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

Predicted mutations
evidence	position	mutation	annotation	gene	description
RA	6,610	G→A	R450R (CGC→CGT)	yaaJ ←	inner membrane transport protein
RA	9,278	A→G	intergenic (+87/‑28)	talB → / → mog	transaldolase B/hypothetical protein
RA	10,583	A→G	intergenic (‑89/+60)	yaaH ← / ← b0011	hypothetical protein/putative oxidoreductase
RA	11,000	T→C	E119E (GAA→GAG)  C92C (TGT→TGC)	b0011 ← htgA →	putative oxidoreductase HtgA
RA	11,852	A→G	intergenic (‑66/‑311)	yaaI ← / → dnaK	hypothetical protein/chaperone Hsp70
RA	17,359	C→T	intergenic (‑399/‑130)	gef ← / → nhaA	Gef/pH dependent Na+/H antiporter
RA	19,161	T→C	I149I (ATT→ATC)	nhaR →	NhaR
RA	28,729	C→T	A119V (GCC→GTC)	dapB →	dihydrodipicolinate reductase
RA	30,594	C→T	A315V (GCG→GTG)	carA →	carbamoyl‑phosphate synthetase
RA	31,345	A→G	S177G (AGC→GGC)	carB →	carbamoyl‑phosphate synthase large subunit
RA	33,732	T→C	D972D (GAT→GAC)	carB →	carbamoyl‑phosphate synthase large subunit
RA	49,119	A→G	T451A (ACG→GCG)	kefC →	K+ efflux antiporter glutathione‑regulated
RA	49,165	T→C	V466A (GTG→GCG)	kefC →	K+ efflux antiporter glutathione‑regulated
RA	62,312	T→C	Q318R (CAG→CGG)	hepA ←	putative ATP‑dependent RNA helicase
RA	66,456	A→G	V32A (GTT→GCT)	araD ←	L‑ribulose‑5‑phosphate 4‑epimerase
RA	66,528	T→C	Q8R (CAG→CGG)	araD ←	L‑ribulose‑5‑phosphate 4‑epimerase
MC JC	66,533	3540 bp→27 bp		[araD]–araB	[araD], araA, araB
RA	70,289	G→T	intergenic (‑241/‑98)	araB ← / → araC	L‑ribulokinase/transcriptional regulator for ara operon
RA	78,003	A→C	E128A (GAG→GCG)	yabM →	putative transport protein
RA	83,095	A→G	R145R (CGT→CGC)	leuA ←	2‑isopropylmalate synthase
RA	87,311	(G)5→6	coding (1682/1725 nt)	ilvI →	acetolactate synthase isozyme III large subunit
RA	88,957	A→G	E310E (GAA→GAG)	fruR →	FruR
RA	95,362	G→A	R238H (CGT→CAT)	murF →	D‑alanine:D‑alanine‑adding enzyme
RA	107,212	A→G	D219G (GAC→GGC)	lpxC →	UDP‑3‑O‑acyl N‑acetylglucosamine deacetylase
RA	111,615	T→C	intergenic (+182/+34)	mutT → / ← yacG	7,8‑dihydro‑8‑oxoguanine‑triphosphatase/hypothetical protein
RA	112,770	C→T	E150E (GAG→GAA)	yacE ←	putative DNA repair protein
RA	120,248	A→G	V435A (GTA→GCA)	aroP ←	aromatic amino acid transport protein
RA	121,433	A→G	V40A (GTA→GCA)	aroP ←	aromatic amino acid transport protein
RA	138,226	A→G	S382G (AGC→GGC)	yacK →	hypothetical protein
RA	138,888	T→C	T780A (ACG→GCG)	gcd ←	glucose dehydrogenase
RA	144,241	A→G	P180P (CCA→CCG)	yadH →	hypothetical protein
RA	147,141	A→G	G58G (GGA→GGG)	yadD →	hypothetical protein
RA	148,799	G→A	intergenic (‑4/+8)	panC ← / ← panB	pantothenate synthetase/3‑methyl‑2‑oxobutanoate hydroxymethyltransferase
RA	156,827	A→G	G19G (GGT→GGC)	yadN ←	putative fimbrial‑like protein
RA	159,762	A→G	R117R (CGT→CGC)	yadB ←	putative tRNA synthetase
RA	171,718	C→T	P86L (CCG→CTG)	fhuB →	FhuB
RA	182,747	A→G	T95T (ACA→ACG)	yaeG →	hypothetical protein
RA	196,422	A→G	D213G (GAC→GGC)	cdsA →	CDP‑diglyceride synthetase
RA	202,345	T→C	V82A (GTA→GCA)	fabZ →	(3R)‑hydroxymyristol acyl carrier protein dehydratase
RA	231,829	T→C	G236G (GGT→GGC)	yafD →	hypothetical protein
RA	235,988	T→C	V5V (GTA→GTG)	rnhA ←	RNase HI
RA	241,745	A→G	V532A (GTG→GCG)	yafH ←	putative acyl‑CoA dehydrogenase
RA	250,749	T→C	G236G (GGT→GGC)	mbhA →	putative motility protein
RA	253,831	T→C	Y44H (TAT→CAT)	prfH →	putative peptide chain release factor
RA	254,298	T→C	T473T (ACA→ACG)	pepD ←	aminoacyl‑histidine dipeptidase
RA	256,955	T→C	D143D (GAT→GAC)	yafA →	hypothetical protein
RA	262,642	T→C	E84E (GAA→GAG)	b0245 ←	hypothetical protein
RA	269,425	A→G	intergenic (‑19/‑41)	perR ← / → yi91a	putative transcriptional regulator LYSR‑type/hypothetical protein
RA	272,747	T→C	L221P (CTA→CCA)	ykfC →	hypothetical protein
RA	276,473	T→C	L179L (TTG→CTG)	yagD →	YagD
RA	281,747	C→T	T89T (ACC→ACT)	yagE →	putative lyase/synthase
RA	283,609	A→G	E395E (GAA→GAG)	yagF →	putative dehydratase
RA	289,272	A→G	H86H (CAT→CAC)	argF ←	ornithine carbamoyltransferase 2 chain F
RA	296,697	A→G	F107L (TTC→CTC)	yagP ←	putative transcriptional regulator LYSR‑type
RA	301,283	A→G	V172A (GTG→GCG)	yagT ←	putative xanthine dehydrogenase
RA	304,069	C→G	V136L (GTC→CTC)	yagV ←	hypothetical protein
RA	307,659	T→C	T300A (ACC→GCC)	yagX ←	hypothetical protein
RA	318,936	C→T	G106D (GGC→GAC)	ykgC ←	putative oxidoreductase
RA	320,122	T→C	A224A (GCT→GCC)	ykgD →	putative ARAC‑type regulatory protein
RA	323,407	A→G	G142G (GGA→GGG)	ykgG →	putative transporter
RA	338,761	G→A	V405I (GTC→ATC)	yahG →	hypothetical protein
RA	355,588	T→C	L65P (CTG→CCG)	codA →	cytosine deaminase
RA	358,162	A→G	E47G (GAG→GGG)	cynT →	carbonic anhydrase
RA	361,958	A→G	V149A (GTT→GCT)	lacY ←	galactoside permease
RA	363,169	A→G	R787R (CGT→CGC)	lacZ ←	beta‑D‑galactosidase
RA	368,911	G→A	V359V (GTG→GTA)	mhpA →	3‑(3‑hydroxyphenyl)propionate hydroxylase
RA	376,616	A→G	intergenic (+81/+143)	yaiL → / ← yaiM	nucleoprotein/polynucleotide‑associated enzyme/putative esterase
RA	394,595	T→C	D306G (GAT→GGT)	yaiH ←	hypothetical protein
RA	400,205	A→G	intergenic (‑58/‑405)	ddlA ← / → yaiB	D‑alanine‑D‑alanine ligase A/hypothetical protein
RA	403,861	T→C	V312A (GTG→GCG)	yaiC →	hypothetical protein
RA	418,805	A→G	intergenic (+397/‑10)	phoR → / → brnQ	positive and negative sensor protein for pho regulon/branched chain amino acid transport system II carrier protein
RA	434,599	T→C	V80A (GTA→GCA)	nusB →	transcription termination
RA	434,687	A→G	E109E (GAA→GAG)	nusB →	transcription termination
RA	440,252	A→G	L25P (CTG→CCG)	ispA ←	geranyltranstransferase
RA	440,417	C→T	A51T (GCC→ACC)	xseB ←	exonuclease VII small subunit
RA	444,504	A→G	intergenic (+106/+22)	yajQ → / ← yajR	hypothetical protein/putative transport protein
RA	459,573	A→G	I488V (ATT→GTT)	lon →	ATP‑dependent protease La
RA	480,099	A→G	intergenic (‑167/+379)	ybaJ ← / ← acrB	hypothetical protein/acridine efflux pump
RA	484,107	A→G	L246P (CTG→CCG)	acrA ←	acridine efflux pump
RA	487,376	T→C	G539G (GGT→GGC)	aefA →	putative alpha helix protein
RA	489,570	A→G	L156P (CTG→CCG)	priC ←	primosomal replication protein N''
RA	500,364	A→G	H339R (CAC→CGC)	gsk →	inosine‑guanosine kinase
RA	502,653	C→T	intergenic (‑191/+47)	ybaL ← / ← fsr	putative transport protein/fosmidomycin resistance protein
RA	509,575	T→C	P343P (CCA→CCG)	ybaR ←	putative ATPase
RA	509,606	(T)6→5	coding (998/2505 nt)	ybaR ←	putative ATPase
RA	517,700	A→G	V225A (GTG→GCG)	ybbO ←	putative oxidoreductase
RA	518,231	T→C	K48R (AAA→AGA)	ybbO ←	putative oxidoreductase
JC	521,090	(AGC)3→2	coding (1451‑1453/2415 nt)	ybbP →	putative oxidoreductase
RA	527,625	T→C	G151G (GGT→GGC)	b0499 →	hypothetical protein
RA	528,763	T→C	intergenic (+409/+106)	b0501 → / ← b0502	hypothetical protein/hypothetical protein
RA	531,406	C→T	A14T (GCT→ACT)	ybbS ←	putative transcriptional regulator LYSR‑type
RA	536,980	A→G	I87M (ATA→ATG)  N42D (AAC→GAC)	ybbV → ybbW →	hypothetical protein putative transport protein
RA	542,052	A→G	Q314R (CAG→CGG)	ybbZ →	hypothetical protein
RA	547,645	A→G	H22R (CAC→CGC)	b4507 →	hypothetical protein
RA	547,694	A→G	E38E (GAA→GAG)	b4507 →	hypothetical protein
RA	547,835	+G	coding (255/261 nt)	b4507 →	hypothetical protein
RA	552,300	C→T	A8A (GCG→GCA)	purE ←	phosphoribosylaminoimidazole carboxylase
RA	556,636	A→G	V110A (GTG→GCG)	folD ←	5,10‑methylene‑tetrahydrofolate dehydrogenase
RA	559,101	A→G	N61S (AAT→AGT)	sfmD →	putative outer membrane protein
RA	562,546	A→G	intergenic (+4/‑7)	sfmH → / → sfmF	involved in fimbrial asembly/putative fimbrial‑like protein
RA	577,681	(C)6→7	coding (352/462 nt)	ybcT →	endopeptidase‑like protein
RA	578,027	T→C	A30A (GCA→GCG)	ybcU ←	Bor‑like protein
RA	582,225	A→G	Q43R (CAG→CGG)	ylcE →	hypothetical protein
RA	611,741	A→G	intergenic (‑24/‑297)	fepA ← / → fes	FepA/enterochelin esterase
RA	612,751	T→C	A238A (GCT→GCC)	fes →	enterochelin esterase
RA	618,600	A→G	H375R (CAC→CGC)	fepE →	FepE
RA	621,553	A→G	S11G (AGC→GGC)	ybdA →	putative transport
RA	624,133	T→C	V9A (GTA→GCA)	entC →	isochorismate hydroxymutase 2
RA	638,137	A→G	intergenic (‑281/‑31)	dsbG ← / → ahpC	thiol:disulfide interchange protein/alkyl hydroperoxide reductase C22 subunit
RA	642,964	A→G	H112R (CAC→CGC)  V76A (GTG→GCG)	b0609 → rnk ←	hypothetical protein regulator of nucleoside diphosphate kinase
RA	654,113	A→G	L360P (CTG→CCG)	dcuC ←	DcuC
RA	662,679	C→T	G170S (GGC→AGC)	dacA ←	D‑alanyl‑D‑alanine carboxypeptidase fraction A
RA	669,635	A→G	V54A (GTG→GCG)	ybeN ←	hypothetical protein
RA	670,528	T→C	T101A (ACC→GCC)	holA ←	DNA polymerase III delta subunit
RA	683,225	A→G	H137H (CAT→CAC)	ybeK ←	putative tRNA synthetase
RA	697,801	A→G	D200D (GAT→GAC)	asnB ←	asparagine synthetase B
RA	704,130	A→G	I322V (ATC→GTC)	nagE →	PTS system, N‑acetylglucosamine‑specific enzyme IIABC
RA	704,236	T→C	L357S (TTG→TCG)	nagE →	PTS system, N‑acetylglucosamine‑specific enzyme IIABC
RA	704,311	A→G	N382S (AAC→AGC)	nagE →	PTS system, N‑acetylglucosamine‑specific enzyme IIABC
RA	705,360	C→T	I15I (ATC→ATT)	glnS →	glutamine tRNA synthetase
RA	708,421	G→A	G289S (GGC→AGC)	ybfM →	hypothetical protein
RA	708,813	C→T	D419D (GAC→GAT)	ybfM →	hypothetical protein
RA	709,321	A→G	I103M (ATA→ATG)	ybfN →	hypothetical protein
RA	715,139	T→C	intergenic (+10/+31)	ybfP → / ← ybfG	putative pectinase/hypothetical protein
RA	717,441	T→C	I16M (ATA→ATG)	potE ←	putrescine transport protein
RA	719,820	A→G	L5L (TTA→TTG)	ybfK →	hypothetical protein
RA	729,698	A→G	H298R (CAC→CGC)	rhsC →	RhsC
RA	765,778	C→T	A191V (GCC→GTC)	hrsA →	PTS system fructose specific IIABC component
RA	788,889	A→G	L105P (CTG→CCG)	galK ←	galactokinase
RA	791,797	T→C	G405G (GGA→GGG)	modF ←	ModF
RA	795,202	A→G	T40A (ACG→GCG)	modB →	molybdate transport permease protein
RA	826,265	T→C	T71A (ACC→GCC)	ybhS ←	hypothetical protein
RA	829,262	A→G	L206P (CTG→CCG)	ybiH ←	putative transcriptional regulator
RA	831,133	T→C	S347P (TCG→CCG)	rhlE →	putative ATP‑dependent RNA helicase
RA	836,115	A→G	Y181C (TAC→TGC)	ybiC →	putative dehydrogenase
RA	839,256	G→A	P500L (CCG→CTG)	b0805 ←	putative outer membrane receptor for iron transport
RA	844,809	A→G	intergenic (‑106/+155)	ybiO ← / ← glnQ	putative transport protein/ATP‑binding component of glutamine high‑affinity transport system
RA	853,690	A→G	N274S (AAC→AGC)	ybiR →	hypothetical protein
RA	867,645	(C)8→7	coding (870/1839 nt)	b0829 →	hypothetical protein
RA	878,191	A→G	D76G (GAC→GGC)	yliI →	putative dehydrogenase
RA	878,307	A→G	T115A (ACT→GCT)	yliI →	putative dehydrogenase
RA	879,780	A→G	intergenic (‑77/‑170)	yliJ ← / → dacC	putative transferase/D‑alanyl‑D‑alanine carboxypeptidase
RA	883,244	A→G	I117V (ATA→GTA)	cmr →	proton motive force efflux pump
RA	884,046	A→G	N384S (AAC→AGC)	cmr →	proton motive force efflux pump
RA	887,275	A→G	intergenic (+93/+82)	b0846 → / ← b0847	putative DEOR‑type transcriptional regulator/putative transport protein
RA	888,260	A→G	D261D (GAT→GAC)	b0847 ←	putative transport protein
RA	888,802	(A)7→6	coding (241/1686 nt)	b0847 ←	putative transport protein
RA	898,377	A→G	T213A (ACT→GCT)	ybjF →	hypothetical protein
RA	899,581	A→T	I73N (ATC→AAC)	artJ ←	arginine 3rd transport system periplasmic binding protein
RA	901,907	Δ1 bp	coding (305/732 nt)	artI ←	arginine 3rd transport system periplasmic binding protein
RA	905,689	G→A	R108R (CGC→CGT)	b0868 ←	putative nucleotide di‑P‑sugar epimerase or dehydratase
RA	905,792	A→G	V74A (GTG→GCG)	b0868 ←	putative nucleotide di‑P‑sugar epimerase or dehydratase
RA	908,654	A→G	L540P (CTC→CCC)	poxB ←	pyruvate oxidase
RA	914,422	A→G	intergenic (‑294/+153)	ybjE ← / ← aqpZ	putative surface protein/transmembrane water channel
RA	914,564	T→C	intergenic (‑436/+11)	ybjE ← / ← aqpZ	putative surface protein/transmembrane water channel
RA	934,133	G→A	G563R (GGG→AGG)	ftsK →	cell division protein
RA	934,731	A→G	Q762R (CAG→CGG)	ftsK →	cell division protein
RA	943,049	(A)5→4	coding (413/618 nt)	dmsB →	anaerobic dimethyl sulfoxide reductase subunit B
RA	946,689	A→G	T144A (ACG→GCG)	b0899 →	putative transport
RA	949,354	A→G	Y155C (TAT→TGT)	ycaK →	hypothetical protein
RA	961,423	A→G	D69G (GAC→GGC)	rpsA →	30S ribosomal subunit protein S1
RA	962,413	A→G	N399S (AAC→AGC)	rpsA →	30S ribosomal subunit protein S1
RA	969,158	C→T	R183C (CGC→TGC)	ycaQ →	hypothetical protein
RA	972,900	T→C	R47R (CGT→CGC)	smtA →	S‑adenosylmethionine‑dependent methyltransferase
RA	974,456	A→G	V305V (GTA→GTG)	mukF →	MukF
RA	978,817	A→G	D1090G (GAC→GGC)	mukB →	MukB
RA	979,652	T→C	G1368G (GGT→GGC)	mukB →	MukB
RA	981,066	A→T	D266V (GAC→GTC)	ycbB →	putative amidase
RA	981,566	C→T	R433C (CGC→TGC)	ycbB →	putative amidase
RA	1,003,383	(G)7→8	coding (184/681 nt)	ycbF →	putative chaperone
RA	1,015,850	T→C	Q558R (CAG→CGG)	b0955 ←	putative ATP‑dependent protease
RA	1,016,180	A→G	I448T (ATA→ACA)	b0955 ←	putative ATP‑dependent protease
RA	1,019,358	T→C	intergenic (‑82/+275)	ompA ← / ← sulA	outer membrane protein 3a/suppressor of lon
RA	1,021,662	A→G	V485A (GTG→GCG)	b0960 ←	hypothetical protein
RA	1,032,328	A→G	T323A (ACC→GCC)	hyaA →	hydrogenase‑1 small subunit
RA	1,033,040	(G)5→6	coding (564/1794 nt)	hyaB →	hydrogenase‑1 large subunit
RA	1,038,386	T→C	L475P (CTG→CCG)	appC →	putative third cytochrome oxidase subunit I
RA	1,046,049	T→C	M374V (ATG→GTG)	ymcA ←	hypothetical protein
RA	1,051,163	Δ1 bp	coding (94/231 nt)	sfa →	Sfa
RA	1,053,820	T→C	T518A (ACC→GCC)	torS ←	TorS
RA	1,056,041	A→G	E186E (GAA→GAG)	torT →	TorT
RA	1,064,328	A→G	N357S (AAT→AGT)	yccE →	hypothetical protein
RA	1,065,252	T→C	F149L (TTT→CTT)	agp →	periplasmic glucose‑1‑phosphatase
RA	1,066,017	T→C	F404L (TTT→CTT)	agp →	periplasmic glucose‑1‑phosphatase
RA	1,074,187	T→C	T1307A (ACC→GCC)	putA ←	proline dehydrogenase
RA	1,079,087	A→G	D187G (GAC→GGC)	putP →	major sodium/proline symporter
RA	1,086,170	A→G	G300G (GGT→GGC)	ycdQ ←	hypothetical protein
RA	1,086,330	T→C	Y247C (TAC→TGC)	ycdQ ←	hypothetical protein
RA	1,089,129	T→C	H795R (CAC→CGC)	ycdS ←	putative outer membrane protein
RA	1,090,676	A→G	R279R (CGT→CGC)	ycdS ←	putative outer membrane protein
RA	1,098,156	A→G	T19A (ACA→GCA)	ycdX →	hypothetical protein
RA	1,101,826	T→C	I198M (ATA→ATG)	csgD ←	CsgD
RA	1,106,363	A→G	K282K (AAA→AAG)	ymdC →	putative synthase
RA	1,119,304	T→C	N169S (AAC→AGC)	solA ←	sarcosine oxidase‑like protein
RA	1,120,179	C→T	M1M (ATG→ATA) †	yceP ←	hypothetical protein
RA	1,127,881	T→C	F274L (TTT→CTT)	mviN →	putative virulence factor
RA	1,134,313	A→G	Q121R (CAG→CGG)	flgG →	FlgG
RA	1,138,489	A→G	T297A (ACG→GCG)	flgK →	hook‑filament junction protein 1
RA	1,140,817	T→C	Q925R (CAG→CGG)	rne ←	RNase E
RA	1,141,015	T→C	Q859R (CAG→CGG)	rne ←	RNase E
RA	1,142,917	T→C	D225G (GAC→GGC)	rne ←	RNase E
RA	1,143,101	T→C	M164V (ATG→GTG)	rne ←	RNase E
RA	1,154,920	C→T	P192S (CCG→TCG)	tmk →	thymidylate kinase
RA	1,155,780	A→G	T266A (ACC→GCC)	holB →	DNA polymerase III delta prime subunit
RA	1,156,390	A→G	T131A (ACC→GCC)	ycfH →	hypothetical protein
RA	1,157,019	A→G	intergenic (+222/‑73)	ycfH → / → ptsG	hypothetical protein/PTS system, glucose‑specific IIBC component
RA	1,158,246	T→C	G385G (GGT→GGC)	ptsG →	PTS system, glucose‑specific IIBC component
RA	1,158,718	T→C	Q686R (CAG→CGG)	fhuE ←	outer membrane receptor for ferric iron uptake
RA	1,175,607	A→G	S320G (AGC→GGC)	ycfU →	hypothetical protein
RA	1,176,507	T→C	R222R (CGT→CGC)	ycfV →	putative ATP‑binding component of a transport system
RA	1,192,497	A→G	L167P (CTG→CCG)	ycfB ←	hypothetical protein
RA	1,192,608	A→G	V130A (GTA→GCA)	ycfB ←	hypothetical protein
RA	1,199,211	T→C	V273V (GTA→GTG)	intE ←	prophage e14 integrase
RA	1,202,871	A→G	E131E (GAA→GAG)	ymfL →	hypothetical protein
RA	1,207,165	(G)7→8	coding (442/630 nt)	ycfK →	hypothetical protein
RA	1,210,134	A→G	Y189C (TAT→TGT)	mcrA →	McrA
RA	1,210,786	A→G	intergenic (+384/+117)	mcrA → / ← ycgW	McrA/hypothetical protein
RA	1,211,165	A→G	I21T (ATA→ACA)	ycgW ←	hypothetical protein
RA	1,212,474	A→G	intergenic (‑144/+77)	ycgX ← / ← ycgE	hypothetical protein/putative transcriptional regulator
RA	1,229,837	C→T	intergenic (‑214/‑153)	hlyE ← / → umuD	hemolysin E/UmuD
RA	1,235,692	T→C	Q258R (CAG→CGG)	ycgB ←	putative sporulation protein
RA	1,238,083	A→G	A430A (GCA→GCG)	dadA →	D‑amino acid dehydrogenase subunit
RA	1,252,715	A→G	S821P (TCC→CCC)	b1202 ←	putative adhesion and penetration protein
RA	1,259,418	G→A	G194G (GGC→GGT)	ychM ←	hypothetical protein
RA	1,275,669	A→G	R391R (CGT→CGC)	narX ←	NarX
RA	1,281,011	A→G	H642R (CAC→CGC)	narG →	nitrate reductase 1 alpha subunit
RA	1,282,099	C→T	R1005C (CGC→TGC)	narG →	nitrate reductase 1 alpha subunit
RA	1,288,263	T→C	E31E (GAA→GAG)	ychJ ←	hypothetical protein
RA	1,298,679	T→C	intergenic (+211/‑527)	ychE → / → oppA	putative channel protein/OppA
RA	1,302,782	A→G	N2S (AAC→AGC)	oppD →	OppD
RA	1,320,156	A→G	L272P (CTG→CCG)	trpE ←	anthranilate synthase component I
RA	1,326,196	C→T	V62V (GTG→GTA)	btuR ←	cob(I)alamin adenolsyltransferase
RA	1,329,903	A→G	S278G (AGT→GGT)	topA →	DNA topoisomerase type I omega protein
RA	1,330,060	A→G	D330G (GAC→GGC)	topA →	DNA topoisomerase type I omega protein
RA	1,332,547	G→A	T223T (ACG→ACA)	cysB →	positive transcriptional regulator for cysteine regulon
RA	1,335,418	A→G	S522G (AGC→GGC)	acnA →	aconitate hydrase 1
RA	1,342,077	A→G	N98N (AAT→AAC)	b1284 ←	putative DEOR‑type transcriptional regulator
RA	1,342,604	G→A	A10A (GCC→GCT)	b4523 ←	hypothetical protein
RA	1,348,410	A→G	R218R (CGT→CGC)	fabI ←	enoyl‑[acyl‑carrier‑protein] reductase (NADH)
RA	1,356,907	A→G	V102A (GTC→GCC)	ycjJ ←	putative amino acid/amine transport protein
RA	1,358,270	G→A	G221G (GGC→GGT)	b1297 ←	putative glutamine synthetase
RA	1,358,630	A→G	V101V (GTT→GTC)	b1297 ←	putative glutamine synthetase
RA	1,372,245	A→G	S44S (TCA→TCG)	ycjP →	putative transport system permease protein
RA	1,381,611	A→G	I125I (ATT→ATC)	ycjW ←	putative LACI‑type transcriptional regulator
RA	1,383,611	A→G	Q26R (CAG→CGG)	ycjF →	hypothetical protein
RA	1,390,132	C→T	R40C (CGT→TGT)	ycjZ →	putative transcriptional regulator LYSR‑type
RA	1,391,027	A→G	intergenic (+113/‑203)	ycjZ → / → b1329	putative transcriptional regulator LYSR‑type/putative transport periplasmic protein
RA	1,391,480	A→G	E84G (GAG→GGG)	b1329 →	putative transport periplasmic protein
RA	1,396,204	T→C	Q148R (CAG→CGG)	ydaA ←	hypothetical protein
RA	1,397,365	A→G	G62G (GGT→GGC)	fnr ←	Fnr
RA	1,398,000	C→T	T87T (ACG→ACA)	ogt ←	O‑6‑alkylguanine‑DNA/cysteine‑protein methyltransferase
RA	1,407,401	G→A	intergenic (+344/‑134)	b1342 → / → dbpA	hypothetical protein/ATP‑dependent RNA helicase
RA	1,408,072	A→G	T180A (ACG→GCG)	dbpA →	ATP‑dependent RNA helicase
RA	1,415,570	(T)8→9	coding (218/276 nt)	racC ←	defective prophage rac
RA	1,415,996	(T)6→7	coding (37/171 nt)	ydaE ←	hypothetical protein
RA	1,434,318	C→T	W200* (TGG→TGA)	b1377 ←	putative outer membrane protein
RA	1,437,025	T→C	Q595R (CAG→CGG)	ydbK ←	putative oxidoreductase Fe‑S subunit
RA	1,442,757	C→T	D561D (GAC→GAT)	ydbH →	hypothetical protein
RA	1,445,328	A→G	intergenic (‑21/‑215)	feaR ← / → feaB	FeaR/phenylacetaldehyde dehydrogenase
RA	1,456,536	A→G	S83S (TCA→TCG)	b1394 →	hypothetical protein
RA	1,457,617	T→C	P180P (CCT→CCC)	ydbU →	hypothetical protein
RA	1,460,324	A→G	D59G (GAC→GGC)	b1398 →	hypothetical protein
RA	1,460,607	T→C	R153R (CGT→CGC)	b1398 →	hypothetical protein
RA	1,473,007	A→G	T255A (ACG→GCG)	ydbC →	putative dehydrogenase
RA	1,475,087	T→C	R642R (CGT→CGC)	ydbD →	hypothetical protein
RA	1,476,433	A→G	T62A (ACG→GCG)	b1409 →	putative phosphatidate cytidiltransferase
RA	1,492,778	A→G	G153G (GGT→GGC)	b1422 ←	putative transcriptional regulator LYSR‑type
RA	1,503,894	T→C	T71A (ACC→GCC)	b1433 ←	putative membrane transport protein
RA	1,507,063	A→G	V9A (GTC→GCC)	b1436 ←	hypothetical protein
RA	1,520,878	A→G	V71A (GTG→GCG)	b1451 ←	putative outer membrane receptor for iron transport
RA	1,520,926	A→G	M55T (ATG→ACG)	b1451 ←	putative outer membrane receptor for iron transport
RA	1,523,536	T→C	T157A (ACC→GCC)	ansP ←	L‑asparagine permease
RA	1,533,898	A→G	intergenic (‑16/+63)	yddE ← / ← narV	hypothetical protein/cryptic nitrate reductase 2 gamma subunit
RA	1,534,038	T→C	T202A (ACC→GCC)	narV ←	cryptic nitrate reductase 2 gamma subunit
RA	1,536,063	A→G	L272P (CTG→CCG)	narY ←	cryptic nitrate reductase 2 beta subunit
RA	1,538,045	G→A	P857L (CCG→CTG)	narZ ←	cryptic nitrate reductase 2 alpha subunit
RA	1,545,666	A→G	D81G (GAC→GGC)  D81G (GAC→GGC)	b4525 → fdnG →	hypothetical protein formate dehydrogenase‑N, nitrate‑inducible, alpha subunit
RA	1,548,911	T→C	C143R (TGT→CGT)	fdnH →	formate dehydrogenase‑N, nitrate‑inducible, iron‑sulfur beta subunit
RA	1,564,047	T→C	Y373C (TAC→TGC)	b1490 ←	hypothetical protein
RA	1,568,135	G→A	P127S (CCC→TCC)	xasA ←	acid sensitivity protein
RA	1,571,055	T→C	L724L (TTA→TTG)	pqqL ←	putative peptidase
RA	1,592,738	T→C	T1125A (ACG→GCG)	ydeK ←	hypothetical protein
RA	1,598,357	T→C	A303A (GCA→GCG)	ydeW ←	putative transcriptional regulator, sorC family
RA	1,603,543	T→C	F157L (TTT→CTT)	b1516 →	putative LACI‑type transcriptional regulator
RA	1,605,226	G→A	T68T (ACG→ACA)	b1518 →	hypothetical protein
RA	1,607,710	A→G	L332P (CTT→CCT)	uxaB ←	altronate oxidoreductase
RA	1,608,034	A→G	V224A (GTG→GCG)	uxaB ←	altronate oxidoreductase
RA	1,616,532	G→A	T134I (ACC→ATC)	ydeB ←	hypothetical protein
RA	1,634,017	A→T	I125I (ATT→ATA)	nohA ←	NohA
RA	1,636,465	T→C	intergenic (‑296/+14)	b1551 ← / ← cspI	hypothetical protein/cold shock‑like protein
RA	1,650,355	T→C	F274L (TTC→CTC)	b1579 →	putative transposase
RA	1,652,626	T→C	E180E (GAA→GAG)	rspA ←	starvation sensing protein
RA	1,658,150	A→G	P686P (CCA→CCG)	b1587 →	putative oxidoreductase major subunit
RA	1,666,596	T→C	intergenic (‑8/+127)	mlc ← / ← ynfL	putative NAGC‑like transcriptional regulator/putative transcriptional regulator LYSR‑type
RA	1,668,733	A→G	S337S (TCA→TCG)	ynfM →	putative transport protein
RA	1,671,621	A→G	intergenic (‑96/‑316)	b1600 ← / → b1601	putative chaperone/putative transport protein
RA	1,672,622	T→C	L229P (CTG→CCG)	b1601 →	putative transport protein
RA	1,679,869	A→G	S62S (AGT→AGC)	ydgC ←	hypothetical protein
RA	1,680,328	T→C	V52A (GTG→GCG)	rstA →	response transcriptional regulatory protein
RA	1,681,154	T→C	S83S (AGT→AGC)	rstB →	sensor histidine protein kinase
RA	1,691,941	T→C	Y116C (TAC→TGC)	uidB ←	glucuronide permease
RA	1,705,052	T→C	V37A (GTA→GCA)	b1629 →	putative membrane protein
RA	1,718,191	A→G	T98A (ACT→GCT)	slyB →	putative outer membrane protein
RA	1,722,918	T→A	N247Y (AAC→TAC)	b1647 ←	hypothetical protein
RA	1,724,901	T→C	P73P (CCT→CCC)	nemA →	N‑ethylmaleimide reductase
RA	1,727,400	T→C	L97P (CTG→CCG)	lhr →	Lhr
RA	1,728,403	T→C	R431R (CGT→CGC)	lhr →	Lhr
RA	1,730,968	T→C	S1286S (AGT→AGC)	lhr →	Lhr
RA	1,739,051	A→G	M373V (ATG→GTG)	ydhC →	putative transport protein
RA	1,741,574	2 bp→GA	coding (94‑95/1374 nt)	ydhE →	putative transport protein
RA	1,746,233	T→C	V360A (GTA→GCA)	b1668 →	hypothetical protein
RA	1,749,920	T→C	E645E (GAA→GAG)	b1673 ←	hypothetical protein
RA	1,755,127	T→C	V469A (GTC→GCC)	pykF →	pyruvate kinase I
RA	1,764,932	A→G	M593T (ATG→ACG)	ydiJ ←	putative oxidase
RA	1,766,232	T→C	T160A (ACC→GCC)	ydiJ ←	putative oxidase
RA	1,769,881	A→G	I263V (ATT→GTT)	b1690 →	putative transport system permease protein
RA	1,778,705	T→C	L94P (CTG→CCG)	ydiR →	putative flavoprotein
RA	1,782,304	A→T	D417V (GAT→GTT)	ydiD →	putative ligase/synthetase
RA	1,799,252	T→C	N448S (AAC→AGC)	thrS ←	threonine tRNA synthetase
RA	1,812,482	T→C	F198L (TTC→CTC)	katE →	catalase
RA	1,818,468	T→C	A257A (GCA→GCG)	celB ←	PTS system cellobiose‑specific enzyme IIC component
RA	1,835,432	T→C	V66A (GTC→GCC)	b1755 →	putative transport system permease protein
RA	1,836,044	T→C	V270A (GTA→GCA)	b1755 →	putative transport system permease protein
RA	1,846,045	T→C	intergenic (‑13/+104)	selD ← / ← ydjA	selenophosphate synthase/hypothetical protein
RA	1,848,059	T→C	V400A (GTT→GCT)	sppA →	protease IV
RA	1,852,569	T→C	T104A (ACC→GCC)	b1770 ←	putative DEOR‑type transcriptional regulator
RA	1,858,723	C→T	A212T (GCG→ACG)	b1776 ←	putative oxidoreductase
RA	1,858,802	T→C	P185P (CCA→CCG)	b1776 ←	putative oxidoreductase
RA	1,860,370	T→C	E28E (GAA→GAG)	yeaA ←	hypothetical protein
RA	1,862,301	T→C	V143A (GTG→GCG)	yeaD →	hypothetical protein
RA	1,863,764	T→C	T245A (ACC→GCC)	yeaF ←	hypothetical protein
RA	1,868,376	T→C	intergenic (+114/‑33)	yeaH → / → yeaI	hypothetical protein/hypothetical protein
RA	1,870,741	T→C	V286A (GTA→GCA)	yeaJ →	hypothetical protein
RA	1,871,827	C→T	A77V (GCC→GTC)	yeaK →	hypothetical protein
RA	1,873,080	(C)6→7	coding (521/822 nt)	yeaM ←	putative ARAC‑type regulatory protein
RA	1,880,593	A→G	K220E (AAG→GAG)	yeaU →	putative tartrate dehydrogenase
RA	1,884,922	G→A	A365V (GCA→GTA)	rnd ←	RNase D
RA	1,885,627	A→G	L130P (CTG→CCG)	rnd ←	RNase D
RA	1,890,598	A→G	V221A (GTC→GCC)	b1808 ←	hypothetical protein
RA	1,893,186	T→C	S120P (TCA→CCA)	pabB →	p‑aminobenzoate synthetase component I
RA	1,899,288	G→A	R108W (CGG→TGG)	yoaE ←	putative transport protein
RA	1,902,757	T→C	L280P (CTG→CCG)	b1819 →	PTS enzyme IID, mannose‑specific
RA	1,902,950	T→C	R42R (CGT→CGC)	b1820 →	hypothetical protein
RA	1,904,845	T→C	E80E (GAA→GAG)	yebH ←	hypothetical protein
RA	1,905,091	T→C	intergenic (‑7/+159)	yebH ← / ← cspC	hypothetical protein/cold shock protein
RA	1,909,232	A→G	T311T (ACA→ACG)	b1828 →	putative transport protein
RA	1,911,765	A→G	V359A (GTG→GCG)	prc ←	carboxy‑terminal protease for penicillin‑binding protein 3
RA	1,930,950	G→A	A560V (GCG→GTG)	edd ←	6‑phosphogluconate dehydratase
RA	1,933,325	A→G	G338G (GGT→GGC)	zwf ←	glucose‑6‑phosphate dehydrogenase
RA	1,934,800	T→C	L42P (CTG→CCG)	yebK →	hypothetical protein
RA	1,973,386	A→G	S298S (AGT→AGC)	motB ←	MotB
MC JC	1,976,527	Δ776 bp		insB5–insA5	insB5, insA5
RA	1,980,940	+C	coding (1/363 nt) coding (627/627 nt)	araH ← araH ←	ABC‑type arabinose transport system permease component ABC‑type arabinose transport system permease component
RA	1,981,668	A→G	G475G (GGT→GGC)	araG ←	ATP‑binding component of high‑affinity L‑arabinose transport system
RA	1,982,766	C→T	P109P (CCG→CCA)	araG ←	ATP‑binding component of high‑affinity L‑arabinose transport system
RA	1,984,089	A→G	A21A (GCT→GCC)	araF ←	L‑arabinose‑binding periplasmic protein
RA	1,995,537	T→C	T101A (ACG→GCG)	yecC ←	putative ATP‑binding component of a transport system
RA	1,995,724	A→G	S38S (AGT→AGC)	yecC ←	putative ATP‑binding component of a transport system
RA	1,998,893	A→G	L64P (CTG→CCG)	fliZ ←	hypothetical protein
RA	2,006,874	A→G	Q192R (CAG→CGG)	yedE →	putative transport system permease protein
RA	2,008,480	+A	coding (637/654 nt)	yedK →	hypothetical protein
RA	2,025,451	T→C	T202A (ACG→GCG)	b1956 ←	hypothetical protein
RA	2,027,751	(C)6→7	coding (191/921 nt)	yedA →	putative transmembrane subunit
RA	2,029,060	T→C	D427G (GAC→GGC)	dcm ←	DNA cytosine methylase
RA	2,031,743	A→G	intergenic (‑219/‑330)	b1963 ← / → b1964	hypothetical protein/putative outer membrane protein
RA	2,033,600	A→G	intergenic (+335/‑257)	b1966 → / → yedU	putative outer membrane protein/hypothetical protein
RA	2,034,882	T→C	G431G (GGA→GGG)	yedV ←	putative 2‑component sensor protein
RA	2,037,676	(C)5→6	coding (177/1005 nt)	b1971 →	putative reductase
RA	2,043,272	A→G	S130G (AGT→GGT)	b1978 →	hypothetical protein
RA	2,049,323	A→G	I2147V (ATC→GTC)	b1978 →	hypothetical protein
RA	2,056,134	A→G	intergenic (‑10/+91)	asnW ← / ← yeeO	tRNA‑Asn/hypothetical protein
RA	2,056,815	T→C	M352V (ATG→GTG)	yeeO ←	hypothetical protein
RA	2,059,510	T→C	E149G (GAG→GGG)	nac ←	nitrogen assimilation control protein
RA	2,069,211	T→C	V230A (GTA→GCA)	yeeP →	putative histone
RA	2,072,030	T→A	C824S (TGC→AGC)	b2000 →	outer membrane fluffing protein
RA	2,086,377	T→C	E258E (GAA→GAG)	b2016 ←	hypothetical protein
RA	2,094,047	T→C	V61A (GTA→GCA)	hisF →	imidazole glycerol phosphate synthase holoenzyme
RA	2,102,539	T→C	T190A (ACC→GCC)	wbbJ ←	putative O‑acetyl transferase
RA	2,108,221	A→G	V274A (GTA→GCA)	rfbA ←	glucose‑1‑phosphate thymidylyltransferase
RA	2,111,112	T→C	intergenic (‑29/+344)	rfbB ← / ← galF	dTDP‑glucose 4,6 dehydratase/putative a UDP‑gal transferase
RA	2,115,568	T→C	S287G (AGC→GGC)	wcaK ←	putative galactokinase
RA	2,116,149	A→G	V93A (GTC→GCC)	wcaK ←	putative galactokinase
RA	2,132,238	A→G	R479R (CGT→CGC)	b2060 ←	hypothetical protein
RA	2,144,314	C→T	G1009G (GGC→GGT)	yegE →	putative sensor‑type protein
RA	2,147,941	A→G	V356A (GTC→GCC)	b2070 ←	putative chaperonin
RA	2,151,362	(C)5→4	intergenic (‑212/‑529)	b2073 ← / → b2074	hypothetical protein/putative membrane protein
RA	2,152,717	T→C	V276A (GTG→GCG)	b2074 →	putative membrane protein
RA	2,154,032	T→C	Y250H (TAT→CAT)	yegN →	hypothetical protein
RA	2,161,324	G→A	V143M (GTG→ATG)	baeS →	BaeS
RA	2,171,956	T→C	M115V (ATG→GTG)	gatC ←	PTS system galactitol‑specific enzyme IIC
RA	2,175,347	(A)7→6	intergenic (‑117/+185)	gatY ← / ← b2097	tagatose‑bisphosphate aldolase 1/hypothetical protein
RA	2,176,450	G→A	R45R (CGC→CGT)	b2097 ←	hypothetical protein
RA	2,184,398	A→G	A154A (GCA→GCG)	yohM →	hypothetical protein
RA	2,184,686	(C)5→6	coding (750/825 nt)	yohM →	hypothetical protein
RA	2,202,504	(T)7→6	intergenic (+195/‑46)	yehK → / → yehL	hypothetical protein/hypothetical protein
RA	2,202,945	C→T	G132G (GGC→GGT)	yehL →	hypothetical protein
RA	2,209,048	A→G	intergenic (+84/‑185)	b2122 → / → yehR	hypothetical protein/hypothetical protein
RA	2,210,202	A→G	D5D (GAT→GAC)	yehS ←	hypothetical protein
RA	2,211,217	A→G	L483P (CTG→CCG)	yehU ←	putative 2‑component sensor protein
RA	2,216,746	G→C	S252S (TCC→TCG)	yehZ ←	putative transport system permease protein
RA	2,218,895	T→C	D372G (GAC→GGC)	bglX ←	beta‑D‑glucoside glucohydrolase
RA	2,219,147	T→C	H288R (CAC→CGC)	bglX ←	beta‑D‑glucoside glucohydrolase
RA	2,221,058	A→G	Q285R (CAG→CGG)	dld →	D‑lactate dehydrogenase
RA	2,223,035	A→G	intergenic (‑136/+29)	pbpG ← / ← yohC	penicillin‑binding protein 7/hypothetical protein
RA	2,234,921	T→C	T285A (ACG→GCG)	mglC ←	MglC
RA	2,239,132	T→C	H186R (CAC→CGC)	galS ←	mgl repressor
RA	2,252,917	C→T	R97H (CGC→CAC)	yeiK ←	hypothetical protein
RA	2,258,207	A→G	G408G (GGT→GGC)	fruA ←	PTS system, fructose‑specific transport protein
RA	2,258,992	C→T	A147T (GCG→ACG)	fruA ←	PTS system, fructose‑specific transport protein
RA	2,265,000	(G)5→6	coding (736/1467 nt)	yeiQ →	putative oxidoreductase
RA	2,266,085	A→G	L79L (TTA→TTG)	yeiR →	hypothetical protein
RA	2,272,980	T→C	V261A (GTG→GCG)	yejB →	putative transport system permease protein
RA	2,281,041	T→C	P309P (CCA→CCG)	yejK ←	hypothetical protein
RA	2,286,581	(C)7→8	coding (340/2511 nt)	yejO ←	putative ATP‑binding component of a transport system
RA	2,289,064	A→G	E182G (GAG→GGG)	narP →	nitrate/nitrite response regulator
RA	2,295,134	(C)7→8	coding (525/618 nt)	ccmA ←	ATP binding protein of heme exporter A
RA	2,295,407	C→T	G84G (GGG→GGA)	ccmA ←	ATP binding protein of heme exporter A
RA	2,295,753	C→T	G176E (GGG→GAG)	napC ←	cytochrome c‑type protein
RA	2,296,868	G→A	A244V (GCC→GTC)	napH ←	ferredoxin‑type protein: electron transfer
RA	2,298,169	T→C	T38A (ACC→GCC)	napG ←	ferredoxin‑type protein
RA	2,306,548	T→C	I30V (ATT→GTT)	yojI ←	putative ATP‑binding component of a transport system
RA	2,308,644	C→T	G304D (GGC→GAC)	yojL ←	hypothetical protein
RA	2,315,444	G→C	A802G (GCG→GGG)	rcsC ←	RcsC
RA	2,327,579	T→C	Y80C (TAC→TGC)	b2226 ←	hypothetical protein
RA	2,330,581	T→C	intergenic (‑2764/+1775)	b2226 ← / ← b2229	hypothetical protein/hypothetical protein
RA	2,332,505	A→G	Y159H (TAC→CAC)	b2229 ←	hypothetical protein
RA	2,348,653	(T)6→7	coding (379/1077 nt)	glpQ ←	glycerophosphodiester phosphodiesterase
RA	2,355,276	T→C	V118A (GTG→GCG)	yfaD →	hypothetical protein
RA	2,356,126	A→G	L247P (CTG→CCG)	b2245 ←	hypothetical protein
RA	2,359,592	T→C	T214A (ACC→GCC)	b2248 ←	putative regulator
RA	2,372,976	T→C	G16G (GGA→GGG)	menE ←	o‑succinylbenzoate‑CoA ligase
RA	2,375,218	A→G	V132A (GTG→GCG)	yfbB ←	hyptothetical protein
RA	2,376,124	A→G	L386L (TTG→CTG)	menD ←	2‑oxoglutarate decarboxylase
RA	2,378,232	G→A	I144I (ATC→ATT)	b2265 ←	isochorismate hydroxymutase 2
RA	2,389,856	A→G	G402G (GGT→GGC)	nuoM ←	NADH dehydrogenase I chain M
RA	2,409,331	A→G	V14V (GTT→GTC)	yfbS ←	putative transport protein
RA	2,415,422	A→G	T115A (ACA→GCA)	yfcC →	putative S‑transferase
RA	2,417,173	A→G	S8S (AGT→AGC)	b2299 ←	putative regulator
RA	2,420,432	T→C	H235H (CAT→CAC)	b2304 →	putative sugar nucleotide epimerase
RA	2,429,483	T→C	E65E (GAA→GAG)	dedD ←	putative lipoprotein
RA	2,430,676	T→C	Q96R (CAG→CGG)	folC ←	dihydrofolate:folylpolyglutamate synthetase
RA	2,438,697	A→C	L310R (CTG→CGG)	fabB ←	3‑oxoacyl‑[acyl‑carrier‑protein] synthase I
RA	2,453,091	T→C	intergenic (‑70/+12)	b4534 ← / ← b2339	hypothetical protein/putative fimbrial‑like protein
RA	2,453,196	A→G	T157T (ACT→ACC)	b2339 ←	putative fimbrial‑like protein
RA	2,457,112	A→G	V23A (GTA→GCA)	b2341 ←	hypothetical protein
RA	2,462,920	G→A	N36N (AAC→AAT)	vacJ ←	lipoprotein precursor
RA	2,469,675	A→G	S136S (AGT→AGC)	yfdL ←	putative RNA polymerase beta
RA	2,471,443	A→G	intergenic (‑177/‑181)	yfdO ← / → b2359	hypothetical protein/hypothetical protein
RA	2,486,394	T→C	A278A (GCA→GCG)	yfdE ←	hypothetical protein
RA	2,495,696	A→G	V207A (GTG→GCG)	b2379 ←	putative aminotransferase
RA	2,497,463	T→C	V258A (GTG→GCG)	b2380 →	putative sensor protein
RA	2,506,541	G→A	D302D (GAC→GAT)	glk ←	glucokinase
RA	2,506,868	A→G	P193P (CCT→CCC)	glk ←	glucokinase
RA	2,530,303	+C	intergenic (+59/‑126)	cysZ → / → cysK	CysZ/cysteine synthase A, O‑acetylserine sulfhydrolase A
RA	2,548,591	A→G	intergenic (‑26/+70)	b2431 ← / ← b2432	hypothetical protein/hypothetical protein
RA	2,551,460	T→C	A72A (GCT→GCC)	hemF →	coproporphyrinogen III oxidase
RA	2,556,608	T→C	D31G (GAT→GGT)	b2441 ←	ethanolamine ammonia‑lyase, heavy chain
RA	2,578,097	A→G	T148A (ACC→GCC)	tktB →	transketolase 2 isozyme
RA	2,578,875	G→A	G407E (GGG→GAG)	tktB →	transketolase 2 isozyme
RA	2,586,923	C→T	Q437* (CAG→TAG)	acrD →	AcrD
RA	2,592,725	T→C	L385L (TTA→TTG)	ypfI ←	hypothetical protein
RA	2,594,634	T→C	I42V (ATA→GTA)	b2475 ←	hypothetical protein
RA	2,610,461	T→C	I181T (ATC→ACC)	b2491 →	HyfR
RA	2,616,953	T→C	S410G (AGT→GGT)	uraA ←	UraA
RA	2,620,042	T→C	W276R (TGG→CGG)	purM →	phosphoribosylaminoimidazole synthetase
RA	2,621,256	G→A	E65K (GAA→AAA)	ppk →	polyphosphate kinase
RA	2,637,648	T→C	V316V (GTA→GTG)	hisS ←	histidine tRNA synthetase
RA	2,647,757	G→A	P851S (CCG→TCG)	b2520 ←	hypothetical protein
RA	2,647,924	G→A	P795L (CCG→CTG)	b2520 ←	hypothetical protein
RA	2,649,291	+C	coding (1017/4962 nt)	b2520 ←	hypothetical protein
RA	2,654,241	A→G	R46R (CGT→CGC)	b2523 ←	putative peptidase
RA	2,659,748	A→G	V135A (GTG→GCG)	b2531 ←	hypothetical protein
RA	2,664,734	G→A	*434* (TGA→TAA)  S378L (TCA→TTA)	csiE → hcaT ←	hypothetical protein HcaT
RA	2,672,460	G→A	H83H (CAC→CAT)	yphB ←	hypothetical protein
RA	2,680,768	T→C	T31A (ACC→GCC)	yphG ←	hypothetical protein
RA	2,686,423	T→C	E134G (GAG→GGG)	yfhA ←	putative 2‑component transcriptional regulator
RA	2,686,480	T→C	Q115R (CAG→CGG)	yfhA ←	putative 2‑component transcriptional regulator
RA	2,688,940	G→A	A81V (GCG→GTG)	yfhK ←	putative 2‑component sensor protein
RA	2,691,024	A→T	F847Y (TTT→TAT)	purL ←	phosphoribosylformyl‑glycineamide synthetase
RA	2,694,131	T→C	L58P (CTG→CCG)	yfhD →	putative periplasmic binding transport protein
RA	2,701,551	T→C	Q178R (CAG→CGG)	rnc ←	RNase III
RA	2,711,990	C→T	L359L (CTG→TTG)	srmB →	ATP‑dependent RNA helicase
RA	2,719,936	A→G	Q655R (CAG→CGG)	yfiQ →	hypothetical protein
RA	2,723,253	C→T	G172R (GGA→AGA)	kgtP ←	alpha‑ketoglutarate permease
RA	2,729,373	+C	intergenic (‑195/+247)	rrsG ← / ← clpB	16S ribosomal RNA/ClpB
RA	2,744,244	G→A	intergenic (‑39/+210)	rpsP ← / ← ffh	30S ribosomal subunit protein S16/FFh
RA	2,744,399	T→C	intergenic (‑194/+55)	rpsP ← / ← ffh	30S ribosomal subunit protein S16/FFh
RA	2,747,389	Δ1 bp	coding (572/591 nt)	b4540 →	hypothetical protein
RA	2,747,477	G→A	intergenic (+69/+659)	b4540 → / ← grpE	hypothetical protein/GrpE
RA	2,751,091	G→C	A426P (GCT→CCT)	recN →	RecN
RA	2,766,382	C→G	P218A (CCC→GCC)	b2632 →	putative GTP‑binding protein
RA	2,766,423	G→A	R231R (CGG→CGA)	b2632 →	putative GTP‑binding protein
RA	2,766,427	2 bp→AC	coding (697‑698/864 nt)	b2632 →	putative GTP‑binding protein
RA	2,766,473	A→G	D248G (GAT→GGT)	b2632 →	putative GTP‑binding protein
RA	2,766,475	A→G	T249A (ACC→GCC)	b2632 →	putative GTP‑binding protein
RA	2,773,076	T→C	intergenic (+34/‑864)	yfjW → / → yfjX	hypothetical protein/hypothetical protein
RA	2,781,020	+G	intergenic (‑144/+65)	ypjA ← / ← b2648	putative ATP‑binding component of a transport system/hypothetical protein
RA	2,781,027	C→G	intergenic (‑151/+58)	ypjA ← / ← b2648	putative ATP‑binding component of a transport system/hypothetical protein
RA	2,785,180	Δ1 bp	coding (413/495 nt)	b2655 →	hypothetical protein
RA	2,796,560	T→C	intergenic (‑44/‑625)	stpA ← / → b2670	StpA/hypothetical protein
RA	2,796,565	T→C	intergenic (‑49/‑620)	stpA ← / → b2670	StpA/hypothetical protein
RA	2,805,526	A→G	D125G (GAC→GGC)	proX →	high‑affinity transport system for glycine betaine and proline
RA	2,810,132	C→T	R229C (CGC→TGC)	emrA →	EmrA
RA	2,812,859	Δ1 bp	intergenic (‑105/+46)	ygaG ← / ← gshA	hypothetical protein/gamma‑glutamate‑cysteine ligase
RA	2,815,038	A→G	V163A (GTG→GCG)	yqaB ←	putative phosphatase
RA	2,819,446	G→C	G196G (GGC→GGG)	alaS ←	alanyl‑tRNA synthetase
RA	2,820,144	Δ1 bp	intergenic (+24/+18)	b4542 → / ← oraA	hypothetical protein/OraA
RA	2,820,318	G→A	I115I (ATC→ATT)	oraA ←	OraA
RA	2,823,571	A→G	L10P (CTT→CCT)	mltB ←	membrane‑bound lytic murein transglycosylase B
RA	2,823,915	A→G	K21E (AAG→GAG)	srlA →	PTS system, glucitol/sorbitol‑specific IIC component
RA	2,824,797	T→C	F128S (TTT→TCT)	srlE →	PTS system glucitol/sorbitol‑specific enzyme IIBC component
RA	2,825,102	T→C	F230L (TTC→CTC)	srlE →	PTS system glucitol/sorbitol‑specific enzyme IIBC component
RA	2,830,091	T→C	P99P (CCA→CCG)	ygaA ←	putative 2‑component transcriptional regulator
RA	2,838,044	+G	coding (498/1458 nt)	ascF →	PTS system enzyme IIBC
RA	2,838,055	Δ1 bp	coding (509/1458 nt)	ascF →	PTS system enzyme IIBC
RA	2,841,271	T→C	S67G (AGT→GGT)	hycH ←	HycH
RA	2,842,033	G→T	R67R (CGC→CGA)	hycG ←	hydrogenase activity
RA	2,853,930	G→A	D524N (GAT→AAT)	fhlA →	FhlA
RA	2,854,119	C→T	R587C (CGC→TGC)	fhlA →	FhlA
RA	2,856,284	T→C	V390A (GTA→GCA)	mutS →	MutS
RA	2,865,091	T→C	T162A (ACC→GCC)	rpoS ←	sigma S factor
RA	2,871,779	A→G	D79D (GAT→GAC)	cysC ←	adenosine 5'‑phosphosulfate kinase
RA	2,872,811	T→C	D211G (GAC→GGC)	cysN ←	ATP‑sulfurylase subunit 1
RA	2,872,822	T→C	A207A (GCA→GCG)	cysN ←	ATP‑sulfurylase subunit 1
RA	2,877,536	G→C	A87G (GCT→GGT)	b2755 ←	hypothetical protein
RA	2,888,375	A→G	L516P (CTT→CCT)	cysJ ←	sulfite reductase (NADPH)
RA	2,894,766	A→G	T400T (ACT→ACC)	ygcS ←	putative transport protein
RA	2,896,819	+C	coding (622/657 nt)	ygcU ←	putative oxidoreductase subunit
RA	2,900,224	T→C	W103R (TGG→CGG)	ygcE →	putative kinase
RA	2,917,193	A→G	V72A (GTG→GCG)	ygcX ←	putative glucarate dehydratase
RA	2,923,951	T→C	H194H (CAT→CAC)	yqcD →	hypothetical protein
RA	2,926,421	T→C	A57A (GCT→GCC)	sdaC →	putative serine transporter
RA	2,929,074	A→G	intergenic (+109/‑3)	sdaB → / → b2798	L‑serine dehydratase/Exo
RA	2,956,046	A→C	R287R (CGT→CGG)	ptr ←	protease III
RA	2,960,777	A→G	S4P (TCC→CCC)  L134L (CTT→CTC)	ppdC ← b2824 ←	prepilin peptidase dependent protein C hypothetical protein
RA	2,961,511	C→T	G76G (GGG→GGA)	ppdB ←	prepilin peptidase dependent protein B
RA	2,963,770	T→C	D97G (GAC→GGC)	lgt ←	phosphatidylglycerol‑prolipoprotein diacylglyceryl transferase
RA	2,967,341	T→C	intergenic (‑342/‑343)	ygdP ← / → mutH	putative invasion protein/methyl‑directed mismatch repair
RA	2,968,005	T→A	W108R (TGG→AGG)	mutH →	methyl‑directed mismatch repair
RA	2,980,709	A→G	M191T (ATG→ACG)	kduD ←	2‑deoxy‑D‑gluconate 3‑dehydrogenase
RA	2,985,029	G→A	W387* (TGG→TGA)	b2845 →	putative transporter protein
RA	2,996,557	T→C	K112K (AAA→AAG)	b2863 ←	hypothetical protein
RA	3,005,399	+C	coding (1044/1092 nt)	ygeW →	putative carbamoyl transferase
RA	3,007,730	T→C	W316R (TGG→CGG)	ygeY →	putative deacetylase
RA	3,012,261	A→G	intergenic (‑1/+47)	b2875 ← / ← b2876	putative synthases/hypothetical protein
RA	3,013,656	T→C	M159T (ATG→ACG)	ygfJ →	hypothetical protein
RA	3,014,968	G→A	M296I (ATG→ATA)	b2878 →	putative oxidoreductase Fe‑S subunit
RA	3,025,676	+C	coding (535/570 nt)	ygfQ →	hypothetical protein
RA	3,030,024	T→C	L236P (CTG→CCG)	ygfU →	putative permease
RA	3,070,377	A→G	V89A (GTT→GCT)	pgk ←	phosphoglycerate kinase
RA	3,074,951	C→T	G80S (GGC→AGC)	b2931 ←	putative oxidoreductase
RA	3,075,220	(T)5→6	coding (256/357 nt)	yggP ←	hypothetical protein
RA	3,077,340	T→C	S4G (AGT→GGT)	cmtB ←	PTS system mannitol‑specific enzyme IIA component
RA	3,077,514	Δ1 bp	intergenic (‑165/+149)	cmtB ← / ← tktA	PTS system mannitol‑specific enzyme IIA component/transketolase 1 isozyme
RA	3,077,640	+G	intergenic (‑291/+23)	cmtB ← / ← tktA	PTS system mannitol‑specific enzyme IIA component/transketolase 1 isozyme
RA	3,077,905	A→G	S584P (TCG→CCG)	tktA ←	transketolase 1 isozyme
RA	3,078,245	C→G	G470G (GGG→GGC)	tktA ←	transketolase 1 isozyme
RA	3,082,631	C→T	G434S (GGC→AGC)	speA ←	biosynthetic arginine decarboxylase
RA	3,085,060	G→A	P112P (CCG→CCA)	metK →	methionine adenosyltransferase 1
RA	3,093,303	+G	coding (187/705 nt)	yggS →	hypothetical protein
RA	3,099,661	(A)5→6	intergenic (‑19/+164)	yggN ← / ← b2959	hypothetical protein/hypothetical protein
RA	3,107,469	+C	intergenic (‑296/‑101)	b2965 ← / → yqgA	ornithine decarboxylase isozyme/putative transport protein
RA	3,108,438	C→A	noncoding (56/76 nt)	pheV →	tRNA‑Phe
RA	3,114,866	T→C	N83S (AAC→AGC)	b2973 ←	hypothetical protein
RA	3,115,116	+C	coding (2013/2028 nt)	b2974 ←	putative endoglucanase
RA	3,116,492	C→T	E213K (GAA→AAA)	b2974 ←	putative endoglucanase
RA	3,123,585	+G	coding (953/2286 nt)	glcF ←	glycolate oxidase iron‑sulfur subunit
RA	3,130,334	A→G	V30V (GTT→GTC)	b2983 ←	hypothetical protein
RA	3,130,671	T→C	D186G (GAT→GGT)	yghR ←	hypothetical protein
RA	3,132,550	T→C	G135G (GGT→GGC)	yghT →	hypothetical protein
RA	3,132,556	T→C	R137R (CGT→CGC)	yghT →	hypothetical protein
RA	3,142,620	T→C	Q179R (CAG→CGG)	hybA ←	hydrogenase‑2 small subunit
RA	3,150,581	T→C	Y111H (TAT→CAT)	metC →	cystathionine beta‑lyase
RA	3,151,557	C→T	intergenic (+119/‑21)	metC → / → yghB	cystathionine beta‑lyase/hypothetical protein
RA	3,152,247	+C	intergenic (+10/+29)	yghB → / ← yqhC	hypothetical protein/putative ARAC‑type regulatory protein
MC JC	3,156,257	(CCA)2→1	coding (594‑596/930 nt)	yqhG →	hypothetical protein
RA	3,158,202	+C	coding (961/975 nt)	ygiRQ ←	Fe‑S oxidoreductase
RA	3,158,281	C→T	L294L (CTG→CTA)	ygiRQ ←	Fe‑S oxidoreductase
RA	3,166,935	2 bp→CG	coding (312‑313/483 nt)	b3023 ←	hypothetical protein
RA	3,167,940	G→A	G33S (GGT→AGT)	qseB →	quorum sensing regulator B
RA	3,185,776	T→C	F121L (TTC→CTC)	yqiG →	putative membrane protein
RA	3,185,807	T→C	F131S (TTT→TCT)	yqiG →	putative membrane protein
RA	3,186,925	A→G	T504A (ACT→GCT)	yqiG →	putative membrane protein
RA	3,190,239	G→A	D6N (GAC→AAC)	b3050 →	putative oxidoreductase
RA	3,195,775	A→G	V503A (GTG→GCG)	glnE ←	GlnE
RA	3,195,844	A→G	V480A (GTG→GCG)	glnE ←	GlnE
RA	3,197,947	A→G	D220D (GAT→GAC)	ygiF ←	hypothetical protein
RA	3,206,609	C→T	S315S (AGC→AGT)	ygjE →	hypothetical protein
RA	3,206,988	A→G	T442A (ACC→GCC)	ygjE →	hypothetical protein
RA	3,208,504	T→C	V28A (GTT→GCT)	rpsU →	30S ribosomal subunit protein S21
RA	3,209,171	T→C	Y142H (TAT→CAT)	dnaG →	DNA primase
RA	3,221,097	2 bp→GC	coding (824‑825/3093 nt)	b3076 →	evolved beta‑D‑galactosidase alpha subunit
RA	3,221,392	T→C	R373R (CGT→CGC)	b3076 →	evolved beta‑D‑galactosidase alpha subunit
RA	3,222,061	A→G	K596K (AAA→AAG)	b3076 →	evolved beta‑D‑galactosidase alpha subunit
RA	3,222,944	4 bp→AGCA	coding (2671‑2674/3093 nt)	b3076 →	evolved beta‑D‑galactosidase alpha subunit
RA	3,224,879	Δ1 bp	coding (1005/1434 nt)	ygjI →	putative oxidoreductase
RA	3,224,926	+C	coding (1052/1434 nt)	ygjI →	putative oxidoreductase
RA	3,225,194	C→T	V440V (GTC→GTT)	ygjI →	putative oxidoreductase
RA	3,229,223	T→C	intergenic (+343/‑83)	ygjK → / → ygjL	putative isomerase/putative NADPH dehydrogenase
RA	3,234,507	G→A	M109I (ATG→ATA)	ygjQ →	hypothetical protein
RA	3,236,177	Δ1 bp	intergenic (+239/‑45)	ygjR → / → ygjT	hypothetical protein/putative transport protein
RA	3,236,735	+C	coding (514/966 nt)	ygjT →	putative transport protein
RA	3,236,758	Δ1 bp	coding (537/966 nt)	ygjT →	putative transport protein
RA	3,237,242	+C	intergenic (+55/‑342)	ygjT → / → ygjU	putative transport protein/putative transport protein
RA	3,237,247	+C	intergenic (+60/‑337)	ygjT → / → ygjU	putative transport protein/putative transport protein
RA	3,238,220	T→C	W213R (TGG→CGG)	ygjU →	putative transport protein
RA	3,240,123	T→C	M278V (ATG→GTG)	uxaA ←	altronate hydrolase
RA	3,242,993	A→G	T84A (ACC→GCC)	exuT →	ExuT
RA	3,250,165	C→T	R74R (CGC→CGT)	yhaH →	putative cytochrome
RA	3,253,742	Δ1 bp	coding (551/552 nt)	yhaNM ←	hypothetical protein
RA	3,255,594	Δ1 bp	coding (4/1278 nt)	yhaO ←	putative transport system permease protein
RA	3,255,616	Δ1 bp	intergenic (‑19/+312)	yhaO ← / ← yhaP	putative transport system permease protein/putative L‑serine dehydratase
RA	3,256,893	+C	coding (405/423 nt)	yhaQ ←	putative L‑serine dehydratase
RA	3,257,838	+G	coding (2222/2241 nt)	tdcE ←	putative formate acetyltransferase 3
RA	3,269,236	G→C	A59G (GCT→GGT)	b3124 ←	hypothetical protein
RA	3,278,453	T→C	L38L (TTG→CTG)	agaW →	PTS system N‑acetylgalactosameine‑specific IIC component 2
RA	3,279,197	A→C	R145S (AGA→AGC)	agaA →	putative N‑acetylgalactosamine‑6‑phosphate deacetylase
RA	3,282,191	C→T	D127D (GAC→GAT)	agaB →	PTS system galactosamine‑specific IIB component 1
RA	3,291,253	T→C	R71R (CGT→CGC)	yraM →	putative glycosylase
RA	3,302,454	(C)7→8	coding (1005/1245 nt)	mtr ←	tryptophan‑specific transport protein
RA	3,304,497	A→G	R352R (CGT→CGC)	deaD ←	inducible ATP‑independent RNA helicase
RA	3,310,422	T→C	D133G (GAC→GGC)	rbfA ←	ribosome‑binding factor A
RA	3,312,106	T→C	Y517C (TAC→TGC)	infB ←	protein chain initiation factor IF‑2
RA	3,312,754	T→C	K301R (AAG→AGG)	infB ←	protein chain initiation factor IF‑2
RA	3,317,651	G→A	P535L (CCC→CTC)	b3173 ←	putative alkaline phosphatase I
RA	3,319,717	A→G	noncoding (83/87 nt)	leuU ←	tRNA‑Leu
RA	3,324,185	G→A	A131V (GCC→GTC)	hflB ←	HflB
RA	3,334,367	G→A	S31S (AGC→AGT)	yrbA ←	hypothetical protein
RA	3,342,129	A→G	H182R (CAC→CGC)	yhbG →	putative ATP‑binding component of a transport system
RA	3,345,093	A→G	E113G (GAA→GGA)	yhbJ →	hypothetical protein
RA	3,347,825	C→T	P95P (CCG→CCA)	yhbL ←	sigma cross‑reacting protein 27A
RA	3,352,254	2 bp→GC	intergenic (‑569/‑12)	yhcC ← / → gltB	hypothetical protein/glutamate synthase large subunit
RA	3,362,606	A→G	D722G (GAC→GGC)	yhcD →	putative outer membrane protein
RA	3,368,253	A→G	L140P (CTG→CCG)	yhcJ ←	hypothetical protein
RA	3,389,812	Δ1 bp	intergenic (‑149/+4151)	tldD ← / ← cafA	TldD/CafA
RA	3,393,106	Δ1 bp	intergenic (‑3443/+857)	tldD ← / ← cafA	TldD/CafA
RA	3,406,487	T→C	L415P (CTT→CCT)	b3258 →	sodium/pantothenate symporter
RA	3,412,612	A→G	Q371R (CAG→CGG)	acrE →	AcrE
RA	3,413,723	T→C	F352L (TTC→CTC)	acrF →	AcrF
RA	3,418,840	+G	coding (1070/1089 nt)	b3269 →	putative transport system permease protein
RA	3,421,120	Δ1 bp	noncoding (60/121 nt)	rrfF ←	5S ribosomal RNA
RA	3,429,168	A→G	A133A (GCT→GCC)	yrdD ←	putative DNA topoisomerase
RA	3,429,527	Δ1 bp	coding (40/510 nt)	yrdD ←	putative DNA topoisomerase
RA	3,430,453	+C	coding (745/747 nt)	smf ←	putative Rossmann‑fold nucleotide‑binding protein
RA	3,432,762	T→C	R304R (CGT→CGC)	fmt →	10‑formyltetrahydrofolate:L‑methionyl‑tRNA(fMet) N‑formyltransferase
RA	3,440,503	A→G	V411A (GTC→GCC)	prlA ←	putative ATPase subunit of translocase
RA	3,446,406	G→A	T134M (ACG→ATG)	rplP ←	50S ribosomal subunit protein L16
RA	3,446,647	T→C	T54A (ACC→GCC)	rplP ←	50S ribosomal subunit protein L16
RA	3,455,292	T→C	W427R (TGG→CGG)	b3325 →	YheF
RA	3,458,811	C→T	A51V (GCG→GTG)	hofG →	putative general protein secretion protein
RA	3,464,165	T→C	E66E (GAA→GAG)	bfr ←	bacterioferrin
RA	3,471,916	C→T	G92S (GGT→AGT)	rpsL ←	30S ribosomal subunit protein S12
RA	3,472,072	T→C	T40A (ACC→GCC)	rpsL ←	30S ribosomal subunit protein S12
RA	3,477,397	T→C	N283S (AAC→AGC)	kefB ←	KefB
RA	3,481,792	T→C	H318H (CAT→CAC)	yheT →	hypothetical protein
RA	3,483,905	T→C	V50A (GTG→GCG)	crp →	cyclic AMP receptor protein
RA	3,494,555	T→C	intergenic (+41/‑85)	nirD → / → nirC	nitrite reductase (NAD(P)H) subunit/Nitrite transporter
RA	3,500,011	G→A	R12Q (CGG→CAG)	b3372 →	hypothetical protein
RA	3,500,309	Δ1 bp	coding (333/363 nt)	b3372 →	hypothetical protein
RA	3,503,532	T→C	T43A (ACG→GCG)	yhfS ←	hypothetical protein
RA	3,505,916	T→C	M105V (ATG→GTG)	yhfV ←	putative hydrolase
RA	3,506,318	(C)5→6	coding (1134/1227 nt)	yhfW ←	putative mutase
RA	3,509,198	A→G	V189A (GTG→GCG)	yhfZ ←	hypothetical protein
RA	3,509,958	Δ1 bp	intergenic (‑195/+314)	yhfZ ← / ← trpS	hypothetical protein/tryptophan tRNA synthetase
RA	3,510,121	+G	intergenic (‑358/+151)	yhfZ ← / ← trpS	hypothetical protein/tryptophan tRNA synthetase
RA	3,522,256	G→C	G591A (GGC→GCC)	mrcA →	penicillin‑binding protein 1A
RA	3,522,805	A→G	Y774C (TAC→TGC)	mrcA →	penicillin‑binding protein 1A
RA	3,537,405	+GC	intergenic (+61/‑394)	b3407 → / → feoA	hypothetical protein/ferrous iron transport protein A
RA	3,542,788	A→G	S107G (AGC→GGC)	yhgH →	hypothetical protein
RA	3,544,357	+G	coding (163/1314 nt)	gntT →	gluconate permease
RA	3,544,360	+G	coding (166/1314 nt)	gntT →	gluconate permease
RA	3,544,363	+C	coding (169/1314 nt)	gntT →	gluconate permease
RA	3,548,005	C→T	G701D (GGT→GAT)	malP ←	maltodextrin phosphorylase
RA	3,554,088	+C	coding (2/624 nt)	yhgKJ ←	RNA phosphage cyclase
RA	3,554,113	Δ1 bp	coding (372/396 nt)	yhgKJ ←	RNA phosphage cyclase
RA	3,554,118	+C	coding (367/396 nt)	yhgKJ ←	RNA phosphage cyclase
RA	3,558,932	2 bp→GC	coding (153‑154/831 nt)	glpG ←	GlpG
RA	3,573,700	+C	intergenic (+403/+997)	yhgN → / ← gntK	hypothetical protein/gluconokinase 2
RA	3,575,446	+G	coding (912/942 nt)	gntR ←	GntR
RA	3,579,035	T→C	R89R (CGT→CGC)	yhhY →	hypothetical protein
RA	3,580,138	A→G	L215L (CTA→CTG)	yhhZ →	hypothetical protein
RA	3,584,684	G→A	Q37Q (CAG→CAA)	yhhA →	hypothetical protein
RA	3,598,512	A→G	intergenic (‑98/+147)	rpoH ← / ← ftsX	sigma(32) factor/cell division membrane protein
RA	3,609,245	T→C	L54L (TTA→TTG)	yhhS ←	putative transport
RA	3,610,653	A→G	P18P (CCA→CCG)	yhhU →	hypothetical protein
RA	3,621,612	T→C	intergenic (+199/‑397)	yhhH → / → yhhI	hypothetical protein/putative receptor
RA	3,624,949	C→T	E724K (GAA→AAA)	yhiH ←	putative ATP‑binding component of a transport system, fragment 1
RA	3,624,985	T→C	I712V (ATC→GTC)	yhiH ←	putative ATP‑binding component of a transport system, fragment 1
RA	3,627,142	+G	intergenic (‑24/+23)	yhiH ← / ← yhiI	putative ATP‑binding component of a transport system, fragment 1/putative membrane protein
RA	3,629,183	T→C	K346K (AAA→AAG)	yhiJ ←	hypothetical protein
RA	3,629,781	A→G	V147A (GTT→GCT)	yhiJ ←	hypothetical protein
RA	3,654,259	T→C	T38A (ACC→GCC)	hdeA ←	hypothetical protein
RA	3,663,007	G→A	T145I (ACA→ATA)	yhiX ←	putative ARAC‑type regulatory protein
RA	3,665,449	T→C	Y457C (TAC→TGC)	yhjA ←	putative cytochrome C peroxidase
RA	3,667,169	T→C	intergenic (‑351/‑53)	yhjA ← / → treF	putative cytochrome C peroxidase/cytoplasmic trehalase
RA	3,670,236	T→C	Y89H (TAT→CAT)	yhjC →	putative transcriptional regulator LYSR‑type
RA	3,675,076	+G	coding (920/2076 nt)	yhjG ←	hypothetical protein
RA	3,677,270	T→C	T147T (ACT→ACC)	kdgK →	ketodeoxygluconokinase
RA	3,682,619	A→G	R199R (CGT→CGC)	yhjK ←	hypothetical protein
RA	3,686,775	+T	intergenic (‑23/+9)	b3530 ← / ← yhjM	putative oxidoreductase subunit/putative endoglucanase
RA	3,689,910	C→T	T109T (ACG→ACA)	yhjN ←	hypothetical protein
RA	3,693,594	(C)5→4	intergenic (‑4/+32)	yhjQ ← / ← yhjR	hypothetical protein/hypothetical protein
RA	3,694,167	C→T	G27G (GGC→GGT)	yhjS →	putative protease
RA	3,703,602	2 bp→GC	intergenic (‑183/+124)	dppB ← / ← dppA	dipeptide transport system permease protein 1/dipeptide transport protein
RA	3,706,723	T→C	Y472C (TAC→TGC)	yhjW ←	hypothetical protein
RA	3,706,941	A→G	G399G (GGT→GGC)	yhjW ←	hypothetical protein
RA	3,710,261	T→C	E101E (GAA→GAG)	b3548 ←	putative lipase
RA	3,714,436	2 bp→GC	coding (261‑262/660 nt)	yiaD →	putative outer membrane protein
RA	3,719,494	T→C	V223A (GTG→GCG)	t150 →	IS150 putative transposase
RA	3,722,055	A→G	M298T (ATG→ACG)	glyQ ←	glycine tRNA synthetase alpha subunit
RA	3,726,481	T→C	T174A (ACC→GCC)	xylB ←	xylulokinase
RA	3,734,264	2 bp→GC	coding (542‑543/825 nt)	bax ←	putative ATP‑binding protein
RA	3,735,666	T→C	S181P (TCC→CCC)	malS →	alpha‑amylase
RA	3,737,956	2 bp→CG	coding (623‑624/1254 nt)	avtA →	alanine‑alpha‑ketoisovalerate transaminase
RA	3,738,723	A→G	intergenic (+136/+15)	avtA → / ← yiaI	alanine‑alpha‑ketoisovalerate transaminase/hypothetical protein
RA	3,739,262	T→C	intergenic (‑51/+51)	yiaI ← / ← yiaJ	hypothetical protein/putative regulator
RA	3,741,875	G→A	intergenic (+36/‑82)	yiaL → / → yiaM	putative lipase/hypothetical protein
RA	3,743,603	Δ1 bp	coding (1171/1275 nt)	yiaN →	putative membrane protein
RA	3,751,162	T→C	S190G (AGC→GGC)	yiaV ←	putative membrane protein
RA	3,754,310	C→A	R382M (AGG→ATG)	yiaY ←	putative oxidoreductase
JC	3,754,317	+GCG	coding (1138/1149 nt)	yiaY ←	putative oxidoreductase
RA	3,754,634	T→C	N274S (AAC→AGC)	yiaY ←	putative oxidoreductase
RA	3,754,708	G→A	L249L (CTC→CTT)	yiaY ←	putative oxidoreductase
RA	3,758,509	T→C	D123G (GAC→GGC)	selA ←	selenocysteine synthase
RA	3,759,720	T→C	intergenic (‑138/‑90)	yibF ← / → rhsA	putative S‑transferase/RhsA
RA	3,764,283	T→C	V107A (GTT→GCT)	yibA →	hypothetical protein
RA	3,765,203	A→T	Q119L (CAG→CTG)	yibJ →	hypothetical protein
RA	3,765,225	T→A	D126E (GAT→GAA)	yibJ →	hypothetical protein
RA	3,765,234	G→A	G129G (GGG→GGA)	yibJ →	hypothetical protein
RA	3,766,847	T→C	intergenic (+582/‑125)	yibG → / → b4549	hypothetical protein/hypothetical protein
RA	3,771,793	T→C	V629A (GTG→GCG)	mtlA →	PTS system, mannitol‑specific enzyme IIABC components
RA	3,778,301	T→C	V283A (GTA→GCA)	lldD →	L‑lactate dehydrogenase
RA	3,782,476	A→G	V56A (GTT→GCT)	yibN ←	hypothetical protein
RA	3,783,092	T→C	V69A (GTT→GCT)	yibO →	putative 2,3‑bisphosphoglycerate‑independent phosphoglycerate mutase
RA	3,783,479	A→G	D198G (GAT→GGT)	yibO →	putative 2,3‑bisphosphoglycerate‑independent phosphoglycerate mutase
RA	3,787,955	A→G	W340R (TGG→CGG)	tdh ←	threonine dehydrogenase
RA	3,788,398	A→G	V192A (GTG→GCG)	tdh ←	threonine dehydrogenase
RA	3,793,926	G→A	A107A (GCG→GCA)	rfaC →	heptosyl transferase I
RA	3,795,756	A→G	A394A (GCA→GCG)	rfaL →	O‑antigen ligase
RA	3,808,645	G→A	S45S (AGC→AGT)	mutM ←	formamidopyrimidine DNA glycosylase
RA	3,809,063	A→G	intergenic (‑19/+2)	rpmG ← / ← rpmB	50S ribosomal subunit protein L33/50S ribosomal subunit protein L28
RA	3,822,370	C→T	R77C (CGC→TGC)	spoU →	putative RNA methylase
RA	3,822,659	G→A	R173H (CGT→CAT)	spoU →	putative RNA methylase
RA	3,823,984	A→G	Q383R (CAG→CGG)	recG →	DNA helicase
RA	3,825,188	T→C	M369V (ATG→GTG)	gltS ←	glutamate transport
RA	3,829,956	A→G	C737R (TGC→CGC)	yicI ←	hypothetical protein
RA	3,840,766	G→A	C243C (TGC→TGT)	yicO ←	hypothetical protein
RA	3,842,228	G→A	G213D (GGT→GAT)	yicP →	putative adenine deaminase
RA	3,847,419	(C)5→6	coding (345/1503 nt)	b3668 ←	sensor histidine protein kinase
RA	3,853,551	T→C	Q16R (CAG→CGG)	yidG ←	hypothetical protein
RA	3,854,698	T→C	Y445C (TAC→TGC)	yidJ ←	putative sulfatase
RA	3,856,410	A→G	I445T (ATC→ACC)	yidK ←	putative cotransporter
RA	3,857,430	A→G	I105T (ATC→ACC)	yidK ←	putative cotransporter
RA	3,859,397	A→G	V73A (GTG→GCG)	glvG ←	putative 6‑phospho‑beta‑glucosidase
RA	3,866,583	A→G	S119S (AGT→AGC)	yidR ←	hypothetical protein
RA	3,866,718	T→C	A74A (GCA→GCG)	yidR ←	hypothetical protein
RA	3,867,186	T→C	D68D (GAT→GAC)	yidS →	hypothetical protein
RA	3,867,236	T→C	V85A (GTC→GCC)	yidS →	hypothetical protein
RA	3,870,631	Δ1 bp	coding (610/1764 nt)	dgoA ←	2‑oxo‑3‑deoxygalactonate 6‑phosphate aldolase
RA	3,870,765	+G	coding (476/1764 nt)	dgoA ←	2‑oxo‑3‑deoxygalactonate 6‑phosphate aldolase
RA	3,870,876	Δ1 bp	coding (365/1764 nt)	dgoA ←	2‑oxo‑3‑deoxygalactonate 6‑phosphate aldolase
RA	3,872,450	+G	coding (338/387 nt)	yidW ←	regulator protein for dgo operon
RA	3,873,209	A→G	T30A (ACT→GCT)	yidX →	putative replicase
RA	3,873,627	Δ1 bp	coding (506/672 nt)	yidX →	putative replicase
RA	3,873,986	T→C	T199A (ACG→GCG)	yidA ←	hypothetical protein
RA	3,876,595	G→C	P385A (CCG→GCG)	gyrB ←	DNA gyrase subunit B
RA	3,878,432	A→G	C140R (TGC→CGC)	recF ←	RecF
RA	3,881,483	Δ1 bp	intergenic (‑126/‑482)	dnaA ← / → rpmH	DnaA/50S ribosomal subunit protein L34
RA	3,881,885	G→A	intergenic (‑528/‑80)	dnaA ← / → rpmH	DnaA/50S ribosomal subunit protein L34
RA	3,881,913	G→A	intergenic (‑556/‑52)	dnaA ← / → rpmH	DnaA/50S ribosomal subunit protein L34
RA	3,887,809	A→G	intergenic (+35/‑56)	b3708 → / → tnaB	tryptophanase/low affinity tryptophan permease
RA	3,888,054	A→G	N64D (AAT→GAT)	tnaB →	low affinity tryptophan permease
RA	3,888,277	C→T	A138V (GCC→GTC)	tnaB →	low affinity tryptophan permease
RA	3,893,920	C→T	G107S (GGC→AGC)	yieG ←	putative membrane/transport protein
RA	3,895,750	T→C	C34R (TGT→CGT)	yieJ →	hypothetical protein
RA	3,896,324	+G	coding (698/711 nt)	b3718 ←	putative isomerase
RA	3,896,435	G→A	A196V (GCG→GTG)	b3718 ←	putative isomerase
RA	3,897,358	T→C	Y294C (TAC→TGC)	yieL ←	putative xylanase
RA	3,899,440	T→C	T137A (ACC→GCC)	yieC ←	putative receptor protein
RA	3,911,336	T→C	intergenic (‑40/+122)	glmS ← / ← glmU	L‑glutamine:D‑fructose‑6‑phosphate aminotransferase/N‑acetyl glucosamine‑1‑phosphate uridyltransferase
RA	3,911,433	A→G	intergenic (‑137/+25)	glmS ← / ← glmU	L‑glutamine:D‑fructose‑6‑phosphate aminotransferase/N‑acetyl glucosamine‑1‑phosphate uridyltransferase
RA	3,912,152	A→G	V226A (GTG→GCG)	glmU ←	N‑acetyl glucosamine‑1‑phosphate uridyltransferase
RA	3,915,980	G→A	G502G (GGC→GGT)	atpA ←	membrane‑bound ATP synthase, F1 sector, alpha‑subunit
RA	3,916,949	A→G	A179A (GCT→GCC)	atpA ←	membrane‑bound ATP synthase, F1 sector, alpha‑subunit
RA	3,917,345	A→G	C47C (TGT→TGC)	atpA ←	membrane‑bound ATP synthase, F1 sector, alpha‑subunit
RA	3,923,014	A→G	I83T (ATA→ACA)	gidA ←	glucose‑inhibited division
RA	3,923,701	T→C	H128R (CAC→CGC)	mioC ←	MioC
RA	3,927,062	+G	coding (2/1284 nt) coding (169/183 nt)	yieM ← b4564 ←	hypothetical protein hypothetical protein
RA	3,929,523	T→C	V194A (GTG→GCG)	kup →	low affinity potassium transport system
RA	3,929,607	T→C	V222A (GTG→GCG)	kup →	low affinity potassium transport system
RA	3,930,457	Δ1 bp	coding (1515/1560 nt)	kup →	low affinity potassium transport system
RA	3,930,568	+G	intergenic (+66/‑373)	kup → / → rbsD	low affinity potassium transport system/RbsD
RA	3,930,677	+G	intergenic (+175/‑264)	kup → / → rbsD	low affinity potassium transport system/RbsD
RA	3,931,725	A→G	N108D (AAT→GAT)	rbsA →	ATP‑binding component of D‑ribose high‑affinity transport system
RA	3,935,303	A→G	Q128Q (CAA→CAG)	rbsK →	ribokinase
RA	3,935,434	A→G	E172G (GAA→GGA)	rbsK →	ribokinase
RA	3,935,895	A→G	T15A (ACC→GCC)	rbsR →	RbsR
RA	3,937,900	G→A	G113G (GGC→GGT)	yieO ←	putative transport protein
JC	3,938,587	+TGC	coding (220/546 nt)	yiePs ←	hypothetical protein
RA	3,941,734	Δ1 bp	noncoding (409/2906 nt)	rrlC →	23S ribosomal RNA
RA	3,944,244	C→A	intergenic (+13/‑80)	rrlC → / → rrfC	23S ribosomal RNA/5S ribosomal RNA
RA	3,944,676	2 bp→GC	intergenic (+20/+75)	trpT → / ← yifDA	tRNA‑Trp/transcription regulator
RA	3,945,351	+C	coding (1/600 nt) coding (240/240 nt)	yifDA ← yifDA ←	transcription regulator transcription regulator
RA	3,950,557	2 bp→GC	coding (451‑452/930 nt)	ilvE →	branched‑chain amino‑acid aminotransferase
RA	3,951,166	+C	coding (35/1818 nt)	ilvD →	dihydroxyacid dehydratase
RA	3,951,168	+G	coding (37/1818 nt)	ilvD →	dihydroxyacid dehydratase
RA	3,957,092	+CC	intergenic (+26/+58)	ilvC → / ← ppiC	ketol‑acid reductoisomerase/peptidyl‑prolyl cis‑trans isomerase C
RA	3,957,124	+G	intergenic (+58/+26)	ilvC → / ← ppiC	ketol‑acid reductoisomerase/peptidyl‑prolyl cis‑trans isomerase C
RA	3,957,548	1 bp→GG	intergenic (‑117/‑744)	ppiC ← / → rep	peptidyl‑prolyl cis‑trans isomerase C/rep helicase
RA	3,957,551	+T	intergenic (‑120/‑741)	ppiC ← / → rep	peptidyl‑prolyl cis‑trans isomerase C/rep helicase
RA	3,957,560	+C	intergenic (‑129/‑732)	ppiC ← / → rep	peptidyl‑prolyl cis‑trans isomerase C/rep helicase
RA	3,958,877	2 bp→CG	coding (586‑587/2022 nt)	rep →	rep helicase
RA	3,960,578	2 bp→CG	coding (1266‑1267/1485 nt)	gppA ←	guanosine pentaphosphatase
RA	3,961,588	C→G	R86T (AGG→ACG)	gppA ←	guanosine pentaphosphatase
RA	3,964,491	A→G	T154A (ACT→GCT)	rho →	transcription termination factor Rho
RA	3,967,593	A→G	K317K (AAA→AAG)	wzzE →	putative transport protein
JC	3,968,317	+CGT	coding (612/1170 nt)	wecB →	UDP‑N‑acetyl glucosamine ‑2‑epimerase
RA	3,969,103	2 bp→GC	coding (232‑233/1263 nt)	wecC →	UDP‑N‑acetyl‑D‑mannosaminuronic acid dehydrogenase
RA	3,971,075	2 bp→GC	coding (942‑943/1068 nt)	rffG →	dTDP‑glucose 4,6‑dehydratase
RA	3,972,637	2 bp→GC	coding (430‑431/546 nt)	wecD →	hypothetical protein
RA	3,975,313	Δ1 bp	intergenic (+173/‑901)	wzxE → / → wecF	putative cytochrome/TDP‑Fuc4NAc:lipidII transferase
RA	3,978,702	C→T	S68F (TCC→TTC)	yifK →	putative amino acid/amine transport protein
RA	3,979,535	+G	coding (1036/1386 nt)	yifK →	putative amino acid/amine transport protein
RA	3,979,546	Δ1 bp	coding (1047/1386 nt)	yifK →	putative amino acid/amine transport protein
RA	3,980,297	(C)8→9	noncoding (79/87 nt)	leuT →	tRNA‑Leu
RA	3,980,918	2 bp→CG	coding (348‑349/1236 nt)	aslB →	putative arylsulfatase regulator
RA	3,987,586	2 bp→GC	coding (814‑815/963 nt)	hemC ←	porphobilinogen deaminase
RA	3,987,822	2 bp→CG	coding (578‑579/963 nt)	hemC ←	porphobilinogen deaminase
RA	3,998,290	+G	coding (379/486 nt)	b4566 ←	hypothetical protein
RA	4,001,421	2 bp→GC	coding (381‑382/903 nt)	rarD ←	hypothetical protein
RA	4,001,486	2 bp→GC	coding (316‑317/903 nt)	rarD ←	hypothetical protein
RA	4,001,717	+C	coding (86/903 nt)	rarD ←	hypothetical protein
RA	4,004,979	+G	coding (1511/1833 nt)	recQ →	ATP‑dependent DNA helicase
RA	4,004,984	+CG	coding (1516/1833 nt)	recQ →	ATP‑dependent DNA helicase
RA	4,005,601	+C	coding (237/282 nt)	b4568 →	hypothetical protein
RA	4,006,483	+C	coding (183/207 nt)	b4554 ←	hypothetical protein
RA	4,007,718	2 bp→CG	coding (943‑944/1023 nt)	pldB →	lysophospholipase L(2)
RA	4,007,907	+GG	intergenic (+109/‑11)	pldB → / → b4555	lysophospholipase L(2)/hypothetical protein
RA	4,008,375	+A	coding (458/516 nt)	b4555 →	hypothetical protein
RA	4,008,391	+C	coding (474/516 nt)	b4555 →	hypothetical protein
RA	4,008,393	C→G	A159G (GCT→GGT)	b4555 →	hypothetical protein
RA	4,008,400	+GAAA	coding (483/516 nt)	b4555 →	hypothetical protein
RA	4,008,404	+G	coding (487/516 nt)	b4555 →	hypothetical protein
RA	4,008,411	+C	coding (494/516 nt)	b4555 →	hypothetical protein
RA	4,008,421	+T	coding (504/516 nt)	b4555 →	hypothetical protein
RA	4,008,429	+TG	coding (512/516 nt)	b4555 →	hypothetical protein
RA	4,008,469	+G	intergenic (+36/‑197)	b4555 → / → yigM	hypothetical protein/hypothetical protein
RA	4,008,473	+G	intergenic (+40/‑193)	b4555 → / → yigM	hypothetical protein/hypothetical protein
RA	4,008,491	2 bp→CG	intergenic (+58/‑174)	b4555 → / → yigM	hypothetical protein/hypothetical protein
RA	4,008,525	+G	intergenic (+92/‑141)	b4555 → / → yigM	hypothetical protein/hypothetical protein
RA	4,013,176	C→G	G182R (GGA→CGA)	ysgA ←	hypothetical protein
RA	4,013,177	+C	coding (543/999 nt)	ysgA ←	hypothetical protein
RA	4,013,717	+G	coding (3/999 nt)	ysgA ←	hypothetical protein
RA	4,013,772	+C	intergenic (‑53/‑246)	ysgA ← / → udp	hypothetical protein/uridine phosphorylase
RA	4,016,743	C→T	P101L (CCC→CTC)	ubiE →	UbiE
RA	4,019,857	C→T	intergenic (+56/‑28)	b3836 → / → b3838	hypothetical protein/hypothetical protein
RA	4,019,860	Δ2 bp	intergenic (+59/‑24)	b3836 → / → b3838	hypothetical protein/hypothetical protein
RA	4,021,684	Δ1 bp	coding (542/609 nt)|coding (1/243 nt)	b4556 → tatD →	hypothetical protein Mg‑dependent DNase
RA	4,026,252	2 bp→GC	coding (110‑111/1164 nt)	fadA ←	thiolase I
RA	4,031,984	+C	coding (1250/1299 nt)	trkH →	TrkH
RA	4,039,349	T→C	P77P (CCA→CCG)	mobA ←	MobA
RA	4,039,960	Δ1 bp	intergenic (+42/‑36)	yihD → / → yihE	hypothetical protein/hypothetical protein
RA	4,041,654	G→A	intergenic (+29/‑125)	dsbA → / → b3861	protein disulfide isomerase I/putative GTP‑binding protein
RA	4,041,671	(T)6→7	intergenic (+46/‑108)	dsbA → / → b3861	protein disulfide isomerase I/putative GTP‑binding protein
RA	4,051,144	Δ1 bp	intergenic (+146/+305)	hemN → / ← glnG	O2‑independent coproporphyrinogen III oxidase/GlnG
RA	4,051,170	+C	intergenic (+172/+279)	hemN → / ← glnG	O2‑independent coproporphyrinogen III oxidase/GlnG
RA	4,057,759	+C	coding (1773/1776 nt)	yihK →	putative GTP‑binding factor
RA	4,057,859	(T)9→8	intergenic (+97/‑167)	yihK → / → yihL	putative GTP‑binding factor/putative transcriptional regulator
RA	4,058,326	A→G	T101A (ACC→GCC)	yihL →	putative transcriptional regulator
RA	4,059,768	A→G	intergenic (+44/‑58)	yihM → / → yihN	hypothetical protein/putative resistance protein
RA	4,061,961	Δ1 bp	coding (1386/1458 nt)	b3876 ←	putative permease
RA	4,062,187	A→G	L387S (TTG→TCG)	b3876 ←	putative permease
RA	4,066,222	T→C	Y212C (TAC→TGC)	yihQ ←	putative glycosidase
RA	4,071,652	A→G	S114G (AGC→GGC)	yihV →	putative kinase
RA	4,080,831	G→A	L858L (CTG→TTG)	fdoG ←	formate dehydrogenase‑O, major subunit
RA	4,085,675	Δ1 bp	intergenic (+38/+13)	yiiG → / ← frvR	hypothetical protein/putative frv operon regulatory protein
RA	4,088,793	T→C	T385T (ACA→ACG)	frvB ←	PTS system, fructose‑like enzyme IIBC component
RA	4,091,351	C→T	G168D (GGC→GAC)	rhaD ←	rhamnulose‑phosphate aldolase
MC JC	4,091,572	3461 bp→29 bp		[rhaD]–rhaB	[rhaD], rhaA, rhaB
JC	4,099,309	(G)7→10	coding (48/993 nt)	kdgT →	2‑keto‑3‑deoxy‑D‑gluconate transport system
RA	4,099,449	C→T	A63V (GCG→GTG)	kdgT →	2‑keto‑3‑deoxy‑D‑gluconate transport system
RA	4,102,870	C→T	D128N (GAC→AAC)	cpxR ←	transcriptional regulator in 2‑component system
RA	4,103,519	+T	intergenic (‑268/‑530)	cpxR ← / → yiiP	transcriptional regulator in 2‑component system/putative transport system permease protein
RA	4,108,732	T→C	Q119R (CAG→CGG)	tpiA ←	triosephosphate isomerase
RA	4,109,226	A→G	L190P (CTA→CCA)	yiiQ ←	hypothetical protein
RA	4,110,991	A→G	D40G (GAT→GGT)	yiiT →	putative regulator
RA	4,113,766	A→G	V346A (GTT→GCT)	glpK ←	glycerol kinase
RA	4,114,335	T→C	A156A (GCA→GCG)	glpK ←	glycerol kinase
RA	4,118,257	T→C	A357A (GCA→GCG)	hslU ←	heat shock protein hslVU ATPase subunit
RA	4,119,382	A→G	Y162Y (TAT→TAC)	hslV ←	heat shock protein hslVU proteasome‑related peptidase subunit
RA	4,130,398	A→G	D68G (GAC→GGC)	metF →	5,10‑methylenetetrahydrofolate reductase
RA	4,132,580	T→A	I389N (ATC→AAC)	katG →	catalase
RA	4,133,793	A→G	I36V (ATC→GTC)	b3943 →	hypothetical protein
RA	4,139,436	G→A	intergenic (‑1/‑1)	ptsA ← / → yijI	PEP‑protein phosphotransferase system enzyme I/IIA/hypothetical protein
RA	4,139,669	+C	coding (233/330 nt) coding (132/159 nt)	yijI → b4558 ←	hypothetical protein hypothetical protein
RA	4,145,321	T→C	A192A (GCA→GCG)	yijO ←	putative ARAC‑type regulatory protein
RA	4,147,430	A→G	W139R (TGG→CGG)	yijP ←	hypothetical protein
RA	4,151,054	T→C	intergenic (‑377/+221)	ppc ← / ← argE	phosphoenolpyruvate carboxylase/acetylornithine deacetylase
RA	4,155,035	A→G	T203A (ACG→GCG)	argH →	argininosuccinate lyase
RA	4,158,827	G→T	G61V (GGC→GTC)	yijC →	hypothetical protein
RA	4,161,702	C→G	A162G (GCA→GGA)	btuB →	BtuB
RA	4,162,448	A→G	T411A (ACA→GCA)	btuB →	BtuB
RA	4,170,208	T→C	G191G (GGT→GGC)	murB →	UDP‑N‑acetylenolpyruvoylglucosamine reductase
RA	4,171,680	A→G	V309A (GTA→GCA)	coaA ←	pantothenate kinase
RA	4,175,949	+G	intergenic (+82/‑76)	nusG → / → rplK	NusG/50S ribosomal subunit protein L11
RA	4,182,169	A→G	H1116R (CAC→CGC)	rpoB →	RNA polymerase beta subunit
RA	4,185,997	A→G	T1024A (ACC→GCC)	rpoC →	RNA polymerase beta prime subunit
RA	4,194,577	2 bp→GC	coding (97‑98/774 nt)	yjaD →	hypothetical protein
RA	4,199,347	T→C	R21G (AGA→GGA)	yjaI ←	hypothetical protein
RA	4,200,901	A→G	*466W (TGA→TGG)  T2A (ACG→GCG)	hydH → hydG →	HydH HydG
RA	4,202,136	G→A	A413A (GCG→GCA)	hydG →	HydG
RA	4,220,652	A→G	Y199H (TAT→CAT)	iclR ←	IclR
RA	4,224,188	C→T	R928C (CGT→TGT)	metH →	B12‑dependent homocysteine‑N5‑methyltetrahydrofolate transmethylase
RA	4,228,096	A→G	N55S (AAC→AGC)	yjbC →	hypothetical protein
RA	4,235,656	(G)5→6	coding (444/2097 nt)	yjbH →	hypothetical protein
RA	4,236,190	C→T	G326G (GGC→GGT)	yjbH →	hypothetical protein
RA	4,247,622	A→G	T164A (ACG→GCG)	malM →	MalM
RA	4,248,121	T→C	intergenic (+68/‑161)	malM → / → b4559	MalM/hypothetical protein
RA	4,255,670	C→T	A117V (GCT→GTT)	dinF →	DNA‑damage‑inducible protein F
RA	4,262,748	A→G	T286A (ACC→GCC)	dnaB →	replicative DNA helicase
RA	4,293,107	A→G	T350A (ACC→GCC)	gltP →	glutamate‑aspartate symport protein
RA	4,293,960	+GC	intergenic (+587/+55)	gltP → / ← yjcO	glutamate‑aspartate symport protein/hypothetical protein
RA	4,298,395	A→G	L72P (CTG→CCG)	yjcP ←	hypothetical protein
RA	4,311,496	+C	coding (301/408 nt)	phnQ ←	hypothetical protein
RA	4,312,334	A→G	L116P (CTG→CCG)	phnP ←	PhnP
RA	4,314,600	C→T	R66H (CGC→CAC)	phnM ←	PhnM
RA	4,316,203	T→G	Q47P (CAG→CCG)	phnK ←	ATP‑binding component of phosphonate transport
RA	4,325,494	C→G	A261G (GCG→GGG)	yjdA →	putative vimentin
RA	4,334,019	A→G	L197L (CTT→CTC)	yjdE ←	putative amino acid/amine transport protein
RA	4,337,626	T→C	A159A (GCA→GCG)	adiA ←	biodegradative arginine decarboxylase
RA	4,337,885	A→G	V73A (GTC→GCC)	adiA ←	biodegradative arginine decarboxylase
RA	4,354,595	A→G	L534P (CTG→CCG)	cadA ←	lysine decarboxylase 1
RA	4,362,298	T→C	Q108R (CAG→CGG)	dsbD ←	thiol:disulfide interchange protein
RA	4,369,168	T→C	V189A (GTG→GCG)	mopA →	GroEL
RA	4,375,376	A→G	intergenic (‑76/+13)	blc ← / ← ampC	outer membrane lipoprotein/beta‑lactamase
RA	4,384,043	A→G	V969A (GTG→GCG)	yjeP ←	putative periplasmic binding protein
RA	4,386,329	C→T	R207H (CGC→CAC)	yjeP ←	putative periplasmic binding protein
RA	4,389,966	A→G	noncoding (29/76 nt)	glyV →	tRNA‑Gly
RA	4,392,651	(G)5→4	coding (1008/1548 nt)	yjeF →	hypothetical protein
RA	4,395,798	A→G	H270R (CAC→CGC)	mutL →	MutL
RA	4,402,284	T→C	V7A (GTA→GCA)	purA →	adenylosuccinate synthetase
RA	4,402,992	A→G	N243S (AAC→AGC)	purA →	adenylosuccinate synthetase
RA	4,404,526	C→T	L99L (CTG→TTG)	b4179 →	hypothetical protein
RA	4,413,828	A→G	Y19H (TAT→CAT)	b4188 ←	hypothetical protein
RA	4,422,664	A→G	intergenic (‑295/‑32)	yjfY ← / → rpsF	hypothetical protein/30S ribosomal subunit protein S6
RA	4,424,677	A→G	G108G (GGT→GGC)	yjfZ ←	hypothetical protein
RA	4,433,048	A→G	Y366H (TAT→CAT)	cpdB ←	2',3'‑cyclic‑nucleotide 2'‑phosphodiesterase
RA	4,435,684	+A	coding (400/501 nt)	ytfI →	hypothetical protein
RA	4,440,773	T→C	V272A (GTC→GCC)	ytfM →	hypothetical protein
RA	4,444,741	A→G	E1018G (GAG→GGG)	ytfN →	hypothetical protein
RA	4,448,541	+C	intergenic (+46/‑92)	ytfQ → / → ytfR	putative LACI‑type transcriptional regulator/YtfR
RA	4,448,543	+C	intergenic (+48/‑90)	ytfQ → / → ytfR	putative LACI‑type transcriptional regulator/YtfR
RA	4,449,738	+G	coding (1106/1254 nt)	ytfR →	YtfR
RA	4,456,991	A→G	intergenic (+106/‑91)	pmbA → / → b4236	PmbA/cytochrome b(562)
RA	4,459,408	T→C	Y276C (TAC→TGC)	nrdD ←	anaerobic ribonucleoside‑triphosphate reductase
RA	4,467,145	A→G	L649L (TTA→TTG)	mgtA →	Mg2+ transport ATPase, P‑type 1
RA	4,472,408	A→G	intergenic (+117/‑28)	b4251 → / → b4252	hypothetical protein/hypothetical protein
RA	4,474,826	+A	intergenic (+1/+44)	yjgL → / ← argI	hypothetical protein/ornithine carbamoyltransferase 1
MC JC	4,474,849	20 bp→30 bp	intergenic (+24/+2)	yjgL → / ← argI	hypothetical protein/ornithine carbamoyltransferase 1
RA	4,476,406	A→G	D124G (GAC→GGC)	yjgD →	hypothetical protein
RA	4,477,041	Δ1 bp	intergenic (‑151/‑269)	b4256 ← / → yjgN	hypothetical protein/hypothetical protein
RA	4,477,068	+C	intergenic (‑178/‑242)	b4256 ← / → yjgN	hypothetical protein/hypothetical protein
RA	4,477,281	Δ1 bp	intergenic (‑391/‑29)	b4256 ← / → yjgN	hypothetical protein/hypothetical protein
RA	4,477,321	Δ1 bp	coding (12/1182 nt)	yjgN →	hypothetical protein
RA	4,478,503	(A)7→6	intergenic (+12/+47)	yjgN → / ← valS	hypothetical protein/valine tRNA synthetase
RA	4,478,511	Δ1 bp	intergenic (+20/+39)	yjgN → / ← valS	hypothetical protein/valine tRNA synthetase
RA	4,478,527	Δ1 bp	intergenic (+36/+23)	yjgN → / ← valS	hypothetical protein/valine tRNA synthetase
RA	4,486,588	A→G	D348D (GAT→GAC)	yjgR ←	hypothetical protein
RA	4,502,680	C→T	A352V (GCA→GTA)	b4279 →	putative transport protein
RA	4,506,550	T→C	C9R (TGT→CGT)	b4285 →	putative transposase
RA	4,522,805	G→A	A189A (GCC→GCT)	yjhI ←	putative regulator
RA	4,527,603	A→G	L70P (CTA→CCA)	sgcC ←	putative PTS system enzyme IIC component
RA	4,531,073	T→C	M94V (ATG→GTG)	yjhQ ←	hypothetical protein
RA	4,532,411	A→G	intergenic (‑1059/‑172)	yjhQ ← / → yjhR	hypothetical protein/putative frameshift suppressor
RA	4,542,643	Δ1 bp	intergenic (+46/‑22)	b4316 → / → fimD	Pil/FimD
RA	4,544,170	T→C	I502I (ATT→ATC)	fimD →	FimD
RA	4,549,377	T→C	V58A (GTG→GCG)	uxuA →	mannonate hydrolase
RA	4,551,074	T→C	L202P (CTG→CCG)	uxuB →	D‑mannonate oxidoreductase
RA	4,555,245	T→C	Y205C (TAC→TGC)	yjiE ←	putative transcriptional regulator LYSR‑type
RA	4,556,716	C→T	G127D (GGC→GAC)	iadA ←	isoaspartyl dipeptidase
RA	4,568,665	A→G	L160P (CTC→CCC)	yjiR ←	putative regulator
RA	4,572,272	G→A	G190E (GGG→GAG)	yjiU →	hypothetical protein
RA	4,573,190	Δ1 bp	coding (1487/1542 nt)	yjiU →	hypothetical protein
RA	4,583,050	G→A	Q446* (CAA→TAA)	hsdR ←	endonuclease R
RA	4,593,254	2 bp→GC	coding (59‑60/807 nt)	yjjM ←	hypothetical protein
RA	4,593,336	+G	intergenic (‑23/‑208)	yjjM ← / → yjjN	hypothetical protein/putative oxidoreductase
RA	4,595,908	T→C	Q355R (CAG→CGG)	mdoB ←	phosphoglycerol transferase I
RA	4,600,078	C→T	W135* (TGG→TAG)	yjjP ←	putative structural protein
RA	4,601,332	A→G	Q96R (CAG→CGG)	yjjQ →	putative regulator
RA	4,603,663	(G)8→9	noncoding (72/88 nt)	leuV ←	tRNA‑Leu
RA	4,606,898	Δ1 bp	intergenic (+6/‑85)	yjjG → / → prfC	putative phosphatase/peptide chain release factor RF‑3
RA	4,608,595	2 bp→GC	intergenic (+23/‑369)	prfC → / → osmY	peptide chain release factor RF‑3/OsmY
RA	4,614,238	G→T	L133I (CTA→ATA)	yjjI ←	hypothetical protein
RA	4,614,723	C→T	intergenic (‑89/‑169)	yjjI ← / → deoC	hypothetical protein/2‑deoxyribose‑5‑phosphate aldolase
RA	4,618,604	T→C	G51G (GGT→GGC)	deoD →	purine‑nucleoside phosphorylase
RA	4,620,966	T→C	S241G (AGC→GGC)	lplA ←	lipoate‑protein ligase A
RA	4,632,259	T→C	A207A (GCA→GCG)	rob ←	right origin‑binding protein
RA	4,632,611	C→T	R90H (CGC→CAC)	rob ←	right origin‑binding protein
RA	4,634,093	T→C	V173A (GTC→GCC)	creB →	CreB
RA	4,636,923	T→C	W393R (TGG→CGG)	creD →	CreD

Unassigned missing coverage evidence
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	363557	365526	1970	169 [165]	[20] 289	lacZ	beta‑D‑galactosidase
*	*	÷	NC_000913	2518968–2519023	2519122–2519071	49–155	166 [164]	[163] 167	[valU]–[valX]	[valU],[valX]
*	*	÷	NC_000913	2727634–2728586	2728926–2728591	6–1293	172 [157]	[164] 167	[rrsG]	[rrsG]
*	*	÷	NC_000913	3421332–3421870	3422240–3421880	11–909	166 [164]	[162] 168	[rrfD]–[rrlD]	[rrfD],[rrlD]
*	*	÷	NC_000913	3943609–3943706	3943791–3943771	66–183	166 [152]	[163] 170	rrlC	23S ribosomal RNA

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	269765 =	NA (NA)	302 (1.030)	141/184	0.1	98.7%	coding (300/405 nt)	yi91a	hypothetical protein
	?	NC_000913	= 370983	4 (0.010)					coding (536/882 nt)	mhpC	2‑hydroxy‑6‑ketonona‑2,4‑dienedioic acid hydrolase
*	?	NC_000913	= 279335	NA (NA)	302 (1.030)	142/184	0.1	97.7%	coding (252/339 nt)	b4505	hypothetical protein
	?	NC_000913	370982 =	7 (0.020)					coding (535/882 nt)	mhpC	2‑hydroxy‑6‑ketonona‑2,4‑dienedioic acid hydrolase
*	?	NC_000913	365527 =	20 (0.070)	252 (0.880)	124/178	0.4	68.0%	coding (3/3075 nt)	lacZ	beta‑D‑galactosidase
	?	NC_000913	4589230 =	218 (0.770)					coding (4/1656 nt)	tsr	methyl‑accepting chemotaxis protein I
*	?	NC_000913	1207013 =	101 (0.340)	149 (0.610)	93/152	1.4	61.3%	coding (290/630 nt)	ycfK	hypothetical protein
	?	NC_000913	1208842 =	105 (0.430)					coding (40/540 nt)	b1157	putative tail fiber protein
*	?	NC_000913	= 1207028	101 (0.340)	146 (0.600)	86/152	2.1	60.8%	coding (305/630 nt)	ycfK	hypothetical protein
	?	NC_000913	= 1208825	105 (0.430)					coding (57/540 nt)	b1157	putative tail fiber protein
*	?	NC_000913	3192559 =	280 (0.950)	207 (0.890) +ATGTGTTAATGAAACCTTC	83/146	2.0	48.9%	intergenic (+18/+402)	b3051/b3052	putative membrane protein/putative kinase
	?	NC_000913	= 3192916	266 (0.900)					intergenic (+375/+45)	b3051/b3052	putative membrane protein/putative kinase
*	?	NC_000913	3349258 =	19 (0.060)	340 (1.150)	142/184	0.1	94.7%	coding (1403/2331 nt)	arcB	aerobic respiration sensor‑response protein
	?	NC_000913	= 3349263	NA (NA)					coding (1398/2331 nt)	arcB	aerobic respiration sensor‑response protein
*	?	NC_000913	= 3967641	265 (0.960)	224 (0.790) +GGG	98/166	1.7	45.1%	coding (999/1050 nt)	wzzE	putative transport protein
	?	NC_000913	3967642 =	279 (0.950)					coding (1000/1050 nt)	wzzE	putative transport protein
*	?	NC_000913	3980290 =	320 (1.090)	191 (0.690)	94/174	2.7	43.4%	noncoding (72/87 nt)	leuT	tRNA‑Leu
	?	NC_000913	4603661 =	195 (0.700)					noncoding (74/88 nt)	leuV	tRNA‑Leu