA	2,352,573	C→A	100%	P353P (CCG→CCT)	rhmT ←	putative L‑rhamnonate transporter
RA	2,359,673	G→T	100%	M89I (ATG→ATT)	arnB →	uridine 5'‑(beta‑1‑threo‑pentapyranosyl‑4‑ulose diphosphate) aminotransferase, PLP‑dependent
RA	2,361,434	C→T	8.0%	I295I (ATC→ATT)	arnC →	undecaprenyl phosphate‑L‑Ara4FN transferase
RA	2,362,338	T→A	100%	L274Q (CTG→CAG)	arnA →	fused UDP‑L‑Ara4N formyltransferase/UDP‑GlcA C‑4'‑decarboxylase
RA	2,364,394	C→A	16.1%	S3* (TCG→TAG)	arnT →	4‑amino‑4‑deoxy‑L‑arabinose transferase
RA	2,366,555	T→G	12.1%	F62C (TTT→TGT)	arnF →	undecaprenyl phosphate‑alpha‑L‑ara4N exporter; flippase ArnEF subunit
RA	2,369,088	G→A	30.0%	I118I (ATC→ATT)	menC ←	O‑succinylbenzoyl‑CoA synthase
RA	2,370,361:1	+G	100%	coding (711/759 nt)	menH ←	2‑succinyl‑6‑hydroxy‑2, 4‑cyclohexadiene‑1‑carboxylate synthase
RA	2,370,987	C→A	100%	E29* (GAA→TAA)	menH ←	2‑succinyl‑6‑hydroxy‑2, 4‑cyclohexadiene‑1‑carboxylate synthase
RA	2,372,282	C→A	10.3%	D153Y (GAC→TAC)	menD ←	2‑succinyl‑5‑enolpyruvyl‑6‑hydroxy‑3‑ cyclohexene‑1‑carboxylate synthase; SEPHCHC synthase
RA	2,373,129	C→A	10.5%	D332Y (GAT→TAT)	menF ←	isochorismate synthase 2
RA	2,378,963	A→T	15.8%	L80* (TTG→TAG)	yfbK ←	Von Willebrand factor domain putative lipoprotein
RA	2,380,078	C→T	89.6%	S247F (TCT→TTT)	yfbL →	putative peptidase
RA	2,380,320	C→A	16.0%	intergenic (+10/‑93)	yfbL → / → yfbM	putative peptidase/DUF1877 family protein
RA	2,383,897	C→A	94.1%	R363L (CGC→CTC)	nuoN ←	NADH:ubiquinone oxidoreductase, membrane subunit N
RA	2,392,190	G→T	19.0%	V485V (GTC→GTA)	nuoG ←	NADH:ubiquinone oxidoreductase, chain G
RA	2,395,151	C→A	56.6%	T127T (ACG→ACT)	nuoE ←	NADH:ubiquinone oxidoreductase, chain E
RA	2,399,210	G→T	94.9%	S304* (TCA→TAA)	lrhA ←	transcriptional repressor of flagellar, motility and chemotaxis genes
RA	2,403,485	C→A	35.4%	L449L (CTG→CTT)	yfbS ←	putative transporter
RA	2,404,742	A→C	13.3%	A30A (GCT→GCG)	yfbS ←	putative transporter
RA	2,405,946	T→G	94.2%	Q43P (CAG→CCG)	yfbU ←	UPF0304 family protein
RA	2,412,205	C→A	90.6%	D151Y (GAT→TAT)	yfcD ←	putative NUDIX hydrolase
RA	2,412,692	G→T	33.4%	intergenic (‑37/+21)	yfcD ← / ← yfcE	putative NUDIX hydrolase/phosphodiesterase activity on bis‑pNPP
RA	2,416,101	C→A	100%	intergenic (+21/+27)	yfcH → / ← yfcI	putative NAD‑dependent nucleotide‑sugar epimerase/transposase_31 family protein
RA	2,417,358	C→A	55.1%	E211* (GAA→TAA)	hisP ←	histidine/lysine/arginine/ornithine transporter subunit
RA	2,421,032	G→T	7.5%	S80* (TCA→TAA)	argT ←	lysine/arginine/ornithine transporter subunit
RA	2,422,841	C→A	94.3%	D293Y (GAT→TAT)	purF ←	amidophosphoribosyltransferase
RA	2,423,034	G→T	13.3%	G228G (GGC→GGA)	purF ←	amidophosphoribosyltransferase
RA	2,424,074	C→T	100%	D57N (GAC→AAC)	cvpA ←	colicin V production membrane protein
RA	2,424,254	G→T	8.7%	intergenic (‑12/+247)	cvpA ← / ← dedD	colicin V production membrane protein/membrane‑anchored periplasmic protein involved in septation
RA	2,425,587	C→A	8.7%	D279Y (GAC→TAC)	folC ←	bifunctional folylpolyglutamate synthase/ dihydrofolate synthase
RA	2,437,156	G→T	14.0%	P638P (CCG→CCT)	mnmC →	fused 5‑methylaminomethyl‑2‑thiouridine‑forming enzyme methyltransferase and FAD‑dependent demodification enzyme
RA	2,438,410	C→A	20.5%	A210A (GCG→GCT)	yfcA ←	UPF0721 family inner membrane protein
RA	2,442,971	C→A	61.5%	E186D (GAG→GAT)	yfcO ←	DUF2544 family putative outer membrane protein
RA	2,443,918	T→G	19.2%	Y51S (TAT→TCT)	yfcP ←	putative fimbrial‑like adhesin protein
RA	2,444,107	T→G	19.4%	N150H (AAT→CAT)	yfcQ ←	putative fimbrial‑like adhesin protein
RA	2,450,335	C→T	100%	intergenic (‑44/+159)	sixA ← / ← fadJ	phosphohistidine phosphatase/fused enoyl‑CoA hydratase and epimerase and isomerase/3‑hydroxyacyl‑CoA dehydrogenase
RA	2,450,346	G→T	100%	intergenic (‑55/+148)	sixA ← / ← fadJ	phosphohistidine phosphatase/fused enoyl‑CoA hydratase and epimerase and isomerase/3‑hydroxyacyl‑CoA dehydrogenase
RA	2,452,454	G→T	100%	P62Q (CCG→CAG)	fadJ ←	fused enoyl‑CoA hydratase and epimerase and isomerase/3‑hydroxyacyl‑CoA dehydrogenase
RA	2,453,358	G→T	13.9%	I197I (ATC→ATA)	fadI ←	beta‑ketoacyl‑CoA thiolase, anaerobic, subunit
RA	2,454,297	T→G	100%	E39D (GAA→GAC)	yfcZ ←	UPF0381 family protein
RA	2,456,508	A→T	17.6%	S6S (TCA→TCT)	yfdF →	uncharacterized protein
RA	2,457,130	C→A	5.4%	R214S (CGT→AGT)	yfdF →	uncharacterized protein
RA	2,459,304	C→A	6.3%	I175I (ATC→ATA)	yfdC →	putative inner membrane protein
RA	2,460,619	T→A	7.9%	F199Y (TTT→TAT)	intS →	CPS‑53 (KpLE1) prophage; putative prophage CPS‑53 integrase
RA	2,463,760	T→A	15.6%	V384E (GTA→GAA)	gtrS →	serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
RA	2,463,906	C→A	20.9%	Q433K (CAA→AAA)	gtrS →	serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
RA	2,472,897	A→T	14.3%	T73S (ACT→TCT)	dsdA →	D‑serine dehydratase
RA	2,474,418	G→T	100%	S413* (TCA→TAA)	emrY ←	putative multidrug efflux system
RA	2,487,835	G→T	11.9%	S16Y (TCT→TAT)	yfdX ←	uncharacterized protein
RA	2,491,279	G→T	54.5%	R166S (CGT→AGT)	alaC ←	valine‑pyruvate aminotransferase 3
RA	2,494,310	C→A	14.2%	T150K (ACG→AAG)	ypdB →	response regulator activating yhjX; pyruvate‑responsive YpdAB two‑component system
RA	2,495,918	C→A	5.2%	V683F (GTT→TTT)	fryA ←	putative PTS enzyme, Hpr component/enzyme I component/enzyme IIA component
RA	2,498,349	C→A	5.5%	A226A (GCG→GCT)	ypdE ←	aminopeptidase
RA	2,501,358	G→T	17.1%	R6S (CGC→AGC)	fryC ←	putative enzyme IIC component of PTS
RA	2,511,317	C→A	63.1%	intergenic (‑6/+203)	yfeA ← / ← alaX	putative diguanylate cyclase/tRNA‑Ala
RA	2,516,301	G→T	13.2%	L348L (CTC→CTA)	xapB ←	xanthosine transporter
RA	2,520,652	C→A	100%	I116I (ATC→ATA)	yfeH →	putative inorganic ion transporter
RA	2,521,860	T→A	12.6%	H559L (CAC→CTC)	ligA ←	DNA ligase, NAD(+)‑dependent
RA	2,522,624	C→A	15.9%	A304A (GCG→GCT)	ligA ←	DNA ligase, NAD(+)‑dependent
RA	2,526,794	C→T	5.1%	intergenic (+55/‑329)	cysK → / → ptsH	cysteine synthase A, O‑acetylserine sulfhydrolase A subunit/phosphohistidinoprotein‑hexose phosphotransferase component of PTS system (Hpr)
RA	2,526,851	A→T	52.1%	intergenic (+112/‑272)	cysK → / → ptsH	cysteine synthase A, O‑acetylserine sulfhydrolase A subunit/phosphohistidinoprotein‑hexose phosphotransferase component of PTS system (Hpr)
RA	2,542,627	T→G	90.1%	I389M (ATT→ATG)	yfeW →	penicillin binding protein PBP4B; weak DD‑carboxypeptidase activity
RA	2,545,086	C→A	10.8%	D138Y (GAT→TAT)	ypeA ←	putative acyl‑CoA transferase
RA	2,549,676	C→A	100%	L28L (CTG→CTT)	eutL ←	putative ethanol utilization carboxysome structural protein
RA	2,549,778	C→A	12.7%	M293I (ATG→ATT)	eutC ←	ethanolamine ammonia‑lyase, small subunit (light chain)
RA	2,552,999	A→T	14.9%	A261A (GCA→GCT)	intZ →	CPZ‑55 prophage; putative phage integrase
RA	2,555,542	C→A	12.5%	R25R (CGG→AGG)	yffO →	CPZ‑55 prophage; uncharacterized protein
RA	2,561,221	C→A	19.2%	P82P (CCG→CCT)	eutH ←	ethanolamine transporter
RA	2,562,068	G→T	7.6%	A268E (GCG→GAG)	eutG ←	ethanol dehydrogenase involved in ethanolamine utilization; aldehyde reductase, converts acetaldehyde to ethanol
RA	2,568,720	C→T	100%	A33T (GCC→ACC)	eutP ←	putative P‑loop NTPase ethanolamine utilization protein
RA	2,569,792	G→T	13.3%	R649S (CGT→AGT)	maeB ←	malic enzyme: putative oxidoreductase/putative phosphotransacetylase
RA	2,576,325	C→A	100%	E171D (GAG→GAT)	nudK ←	GDP‑mannose pyrophosphatase
RA	2,576,567	C→A	30.9%	D91Y (GAC→TAC)	nudK ←	GDP‑mannose pyrophosphatase
RA	2,587,029:1	+G	100%	coding (101/699 nt)	ypfH ←	palmitoyl‑CoA esterase activity, uncertain physiological substrate
RA	2,589,808	G→T	53.8%	Q97K (CAG→AAG)	ypfJ ←	putative neutral zinc metallopeptidase
RA	2,589,933	G→A	100%	T55I (ACC→ATC)	ypfJ ←	putative neutral zinc metallopeptidase
RA	2,595,418	C→A	39.7%	S81* (TCG→TAG)	hyfB →	hydrogenase 4, membrane subunit
RA	2,597,173	T→G	90.3%	L666R (CTG→CGG)	hyfB →	hydrogenase 4, membrane subunit
RA	2,599,673	C→A	11.1%	S18* (TCG→TAG)	hyfE →	hydrogenase 4, membrane subunit
RA	2,601,404	C→T	55.9%	L377F (CTC→TTC)	hyfF →	hydrogenase 4, membrane subunit
RA	2,603,728	A→C	14.8%	Q69P (CAG→CCG)	hyfH →	hydrogenase 4, Fe‑S subunit
RA	2,606,516	G→T	100%	D420Y (GAC→TAC)	hyfR →	hydrogenase‑4 transcriptional activator
RA	2,610,919	C→A	100%	intergenic (+3/‑18)	bepA → / → yfgD	periplasmic metalloprotease and chaperone for OM protein maintenance and assembly/putative oxidoreductase
RA	2,614,168	C→A	100%	D22Y (GAT→TAT)	upp ←	uracil phosphoribosyltransferase
RA	2,614,721	C→A	40.2%	R56S (CGT→AGT)	purM →	phosphoribosylaminoimidazole synthetase
RA	2,615,370	C→A	14.5%	S272Y (TCT→TAT)	purM →	phosphoribosylaminoimidazole synthetase
RA	2,617,515	T→G	5.5%	I371M (ATT→ATG)	ppk →	polyphosphate kinase, component of RNA degradosome
RA	2,618,693	G→T	91.3%	E74* (GAA→TAA)	ppx →	exopolyphosphatase
RA	2,632,012	C→A	90.8%	intergenic (‑1/+10)	bamB ← / ← yfgM	BamABCDE complex OM biogenesis lipoprotein/putative anti‑RcsB factor
RA	2,636,214	T→A	43.4%	intergenic (‑11/+274)	rodZ ← / ← rlmN	MreB assembly cytoskeletal protein/dual specificity 23S rRNA m(2)A2503, tRNA m(2)A37 methyltransferase, SAM‑dependent
RA	2,651,665	G→T	100%	G210G (GGC→GGA)	hscA ←	DnaK‑like molecular chaperone specific for IscU
RA	2,658,679	G→T	12.6%	intergenic (+76/‑115)	yfhR → / → csiE	putative S9 family prolyl oligopeptidase/stationary phase inducible protein
RA	2,669,978	C→A	87.8%	A69A (GCG→GCT)	yphD ←	inner membrane putative ABC superfamily sugar transporter permease
RA	2,670,769	C→A	37.1%	E318* (GAA→TAA)	yphE ←	putative sugar transporter subunit of ABC superfamily, ATP‑binding component
RA	2,671,274	C→A	100%	T149T (ACG→ACT)	yphE ←	putative sugar transporter subunit of ABC superfamily, ATP‑binding component
RA	2,678,030	C→A	7.3%	A279A (GCG→GCT)	glyA ←	serine hydroxymethyltransferase
RA	2,681,873	T→A	100%	Q97L (CAG→CTG)	glrR ←	response regulator regulating glmY sRNA in two‑component system with sensor protein GlrK
RA	2,683,829	C→A	100%	R210L (CGT→CTT)	glrK ←	sensor protein kinase regulating glmY sRNA in two‑component system with response regulator GlrR
RA	2,687,073	C→A	10.9%	P610P (CCG→CCT)	purL ←	phosphoribosylformyl‑glycineamide synthetase
RA	2,690,778	C→A	33.9%	D147Y (GAC→TAC)	tadA ←	tRNA‑specific adenosine deaminase
RA	2,692,793	C→A	92.3%	H226N (CAT→AAT)	yfhH →	putative DNA‑binding transcriptional regulator
RA	2,694,843	G→T	82.2%	I82I (ATC→ATA)	pdxJ ←	pyridoxine 5'‑phosphate synthase
RA	2,699,380	C→A	87.4%	P368P (CCG→CCT)	lepA ←	back‑translocating elongation factor EF4, GTPase
RA	2,709,841	T→A	13.5%	intergenic (‑33/‑272)	grcA ← / → ung	autonomous glycyl radical cofactor/uracil‑DNA‑glycosylase
RA	2,715,643	G→T	100%	E778* (GAA→TAA)	pka →	protein lysine acetyltransferase
RA	2,719,168	A→T	5.2%	intergenic (‑63/+260)	kgtP ← / ← rrfG	alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon
RA	2,719,426	T→C	100%	intergenic (‑321/+2)	kgtP ← / ← rrfG	alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon
RA	2,725,657	C→A	19.5%	D626Y (GAC→TAC)	clpB ←	protein disaggregation chaperone
RA	2,726,786	C→A	100%	A249A (GCG→GCT)	clpB ←	protein disaggregation chaperone
RA	2,733,753	C→T	100%	E253K (GAG→AAG)	aroF ←	3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, tyrosine‑repressible
RA	2,740,948	C→A	18.7%	T69T (ACG→ACT)	ffh ←	Signal Recognition Particle (SRP) component with 4.5S RNA (ffs)
RA	2,741,288	C→A	18.2%	intergenic (‑134/‑33)	ffh ← / → ypjD	Signal Recognition Particle (SRP) component with 4.5S RNA (ffs)/cytochrome c assembly protein family inner membrane protein
RA	2,741,442	C→A	5.5%	A41E (GCG→GAG)	ypjD →	cytochrome c assembly protein family inner membrane protein
RA	2,748,332	C→A	12.3%	I26I (ATC→ATA)	smpB →	trans‑translation protein
RA	2,750,424	G→T	15.4%	E303* (GAA→TAA)	intA →	CP4‑57 prophage; integrase
RA	2,753,424	G→T	57.8%	G361* (GGA→TGA)	yfjI →	CP4‑57 prophage; uncharacterized protein
RA	2,753,629	C→A	32.5%	P429Q (CCA→CAA)	yfjI →	CP4‑57 prophage; uncharacterized protein
RA	2,754,840	T→A	16.9%	E687V (GAA→GTA)	yfjK ←	DEAD/H helicase‑like protein, CP4‑57 putative defective prophage
RA	2,756,683	G→T	16.5%	L73I (CTC→ATC)	yfjK ←	DEAD/H helicase‑like protein, CP4‑57 putative defective prophage
RA	2,761,733	T→A	6.8%	V222E (GTA→GAA)	yfjP →	CP4‑57 prophage; 50S ribosome‑binding GTPase family protein
RA	2,762,153	C→A	24.0%	R44S (CGC→AGC)	yfjQ →	CP4‑57 prophage; uncharacterized protein
RA	2,771,358	G→A	100%	intergenic (+217/+147)	ypjF → / ← ypjA	CP4‑57 prophage; toxin of the YpjF‑YfjZ toxin‑antitoxin system/adhesin‑like autotransporter
RA	2,771,366	G→A	16.2%	intergenic (+225/+139)	ypjF → / ← ypjA	CP4‑57 prophage; toxin of the YpjF‑YfjZ toxin‑antitoxin system/adhesin‑like autotransporter
RA	2,776,219	C→A	54.1%	intergenic (‑134/+205)	ypjA ← / ← pinH	adhesin‑like autotransporter/pseudogene, invertase resolvase family
RA	2,778,260	T→A	29.3%	pseudogene (111/1374 nt)	ypjC ←	pseudogene
RA	2,778,281	C→T	12.9%	pseudogene (90/1374 nt)	ypjC ←	pseudogene
RA	2,779,067	C→A	100%	intergenic (‑697/+54)	ypjC ← / ← ileY	pseudogene/tRNA‑Ile
RA	2,779,767	A→T	6.6%	pseudogene (12/2253 nt)	ygaQ →	uncharacterized protein; putative enzyme
RA	2,780,661	C→A	15.8%	pseudogene (906/2253 nt)	ygaQ →	uncharacterized protein; putative enzyme
RA	2,783,587	C→A	19.7%	R83S (CGC→AGC)	lhgO →	L‑2‑hydroxyglutarate oxidase
RA	2,790,370	G→T	36.4%	I6I (ATC→ATA)	yqaE ←	cyaR sRNA‑regulated protein
RA	2,799,737	C→A	12.2%	V123V (GTC→GTA)	proW →	glycine betaine transporter subunit
RA	2,801,706	C→A	6.1%	pseudogene (32/1178 nt)	ygaY →	pseudogene, major facilitator transporter superfamily;putative transport; Not classified; putative transport protein
RA	2,805,420	C→A	51.4%	A212E (GCG→GAG)	emrA →	multidrug efflux system
RA	2,808,737	C→A	11.9%	M354I (ATG→ATT)	gshA ←	glutamate‑cysteine ligase
RA	2,808,987	G→T	74.9%	S271* (TCG→TAG)	gshA ←	glutamate‑cysteine ligase
RA	2,812,678	G→T	9.4%	intergenic (‑173/+62)	csrA ← / ← alaS	pleiotropic regulatory protein for carbon source metabolism/alanyl‑tRNA synthetase
RA	2,812,689	C→A	5.1%	intergenic (‑184/+51)	csrA ← / ← alaS	pleiotropic regulatory protein for carbon source metabolism/alanyl‑tRNA synthetase
RA	2,819,067	C→A	18.6%	intergenic (‑132/‑124)	mltB ← / → srlA	membrane‑bound lytic murein transglycosylase B/glucitol/sorbitol‑specific enzyme IIC component of PTS
RA	2,819,102	G→T	24.1%	intergenic (‑167/‑89)	mltB ← / → srlA	membrane‑bound lytic murein transglycosylase B/glucitol/sorbitol‑specific enzyme IIC component of PTS
RA	2,823,071	T→A	16.1%	L222L (CTT→CTA)	srlR →	sorbitol‑inducible srl operon transcriptional repressor
RA	2,825,160	A→T	34.8%	I163I (ATT→ATA)	norR ←	anaerobic nitric oxide reductase DNA‑binding transcriptional activator
RA	2,825,783	C→T	100%	intergenic (‑135/‑52)	norR ← / → norV	anaerobic nitric oxide reductase DNA‑binding transcriptional activator/anaerobic nitric oxide reductase flavorubredoxin
RA	2,828,952	C→A	100%	T611T (ACG→ACT)	hypF ←	carbamoyl phosphate phosphatase and maturation protein for [NiFe] hydrogenases
RA	2,831,086	C→A	88.0%	E127* (GAA→TAA)	hydN ←	formate dehydrogenase‑H, [4Fe‑4S] ferredoxin subunit
RA	2,833,263	C→A	28.3%	V127V (GTC→GTA)	ascF →	fused cellobiose/arbutin/salicin‑specific PTS enzymes: IIB component/IC component
RA	2,835,094	C→A	86.5%	P249Q (CCG→CAG)	ascB →	cryptic 6‑phospho‑beta‑glucosidase
RA	2,836,192	C→T	10.9%	G71S (GGC→AGC)	hycI ←	protease involved in processing C‑terminal end of HycE
RA	2,840,562	C→A	59.1%	V70V (GTG→GTT)	hycD ←	hydrogenase 3, membrane subunit
RA	2,841,044	C→A	100%	A519A (GCG→GCT)	hycC ←	hydrogenase 3, membrane subunit
RA	2,846,112	C→A	87.1%	I206I (ATC→ATA)	hypD →	hydrogenase maturation protein
RA	2,846,721	G→T	31.9%	D37Y (GAT→TAT)	hypE →	carbamoyl dehydratase, hydrogenases 1,2,3 maturation protein
RA	2,850,790	C→A	100%	I113I (ATC→ATA)	mutS →	methyl‑directed mismatch repair protein
RA	2,860,460	G→T	11.8%	R151S (CGC→AGC)	rpoS ←	RNA polymerase, sigma S (sigma 38) factor
RA	2,873,087	G→T	100%	V15V (GTC→GTA)	ygbT ←	multifunctional endonuclease Cas1, CRISPR adaptation protein; DNA repair enzyme
RA	2,876,760	C→T	100%	G246G (GGG→GGA)	casA ←	CRISP RNA (crRNA) containing Cascade antiviral complex protein
RA	2,878,668	G→T	100%	V637V (GTC→GTA)	ygcB ←	R‑loop helicase‑annealase Cas3 needed for Cascade anti‑viral activity
RA	2,879,449	G→T	100%	S377* (TCA→TAA)	ygcB ←	R‑loop helicase‑annealase Cas3 needed for Cascade anti‑viral activity
RA	2,882,865	G→T	15.3%	V198V (GTC→GTA)	cysI ←	sulfite reductase, beta subunit, NAD(P)‑binding, heme‑binding
RA	2,886,199	C→A	18.9%	H62N (CAT→AAT)	ygcN →	putative oxidoreductase
RA	2,888,584	G→T	100%	I185I (ATC→ATA)	ygcQ ←	putative flavoprotein
RA	2,893,446	T→A	92.3%	K63* (AAA→TAA)	ygcW ←	putative dehydrogenase
RA	2,893,624	G→T	36.1%	I3I (ATC→ATA)	ygcW ←	putative dehydrogenase
RA	2,902,059	C→T	14.7%	V323I (GTC→ATC)	pyrG ←	CTP synthetase
RA	2,904,743	C→T	11.8%	intergenic (‑45/+33)	mazE ← / ← relA	antitoxin of the ChpA‑ChpR toxin‑antitoxin system/(p)ppGpp synthetase I/GTP pyrophosphokinase
RA	2,919,067	A→T	36.8%	T121S (ACT→TCT)	queF →	7‑cyano‑7‑deazaguanine reductase (NADPH‑dependent)
RA	2,931,717	C→A	94.9%	N307K (AAC→AAA)	fucK →	L‑fuculokinase
RA	2,932,832	C→A	5.6%	R36S (CGT→AGT)	fucR →	l‑fucose operon activator
RA	2,932,835	C→T	89.7%	R37C (CGC→TGC)	fucR →	l‑fucose operon activator
RA	2,934,843	G→T	100%	H50N (CAT→AAT)	ygdD ←	UPF0382 family inner membrane protein
RA	2,937,613	G→T	13.4%	T306T (ACG→ACT)	csdA →	cysteine sulfinate desulfinase
RA	2,938,035	G→T	62.8%	P45P (CCG→CCT)	csdE →	CsdA‑binding activator; Fe‑S protein
RA	2,938,640	C→A	5.1%	D188Y (GAT→TAT)	tcdA ←	tRNA threonylcarbamoyladenosine dehydratase; sulfur acceptor for CsdA
RA	2,950,594	G→T	36.1%	V550V (GTC→GTA)	ptrA ←	protease III
RA	2,956,284	C→A	29.2%	D78Y (GAT→TAT)	ygdB ←	DUF2509 family protein
RA	2,959,004	G→A	100%	I131I (ATC→ATT)	lgt ←	phosphatidylglycerol‑prolipoprotein diacylglyceryl transferase
RA	2,961,295	G→T	48.0%	R167S (CGC→AGC)	ptsP ←	fused PTS enzyme: PEP‑protein phosphotransferase (enzyme I)/GAF domain containing protein
RA	2,962,962	T→A	87.6%	intergenic (‑626/‑59)	rppH ← / → mutH	RNA pyrophosphohydrolase/methyl‑directed mismatch repair protein
RA	2,965,691	C→A	26.4%	L246I (CTC→ATC)	tas →	putative NADP(H)‑dependent aldo‑keto reductase
RA	2,969,113	A→T	11.9%	I87I (ATT→ATA)	aas ←	fused 2‑acylglycerophospho‑ethanolamine acyl transferase/acyl‑acyl carrier protein synthetase
RA	2,970,031	C→A	10.9%	S25* (TCA→TAA)	galR →	galactose‑inducible d‑galactose regulon transcriptional repressor; autorepressor
RA	2,970,703	C→A	37.2%	A249E (GCG→GAG)	galR →	galactose‑inducible d‑galactose regulon transcriptional repressor; autorepressor
RA	2,978,850	C→A	16.9%	V34V (GTG→GTT)	yqeF ←	short chain acyltransferase
RA	2,979,222	C→T	18.4%	S6F (TCT→TTT)	yqeG →	putative transporter
RA	2,985,884	C→T	89.5%	I144I (ATC→ATT)	ygeH →	putative transcriptional regulator
RA	2,987,928	C→A	15.3%	pseudogene (524/633 nt)	ygeK ←	pseudogene; putative 2‑component transcriptional regulator
RA	2,988,554	G→A	94.1%	intergenic (‑103/+119)	ygeK ← / ← ygeN	pseudogene; putative 2‑component transcriptional regulator/pseudogene
RA	2,988,641	T→C	61.4%	intergenic (‑190/+32)	ygeK ← / ← ygeN	pseudogene; putative 2‑component transcriptional regulator/pseudogene
RA	2,989,295	C→A	100%	pseudogene (85/261 nt)	ygeN ←	pseudogene
RA	2,993,211	C→A	100%	V14L (GTG→TTG)	ygeR ←	LysM domain‑containing M23 family putative peptidase; septation lipoprotein
RA	2,993,699	C→A	100%	intergenic (‑449/‑5)	ygeR ← / → xdhA	LysM domain‑containing M23 family putative peptidase; septation lipoprotein/xanthine dehydrogenase, molybdenum binding subunit
RA	3,007,405	A→T	12.4%	L65* (TTG→TAG)	yqeB ←	XdhC‑CoxI family protein with NAD(P)‑binding Rossman fold
RA	3,009,187	G→T	88.7%	intergenic (+90/‑232)	mocA → / → ygfK	CTP:molybdopterin cytidylyltransferase/putative Fe‑S subunit oxidoreductase subunit
RA	3,017,285	G→T	100%	D871Y (GAC→TAC)	xdhD →	putative hypoxanthine oxidase, molybdopterin‑binding/Fe‑S binding
RA	3,021,141	T→C	16.2%	I221T (ATC→ACC)	ygfQ →	putative purine permease
RA	3,024,081	A→C	89.9%	V70V (GTT→GTG)	ygfT ←	putative oxidoreductase, Fe‑S subunit/nucleotide‑binding subunit
RA	3,024,983	C→G	100%	G86G (GGC→GGG)	uacT →	uric acid permease
RA	3,025,678	A→T	7.4%	Q318L (CAA→CTA)	uacT →	uric acid permease
RA	3,028,224	G→T	11.4%	L104I (CTC→ATC)	lysS ←	lysine tRNA synthetase, constitutive
RA	3,030,181	G→T	90.8%	H429N (CAT→AAT)	recJ ←	ssDNA exonuclease, 5' ‑‑> 3'‑specific
RA	3,030,376	C→A	8.8%	E364* (GAA→TAA)	recJ ←	ssDNA exonuclease, 5' ‑‑> 3'‑specific
RA	3,030,978	A→T	43.1%	L163* (TTG→TAG)	recJ ←	ssDNA exonuclease, 5' ‑‑> 3'‑specific
RA	3,035,271	G→T	16.4%	V200V (GTG→GTT)	ygfZ →	iron‑sulfur cluster repair protein, plumbagin resistance
RA	3,036,052	C→A	18.1%	S152S (TCG→TCT)	yqfA ←	hemolysin III family HylIII inner membrane protein
RA	3,038,798	C→A	30.1%	D155Y (GAT→TAT)	ygfF ←	putative NAD(P)‑dependent oxidoreductase with NAD(P)‑binding Rossmann‑fold domain
RA	3,041,026	C→A	11.0%	D459Y (GAC→TAC)	gcvP ←	glycine decarboxylase, PLP‑dependent, subunit (protein P) of glycine cleavage complex
RA	3,042,913	C→A	29.6%	intergenic (‑5/+19)	gcvH ← / ← gcvT	glycine cleavage complex lipoylprotein/aminomethyltransferase, tetrahydrofolate‑dependent, subunit (T protein) of glycine cleavage complex
RA	3,044,281	G→A	8.7%	intergenic (‑255/+193)	gcvT ← / ← ubiI	aminomethyltransferase, tetrahydrofolate‑dependent, subunit (T protein) of glycine cleavage complex/2‑octaprenylphenol hydroxylase, FAD‑dependent
RA	3,044,437	T→A	17.0%	intergenic (‑411/+37)	gcvT ← / ← ubiI	aminomethyltransferase, tetrahydrofolate‑dependent, subunit (T protein) of glycine cleavage complex/2‑octaprenylphenol hydroxylase, FAD‑dependent
RA	3,044,464	G→A	100%	intergenic (‑438/+10)	gcvT ← / ← ubiI	aminomethyltransferase, tetrahydrofolate‑dependent, subunit (T protein) of glycine cleavage complex/2‑octaprenylphenol hydroxylase, FAD‑dependent
RA	3,046,245	C→A	31.0%	A211A (GCG→GCT)	ubiH ←	2‑octaprenyl‑6‑methoxyphenol hydroxylase, FAD/NAD(P)‑binding
RA	3,046,473	G→T	16.5%	N135K (AAC→AAA)	ubiH ←	2‑octaprenyl‑6‑methoxyphenol hydroxylase, FAD/NAD(P)‑binding
RA	3,048,273	A→T	5.4%	T177T (ACT→ACA)	ygfB ←	UPF0149 family protein
RA	3,048,490	A→T	10.2%	L105* (TTG→TAG)	ygfB ←	UPF0149 family protein
RA	3,055,069	C→A	5.8%	V287V (GTC→GTA)	scpA →	methylmalonyl‑CoA mutase
RA	3,058,692	C→T	5.1%	P178S (CCT→TCT)	scpC →	propionyl‑CoA:succinate CoA transferase
RA	3,058,769	C→T	86.4%	I203I (ATC→ATT)	scpC →	propionyl‑CoA:succinate CoA transferase
RA	3,059,577	G→T	64.4%	D473Y (GAT→TAT)	scpC →	propionyl‑CoA:succinate CoA transferase
RA	3,064,483	C→A	13.8%	D41Y (GAC→TAC)	fbaA ←	fructose‑bisphosphate aldolase, class II
RA	3,064,914	G→T	100%	I356I (ATC→ATA)	pgk ←	phosphoglycerate kinase
RA	3,065,300	C→A	15.8%	D228Y (GAT→TAT)	pgk ←	phosphoglycerate kinase
RA	3,066,295	C→A	7.4%	K252N (AAG→AAT)	epd ←	D‑erythrose 4‑phosphate dehydrogenase
RA	3,068,854	C→A	19.1%	E230* (GAG→TAG)	yggF ←	fructose 1,6 bisphosphatase isozyme
RA	3,074,352	C→T	15.7%	D215N (GAC→AAC)	tktA ←	transketolase 1, thiamine triphosphate‑binding
RA	3,075,114	C→A	100%	intergenic (‑120/‑158)	tktA ← / → loiP	transketolase 1, thiamine triphosphate‑binding/Phe‑Phe periplasmic metalloprotease, OM lipoprotein; low salt‑inducible; heat shock protein that binds Era
RA	3,076,526	C→A	100%	D211Y (GAC→TAC)	speB ←	agmatinase
RA	3,080,098	T→G	18.6%	S12A (TCT→GCT)	metK →	S‑adenosylmethionine synthetase
RA	3,080,618	T→A	94.0%	V185E (GTG→GAG)	metK →	S‑adenosylmethionine synthetase
RA	3,081,697	T→A	17.2%	C19S (TGC→AGC)	galP →	D‑galactose transporter
RA	3,085,649	C→A	14.2%	T138K (ACG→AAG)	gshB →	glutathione synthetase
RA	3,088,065	C→A	92.6%	V125V (GTG→GTT)	yggR ←	putative PilT family AAA+ ATPase
RA	3,089,392	C→A	14.8%	L72I (CTC→ATC)	yggT →	putative inner membrane protein; compensates for loss in K+ uptake
RA	3,091,476	C→A	41.7%	T284K (ACG→AAG)	yggW →	HemN family putative oxidoreductase
RA	3,092,182	C→A	9.1%	C248F (TGT→TTT)	yggM ←	DUF1202 family putative secreted protein
RA	3,096,445	A→T	21.4%	Q25L (CAA→CTA)	mutY →	adenine DNA glycosylase
RA	3,097,262	C→T	91.5%	F297F (TTC→TTT)	mutY →	adenine DNA glycosylase
RA	3,099,851	C→A	23.7%	S260* (TCG→TAG)	nupG →	nucleoside transporter
RA	3,100,053	C→T	16.2%	I327I (ATC→ATT)	nupG →	nucleoside transporter
RA	3,104,247	C→A	13.8%	R80L (CGA→CTA)	yghD ←	putative membrane‑anchored secretion pathway M‑type protein
RA	3,110,751	C→A	100%	R574L (CGT→CTT)	yghJ ←	DUF4092 family putative lipoprotein peptidase
RA	3,111,434	C→A	100%	A346A (GCG→GCT)	yghJ ←	DUF4092 family putative lipoprotein peptidase
RA	3,113,973	C→A	38.6%	E222D (GAG→GAT)	glcA ←	glycolate transporter
RA	3,118,925	C→A	15.9%	P319P (CCG→CCT)	glcE ←	glycolate oxidase FAD binding subunit
RA	3,120,216	C→A	100%	D389Y (GAT→TAT)	glcD ←	glycolate oxidase subunit, FAD‑linked
RA	3,121,242	C→A	13.1%	D47Y (GAC→TAC)	glcD ←	glycolate oxidase subunit, FAD‑linked
RA	3,129,198	C→A	32.6%	R178L (CGA→CTA)	pitB ←	phosphate transporter
RA	3,130,516	C→A	31.1%	D456Y (GAC→TAC)	gss ←	fused glutathionylspermidine amidase/glutathionylspermidine synthetase
RA	3,132,601	T→G	5.7%	I172M (ATT→ATG)	yghU →	putative S‑transferase
RA	3,132,984	G→A	57.9%	intergenic (+32/+91)	yghU → / ← hybG	putative S‑transferase/hydrogenase 2 accessory protein
RA	3,133,918	C→A	12.4%	E81* (GAA→TAA)	hybE ←	hydrogenase 2‑specific chaperone
RA	3,136,368	G→T	55.7%	R386S (CGT→AGT)	hybB ←	putative hydrogenase 2 cytochrome b type component
RA	3,142,668	G→T	82.9%	L55I (CTC→ATC)	yqhA ←	UPF0114 family putative inner membrane protein
RA	3,144,158	C→A	93.9%	intergenic (+253/+19)	yghA → / ← exbD	putative oxidoreductase/membrane spanning protein in TonB‑ExbB‑ExbD complex
RA	3,147,360	G→T	9.8%	G147C (GGT→TGT)	yghB →	general envelope maintenance protein; DedA family inner membrane protein
RA	3,149,310	C→A	17.4%	T199T (ACC→ACA)	yqhD →	aldehyde reductase, NADPH‑dependent
RA	3,151,225	A→T	36.2%	N73Y (AAT→TAT)	yqhG →	DUF3828 family putative periplasmic protein
RA	3,157,088	C→A	35.2%	D749Y (GAT→TAT)	parC ←	DNA topoisomerase IV, subunit A
RA	3,164,049	G→T	16.8%	M69I (ATG→ATT)	qseC →	quorum sensing sensory histidine kinase in two‑component regulatory system with QseB
RA	3,164,230	C→A	91.2%	R130S (CGT→AGT)	qseC →	quorum sensing sensory histidine kinase in two‑component regulatory system with QseB
RA	3,169,865	T→G	10.2%	I110L (ATC→CTC)	cpdA ←	3',5' cAMP phosphodiesterase
RA	3,173,537	G→T	5.3%	P145P (CCG→CCT)	ygiB →	DUF1190 family protein
RA	3,173,669	G→T	100%	A189A (GCG→GCT)	ygiB →	DUF1190 family protein
RA	3,176,051	C→A	13.8%	S48* (TCA→TAA)	zupT →	zinc transporter
RA	3,176,733	G→T	92.4%	intergenic (+51/+439)	zupT → / ← ribB	zinc transporter/3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase
RA	3,181,323	C→A	7.9%	pseudogene (544/2445 nt)	yqiG →	pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein
RA	3,184,654	A→T	14.5%	N222Y (AAT→TAT)	yqiI →	fimbrial protein
RA	3,203,599	A→T	20.5%	W102R (TGG→AGG)	tsaD ←	tRNA(ANN) t(6)A37 threonylcarbamoyladenosine modification protein; glycation binding protein
RA	3,208,550	T→A	42.5%	K95* (AAA→TAA)	mug ←	G/U mismatch‑specific DNA glycosylase; xanthine DNA glycosylase
RA	3,208,581	C→A	14.7%	E84D (GAG→GAT)	mug ←	G/U mismatch‑specific DNA glycosylase; xanthine DNA glycosylase
RA	3,213,497	C→A	8.3%	I215I (ATC→ATA)	patA →	putrescine:2‑oxoglutaric acid aminotransferase, PLP‑dependent
RA	3,214,709	C→A	18.4%	intergenic (‑103/‑116)	ygjH ← / → ebgR	putative tRNA binding protein; putative tRNA corner chaperone/transcriptional repressor
RA	3,217,098	C→A	18.4%	I369I (ATC→ATA)	ebgA →	evolved beta‑D‑galactosidase, alpha subunit
RA	3,217,289	A→T	93.0%	H433L (CAC→CTC)	ebgA →	evolved beta‑D‑galactosidase, alpha subunit
RA	3,219,616	A→T	16.3%	T8T (ACA→ACT)	ygjI →	putative transporter
RA	3,224,927	C→A	100%	intergenic (+329/‑97)	ygjK → / → fadH	alpha‑glucosidase/2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked
RA	3,225,300	C→A	11.9%	Q93K (CAG→AAG)	fadH →	2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked
RA	3,229,926	C→A	20.2%	L10I (CTC→ATC)	ygjQ →	DUF218 superfamily protein
RA	3,230,857	C→G	90.6%	A63G (GCC→GGC)	ygjR →	putative NAD(P)‑dependent dehydrogenase
RA	3,231,349	A→C	91.7%	Q227P (CAG→CCG)	ygjR →	putative NAD(P)‑dependent dehydrogenase
RA	3,233,218	C→A	57.0%	intergenic (+314/‑85)	alx → / → sstT	putative membrane‑bound redox modulator/sodium:serine/threonine symporter
RA	3,233,271	G→T	31.1%	intergenic (+367/‑32)	alx → / → sstT	putative membrane‑bound redox modulator/sodium:serine/threonine symporter
RA	3,237,654	C→A	14.7%	M149I (ATG→ATT)	uxaC ←	uronate isomerase
RA	3,243,361	C→A	9.3%	S107* (TCG→TAG)	yqjE →	DUF1469 family inner membrane protein
RA	3,245,848	G→T	100%	L62L (CTG→CTT)	yhaH →	DUF805 family inner membrane protein
RA	3,246,634	A→T	5.7%	intergenic (+8/+43)	yhaI → / ← yhaJ	DUF805 family inner membrane protein/LysR family putative transcriptional regulator
RA	3,248,241	G→A	37.7%	G188G (GGG→GGA)	yhaK →	redox‑sensitive bicupin
RA	3,251,070	C→A	15.1%	P100P (CCG→CCT)	yhaO ←	putative transporter
RA	3,252,258	C→A	100%	D251Y (GAT→TAT)	tdcG ←	L‑serine dehydratase 3, anaerobic
RA	3,254,793	C→A	10.0%	D329Y (GAT→TAT)	tdcE ←	pyruvate formate‑lyase 4/2‑ketobutyrate formate‑lyase
RA	3,257,209	C→A	60.7%	E390* (GAA→TAA)	tdcC ←	L‑threonine/L‑serine transporter
RA	3,260,550	C→T	11.4%	intergenic (‑126/‑189)	tdcA ← / → tdcR	tdc operon transcriptional activator/L‑threonine dehydratase operon activator protein
RA	3,262,367	T→G	5.1%	F198L (TTT→TTG)	yhaC →	pentapetide repeats‑related protein
RA	3,262,436	C→T	12.2%	S221S (AGC→AGT)	yhaC →	pentapetide repeats‑related protein
RA	3,263,315	T→C	5.5%	intergenic (+354/+260)	yhaC → / ← rnpB	pentapetide repeats‑related protein/RNase P, M1 RNA component
RA	3,263,466	G→T	6.1%	intergenic (+505/+109)	yhaC → / ← rnpB	pentapetide repeats‑related protein/RNase P, M1 RNA component
RA	3,266,646	C→A	100%	G91C (GGT→TGT)	garL ←	alpha‑dehydro‑beta‑deoxy‑D‑glucarate aldolase
RA	3,267,286	C→A	58.3%	P327P (CCG→CCT)	garP ←	putative (D)‑galactarate transporter
RA	3,271,233	C→A	12.5%	V264V (GTG→GTT)	agaR ←	transcriptional repressor of the aga regulon
RA	3,275,820	C→A	5.7%	P162P (CCC→CCA)	agaS →	tagatose‑6‑phosphate ketose/aldose isomerase
RA	3,292,182	G→T	14.9%	G8G (GGC→GGA)	yraR ←	putative nucleoside‑diphosphate‑sugar epimerase
RA	3,292,914	C→A	55.6%	D121Y (GAT→TAT)	yhbP ←	UPF0306 family protein
RA	3,296,612	G→T	90.6%	A255A (GCG→GCT)	yhbV →	U32 peptidase family protein
RA	3,298,059	C→A	53.1%	R373L (CGC→CTC)	mtr ←	tryptophan transporter of high affinity
RA	3,302,027	G→T	93.9%	S86* (TCG→TAG)	nlpI ←	lipoprotein involved in osmotic sensitivity and filamentation
RA	3,311,488	G→T	36.8%	intergenic (‑123/+84)	rimP ← / ← metY	ribosome maturation factor for 30S subunits/tRNA‑Met
RA	3,311,841	C→A	11.3%	intergenic (‑193/‑155)	metY ← / → argG	tRNA‑Met/argininosuccinate synthetase
RA	3,312,862	T→A	6.7%	R289R (CGT→CGA)	argG →	argininosuccinate synthetase
RA	3,314,870	C→A	100%	A35S (GCG→TCG)	yhbX ←	putative EptAB family phosphoethanolamine transferase, inner membrane protein
RA	3,318,271	G→T	20.3%	intergenic (‑1/+89)	folP ← / ← ftsH	7,8‑dihydropteroate synthase/protease, ATP‑dependent zinc‑metallo
RA	3,324,066	C→A	15.9%	E350* (GAA→TAA)	obgE ←	GTPase involved in cell partioning and DNA repair
RA	3,329,704	G→T	15.6%	V50V (GTC→GTA)	murA ←	UDP‑N‑acetylglucosamine 1‑carboxyvinyltransferase
RA	3,332,632	G→T	59.7%	L265I (CTT→ATT)	mlaF ←	ABC transporter maintaining OM lipid asymmetry, ATP‑binding protein
RA	3,334,892	G→T	18.2%	D90Y (GAT→TAT)	kdsD →	D‑arabinose 5‑phosphate isomerase
RA	3,335,651	C→A	49.8%	S7* (TCG→TAG)	kdsC →	3‑deoxy‑D‑manno‑octulosonate 8‑phosphate phosphatase
RA	3,341,351	C→A	7.9%	I9I (ATC→ATA)	npr →	phosphohistidinoprotein‑hexose phosphotransferase component of N‑regulated PTS system (Npr)
RA	3,345,737	A→C	11.2%	D216E (GAT→GAG)	arcB ←	aerobic respiration control sensor histidine protein kinase, cognate to two‑component response regulators ArcA and RssB
RA	3,347,740	C→A	40.6%	intergenic (‑331/‑344)	yhcC ← / → gltB	putative Fe‑S oxidoreductase, Radical SAM superfamily protein/glutamate synthase, large subunit
RA	3,347,778	G→A	100%	intergenic (‑369/‑306)	yhcC ← / → gltB	putative Fe‑S oxidoreductase, Radical SAM superfamily protein/glutamate synthase, large subunit
RA	3,351,650	G→T	88.4%	E1189D (GAG→GAT)	gltB →	glutamate synthase, large subunit
RA	3,354,405	C→T	100%	intergenic (+430/‑130)	gltD → / → gltF	glutamate synthase, 4Fe‑4S protein, small subunit/periplasmic protein
RA	3,360,045	G→T	21.9%	F11L (TTC→TTA)	insH1 ←	IS5 transposase and trans‑activator
RA	3,365,253	G→T	34.8%	I227I (ATC→ATA)	nanT ←	sialic acid transporter
RA	3,365,607	G→T	100%	I109I (ATC→ATA)	nanT ←	sialic acid transporter
RA	3,368,168	C→T	11.6%	intergenic (‑320/‑60)	nanR ← / → dcuD	transcriptional repressor of the nan operon, induced by sialic acid/putative transporter
RA	3,372,318	G→T	14.7%	R347R (CGG→AGG)	yhcM ←	putative AFG1‑like family P‑loop ATPase
RA	3,373,985	C→A	100%	intergenic (+37/‑117)	yhcB → / → degQ	DUF1043 family inner membrane‑anchored protein/serine endoprotease, periplasmic
RA	3,375,260	G→T	100%	D387Y (GAT→TAT)	degQ →	serine endoprotease, periplasmic
RA	3,381,195	G→T	13.9%	S118* (TCG→TAG)	aaeB ←	p‑hydroxybenzoic acid efflux system component
RA	3,385,662	C→G	8.0%	intergenic (‑275/+155)	tldD ← / ← yhdP	putative peptidase/DUF3971‑AsmA2 domains protein
RA	3,389,148	G→T	38.4%	T157K (ACG→AAG)	yhdP ←	DUF3971‑AsmA2 domains protein
RA	3,392,238	T→A	9.2%	Q367L (CAA→CTA)	mreC ←	cell wall structural complex MreBCD transmembrane component MreC
RA	3,392,935	C→T	19.7%	V135I (GTT→ATT)	mreC ←	cell wall structural complex MreBCD transmembrane component MreC
RA	3,395,059	C→A	14.3%	V545F (GTC→TTC)	csrD ←	targeting factor for csrBC sRNA degradation
RA	3,396,082	G→T	100%	R204S (CGT→AGT)	csrD ←	targeting factor for csrBC sRNA degradation
RA	3,397,077	G→T	32.5%	A79S (GCC→TCC)	acuI →	putative acryloyl‑CoA reductase
RA	3,397,316	C→A	14.9%	G158G (GGC→GGA)	acuI →	putative acryloyl‑CoA reductase
RA	3,398,168	C→A	9.6%	pseudogene (78/300 nt)	yrdE →	pseudogene, yedZ paralog
RA	3,399,100	C→A	13.3%	F102L (TTC→TTA)	accB →	acetyl CoA carboxylase, BCCP subunit
RA	3,407,007	G→A	93.0%	intergenic (‑183/‑216)	acrS ← / → acrE	acrAB operon transcriptional repressor/cytoplasmic membrane lipoprotein
RA	3,412,733	G→T	18.1%	pseudogene (268/960 nt)	yhdW →	pseudogene, amino‑acid transporter homology;putative transport; Not classified; putative periplasmic binding transport protein; periplasmic‑binding component of ABC superfamily
RA	3,416,890	T→G	8.0%	noncoding (12/120 nt)	rrfF ←	5S ribosomal RNA of rrnD operon
RA	3,432,676	C→A	13.1%	E65* (GAA→TAA)	yhdN ←	DUF1992 family protein
RA	3,432,840	C→A	17.2%	R10L (CGC→CTC)	yhdN ←	DUF1992 family protein
RA	3,433,018	T→G	55.8%	E114A (GAG→GCG)	rplQ ←	50S ribosomal subunit protein L17
RA	3,437,638	G→T	14.6%	G87G (GGC→GGA)	rplO ←	50S ribosomal subunit protein L15
RA	3,440,151	G→T	100%	I31I (ATC→ATA)	rpsN ←	30S ribosomal subunit protein S14
RA	3,440,444	G→T	100%	S118S (TCC→TCA)	rplE ←	50S ribosomal subunit protein L5
RA	3,440,832	T→C	100%	N99D (AAC→GAC)	rplX ←	50S ribosomal subunit protein L24
RA	3,442,244	C→A	30.6%	L95F (TTG→TTT)	rplP ←	50S ribosomal subunit protein L16
RA	3,451,616	T→G	17.5%	V627V (GTT→GTG)	gspD →	general secretory pathway component, cryptic
RA	3,452,566	C→A	21.0%	T290K (ACG→AAG)	gspE →	general secretory pathway component, cryptic
RA	3,455,789	G→T	38.1%	M29I (ATG→ATT)	gspJ →	putative general secretory pathway component, cryptic
RA	3,455,867	C→A	100%	I55I (ATC→ATA)	gspJ →	putative general secretory pathway component, cryptic
RA	3,457,607	G→T	53.5%	V109V (GTG→GTT)	gspL →	general secretory pathway component, cryptic
RA	3,457,896	C→A	55.8%	P206T (CCT→ACT)	gspL →	general secretory pathway component, cryptic
RA	3,473,139	G→T	100%	I276I (ATC→ATA)	kefB ←	potassium:proton antiporter
RA	3,479,769	A→T	100%	E97D (GAA→GAT)	crp →	cAMP‑activated global transcription factor, mediator of catabolite repression
RA	3,480,538	C→A	31.7%	A130E (GCG→GAG)	yhfK →	putative transporter, FUSC superfamily inner membrane protein, tandem domains
RA	3,484,469	C→A	31.5%	A118A (GCG→GCT)	fic ←	stationary‑phase adenosine monophosphate‑protein transferase domain protein
RA	3,487,320	G→A	53.0%	intergenic (+212/‑50)	tsgA → / → nirB	putative transporter/nitrite reductase, large subunit, NAD(P)H‑binding
RA	3,488,966	G→C	100%	A533P (GCC→CCC)	nirB →	nitrite reductase, large subunit, NAD(P)H‑binding
RA	3,489,397	C→A	100%	F676L (TTC→TTA)	nirB →	nitrite reductase, large subunit, NAD(P)H‑binding
RA	3,494,830	C→T	34.1%	R68R (CGC→CGT)	frlB →	fructoselysine‑6‑P‑deglycase
RA	3,495,516	C→A	50.0%	S297* (TCG→TAG)	frlB →	fructoselysine‑6‑P‑deglycase
RA	3,498,214	T→G	8.5%	intergenic (+72/+80)	frlR → / ← yhfS	putative DNA‑binding transcriptional regulator/FNR‑regulated pyridoxal phosphate‑dependent aminotransferase family protein
RA	3,498,239	A→C	9.5%	intergenic (+97/+55)	frlR → / ← yhfS	putative DNA‑binding transcriptional regulator/FNR‑regulated pyridoxal phosphate‑dependent aminotransferase family protein
RA	3,500,138	G→T	37.7%	I186I (ATC→ATA)	yhfT ←	inner membrane protein
RA	3,501,571	C→A	93.9%	G127C (GGC→TGC)	php ←	phosphotriesterase homology protein
RA	3,504,143	G→T	91.5%	R65S (CGT→AGT)	yhfX ←	putative pyridoxal 5'‑phosphate binding protein
RA	3,507,017	G→T	6.3%	S244R (AGC→AGA)	gph ←	phosphoglycolate phosphatase
RA	3,507,749	G→T	92.5%	H224N (CAT→AAT)	rpe ←	D‑ribulose‑5‑phosphate 3‑epimerase
RA	3,508,852	G→T	12.5%	P141T (CCC→ACC)	dam ←	DNA adenine methyltransferase
RA	3,513,238	A→T	38.1%	I275I (ATT→ATA)	hofQ ←	DNA catabolic putative fimbrial transporter
RA	3,513,424	A→T	90.3%	V213V (GTT→GTA)	hofQ ←	DNA catabolic putative fimbrial transporter
RA	3,513,975	C→A	10.8%	D30Y (GAC→TAC)  *135L (TGA→TTA)	hofQ ← hofP ←	DNA catabolic putative fimbrial transporter DNA catabolic protein
RA	3,519,657	G→T	100%	intergenic (‑149/‑171)	nudE ← / → yrfF	adenosine nucleotide hydrolase; substrates include Ap3A, Ap2A, ADP‑ribose, NADH/inner membrane protein
RA	3,521,598	C→A	18.2%	Q591K (CAG→AAG)	yrfF →	inner membrane protein
RA	3,525,950	C→T	5.7%	intergenic (‑152/‑227)	yhgE ← / → pck	DUF4153 family putative inner membrane protein/phosphoenolpyruvate carboxykinase
RA	3,536,360	C→A	15.0%	intergenic (+37/‑166)	feoC → / → yhgA	putative DNA‑binding transcriptional regulator/transposase_31 family protein
RA	3,541,936	G→T	11.4%	L498L (CTC→CTA)	malQ ←	4‑alpha‑glucanotransferase (amylomaltase)
RA	3,542,876	T→G	27.5%	N185T (AAC→ACC)	malQ ←	4‑alpha‑glucanotransferase (amylomaltase)
RA	3,543,959	G→T	100%	A625E (GCG→GAG)	malP ←	maltodextrin phosphorylase
RA	3,544,369	T→A	18.6%	E488D (GAA→GAT)	malP ←	maltodextrin phosphorylase
RA	3,544,521	G→T	14.2%	H438N (CAC→AAC)	malP ←	maltodextrin phosphorylase
RA	3,549,303	G→T	14.1%	V302V (GTC→GTA)	rtcA ←	RNA 3'‑terminal phosphate cyclase
RA	3,557,815	T→A	57.1%	K709N (AAA→AAT)	glgP ←	glycogen phosphorylase
RA	3,559,991	G→T	17.9%	S468* (TCG→TAG)	glgA ←	glycogen synthase
RA	3,561,258	C→A	35.4%	D46Y (GAT→TAT)	glgA ←	glycogen synthase
RA	3,561,574	C→A	100%	W372L (TGG→TTG)	glgC ←	glucose‑1‑phosphate adenylyltransferase
RA	3,562,409	C→A	13.8%	E94* (GAA→TAA)	glgC ←	glucose‑1‑phosphate adenylyltransferase
RA	3,563,911	C→A	52.2%	E257* (GAA→TAA)	glgX ←	glycogen debranching enzyme
RA	3,564,984	C→A	33.8%	E627* (GAA→TAA)	glgB ←	1,4‑alpha‑glucan branching enzyme
RA	3,568,708	C→A	18.2%	S93* (TCA→TAA)	yhgN →	UPF0056 family inner membrane protein
RA	3,571,118	G→T	32.4%	F323L (TTC→TTA)	gntR ←	d‑gluconate inducible gluconate regulon transcriptional repressor
RA	3,571,612	C→T	11.8%	A159T (GCC→ACC)	gntR ←	d‑gluconate inducible gluconate regulon transcriptional repressor
RA	3,571,618	C→A	16.9%	D157Y (GAT→TAT)	gntR ←	d‑gluconate inducible gluconate regulon transcriptional repressor
RA	3,571,950	T→A	38.6%	E46V (GAA→GTA) ‡	gntR ←	d‑gluconate inducible gluconate regulon transcriptional repressor
RA	3,571,951	C→A	20.7%	E46* (GAA→TAA) ‡	gntR ←	d‑gluconate inducible gluconate regulon transcriptional repressor
RA	3,574,500	G→T	17.1%	M1M (ATG→ATT) †	yhhY →	putative acetyltransferase
RA	3,577,507	C→A	19.1%	I157I (ATC→ATA)	insB1 →	IS1 transposase B
RA	3,580,302	G→T	11.1%	intergenic (‑119/‑1)	ggt ← / → yhhA	gamma‑glutamyltranspeptidase/DUF2756 family protein
RA	3,584,639	G→T	18.8%	I349I (ATC→ATA)	ugpB ←	glycerol‑3‑phosphate transporter subunit
RA	3,590,930	T→A	60.0%	intergenic (‑10/‑414)	livK ← / → panM	leucine transporter subunit/PanD autocleavage accelerator, panothenate synthesis
RA	3,591,211	C→A	5.7%	intergenic (‑291/‑133)	livK ← / → panM	leucine transporter subunit/PanD autocleavage accelerator, panothenate synthesis
RA	3,598,440	C→A	16.6%	N34K (AAC→AAA)	yhhL →	DUF1145 family protein
RA	3,600,766	C→A	27.1%	S319* (TCA→TAA)	zntA →	zinc, cobalt and lead efflux system
RA	3,609,958	C→A	12.9%	I139I (ATC→ATA)	nikC →	nickel transporter subunit
RA	3,612,708	C→A	12.3%	L53I (CTC→ATC)	rhsB →	Rhs family putative polymorphic toxin, putative neighboring cell growth inhibitor
RA	3,616,947	A→T	8.0%	E63D (GAA→GAT)	yhhH →	putative immunity protein for putative polymorphic toxin RhsB
RA	3,618,622	C→A	6.9%	F295L (TTC→TTA)	yhhI →	putative transposase
RA	3,622,863	G→T	20.7%	V12V (GTC→GTA)	rbbA ←	ribosome‑associated ATPase: ATP‑binding protein/ATP‑binding membrane protein
RA	3,629,439	C→A	15.9%	intergenic (+186/+129)	yhiM → / ← yhiN	acid resistance protein, inner membrane/putative oxidoreductase
RA	3,632,600	T→G	7.9%	intergenic (+99/+145)	pitA → / ← uspB	phosphate transporter, low‑affinity; tellurite importer/universal stress (ethanol tolerance) protein B
RA	3,634,084	C→A	33.9%	intergenic (+179/‑138)	uspA → / → dtpB	universal stress global response regulator/dipeptide and tripeptide permease B
RA	3,640,170	C→A	12.3%	A171E (GCG→GAG)	gor →	glutathione oxidoreductase
RA	3,649,637	G→A	14.0%	L6F (CTC→TTC)	hdeB ←	acid‑resistance protein
RA	3,652,308	G→T	40.8%	intergenic (+55/‑284)	gadE → / → mdtE	gad regulon transcriptional activator/anaerobic multidrug efflux transporter, ArcA‑regulated
RA	3,652,706	G→T	13.2%	V39F (GTC→TTC)	mdtE →	anaerobic multidrug efflux transporter, ArcA‑regulated
RA	3,661,179	T→A	27.7%	Y457F (TAC→TTC)	yhjA ←	putative cytochrome C peroxidase
RA	3,662,660	T→C	100%	intergenic (‑112/‑292)	yhjA ← / → treF	putative cytochrome C peroxidase/cytoplasmic trehalase
RA	3,667,977	C→T	14.0%	intergenic (+242/‑169)	yhjD → / → yhjE	inner membrane putative BrbK family alternate lipid exporter/MFS superfamily sugar transport 1 family protein
RA	3,668,106	G→A	12.1%	intergenic (+371/‑40)	yhjD → / → yhjE	inner membrane putative BrbK family alternate lipid exporter/MFS superfamily sugar transport 1 family protein
RA	3,670,418	C→A	15.0%	P431P (CCG→CCT)	yhjG ←	putative inner membrane‑anchored periplasmic AsmA family protein
RA	3,672,064	T→A	34.9%	T162S (ACC→TCC)	yhjH ←	cyclic‑di‑GMP phosphodiesterase, FlhDC‑regulated
RA	3,673,169	C→A	18.1%	L131I (CTC→ATC)	kdgK →	2‑dehydro‑3‑deoxygluconokinase
RA	3,676,886	C→A	40.0%	intergenic (‑79/+104)	dctA ← / ← yhjK	C4‑dicarboxylic acid, orotate and citrate transporter/cyclic‑di‑GMP phosphodiesterase
RA	3,679,301	T→G	100%	Q1078P (CAG→CCG)	bcsC ←	cellulose synthase subunit
RA	3,679,324	C→A	100%	M1070I (ATG→ATT)	bcsC ←	cellulose synthase subunit
RA	3,680,907	C→A	18.1%	D543Y (GAC→TAC)	bcsC ←	cellulose synthase subunit
RA	3,680,910	G→T	100%	H542N (CAT→AAT)	bcsC ←	cellulose synthase subunit
RA	3,681,855	C→A	30.4%	D227Y (GAC→TAC)	bcsC ←	cellulose synthase subunit
RA	3,689,369	C→A	19.6%	A59A (GCG→GCT)	yhjR ←	DUF2629 family protein
RA	3,694,707	C→A	9.4%	S262* (TCG→TAG)	yhjV →	putative transporter
RA	3,698,875	G→T	90.9%	F92L (TTC→TTA)	dppB ←	dipeptide/heme transporter
RA	3,699,362	C→T	10.0%	intergenic (‑212/+96)	dppB ← / ← dppA	dipeptide/heme transporter/dipeptide transporter
RA	3,701,444	G→A	9.8%	intergenic (‑379/+532)	dppA ← / ← proK	dipeptide transporter/tRNA‑Pro
RA	3,701,561	G→A	6.0%	intergenic (‑496/+415)	dppA ← / ← proK	dipeptide transporter/tRNA‑Pro
RA	3,708,413	G→T	17.6%	P448T (CCG→ACG)	bisC ←	biotin sulfoxide reductase
RA	3,710,665	G→T	11.2%	intergenic (+99/‑5)	yiaD → / → ghrB	multicopy suppressor of bamB; outer membrane lipoprotein/glyoxylate/hydroxypyruvate reductase B
RA	3,716,399	C→A	12.8%	A453A (GCG→GCT)	glyS ←	glycine tRNA synthetase, beta subunit
RA	3,717,788	C→A	100%	P297P (CCG→CCT)	glyQ ←	glycine tRNA synthetase, alpha subunit
RA	3,736,058	C→A	13.7%	intergenic (‑166/‑35)	yiaJ ← / → yiaK	transcriptional repressor of yiaK‑S operon/2,3‑diketo‑L‑gulonate reductase, NADH‑dependent
RA	3,738,431	C→A	100%	P90T (CCA→ACA)	yiaN →	2,3‑diketo‑L‑gulonate TRAP transporter large permease protein
RA	3,740,731	G→T	54.9%	G96G (GGG→GGT)	lyxK →	L‑xylulose kinase
RA	3,740,770	C→A	14.4%	I109I (ATC→ATA)	lyxK →	L‑xylulose kinase
RA	3,744,809	C→A	52.5%	E140D (GAG→GAT)	yiaT ←	putative outer membrane protein
RA	3,759,323	C→T	15.7%	P1261S (CCC→TCC)	rhsA →	Rhs family protein, putative polymorphic toxin; putative polysaccharide synthesis/export protein; putative neighboring cell growth inhibitor
RA	3,761,602	G→A	20.1%	V22V (GTG→GTA)	yibG →	TPR‑like repeat protein
RA	3,767,000	G→T	86.4%	D454Y (GAC→TAC)	mtlA →	fused mannitol‑specific PTS enzymes: IIA components/IIB components/IIC components
RA	3,770,645	C→A	42.6%	intergenic (+258/‑114)	yibL → / → lldP	ribosome‑associated DUF2810 family protein/L‑lactate permease
RA	3,777,581	T→G	12.8%	A74A (GCA→GCC)	grxC ←	glutaredoxin 3
RA	3,777,924	C→A	58.8%	intergenic (‑122/+20)	grxC ← / ← yibN	glutaredoxin 3/putative rhodanese‑related sulfurtransferase
RA	3,778,219	C→A	11.6%	D53Y (GAC→TAC)	yibN ←	putative rhodanese‑related sulfurtransferase
RA	3,779,324	C→A	17.5%	F235L (TTC→TTA)	gpmM →	phosphoglycero mutase III, cofactor‑independent
RA	3,785,915	G→T	100%	intergenic (‑4/+271)	kbl ← / ← yibB	glycine C‑acetyltransferase/YibB family protein, function unknown
RA	3,793,653	G→T	5.3%	R225S (CGT→AGT)	waaY ←	lipopolysaccharide core biosynthesis protein
RA	3,796,691	T→A	37.9%	P269P (CCA→CCT)	waaB ←	UDP‑D‑galactose:(glucosyl)lipopolysaccharide‑1, 6‑D‑galactosyltransferase
RA	3,797,033	C→A	16.1%	T155T (ACG→ACT)	waaB ←	UDP‑D‑galactose:(glucosyl)lipopolysaccharide‑1, 6‑D‑galactosyltransferase
RA	3,797,907	G→T	35.8%	V190V (GTC→GTA)	waaS ←	lipopolysaccharide core biosynthesis protein
RA	3,798,296	G→A	13.7%	L61F (CTC→TTC)	waaS ←	lipopolysaccharide core biosynthesis protein
RA	3,799,108	C→A	18.0%	R68L (CGG→CTG)	waaP ←	kinase that phosphorylates core heptose of lipopolysaccharide
RA	3,799,227	G→T	17.9%	V28V (GTC→GTA)	waaP ←	kinase that phosphorylates core heptose of lipopolysaccharide
RA	3,809,236	G→T	43.3%	pseudogene (6/48 nt)	rph ←	ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH
RA	3,810,195	C→A	100%	R54S (CGT→AGT)	yicC →	UPF0701 family protein
RA	3,815,043	C→A	18.3%	R86S (CGT→AGT)	gmk →	guanylate kinase
RA	3,816,601	A→T	100%	H281L (CAC→CTC)	spoT →	bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase
RA	3,816,686	G→T	60.0%	S309S (TCG→TCT)	spoT →	bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase
RA	3,818,010	C→A	100%	H46N (CAT→AAT)	trmH →	tRNA mG18‑2'‑O‑methyltransferase, SAM‑dependent
RA	3,819,936	C→A	13.1%	T456K (ACG→AAG)	recG →	ATP‑dependent DNA helicase
RA	3,822,340	A→C	7.4%	Q12H (CAA→CAC)	xanP →	xanthine permease
RA	3,825,702	C→A	100%	K732N (AAG→AAT)	yicI ←	putative alpha‑glucosidase
RA	3,826,122	C→A	29.8%	M592I (ATG→ATT)	yicI ←	putative alpha‑glucosidase
RA	3,828,206	T→A	13.6%	S362C (AGT→TGT)	yicJ ←	putative transporter
RA	3,829,020	G→T	59.0%	F90L (TTC→TTA)	yicJ ←	putative transporter
RA	3,829,113	C→A	38.2%	A59A (GCG→GCT)	yicJ ←	putative transporter
RA	3,830,197	C→A	100%	intergenic (+281/‑116)	yicT → / → setC	pseudogene/putative arabinose efflux transporter
RA	3,830,311	G→T	100%	intergenic (+395/‑2)	yicT → / → setC	pseudogene/putative arabinose efflux transporter
RA	3,834,958	G→T	57.2%	Q48K (CAG→AAG)	nepI ←	putative transporter
RA	3,837,177	C→T	16.5%	intergenic (‑28/‑147)	yicO ← / → ade	putative adenine permease/cryptic adenine deaminase
RA	3,838,587	T→A	12.9%	S422T (TCC→ACC)	ade →	cryptic adenine deaminase
RA	3,839,034	C→A	54.6%	Q571K (CAG→AAG)	ade →	cryptic adenine deaminase
JC	3,841,409	+CAACCAG	10.3%	coding (576/1320 nt)	uhpC ←	membrane protein regulates uhpT expression
RA	3,846,307	C→A	14.6%	A14A (GCG→GCT)	ivbL ←	ilvB operon leader peptide
RA	3,848,953	T→A	6.5%	I7F (ATT→TTT)	yidF ←	putative Cys‑type oxidative YidJ‑maturating enzyme
RA	3,851,275	G→T	11.4%	H164N (CAT→AAT)	yidJ ←	sulfatase/phosphatase superfamily protein
RA	3,851,696	G→T	5.2%	S23R (AGC→AGA)	yidJ ←	sulfatase/phosphatase superfamily protein
RA	3,857,220	C→A	12.1%	intergenic (‑257/‑39)	glvC ← / → yidP	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/UTRA domain‑containing GntR family putative transcriptional regulator
RA	3,858,963	A→T	59.7%	V224E (GTA→GAA)	yidE ←	putative transporter
RA	3,860,159	C→A	100%	P33P (CCG→CCT)	ibpB ←	heat shock chaperone
RA	3,860,327	C→A	91.1%	intergenic (‑70/+42)	ibpB ← / ← ibpA	heat shock chaperone/heat shock chaperone
RA	3,860,653	C→A	91.6%	E44* (GAA→TAA)	ibpA ←	heat shock chaperone
RA	3,864,463	C→A	35.6%	D210Y (GAT→TAT)	dgoT ←	D‑galactonate transporter
RA	3,865,120	C→A	90.0%	intergenic (‑30/+90)	dgoT ← / ← dgoD	D‑galactonate transporter/galactonate dehydratase
RA	3,867,062	C→A	14.3%	R258L (CGC→CTC)	dgoK ←	2‑oxo‑3‑deoxygalactonate kinase
RA	3,874,397	C→A	13.8%	R62L (CGC→CTC)	recF ←	gap repair protein
RA	3,879,461	A→T	31.9%	K342N (AAA→AAT)	yidC →	membrane protein insertase
RA	3,879,501	T→A	14.9%	F356I (TTC→ATC)	yidC →	membrane protein insertase
RA	3,882,020	G→T	51.3%	intergenic (+151/‑70)	tnaC → / → tnaA	tryptophanase leader peptide/tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent
RA	3,885,881	G→T	5.6%	A303S (GCC→TCC)	mdtL →	multidrug efflux system protein
RA	3,888,563	G→T	31.2%	Q184H (CAG→CAT)	chrR →	chromate reductase, Class I, flavoprotein
RA	3,889,578	C→A	16.0%	R131L (CGC→CTC)	purP ←	adenine permease, high affinity; adenine:H+ symporter
RA	3,891,421	C→A	15.3%	H14N (CAT→AAT)	cbrC →	UPF0167 family protein
RA	3,896,944	C→A	15.3%	V40L (GTA→TTA)	bglB ←	cryptic phospho‑beta‑glucosidase B
RA	3,902,909	C→A	11.7%	V284F (GTT→TTT)	pstC ←	phosphate transporter subunit
RA	3,910,487	C→A	18.0%	A83A (GCG→GCT)	atpD ←	F1 sector of membrane‑bound ATP synthase, beta subunit
RA	3,910,894	C→A	100%	M244I (ATG→ATT)	atpG ←	F1 sector of membrane‑bound ATP synthase, gamma subunit
RA	3,911,056	C→A	12.8%	P190P (CCG→CCT)	atpG ←	F1 sector of membrane‑bound ATP synthase, gamma subunit
RA	3,916,052	C→A	5.1%	intergenic (‑252/+365)	atpI ← / ← rsmG	ATP synthase, membrane‑bound accessory factor/16S rRNA m(7)G527 methyltransferase, SAM‑dependent; glucose‑inhibited cell‑division protein
RA	3,916,830	C→A	100%	D71Y (GAT→TAT)	rsmG ←	16S rRNA m(7)G527 methyltransferase, SAM‑dependent; glucose‑inhibited cell‑division protein
RA	3,918,039	C→A	9.3%	D319Y (GAT→TAT)	mnmG ←	5‑methylaminomethyl‑2‑thiouridine modification at tRNA U34
RA	3,923,028	C→A	92.0%	D476Y (GAC→TAC)	ravA ←	hexameric AAA+ MoxR family ATPase, putative molecular chaperone
RA	3,923,775	G→T	9.0%	H227N (CAT→AAT)	ravA ←	hexameric AAA+ MoxR family ATPase, putative molecular chaperone
RA	3,925,420	A→T	31.2%	T249S (ACC→TCC)	kup →	potassium transporter
RA	3,926,618	G→T	30.1%	intergenic (+74/‑93)	kup → / → rbsD	potassium transporter/putative cytoplasmic sugar‑binding protein
RA	3,926,831	G→T	94.6%	D41Y (GAT→TAT)	rbsD →	putative cytoplasmic sugar‑binding protein
RA	3,927,972	G→T	91.5%	E279* (GAA→TAA)	rbsA →	fused D‑ribose transporter subunits of ABC superfamily: ATP‑binding components
RA	3,933,204	C→T	7.8%	D257N (GAT→AAT)	hsrA ←	putative multidrug or homocysteine efflux system
RA	3,933,680	G→T	11.2%	S98* (TCG→TAG)	hsrA ←	putative multidrug or homocysteine efflux system
RA	3,935,100	G→T	93.6%	intergenic (‑413/‑68)	yieP ← / → rrsC	putative transcriptional regulator/16S ribosomal RNA of rrnC operon
RA	3,940,333	T→A	10.6%	noncoding (17/76 nt)	trpT →	tRNA‑Trp
RA	3,945,503	A→T	16.8%	pseudogene (602/663 nt)	ilvG →	pseudogene, acetolactate synthase 2 large subunit, valine‑insensitive; acetolactate synthase II, large subunit, cryptic, interrupted
RA	3,945,552	G→T	6.3%	pseudogene (651/663 nt)	ilvG →	pseudogene, acetolactate synthase 2 large subunit, valine‑insensitive; acetolactate synthase II, large subunit, cryptic, interrupted
RA	3,948,854	G→T	10.5%	R55L (CGC→CTC)	ilvA →	L‑threonine dehydratase, biosynthetic; also known as threonine deaminase
RA	3,952,842	A→C	9.7%	intergenic (+37/+50)	ilvC → / ← ppiC	ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C)
RA	3,956,165	C→A	18.3%	E475D (GAG→GAT)	gpp ←	guanosine pentaphosphatase/exopolyphosphatase
RA	3,960,036	G→A	100%	R87H (CGC→CAC)	rho →	transcription termination factor
RA	3,966,854	C→A	100%	R325S (CGT→AGT)	rffG →	dTDP‑glucose 4,6‑dehydratase
RA	3,967,474	G→T	91.8%	A169A (GCG→GCT)	rffH →	glucose‑1‑phosphate thymidylyltransferase
RA	3,968,673	C→A	6.1%	T56T (ACC→ACA)	wecE →	TDP‑4‑oxo‑6‑deoxy‑D‑glucose transaminase
RA	3,968,711	A→T	6.4%	Q69L (CAG→CTG)	wecE →	TDP‑4‑oxo‑6‑deoxy‑D‑glucose transaminase
RA	3,969,710	G→T	100%	G25C (GGT→TGT)	wzxE →	O‑antigen translocase
RA	3,977,650	A→T	17.6%	intergenic (+97/+62)	aslB → / ← aslA	putative AslA‑specific sulfatase‑maturating enzyme/putative Ser‑type periplasmic non‑aryl sulfatase
RA	3,978,003	C→A	18.8%	E455D (GAG→GAT)	aslA ←	putative Ser‑type periplasmic non‑aryl sulfatase
RA	3,978,810	G→T	16.7%	I186I (ATC→ATA)	aslA ←	putative Ser‑type periplasmic non‑aryl sulfatase
RA	3,984,342	G→T	57.8%	intergenic (‑216/‑171)	hemC ← / → cyaA	hydroxymethylbilane synthase/adenylate cyclase
RA	3,987,104	G→T	12.3%	R106S (CGC→AGC)	cyaY ←	iron‑dependent inhibitor of iron‑sulfur cluster formation; frataxin; iron‑binding and oxidizing protein
RA	3,988,075	T→A	100%	V65E (GTG→GAG)	yifL →	putative lipoprotein
RA	3,990,572	C→A	13.4%	I10I (ATC→ATA)	yigB →	5‑amino‑6‑(5‑phospho‑D‑ribitylamino)uracil phosphatase; pyrimidine phosphatase; riboflavin synthesis
RA	3,994,076	A→T	100%	L114* (TTA→TAA)	yigE ←	DUF2233 family protein
RA	3,994,247	A→T	100%	V57E (GTG→GAG)	yigE ←	DUF2233 family protein
RA	3,994,758	G→T	59.1%	intergenic (‑342/‑28)	yigE ← / → corA	DUF2233 family protein/magnesium/nickel/cobalt transporter
RA	3,996,070	G→T	14.7%	F30L (TTC→TTA)	yigF ←	putative inner membrane protein
RA	3,997,144	G→T	22.7%	A132E (GCG→GAG)	rarD ←	putative chloramphenical resistance permease
RA	3,999,692	G→T	12.1%	D157Y (GAT→TAT)	recQ →	ATP‑dependent DNA helicase
RA	4,001,030	G→T	33.5%	V603F (GTT→TTT)	recQ →	ATP‑dependent DNA helicase
RA	4,009,705	G→A	93.3%	intergenic (‑176/‑86)	ysgA ← / → udp	putative carboxymethylenebutenolidase/uridine phosphorylase
RA	4,011,961	G→T	15.2%	A423A (GCG→GCT)	rmuC →	DNA recombination protein
RA	4,023,757	T→A	60.6%	K192I (AAA→ATA)	fadB ←	fused 3‑hydroxybutyryl‑CoA epimerase/delta(3)‑cis‑delta(2)‑trans‑enoyl‑CoA isomerase/enoyl‑CoA hydratase/3‑hydroxyacyl‑CoA dehydrogenase
RA	4,024,233	A→C	51.1%	T33T (ACT→ACG)	fadB ←	fused 3‑hydroxybutyryl‑CoA epimerase/delta(3)‑cis‑delta(2)‑trans‑enoyl‑CoA isomerase/enoyl‑CoA hydratase/3‑hydroxyacyl‑CoA dehydrogenase
RA	4,024,827	G→T	91.6%	D103Y (GAT→TAT)	pepQ →	proline dipeptidase
RA	4,035,421	G→T	92.4%	intergenic (‑62/‑8)	mobA ← / → yihD	molybdopterin‑guanine dinucleotide synthase/DUF1040 protein YihD
RA	4,039,399	G→T	43.5%	F188L (TTC→TTA)	yihG ←	inner membrane protein, inner membrane acyltransferase
RA	4,041,798	C→A	14.2%	L491L (CTC→CTA)	polA →	fused DNA polymerase I 5'‑>3' polymerase/3'‑>5' exonuclease/5'‑>3' exonuclease
RA	4,046,172	A→T	86.6%	K256N (AAA→AAT)	hemN →	coproporphyrinogen III oxidase, SAM and NAD(P)H dependent, oxygen‑independent
RA	4,050,102	G→T	12.8%	A431A (GCC→GCA)	glnA ←	glutamine synthetase
RA	4,054,222	T→A	55.8%	V139D (GTT→GAT)	yihL →	putative DNA‑binding transcriptional regulator
RA	4,056,018	T→A	100%	F138I (TTC→ATC)	yihN →	MFS transporter family protein
RA	4,056,425	G→T	36.1%	P273P (CCG→CCT)	yihN →	MFS transporter family protein
RA	4,062,424	G→T	100%	I71I (ATC→ATA)	yihQ ←	alpha‑glucosidase
RA	4,066,133	T→G	100%	S267R (AGC→CGC)	yihU ←	gamma‑hydroxybutyrate dehydrogenase, NADH‑dependent
RA	4,068,208	C→A	100%	G60G (GGC→GGA)	yihW →	DeoR family putative transcriptional regulator
RA	4,077,665	G→T	20.2%	V506V (GTC→GTA)	fdoG ←	formate dehydrogenase‑O, large subunit
RA	4,078,536	T→A	25.9%	H216L (CAC→CTC)	fdoG ←	formate dehydrogenase‑O, large subunit
RA	4,078,761	C→A	55.0%	R141L (CGC→CTC)	fdoG ←	formate dehydrogenase‑O, large subunit
RA	4,086,311	A→T	29.9%	intergenic (‑128/+173)	frvA ← / ← rhaM	putative enzyme IIA component of PTS/L‑rhamnose mutarotase
RA	4,087,476	A→T	8.9%	intergenic (‑126/‑188)	rhaD ← / → rhaS	pseudogene, truncated, rhamnulose‑phosphate aldolase/transcriptional activator of rhaBAD and rhaT
RA	4,087,754	C→A	16.5%	H31N (CAT→AAT)	rhaS →	transcriptional activator of rhaBAD and rhaT
RA	4,089,371	A→T	37.0%	E266D (GAA→GAT)	rhaR →	transcriptional activator of rhaSR
RA	4,092,998	G→T	39.9%	A83A (GCG→GCT)	yiiM →	6‑N‑hydroxylaminopurine resistance protein
RA	4,094,362	C→A	100%	W181L (TGG→TTG)	cpxA ←	sensory histidine kinase in two‑component regulatory system with CpxR
RA	4,095,124	C→T	20.1%	G159S (GGT→AGT)	cpxR ←	response regulator in two‑component regulatory system with CpxA
RA	4,097,282	C→A	15.9%	R296R (CGG→AGG)	fieF →	ferrous iron and zinc transporter
RA	4,097,822	G→T	100%	E115* (GAA→TAA)	pfkA →	6‑phosphofructokinase I
RA	4,105,186	C→A	6.2%	D108Y (GAT→TAT)	glpX ←	fructose 1,6‑bisphosphatase II
RA	4,122,248	A→T	90.7%	intergenic (+53/‑296)	metL → / → metF	Bifunctional aspartokinase/homoserine dehydrogenase 2/5,10‑methylenetetrahydrofolate reductase
RA	4,122,781	C→A	16.5%	R80S (CGC→AGC)	metF →	5,10‑methylenetetrahydrofolate reductase
RA	4,127,022	T→G	100%	E188D (GAA→GAC)	yijF ←	DUF1287 family protein
RA	4,128,613	G→T	15.5%	I117I (ATC→ATA)	gldA ←	glycerol dehydrogenase, NAD+ dependent; 1,2‑propanediol:NAD+ oxidoreductase
RA	4,131,163	C→A	5.4%	T329T (ACG→ACT)	frwA ←	putative PTS enzyme, Hpr component/enzyme I component/enzyme IIA component
RA	4,133,935	A→C	43.6%	I5L (ATC→CTC)	pflD →	putative glycine radical domain‑containing pyruvate formate‑lyase
RA	4,134,111	G→T	14.7%	L63L (CTG→CTT)	pflD →	putative glycine radical domain‑containing pyruvate formate‑lyase
RA	4,141,881	G→T	41.5%	R382R (CGC→CGA)	ppc ←	phosphoenolpyruvate carboxylase
RA	4,143,375	A→G	6.4%	intergenic (‑349/+249)	ppc ← / ← argE	phosphoenolpyruvate carboxylase/acetylornithine deacetylase
RA	4,144,163	C→A	22.1%	A205S (GCT→TCT)	argE ←	acetylornithine deacetylase
RA	4,145,195	G→T	13.2%	A89A (GCG→GCT)	argC →	N‑acetyl‑gamma‑glutamylphosphate reductase, NAD(P)‑binding
RA	4,150,197	G→T	10.6%	H174Q (CAC→CAA)	sthA ←	pyridine nucleotide transhydrogenase, soluble
RA	4,167,995	G→T	29.5%	D109Y (GAT→TAT)	nusG →	transcription termination factor
RA	4,168,773	A→T	5.3%	A133A (GCA→GCT)	rplK →	50S ribosomal subunit protein L11
RA	4,172,414	C→A	33.2%	I414I (ATC→ATA)	rpoB →	RNA polymerase, beta subunit
RA	4,173,059	C→A	19.6%	F629L (TTC→TTA)	rpoB →	RNA polymerase, beta subunit
RA	4,173,145	A→T	92.8%	Q658L (CAG→CTG)	rpoB →	RNA polymerase, beta subunit
RA	4,176,417	C→A	37.8%	F380L (TTC→TTA)	rpoC →	RNA polymerase, beta prime subunit
RA	4,176,823	G→T	100%	D516Y (GAC→TAC)	rpoC →	RNA polymerase, beta prime subunit
RA	4,179,520	C→A	40.4%	intergenic (+19/‑194)	rpoC → / → yjaZ	RNA polymerase, beta prime subunit/stationary phase growth adaptation protein
RA	4,183,071	G→T	16.7%	P145Q (CCG→CAG)	thiF ←	adenylyltransferase, modifies ThiS C‑terminus
RA	4,186,367	G→T	15.5%	Q124K (CAA→AAA)	rsd ←	stationary phase protein, binds sigma 70 RNA polymerase subunit
RA	4,189,766	C→A	52.7%	T112K (ACG→AAG)	yjaG →	DUF416 domain protein
RA	4,207,552	G→T	94.2%	M172I (ATG→ATT)	aceA →	isocitrate lyase
RA	4,208,942	C→A	52.8%	A140E (GCG→GAG)	aceK →	isocitrate dehydrogenase kinase/phosphatase
RA	4,208,975	C→A	23.0%	S151Y (TCT→TAT)	aceK →	isocitrate dehydrogenase kinase/phosphatase
RA	4,210,835	G→C	15.7%	C527W (TGC→TGG)	arpA ←	ankyrin repeat protein
RA	4,211,576	G→T	100%	S280R (AGC→AGA)	arpA ←	ankyrin repeat protein
RA	4,211,803	G→A	100%	P205S (CCT→TCT)	arpA ←	ankyrin repeat protein
RA	4,214,563	A→T	87.9%	T270S (ACC→TCC)	metH →	homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent
RA	4,215,252	G→T	14.2%	E499D (GAG→GAT)	metH →	homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent
RA	4,217,818	G→T	60.3%	V54F (GTT→TTT)	yjbB →	putative Na+/Pi‑cotransporter
RA	4,219,550	C→A	16.2%	R174L (CGT→CTT)	pepE ←	(alpha)‑aspartyl dipeptidase
RA	4,222,149	G→T	20.1%	S338* (TCG→TAG)	lysC ←	lysine‑sensitive aspartokinase 3
RA	4,230,913	A→T	100%	W424R (TGG→AGG)	xylE ←	D‑xylose transporter
RA	4,235,869	G→T	90.1%	A160E (GCG→GAG)	malE ←	maltose transporter subunit
RA	4,242,509	C→T	90.3%	L26F (CTC→TTC)	ubiC →	chorismate‑‑pyruvate lyase
RA	4,245,537	G→T	5.8%	N286K (AAC→AAA)	plsB ←	glycerol‑3‑phosphate O‑acyltransferase
RA	4,247,427	G→T	16.2%	D129Y (GAC→TAC)	lexA →	transcriptional repressor of SOS regulon
RA	4,256,589	G→T	57.7%	E294* (GAA→TAA)	alr →	alanine racemase, biosynthetic, PLP‑binding
RA	4,257,593	C→T	15.3%	N184N (AAC→AAT)	tyrB →	tyrosine aminotransferase, tyrosine‑repressible, PLP‑dependent
RA	4,258,418	G→A	57.4%	intergenic (+183/+319)	tyrB → / ← yjbS	tyrosine aminotransferase, tyrosine‑repressible, PLP‑dependent/uncharacterized protein
RA	4,259,065	C→A	52.0%	intergenic (‑125/‑277)	yjbS ← / → aphA	uncharacterized protein/acid phosphatase/phosphotransferase, class B, non‑specific
RA	4,261,049	G→T	31.7%	V917V (GTC→GTA)	uvrA ←	ATPase and DNA damage recognition protein of nucleotide excision repair excinuclease UvrABC
RA	4,265,064	C→A	100%	intergenic (‑95/‑335)	yjcB ← / → yjcC	putative inner membrane protein/putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	4,265,415	G→T	8.9%	R6L (CGA→CTA)	yjcC →	putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	4,266,665	G→T	13.7%	D423Y (GAT→TAT)	yjcC →	putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	4,270,316	G→T	66.2%	E137* (GAA→TAA)	yjcE →	putative cation/proton antiporter
RA	4,272,983	A→C	29.0%	N7K (AAT→AAG)	yjcF ←	pentapeptide repeats protein
RA	4,273,297	A→T	5.0%	W512R (TGG→AGG)	actP ←	acetate transporter
RA	4,274,748	C→A	58.5%	R28L (CGC→CTC)	actP ←	acetate transporter
RA	4,274,926	A→C	100%	I72M (ATT→ATG)	yjcH ←	DUF485 family inner membrane protein
RA	4,275,142	C→A	94.3%	intergenic (‑1/+199)	yjcH ← / ← acs	DUF485 family inner membrane protein/acetyl‑CoA synthetase
RA	4,276,940	G→T	56.2%	F120L (TTC→TTA)	acs ←	acetyl‑CoA synthetase
RA	4,277,386	G→T	23.5%	intergenic (‑87/‑306)	acs ← / → nrfA	acetyl‑CoA synthetase/nitrite reductase, formate‑dependent, cytochrome
RA	4,278,846	C→A	5.8%	I385I (ATC→ATA)	nrfA →	nitrite reductase, formate‑dependent, cytochrome
RA	4,281,581	G→T	60.9%	D48Y (GAT→TAT)	nrfE →	heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfE
RA	4,285,213	G→T	12.7%	D269Y (GAT→TAT)	gltP →	glutamate/aspartate:proton symporter
RA	4,286,311	C→A	14.8%	S211I (AGC→ATC)	yjcO ←	Sel1 family TPR‑like repeat protein
RA	4,290,080	G→T	100%	I256I (ATC→ATA)	mdtP ←	outer membrane factor of efflux pump
RA	4,294,402	C→T	14.6%	intergenic (‑182/+27)	ytcA ← / ← yjcS	putative inner membrane DUF1656 family protein; efflux pump associated/metallo‑beta‑lactamase superfamily protein
RA	4,297,485	G→C	92.2%	G44G (GGC→GGG)	alsK ←	D‑allose kinase
RA	4,297,846	C→A	100%	M150I (ATG→ATT)	alsE ←	allulose‑6‑phosphate 3‑epimerase
RA	4,301,569	G→T	16.9%	V97V (GTC→GTA)	alsB ←	D‑allose transporter subunit
RA	4,303,358	G→T	11.8%	L64F (TTG→TTT)	rpiB →	ribose 5‑phosphate isomerase B/allose 6‑phosphate isomerase
RA	4,303,614	T→A	100%	*150R (TGA→AGA)	rpiB →	ribose 5‑phosphate isomerase B/allose 6‑phosphate isomerase
RA	4,316,794	G→A	18.2%	intergenic (‑243/‑158)	yjdM ← / → crfC	zinc‑ribbon family protein/clamp‑binding sister replication fork colocalization protein, dynamin‑related
RA	4,317,243	C→A	54.5%	R98S (CGT→AGT)	crfC →	clamp‑binding sister replication fork colocalization protein, dynamin‑related
RA	4,317,249	C→A	40.1%	R100S (CGC→AGC)	crfC →	clamp‑binding sister replication fork colocalization protein, dynamin‑related
RA	4,330,426	Δ1 bp	100%	intergenic (‑88/+111)	adiA ← / ← melR	arginine decarboxylase/melibiose operon transcriptional regulator; autoregulator
RA	4,333,400	G→T	18.5%	R72L (CGA→CTA)	melB →	melibiose:sodium symporter
RA	4,335,003	A→T	13.5%	Y125N (TAC→AAC)	yjdF ←	DUF2238 family inner membrane protein
RA	4,335,195	G→T	5.8%	L61I (CTC→ATC)	yjdF ←	DUF2238 family inner membrane protein
RA	4,336,196	G→T	14.0%	V316V (GTC→GTA)	fumB ←	anaerobic class I fumarate hydratase (fumarase B)
RA	4,336,681	A→T	7.1%	Y155N (TAC→AAC)	fumB ←	anaerobic class I fumarate hydratase (fumarase B)
RA	4,337,717	G→T	13.3%	A282E (GCG→GAG)	dcuB ←	C4‑dicarboxylate transporter, anaerobic; DcuS co‑sensor
RA	4,341,023	A→T	100%	Y153N (TAC→AAC)	dcuS ←	sensory histidine kinase in two‑component regulatory system with DcuR, regulator of anaerobic fumarate respiration
RA	4,346,015	G→T	27.0%	L72I (CTC→ATC)	dtpC ←	dipeptide and tripeptide permease
RA	4,346,500	G→T	12.3%	N645K (AAC→AAA)	cadA ←	lysine decarboxylase, acid‑inducible
RA	4,354,610	A→T	5.1%	W84R (TGG→AGG)	dsbD ←	fused thiol:disulfide interchange protein: activator of DsbC/conserved protein
RA	4,355,939	C→A	19.9%	E218* (GAA→TAA)	dcuA ←	C4‑dicarboxylate antiporter
RA	4,357,095	A→C	16.5%	V350V (GTT→GTG)	aspA ←	aspartate ammonia‑lyase
RA	4,358,920	G→T	86.2%	R147L (CGC→CTC)	fxsA →	suppressor of F exclusion of phage T7
RA	4,358,943	G→T	36.8%	D155Y (GAT→TAT)	fxsA →	suppressor of F exclusion of phage T7
RA	4,366,263	T→G	41.5%	intergenic (+4/‑107)	ecnA → / → ecnB	entericidin A membrane lipoprotein, antidote entericidin B/entericidin B membrane lipoprotein
RA	4,371,101	A→T	39.4%	V345V (GTT→GTA)	frdA ←	fumarate reductase (anaerobic) catalytic and NAD/flavoprotein subunit
RA	4,372,891	A→T	6.0%	A144A (GCA→GCT)	epmA →	Elongation Factor P Lys34 lysyltransferase
RA	4,373,522	C→T	60.7%	intergenic (+85/‑134)	epmA → / → yjeM	Elongation Factor P Lys34 lysyltransferase/putative transporter
RA	4,373,880	G→T	14.9%	M75I (ATG→ATT)	yjeM →	putative transporter
RA	4,376,178	C→A	92.6%	E1004* (GAA→TAA)	mscM ←	mechanosensitive channel protein, miniconductance
RA	4,378,778	G→T	92.2%	S137* (TCG→TAG)	mscM ←	mechanosensitive channel protein, miniconductance
RA	4,381,462	G→A	19.6%	E14E (GAG→GAA)	orn →	oligoribonuclease
RA	4,388,902	G→T	100%	A558A (GCG→GCT)	mutL →	methyl‑directed mismatch repair protein
RA	4,394,875	G→T	91.6%	A124A (GCG→GCT)	purA →	adenylosuccinate synthetase
RA	4,396,598	A→T	100%	E43V (GAA→GTA)	rnr →	exoribonuclease R, RNase R
RA	4,399,304	C→A	12.1%	I71I (ATC→ATA)	rlmB →	23S rRNA mG2251 2'‑O‑ribose methyltransferase, SAM‑dependent
RA	4,401,343	A→T	55.8%	S75S (TCA→TCT)	yjfK →	DUF2491 family protein
RA	4,402,105	A→T	11.5%	I104F (ATT→TTT)	yjfL →	UPF0719 family inner membrane protein
RA	4,402,850	G→T	100%	L2L (CTG→CTT)	yjfC →	ATP‑Grasp family ATPase
RA	4,405,735	G→T	7.4%	intergenic (+18/+99)	aidB → / ← yjfN	DNA alkylation damage repair protein; flavin‑containing DNA binding protein, weak isovaleryl CoA dehydrogenase/DUF1471 family periplasmic protein
RA	4,407,017	C→T	60.1%	I83I (ATC→ATT)	yjfP →	acyl CoA esterase
RA	4,408,612	C→A	10.3%	V277V (GTG→GTT)	ulaG ←	L‑ascorbate 6‑phosphate lactonase
RA	4,413,195	C→A	6.2%	P178Q (CCG→CAG)	ulaE →	L‑xylulose 5‑phosphate 3‑epimerase
RA	4,413,724	C→A	37.8%	R70S (CGC→AGC)	ulaF →	L‑ribulose 5‑phosphate 4‑epimerase
RA	4,417,551	A→C	100%	pseudogene (41/402 nt)	ytfA →	pseudogene, related to transcriptional regulators
RA	4,419,557	C→T	12.7%	intergenic (+185/‑124)	fklB → / → cycA	FKBP‑type peptidyl‑prolyl cis‑trans isomerase (rotamase)/D‑alanine/D‑serine/glycine transporter
RA	4,421,791	G→T	9.6%	R4S (CGC→AGC)	ytfE ←	iron‑sulfur cluster repair protein RIC
RA	4,427,647	G→A	100%	D42N (GAT→AAT)	ytfI →	uncharacterized protein
RA	4,428,092	G→T	88.8%	G190V (GGA→GTA)	ytfI →	uncharacterized protein
RA	4,442,839	C→A	15.4%	A151E (GCG→GAG)	ytfT →	inner membrane putative ABC superfamily sugar transporter permease
RA	4,449,002	C→A	14.6%	I409I (ATC→ATA)	pmbA →	putative antibiotic peptide MccB17 maturation peptidase
RA	4,458,254	T→A	100%	V271V (GTT→GTA)	mgtA →	magnesium transporter
RA	4,458,609	G→T	100%	D390Y (GAT→TAT)	mgtA →	magnesium transporter
RA	4,461,317	G→T	60.8%	A299E (GCG→GAG)	pyrB ←	aspartate carbamoyltransferase, catalytic subunit
RA	4,465,624	C→T	6.1%	S124F (TCC→TTC)	yjgL →	uncharacterized protein
RA	4,465,836	C→T	12.1%	L195L (CTA→TTA)	yjgL →	uncharacterized protein
RA	4,468,165	A→G	100%	intergenic (‑37/‑125)	argI ← / → rraB	ornithine carbamoyltransferase 1/protein inhibitor of RNase E
RA	4,469,532	A→G	7.7%	intergenic (‑178/‑15)	yjgM ← / → yjgN	putative acetyltransferase/DUF898 family inner membrane protein
RA	4,469,550	G→A	100%	A2T (GCT→ACT)	yjgN →	DUF898 family inner membrane protein
RA	4,470,017	G→A	100%	M157I (ATG→ATA)	yjgN →	DUF898 family inner membrane protein
RA	4,470,873	G→T	84.1%	R928S (CGT→AGT)	valS ←	valyl‑tRNA synthetase
RA	4,474,993	G→T	19.1%	S259* (TCG→TAG)	pepA ←	multifunctional aminopeptidase A: a cyteinylglycinase, transcription regulator and site‑specific recombination factor
RA	4,475,510	G→T	10.6%	R87S (CGT→AGT)	pepA ←	multifunctional aminopeptidase A: a cyteinylglycinase, transcription regulator and site‑specific recombination factor
RA	4,481,249	A→T	7.7%	V365E (GTG→GAG)	idnT ←	L‑idonate and D‑gluconate transporter
RA	4,481,791	C→A	12.6%	P184P (CCG→CCT)	idnT ←	L‑idonate and D‑gluconate transporter
RA	4,482,573	A→T	10.2%	L199Q (CTG→CAG)	idnO ←	5‑keto‑D‑gluconate‑5‑reductase
RA	4,494,721	G→A	91.0%	A283T (GCC→ACC)	yjhB →	putative transporter
RA	4,494,928	G→T	12.0%	A352S (GCA→TCA)	yjhB →	putative transporter
RA	4,495,349	G→T	12.1%	K82N (AAG→AAT)	yjhC →	putative oxidoreductase
RA	4,495,560	A→T	6.8%	N153Y (AAC→TAC)	yjhC →	putative oxidoreductase
RA	4,510,255	G→T	7.5%	intergenic (‑114/+233)	yjhU ← / ← yjhF	putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter
RA	4,512,693	T→A	100%	K407* (AAG→TAG)	yjhG ←	putative dehydratase
RA	4,514,180	A→T	10.1%	A216A (GCT→GCA)	yjhH ←	putative lyase/synthase
RA	4,516,177	C→A	13.1%	D177Y (GAT→TAT)	sgcR ←	putative DNA‑binding transcriptional regulator
RA	4,519,217	A→T	57.1%	F282I (TTC→ATC)	sgcC ←	putative PTS system EIIC permease component
RA	4,522,074	T→A	17.3%	pseudogene (54/261 nt)	yjhY ←	pseudogene, zinc finger protein family
RA	4,523,001	T→A	92.4%	intergenic (‑1/+55)	yjhP ← / ← yjhQ	putative methyltransferase/putative acetyltransferase
RA	4,525,234	G→A	100%	pseudogene (415/1029 nt)	yjhR →	pseudogene, helicase family; putative frameshift suppressor
RA	4,525,278	G→T	15.0%	pseudogene (459/1029 nt)	yjhR →	pseudogene, helicase family; putative frameshift suppressor
RA	4,530,308	G→T	31.6%	intergenic (‑990/‑466)	nanC ← / → fimB	N‑acetylnuraminic acid outer membrane channel protein/tyrosine recombinase/inversion of on/off regulator of fimA
RA	4,531,143	A→T	100%	I124F (ATT→TTT)	fimB →	tyrosine recombinase/inversion of on/off regulator of fimA
RA	4,531,461	G→A	22.2%	intergenic (+85/‑393)	fimB → / → fimE	tyrosine recombinase/inversion of on/off regulator of fimA/tyrosine recombinase/inversion of on/off regulator of fimA
RA	4,535,507	C→A	18.5%	R199R (CGG→AGG)	fimD →	fimbrial usher outer membrane porin protein; FimCD chaperone‑usher
RA	4,535,723	G→T	15.3%	D271Y (GAT→TAT)	fimD →	fimbrial usher outer membrane porin protein; FimCD chaperone‑usher
RA	4,541,449	A→T	87.6%	intergenic (‑336/‑4)	gntP ← / → uxuA	fructuronate transporter/mannonate hydrolase
RA	4,546,426	G→T	38.2%	intergenic (‑289/‑384)	yjiC ← / → iraD	uncharacterized protein/RpoS stabilzer after DNA damage, anti‑RssB factor
RA	4,547,687	G→T	37.8%	V140V (GTC→GTA)	hypT ←	hypochlorite‑responsive transcription factor
RA	4,555,156	G→T	100%	A171E (GCG→GAG)	yjiM ←	putative 2‑hydroxyglutaryl‑CoA dehydratase
RA	4,555,620	T→G	12.1%	E16D (GAA→GAC)	yjiM ←	putative 2‑hydroxyglutaryl‑CoA dehydratase
RA	4,559,831	G→T	17.3%	intergenic (+96/+148)	yjiP → / ← yjiR	pseudogene, transposase_31 family protein/putative DNA‑binding transcriptional regulator/putative aminotransferase
RA	4,562,043	C→A	100%	intergenic (+311/‑188)	yjiS → / → yjiT	DUF1127 family protein/pseudogene
RA	4,564,939	G→T	20.5%	pseudogene (1204/2937 nt)	yjiV →	pseudogene; conserved hypothetical protein
RA	4,565,742	C→A	5.4%	pseudogene (2007/2937 nt)	yjiV →	pseudogene; conserved hypothetical protein
RA	4,567,114	G→A	10.4%	S221F (TCT→TTT)	mcrC ←	5‑methylcytosine‑specific restriction enzyme McrBC, subunit McrC
RA	4,567,552	C→A	10.6%	R75L (CGA→CTA)	mcrC ←	5‑methylcytosine‑specific restriction enzyme McrBC, subunit McrC
RA	4,571,233	G→A	92.3%	S16F (TCT→TTT)	hsdS ←	specificity determinant for hsdM and hsdR
RA	4,572,227	G→T	55.9%	I213I (ATC→ATA)	hsdM ←	DNA methyltransferase M
RA	4,572,800	A→T	15.0%	V22V (GTT→GTA)	hsdM ←	DNA methyltransferase M
RA	4,575,640	C→A	11.2%	pseudogene (993/3567 nt)	hsdR ←	pseudogene, premature stop codon, host restriction; endonuclease R
RA	4,577,095	G→T	37.1%	V110V (GTG→GTT)	mrr →	methylated adenine and cytosine restriction protein
RA	4,580,729	A→T	31.6%	L123Q (CTG→CAG)	yjiY ←	putative transporter
RA	4,584,381	G→T	94.3%	I53I (ATC→ATA)	yjjL ←	L‑galactonate transporter
RA	4,584,756	A→T	92.9%	*305K (TAA→AAA)	yjjM ←	yjjMN operon transcriptional activator
RA	4,585,338	A→T	100%	S111T (TCT→ACT)	yjjM ←	yjjMN operon transcriptional activator
RA	4,586,074	G→T	41.4%	V90F (GTT→TTT)	yjjN →	L‑galactonate oxidoreductase
RA	4,586,139	C→A	18.3%	V111V (GTC→GTA)	yjjN →	L‑galactonate oxidoreductase
RA	4,586,861	G→T	51.5%	intergenic (+32/+106)	yjjN → / ← opgB	L‑galactonate oxidoreductase/phosphoglycerol transferases I and II
RA	4,591,139	C→A	90.6%	D66Y (GAT→TAT)	dnaT ←	DNA biosynthesis protein (primosomal protein I)
RA	4,593,513	T→G	14.8%	Y74D (TAT→GAT)	yjjQ →	putative transcriptional regulator
RA	4,596,008	C→A	22.7%	intergenic (‑26/+9)	leuV ← / ← leuP	tRNA‑Leu/tRNA‑Leu
RA	4,596,108	T→A	5.6%	intergenic (‑5/+24)	leuP ← / ← leuQ	tRNA‑Leu/tRNA‑Leu
RA	4,596,243	T→A	86.6%	intergenic (‑25/+243)	leuQ ← / ← rsmC	tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase, SAM‑dependent
RA	4,602,307	T→A	19.1%	L27Q (CTG→CAG)	yjjU →	putative patatin‑like family phospholipase
RA	4,612,781	C→A	11.9%	A399E (GCG→GAG)	yjjJ →	putative protein kinase
RA	4,616,323	G→T	21.5%	E199* (GAA→TAA)	radA →	DNA repair protein
RA	4,617,009	G→T	12.6%	A427A (GCG→GCT)	radA →	DNA repair protein
RA	4,617,366	G→T	13.2%	G79* (GGA→TGA)	nadR →	trifunctional protein: nicotinamide mononucleotide adenylyltransferase, ribosylnicotinamide kinase, transcriptional repressor
RA	4,617,708	G→T	6.2%	E193* (GAG→TAG)	nadR →	trifunctional protein: nicotinamide mononucleotide adenylyltransferase, ribosylnicotinamide kinase, transcriptional repressor
RA	4,618,017	G→T	5.7%	D296Y (GAT→TAT)	nadR →	trifunctional protein: nicotinamide mononucleotide adenylyltransferase, ribosylnicotinamide kinase, transcriptional repressor
RA	4,624,764	C→A	35.8%	E122* (GAA→TAA)	rob ←	right oriC‑binding transcriptional activator, AraC family
RA	4,625,288	T→C	94.8%	intergenic (‑161/‑50)	rob ← / → creA	right oriC‑binding transcriptional activator, AraC family/putative periplasmic protein

Unassigned missing coverage evidence
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	CP009273	373844	375108	1265	187 [182]	[182] 186	frmA–[frmR]	frmA,[frmR]
*	*	÷	CP009273	4100592	4101525	934	185 [182]	[179] 187	[cdh]–tpiA	[cdh],tpiA

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	360104 =	212 (0.800)	228 (0.860)	128/278	NT	51.8%	intergenic (‑38/+557)	lacZ/lacI	pseudogene, truncated/DNA‑binding transcriptional repressor
	?	CP009273	= 360286	NA (NA)					intergenic (‑220/+375)	lacZ/lacI	pseudogene, truncated/DNA‑binding transcriptional repressor
*	?	CP009273	= 360278	NA (NA)	6406 (25.550) +TTAATTAA	195/262	NT	95.9%	intergenic (‑212/+383)	lacZ/lacI	pseudogene, truncated/DNA‑binding transcriptional repressor
	?	CP009273	= 361823	288 (1.080)					coding (831/834 nt)	mhpR	mhp operon transcriptional activator
*	?	CP009273	360652 =	274 (1.030)	6204 (34.960) +46 bp	186/186	NT	97.4%	intergenic (‑586/+9)	lacZ/lacI	pseudogene, truncated/DNA‑binding transcriptional repressor
	?	CP009273	= 1317577	220 (0.830)					coding (101/882 nt)	yciV	PHP domain protein
*	?	CP009273	376716 =	NA (NA)	283 (1.060)	136/278	NT	99.3%	intergenic (‑1/‑91)	yaiX/insC1	pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase/IS2 repressor TnpA
	?	CP009273	566411 =	2 (0.010)					coding (63/552 nt)	ybcL	inactive polymorphonuclear leukocyte migration suppressor; DLP12 prophage; secreted protein, UPF0098 family
*	?	CP009273	= 378046	NA (NA)	258 (0.970)	141/278	NT	99.2%	intergenic (+11/+1)	insD1/yaiX	IS2 transposase TnpB/pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase
	?	CP009273	= 566415	2 (0.010)					coding (67/552 nt)	ybcL	inactive polymorphonuclear leukocyte migration suppressor; DLP12 prophage; secreted protein, UPF0098 family
*	?	CP009273	776825 =	144 (0.540)	26 (0.100) +G	12/276	NT	13.0%	noncoding (1/76 nt)	lysZ	tRNA‑Lys
	?	CP009273	= 2514488	205 (0.770)					noncoding (216/1345 nt)	IS186	repeat region
*	?	CP009273	= 776902	160 (0.600)	9 (0.040)	6/238	NT	5.3%	intergenic (+2/‑131)	lysZ/lysQ	tRNA‑Lys/tRNA‑Lys
	?	CP009273	777267 =	186 (0.820)					intergenic (+159/‑274)	lysQ/nadA	tRNA‑Lys/quinolinate synthase, subunit A
*	?	CP009273	1089701 =	NA (NA)	6 (0.020)	5/278	NT	23.1%	noncoding (1258/1258 nt)	IS3	repeat region
	?	CP009273	= 1194571	20 (0.080)					coding (421/894 nt)	lit	e14 prophage; cell death peptidase, inhibitor of T4 late gene expression
*	?	CP009273	1203246 =	8 (0.030)	11 (0.050)	8/246	NT	52.3%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	CP009273	1205075 =	13 (0.060)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	CP009273	= 1203261	7 (0.030)	13 (0.060)	7/246	NT	57.5%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	CP009273	= 1205058	13 (0.060)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	CP009273	1635219 =	5 (0.020)	241 (0.920)	124/274	NT	98.0%	intergenic (‑377/+377)	essQ/cspB	Qin prophage; putative S lysis protein/Qin prophage; cold shock protein
	?	CP009273	= 2063752	NA (NA)					noncoding (1/1331 nt)	IS2	repeat region
*	?	CP009273	= 1635223	5 (0.020)	237 (0.890)	131/278	NT	97.9%	intergenic (‑381/+373)	essQ/cspB	Qin prophage; putative S lysis protein/Qin prophage; cold shock protein
	?	CP009273	= 1645805	NA (NA)					intergenic (+11/‑3)	insD1/intQ	IS2 transposase TnpB;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related/pseudogene, Qin prophage; phage integrase family;Phage or Prophage Related
*	?	CP009273	= 3180783	NA (NA)	265 (1.010)	129/274	NT	92.4%	pseudogene (4/2445 nt)	yqiG	pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein
	?	CP009273	= 3833569	22 (0.080)					intergenic (‑216/‑6)	nlpA/yicS	cytoplasmic membrane lipoprotein‑28/putative periplasmic protein
*	?	CP009273	= 3180785	NA (NA)	107 (0.400)	72/278	NT	43.5%	pseudogene (6/2445 nt)	yqiG	pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein
	?	CP009273	= 4096069	139 (0.520)					coding (322/501 nt)	cpxP	inhibitor of the cpx response; periplasmic adaptor protein
*	?	CP009273	3744959 =	268 (1.010)	422 (1.590)	177/278	NT	60.2%	coding (270/741 nt)	yiaT	putative outer membrane protein
	?	CP009273	= 3752673	289 (1.090)					coding (549/1845 nt)	selB	selenocysteinyl‑tRNA‑specific translation factor
*	?	CP009273	3833562 =	26 (0.100)	286 (1.080)	143/276	NT	91.7%	intergenic (‑209/‑13)	nlpA/yicS	cytoplasmic membrane lipoprotein‑28/putative periplasmic protein
	?	CP009273	4487999 =	NA (NA)					intergenic (+242/‑90)	intB/insC1	pseudogene, integrase homology;IS, phage, Tn; Phage‑related functions and prophages; KpLE2 phage‑like element; P4‑like integrase/IS2 repressor TnpA
*	?	CP009273	3920822 =	223 (0.840)	19 (0.070)	16/278	NT	7.1%	coding (308/993 nt)	asnA	asparagine synthetase A
	?	CP009273	= 3921005	277 (1.040)					coding (491/993 nt)	asnA	asparagine synthetase A
*	?	CP009273	4096064 =	143 (0.540)	83 (0.310)	57/276	NT	36.9%	coding (317/501 nt)	cpxP	inhibitor of the cpx response; periplasmic adaptor protein
	?	CP009273	4487999 =	NA (NA)					intergenic (+242/‑90)	intB/insC1	pseudogene, integrase homology;IS, phage, Tn; Phage‑related functions and prophages; KpLE2 phage‑like element; P4‑like integrase/IS2 repressor TnpA