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	2,577	C→A	52.9%	G747G (GGC→GGA)	thrA →	Bifunctional aspartokinase/homoserine dehydrogenase 1
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	25,013	G→T	5.3%	D875Y (GAC→TAC)	ileS →	isoleucyl‑tRNA 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	31,450	G→T	8.5%	G212C (GGC→TGC)	carB →	carbamoyl‑phosphate synthase large subunit
RA	32,641	G→A	5.6%	D609N (GAC→AAC)	carB →	carbamoyl‑phosphate synthase large subunit
RA	41,442	G→T	41.4%	R164S (CGC→AGC)	caiT ←	putative transporter
RA	42,150	G→A	58.4%	intergenic (‑219/‑253)	caiT ← / → fixA	putative transporter/anaerobic carnitine reduction putative electron transfer flavoprotein subunit
RA	46,091	G→T	5.8%	V95V (GTG→GTT)	yaaU →	putative transporter
RA	49,840	G→T	100%	A6A (GCG→GCT)	folA →	dihydrofolate reductase
RA	51,352	A→T	35.3%	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	70,249	A→C	35.2%	C254G (TGC→GGC)	thiP ←	thiamine, thiamine pyrophosphate ABC transporter permease; ThiBPQ thiamine, thiamine pyrophosphate importer
RA	76,821	G→T	12.1%	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	5.2%	intergenic (+146/‑34)	ilvH → / → cra	acetolactate synthase 3, small subunit, valine‑sensitive/transcriptional repressor‑activator for carbon metabolism
RA	85,890	G→T	40.5%	intergenic (+371/‑231)	cra → / → mraZ	transcriptional repressor‑activator for carbon metabolism/RsmH methytransferase inhibitor
RA	86,729	G→T	6.3%	R50L (CGT→CTT)	rsmH →	16S rRNA m(4)C1402 methyltransferase, SAM‑dependent
RA	92,294	C→A	37.5%	R386R (CGC→CGA)	murF →	UDP‑N‑acetylmuramoyl‑tripeptide:D‑alanyl‑D‑ alanine ligase
RA	93,391	G→T	58.6%	T301T (ACG→ACT)	mraY →	phospho‑N‑acetylmuramoyl‑pentapeptide transferase
RA	95,873	G→T	45.6%	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	39.6%	F214L (TTT→TTA)	murC →	UDP‑N‑acetylmuramate:L‑alanine ligase
RA	103,467	G→T	100%	D142Y (GAT→TAT)	lpxC →	UDP‑3‑O‑acyl N‑acetylglucosamine deacetylase
RA	103,902	T→A	5.1%	F287I (TTC→ATC)	lpxC →	UDP‑3‑O‑acyl N‑acetylglucosamine deacetylase
RA	104,561	G→T	100%	A124S (GCG→TCG)	secM →	regulator of secA translation
RA	104,582	A→T	36.7%	T131S (ACG→TCG)	secM →	regulator of secA translation
RA	110,883	A→T	8.7%	Y318F (TAC→TTC)	guaC →	GMP reductase
RA	116,052	G→T	5.8%	L95L (CTG→CTT)	ampE →	ampicillin resistance inner membrane protein; putative signaling protein in beta‑lactamase regulation
RA	118,873	G→T	100%	D99Y (GAC→TAC)	pdhR →	pyruvate dehydrogenase complex repressor; autorepressor
RA	119,467	G→T	52.4%	intergenic (+124/‑37)	pdhR → / → aceE	pyruvate dehydrogenase complex repressor; autorepressor/pyruvate dehydrogenase, decarboxylase component E1, thiamine triphosphate‑binding
RA	124,371	C→A	43.0%	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	5.4%	R361R (CGG→AGG)	yacH ←	uncharacterized protein
RA	134,028	G→T	56.2%	A153A (GCG→GCT)	cueO →	multicopper oxidase (laccase)
RA	134,203	G→T	8.9%	D212Y (GAT→TAT)	cueO →	multicopper oxidase (laccase)
RA	134,652	G→T	35.2%	M361I (ATG→ATT)	cueO →	multicopper oxidase (laccase)
RA	142,460	T→A	100%	F298Y (TTC→TAC)	yadE →	putative polysaccharide deacetylase lipoprotein
RA	146,343	G→T	43.2%	T366T (ACC→ACA)	yadC ←	putative fimbrial‑like adhesin protein
RA	151,620	C→A	36.7%	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	161,068	A→C	11.8%	intergenic (+47/‑149)	hrpB → / → mrcB	putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase
RA	172,107	G→T	35.7%	E172* (GAA→TAA)	clcA →	H(+)/Cl(‑) exchange transporter
RA	172,979	G→T	30.8%	A462A (GCG→GCT)	clcA →	H(+)/Cl(‑) exchange transporter
RA	175,636	T→G	11.2%	K2T (AAA→ACA)	mtn ←	5'‑methylthioadenosine/S‑adenosylhomocysteine nucleosidase
RA	176,783	G→T	54.5%	D354Y (GAT→TAT)	dgt →	deoxyguanosine triphosphate triphosphohydrolase
RA	176,864	C→T	34.4%	L381L (CTA→TTA)	dgt →	deoxyguanosine triphosphate triphosphohydrolase
RA	183,669	C→A	5.2%	R490L (CGC→CTC)	glnD ←	uridylyltransferase
RA	186,279	A→T	36.2%	noncoding (81/136 nt)	tff →	novel sRNA, function unknown
RA	189,654	G→T	5.4%	R99L (CGT→CTT)	frr →	ribosome recycling factor
RA	194,124	C→A	39.1%	I364I (ATC→ATA)	rseP →	inner membrane zinc RIP metalloprotease; RpoE activator, by degrading RseA; cleaved signal peptide endoprotease
RA	201,962	A→T	57.4%	D117V (GAT→GTT)	dnaE →	DNA polymerase III alpha subunit
RA	207,624	G→T	5.2%	D487Y (GAT→TAT)	ldcC →	lysine decarboxylase 2, constitutive
RA	215,833	G→T	28.3%	N83K (AAC→AAA)	tsaA ←	tRNA‑Thr(GGU) m(6)t(6)A37 methyltransferase, SAM‑dependent
RA	217,932	A→C	59.7%	I59M (ATT→ATG)	metI ←	DL‑methionine transporter subunit
RA	222,983	G→T	5.8%	noncoding (738/2904 nt)	rrlH →	23S ribosomal RNA of rrnH operon
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	233,931	G→A	28.9%	S37N (AGT→AAT)	yafT →	lipoprotein
RA	236,234	A→T	53.2%	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	247,002	G→T	36.1%	pseudogene (444/756 nt)	lafU →	pseudogene, lateral flagellar motor protein fragment
RA	250,880	G→T	34.5%	P442T (CCG→ACG)	pepD ←	aminoacyl‑histidine dipeptidase (peptidase D)
RA	253,769	C→T	8.8%	V252V (GTC→GTT)	frsA →	fermentation‑respiration switch protein; PTS Enzyme IIA(Glc)‑binding protein; pNP‑butyrate esterase activity
RA	258,054	G→T	49.2%	G281C (GGC→TGC)	proA →	gamma‑glutamylphosphate reductase
RA	262,114	C→A	57.0%	D51Y (GAT→TAT)	yafY ←	lipoprotein, inner membrane; overproduction stimulates degP expression; CP4‑6 prophage
RA	266,127	C→A	36.5%	pseudogene (139/258 nt)	insN →	pseudogene, IS911 transposase A;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related
RA	274,735	A→T	100%	pseudogene (138/348 nt)	afuB ←	pseudogene, CP4‑6 prophage; ABC transporter permease family;Phage or Prophage Related
RA	278,052	G→T	17.4%	G22C (GGC→TGC)	yagE →	2‑keto‑3‑deoxy gluconate (KDG) aldolase; CP4‑6 prophage
RA	291,453	A→T	8.1%	L452* (TTA→TAA)	intF ←	CP4‑6 prophage; putative phage integrase
RA	295,092	G→T	31.1%	G518G (GGC→GGA)	paoC ←	PaoABC aldehyde oxidoreductase, Moco‑containing subunit
RA	302,428	G→T	5.1%	P34Q (CCG→CAG)	ecpD ←	polymerized tip adhesin of ECP fibers
RA	312,532	G→A	100%	pseudogene (349/684 nt)	ykgA ←	pseudogene, AraC family;putative regulator; Not classified; putative ARAC‑type regulatory protein
RA	314,408	A→G	40.3%	D435D (GAT→GAC)	rclA ←	reactive chlorine stress species (RCS) resistance protein; pyridine nucleotide‑dependent disulfide oxidoreductase family
RA	317,205	G→A	50.6%	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	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	40.7%	P404P (CCG→CCT)	betT →	choline transporter of high affinity
RA	344,800	G→T	100%	E136D (GAG→GAT)	prpB →	2‑methylisocitrate lyase
RA	345,384	G→C	5.3%	intergenic (+101/‑339)	prpB → / → prpC	2‑methylisocitrate lyase/2‑methylcitrate synthase
RA	347,382	G→T	44.4%	E153* (GAA→TAA)	prpD →	2‑methylcitrate dehydratase
RA	360,317	C→A	48.2%	intergenic (‑251/+344)	lacZ ← / ← lacI	pseudogene, truncated/DNA‑binding transcriptional repressor
RA	360,752	A→G	100%	V331A (GTG→GCG)	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	376,412	G→A	9.0%	pseudogene (304/416 nt)	yaiX ←	pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase
RA	385,815	G→T	59.9%	pseudogene (109/1458 nt)	yaiT →	pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein
RA	388,341	G→T	8.8%	S6* (TCA→TAA)	insE1 ←	IS3 transposase A
RA	395,951	G→T	40.7%	V143V (GTC→GTA)	ddlA ←	D‑alanine‑D‑alanine ligase A
RA	396,883	A→G	92.9%	Q14Q (CAA→CAG)	iraP →	anti‑RssB factor, RpoS stabilzer during Pi starvation; anti‑adapter protein
RA	397,959	G→A	54.8%	A253T (GCG→ACG)	phoA →	bacterial alkaline phosphatase
RA	399,531	G→T	9.0%	A125S (GCG→TCG)	yaiC →	diguanylate cyclase, cellulose regualtor
RA	402,340	G→T	100%	V160V (GTG→GTT)	aroL →	shikimate kinase II
RA	406,075	C→A	100%	P159Q (CCG→CAG)	mak →	manno(fructo)kinase
RA	411,027	G→T	100%	L61L (CTC→CTA)	sbcC ←	exonuclease, dsDNA, ATP‑dependent
RA	421,799	C→A	100%	I69I (ATC→ATA)	tgt →	tRNA‑guanine transglycosylase
RA	425,143	G→T	57.9%	T61T (ACG→ACT)	secF →	SecYEG protein translocase auxillary subunit
RA	427,603	C→T	30.8%	intergenic (‑134/+165)	tsx ← / ← yajI	nucleoside channel, receptor of phage T6 and colicin K/putative lipoprotein
RA	433,551	G→T	100%	S14Y (TCC→TAC)	yajO ←	2‑carboxybenzaldehyde reductase
RA	433,738	A→C	48.4%	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	437,672	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	54.5%	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	32.8%	T422N (ACC→AAC)	tig →	peptidyl‑prolyl cis/trans isomerase (trigger factor)
RA	453,656	T→A	44.0%	S259T (TCC→ACC)	clpX →	ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease
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	462,982	A→T	24.8%	T39S (ACT→TCT)	cof →	thiamine pyrimidine pyrophosphate hydrolase; HMP‑PP phosphatase
RA	465,341	A→C	41.8%	I339L (ATT→CTT)	mdlA →	putative multidrug transporter subunit of ABC superfamily, ATP‑binding component
RA	474,138	G→T	100%	intergenic (‑65/+99)	ylaB ← / ← ylaC	putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase/DUF1449 family inner membrane protein
RA	475,502	T→A	37.9%	intergenic (‑128/+44)	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	479,244	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	486,912	C→A	40.6%	I15I (ATC→ATA)	apt →	adenine phosphoribosyltransferase
RA	498,579	G→T	45.6%	A39E (GCG→GAG)	ybaL ←	inner membrane putative NAD(P)‑binding transporter
RA	500,613	G→T	7.7%	G82C (GGT→TGT)	ushA →	bifunctional UDP‑sugar hydrolase/5'‑nucleotidase
RA	507,163	G→T	6.7%	G23C (GGC→TGC)	glsA →	glutaminase 1
RA	509,737	G→A	57.4%	E97K (GAG→AAG)	cueR →	copper‑responsive regulon transcriptional regulator
RA	511,170	G→T	32.3%	V20V (GTC→GTA)	qmcA ←	PHB domain membrane‑anchored putative protease
RA	511,619	A→T	33.7%	Q82L (CAA→CTA)	fetA →	iron exporter, ATP‑binding subunit, ABC transporter FetAB subunit; peroxide resistance protein
RA	522,859	T→G	10.3%	S1381R (AGT→AGG)	rhsD →	Rhs family putative polymorphic toxin
RA	523,413	G→T	5.8%	pseudogene (6/708 nt)	rhsH →	pseudogene, Rhs familly protein
RA	523,781	G→T	13.4%	pseudogene (374/708 nt)	rhsH →	pseudogene, Rhs familly protein
RA	524,334:1	+T	100%	pseudogene (239/491 nt)	ybbD →	pseudogene
RA	525,631	C→A	6.0%	R351L (CGC→CTC)	mnmH ←	tRNA 2‑selenouridine synthase, selenophosphate‑dependent
RA	530,466	C→A	100%	F365L (TTC→TTA)	gcl →	glyoxylate carboligase
RA	538,153	A→C	5.4%	E270D (GAA→GAC)	glxK →	glycerate kinase II
RA	538,400	G→T	5.2%	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	546,491	G→T	100%	V199V (GTG→GTT)	ybcF →	putative carbonate kinase
RA	546,782	G→T	6.7%	S296S (TCG→TCT)	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	38.9%	F123I (TTC→ATC)	folD ←	bifunctional 5,10‑methylene‑tetrahydrofolate dehydrogenase/ 5,10‑methylene‑tetrahydrofolate cyclohydrolase
RA	557,303	A→T	37.0%	E717D (GAA→GAT)	sfmD →	putative outer membrane export usher protein
RA	557,592	G→T	57.2%	D814Y (GAC→TAC)	sfmD →	putative outer membrane export usher protein
RA	560,966	G→T	10.0%	L157I (CTC→ATC)	intD ←	DLP12 prophage; putative phage integrase
RA	564,074	A→C	14.0%	N102H (AAT→CAT)	emrE →	DLP12 prophage; multidrug resistance protein
RA	566,710	G→T	43.1%	G121V (GGC→GTC)	ybcL →	inactive polymorphonuclear leukocyte migration suppressor; DLP12 prophage; secreted protein, UPF0098 family
RA	571,745	G→T	44.1%	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	576,653	G→T	39.7%	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	580,102	G→T	41.7%	intergenic (+216/+34)	appY → / ← ompT	global transcriptional activator; DLP12 prophage/DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
RA	581,203	A→T	100%	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	607,931	G→A	100%	S7F (TCC→TTC)	fepA ←	iron‑enterobactin outer membrane transporter
RA	615,143	C→A	6.9%	T171T (ACG→ACT)	fepC ←	iron‑enterobactin transporter subunit
RA	619,048	C→A	61.2%	A307S (GCC→TCC)	fepB ←	iron‑enterobactin transporter subunit
RA	625,364	G→T	100%	G5G (GGG→GGT)	cstA →	carbon starvation protein involved in peptide utilization; APC peptide transporter family protein
RA	630,742	C→A	39.8%	E31* (GAA→TAA)	ybdM ←	Spo0J family protein, ParB‑like nuclease domain
RA	631,999	C→A	36.1%	P9P (CCG→CCT)	ybdN ←	PAPS reductase‑like domain protein
RA	632,286	C→A	50.5%	E263D (GAG→GAT)	ybdO ←	putative DNA‑binding transcriptional regulator
RA	639,231	G→A	100%	L65F (CTT→TTT)	rnk ←	regulator of nucleoside diphosphate kinase
RA	647,234	C→T	53.8%	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	648,056	C→A	100%	F122L (TTC→TTA)	citA →	sensory histidine kinase in two‑component regulatory system with CitB
RA	648,368	G→T	5.9%	A226A (GCG→GCT)	citA →	sensory histidine kinase in two‑component regulatory system with CitB
RA	651,666	G→A	8.0%	intergenic (‑242/‑347)	dcuC ← / → pagP	anaerobic C4‑dicarboxylate transport/phospholipid:lipid A palmitoyltransferase
RA	652,865	Δ1 bp	100%	coding (118/210 nt)	cspE →	constitutive cold shock family transcription antitermination protein; negative regulator of cspA transcription; RNA melting protein; ssDNA‑binding protein
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	664,243	C→A	40.4%	D84Y (GAT→TAT)	rsfS ←	ribosomal silencing factor
RA	666,998	G→T	35.2%	L22I (CTT→ATT)	holA ←	DNA polymerase III, delta subunit
RA	667,348	G→T	62.9%	Q99K (CAG→AAG)	lptE ←	LPS assembly OM complex LptDE, lipoprotein component
RA	668,230	C→A	5.0%	L670L (CTG→CTT)	leuS ←	leucyl‑tRNA synthetase
RA	672,142	T→A	55.5%	intergenic (‑139/‑25)	ybeQ ← / → ybeR	Sel1 family TPR‑like repeat protein/uncharacterized protein
RA	679,765	G→T	41.7%	S35Y (TCT→TAT)	rihA ←	ribonucleoside hydrolase 1
RA	693,739	G→T	54.2%	H299N (CAC→AAC)	asnB ←	asparagine synthetase B
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	62.2%	T2T (ACT→ACG)  *29G (TGA→GGA)	fur ← uof ←	ferric iron uptake regulon transcriptional repressor; autorepressor ryhB‑regulated fur leader peptide
RA	709,827	G→T	41.9%	D272Y (GAT→TAT)	pgm →	phosphoglucomutase
RA	723,846	A→C	37.5%	W115G (TGG→GGG)	kdpA ←	potassium translocating ATPase, subunit A
RA	724,813	A→T	100%	intergenic (+17/‑226)	ybfA → / → rhsC	DUF2517 family protein/Rhs family putative polymorphic toxin
RA	725,650	G→T	30.4%	P204P (CCG→CCT)	rhsC →	Rhs family putative polymorphic toxin
RA	729,456	G→A	54.7%	R75R (AGG→AGA)	ybfB →	putative membrane protein
RA	732,494	G→T	56.9%	pseudogene (214/1137 nt)	ybfL →	pseudogene, DDE domain transposase family;putative factor; Not classified; putative receptor protein
RA	733,539	G→A	9.0%	intergenic (+122/‑9)	ybfL → / → ybfD	pseudogene, DDE domain transposase family;putative factor; Not classified; putative receptor protein/H repeat‑associated putative transposase
RA	734,498	C→A	6.7%	I14I (ATC→ATA)	ybgA →	DUF1722 family protein
RA	735,817	G→T	37.6%	L285L (CTG→CTT)	phr →	deoxyribodipyrimidine photolyase, FAD‑binding
RA	738,124:1	+T	44.7%	intergenic (‑112/‑159)	dtpD ← / → ybgI	dipeptide and tripeptide permease D/NIF3 family metal‑binding protein
RA	741,706	G→T	8.5%	A106S (GCC→TCC)	nei →	endonuclease VIII/ 5‑formyluracil/5‑hydroxymethyluracil DNA glycosylase
RA	742,840	G→T	26.8%	A129E (GCG→GAG)	abrB ←	regulator of aidB expression; inner membrane protein
RA	743,278	G→A	34.5%	intergenic (‑53/+99)	abrB ← / ← ybgO	regulator of aidB expression; inner membrane protein/putative fimbrial protein
RA	747,597	G→A	6.3%	S10F (TCC→TTC)	ybgQ ←	putative outer membrane protein
RA	748,327	G→A	6.5%	intergenic (‑76/+314)	ybgD ← / ← gltA	putative fimbrial‑like adhesin protein/citrate synthase
RA	750,112	A→T	37.6%	intergenic (‑188/‑521)	gltA ← / → sdhC	citrate synthase/succinate dehydrogenase, membrane subunit, binds cytochrome b556
RA	750,558	C→A	5.2%	intergenic (‑634/‑75)	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	41.2%	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	10.1%	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	46.5%	E261K (GAA→AAA)	cydA →	cytochrome d terminal oxidase, subunit I
RA	779,699	G→T	33.7%	S194* (TCG→TAG)	zitB ←	zinc efflux system
RA	788,902	G→T	100%	R115S (CGT→AGT)	modF ←	fused molybdate transporter subunits of ABC superfamily: ATP‑binding components
RA	789,044	G→T	39.1%	I67I (ATC→ATA)	modF ←	fused molybdate transporter subunits of ABC superfamily: ATP‑binding components
RA	792,351	G→T	36.8%	A114A (GCG→GCT)	modC →	molybdate transporter subunit
RA	792,957	C→A	5.0%	V316V (GTC→GTA)	modC →	molybdate transporter subunit
RA	796,821	G→T	13.4%	A203S (GCT→TCT)	ybhH →	putative PrpF family isomerase
RA	800,488	G→T	100%	V510V (GTG→GTT)	ybhJ →	putative hydratase
RA	800,779	G→T	100%	E607D (GAG→GAT)	ybhJ →	putative hydratase
RA	816,152	C→A	38.7%	intergenic (+108/‑97)	ybhL → / → ybhM	UPF0005 family inner membrane protein/UPF0005 family inner membrane protein
RA	816,292	A→T	36.4%	H15L (CAC→CTC)	ybhM →	UPF0005 family inner membrane protein
RA	818,362	G→T	7.8%	G278G (GGC→GGA)	clsB ←	cardiolipin synthase 2
RA	825,641	G→T	40.5%	A153A (GCC→GCA)	ybiH ←	DUF1956 domain‑containing tetR family putative transcriptional regulator
RA	828,374	G→T	100%	V11V (GTC→GTA)	ybiA ←	DUF1768 family protein
RA	828,819	G→T	5.3%	P98P (CCG→CCT)	dinG →	ATP‑dependent DNA helicase
RA	832,445	G→T	100%	P213P (CCG→CCT)	ybiC →	putative dehydrogenase
RA	834,794	C→A	5.1%	D732Y (GAT→TAT)	fiu ←	catecholate siderophore receptor Fiu
RA	837,698	G→A	36.2%	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	42.5%	K122* (AAA→TAA)	ybiT →	putative transporter subunit of ABC superfamily: ATP‑binding component
RA	863,745	T→A	40.3%	F257Y (TTT→TAT)	gsiA →	glutathione transporter ATP‑binding protein, ABC superfamily
RA	868,897	G→T	37.4%	D155Y (GAC→TAC)	yliE →	putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	870,070	G→T	6.4%	V546F (GTC→TTC)	yliE →	putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	876,447	G→A	100%	D89N (GAT→AAT)	dacC →	D‑alanyl‑D‑alanine carboxypeptidase (penicillin‑binding protein 6a)
RA	877,482	C→A	39.6%	D237Y (GAT→TAT)	deoR ←	deoxyribose‑5‑phosphate‑inducible deoxyribose operon transcriptional repressor; repressor of nupG and tsx
RA	879,085	G→T	100%	intergenic (‑241/‑44)	ybjG ← / → mdfA	undecaprenyl pyrophosphate phosphatase/multidrug efflux system protein
RA	879,590	G→T	7.4%	P154P (CCG→CCT)	mdfA →	multidrug efflux system protein
RA	884,152	G→T	33.0%	S375* (TCG→TAG)	ybjL ←	putative transporter
RA	889,044	G→T	32.5%	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	42.5%	D37Y (GAT→TAT)	potG →	putrescine transporter subunit: ATP‑binding component of ABC superfamily
RA	898,457	G→T	41.7%	intergenic (‑13/+5)	artI ← / ← artP	arginine transporter subunit/arginine transporter subunit
RA	907,596	G→T	43.6%	P4Q (CCA→CAA)	hcr ←	HCP oxidoreductase, NADH‑dependent
RA	911,375	G→T	5.3%	F43L (TTC→TTA)	aqpZ ←	aquaporin Z
RA	912,119	C→A	10.1%	P64Q (CCG→CAG)	ybjD →	putative OLD family ATP‑dependent endonuclease; DUF2813 family protein
RA	919,422	G→T	6.5%	D235Y (GAT→TAT)	clpA →	ATPase and specificity subunit of ClpA‑ClpP ATP‑dependent serine protease, chaperone activity
RA	920,805	G→T	5.0%	D696Y (GAC→TAC)	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	925,355	A→T	37.5%	L355Q (CTG→CAG)	cydD ←	fused glutathione, cysteine exporter subunits of ABC superfamily: membrane component/ATP‑binding component
RA	925,957	A→T	37.5%	I154I (ATT→ATA)	cydD ←	fused glutathione, cysteine exporter subunits of ABC superfamily: membrane component/ATP‑binding component
RA	932,814	T→A	7.8%	intergenic (+145/‑14)	ftsK → / → lolA	DNA translocase at septal ring sorting daughter chromsomes/lipoprotein chaperone
RA	943,573	G→T	100%	A297S (GCC→TCC)	ycaM →	putative transporter
RA	954,765	C→A	45.5%	G166G (GGC→GGA)	aroA →	5‑enolpyruvylshikimate‑3‑phosphate synthetase
RA	955,568	A→T	59.6%	intergenic (+17/‑152)	aroA → / → ycaL	5‑enolpyruvylshikimate‑3‑phosphate synthetase/putative peptidase‑related chaperone
RA	963,256	G→A	37.0%	D394N (GAT→AAT)	msbA →	fused lipid transporter subunits of ABC superfamily: membrane component/ATP‑binding component
RA	968,415	G→T	100%	S148* (TCG→TAG)	ycbC ←	DUF218 superfamily protein
RA	976,873	C→A	36.5%	A124E (GCG→GAG)	ldtD →	murein L,D‑transpeptidase
RA	991,613	G→C	6.8%	A263G (GCC→GGC)	ssuA ←	aliphatic sulfonate binding protein, SsuABC ABC transporter
RA	997,965	G→T	62.6%	D235Y (GAT→TAT)	elfG →	putative fimbrial‑like adhesin protein
RA	1,011,409	C→A	6.3%	*173L (TGA→TTA)	fabA ←	beta‑hydroxydecanoyl thioester dehydrase
RA	1,016,392	G→A	6.2%	intergenic (‑17/‑202)	sulA ← / → sxy	SOS cell division inhibitor/CRP‑S‑dependent promoter expression factor
RA	1,024,703	G→T	61.1%	G241G (GGC→GGA)	rlmI ←	23S rRNA m(5)C1962 methyltransferase, SAM‑dependent
RA	1,040,472	A→T	6.1%	V263E (GTG→GAG)	gfcE ←	putative O‑antigen capsule outer membrane auxillary protein export channel
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	100%	T743K (ACG→AAG)	torS ←	hybrid sensory histidine kinase in two‑component regulatory system with TorR
RA	1,073,243	C→A	37.3%	G366C (GGT→TGT)	putA ←	fused DNA‑binding transcriptional regulator/proline dehydrogenase/pyrroline‑5‑carboxylate dehydrogenase
RA	1,073,863	G→T	7.2%	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	1,083,443	G→T	56.8%	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	94.5%	L404* (TTA→TAA)	pgaB ←	poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine (PGA) N‑deacetylase outer membrane export lipoprotein
RA	1,087,360	G→T	49.1%	P129Q (CCG→CAG)	pgaA ←	biofilm adhesin polysaccharide PGA secretin; OM porin; poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine export protein
RA	1,095,709	C→A	14.2%	intergenic (+59/‑43)	ycdY → / → ycdZ	redox enzyme maturation protein (REMP) chaperone for YcdX/DUF1097 family inner membrane protein
RA	1,098,939	A→T	17.1%	intergenic (‑287/‑468)	csgD ← / → csgB	csgBAC operon transcriptional regulator/curlin nucleator protein, minor subunit in curli complex
RA	1,105,607	G→T	5.3%	D273Y (GAC→TAC)	opgG →	osmoregulated periplasmic glucan (OPG) biosynthesis periplasmic protein
RA	1,116,601	T→A	35.5%	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	1,132,098	G→T	43.5%	M123I (ATG→ATT)	flgI →	putative flagellar basal body protein
RA	1,132,494	T→A	40.3%	I255I (ATT→ATA)	flgI →	putative flagellar basal body protein
RA	1,151,485	G→T	8.4%	V90F (GTT→TTT)	holB →	DNA polymerase III, delta prime subunit
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	1,161,438	C→A	33.8%	intergenic (+297/‑103)	ycfP → / → ndh	putative UPF0227 family esterase/respiratory NADH dehydrogenase 2/cupric reductase
RA	1,164,454	G→A	36.1%	intergenic (‑166/‑75)	ycfQ ← / → bhsA	repressor for bhsA(ycfR)/biofilm, cell surface and signaling protein
RA	1,173,073	T→A	8.7%	F100I (TTC→ATC)	lolE →	lipoprotein‑releasing system transmembrane protein
RA	1,175,193	A→T	37.9%	E36V (GAA→GTA)	cobB →	deacetylase of acs and cheY, chemotaxis regulator
RA	1,176,357	G→T	9.8%	L123I (CTC→ATC)	ycfZ ←	inner membrane protein
RA	1,191,676	C→T	49.0%	H366H (CAC→CAT)	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,688	C→T	47.3%	T370T (ACC→ACT)	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,701	T→C	42.3%	L375L (TTA→CTA) ‡	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,703	A→G	41.8%	L375L (TTA→TTG) ‡	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,733	C→T	25.0%	N385N (AAC→AAT)	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,736	G→C	25.0%	A386A (GCG→GCC)	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,739	A→G	23.5%	K387K (AAA→AAG)	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,748	C→T	20.9%	T390T (ACC→ACT)	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,191,760	G→A	13.5%	E394E (GAG→GAA)	icd →	e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA	1,192,153	G→T	5.1%	intergenic (+324/+170)	icd → / ← ymfD	e14 prophage; isocitrate dehydrogenase, specific for NADP+/e14 prophage; putative SAM‑dependent methyltransferase
RA	1,193,041	T→C	7.0%	K218R (AAA→AGA)	ymfE ←	e14 prophage; putative inner membrane protein
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	1,195,030	C→A	6.9%	L294I (CTT→ATT)	lit →	e14 prophage; cell death peptidase, inhibitor of T4 late gene expression
RA	1,196,362	G→A	10.9%	R43W (CGG→TGG)	xisE ←	e14 prophage; putative excisionase
RA	1,201,506	T→G	7.3%	pseudogene (320/412 nt)	beeE →	pseudogene, portal protein family, e14 prophage;Phage or Prophage Related
RA	1,204,284	C→A	89.9%	D98Y (GAT→TAT)	tfaE ←	e14 prophage; putative tail fiber assembly protein
RA	1,204,620	C→A	8.1%	pseudogene (456/501 nt)	stfE ←	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
RA	1,206,494	T→A	5.4%	I231I (ATT→ATA)	mcrA →	putative 5‑methylcytosine/5‑hydroxymethylcytosine‑specific restriction nuclease; 5‑methylcytosine DNA binding protein; e14 prophage gene
RA	1,211,169	C→A	93.1%	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	1,214,456	T→C	35.2%	N6N (AAT→AAC)	ymgF →	inner membrane division septum protein
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	1,224,528	G→T	8.2%	L86L (CTG→CTT)	ycgN →	UPF0153 family cysteine cluster protein
RA	1,226,292	T→A	100%	C24S (TGT→AGT)	umuD →	DNA polymerase V, subunit D
RA	1,227,613	C→A	38.6%	N324K (AAC→AAA)	umuC →	DNA polymerase V, subunit C
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	1,238,721	C→A	30.5%	A29E (GCG→GAG)	emtA →	lytic murein endotransglycosylase E
RA	1,251,120	T→A	44.0%	T97S (ACC→TCC)	ycgV ←	putative adhesin
RA	1,266,853	C→A	5.0%	A151A (GCG→GCT)	chaA ←	calcium/sodium:proton antiporter
RA	1,277,786	G→A	100%	D823N (GAC→AAC)	narG →	nitrate reductase 1, alpha subunit
RA	1,282,249	A→G	6.2%	intergenic (+267/+273)	narI → / ← rttR	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
RA	1,282,421	A→G	11.0%	intergenic (+439/+101)	narI → / ← rttR	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
RA	1,282,439	A→G	6.0%	intergenic (+457/+83)	narI → / ← rttR	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
RA	1,288,669	A→T	58.4%	intergenic (‑291/‑314)	hns ← / → tdk	global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
RA	1,310,130	T→A	5.6%	K55* (AAA→TAA)	yciG ←	KGG family protein
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	54.2%	D290Y (GAT→TAT)	acnA →	aconitate hydratase 1
RA	1,332,486	G→T	41.1%	R800L (CGA→CTA)	acnA →	aconitate hydratase 1
RA	1,334,048	G→T	36.5%	E154D (GAG→GAT)	pgpB →	phosphatidylglycerophosphatase B
RA	1,337,498	G→T	7.2%	R30R (CGG→AGG)	osmB ←	lipoprotein
RA	1,337,533	G→T	93.9%	A18E (GCA→GAA)	osmB ←	lipoprotein
RA	1,340,820	G→T	39.8%	I60I (ATC→ATA)	gmr ←	cyclic‑di‑GMP phosphodiesterase; csgD regulator; modulator of Rnase II stability
RA	1,340,901	A→T	38.1%	S33S (TCT→TCA)	gmr ←	cyclic‑di‑GMP phosphodiesterase; csgD regulator; modulator of Rnase II stability
RA	1,365,283	G→T	100%	E271* (GAG→TAG)	ycjM →	alpha amylase catalytic domain family protein
RA	1,372,069	G→T	45.2%	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	1,386,008	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	1,392,834	C→A	5.0%	D16Y (GAC→TAC)	uspE ←	stress‑induced protein
RA	1,406,275	C→A	12.9%	L406F (TTG→TTT)	intR ←	Rac prophage; integrase
RA	1,417,454	C→A	41.6%	pseudogene (497/500 nt)	ydaW →	Rac prophage; pseudogene, DNA‑binding protein family;Phage or Prophage Related
RA	1,424,234	C→A	93.0%	S310* (TCA→TAA)	stfR →	Rac prophage; putative tail fiber protein
RA	1,424,558	C→A	42.1%	A418E (GCG→GAG)	stfR →	Rac prophage; putative tail fiber protein
JC JC	1,428,894	IS2 (–) +5 bp	100%	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	6.6%	I120I (ATC→ATA)	uspF ←	stress‑induced protein, ATP‑binding protein
RA	1,439,518	C→A	100%	S737S (TCC→TCA)	ydbH →	putative membrane‑anchored protein, function unknown
RA	1,443,093	C→A	32.9%	L440I (CTC→ATC)	feaB →	phenylacetaldehyde dehydrogenase
RA	1,443,196	A→T	47.0%	Q474L (CAG→CTG)	feaB →	phenylacetaldehyde dehydrogenase
RA	1,444,739	G→A	30.6%	P290S (CCC→TCC)	tynA ←	tyramine oxidase, copper‑requiring
RA	1,448,466	C→A	8.3%	Q95K (CAA→AAA)	paaA →	ring 1,2‑phenylacetyl‑CoA epoxidase subunit
RA	1,451,422	A→T	59.1%	T246S (ACG→TCG)	paaE →	ring 1,2‑phenylacetyl‑CoA epoxidase, NAD(P)H oxidoreductase component
RA	1,454,724	G→T	100%	G472C (GGT→TGT)	paaH →	3‑hydroxyadipyl‑CoA dehydrogenase, NAD+‑dependent
RA	1,457,811	A→T	43.5%	T6S (ACT→TCT)	paaX →	transcriptional repressor of phenylacetic acid degradation paa operon, phenylacetyl‑CoA inducer
RA	1,460,458	T→C	7.0%	pseudogene (810/2513 nt)	ydbA →	pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA	1,460,467	G→A	5.0%	pseudogene (819/2513 nt)	ydbA →	pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA	1,460,593	C→G	9.8%	pseudogene (945/2513 nt)	ydbA →	pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA	1,460,602	T→C	8.2%	pseudogene (954/2513 nt)	ydbA →	pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA	1,460,689	A→G	6.0%	pseudogene (1041/2513 nt)	ydbA →	pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA	1,460,695	T→G	7.8%	pseudogene (1047/2513 nt)	ydbA →	pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA	1,460,752	C→T	5.3%	pseudogene (1104/2513 nt)	ydbA →	pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA	1,460,861	G→A	7.7%	pseudogene (1213/2513 nt)	ydbA →	pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA	1,460,887	G→C	7.2%	pseudogene (1239/2513 nt)	ydbA →	pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA	1,481,236	G→T	49.3%	intergenic (+16/‑256)	hrpA → / → ydcF	putative ATP‑dependent helicase/DUF218 superfamily protein, SAM‑binding
RA	1,488,630	C→A	35.2%	T233T (ACG→ACT)	ydcI ←	putative DNA‑binding transcriptional regulator
RA	1,493,345	A→T	13.3%	T51S (ACG→TCG)	rimL →	ribosomal‑protein‑L7/L12‑serine acetyltransferase
RA	1,499,199	A→T	41.6%	V380E (GTG→GAG)	ydcO ←	BenE family inner membrane putative transporter
RA	1,503,867	G→A	9.5%	A35T (GCG→ACG)	hicB →	antitoxin for the HicAB toxin‑antitoxin system
RA	1,519,349	T→A	100%	K297* (AAA→TAA)	ansP ←	L‑asparagine transporter
RA	1,520,062	G→T	11.3%	A59E (GCG→GAG)	ansP ←	L‑asparagine transporter
RA	1,521,126	G→A	9.7%	intergenic (+5/‑71)	yncG → / → yncH	glutathione S‑transferase homolog/IPR020099 family protein
RA	1,529,506	C→T	10.4%	G204S (GGC→AGC)	yddE ←	PhzC‑PhzF family protein
RA	1,533,556	G→T	12.3%	H1098N (CAC→AAC)	narZ ←	nitrate reductase 2 (NRZ), alpha subunit
RA	1,540,526	C→A	43.4%	intergenic (‑241/+19)	yddL ← / ← yddG	putative lipoprotein;putative membrane; Not classified; putative outer membrane porin protein/aromatic amino acid exporter
RA	1,542,441	T→A	31.7%	F262I (TTT→ATT)	fdnG →	formate dehydrogenase‑N, alpha subunit, nitrate‑inducible
RA	1,545,413	T→A	5.9%	D232E (GAT→GAA)	fdnH →	formate dehydrogenase‑N, Fe‑S (beta) 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	53.8%	D216Y (GAT→TAT)	ddpD ←	D,D‑dipeptide permease system, ATP‑binding component
RA	1,554,588	G→T	38.3%	A200E (GCG→GAG)	ddpB ←	D‑ala‑D‑ala transporter subunit
RA	1,563,276	G→T	100%	H491N (CAC→AAC)	gadC ←	glutamate:gamma‑aminobutyric acid antiporter
RA	1,564,175	G→T	32.5%	S191* (TCG→TAG)	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	36.6%	intergenic (‑90/+272)	gadB ← / ← pqqL	glutamate decarboxylase B, PLP‑dependent/putative periplasmic M16 family zinc metalloendopeptidase
RA	1,572,192	G→T	37.7%	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	1,586,871	G→T	6.0%	intergenic (‑172/+51)	hipB ← / ← yneO	antitoxin of HipAB toxin‑antitoxin system/pseudogene, AidA homolog
RA	1,588,516	G→T	9.2%	pseudogene (3729/5323 nt)	yneO ←	pseudogene, AidA homolog
RA	1,591,853	C→A	39.9%	pseudogene (392/5323 nt)	yneO ←	pseudogene, AidA homolog
RA	1,591,894	C→A	36.2%	pseudogene (351/5323 nt)	yneO ←	pseudogene, AidA homolog
RA	1,593,900	G→T	27.0%	N189K (AAC→AAA)	lsrK ←	autoinducer‑2 (AI‑2) kinase
RA	1,602,131	G→T	44.0%	D177Y (GAT→TAT)	tam →	trans‑aconitate methyltransferase
RA	1,603,440	G→A	94.5%	intergenic (‑161/+46)	yneE ← / ← uxaB	bestrophin family putative inner membrane protein/altronate oxidoreductase, NAD‑dependent
RA	1,604,655	C→A	6.0%	E95* (GAA→TAA)	uxaB ←	altronate oxidoreductase, NAD‑dependent
RA	1,605,105	C→T	43.0%	intergenic (‑168/+59)	uxaB ← / ← yneF	altronate oxidoreductase, NAD‑dependent/putative membrane‑bound diguanylate cyclase
RA	1,620,961	T→G	100%	Q226P (CAA→CCA)	dcp ←	dipeptidyl carboxypeptidase II
RA	1,628,207	G→A	100%	G110E (GGA→GAA)	pinQ →	Qin prophage; putative site‑specific recombinase
RA	1,646,993	C→T	46.8%	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	1,660,918	C→A	13.0%	V187L (GTG→TTG)	ynfK ←	putative dethiobiotin synthetase
RA	1,661,110	C→A	5.5%	D123Y (GAT→TAT)	ynfK ←	putative dethiobiotin synthetase
RA	1,661,763	C→A	100%	P353P (CCG→CCT)	mlc ←	glucosamine anaerobic growth regulon transcriptional repressor; autorepressor
RA	1,663,639	G→T	30.8%	R71R (CGG→AGG)	ynfL ←	LysR family putative transcriptional regulator
RA	1,670,193	G→T	6.8%	A142E (GCG→GAG)	pntB ←	pyridine nucleotide transhydrogenase, beta subunit
RA	1,680,642	C→A	9.6%	E68D (GAG→GAT)	fumC ←	fumarate hydratase (fumarase C),aerobic Class II
RA	1,689,180	T→G	56.4%	E383D (GAA→GAC)	uidA ←	beta‑D‑glucuronidase
RA	1,690,981	G→T	6.2%	A110E (GCG→GAG)	uidR ←	transcriptional repressor
RA	1,692,573	C→A	56.1%	D289Y (GAT→TAT)	malI ←	transcriptional repressor of Mal regulon
RA	1,696,612	A→T	100%	E41D (GAA→GAT)	add →	adenosine deaminase
RA	1,698,343	C→A	41.2%	D75Y (GAT→TAT)	ydgJ ←	putative oxidoreductase
RA	1,699,862	T→A	63.5%	L119* (TTG→TAG)	ydgK →	DUF2569 family inner membrane protein
RA	1,699,884	C→A	6.2%	T126T (ACC→ACA)	ydgK →	DUF2569 family inner membrane protein
RA	1,702,966	T→A	7.3%	R597R (CGT→CGA)	rsxC →	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA	1,703,008	A→G	5.1%	E611E (GAA→GAG)	rsxC →	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA	1,703,015	G→C	5.2%	E614Q (GAA→CAA)	rsxC →	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA	1,711,397	C→T	100%	R28Q (CGA→CAA)	tyrS ←	tyrosyl‑tRNA synthetase
RA	1,718,636	G→T	46.7%	L93I (CTT→ATT)	sodC ←	superoxide dismutase, Cu, Zn, periplasmic
RA	1,723,809	G→T	63.5%	E156* (GAA→TAA)	lhr →	putative ATP‑dependent helicase
RA	1,725,272	G→T	5.2%	A643A (GCG→GCT)	lhr →	putative ATP‑dependent helicase
RA	1,727,497	G→T	9.2%	R1385L (CGA→CTA)	lhr →	putative ATP‑dependent helicase
RA	1,732,758	G→T	45.4%	D220Y (GAC→TAC)	purR →	transcriptional repressor, hypoxanthine‑binding
RA	1,747,774	A→T	6.4%	F105Y (TTC→TAC)	ydhV ←	putative oxidoreductase subunit
RA	1,751,673	T→G	39.2%	intergenic (+306/‑5)	pykF → / → lpp	pyruvate kinase I/murein lipoprotein
RA	1,752,893	T→A	38.7%	P30P (CCA→CCT)	ldtE ←	murein L,D‑transpeptidase
RA	1,753,293	G→T	40.5%	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	1,764,150	G→T	54.8%	D274Y (GAT→TAT)	ydiK →	UPF0118 family inner membrane protein
RA	1,769,440	C→A	38.2%	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	1,777,451	C→A	59.0%	A55E (GCG→GAG)	fadK →	short chain acyl‑CoA synthetase, anaerobic
RA	1,778,497	G→T	13.0%	A404S (GCC→TCC)	fadK →	short chain acyl‑CoA synthetase, anaerobic
RA	1,788,981	A→T	41.6%	S143R (AGT→AGA)	btuC ←	vitamin B12 transporter subunit: membrane component of ABC superfamily
RA	1,791,509	C→A	33.4%	P231P (CCG→CCT)	pheT ←	phenylalanine tRNA synthetase, beta subunit
RA	1,795,267	A→T	33.6%	F521I (TTC→ATC)	thrS ←	threonyl‑tRNA synthetase
RA	1,795,354	G→T	5.4%	R492S (CGT→AGT)	thrS ←	threonyl‑tRNA synthetase
RA	1,798,234	G→T	47.5%	pseudogene (460/1476 nt)	arpB →	pseudogene, ankyrin repeats
RA	1,798,834	G→A	37.5%	pseudogene (1060/1476 nt)	arpB →	pseudogene, ankyrin repeats
RA	1,802,047	G→A	100%	intergenic (+100/‑6)	ydiZ → / → yniA	uncharacterized protein/fructosamine kinase family protein
RA	1,803,109	C→T	54.2%	A128T (GCC→ACC)	yniB ←	putative inner membrane protein
RA	1,805,246	T→A	6.1%	L19Q (CTG→CAG)	ydjN →	putative transporter
RA	1,813,263	C→A	40.6%	E148* (GAG→TAG)	chbR ←	repressor of chb operon for N,N'‑diacetylchitobiose utilization
RA	1,813,497	C→A	11.2%	D70Y (GAT→TAT)	chbR ←	repressor of chb operon for N,N'‑diacetylchitobiose utilization
RA	1,816,882	C→A	10.8%	A56A (GCC→GCA)	nadE →	NAD synthetase, NH3/glutamine‑dependent
RA	1,821,696	A→T	55.7%	L274Q (CTG→CAG)	astB ←	succinylarginine dihydrolase
RA	1,822,975	C→A	47.4%	A339A (GCG→GCT)	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	1,836,072	C→A	31.7%	A109E (GCG→GAG)	nudG →	CTP pyrophosphohydrolase; also hydrolyzes 2‑hydroxy‑dATP, 8‑hydroxy‑dGTP, 5‑hydroxy‑CTP, dCTP and 5‑methyl‑dCTP
RA	1,838,201	C→A	6.9%	E310* (GAA→TAA)	ynjI ←	inner membrane protein
RA	1,838,387	T→A	6.3%	I248F (ATC→TTC)	ynjI ←	inner membrane protein
RA	1,842,604	A→T	5.8%	S110S (TCT→TCA)	ydjA ←	putative oxidoreductase
RA	1,850,880	C→A	38.4%	V102V (GTG→GTT)	ydjH ←	putative kinase
RA	1,855,538	C→A	6.3%	D18Y (GAT→TAT)	ydjL ←	putative Zn‑dependent NAD(P)‑binding oxidoreductase
RA	1,862,404	G→T	37.5%	E414* (GAA→TAA)	yeaG →	protein kinase, endogenous substrate unidentified; autokinase
RA	1,864,752	C→A	23.2%	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	1,868,749	A→C	7.1%	E47D (GAA→GAC)	yeaL →	UPF0756 family putative inner membrane protein
RA	1,872,520	G→T	100%	P183P (CCG→CCT)	yeaP →	diguanylate cyclase
RA	1,872,542	A→T	5.4%	N191Y (AAT→TAT)	yeaP →	diguanylate cyclase
RA	1,873,569	C→A	7.0%	intergenic (‑57/+91)	yeaQ ← / ← yoaG	UPF0410 family protein/uncharacterized protein
RA	1,904,572	C→A	6.2%	R14R (CGA→AGA)	yebQ →	putative transporter
RA	1,909,063	A→C	5.4%	F4C (TTT→TGT)	prc ←	carboxy‑terminal protease for penicillin‑binding protein 3
RA	1,909,342	T→A	100%	E150D (GAA→GAT)	proQ ←	RNA chaperone, putative ProP translation regulator
RA	1,929,069	A→G	32.0%	intergenic (‑208/+27)	edd ← / ← zwf	6‑phosphogluconate dehydratase/glucose‑6‑phosphate 1‑dehydrogenase
RA	1,932,672	A→T	6.8%	E256V (GAA→GTA)	pykA →	pyruvate kinase II
RA	1,934,464	C→A	36.7%	intergenic (‑14/+106)	lpxM ← / ← mepM	myristoyl‑acyl carrier protein (ACP)‑dependent acyltransferase/murein DD‑endopeptidase, space‑maker hydrolase, septation protein
RA	1,937,083	A→T	15.8%	T55T (ACA→ACT)	znuC →	zinc transporter subunit: ATP‑binding component of ABC superfamily
RA	1,942,066	G→T	31.5%	H115N (CAT→AAT)	yebC ←	UPF0082 family protein
RA	1,943,414	C→A	5.2%	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	49.2%	D119Y (GAT→TAT)	yecE →	UPF0759 family protein
RA	1,948,050	C→A	30.8%	L118I (CTT→ATT)	cmoB →	tRNA (cmo5U34)‑carboxymethyltransferase, carboxy‑SAM‑dependent
RA	1,959,915	C→A	57.4%	P178P (CCG→CCT)	flhB ←	flagellin export apparatus, substrate specificity protein
RA	1,963,108	C→A	6.6%	E172* (GAG→TAG)	cheR ←	chemotaxis regulator, protein‑glutamate methyltransferase
RA	1,967,264	C→A	5.9%	L111F (TTG→TTT)	cheW ←	purine‑binding chemotaxis 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	1,973,690	A→G	5.0%	A468A (GCT→GCC)	otsA ←	trehalose‑6‑phosphate synthase
RA	1,978,094	C→T	10.5%	E153K (GAA→AAA)	araG ←	fused L‑arabinose transporter subunits of ABC superfamily: ATP‑binding components
RA	1,984,478	G→T	47.8%	P208Q (CCG→CAG)	yecA ←	UPF0149 family protein
RA	1,984,987	C→A	55.1%	T38T (ACG→ACT)	yecA ←	UPF0149 family protein
RA	1,986,289	T→A	100%	N4Y (AAT→TAT)	pgsA ←	phosphatidylglycerophosphate synthetase
RA	1,991,843	G→A	9.2%	L40F (CTC→TTC)	yecS ←	ABC family putative inner membrane permease
RA	1,997,314	G→T	100%	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	2,007,547	C→A	41.5%	R280S (CGC→AGC)	fliF →	flagellar basal‑body MS‑ring and collar protein
RA	2,015,451	T→A	43.7%	G34G (GGT→GGA)	fliP →	flagellar biosynthesis protein
RA	2,018,405	G→T	11.0%	intergenic (‑101/‑62)	dsrB ← / → yodD	uncharacterized protein/uncharacterized protein
RA	2,018,422	T→A	39.7%	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	2,034,060	G→T	37.7%	G33C (GGT→TGT)	yedZ →	inner membrane heme subunit for periplasmic YedYZ reductase
RA	2,035,090	C→A	92.2%	Q79K (CAG→AAG)	zinT →	zinc and cadmium binding protein, periplasmic
RA	2,040,800	C→A	37.1%	T794T (ACC→ACA)	yeeJ →	putative adhesin
RA	2,043,389	G→T	7.5%	L1657F (TTG→TTT)	yeeJ →	putative adhesin
RA	2,046,371	A→T	10.6%	pseudogene (439/1053 nt)	yeeL ←	pseudogene, glycosyltransferase homology
RA	2,050,363	G→A	9.6%	V9I (GTT→ATT)	yeeN →	UPF0082 family protein
RA	2,050,864	G→T	5.0%	D176Y (GAC→TAC)	yeeN →	UPF0082 family protein
RA	2,060,661	T→A	38.0%	N48Y (AAC→TAC)	insH1 ←	IS5 transposase and trans‑activator
RA	2,061,545	C→A	41.5%	intergenic (‑172/+197)	yoeG ← / ← yoeH	pseudogene, CP4‑44 putative prophage remnant;Phage or Prophage Related/pseudogene, CP4‑44 putative prophage remnant;Phage or Prophage Related
RA	2,068,098	G→T	35.1%	E1027* (GAA→TAA)	flu →	CP4‑44 prophage; antigen 43 (Ag43) phase‑variable biofilm formation autotransporter
RA	2,074,680	A→T	100%	W22R (TGG→AGG)	sbmC ←	DNA gyrase inhibitor
RA	2,075,255	T→A	5.7%	V258V (GTA→GTT)	dacD ←	D‑alanyl‑D‑alanine carboxypeptidase (penicillin‑binding protein 6b)
RA	2,077,212	A→T	51.9%	N326Y (AAT→TAT)	sbcB →	exodeoxyribonuclease I; exonuclease I
RA	2,078,671	C→A	9.7%	A112A (GCG→GCT)	yeeE ←	UPF0394 family inner membrane protein
RA	2,082,619	C→T	42.2%	intergenic (‑10/+73)	yeeZ ← / ← yoeB	putative epimerase/toxin of the YoeB‑YefM toxin‑antitoxin system
RA	2,096,834	C→A	6.0%	pseudogene (37/446 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	44.0%	V94I (GTT→ATT)	wzxB ←	putative polisoprenol‑linked O‑antigen transporter
RA	2,102,969	G→A	7.0%	L33F (CTT→TTT)	wzxB ←	putative polisoprenol‑linked O‑antigen transporter
RA	2,108,219:1	+A	100%	coding (1159/1395 nt)	wcaM ←	colanic acid biosynthesis protein
RA	2,110,346	G→A	55.8%	T88I (ACC→ATC)	wcaL ←	putative glycosyl transferase
RA	2,111,376	C→A	7.1%	A170A (GCG→GCT)	wcaK ←	colanic acid biosynthesis protein
RA	2,114,414	C→A	5.3%	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	42.7%	R367L (CGC→CTC)	cpsG ←	phosphomannomutase
RA	2,121,234	C→A	36.1%	E188* (GAA→TAA)	gmd ←	GDP‑D‑mannose dehydratase, NAD(P)‑binding
RA	2,122,216	C→A	7.6%	A52S (GCA→TCA)	wcaF ←	putative acyl transferase
RA	2,130,684	G→T	6.4%	S14* (TCA→TAA)	wza ←	colanic acid export protein; outer membrane auxillary lipoprotein
RA	2,135,016	C→A	6.9%	V26V (GTG→GTT)	asmA ←	suppressor of OmpF assembly mutants; putative outer membrane protein assembly factor; inner membrane‑anchored periplasmic protein
RA	2,135,194	A→T	12.8%	V168E (GTG→GAG)	dcd ←	2'‑deoxycytidine 5'‑triphosphate deaminase
RA	2,135,719	C→A	9.2%	intergenic (‑23/+69)	dcd ← / ← udk	2'‑deoxycytidine 5'‑triphosphate deaminase/uridine/cytidine kinase
RA	2,139,450	G→T	17.8%	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	2,148,615	C→A	39.9%	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	44.9%	I275T (ATT→ACT)	mdtD →	putative arabinose efflux transporter
RA	2,162,105	T→A	11.3%	intergenic (‑318/‑88)	yegR ← / → yegS	uncharacterized protein/phosphatidylglycerol kinase, metal‑dependent
RA	2,163,087	C→A	33.0%	R299S (CGT→AGT)	yegS →	phosphatidylglycerol kinase, metal‑dependent
RA	2,168,487	A→T	38.5%	D14E (GAT→GAA)	gatA ←	galactitol‑specific enzyme IIA component of PTS
RA	2,168,795	C→A	100%	D336Y (GAT→TAT)	gatZ ←	D‑tagatose 1,6‑bisphosphate aldolase 2, subunit
RA	2,179,205	G→T	100%	A24E (GCG→GAG)	rcnR ←	transcriptional repressor of rcnA
RA	2,181,645	A→G	93.1%	N83N (AAT→AAC)	yehA ←	putative fimbrial‑like adhesin protein
RA	2,191,496	C→A	37.0%	pseudogene (1544/2847 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	2,197,797	A→T	31.9%	intergenic (+29/‑278)	yehK → / → yehL	uncharacterized protein/putative ABC superfamily transporter ATP‑binding subunit
RA	2,208,664	G→T	9.5%	R107L (CGC→CTC)	mlrA →	transcriptional activator of csgD and csgBA
RA	2,209,162	C→A	60.1%	I9I (ATC→ATA)	yohO →	putative membrane protein
RA	2,216,296	C→A	100%	I211I (ATC→ATA)	dld →	D‑lactate dehydrogenase, FAD‑binding, NADH independent
RA	2,220,503	C→T	34.9%	V83M (GTG→ATG)	yohF ←	putative oxidoreductase
RA	2,223,247	C→T	58.9%	W206* (TGG→TGA)	dusC ←	tRNA‑dihydrouridine synthase C
RA	2,224,396	T→A	29.7%	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	2,235,258	G→A	11.5%	intergenic (‑111/+31)	galS ← / ← yeiB	galactose‑ and fucose‑inducible galactose regulon transcriptional isorepressor; mgl operon transcriptional repressor; autorepressor/DUF418 family putative inner membrane protein
RA	2,237,098	G→T	100%	H12N (CAT→AAT)	folE ←	GTP cyclohydrolase I
RA	2,240,361	C→A	5.4%	intergenic (‑113/+181)	cirA ← / ← lysP	colicin IA outer membrane receptor and translocator; ferric iron‑catecholate transporter/lysine transporter
RA	2,240,937	A→T	6.0%	C359S (TGC→AGC)	lysP ←	lysine transporter
RA	2,253,140	C→A	12.9%	intergenic (‑365/+58)	psuK ← / ← fruA	pseudouridine kinase/fused fructose‑specific PTS enzymes: IIBcomponent/IIC components
RA	2,263,137	C→A	54.9%	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	2,270,338	T→A	39.1%	L187Q (CTG→CAG)	yejF →	microcin C transporter, ATP‑binding subunit; ABC family
RA	2,281,503	C→A	5.8%	pseudogene (891/2525 nt)	yejO ←	pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system
RA	2,287,829	C→A	52.6%	S185S (TCG→TCT)	ccmF ←	heme lyase, CcmF subunit
RA	2,289,043	C→A	55.6%	W8L (TGG→TTG)	ccmD ←	cytochrome c biogenesis protein
RA	2,289,374	C→A	100%	V142V (GTG→GTT)	ccmC ←	heme exporter subunit
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	48.1%	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	2,306,671	C→T	6.5%	intergenic (+16/‑296)	micF → / → rcsD	sRNA antisense regulator affecting ompF expression, Hfq‑dependent/phosphotransfer intermediate protein in two‑component regulatory system with RcsBC
RA	2,310,213	G→T	56.5%	K186N (AAG→AAT)	rcsB →	response regulator in two‑component regulatory system with RcsC and YojN
RA	2,311,008	T→A	9.2%	H783L (CAC→CTC)	rcsC ←	hybrid sensory kinase in two‑component regulatory system with RcsB and YojN
RA	2,312,708	C→A	6.6%	A216A (GCG→GCT)	rcsC ←	hybrid sensory kinase in two‑component regulatory system with RcsB and YojN
RA	2,313,924	C→A	34.0%	R135S (CGC→AGC)	atoS →	sensory histidine kinase in two‑component regulatory system with AtoC
RA	2,319,204	G→T	7.8%	G324C (GGT→TGT)	atoE →	short chain fatty acid transporter
RA	2,330,502	C→A	100%	D800Y (GAT→TAT)	gyrA ←	DNA gyrase (type II topoisomerase), subunit A
RA	2,331,288	C→T	25.2%	D538N (GAT→AAT)	gyrA ←	DNA gyrase (type II topoisomerase), subunit A
RA	2,341,217	C→A	35.2%	H119N (CAT→AAT)	nrdB →	ribonucleoside‑diphosphate reductase 1, beta subunit, ferritin‑like protein
RA	2,344,807	G→T	5.4%	V349V (GTC→GTA)	glpT ←	sn‑glycerol‑3‑phosphate transporter
RA	2,346,906	G→T	13.7%	D261Y (GAT→TAT)	glpA →	sn‑glycerol‑3‑phosphate dehydrogenase (anaerobic), large subunit, FAD/NAD(P)‑binding
RA	2,348,894	T→A	54.7%	V384E (GTG→GAG)	glpB →	sn‑glycerol‑3‑phosphate dehydrogenase (anaerobic), membrane anchor subunit
RA	2,352,573	C→A	100%	P353P (CCG→CCT)	rhmT ←	putative L‑rhamnonate transporter
RA	2,353,889	C→A	34.0%	V335V (GTG→GTT)	rhmD ←	L‑rhamnonate dehydratase
RA	2,359,673	G→T	100%	M89I (ATG→ATT)	arnB →	uridine 5'‑(beta‑1‑threo‑pentapyranosyl‑4‑ulose diphosphate) aminotransferase, PLP‑dependent
RA	2,362,338	T→A	100%	L274Q (CTG→CAG)	arnA →	fused UDP‑L‑Ara4N formyltransferase/UDP‑GlcA C‑4'‑decarboxylase
RA	2,366,555	T→G	6.3%	F62C (TTT→TGT)	arnF →	undecaprenyl phosphate‑alpha‑L‑ara4N exporter; flippase ArnEF subunit
RA	2,370,361:1	+G	100%	coding (711/759 nt)	menH ←	2‑succinyl‑6‑hydroxy‑2, 4‑cyclohexadiene‑1‑carboxylate synthase
RA	2,370,837	Δ1 bp	40.8%	coding (235/759 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	2,373,129	C→A	7.2%	D332Y (GAT→TAT)	menF ←	isochorismate synthase 2
RA	2,380,078	C→T	54.2%	S247F (TCT→TTT)	yfbL →	putative peptidase
RA	2,383,897	C→A	59.0%	R363L (CGC→CTC)	nuoN ←	NADH:ubiquinone oxidoreductase, membrane subunit N
RA	2,399,210	G→T	100%	S304* (TCA→TAA)	lrhA ←	transcriptional repressor of flagellar, motility and chemotaxis genes
RA	2,400,861	G→A	8.0%	intergenic (‑741/‑179)	lrhA ← / → alaA	transcriptional repressor of flagellar, motility and chemotaxis genes/valine‑pyruvate aminotransferase 2
RA	2,405,946	T→G	100%	Q43P (CAG→CCG)	yfbU ←	UPF0304 family protein
RA	2,407,678	T→A	38.1%	S244T (TCT→ACT)	ackA →	acetate kinase A and propionate kinase 2
RA	2,412,205	C→A	56.4%	D151Y (GAT→TAT)	yfcD ←	putative NUDIX hydrolase
RA	2,415,498	G→T	37.4%	T104T (ACG→ACT)	yfcH →	putative NAD‑dependent nucleotide‑sugar epimerase
RA	2,416,101	C→A	100%	intergenic (+21/+27)	yfcH → / ← yfcI	putative NAD‑dependent nucleotide‑sugar epimerase/transposase_31 family protein
RA	2,422,841	C→A	100%	D293Y (GAT→TAT)	purF ←	amidophosphoribosyltransferase
RA	2,423,034	G→T	46.7%	G228G (GGC→GGA)	purF ←	amidophosphoribosyltransferase
RA	2,424,074	C→T	100%	D57N (GAC→AAC)	cvpA ←	colicin V production membrane protein
RA	2,425,016	G→T	5.1%	R50S (CGT→AGT)	dedD ←	membrane‑anchored periplasmic protein involved in septation
RA	2,425,587	C→A	14.5%	D279Y (GAC→TAC)	folC ←	bifunctional folylpolyglutamate synthase/ dihydrofolate synthase
RA	2,426,731	G→T	33.7%	I225I (ATC→ATA)	accD ←	acetyl‑CoA carboxylase, beta (carboxyltransferase) subunit
RA	2,434,701	C→A	5.4%	A128A (GCG→GCT)	fabB ←	3‑oxoacyl‑[acyl‑carrier‑protein] synthase I
RA	2,442,770	A→C	40.5%	D253E (GAT→GAG)	yfcO ←	DUF2544 family putative outer membrane protein
RA	2,442,790	C→A	37.6%	D247Y (GAT→TAT)	yfcO ←	DUF2544 family putative outer membrane protein
RA	2,444,107	T→G	50.2%	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	7.4%	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	2,456,282	C→A	45.9%	intergenic (+157/‑209)	fadL → / → yfdF	long‑chain fatty acid outer membrane transporter/uncharacterized protein
RA	2,463,910	G→T	10.2%	R434I (AGA→ATA)	gtrS →	serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
RA	2,463,920	C→A	5.4%	D437E (GAC→GAA)	gtrS →	serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
RA	2,466,183	G→T	12.9%	H60N (CAT→AAT)	yfdN ←	CPS‑53 (KpLE1) prophage; uncharacterized protein
RA	2,472,897	A→T	47.9%	T73S (ACT→TCT)	dsdA →	D‑serine dehydratase
RA	2,474,418	G→T	100%	S413* (TCA→TAA)	emrY ←	putative multidrug efflux system
RA	2,475,340	G→T	7.1%	L106I (CTT→ATT)	emrY ←	putative multidrug efflux system
RA	2,494,310	C→A	5.9%	T150K (ACG→AAG)	ypdB →	response regulator activating yhjX; pyruvate‑responsive YpdAB two‑component system
RA	2,495,918	C→A	38.4%	V683F (GTT→TTT)	fryA ←	putative PTS enzyme, Hpr component/enzyme I component/enzyme IIA component
RA	2,503,015	C→A	39.9%	intergenic (‑110/‑94)	glk ← / → yfeO	glucokinase/putative ion channel protein
RA	2,503,813	A→C	5.0%	A235A (GCA→GCC)	yfeO →	putative ion channel protein
RA	2,504,065	C→T	38.7%	G319G (GGC→GGT)	yfeO →	putative ion channel protein
RA	2,505,337	T→A	29.0%	L283F (TTA→TTT)	mntH ←	manganese/divalent cation transporter
RA	2,514,152	G→T	5.4%	intergenic (‑1/‑258)	gltX ← / → valU	glutamyl‑tRNA synthetase/tRNA‑Val
RA	2,520,652	C→A	100%	I116I (ATC→ATA)	yfeH →	putative inorganic ion transporter
RA	2,522,624	C→A	38.1%	A304A (GCG→GCT)	ligA ←	DNA ligase, NAD(+)‑dependent
RA	2,526,583	C→A	9.9%	I272I (ATC→ATA)	cysK →	cysteine synthase A, O‑acetylserine sulfhydrolase A subunit
RA	2,541,934	C→A	9.5%	S158R (AGC→AGA)	yfeW →	penicillin binding protein PBP4B; weak DD‑carboxypeptidase activity
RA	2,542,627	T→G	58.3%	I389M (ATT→ATG)	yfeW →	penicillin binding protein PBP4B; weak DD‑carboxypeptidase activity
RA	2,545,086	C→A	42.6%	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	2,561,221	C→A	52.0%	P82P (CCG→CCT)	eutH ←	ethanolamine transporter
RA	2,563,208	C→A	5.6%	A163A (GCG→GCT)	eutJ ←	ethanolamine utilization protein, HSP70/actin superfamily protein
RA	2,568,720	C→T	100%	A33T (GCC→ACC)	eutP ←	putative P‑loop NTPase ethanolamine utilization protein
RA	2,576,325	C→A	100%	E171D (GAG→GAT)	nudK ←	GDP‑mannose pyrophosphatase
RA	2,586,791	G→T	39.7%	G113G (GGC→GGA)	ypfH ←	palmitoyl‑CoA esterase activity, uncertain physiological substrate
RA	2,587,029:1	+G	100%	coding (101/699 nt)	ypfH ←	palmitoyl‑CoA esterase activity, uncertain physiological substrate
RA	2,589,933	G→A	100%	T55I (ACC→ATC)	ypfJ ←	putative neutral zinc metallopeptidase
RA	2,596,912	C→A	10.4%	S579* (TCA→TAA)	hyfB →	hydrogenase 4, membrane subunit
RA	2,597,173	T→G	58.2%	L666R (CTG→CGG)	hyfB →	hydrogenase 4, membrane subunit
RA	2,603,728	A→C	46.3%	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	2,611,391	T→A	33.6%	intergenic (+95/+43)	yfgD → / ← hda	putative oxidoreductase/ATPase regulatory factor involved in DnaA inactivation
RA	2,612,335	C→A	14.5%	A395A (GCG→GCT)	uraA ←	uracil permease
RA	2,614,168	C→A	100%	D22Y (GAT→TAT)	upp ←	uracil phosphoribosyltransferase
RA	2,615,370	C→A	41.7%	S272Y (TCT→TAT)	purM →	phosphoribosylaminoimidazole synthetase
RA	2,617,515	T→G	25.0%	I371M (ATT→ATG)	ppk →	polyphosphate kinase, component of RNA degradosome
RA	2,618,693	G→T	54.3%	E74* (GAA→TAA)	ppx →	exopolyphosphatase
RA	2,619,125	G→T	40.9%	G218C (GGT→TGT)	ppx →	exopolyphosphatase
RA	2,632,012	C→A	54.8%	intergenic (‑1/+10)	bamB ← / ← yfgM	BamABCDE complex OM biogenesis lipoprotein/putative anti‑RcsB factor
RA	2,651,665	G→T	100%	G210G (GGC→GGA)	hscA ←	DnaK‑like molecular chaperone specific for IscU
RA	2,653,259	C→A	8.4%	intergenic (‑14/+3)	iscA ← / ← iscU	FeS cluster assembly protein/iron‑sulfur cluster assembly scaffold protein
RA	2,654,383	A→T	9.4%	C170S (TGC→AGC)	iscS ←	cysteine desulfurase (tRNA sulfurtransferase), PLP‑dependent
RA	2,658,679	G→T	47.8%	intergenic (+76/‑115)	yfhR → / → csiE	putative S9 family prolyl oligopeptidase/stationary phase inducible protein
RA	2,664,115	C→A	26.4%	R123R (CGG→AGG)	hcaF →	3‑phenylpropionate dioxygenase, small (beta) subunit
RA	2,668,994	C→A	35.0%	D43Y (GAT→TAT)	yphC ←	putative Zn‑dependent NAD(P)‑binding oxidoreductase
RA	2,669,191	G→T	10.2%	R332S (CGC→AGC)	yphD ←	inner membrane putative ABC superfamily sugar transporter permease
RA	2,669,978	C→A	48.3%	A69A (GCG→GCT)	yphD ←	inner membrane putative ABC superfamily sugar transporter permease
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	29.9%	A279A (GCG→GCT)	glyA ←	serine hydroxymethyltransferase
RA	2,679,151	C→T	6.8%	intergenic (‑285/‑43)	glyA ← / → hmp	serine hydroxymethyltransferase/fused nitric oxide dioxygenase/dihydropteridine reductase 2
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	2,688,062	C→A	9.3%	D281Y (GAT→TAT)	purL ←	phosphoribosylformyl‑glycineamide synthetase
RA	2,692,793	C→A	58.1%	H226N (CAT→AAT)	yfhH →	putative DNA‑binding transcriptional regulator
RA	2,694,564	G→T	11.2%	I175I (ATC→ATA)	pdxJ ←	pyridoxine 5'‑phosphate synthase
RA	2,694,843	G→T	59.6%	I82I (ATC→ATA)	pdxJ ←	pyridoxine 5'‑phosphate synthase
RA	2,699,380	C→A	52.0%	P368P (CCG→CCT)	lepA ←	back‑translocating elongation factor EF4, GTPase
RA	2,706,575	C→A	7.9%	I107I (ATC→ATA)	srmB →	ATP‑dependent RNA helicase
RA	2,711,249	G→T	8.0%	G213G (GGC→GGA)	yfiF ←	putative methyltransferase
RA	2,715,643	G→T	100%	E778* (GAA→TAA)	pka →	protein lysine acetyltransferase
RA	2,719,426	T→C	100%	intergenic (‑321/+2)	kgtP ← / ← rrfG	alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon
RA	2,726,786	C→A	100%	A249A (GCG→GCT)	clpB ←	protein disaggregation chaperone
RA	2,730,789	G→T	35.8%	E93* (GAA→TAA)	raiA →	cold shock protein associated with 30S ribosomal subunit
RA	2,733,108	G→T	5.2%	G107G (GGC→GGA)	tyrA ←	fused chorismate mutase T/prephenate dehydrogenase
RA	2,733,627	G→T	5.2%	R295S (CGC→AGC)	aroF ←	3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, tyrosine‑repressible
RA	2,733,753	C→T	100%	E253K (GAG→AAG)	aroF ←	3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, tyrosine‑repressible
RA	2,735,293	A→T	38.0%	I20I (ATA→ATT)	yfiR →	putative periplasmic inhibitor of YfiN activity
RA	2,740,948	C→A	39.7%	T69T (ACG→ACT)	ffh ←	Signal Recognition Particle (SRP) component with 4.5S RNA (ffs)
RA	2,740,971	G→T	7.1%	H62N (CAT→AAT)	ffh ←	Signal Recognition Particle (SRP) component with 4.5S RNA (ffs)
RA	2,761,733	T→A	36.3%	V222E (GTA→GAA)	yfjP →	CP4‑57 prophage; 50S ribosome‑binding GTPase family protein
RA	2,762,153	C→A	18.2%	R44S (CGC→AGC)	yfjQ →	CP4‑57 prophage; uncharacterized protein
RA	2,765,545	C→A	6.9%	pseudogene (881/900 nt)	yfjV ←	pseudogene, CP4‑57 prophage;Phage or Prophage Related; putative pump 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	2,778,281	C→T	7.8%	pseudogene (90/1374 nt)	ypjC ←	pseudogene
RA	2,779,067	C→A	100%	intergenic (‑697/+54)	ypjC ← / ← ileY	pseudogene/tRNA‑Ile
RA	2,786,234	G→T	5.8%	A47A (GCG→GCT)	gabT →	4‑aminobutyrate aminotransferase, PLP‑dependent
RA	2,799,737	C→A	39.3%	V123V (GTC→GTA)	proW →	glycine betaine transporter subunit
RA	2,799,851	C→A	5.8%	V161V (GTC→GTA)	proW →	glycine betaine transporter subunit
RA	2,805,849	T→C	7.8%	L355P (CTG→CCG)	emrA →	multidrug efflux system
RA	2,808,987	G→T	52.7%	S271* (TCG→TAG)	gshA ←	glutamate‑cysteine ligase
RA	2,811,405	A→G	5.4%	intergenic (‑186/+13)	argQ ← / ← argZ	tRNA‑Arg/tRNA‑Arg
RA	2,811,408	T→A	8.1%	intergenic (‑189/+10)	argQ ← / ← argZ	tRNA‑Arg/tRNA‑Arg
RA	2,819,102	G→T	44.6%	intergenic (‑167/‑89)	mltB ← / → srlA	membrane‑bound lytic murein transglycosylase B/glucitol/sorbitol‑specific enzyme IIC component of PTS
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	51.1%	E127* (GAA→TAA)	hydN ←	formate dehydrogenase‑H, [4Fe‑4S] ferredoxin subunit
RA	2,831,465	C→A	6.8%	intergenic (‑1/+148)	hydN ← / ← ascG	formate dehydrogenase‑H, [4Fe‑4S] ferredoxin subunit/asc operon transcriptional repressor; prpBC operon repressor
RA	2,835,094	C→A	57.3%	P249Q (CCG→CAG)	ascB →	cryptic 6‑phospho‑beta‑glucosidase
RA	2,835,894	C→A	5.7%	intergenic (+121/+38)	ascB → / ← hycI	cryptic 6‑phospho‑beta‑glucosidase/protease involved in processing C‑terminal end of HycE
RA	2,837,370	C→A	8.4%	R67L (CGA→CTA)	hycG ←	hydrogenase 3 and formate hydrogenase complex, HycG subunit
RA	2,837,725	C→A	10.8%	E129D (GAG→GAT)	hycF ←	formate hydrogenlyase complex iron‑sulfur protein
RA	2,841,044	C→A	93.8%	A519A (GCG→GCT)	hycC ←	hydrogenase 3, membrane subunit
RA	2,842,289	C→T	9.4%	V104V (GTG→GTA)	hycC ←	hydrogenase 3, membrane subunit
RA	2,846,112	C→A	54.6%	I206I (ATC→ATA)	hypD →	hydrogenase maturation protein
RA	2,847,161	C→A	7.3%	I183I (ATC→ATA)	hypE →	carbamoyl dehydratase, hydrogenases 1,2,3 maturation protein
RA	2,848,487	G→T	5.6%	R264L (CGC→CTC)	fhlA →	formate hydrogenlyase transcriptional activator
RA	2,850,790	C→A	100%	I113I (ATC→ATA)	mutS →	methyl‑directed mismatch repair protein
RA	2,854,711	G→A	9.5%	intergenic (‑118/‑78)	ygbI ← / → ygbJ	DeoR family putative transcriptional regulator/putative dehydrogenase
RA	2,854,737:1	+T	6.9%	intergenic (‑144/‑52)	ygbI ← / → ygbJ	DeoR family putative transcriptional regulator/putative dehydrogenase
RA	2,860,460	G→T	7.3%	R151S (CGC→AGC)	rpoS ←	RNA polymerase, sigma S (sigma 38) factor
RA	2,871,140	C→A	7.7%	intergenic (+163/+788)	iap → / ← ygbF	aminopeptidase in alkaline phosphatase isozyme conversion/CRISPR adaptation ssRNA endonuclease
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	2,888,584	G→T	100%	I185I (ATC→ATA)	ygcQ ←	putative flavoprotein
RA	2,890,009	C→A	5.9%	A407A (GCG→GCT)	ygcS ←	putative transporter
RA	2,893,446	T→A	52.8%	K63* (AAA→TAA)	ygcW ←	putative dehydrogenase
RA	2,895,997	C→A	32.0%	A248E (GCG→GAG)	ygcE →	putative kinase
RA	2,896,310	C→A	34.3%	S352R (AGC→AGA)	ygcE →	putative kinase
RA	2,920,080	C→A	5.7%	N138K (AAC→AAA)	ygdH →	UPF0717 family protein
RA	2,927,355	A→C	6.1%	intergenic (‑308/‑239)	fucA ← / → fucP	L‑fuculose‑1‑phosphate aldolase/L‑fucose transporter
RA	2,931,717	C→A	100%	N307K (AAC→AAA)	fucK →	L‑fuculokinase
RA	2,932,832	C→A	37.9%	R36S (CGT→AGT)	fucR →	l‑fucose operon activator
RA	2,932,835	C→T	59.7%	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	2,936,686	G→T	36.9%	intergenic (‑182/‑10)	ygdI ← / → csdA	DUF903 family verified lipoprotein/cysteine sulfinate desulfinase
RA	2,938,640	C→A	37.8%	D188Y (GAT→TAT)	tcdA ←	tRNA threonylcarbamoyladenosine dehydratase; sulfur acceptor for CsdA
RA	2,957,480	C→A	36.9%	L19F (TTG→TTT)	ppdA ←	putative prepilin peptidase‑dependent protein
RA	2,959,004	G→A	100%	I131I (ATC→ATT)	lgt ←	phosphatidylglycerol‑prolipoprotein diacylglyceryl transferase
RA	2,960,713	Δ1 bp	35.8%	coding (1081/2247 nt)	ptsP ←	fused PTS enzyme: PEP‑protein phosphotransferase (enzyme I)/GAF domain containing protein
RA	2,962,962	T→A	57.7%	intergenic (‑626/‑59)	rppH ← / → mutH	RNA pyrophosphohydrolase/methyl‑directed mismatch repair protein
RA	2,967,572	A→G	36.8%	F601S (TTT→TCT)	aas ←	fused 2‑acylglycerophospho‑ethanolamine acyl transferase/acyl‑acyl carrier protein synthetase
RA	2,969,887	C→A	8.7%	intergenic (‑143/‑71)	omrB ← / → galR	sRNA antisense regulator downregulates OM proteins and curli; positively regulated by OmpR/EnvZ, Hfq‑dependent/galactose‑inducible d‑galactose regulon transcriptional repressor; autorepressor
RA	2,978,850	C→A	42.1%	V34V (GTG→GTT)	yqeF ←	short chain acyltransferase
RA	2,979,127	C→T	14.3%	intergenic (‑176/‑79)	yqeF ← / → yqeG	short chain acyltransferase/putative transporter
RA	2,983,700	T→G	7.8%	Q7P (CAG→CCG)	yqeK ←	uncharacterized protein
RA	2,985,884	C→T	55.6%	I144I (ATC→ATT)	ygeH →	putative transcriptional regulator
RA	2,987,787	C→A	6.8%	pseudogene (47/60 nt)	pbl →	pseudogene, peptidoglycan‑binding enzyme family
RA	2,987,928	C→A	5.8%	pseudogene (524/633 nt)	ygeK ←	pseudogene; putative 2‑component transcriptional regulator
RA	2,988,554	G→A	52.9%	intergenic (‑103/+119)	ygeK ← / ← ygeN	pseudogene; putative 2‑component transcriptional regulator/pseudogene
RA	2,988,737	T→G	37.2%	pseudogene (383/447 nt)	ygeN ←	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	2,995,335	C→A	34.4%	V544V (GTC→GTA)	xdhA →	xanthine dehydrogenase, molybdenum binding subunit
RA	3,009,187	G→T	52.3%	intergenic (+90/‑232)	mocA → / → ygfK	CTP:molybdopterin cytidylyltransferase/putative Fe‑S subunit oxidoreductase subunit
RA	3,012,429	A→G	5.4%	N1004S (AAC→AGC)	ygfK →	putative Fe‑S subunit oxidoreductase subunit
RA	3,016,192	G→T	35.5%	M506I (ATG→ATT)	xdhD →	putative hypoxanthine oxidase, molybdopterin‑binding/Fe‑S binding
RA	3,017,285	G→T	100%	D871Y (GAC→TAC)	xdhD →	putative hypoxanthine oxidase, molybdopterin‑binding/Fe‑S binding
RA	3,017,379	C→A	7.0%	P902Q (CCG→CAG)	xdhD →	putative hypoxanthine oxidase, molybdopterin‑binding/Fe‑S binding
RA	3,019,203	G→T	41.6%	E27* (GAG→TAG)	guaD →	guanine deaminase
RA	3,019,343	G→T	36.6%	L73L (CTG→CTT)	guaD →	guanine deaminase
RA	3,024,081	A→C	53.3%	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	41.7%	Q318L (CAA→CTA)	uacT →	uric acid permease
RA	3,028,224	G→T	5.4%	L104I (CTC→ATC)	lysS ←	lysine tRNA synthetase, constitutive
RA	3,030,181	G→T	58.8%	H429N (CAT→AAT)	recJ ←	ssDNA exonuclease, 5' ‑‑> 3'‑specific
RA	3,035,271	G→T	41.7%	V200V (GTG→GTT)	ygfZ →	iron‑sulfur cluster repair protein, plumbagin resistance
RA	3,036,052	C→A	47.0%	S152S (TCG→TCT)	yqfA ←	hemolysin III family HylIII inner membrane protein
RA	3,041,026	C→A	6.8%	D459Y (GAC→TAC)	gcvP ←	glycine decarboxylase, PLP‑dependent, subunit (protein P) of glycine cleavage complex
RA	3,043,625	G→A	5.7%	I134I (ATC→ATT)	gcvT ←	aminomethyltransferase, tetrahydrofolate‑dependent, subunit (T protein) of glycine cleavage complex
RA	3,044,281	G→A	34.6%	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	41.7%	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	3,046,473	G→T	30.7%	N135K (AAC→AAA)	ubiH ←	2‑octaprenyl‑6‑methoxyphenol hydroxylase, FAD/NAD(P)‑binding
RA	3,047,237	G→T	6.8%	I321I (ATC→ATA)	pepP ←	proline aminopeptidase P II
RA	3,049,645	G→A	33.6%	E16K (GAA→AAA)	fau →	5‑formyltetrahydrofolate cyclo‑ligase family protein
RA	3,051,943	A→G	5.7%	intergenic (‑174/+82)	serA ← / ← rpiA	D‑3‑phosphoglycerate dehydrogenase/ribose 5‑phosphate isomerase, constitutive
RA	3,051,973	C→T	5.8%	intergenic (‑204/+52)	serA ← / ← rpiA	D‑3‑phosphoglycerate dehydrogenase/ribose 5‑phosphate isomerase, constitutive
RA	3,055,069	C→A	35.5%	V287V (GTC→GTA)	scpA →	methylmalonyl‑CoA mutase
RA	3,055,407	C→T	10.6%	S400L (TCG→TTG)	scpA →	methylmalonyl‑CoA mutase
RA	3,056,567	T→A	9.3%	F74L (TTT→TTA)	argK →	membrane ATPase/protein kinase
RA	3,058,692	C→T	41.1%	P178S (CCT→TCT)	scpC →	propionyl‑CoA:succinate CoA transferase
RA	3,058,769	C→T	55.7%	I203I (ATC→ATT)	scpC →	propionyl‑CoA:succinate CoA transferase
RA	3,064,914	G→T	92.5%	I356I (ATC→ATA)	pgk ←	phosphoglycerate kinase
RA	3,068,135	G→T	42.2%	F140L (TTC→TTA)	yggD ←	MtlR family putative transcriptional repressor
RA	3,068,854	C→A	42.5%	E230* (GAG→TAG)	yggF ←	fructose 1,6 bisphosphatase isozyme
RA	3,074,352	C→T	36.6%	D215N (GAC→AAC)	tktA ←	transketolase 1, thiamine triphosphate‑binding
RA	3,074,868	C→A	5.6%	D43Y (GAT→TAT)	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	38.3%	S12A (TCT→GCT)	metK →	S‑adenosylmethionine synthetase
RA	3,080,618	T→A	100%	V185E (GTG→GAG)	metK →	S‑adenosylmethionine synthetase
RA	3,080,922	C→A	7.6%	I286I (ATC→ATA)	metK →	S‑adenosylmethionine synthetase
RA	3,081,697	T→A	10.1%	C19S (TGC→AGC)	galP →	D‑galactose transporter
RA	3,088,065	C→A	53.3%	V125V (GTG→GTT)	yggR ←	putative PilT family AAA+ ATPase
RA	3,088,235	C→A	43.1%	A69S (GCC→TCC)	yggR ←	putative PilT family AAA+ ATPase
RA	3,093,737	A→C	31.1%	T117T (ACT→ACG)	ansB ←	periplasmic L‑asparaginase 2
RA	3,097,262	C→T	55.9%	F297F (TTC→TTT)	mutY →	adenine DNA glycosylase
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	3,120,216	C→A	100%	D389Y (GAT→TAT)	glcD ←	glycolate oxidase subunit, FAD‑linked
RA	3,121,999	G→T	5.5%	V123V (GTG→GTT)	glcC →	glycolate‑inducible glc operon transcriptional repressor; autorepressor
RA	3,132,601	T→G	38.3%	I172M (ATT→ATG)	yghU →	putative S‑transferase
RA	3,133,918	C→A	5.9%	E81* (GAA→TAA)	hybE ←	hydrogenase 2‑specific chaperone
RA	3,142,668	G→T	54.0%	L55I (CTC→ATC)	yqhA ←	UPF0114 family putative inner membrane protein
RA	3,144,158	C→A	100%	intergenic (+253/+19)	yghA → / ← exbD	putative oxidoreductase/membrane spanning protein in TonB‑ExbB‑ExbD complex
RA	3,152,523	C→A	6.3%	A661A (GCG→GCT)	ygiQ ←	Radical SAM superfamily protein
RA	3,154,570	A→C	7.1%	intergenic (‑65/+46)	ygiQ ← / ← ftsP	Radical SAM superfamily protein/septal ring component that protects the divisome from stress; multicopy suppressor of ftsI(Ts)
RA	3,164,049	G→T	36.4%	M69I (ATG→ATT)	qseC →	quorum sensing sensory histidine kinase in two‑component regulatory system with QseB
RA	3,164,230	C→A	56.3%	R130S (CGT→AGT)	qseC →	quorum sensing sensory histidine kinase in two‑component regulatory system with QseB
RA	3,173,669	G→T	100%	A189A (GCG→GCT)	ygiB →	DUF1190 family protein
RA	3,176,733	G→T	55.7%	intergenic (+51/+439)	zupT → / ← ribB	zinc transporter/3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase
RA	3,184,654	A→T	10.2%	N222Y (AAT→TAT)	yqiI →	fimbrial protein
RA	3,190,985	C→A	13.2%	P672P (CCG→CCT)	glnE ←	fused deadenylyltransferase/adenylyltransferase for glutamine synthetase
RA	3,208,581	C→A	39.8%	E84D (GAG→GAT)	mug ←	G/U mismatch‑specific DNA glycosylase; xanthine DNA glycosylase
RA	3,211,421	T→A	8.3%	K339* (AAG→TAG)	aer ←	fused signal transducer for aerotaxis sensory component/methyl accepting chemotaxis component
RA	3,214,709	C→A	7.5%	intergenic (‑103/‑116)	ygjH ← / → ebgR	putative tRNA binding protein; putative tRNA corner chaperone/transcriptional repressor
RA	3,217,289	A→T	54.7%	H433L (CAC→CTC)	ebgA →	evolved beta‑D‑galactosidase, alpha subunit
RA	3,221,666	G→T	11.2%	M169I (ATG→ATT)	ygjJ →	putative periplasmic protein
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	13.7%	Q93K (CAG→AAG)	fadH →	2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked
RA	3,226,008	G→T	6.8%	A329S (GCC→TCC)	fadH →	2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked
RA	3,229,926	C→A	45.5%	L10I (CTC→ATC)	ygjQ →	DUF218 superfamily protein
RA	3,230,012	C→A	5.0%	R38R (CGC→CGA)	ygjQ →	DUF218 superfamily protein
RA	3,230,492	C→A	6.5%	A198A (GCC→GCA)	ygjQ →	DUF218 superfamily protein
RA	3,230,857	C→G	57.0%	A63G (GCC→GGC)	ygjR →	putative NAD(P)‑dependent dehydrogenase
RA	3,231,349	A→C	47.7%	Q227P (CAG→CCG)	ygjR →	putative NAD(P)‑dependent dehydrogenase
RA	3,237,654	C→A	5.7%	M149I (ATG→ATT)	uxaC ←	uronate isomerase
RA	3,237,920	T→A	10.1%	K61* (AAA→TAA)	uxaC ←	uronate isomerase
RA	3,245,224	C→A	7.0%	P281Q (CCG→CAG)	yqjG →	putative S‑transferase
RA	3,245,848	G→T	100%	L62L (CTG→CTT)	yhaH →	DUF805 family inner membrane protein
RA	3,246,634	A→T	35.1%	intergenic (+8/+43)	yhaI → / ← yhaJ	DUF805 family inner membrane protein/LysR family putative transcriptional regulator
RA	3,249,389	C→A	10.3%	A208S (GCG→TCG)	yhaM ←	putative L‑serine dehydratase alpha chain
RA	3,252,258	C→A	100%	D251Y (GAT→TAT)	tdcG ←	L‑serine dehydratase 3, anaerobic
RA	3,254,793	C→A	17.9%	D329Y (GAT→TAT)	tdcE ←	pyruvate formate‑lyase 4/2‑ketobutyrate formate‑lyase
RA	3,261,002	A→G	5.6%	intergenic (+45/‑211)	tdcR → / → yhaB	L‑threonine dehydratase operon activator protein/uncharacterized protein
RA	3,263,315	T→C	5.4%	intergenic (+354/+260)	yhaC → / ← rnpB	pentapetide repeats‑related protein/RNase P, M1 RNA component
RA	3,263,466	G→T	43.1%	intergenic (+505/+109)	yhaC → / ← rnpB	pentapetide repeats‑related protein/RNase P, M1 RNA component
RA	3,263,502	C→T	8.6%	intergenic (+541/+73)	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	3,285,476	C→A	10.5%	I259I (ATC→ATA)	yraK →	putative fimbrial‑like adhesin protein
RA	3,296,612	G→T	61.3%	A255A (GCG→GCT)	yhbV →	U32 peptidase family protein
RA	3,299,314	C→A	5.6%	intergenic (‑138/+16)	mtr ← / ← deaD	tryptophan transporter of high affinity/ATP‑dependent RNA helicase
RA	3,302,027	G→T	100%	S86* (TCG→TAG)	nlpI ←	lipoprotein involved in osmotic sensitivity and filamentation
RA	3,312,862	T→A	38.1%	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	3,324,066	C→A	39.8%	E350* (GAA→TAA)	obgE ←	GTPase involved in cell partioning and DNA repair
RA	3,329,704	G→T	11.6%	V50V (GTC→GTA)	murA ←	UDP‑N‑acetylglucosamine 1‑carboxyvinyltransferase
RA	3,332,963	C→A	38.9%	A154A (GCG→GCT)	mlaF ←	ABC transporter maintaining OM lipid asymmetry, ATP‑binding protein
RA	3,334,892	G→T	25.2%	D90Y (GAT→TAT)	kdsD →	D‑arabinose 5‑phosphate isomerase
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	57.1%	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	3,357,229	C→A	29.4%	S355* (TCG→TAG)	yhcD →	putative outer membrane fimbrial subunit usher protein
RA	3,360,045	G→T	20.6%	F11L (TTC→TTA)	insH1 ←	IS5 transposase and trans‑activator
RA	3,360,830	A→T	22.0%	A182A (GCA→GCT)	yhcF →	putative transcriptional regulator
RA	3,365,607	G→T	100%	I109I (ATC→ATA)	nanT ←	sialic acid transporter
RA	3,372,318	G→T	42.9%	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	3,374,563	C→A	6.7%	I154I (ATC→ATA)	degQ →	serine endoprotease, periplasmic
RA	3,375,260	G→T	100%	D387Y (GAT→TAT)	degQ →	serine endoprotease, periplasmic
RA	3,380,174	C→A	36.6%	S458S (TCG→TCT)	aaeB ←	p‑hydroxybenzoic acid efflux system component
RA	3,384,533	G→T	8.0%	V285V (GTC→GTA)	tldD ←	putative peptidase
RA	3,386,672	C→A	39.4%	P982P (CCG→CCT)	yhdP ←	DUF3971‑AsmA2 domains protein
RA	3,389,508	C→A	5.9%	R37L (CGT→CTT)	yhdP ←	DUF3971‑AsmA2 domains protein
RA	3,395,059	C→A	47.0%	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	3,397,316	C→A	7.6%	G158G (GGC→GGA)	acuI →	putative acryloyl‑CoA reductase
RA	3,399,100	C→A	43.9%	F102L (TTC→TTA)	accB →	acetyl CoA carboxylase, BCCP subunit
RA	3,407,007	G→A	55.8%	intergenic (‑183/‑216)	acrS ← / → acrE	acrAB operon transcriptional repressor/cytoplasmic membrane lipoprotein
RA	3,412,733	G→T	40.8%	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	6.7%	noncoding (12/120 nt)	rrfF ←	5S ribosomal RNA of rrnD operon
RA	3,416,899	A→G	6.1%	noncoding (3/120 nt)	rrfF ←	5S ribosomal RNA of rrnD operon
RA	3,425,514	C→A	6.3%	E104* (GAA→TAA)	smg ←	DUF494 family putative periplasmic protein
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	3,451,616	T→G	33.9%	V627V (GTT→GTG)	gspD →	general secretory pathway component, cryptic
RA	3,452,566	C→A	9.5%	T290K (ACG→AAG)	gspE →	general secretory pathway component, cryptic
RA	3,455,867	C→A	100%	I55I (ATC→ATA)	gspJ →	putative general secretory pathway component, cryptic
RA	3,460,771	T→A	13.0%	E814D (GAA→GAT)	chiA ←	periplasmic endochitinase
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	3,481,214	G→T	10.0%	P355P (CCG→CCT)	yhfK →	putative transporter, FUSC superfamily inner membrane protein, tandem domains
RA	3,483,095	C→A	38.7%	V149F (GTT→TTT)	argD ←	bifunctional acetylornithine aminotransferase/ succinyldiaminopimelate aminotransferase
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	3,501,571	C→A	100%	G127C (GGC→TGC)	php ←	phosphotriesterase homology protein
RA	3,504,143	G→T	59.0%	R65S (CGT→AGT)	yhfX ←	putative pyridoxal 5'‑phosphate binding protein
RA	3,507,749	G→T	92.3%	H224N (CAT→AAT)	rpe ←	D‑ribulose‑5‑phosphate 3‑epimerase
RA	3,508,852	G→T	8.6%	P141T (CCC→ACC)	dam ←	DNA adenine methyltransferase
RA	3,510,311	C→A	37.7%	G119C (GGT→TGT)	damX ←	cell division protein that binds to the septal ring
RA	3,513,424	A→T	59.5%	V213V (GTT→GTA)	hofQ ←	DNA catabolic putative fimbrial transporter
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	3,525,950	C→T	33.1%	intergenic (‑152/‑227)	yhgE ← / → pck	DUF4153 family putative inner membrane protein/phosphoenolpyruvate carboxykinase
RA	3,543,775	T→G	9.1%	A686A (GCA→GCC)	malP ←	maltodextrin phosphorylase
RA	3,543,959	G→T	100%	A625E (GCG→GAG)	malP ←	maltodextrin phosphorylase
RA	3,544,521	G→T	24.8%	H438N (CAC→AAC)	malP ←	maltodextrin phosphorylase
RA	3,545,107	G→T	12.4%	A242A (GCC→GCA)	malP ←	maltodextrin phosphorylase
RA	3,561,574	C→A	100%	W372L (TGG→TTG)	glgC ←	glucose‑1‑phosphate adenylyltransferase
RA	3,566,544	C→A	5.1%	E107* (GAA→TAA)	glgB ←	1,4‑alpha‑glucan branching enzyme
RA	3,571,618	C→A	43.7%	D157Y (GAT→TAT)	gntR ←	d‑gluconate inducible gluconate regulon transcriptional repressor
RA	3,577,507	C→A	43.7%	I157I (ATC→ATA)	insB1 →	IS1 transposase B
RA	3,577,849	G→A	11.3%	intergenic (+180/‑270)	yrhA → / → yrhB	pseudogene, interrupted by IS1E/stable heat shock chaperone
RA	3,580,673	G→T	36.6%	R124I (AGA→ATA)	yhhA →	DUF2756 family protein
RA	3,585,079	C→A	33.6%	A203S (GCC→TCC)	ugpB ←	glycerol‑3‑phosphate transporter subunit
RA	3,588,904	A→T	37.0%	L287Q (CTG→CAG)	livH ←	leucine/isoleucine/valine transporter subunit
RA	3,593,024	G→A	5.0%	intergenic (‑6/+265)	livJ ← / ← rpoH	leucine/isoleucine/valine transporter subunit/RNA polymerase, sigma 32 (sigma H) factor
RA	3,595,859	C→A	5.6%	M83I (ATG→ATT)	ftsE ←	putative ABC superfamily transporter ATP‑binding subunit
RA	3,609,958	C→A	45.1%	I139I (ATC→ATA)	nikC →	nickel transporter subunit
RA	3,612,551	G→T	8.3%	intergenic (+202/‑1)	nikR → / → rhsB	transcriptional repressor, Ni‑binding/Rhs family putative polymorphic toxin, putative neighboring cell growth inhibitor
RA	3,612,708	C→A	48.1%	L53I (CTC→ATC)	rhsB →	Rhs family putative polymorphic toxin, putative neighboring cell growth inhibitor
RA	3,620,035	C→A	10.6%	T43T (ACG→ACT)	yhhJ ←	inner membrane putative ABC transporter permease
RA	3,622,863	G→T	30.2%	V12V (GTC→GTA)	rbbA ←	ribosome‑associated ATPase: ATP‑binding protein/ATP‑binding membrane protein
RA	3,629,439	C→A	40.6%	intergenic (+186/+129)	yhiM → / ← yhiN	acid resistance protein, inner membrane/putative oxidoreductase
RA	3,632,600	T→G	40.5%	intergenic (+99/+145)	pitA → / ← uspB	phosphate transporter, low‑affinity; tellurite importer/universal stress (ethanol tolerance) protein B
RA	3,633,738	G→T	7.7%	D90Y (GAC→TAC)	uspA →	universal stress global response regulator
RA	3,639,551	C→A	35.9%	T269T (ACC→ACA)	rlmJ →	23S rRNA m(6)A2030 methyltransferase, SAM‑dependent
RA	3,642,200	C→A	11.3%	R105R (CGA→AGA)	arsR →	arsenical resistance operon transcriptional repressor; autorepressor
RA	3,646,763	C→A	7.9%	pseudogene (173/483 nt)	yhiS →	pseudogene
RA	3,652,706	G→T	10.8%	V39F (GTC→TTC)	mdtE →	anaerobic multidrug efflux transporter, ArcA‑regulated
RA	3,662,660	T→C	100%	intergenic (‑112/‑292)	yhjA ← / → treF	putative cytochrome C peroxidase/cytoplasmic trehalase
RA	3,667,977	C→T	6.0%	intergenic (+242/‑169)	yhjD → / → yhjE	inner membrane putative BrbK family alternate lipid exporter/MFS superfamily sugar transport 1 family protein
RA	3,673,169	C→A	39.5%	L131I (CTC→ATC)	kdgK →	2‑dehydro‑3‑deoxygluconokinase
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	3,680,910	G→T	100%	H542N (CAT→AAT)	bcsC ←	cellulose synthase subunit
RA	3,689,369	C→A	9.9%	A59A (GCG→GCT)	yhjR ←	DUF2629 family protein
RA	3,698,875	G→T	54.6%	F92L (TTC→TTA)	dppB ←	dipeptide/heme transporter
RA	3,701,561	G→A	34.7%	intergenic (‑496/+415)	dppA ← / ← proK	dipeptide transporter/tRNA‑Pro
RA	3,703,272	C→A	35.1%	A188A (GCG→GCT)	eptB ←	KDO phosphoethanolamine transferase, Ca(2+)‑inducible
RA	3,708,861	C→A	37.0%	E298D (GAG→GAT)	bisC ←	biotin sulfoxide reductase
RA	3,710,595	C→A	6.2%	intergenic (+29/‑75)	yiaD → / → ghrB	multicopy suppressor of bamB; outer membrane lipoprotein/glyoxylate/hydroxypyruvate reductase B
RA	3,717,788	C→A	100%	P297P (CCG→CCT)	glyQ ←	glycine tRNA synthetase, alpha subunit
RA	3,718,959	C→A	37.9%	L38F (TTG→TTT)	ysaB ←	uncharacterized protein
RA	3,730,615	C→A	32.4%	intergenic (‑78/‑242)	bax ← / → malS	putative glucosaminidase/alpha‑amylase
RA	3,738,431	C→A	100%	P90T (CCA→ACA)	yiaN →	2,3‑diketo‑L‑gulonate TRAP transporter large permease protein
RA	3,759,388	C→A	32.9%	N1282K (AAC→AAA)	rhsA →	Rhs family protein, putative polymorphic toxin; putative polysaccharide synthesis/export protein; putative neighboring cell growth inhibitor
RA	3,767,000	G→T	51.6%	D454Y (GAC→TAC)	mtlA →	fused mannitol‑specific PTS enzymes: IIA components/IIB components/IIC components
RA	3,767,143	C→A	5.9%	I501I (ATC→ATA)	mtlA →	fused mannitol‑specific PTS enzymes: IIA components/IIB components/IIC components
RA	3,777,313	A→T	5.3%	V59E (GTA→GAA)	secB ←	protein export chaperone
RA	3,779,324	C→A	42.9%	F235L (TTC→TTA)	gpmM →	phosphoglycero mutase III, cofactor‑independent
RA	3,779,927	T→A	6.1%	G436G (GGT→GGA)	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	3,791,588	T→A	36.5%	intergenic (+21/+11)	waaL → / ← waaU	O‑antigen ligase/lipopolysaccharide core biosynthesis
RA	3,793,653	G→T	44.3%	R225S (CGT→AGT)	waaY ←	lipopolysaccharide core biosynthesis protein
RA	3,793,839	G→T	8.5%	R163S (CGT→AGT)	waaY ←	lipopolysaccharide core biosynthesis protein
RA	3,799,108	C→A	40.8%	R68L (CGG→CTG)	waaP ←	kinase that phosphorylates core heptose of lipopolysaccharide
RA	3,801,096	C→A	6.5%	A121A (GCG→GCT)	waaQ ←	lipopolysaccharide core biosynthesis protein
RA	3,810,195	C→A	100%	R54S (CGT→AGT)	yicC →	UPF0701 family protein
RA	3,813,429	T→A	5.7%	S368C (AGC→TGC)	ligB ←	DNA ligase, NAD(+)‑dependent
RA	3,814,302	T→A	38.3%	S77C (AGC→TGC)	ligB ←	DNA ligase, NAD(+)‑dependent
RA	3,816,601	A→T	100%	H281L (CAC→CTC)	spoT →	bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase
RA	3,817,272	C→A	5.0%	Q505K (CAG→AAG)	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	44.3%	T456K (ACG→AAG)	recG →	ATP‑dependent DNA helicase
RA	3,822,340	A→C	7.6%	Q12H (CAA→CAC)	xanP →	xanthine permease
RA	3,825,702	C→A	100%	K732N (AAG→AAT)	yicI ←	putative alpha‑glucosidase
RA	3,828,206	T→A	5.2%	S362C (AGT→TGT)	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	3,835,154	G→A	44.2%	intergenic (‑55/+156)	nepI ← / ← yicN	putative transporter/DUF1198 family protein
RA	3,840,727	C→A	5.5%	A420S (GCC→TCC)	uhpC ←	membrane protein regulates uhpT expression
RA	3,844,347	C→A	11.2%	V36F (GTT→TTT)	ilvN ←	acetolactate synthase 1 small subunit
RA	3,846,307	C→A	8.0%	A14A (GCG→GCT)	ivbL ←	ilvB operon leader peptide
RA	3,847,167	C→A	5.0%	intergenic (+165/‑115)	tisB → / → emrD	toxic membrane persister formation peptide, LexA‑regulated/multidrug efflux system protein
RA	3,851,275	G→T	9.7%	H164N (CAT→AAT)	yidJ ←	sulfatase/phosphatase superfamily protein
RA	3,858,274	A→C	35.6%	F454V (TTT→GTT)	yidE ←	putative transporter
RA	3,860,159	C→A	100%	P33P (CCG→CCT)	ibpB ←	heat shock chaperone
RA	3,860,327	C→A	58.4%	intergenic (‑70/+42)	ibpB ← / ← ibpA	heat shock chaperone/heat shock chaperone
RA	3,860,653	C→A	63.0%	E44* (GAA→TAA)	ibpA ←	heat shock chaperone
RA	3,865,120	C→A	57.2%	intergenic (‑30/+90)	dgoT ← / ← dgoD	D‑galactonate transporter/galactonate dehydratase
RA	3,867,062	C→A	35.3%	R258L (CGC→CTC)	dgoK ←	2‑oxo‑3‑deoxygalactonate kinase
RA	3,877,248	C→A	5.6%	intergenic (‑159/‑448)	dnaA ← / → rpmH	chromosomal replication initiator protein DnaA, DNA‑binding transcriptional dual regulator/50S ribosomal subunit protein L34
RA	3,879,501	T→A	45.2%	F356I (TTC→ATC)	yidC →	membrane protein insertase
RA	3,889,578	C→A	43.9%	R131L (CGC→CTC)	purP ←	adenine permease, high affinity; adenine:H+ symporter
RA	3,890,865	T→A	8.7%	intergenic (+66/‑1)	yieH → / → cbrB	phosphoenolpyruvate and 6‑phosphogluconate phosphatase/PRK09823 family inner membrane protein, creBC regulon
RA	3,894,632	C→A	29.4%	V317F (GTC→TTC)	bglH ←	carbohydrate‑specific outer membrane porin, cryptic
RA	3,900,078	G→A	5.9%	intergenic (‑151/+135)	bglG ← / ← phoU	transcriptional antiterminator of the bgl operon/negative regulator of PhoR/PhoB two‑component regulator
RA	3,901,867	T→G	5.3%	intergenic (‑141/+42)	pstB ← / ← pstA	phosphate transporter subunit/phosphate transporter subunit
RA	3,903,417	G→T	6.7%	I114I (ATC→ATA)	pstC ←	phosphate transporter subunit
RA	3,910,894	C→A	100%	M244I (ATG→ATT)	atpG ←	F1 sector of membrane‑bound ATP synthase, gamma subunit
RA	3,916,052	C→A	39.1%	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	3,921,331	C→A	6.6%	R273S (CGC→AGC)	asnA →	asparagine synthetase A
RA	3,923,028	C→A	50.6%	D476Y (GAC→TAC)	ravA ←	hexameric AAA+ MoxR family ATPase, putative molecular chaperone
RA	3,926,536	G→T	8.7%	E621* (GAA→TAA)	kup →	potassium transporter
RA	3,926,831	G→T	94.1%	D41Y (GAT→TAT)	rbsD →	putative cytoplasmic sugar‑binding protein
RA	3,927,972	G→T	56.6%	E279* (GAA→TAA)	rbsA →	fused D‑ribose transporter subunits of ABC superfamily: ATP‑binding components
RA	3,930,795	G→T	6.6%	A48S (GCT→TCT)	rbsK →	ribokinase
RA	3,933,680	G→T	7.2%	S98* (TCG→TAG)	hsrA ←	putative multidrug or homocysteine efflux system
RA	3,933,862	G→T	41.5%	I37I (ATC→ATA)	hsrA ←	putative multidrug or homocysteine efflux system
RA	3,933,926	G→T	6.4%	A16E (GCG→GAG)	hsrA ←	putative multidrug or homocysteine efflux system
RA	3,935,100	G→T	58.2%	intergenic (‑413/‑68)	yieP ← / → rrsC	putative transcriptional regulator/16S ribosomal RNA of rrnC operon
RA	3,945,503	A→T	45.6%	pseudogene (602/663 nt)	ilvG →	pseudogene, acetolactate synthase 2 large subunit, valine‑insensitive; acetolactate synthase II, large subunit, cryptic, interrupted
RA	3,950,395	C→A	33.9%	E262D (GAG→GAT)	ilvY ←	transcriptional activator of ilvC; autorepressor
RA	3,952,658	C→T	38.2%	D443D (GAC→GAT)	ilvC →	ketol‑acid reductoisomerase, NAD(P)‑binding
RA	3,952,842	A→C	10.6%	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	45.1%	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	57.6%	A169A (GCG→GCT)	rffH →	glucose‑1‑phosphate thymidylyltransferase
RA	3,969,710	G→T	100%	G25C (GGT→TGT)	wzxE →	O‑antigen translocase
RA	3,970,026	C→A	38.0%	A130D (GCC→GAC)	wzxE →	O‑antigen translocase
RA	3,977,650	A→T	45.1%	intergenic (+97/+62)	aslB → / ← aslA	putative AslA‑specific sulfatase‑maturating enzyme/putative Ser‑type periplasmic non‑aryl sulfatase
RA	3,978,810	G→T	15.6%	I186I (ATC→ATA)	aslA ←	putative Ser‑type periplasmic non‑aryl sulfatase
RA	3,988,075	T→A	100%	V65E (GTG→GAG)	yifL →	putative lipoprotein
RA	3,990,572	C→A	45.4%	I10I (ATC→ATA)	yigB →	5‑amino‑6‑(5‑phospho‑D‑ribitylamino)uracil phosphatase; pyrimidine phosphatase; riboflavin synthesis
RA	3,992,341	G→T	7.6%	V333V (GTG→GTT)	uvrD →	DNA‑dependent ATPase I and helicase II
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	4,000,333	G→T	6.9%	A370A (GCG→GCT)	recQ →	ATP‑dependent DNA helicase
RA	4,009,705	G→A	100%	intergenic (‑176/‑86)	ysgA ← / → udp	putative carboxymethylenebutenolidase/uridine phosphorylase
RA	4,019,131	G→T	9.4%	D262Y (GAT→TAT)	ubiD →	3‑octaprenyl‑4‑hydroxybenzoate decarboxylase
RA	4,024,827	G→T	60.7%	D103Y (GAT→TAT)	pepQ →	proline dipeptidase
RA	4,035,421	G→T	54.8%	intergenic (‑62/‑8)	mobA ← / → yihD	molybdopterin‑guanine dinucleotide synthase/DUF1040 protein YihD
RA	4,046,172	A→T	46.5%	K256N (AAA→AAT)	hemN →	coproporphyrinogen III oxidase, SAM and NAD(P)H dependent, oxygen‑independent
RA	4,052,201	C→A	37.3%	F145L (TTC→TTA)	typA →	GTP‑binding protein
RA	4,055,246	T→A	8.4%	L241Q (CTG→CAG)	yihM →	putative sugar phosphate isomerase
RA	4,056,018	T→A	100%	F138I (TTC→ATC)	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	4,069,390	G→T	10.9%	D160Y (GAT→TAT)	yihX →	alpha‑D‑Glucose‑1‑P phosphatase, anomer‑specific
RA	4,077,665	G→T	45.5%	V506V (GTC→GTA)	fdoG ←	formate dehydrogenase‑O, large subunit
RA	4,087,476	A→T	36.4%	intergenic (‑126/‑188)	rhaD ← / → rhaS	pseudogene, truncated, rhamnulose‑phosphate aldolase/transcriptional activator of rhaBAD and rhaT
RA	4,087,754	C→A	44.4%	H31N (CAT→AAT)	rhaS →	transcriptional activator of rhaBAD and rhaT
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	46.1%	G159S (GGT→AGT)	cpxR ←	response regulator in two‑component regulatory system with CpxA
RA	4,096,555	G→T	7.2%	S53S (TCG→TCT)	fieF →	ferrous iron and zinc transporter
RA	4,097,282	C→A	38.0%	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	33.6%	D108Y (GAT→TAT)	glpX ←	fructose 1,6‑bisphosphatase II
RA	4,105,662	A→T	37.8%	W497R (TGG→AGG)	glpK ←	glycerol kinase
RA	4,122,248	A→T	56.0%	intergenic (+53/‑296)	metL → / → metF	Bifunctional aspartokinase/homoserine dehydrogenase 2/5,10‑methylenetetrahydrofolate reductase
RA	4,127,022	T→G	100%	E188D (GAA→GAC)	yijF ←	DUF1287 family protein
RA	4,134,111	G→T	41.4%	L63L (CTG→CTT)	pflD →	putative glycine radical domain‑containing pyruvate formate‑lyase
RA	4,143,375	A→G	8.2%	intergenic (‑349/+249)	ppc ← / ← argE	phosphoenolpyruvate carboxylase/acetylornithine deacetylase
RA	4,143,605	G→T	35.9%	intergenic (‑579/+19)	ppc ← / ← argE	phosphoenolpyruvate carboxylase/acetylornithine deacetylase
RA	4,144,787	C→A	39.4%	intergenic (‑12/‑142)	argE ← / → argC	acetylornithine deacetylase/N‑acetyl‑gamma‑glutamylphosphate reductase, NAD(P)‑binding
RA	4,145,195	G→T	37.9%	A89A (GCG→GCT)	argC →	N‑acetyl‑gamma‑glutamylphosphate reductase, NAD(P)‑binding
RA	4,150,043	G→T	38.4%	H226N (CAC→AAC)	sthA ←	pyridine nucleotide transhydrogenase, soluble
RA	4,150,197	G→T	8.6%	H174Q (CAC→CAA)	sthA ←	pyridine nucleotide transhydrogenase, soluble
RA	4,154,083	G→T	10.2%	D173Y (GAT→TAT)	btuB →	vitamin B12/cobalamin outer membrane transporter
RA	4,163,570	T→A	44.3%	I187I (ATT→ATA)	birA →	bifunctional biotin‑[acetylCoA carboxylase] holoenzyme synthetase/ DNA‑binding transcriptional repressor, bio‑5'‑AMP‑binding
RA	4,168,773	A→T	36.8%	A133A (GCA→GCT)	rplK →	50S ribosomal subunit protein L11
RA	4,173,145	A→T	60.9%	Q658L (CAG→CTG)	rpoB →	RNA polymerase, beta subunit
RA	4,173,546	G→T	8.1%	G792C (GGT→TGT)	rpoB →	RNA polymerase, beta subunit
RA	4,176,823	G→T	100%	D516Y (GAC→TAC)	rpoC →	RNA polymerase, beta prime subunit
RA	4,178,758	G→T	32.4%	G1161C (GGT→TGT)	rpoC →	RNA polymerase, beta prime subunit
RA	4,198,010	T→A	25.7%	intergenic (‑550/‑65)	purH ← / → rrsE	fused IMP cyclohydrolase/phosphoribosylaminoimidazolecarboxamide formyltransferase/16S ribosomal RNA of rrnE operon
RA	4,207,552	G→T	53.0%	M172I (ATG→ATT)	aceA →	isocitrate lyase
RA	4,207,558	G→T	37.6%	A174A (GCG→GCT)	aceA →	isocitrate lyase
RA	4,208,354	G→T	9.6%	intergenic (+13/‑170)	aceA → / → aceK	isocitrate lyase/isocitrate dehydrogenase kinase/phosphatase
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	52.8%	T270S (ACC→TCC)	metH →	homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent
RA	4,218,928	G→A	40.9%	E424K (GAA→AAA)	yjbB →	putative Na+/Pi‑cotransporter
RA	4,220,948	G→T	42.3%	D223Y (GAT→TAT)	rluF →	23S rRNA pseudouridine(2604) synthase
RA	4,222,642	G→T	7.8%	L174I (CTC→ATC)	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	50.1%	A160E (GCG→GAG)	malE ←	maltose transporter subunit
RA	4,241,633	C→T	36.3%	pseudogene (745/1323 nt)	yjbI →	pseudogene, SopA‑related, pentapeptide repeats‑containing
RA	4,242,509	C→T	54.7%	L26F (CTC→TTC)	ubiC →	chorismate‑‑pyruvate lyase
RA	4,247,553	A→T	6.0%	N171Y (AAT→TAT)	lexA →	transcriptional repressor of SOS regulon
RA	4,257,593	C→T	7.0%	N184N (AAC→AAT)	tyrB →	tyrosine aminotransferase, tyrosine‑repressible, PLP‑dependent
RA	4,265,064	C→A	94.7%	intergenic (‑95/‑335)	yjcB ← / → yjcC	putative inner membrane protein/putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	4,271,906	C→T	38.0%	E366E (GAG→GAA)	yjcF ←	pentapeptide repeats protein
RA	4,273,297	A→T	36.7%	W512R (TGG→AGG)	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	100%	intergenic (‑1/+199)	yjcH ← / ← acs	DUF485 family inner membrane protein/acetyl‑CoA synthetase
RA	4,278,325	T→A	38.8%	C212S (TGC→AGC)	nrfA →	nitrite reductase, formate‑dependent, cytochrome
RA	4,284,205	T→C	7.8%	intergenic (+138/‑204)	nrfG → / → gltP	heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfG/glutamate/aspartate:proton symporter
RA	4,285,213	G→T	41.6%	D269Y (GAT→TAT)	gltP →	glutamate/aspartate:proton symporter
RA	4,286,311	C→A	38.5%	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	4,297,485	G→C	57.4%	G44G (GGC→GGG)	alsK ←	D‑allose kinase
RA	4,297,846	C→A	100%	M150I (ATG→ATT)	alsE ←	allulose‑6‑phosphate 3‑epimerase
RA	4,300,333	T→A	37.8%	E155D (GAA→GAT)	alsA ←	fused D‑allose transporter subunits of ABC superfamily: ATP‑binding components
RA	4,303,614	T→A	100%	*150R (TGA→AGA)	rpiB →	ribose 5‑phosphate isomerase B/allose 6‑phosphate isomerase
RA	4,304,151	T→G	5.6%	intergenic (+137/+10)	yjdP → / ← phnP	putative periplasmic protein/5‑phospho‑alpha‑D‑ribosyl 1,2‑cyclic phosphate phosphodiesterase
RA	4,308,395	G→T	32.6%	H63N (CAC→AAC)	phnK ←	carbon‑phosphorus lyase complex subunit, putative ATP transporter ATP‑binding protein
RA	4,315,765	A→G	5.9%	intergenic (‑207/+451)	yjdN ← / ← yjdM	metalloprotein superfamily protein/zinc‑ribbon family protein
RA	4,316,794	G→A	5.7%	intergenic (‑243/‑158)	yjdM ← / → crfC	zinc‑ribbon family protein/clamp‑binding sister replication fork colocalization protein, dynamin‑related
RA	4,317,974	G→T	37.8%	A341A (GCG→GCT)	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	4,331,530	T→A	8.2%	intergenic (‑85/‑198)	melR ← / → melA	melibiose operon transcriptional regulator; autoregulator/alpha‑galactosidase, NAD(P)‑binding
RA	4,335,003	A→T	11.8%	Y125N (TAC→AAC)	yjdF ←	DUF2238 family inner membrane protein
RA	4,335,195	G→T	31.9%	L61I (CTC→ATC)	yjdF ←	DUF2238 family inner membrane protein
RA	4,335,352	T→A	5.1%	L8F (TTA→TTT)	yjdF ←	DUF2238 family inner membrane protein
RA	4,336,681	A→T	40.3%	Y155N (TAC→AAC)	fumB ←	anaerobic class I fumarate hydratase (fumarase B)
RA	4,337,717	G→T	43.1%	A282E (GCG→GAG)	dcuB ←	C4‑dicarboxylate transporter, anaerobic; DcuS co‑sensor
RA	4,341,023	A→T	94.1%	Y153N (TAC→AAC)	dcuS ←	sensory histidine kinase in two‑component regulatory system with DcuR, regulator of anaerobic fumarate respiration
RA	4,345,995	C→A	44.0%	V78V (GTG→GTT)	dtpC ←	dipeptide and tripeptide permease
RA	4,346,015	G→T	41.9%	L72I (CTC→ATC)	dtpC ←	dipeptide and tripeptide permease
RA	4,348,443	C→A	13.1%	intergenic (‑9/+71)	cadA ← / ← cadB	lysine decarboxylase, acid‑inducible/putative lysine/cadaverine transporter
RA	4,354,610	A→T	44.5%	W84R (TGG→AGG)	dsbD ←	fused thiol:disulfide interchange protein: activator of DsbC/conserved protein
RA	4,356,312	G→T	8.5%	I93I (ATC→ATA)	dcuA ←	C4‑dicarboxylate antiporter
RA	4,357,095	A→C	49.5%	V350V (GTT→GTG)	aspA ←	aspartate ammonia‑lyase
RA	4,358,920	G→T	58.9%	R147L (CGC→CTC)	fxsA →	suppressor of F exclusion of phage T7
RA	4,372,891	A→T	42.9%	A144A (GCA→GCT)	epmA →	Elongation Factor P Lys34 lysyltransferase
RA	4,376,178	C→A	59.7%	E1004* (GAA→TAA)	mscM ←	mechanosensitive channel protein, miniconductance
RA	4,378,778	G→T	59.0%	S137* (TCG→TAG)	mscM ←	mechanosensitive channel protein, miniconductance
RA	4,382,399	A→C	8.0%	intergenic (+35/‑1)	glyX → / → glyY	tRNA‑Gly/tRNA‑Gly
RA	4,388,902	G→T	100%	A558A (GCG→GCT)	mutL →	methyl‑directed mismatch repair protein
RA	4,394,391	G→T	6.3%	T63T (ACG→ACT)	yjeT →	DUF2065 family protein
RA	4,394,875	G→T	57.7%	A124A (GCG→GCT)	purA →	adenylosuccinate synthetase
RA	4,396,598	A→T	100%	E43V (GAA→GTA)	rnr →	exoribonuclease R, RNase R
RA	4,402,850	G→T	53.8%	L2L (CTG→CTT)	yjfC →	ATP‑Grasp family ATPase
RA	4,405,735	G→T	40.3%	intergenic (+18/+99)	aidB → / ← yjfN	DNA alkylation damage repair protein; flavin‑containing DNA binding protein, weak isovaleryl CoA dehydrogenase/DUF1471 family periplasmic protein
RA	4,417,551	A→C	100%	pseudogene (41/402 nt)	ytfA →	pseudogene, related to transcriptional regulators
RA	4,421,791	G→T	7.1%	R4S (CGC→AGC)	ytfE ←	iron‑sulfur cluster repair protein RIC
RA	4,428,092	G→T	61.9%	G190V (GGA→GTA)	ytfI →	uncharacterized protein
RA	4,440,321	C→A	34.8%	I181I (ATC→ATA)	ytfQ →	galactofuranose binding proteint: periplasmic‑binding component of ABC superfamily
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	4,463,091	G→T	5.3%	intergenic (‑65/+66)	yjgH ← / ← bdcA	UPF0131 family protein/c‑di‑GMP‑binding biofilm dispersal mediator protein
RA	4,465,624	C→T	35.3%	S124F (TCC→TTC)	yjgL →	uncharacterized protein
RA	4,468,165	A→G	100%	intergenic (‑37/‑125)	argI ← / → rraB	ornithine carbamoyltransferase 1/protein inhibitor of RNase E
RA	4,469,550	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	58.5%	R928S (CGT→AGT)	valS ←	valyl‑tRNA synthetase
RA	4,474,993	G→T	44.5%	S259* (TCG→TAG)	pepA ←	multifunctional aminopeptidase A: a cyteinylglycinase, transcription regulator and site‑specific recombination factor
RA	4,480,249	G→T	8.8%	S236R (AGC→AGA)	idnR ←	transcriptional repressor, 5‑gluconate‑binding
RA	4,481,249	A→T	33.4%	V365E (GTG→GAG)	idnT ←	L‑idonate and D‑gluconate transporter
RA	4,487,680	G→T	7.9%	pseudogene (1189/1266 nt)	intB →	pseudogene, integrase homology;IS, phage, Tn; Phage‑related functions and prophages; KpLE2 phage‑like element; P4‑like integrase
RA	4,494,721	G→A	51.6%	A283T (GCC→ACC)	yjhB →	putative transporter
RA	4,495,349	G→T	48.0%	K82N (AAG→AAT)	yjhC →	putative oxidoreductase
RA	4,495,560	A→T	35.4%	N153Y (AAC→TAC)	yjhC →	putative oxidoreductase
RA	4,512,693	T→A	100%	K407* (AAG→TAG)	yjhG ←	putative dehydratase
RA	4,516,177	C→A	23.3%	D177Y (GAT→TAT)	sgcR ←	putative DNA‑binding transcriptional regulator
RA	4,523,001	T→A	57.2%	intergenic (‑1/+55)	yjhP ← / ← yjhQ	putative methyltransferase/putative acetyltransferase
RA	4,524,073	G→T	8.8%	intergenic (‑203/+174)	yjhX ← / ← yjhZ	UPF0386 family protein/pseudogene, rimK paralog, C‑terminal fragment
RA	4,525,234	G→A	100%	pseudogene (415/1029 nt)	yjhR →	pseudogene, helicase family; putative frameshift suppressor
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	24.5%	intergenic (+85/‑393)	fimB → / → fimE	tyrosine recombinase/inversion of on/off regulator of fimA/tyrosine recombinase/inversion of on/off regulator of fimA
RA	4,534,644	C→T	8.6%	S175F (TCT→TTT)	fimC →	periplasmic chaperone
RA	4,535,507	C→A	38.9%	R199R (CGG→AGG)	fimD →	fimbrial usher outer membrane porin protein; FimCD chaperone‑usher
RA	4,541,445	G→A	11.1%	intergenic (‑332/‑8)	gntP ← / → uxuA	fructuronate transporter/mannonate hydrolase
RA	4,541,449	A→T	54.7%	intergenic (‑336/‑4)	gntP ← / → uxuA	fructuronate transporter/mannonate hydrolase
RA	4,545,657	C→A	8.5%	G161* (GGA→TGA)	yjiC ←	uncharacterized protein
RA	4,552,902	A→T	33.2%	N173K (AAT→AAA)	yjiK ←	SdiA‑regulated family putative membrane‑anchored protein; putative phytase‑like esterase
RA	4,555,156	G→T	100%	A171E (GCG→GAG)	yjiM ←	putative 2‑hydroxyglutaryl‑CoA dehydratase
RA	4,555,620	T→G	7.9%	E16D (GAA→GAC)	yjiM ←	putative 2‑hydroxyglutaryl‑CoA dehydratase
RA	4,562,043	C→A	100%	intergenic (+311/‑188)	yjiS → / → yjiT	DUF1127 family protein/pseudogene
RA	4,565,742	C→A	42.0%	pseudogene (2007/2937 nt)	yjiV →	pseudogene; conserved hypothetical protein
RA	4,571,233	G→A	49.3%	S16F (TCT→TTT)	hsdS ←	specificity determinant for hsdM and hsdR
RA	4,572,581	G→T	37.3%	T95T (ACC→ACA)	hsdM ←	DNA methyltransferase M
RA	4,572,800	A→T	42.1%	V22V (GTT→GTA)	hsdM ←	DNA methyltransferase M
RA	4,583,316	C→A	6.5%	P408P (CCG→CCT)	yjjL ←	L‑galactonate transporter
RA	4,584,381	G→T	100%	I53I (ATC→ATA)	yjjL ←	L‑galactonate transporter
RA	4,584,756	A→T	56.2%	*305K (TAA→AAA)	yjjM ←	yjjMN operon transcriptional activator
RA	4,585,338	A→T	100%	S111T (TCT→ACT)	yjjM ←	yjjMN operon transcriptional activator
RA	4,590,074	A→C	31.8%	V240G (GTA→GGA)	dnaC ←	DNA biosynthesis protein
RA	4,591,139	C→A	54.2%	D66Y (GAT→TAT)	dnaT ←	DNA biosynthesis protein (primosomal protein I)
RA	4,593,035	G→T	6.3%	intergenic (‑360/‑259)	yjjP ← / → yjjQ	pseudogene, premature stop codon, putative structural protein/putative transcriptional regulator
RA	4,593,513	T→G	48.8%	Y74D (TAT→GAT)	yjjQ →	putative transcriptional regulator
RA	4,596,243	T→A	57.2%	intergenic (‑25/+243)	leuQ ← / ← rsmC	tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase, SAM‑dependent
RA	4,602,307	T→A	44.8%	L27Q (CTG→CAG)	yjjU →	putative patatin‑like family phospholipase
RA	4,603,666	G→T	5.7%	A123A (GCG→GCT)	yjjV →	putative DNase
RA	4,604,195	A→G	5.2%	intergenic (+118/+302)	yjjV → / ← yjjW	putative DNase/putative pyruvate formate lyase activating enzyme
RA	4,604,240	T→A	5.2%	intergenic (+163/+257)	yjjV → / ← yjjW	putative DNase/putative pyruvate formate lyase activating enzyme
RA	4,612,781	C→A	7.5%	A399E (GCG→GAG)	yjjJ →	putative protein kinase
RA	4,617,009	G→T	9.2%	A427A (GCG→GCT)	radA →	DNA repair protein
RA	4,618,602	T→C	12.2%	intergenic (+238/+70)	nadR → / ← yjjK	trifunctional protein: nicotinamide mononucleotide adenylyltransferase, ribosylnicotinamide kinase, transcriptional repressor/putative transporter subunit of ABC superfamily: ATP‑binding component
RA	4,625,288	T→C	100%	intergenic (‑161/‑50)	rob ← / → creA	right oriC‑binding transcriptional activator, AraC family/putative periplasmic protein
RA	4,628,799	G→T	5.1%	D269Y (GAT→TAT)	creD →	inner membrane protein
RA	4,629,649	A→T	46.6%	Y159N (TAC→AAC)	arcA ←	response regulator in two‑component regulatory system with ArcB or CpxA

Unassigned missing coverage evidence
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	CP009273	373853	375146	1294	165 [162]	[161] 168	frmA–[frmR]	frmA,[frmR]
*	*	÷	CP009273	4100601	4101530	930	163 [162]	[160] 163	[cdh]–tpiA	[cdh],tpiA

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	360104 =	200 (0.840)	201 (0.840)	115/278	NT	50.1%	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)	6140 (27.240) +TTAATTAA	195/262	NT	96.0%	intergenic (‑212/+383)	lacZ/lacI	pseudogene, truncated/DNA‑binding transcriptional repressor
	?	CP009273	= 361823	271 (1.130)					coding (831/834 nt)	mhpR	mhp operon transcriptional activator
*	?	CP009273	360652 =	234 (0.980)	5897 (36.970) +46 bp	185/186	NT	97.5%	intergenic (‑586/+9)	lacZ/lacI	pseudogene, truncated/DNA‑binding transcriptional repressor
	?	CP009273	= 1317577	211 (0.880)					coding (101/882 nt)	yciV	PHP domain protein
*	?	CP009273	376716 =	NA (NA)	227 (0.950)	125/278	NT	99.6%	intergenic (‑1/‑91)	yaiX/insC1	pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase/IS2 repressor TnpA
	?	CP009273	566411 =	1 (0.000)					coding (63/552 nt)	ybcL	inactive polymorphonuclear leukocyte migration suppressor; DLP12 prophage; secreted protein, UPF0098 family
*	?	CP009273	= 378046	NA (NA)	249 (1.040)	124/278	NT	100%	intergenic (+11/+1)	insD1/yaiX	IS2 transposase TnpB/pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase
	?	CP009273	= 566415	0 (0.000)					coding (67/552 nt)	ybcL	inactive polymorphonuclear leukocyte migration suppressor; DLP12 prophage; secreted protein, UPF0098 family
*	?	CP009273	1203246 =	9 (0.040)	69 (0.330)	50/246	NT	85.2%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	CP009273	1205075 =	16 (0.080)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	CP009273	= 1203261	10 (0.040)	83 (0.390)	53/246	NT	87.0%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	CP009273	= 1205058	16 (0.080)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	CP009273	= 1282540	137 (0.570)	8 (0.040)	6/238	NT	5.4%	noncoding (153/171 nt)	rttR	rtT sRNA, processed from tyrT transcript
	?	CP009273	1283013 =	162 (0.790)					noncoding (66/85 nt)	tyrT	tRNA‑Tyr
*	?	CP009273	1635219 =	0 (0.000)	222 (0.940)	139/274	NT	100%	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	0 (0.000)	202 (0.840)	124/278	NT	100%	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)	131 (0.560)	91/274	NT	54.3%	pseudogene (4/2445 nt)	yqiG	pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein
	?	CP009273	= 3833569	112 (0.470)					intergenic (‑216/‑6)	nlpA/yicS	cytoplasmic membrane lipoprotein‑28/putative periplasmic protein
*	?	CP009273	3833562 =	113 (0.470)	129 (0.540)	79/276	NT	53.5%	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