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	10,620	A→T	5.1%	intergenic (‑126/+23)	satP ← / ← yaaW	succinate‑acetate transporter/UPF0174 family protein
RA	60,259	T→G	5.6%	S30R (AGC→CGC)	rluA ←	dual specificity 23S rRNA pseudouridine(746), tRNA pseudouridine(32) synthase, SAM‑dependent
RA	103,614	A→T	5.2%	K154* (AAG→TAG)	ftsQ →	divisome assembly protein, membrane anchored protein involved in growth of wall at septum
RA	114,507	A→T	5.6%	intergenic (+20/+15)	guaC → / ← hofC	GMP reductase/assembly protein in type IV pilin biogenesis, transmembrane protein
RA	114,510	A→T	5.3%	intergenic (+23/+12)	guaC → / ← hofC	GMP reductase/assembly protein in type IV pilin biogenesis, transmembrane protein
RA	114,511	A→C	5.8%	intergenic (+24/+11)	guaC → / ← hofC	GMP reductase/assembly protein in type IV pilin biogenesis, transmembrane protein
RA	124,856	G→T	5.2%	A614S (GCG→TCG)	aceE →	pyruvate dehydrogenase, decarboxylase component E1, thiamine triphosphate‑binding
RA	124,859	G→C	5.6%	A615P (GCT→CCT) ‡	aceE →	pyruvate dehydrogenase, decarboxylase component E1, thiamine triphosphate‑binding
RA	124,861	T→A	5.8%	A615A (GCT→GCA) ‡	aceE →	pyruvate dehydrogenase, decarboxylase component E1, thiamine triphosphate‑binding
RA	124,863	G→C	5.6%	G616A (GGC→GCC)	aceE →	pyruvate dehydrogenase, decarboxylase component E1, thiamine triphosphate‑binding
RA	124,866	A→C	5.4%	D617A (GAC→GCC)	aceE →	pyruvate dehydrogenase, decarboxylase component E1, thiamine triphosphate‑binding
RA	125,817	A→G	5.9%	K41K (AAA→AAG)	aceF →	pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2
RA	126,093	T→C	6.6%	A133A (GCT→GCC)	aceF →	pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2
RA	136,532	G→C	5.4%	intergenic (‑68/+38)	speE ← / ← yacC	spermidine synthase (putrescine aminopropyltransferase)/PulS_OutS family protein
RA	136,535	G→C	5.4%	intergenic (‑71/+35)	speE ← / ← yacC	spermidine synthase (putrescine aminopropyltransferase)/PulS_OutS family protein
RA	136,537	A→G	5.4%	intergenic (‑73/+33)	speE ← / ← yacC	spermidine synthase (putrescine aminopropyltransferase)/PulS_OutS family protein
RA	165,038	T→G	5.7%	P103P (CCT→CCG)	mrcB →	fused glycosyl transferase and transpeptidase
RA	165,039	G→C	5.8%	A104P (GCG→CCG) ‡	mrcB →	fused glycosyl transferase and transpeptidase
RA	165,040	C→A	6.0%	A104E (GCG→GAG) ‡	mrcB →	fused glycosyl transferase and transpeptidase
RA	209,171	A→G	5.4%	N184S (AAC→AGC) ‡	accA →	acetyl‑CoA carboxylase, carboxytransferase, alpha subunit
RA	209,172	C→G	5.8%	N184K (AAC→AAG) ‡	accA →	acetyl‑CoA carboxylase, carboxytransferase, alpha subunit
RA	209,173	C→T	5.3%	L185L (CTG→TTG)	accA →	acetyl‑CoA carboxylase, carboxytransferase, alpha subunit
RA	231,007	C→A	7.4%	intergenic (‑126/‑115)	yafC ← / → yafD	LysR family putative transcriptional regulator/endo/exonuclease/phosphatase family protein
RA	231,008	T→G	6.3%	intergenic (‑127/‑114)	yafC ← / → yafD	LysR family putative transcriptional regulator/endo/exonuclease/phosphatase family protein
RA	252,589	G→C	6.1%	A97P (GCA→CCA)	yafO →	mRNA interferase toxin of the YafO‑YafN toxin‑antitoxin system
RA	252,594	G→C	5.2%	W98C (TGG→TGC)	yafO →	mRNA interferase toxin of the YafO‑YafN toxin‑antitoxin system
RA	254,223	A→T	5.6%	intergenic (+21/+36)	prfH → / ← pepD	pseudogene, RF‑1 domain family; probable peptide chain release factor/aminoacyl‑histidine dipeptidase (peptidase D)
RA	254,228	A→T	5.2%	intergenic (+26/+31)	prfH → / ← pepD	pseudogene, RF‑1 domain family; probable peptide chain release factor/aminoacyl‑histidine dipeptidase (peptidase D)
RA	254,233	A→T	5.7%	intergenic (+31/+26)	prfH → / ← pepD	pseudogene, RF‑1 domain family; probable peptide chain release factor/aminoacyl‑histidine dipeptidase (peptidase D)
RA	254,238	A→T	6.4%	intergenic (+36/+21)	prfH → / ← pepD	pseudogene, RF‑1 domain family; probable peptide chain release factor/aminoacyl‑histidine dipeptidase (peptidase D)
RA	256,449	T→C	7.9%	intergenic (+14/‑78)	gpt → / → frsA	xanthine phosphoribosyltransferase; xanthine‑guanine phosphoribosyltransferase/fermentation‑respiration switch protein; PTS Enzyme IIA(Glc)‑binding protein; pNP‑butyrate esterase activity
RA	256,454	C→G	7.7%	intergenic (+19/‑73)	gpt → / → frsA	xanthine phosphoribosyltransferase; xanthine‑guanine phosphoribosyltransferase/fermentation‑respiration switch protein; PTS Enzyme IIA(Glc)‑binding protein; pNP‑butyrate esterase activity
RA	256,459	G→A	8.5%	intergenic (+24/‑68)	gpt → / → frsA	xanthine phosphoribosyltransferase; xanthine‑guanine phosphoribosyltransferase/fermentation‑respiration switch protein; PTS Enzyme IIA(Glc)‑binding protein; pNP‑butyrate esterase activity
MC JC	257,908	Δ776 bp	100%		[crl]	[crl]
RA	263,351	T→A	5.8%	S107C (AGC→TGC)	ykfI ←	CP4‑6 prophage; toxin of the YkfI‑YafW toxin‑antitoxin system
RA	263,353	T→A	5.8%	Q106L (CAA→CTA)	ykfI ←	CP4‑6 prophage; toxin of the YkfI‑YafW toxin‑antitoxin system
RA	285,202	T→A	5.1%	intergenic (+34/‑193)	yagF → / → yagG	CP4‑6 prophage; dehydratase family protein/CP4‑6 prophage; putative sugar transporter
RA	304,790	T→G	6.2%	E139A (GAG→GCG)	ecpE ←	ECP production pilus chaperone
RA	304,800	C→G	5.2%	V136L (GTC→CTC)	ecpE ←	ECP production pilus chaperone
RA	304,806	C→A	6.1%	G134C (GGC→TGC)	ecpE ←	ECP production pilus chaperone
RA	314,258	G→A	5.1%	intergenic (‑453/‑99)	ykgP ← / → eaeH	pseudogene, oxidoreductase family/pseudogene, attaching and effacing protein homology;factor; Not classified
RA	318,649	T→C	6.3%	intergenic (‑82/+27)	rclB ← / ← rclA	reactive chlorine species (RCS) stress resistance periplasmic protein/reactive chlorine stress species (RCS) resistance protein; pyridine nucleotide‑dependent disulfide oxidoreductase family
RA	318,651	T→A	6.5%	intergenic (‑84/+25)	rclB ← / ← rclA	reactive chlorine species (RCS) stress resistance periplasmic protein/reactive chlorine stress species (RCS) resistance protein; pyridine nucleotide‑dependent disulfide oxidoreductase family
RA	318,652	T→A	6.5%	intergenic (‑85/+24)	rclB ← / ← rclA	reactive chlorine species (RCS) stress resistance periplasmic protein/reactive chlorine stress species (RCS) resistance protein; pyridine nucleotide‑dependent disulfide oxidoreductase family
RA	318,654	G→A	6.5%	intergenic (‑87/+22)	rclB ← / ← rclA	reactive chlorine species (RCS) stress resistance periplasmic protein/reactive chlorine stress species (RCS) resistance protein; pyridine nucleotide‑dependent disulfide oxidoreductase family
RA	324,585	G→A	5.1%	intergenic (+132/+111)	ykgG → / ← ykgH	LutC family protein; putative electron transport chain YkgEFG component/putative inner membrane protein
RA	324,874	T→G	5.4%	N164T (AAC→ACC) ‡	ykgH ←	putative inner membrane protein
RA	324,875	T→A	5.0%	N164Y (AAC→TAC) ‡	ykgH ←	putative inner membrane protein
RA	324,876	C→A	5.2%	R163S (AGG→AGT)	ykgH ←	putative inner membrane protein
RA	328,375	A→C	5.2%	I120S (ATC→AGC)	betB ←	betaine aldehyde dehydrogenase, NAD‑dependent
RA	329,503	A→G	7.5%	N14S (AAT→AGT)	betT →	choline transporter of high affinity
RA	329,509	T→C	8.0%	V16A (GTG→GCG)	betT →	choline transporter of high affinity
RA	329,512	T→A	6.9%	V17E (GTG→GAG)	betT →	choline transporter of high affinity
RA	329,514	T→G	6.8%	F18V (TTT→GTT) ‡	betT →	choline transporter of high affinity
RA	329,516	T→G	6.8%	F18L (TTT→TTG) ‡	betT →	choline transporter of high affinity
RA	329,519	C→A	6.8%	Y19* (TAC→TAA)	betT →	choline transporter of high affinity
RA	329,521	C→A	6.6%	T20N (ACC→AAC)	betT →	choline transporter of high affinity
RA	329,523	T→A	6.4%	S21T (TCC→ACC)	betT →	choline transporter of high affinity
RA	329,526	G→A	6.8%	A22T (GCC→ACC)	betT →	choline transporter of high affinity
RA	329,532	C→T	7.2%	L24L (CTG→TTG)	betT →	choline transporter of high affinity
RA	357,778	C→T	6.6%	intergenic (+324/+13)	codA → / ← cynR	cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor
RA	361,901	T→G	5.6%	intergenic (‑41/+25)	lacA ← / ← lacY	thiogalactoside acetyltransferase/lactose permease
RA	399,810	A→C	5.3%	intergenic (+5/+19)	yaiZ → / ← ddlA	DUF2754 family putative inner membrane protein/D‑alanine‑D‑alanine ligase A
RA	399,815	C→T	5.2%	intergenic (+10/+14)	yaiZ → / ← ddlA	DUF2754 family putative inner membrane protein/D‑alanine‑D‑alanine ligase A
RA	403,178	T→C	9.6%	intergenic (+16/‑103)	phoA → / → psiF	bacterial alkaline phosphatase/PsiF family protein
RA	403,182	T→A	9.6%	intergenic (+20/‑99)	phoA → / → psiF	bacterial alkaline phosphatase/PsiF family protein
RA	403,183	T→A	9.4%	intergenic (+21/‑98)	phoA → / → psiF	bacterial alkaline phosphatase/PsiF family protein
RA	403,187	G→A	9.3%	intergenic (+25/‑94)	phoA → / → psiF	bacterial alkaline phosphatase/PsiF family protein
RA	431,107	A→T	5.7%	intergenic (+155/+22)	yajD → / ← tsx	HNH nuclease family protein/nucleoside channel, receptor of phage T6 and colicin K
RA	431,109	A→T	6.1%	intergenic (+157/+20)	yajD → / ← tsx	HNH nuclease family protein/nucleoside channel, receptor of phage T6 and colicin K
RA	431,111	A→T	5.8%	intergenic (+159/+18)	yajD → / ← tsx	HNH nuclease family protein/nucleoside channel, receptor of phage T6 and colicin K
RA	441,069	A→T	5.7%	V11V (GTT→GTA) ‡	ispA ←	geranyltranstransferase
RA	441,071	C→A	5.0%	V11F (GTT→TTT) ‡	ispA ←	geranyltranstransferase
RA	443,022	G→A	5.4%	intergenic (+25/+29)	thiI → / ← yajL	tRNA s(4)U8 sulfurtransferase/oxidative‑stress‑resistance chaperone
RA	443,023	T→C	5.5%	intergenic (+26/+28)	thiI → / ← yajL	tRNA s(4)U8 sulfurtransferase/oxidative‑stress‑resistance chaperone
RA	454,853	T→C	7.4%	intergenic (+64/‑280)	bolA → / → tig	stationary‑phase morphogene, transcriptional repressor for mreB; also regulator for dacA, dacC, and ampC/peptidyl‑prolyl cis/trans isomerase (trigger factor)
RA	454,856	G→A	5.8%	intergenic (+67/‑277)	bolA → / → tig	stationary‑phase morphogene, transcriptional repressor for mreB; also regulator for dacA, dacC, and ampC/peptidyl‑prolyl cis/trans isomerase (trigger factor)
RA	475,971	C→G	6.0%	intergenic (+20/+11)	ybaY → / ← ybaZ	outer membrane lipoprotein/excision repair protein, alkyltransferase‑like protein ATL
RA	475,972	C→G	6.1%	intergenic (+21/+10)	ybaY → / ← ybaZ	outer membrane lipoprotein/excision repair protein, alkyltransferase‑like protein ATL
RA	492,230	C→A	5.5%	R47S (CGT→AGT)	dnaX →	DNA polymerase III/DNA elongation factor III, tau and gamma subunits
RA	518,860	A→G	5.0%	F97S (TTC→TCC)	ybbO ←	putative oxidoreductase
RA	525,739	G→C	5.9%	E827Q (GAG→CAG) ‡	rhsD →	Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
RA	525,740	A→T	5.9%	E827V (GAG→GTG) ‡	rhsD →	Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
RA	525,741	G→C	5.9%	E827D (GAG→GAC) ‡	rhsD →	Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
RA	543,091	G→C	6.1%	intergenic (+58/+170)	glxK → / ← allE	glycerate kinase II/S‑ureidoglycine aminohydrolase
RA	556,018	G→A	6.0%	intergenic (+22/+14)	cysS → / ← ybcI	cysteinyl‑tRNA synthetase/DUF457 family inner membrane protein
RA	556,019	T→A	6.0%	intergenic (+23/+13)	cysS → / ← ybcI	cysteinyl‑tRNA synthetase/DUF457 family inner membrane protein
RA	556,020	T→A	6.0%	intergenic (+24/+12)	cysS → / ← ybcI	cysteinyl‑tRNA synthetase/DUF457 family inner membrane protein
RA	556,021	T→C	6.1%	intergenic (+25/+11)	cysS → / ← ybcI	cysteinyl‑tRNA synthetase/DUF457 family inner membrane protein
RA	556,641	G→T	6.2%	intergenic (‑88/+20)	ybcI ← / ← ybcJ	DUF457 family inner membrane protein/ribosome‑associated protein; putative RNA‑binding protein
RA	556,642	A→C	6.0%	intergenic (‑89/+19)	ybcI ← / ← ybcJ	DUF457 family inner membrane protein/ribosome‑associated protein; putative RNA‑binding protein
RA	568,280	C→G	6.0%	intergenic (+33/‑35)	renD → / → emrE	pseudogene, DLP12 prophage;Phage or Prophage Related/DLP12 prophage; multidrug resistance protein
RA	568,285	C→G	6.2%	intergenic (+38/‑30)	renD → / → emrE	pseudogene, DLP12 prophage;Phage or Prophage Related/DLP12 prophage; multidrug resistance protein
RA	603,391	C→G	5.7%	intergenic (+56/+25)	pheP → / ← ybdG	phenylalanine transporter/mechanosensitive channel protein, miniconductance
RA	603,393	T→A	7.7%	intergenic (+58/+23)	pheP → / ← ybdG	phenylalanine transporter/mechanosensitive channel protein, miniconductance
RA	603,395	C→G	5.7%	intergenic (+60/+21)	pheP → / ← ybdG	phenylalanine transporter/mechanosensitive channel protein, miniconductance
RA	613,550	G→C	6.1%	A272P (GCC→CCC) ‡	fes →	enterobactin/ferrienterobactin esterase
RA	613,551	C→A	6.3%	A272D (GCC→GAC) ‡	fes →	enterobactin/ferrienterobactin esterase
RA	622,455	G→C	5.9%	W52C (TGG→TGC)	entS →	enterobactin exporter, iron‑regulated
RA	645,069	G→A	6.2%	intergenic (‑66/+48)	rna ← / ← citT	ribonuclease I/citrate/succinate antiporter; citrate carrier
RA	645,070	G→A	6.2%	intergenic (‑67/+47)	rna ← / ← citT	ribonuclease I/citrate/succinate antiporter; citrate carrier
RA	645,073	T→C	6.3%	intergenic (‑70/+44)	rna ← / ← citT	ribonuclease I/citrate/succinate antiporter; citrate carrier
RA	645,074	T→C	6.3%	intergenic (‑71/+43)	rna ← / ← citT	ribonuclease I/citrate/succinate antiporter; citrate carrier
RA	654,560	A→C	7.6%	intergenic (+18/+23)	citB → / ← dcuC	response regulator in two‑component regulatory system with CitA/anaerobic C4‑dicarboxylate transport
RA	654,563	C→G	7.5%	intergenic (+21/+20)	citB → / ← dcuC	response regulator in two‑component regulatory system with CitA/anaerobic C4‑dicarboxylate transport
RA	654,566	G→T	7.4%	intergenic (+24/+17)	citB → / ← dcuC	response regulator in two‑component regulatory system with CitA/anaerobic C4‑dicarboxylate transport
RA	659,205	A→T	5.0%	intergenic (+55/+46)	tatE → / ← lipA	TatABCE protein translocation system subunit/lipoate synthase
RA	662,683	A→T	5.1%	intergenic (‑41/+69)	ybeD ← / ← dacA	UPF0250 family protein/D‑alanyl‑D‑alanine carboxypeptidase (penicillin‑binding protein 5)
RA	662,684	G→T	5.3%	intergenic (‑42/+68)	ybeD ← / ← dacA	UPF0250 family protein/D‑alanyl‑D‑alanine carboxypeptidase (penicillin‑binding protein 5)
RA	662,685	A→C	5.8%	intergenic (‑43/+67)	ybeD ← / ← dacA	UPF0250 family protein/D‑alanyl‑D‑alanine carboxypeptidase (penicillin‑binding protein 5)
RA	662,686	A→T	5.1%	intergenic (‑44/+66)	ybeD ← / ← dacA	UPF0250 family protein/D‑alanyl‑D‑alanine carboxypeptidase (penicillin‑binding protein 5)
RA	691,858	T→G	6.2%	intergenic (‑74/+16)	ybeX ← / ← ybeY	putative ion transport/ssRNA‑specific endoribonuclease; 16S rRNA 3' end maturation and quality control co‑endoribonuclease working with RNase R; rRNA transcription antitermination factor
RA	691,861	A→T	6.1%	intergenic (‑77/+13)	ybeX ← / ← ybeY	putative ion transport/ssRNA‑specific endoribonuclease; 16S rRNA 3' end maturation and quality control co‑endoribonuclease working with RNase R; rRNA transcription antitermination factor
RA	691,862	A→T	6.2%	intergenic (‑78/+12)	ybeX ← / ← ybeY	putative ion transport/ssRNA‑specific endoribonuclease; 16S rRNA 3' end maturation and quality control co‑endoribonuclease working with RNase R; rRNA transcription antitermination factor
RA	691,865	C→A	5.8%	intergenic (‑81/+9)	ybeX ← / ← ybeY	putative ion transport/ssRNA‑specific endoribonuclease; 16S rRNA 3' end maturation and quality control co‑endoribonuclease working with RNase R; rRNA transcription antitermination factor
RA	696,793	T→A	37.5%	noncoding (38/75 nt)	glnW ←	tRNA‑Gln
RA	696,798	A→G	32.2%	noncoding (33/75 nt)	glnW ←	tRNA‑Gln
RA	696,801	A→T	29.6%	noncoding (30/75 nt)	glnW ←	tRNA‑Gln
RA	715,339	A→G	5.8%	intergenic (+141/‑73)	pgm → / → ybfP	phosphoglucomutase/lipoprotein
RA	715,340	A→C	6.5%	intergenic (+142/‑72)	pgm → / → ybfP	phosphoglucomutase/lipoprotein
RA	715,346	T→G	5.7%	intergenic (+148/‑66)	pgm → / → ybfP	phosphoglucomutase/lipoprotein
RA	715,347	C→A	6.0%	intergenic (+149/‑65)	pgm → / → ybfP	phosphoglucomutase/lipoprotein
RA	715,353	G→T	6.2%	intergenic (+155/‑59)	pgm → / → ybfP	phosphoglucomutase/lipoprotein
RA	715,354	C→T	6.2%	intergenic (+156/‑58)	pgm → / → ybfP	phosphoglucomutase/lipoprotein
RA	723,608	T→G	5.8%	A269A (GCA→GCC)	kdpD ←	fused sensory histidine kinase in two‑component regulatory system with KdpE: signal sensing protein
RA	751,122	G→C	5.7%	Q350E (CAG→GAG)	ybgQ ←	putative outer membrane protein
RA	752,066	T→G	5.2%	D35A (GAC→GCC)	ybgQ ←	putative outer membrane protein
RA	756,643	T→A	5.6%	I246N (ATT→AAT)	sdhA →	succinate dehydrogenase, flavoprotein subunit
RA	774,356	C→G	5.5%	P16P (CCC→CCG)	ybgE →	putative inner membrane protein in cydABX‑ybgE operon
RA	774,358	T→A	5.4%	L17Q (CTG→CAG)	ybgE →	putative inner membrane protein in cydABX‑ybgE operon
RA	803,952	C→T	6.3%	S150S (AGC→AGT)	ybhJ →	aconitase family protein
RA	824,949	T→C	5.6%	L107P (CTG→CCG)	ybhQ →	inner membrane protein
RA	824,957	C→A	5.2%	L110I (CTT→ATT)	ybhQ →	inner membrane protein
RA	848,356	T→A	7.2%	intergenic (‑352/+52)	glnH ← / ← dps	glutamine transporter subunit/Fe‑binding and storage protein; stress‑inducible DNA‑binding protein
RA	848,362	A→G	6.8%	intergenic (‑358/+46)	glnH ← / ← dps	glutamine transporter subunit/Fe‑binding and storage protein; stress‑inducible DNA‑binding protein
RA	850,993	T→C	6.3%	intergenic (+28/+21)	ompX → / ← opgE	outer membrane protein X/OPG biosynthetic transmembrane phosphoethanolamine transferase
RA	850,995	T→G	6.4%	intergenic (+30/+19)	ompX → / ← opgE	outer membrane protein X/OPG biosynthetic transmembrane phosphoethanolamine transferase
RA	850,996	C→A	6.0%	intergenic (+31/+18)	ompX → / ← opgE	outer membrane protein X/OPG biosynthetic transmembrane phosphoethanolamine transferase
RA	850,998	G→A	6.4%	intergenic (+33/+16)	ompX → / ← opgE	outer membrane protein X/OPG biosynthetic transmembrane phosphoethanolamine transferase
RA	858,420	A→C	5.4%	L214L (CTT→CTG) ‡	ybiU ←	DUF1479 family protein
RA	858,421	A→T	6.5%	L214H (CTT→CAT) ‡	ybiU ←	DUF1479 family protein
RA	858,424	A→T	5.3%	L213Q (CTG→CAG) ‡	ybiU ←	DUF1479 family protein
RA	858,425	G→T	5.2%	L213M (CTG→ATG) ‡	ybiU ←	DUF1479 family protein
RA	876,560	C→G	5.5%	A409G (GCA→GGA)	yliF →	putative membrane‑anchored diguanylate cyclase
RA	876,568	A→T	6.4%	N412Y (AAT→TAT) ‡	yliF →	putative membrane‑anchored diguanylate cyclase
RA	876,569	A→T	6.7%	N412I (AAT→ATT) ‡	yliF →	putative membrane‑anchored diguanylate cyclase
RA	876,577	C→G	6.3%	P415A (CCT→GCT)	yliF →	putative membrane‑anchored diguanylate cyclase
RA	892,455	G→C	5.6%	V163V (GTG→GTC)	rimK →	ribosomal protein S6 modification protein
RA	892,457	T→A	5.6%	I164N (ATT→AAT)	rimK →	ribosomal protein S6 modification protein
RA	892,459	G→C	7.3%	D165H (GAC→CAC)	rimK →	ribosomal protein S6 modification protein
RA	894,952	T→A	7.1%	intergenic (+56/‑39)	potF → / → potG	putrescine ABC transporter periplasmic binding protein/putrescine ABC transporter ATPase
RA	900,205	A→T	5.3%	L124Q (CTG→CAG)	artJ ←	arginine ABC transporter periplasmic binding protein
RA	940,751	T→C	5.1%	intergenic (+31/‑208)	serS → / → dmsA	seryl‑tRNA synthetase/dimethyl sulfoxide reductase, anaerobic, subunit A
RA	940,754	G→A	5.2%	intergenic (+34/‑205)	serS → / → dmsA	seryl‑tRNA synthetase/dimethyl sulfoxide reductase, anaerobic, subunit A
RA	958,769	C→G	5.7%	intergenic (+28/‑43)	serC → / → aroA	3‑phosphoserine/phosphohydroxythreonine aminotransferase/5‑enolpyruvylshikimate‑3‑phosphate synthetase
RA	958,771	A→T	6.1%	intergenic (+30/‑41)	serC → / → aroA	3‑phosphoserine/phosphohydroxythreonine aminotransferase/5‑enolpyruvylshikimate‑3‑phosphate synthetase
RA	958,773	C→G	7.6%	intergenic (+32/‑39)	serC → / → aroA	3‑phosphoserine/phosphohydroxythreonine aminotransferase/5‑enolpyruvylshikimate‑3‑phosphate synthetase
RA	959,667	A→C	5.3%	T286P (ACC→CCC)	aroA →	5‑enolpyruvylshikimate‑3‑phosphate synthetase
RA	964,148	T→C	6.0%	intergenic (+36/‑172)	ihfB → / → ycaI	integration host factor (IHF), DNA‑binding protein, beta subunit/ComEC family inner membrane protein
RA	964,150	T→A	5.6%	intergenic (+38/‑170)	ihfB → / → ycaI	integration host factor (IHF), DNA‑binding protein, beta subunit/ComEC family inner membrane protein
RA	964,152	G→A	6.1%	intergenic (+40/‑168)	ihfB → / → ycaI	integration host factor (IHF), DNA‑binding protein, beta subunit/ComEC family inner membrane protein
RA	993,254	A→G	5.3%	intergenic (+20/+23)	pepN → / ← ssuB	aminopeptidase N/aliphatic sulfonate ABC transporter ATPase
RA	993,258	G→T	5.7%	intergenic (+24/+19)	pepN → / ← ssuB	aminopeptidase N/aliphatic sulfonate ABC transporter ATPase
RA	993,259	C→T	5.4%	intergenic (+25/+18)	pepN → / ← ssuB	aminopeptidase N/aliphatic sulfonate ABC transporter ATPase
RA	1,015,912	T→A	6.3%	intergenic (+30/+40)	rmf → / ← fabA	ribosome modulation factor/beta‑hydroxydecanoyl thioester dehydrase
RA	1,086,024	C→A	5.2%	L345I (CTT→ATT)	phoH →	ATP‑binding protein; putative PhoH family P‑loop ATPase
RA	1,101,556	T→G	6.2%	P43P (CCA→CCC) ‡	csgG ←	curli production assembly/transport outer membrane lipoprotein
RA	1,101,557	G→C	5.9%	P43R (CCA→CGA) ‡	csgG ←	curli production assembly/transport outer membrane lipoprotein
RA	1,101,568	C→A	5.6%	L39F (TTG→TTT)	csgG ←	curli production assembly/transport outer membrane lipoprotein
RA	1,104,931	G→T	5.7%	intergenic (+29/‑30)	csgA → / → csgC	curlin subunit, amyloid curli fibers, cryptic/curli assembly protein
RA	1,104,932	C→T	5.9%	intergenic (+30/‑29)	csgA → / → csgC	curlin subunit, amyloid curli fibers, cryptic/curli assembly protein
RA	1,104,933	A→G	5.8%	intergenic (+31/‑28)	csgA → / → csgC	curlin subunit, amyloid curli fibers, cryptic/curli assembly protein
RA	1,104,934	A→C	5.2%	intergenic (+32/‑27)	csgA → / → csgC	curlin subunit, amyloid curli fibers, cryptic/curli assembly protein
RA	1,118,623	C→A	6.0%	G142C (GGT→TGT)	yceJ ←	putative cytochrome b561
RA	1,118,628	A→G	5.6%	F140S (TTT→TCT)	yceJ ←	putative cytochrome b561
RA	1,118,630	G→C	5.6%	D139E (GAC→GAG) ‡	yceJ ←	putative cytochrome b561
RA	1,118,632	C→T	5.5%	D139N (GAC→AAC) ‡	yceJ ←	putative cytochrome b561
RA	1,118,637	T→G	6.9%	Q137P (CAG→CCG)	yceJ ←	putative cytochrome b561
RA	1,131,199	G→C	6.4%	S61T (AGT→ACT) ‡	flgB →	flagellar component of cell‑proximal portion of basal‑body rod
RA	1,131,200	T→A	7.6%	S61R (AGT→AGA) ‡	flgB →	flagellar component of cell‑proximal portion of basal‑body rod
RA	1,131,201	G→C	6.5%	V62L (GTG→CTG)	flgB →	flagellar component of cell‑proximal portion of basal‑body rod
RA	1,134,661	A→G	6.5%	intergenic (+104/‑68)	flgF → / → flgG	flagellar component of cell‑proximal portion of basal‑body rod/flagellar component of cell‑distal portion of basal‑body rod
RA	1,134,662	A→C	6.6%	intergenic (+105/‑67)	flgF → / → flgG	flagellar component of cell‑proximal portion of basal‑body rod/flagellar component of cell‑distal portion of basal‑body rod
RA	1,134,668	T→A	6.7%	intergenic (+111/‑61)	flgF → / → flgG	flagellar component of cell‑proximal portion of basal‑body rod/flagellar component of cell‑distal portion of basal‑body rod
RA	1,134,669	T→A	6.6%	intergenic (+112/‑60)	flgF → / → flgG	flagellar component of cell‑proximal portion of basal‑body rod/flagellar component of cell‑distal portion of basal‑body rod
RA	1,134,675	G→T	5.8%	intergenic (+118/‑54)	flgF → / → flgG	flagellar component of cell‑proximal portion of basal‑body rod/flagellar component of cell‑distal portion of basal‑body rod
RA	1,134,676	C→T	6.1%	intergenic (+119/‑53)	flgF → / → flgG	flagellar component of cell‑proximal portion of basal‑body rod/flagellar component of cell‑distal portion of basal‑body rod
RA	1,141,148	C→T	5.8%	intergenic (+162/+34)	flgL → / ← rne	flagellar hook‑filament junction protein/endoribonuclease; RNA‑binding protein;RNA degradosome binding protein
RA	1,141,150	G→A	5.7%	intergenic (+164/+32)	flgL → / ← rne	flagellar hook‑filament junction protein/endoribonuclease; RNA‑binding protein;RNA degradosome binding protein
RA	1,141,151	T→C	5.8%	intergenic (+165/+31)	flgL → / ← rne	flagellar hook‑filament junction protein/endoribonuclease; RNA‑binding protein;RNA degradosome binding protein
RA	1,141,153	A→G	5.8%	intergenic (+167/+29)	flgL → / ← rne	flagellar hook‑filament junction protein/endoribonuclease; RNA‑binding protein;RNA degradosome binding protein
RA	1,147,690	G→A	5.6%	A24T (GCA→ACA) ‡	plsX →	putative phosphate acyltransferase
RA	1,147,691	C→T	5.6%	A24V (GCA→GTA) ‡	plsX →	putative phosphate acyltransferase
RA	1,147,692	A→G	5.6%	A24A (GCA→GCG) ‡	plsX →	putative phosphate acyltransferase
RA	1,147,693	T→C	5.3%	L25L (TTG→CTG)	plsX →	putative phosphate acyltransferase
RA	1,159,335	G→T	5.4%	intergenic (+33/+27)	ptsG → / ← fhuE	fused glucose‑specific PTS enzymes: IIB component/IIC component/ferric‑rhodotorulic acid outer membrane transporter
RA	1,159,336	A→C	7.4%	intergenic (+34/+26)	ptsG → / ← fhuE	fused glucose‑specific PTS enzymes: IIB component/IIC component/ferric‑rhodotorulic acid outer membrane transporter
RA	1,181,760	A→G	6.0%	intergenic (‑35/+23)	ymfA ← / ← potD	DUF3592 family inner membrane protein/spermidine/putrescine ABC transporter periplasmic binding protein
RA	1,181,761	A→G	6.0%	intergenic (‑36/+22)	ymfA ← / ← potD	DUF3592 family inner membrane protein/spermidine/putrescine ABC transporter periplasmic binding protein
RA	1,181,764	C→T	5.9%	intergenic (‑39/+19)	ymfA ← / ← potD	DUF3592 family inner membrane protein/spermidine/putrescine ABC transporter periplasmic binding protein
RA	1,181,765	C→T	5.9%	intergenic (‑40/+18)	ymfA ← / ← potD	DUF3592 family inner membrane protein/spermidine/putrescine ABC transporter periplasmic binding protein
RA	1,182,771	G→C	5.2%	A20G (GCC→GGC)	potD ←	spermidine/putrescine ABC transporter periplasmic binding protein
RA	1,194,645:1	+A	6.6%	coding (307/654 nt)	rluE ←	23S rRNA pseudouridine(2457) synthase
RA	1,194,650	G→A	6.5%	P101L (CCG→CTG)	rluE ←	23S rRNA pseudouridine(2457) synthase
RA	1,194,653	T→C	6.5%	Q100R (CAG→CGG)	rluE ←	23S rRNA pseudouridine(2457) synthase
RA	1,194,657	Δ1 bp	6.6%	coding (295/654 nt)	rluE ←	23S rRNA pseudouridine(2457) synthase
RA	1,196,803	A→C	7.5%	intergenic (+430/+64)	icd → / ← ymfD	isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase/e14 prophage; putative SAM‑dependent methyltransferase
RA	1,200,910	T→A	6.4%	Q41H (CAA→CAT)	xisE ←	e14 prophage; putative excisionase
RA	1,200,913	T→A	6.0%	K40N (AAA→AAT) ‡	xisE ←	e14 prophage; putative excisionase
RA	1,200,914	T→A	6.5%	K40I (AAA→ATA) ‡	xisE ←	e14 prophage; putative excisionase
RA	1,200,915	T→A	5.9%	K40* (AAA→TAA) ‡	xisE ←	e14 prophage; putative excisionase
RA	1,200,918	T→A	5.7%	M39L (ATG→TTG)	xisE ←	e14 prophage; putative excisionase
RA	1,204,409	T→A	7.6%	pseudogene (6/1134 nt)	aaaE →	pseudogene, phage terminase protein A family, e14 prophage;Phage or Prophage Related
RA	1,217,117	C→A	5.2%	intergenic (+121/‑211)	ymgC → / → ycgG	Blue light, low temperature and stress induced protein/putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	1,217,119	C→A	5.6%	intergenic (+123/‑209)	ymgC → / → ycgG	Blue light, low temperature and stress induced protein/putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	1,224,239	A→T	7.0%	intergenic (+332/+40)	ycgI → / ← minE	pseudogene/cell division topological specificity factor
RA	1,224,242	A→T	7.7%	intergenic (+335/+37)	ycgI → / ← minE	pseudogene/cell division topological specificity factor
RA	1,231,956:1	+G	5.2%	coding (771/1269 nt)	umuC →	translesion error‑prone DNA polymerase V subunit; DNA polymerase activity
RA	1,232,481	C→T	5.9%	intergenic (+27/+19)	umuC → / ← dsbB	translesion error‑prone DNA polymerase V subunit; DNA polymerase activity/oxidoreductase that catalyzes reoxidation of DsbA protein disulfide isomerase I
RA	1,232,484	A→G	5.9%	intergenic (+30/+16)	umuC → / ← dsbB	translesion error‑prone DNA polymerase V subunit; DNA polymerase activity/oxidoreductase that catalyzes reoxidation of DsbA protein disulfide isomerase I
RA	1,233,154	T→A	5.2%	intergenic (‑124/+22)	dsbB ← / ← nhaB	oxidoreductase that catalyzes reoxidation of DsbA protein disulfide isomerase I/sodium:proton antiporter
RA	1,233,157	T→A	5.1%	intergenic (‑127/+19)	dsbB ← / ← nhaB	oxidoreductase that catalyzes reoxidation of DsbA protein disulfide isomerase I/sodium:proton antiporter
RA	1,272,542	T→A	5.4%	C12* (TGT→TGA)	chaC →	cation transport regulator
JC JC	1,293,006	IS5 (+) +3 bp	45.6%	intergenic (‑84/‑519)	hns ← / → tdk	global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
JC JC	1,293,009	IS2 (–) +5 bp	31.0%	intergenic (‑87/‑514)	hns ← / → tdk	global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
JC JC	1,293,032	IS1 (+) +9 bp	38.3%	intergenic (‑110/‑487)	hns ← / → tdk	global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
RA	1,297,267	A→G	5.2%	V285V (GTT→GTC) ‡	adhE ←	fused acetaldehyde‑CoA dehydrogenase/iron‑dependent alcohol dehydrogenase/pyruvate‑formate lyase deactivase
RA	1,297,268	A→T	5.8%	V285D (GTT→GAT) ‡	adhE ←	fused acetaldehyde‑CoA dehydrogenase/iron‑dependent alcohol dehydrogenase/pyruvate‑formate lyase deactivase
MC JC	1,299,499	Δ1,199 bp	100%	intergenic (+254/‑485)	ychE → / → oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
RA	1,311,830	A→G	6.4%	intergenic (+22/+18)	tonB → / ← yciA	membrane spanning protein in TonB‑ExbB‑ExbD transport complex/acyl‑CoA esterase
RA	1,311,831	C→T	5.6%	intergenic (+23/+17)	tonB → / ← yciA	membrane spanning protein in TonB‑ExbB‑ExbD transport complex/acyl‑CoA esterase
RA	1,324,837	A→C	6.5%	Y31S (TAT→TCT) ‡	yciQ →	enhancer of membrane protein expression; putative inner membrane protein
RA	1,324,838	T→A	5.6%	Y31* (TAT→TAA) ‡	yciQ →	enhancer of membrane protein expression; putative inner membrane protein
RA	1,324,839	G→T	5.9%	E32* (GAA→TAA)	yciQ →	enhancer of membrane protein expression; putative inner membrane protein
RA	1,346,957	G→T	5.4%	intergenic (+57/+21)	ymiB → / ← rnb	uncharacterized protein/ribonuclease II
RA	1,354,227	T→G	5.2%	T98P (ACC→CCC)	sapC ←	antimicrobial peptide transport ABC transporter permease
RA	1,388,283	C→T	6.3%	intergenic (+22/+22)	tyrR → / ← tpx	aromatic amino acid biosynthesis and transport regulon transcriptional regulator; autorepressor; ATPase; phosphatase/lipid hydroperoxide peroxidase
RA	1,388,284	A→T	6.4%	intergenic (+23/+21)	tyrR → / ← tpx	aromatic amino acid biosynthesis and transport regulon transcriptional regulator; autorepressor; ATPase; phosphatase/lipid hydroperoxide peroxidase
RA	1,388,285	A→G	6.9%	intergenic (+24/+20)	tyrR → / ← tpx	aromatic amino acid biosynthesis and transport regulon transcriptional regulator; autorepressor; ATPase; phosphatase/lipid hydroperoxide peroxidase
RA	1,413,964	C→T	7.2%	intergenic (‑37/+20)	ralR ← / ← recT	Rac prophage; restriction alleviation protein/Rac prophage; recombination and repair protein
RA	1,413,966	T→A	7.3%	intergenic (‑39/+18)	ralR ← / ← recT	Rac prophage; restriction alleviation protein/Rac prophage; recombination and repair protein
RA	1,413,968	A→G	7.1%	intergenic (‑41/+16)	ralR ← / ← recT	Rac prophage; restriction alleviation protein/Rac prophage; recombination and repair protein
RA	1,441,833	G→C	6.1%	intergenic (‑90/+21)	hslJ ← / ← ldhA	heat‑inducible lipoprotein involved in novobiocin resistance/fermentative D‑lactate dehydrogenase, NAD‑dependent
RA	1,441,835	A→T	5.2%	intergenic (‑92/+19)	hslJ ← / ← ldhA	heat‑inducible lipoprotein involved in novobiocin resistance/fermentative D‑lactate dehydrogenase, NAD‑dependent
RA	1,441,837	G→C	5.4%	intergenic (‑94/+17)	hslJ ← / ← ldhA	heat‑inducible lipoprotein involved in novobiocin resistance/fermentative D‑lactate dehydrogenase, NAD‑dependent
RA	1,443,803	G→A	6.0%	P251P (CCG→CCA)	ydbH →	putative membrane‑anchored protein, function unknown
RA	1,443,804	T→C	6.0%	W252R (TGG→CGG)	ydbH →	putative membrane‑anchored protein, function unknown
RA	1,449,050	T→A	5.6%	intergenic (+32/+26)	feaB → / ← tynA	phenylacetaldehyde dehydrogenase/tyramine oxidase, copper‑requiring
RA	1,449,799	C→G	7.7%	T517T (ACG→ACC)	tynA ←	tyramine oxidase, copper‑requiring
RA	1,449,802	A→G	7.7%	A516A (GCT→GCC) ‡	tynA ←	tyramine oxidase, copper‑requiring
RA	1,449,803	G→C	7.5%	A516G (GCT→GGT) ‡	tynA ←	tyramine oxidase, copper‑requiring
RA	1,449,804	C→T	7.8%	A516T (GCT→ACT) ‡	tynA ←	tyramine oxidase, copper‑requiring
RA	1,449,807	C→G	7.8%	G515R (GGT→CGT)	tynA ←	tyramine oxidase, copper‑requiring
RA	1,457,530	G→T	5.2%	V12L (GTA→TTA)	paaF →	2,3‑dehydroadipyl‑CoA hydratase
RA	1,457,976	A→T	5.6%	G160G (GGA→GGT)	paaF →	2,3‑dehydroadipyl‑CoA hydratase
RA	1,457,979	A→T	5.7%	E161D (GAA→GAT)	paaF →	2,3‑dehydroadipyl‑CoA hydratase
RA	1,457,981	G→C	5.6%	S162T (AGT→ACT)	paaF →	2,3‑dehydroadipyl‑CoA hydratase
RA	1,457,983	A→T	5.8%	I163F (ATC→TTC)	paaF →	2,3‑dehydroadipyl‑CoA hydratase
RA	1,457,986	A→T	5.9%	T164S (ACC→TCC)	paaF →	2,3‑dehydroadipyl‑CoA hydratase
RA	1,466,138	G→A	6.1%	pseudogene (747/2513 nt)	ydbA →	pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA	1,466,144	G→T	9.0%	pseudogene (753/2513 nt)	ydbA →	pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA	1,466,336	C→G	9.2%	pseudogene (945/2513 nt)	ydbA →	pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA	1,466,504	A→G	7.6%	pseudogene (1113/2513 nt)	ydbA →	pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA	1,488,050	T→C	5.7%	intergenic (+15/‑182)	ydcF → / → aldA	DUF218 superfamily protein, SAM‑binding/aldehyde dehydrogenase A, NAD‑linked
RA	1,488,051	G→A	5.7%	intergenic (+16/‑181)	ydcF → / → aldA	DUF218 superfamily protein, SAM‑binding/aldehyde dehydrogenase A, NAD‑linked
RA	1,488,055	C→A	6.5%	intergenic (+20/‑177)	ydcF → / → aldA	DUF218 superfamily protein, SAM‑binding/aldehyde dehydrogenase A, NAD‑linked
RA	1,488,057	C→G	5.5%	intergenic (+22/‑175)	ydcF → / → aldA	DUF218 superfamily protein, SAM‑binding/aldehyde dehydrogenase A, NAD‑linked
RA	1,488,059	T→G	5.5%	intergenic (+24/‑173)	ydcF → / → aldA	DUF218 superfamily protein, SAM‑binding/aldehyde dehydrogenase A, NAD‑linked
RA	1,488,063	T→C	5.8%	intergenic (+28/‑169)	ydcF → / → aldA	DUF218 superfamily protein, SAM‑binding/aldehyde dehydrogenase A, NAD‑linked
RA	1,488,064	G→A	5.4%	intergenic (+29/‑168)	ydcF → / → aldA	DUF218 superfamily protein, SAM‑binding/aldehyde dehydrogenase A, NAD‑linked
RA	1,504,884	T→C	5.0%	intergenic (+19/+21)	insQ → / ← ydcO	IS609 transposase B/BenE family inner membrane putative transporter
RA	1,504,888	T→G	5.1%	intergenic (+23/+17)	insQ → / ← ydcO	IS609 transposase B/BenE family inner membrane putative transporter
RA	1,504,889	C→A	5.1%	intergenic (+24/+16)	insQ → / ← ydcO	IS609 transposase B/BenE family inner membrane putative transporter
RA	1,504,893	G→A	5.1%	intergenic (+28/+12)	insQ → / ← ydcO	IS609 transposase B/BenE family inner membrane putative transporter
RA	1,517,481	C→G	5.0%	R31R (CGC→CGG)	ydcX →	DUF2566 family protein
RA	1,517,484	C→G	5.8%	I32M (ATC→ATG)	ydcX →	DUF2566 family protein
RA	1,530,496	G→T	5.9%	intergenic (+92/‑90)	ydcD → / → yncI	putative immunity protein for RhsE/pseudogene
RA	1,552,191	C→A	24.4%	intergenic (+200/+207)	fdnI → / ← yddM	formate dehydrogenase‑N, cytochrome B556 (gamma) subunit, nitrate‑inducible/putative DNA‑binding transcriptional regulator
RA	1,568,915	G→A	9.8%	intergenic (‑92/+39)	yddW ← / ← gadC	liprotein, glycosyl hydrolase homolog/glutamate:gamma‑aminobutyric acid antiporter
RA	1,568,917	A→T	11.1%	intergenic (‑94/+37)	yddW ← / ← gadC	liprotein, glycosyl hydrolase homolog/glutamate:gamma‑aminobutyric acid antiporter
RA	1,568,919	T→C	9.6%	intergenic (‑96/+35)	yddW ← / ← gadC	liprotein, glycosyl hydrolase homolog/glutamate:gamma‑aminobutyric acid antiporter
RA	1,579,563	G→T	6.4%	intergenic (‑221/+70)	yddA ← / ← ydeM	putative multidrug ABC transporter permease/ATPase/putative YdeN‑specific sulfatase‑maturating enzyme
RA	1,579,564	G→A	6.0%	intergenic (‑222/+69)	yddA ← / ← ydeM	putative multidrug ABC transporter permease/ATPase/putative YdeN‑specific sulfatase‑maturating enzyme
RA	1,579,569	T→C	6.1%	intergenic (‑227/+64)	yddA ← / ← ydeM	putative multidrug ABC transporter permease/ATPase/putative YdeN‑specific sulfatase‑maturating enzyme
RA	1,579,570	A→C	6.1%	intergenic (‑228/+63)	yddA ← / ← ydeM	putative multidrug ABC transporter permease/ATPase/putative YdeN‑specific sulfatase‑maturating enzyme
RA	1,590,599	A→G	8.1%	intergenic (‑63/+255)	yneL ← / ← hipA	pseudogene, AraC family/inactivating GltX kinase facilitating persister formation; toxin of HipAB TA pair; autokinase
RA	1,590,601	G→C	8.5%	intergenic (‑65/+253)	yneL ← / ← hipA	pseudogene, AraC family/inactivating GltX kinase facilitating persister formation; toxin of HipAB TA pair; autokinase
RA	1,590,602	C→G	8.5%	intergenic (‑66/+252)	yneL ← / ← hipA	pseudogene, AraC family/inactivating GltX kinase facilitating persister formation; toxin of HipAB TA pair; autokinase
RA	1,590,603	G→C	8.9%	intergenic (‑67/+251)	yneL ← / ← hipA	pseudogene, AraC family/inactivating GltX kinase facilitating persister formation; toxin of HipAB TA pair; autokinase
RA	1,590,605	C→T	10.0%	intergenic (‑69/+249)	yneL ← / ← hipA	pseudogene, AraC family/inactivating GltX kinase facilitating persister formation; toxin of HipAB TA pair; autokinase
RA	1,602,236	A→T	6.7%	Q249H (CAA→CAT)	lsrA →	autoinducer 2 import ATP‑binding protein
RA	1,602,239	A→T	6.7%	K250N (AAA→AAT)	lsrA →	autoinducer 2 import ATP‑binding protein
RA	1,602,242	A→T	6.5%	L251F (TTA→TTT)	lsrA →	autoinducer 2 import ATP‑binding protein
RA	1,620,224	C→G	5.8%	intergenic (+17/+14)	marB → / ← eamA	periplasmic mar operon regulator/cysteine and O‑acetyl‑L‑serine efflux system
RA	1,620,227	C→G	5.7%	intergenic (+20/+11)	marB → / ← eamA	periplasmic mar operon regulator/cysteine and O‑acetyl‑L‑serine efflux system
RA	1,643,110	T→A	5.9%	K44N (AAA→AAT) ‡	quuQ ←	Qin prophage; putative antitermination protein Q
RA	1,643,111	T→G	5.7%	K44T (AAA→ACA) ‡	quuQ ←	Qin prophage; putative antitermination protein Q
RA	1,643,116	C→A	6.0%	Q42H (CAG→CAT) ‡	quuQ ←	Qin prophage; putative antitermination protein Q
RA	1,643,117	T→A	6.1%	Q42L (CAG→CTG) ‡	quuQ ←	Qin prophage; putative antitermination protein Q
RA	1,650,147	G→A	8.7%	pseudogene (70/765 nt)	ydfE →	Qin prophage; pseudogene;Phage or Prophage Related
RA	1,650,148	T→C	9.5%	pseudogene (71/765 nt)	ydfE →	Qin prophage; pseudogene;Phage or Prophage Related
RA	1,660,194	A→C	6.5%	K709T (AAG→ACG)	ynfE →	putative selenate reductase, periplasmic
RA	1,660,198	T→A	6.6%	A710A (GCT→GCA)	ynfE →	putative selenate reductase, periplasmic
RA	1,660,200	C→G	7.4%	A711G (GCC→GGC)	ynfE →	putative selenate reductase, periplasmic
RA	1,660,202	T→A	6.2%	C712S (TGC→AGC)	ynfE →	putative selenate reductase, periplasmic
RA	1,660,206	G→T	8.1%	R713L (CGT→CTT)	ynfE →	putative selenate reductase, periplasmic
RA	1,666,470	C→A	5.1%	L386I (CTA→ATA)	clcB →	H(+)/Cl(‑) exchange transporter
RA	1,674,171	Δ1 bp	6.3%	coding (259/1035 nt)	tqsA →	pheromone AI‑2 transporter
RA	1,674,177	G→T	6.2%	E89* (GAG→TAG) ‡	tqsA →	pheromone AI‑2 transporter
RA	1,674,178	A→C	6.2%	E89A (GAG→GCG) ‡	tqsA →	pheromone AI‑2 transporter
RA	1,679,644	A→T	5.3%	M30L (ATG→TTG)	ydgI →	putative arginine/ornithine antiporter transporter
RA	1,681,622	T→A	5.5%	L216Q (CTG→CAG)	folM →	dihydromonapterin reductase, NADPH‑dependent; dihydrofolate reductase isozyme
RA	1,699,865	C→G	5.1%	P171A (CCG→GCG)	malX →	maltose and glucose‑specific PTS enzyme IIB component and IIC component
RA	1,703,251	A→T	5.4%	intergenic (+17/+17)	add → / ← ydgJ	adenosine deaminase/putative oxidoreductase
RA	1,703,252	A→T	5.4%	intergenic (+18/+16)	add → / ← ydgJ	adenosine deaminase/putative oxidoreductase
RA	1,707,028	T→G	8.0%	V37G (GTA→GGA) ‡	rsxC →	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA	1,707,029	A→G	7.6%	V37V (GTA→GTG) ‡	rsxC →	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA	1,707,030	C→T	6.7%	P38S (CCC→TCC) ‡	rsxC →	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA	1,707,031	C→A	6.8%	P38H (CCC→CAC) ‡	rsxC →	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA	1,720,364	G→T	9.0%	intergenic (+21/+26)	slyB → / ← slyA	outer membrane lipoprotein/global transcriptional regulator
RA	1,720,366	T→A	9.6%	intergenic (+23/+24)	slyB → / ← slyA	outer membrane lipoprotein/global transcriptional regulator
RA	1,720,367	A→C	5.7%	intergenic (+24/+23)	slyB → / ← slyA	outer membrane lipoprotein/global transcriptional regulator
RA	1,724,279	T→A	6.6%	D126V (GAT→GTT) ‡	sodC ←	superoxide dismutase, Cu, Zn, periplasmic
RA	1,724,280	C→A	6.6%	D126Y (GAT→TAT) ‡	sodC ←	superoxide dismutase, Cu, Zn, periplasmic
RA	1,724,282	G→C	6.8%	T125S (ACC→AGC)	sodC ←	superoxide dismutase, Cu, Zn, periplasmic
RA	1,724,285	G→C	6.7%	A124G (GCT→GGT)	sodC ←	superoxide dismutase, Cu, Zn, periplasmic
RA	1,724,287	T→G	8.0%	K123N (AAA→AAC) ‡	sodC ←	superoxide dismutase, Cu, Zn, periplasmic
RA	1,724,288	T→A	6.7%	K123I (AAA→ATA) ‡	sodC ←	superoxide dismutase, Cu, Zn, periplasmic
RA	1,743,155	C→G	9.2%	D30H (GAC→CAC)	ribC ←	riboflavin synthase, alpha subunit
RA	1,743,157	G→A	9.9%	P29L (CCC→CTC)	ribC ←	riboflavin synthase, alpha subunit
RA	1,743,160	A→T	9.5%	L28* (TTA→TAA)	ribC ←	riboflavin synthase, alpha subunit
RA	1,743,163	T→C	9.9%	E27G (GAG→GGG)	ribC ←	riboflavin synthase, alpha subunit
RA	1,743,165	C→G	9.7%	V26V (GTG→GTC)	ribC ←	riboflavin synthase, alpha subunit
RA	1,757,688	T→A	5.5%	intergenic (+31/+33)	lpp → / ← ldtE	murein lipoprotein/murein L,D‑transpeptidase
RA	1,764,687	T→C	8.5%	intergenic (‑301/+26)	sufA ← / ← rydB	Fe‑S cluster assembly protein/novel sRNA, function unknown
RA	1,764,693	C→T	8.3%	intergenic (‑307/+20)	sufA ← / ← rydB	Fe‑S cluster assembly protein/novel sRNA, function unknown
RA	1,764,694	G→C	9.2%	intergenic (‑308/+19)	sufA ← / ← rydB	Fe‑S cluster assembly protein/novel sRNA, function unknown
RA	1,764,695	A→G	8.4%	intergenic (‑309/+18)	sufA ← / ← rydB	Fe‑S cluster assembly protein/novel sRNA, function unknown
RA	1,764,701	G→A	8.0%	intergenic (‑315/+12)	sufA ← / ← rydB	Fe‑S cluster assembly protein/novel sRNA, function unknown
RA	1,789,497	T→G	6.7%	intergenic (+16/‑116)	aroH → / → ydiE	3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, tryptophan repressible/hemin uptake protein HemP homolog
RA	1,789,498	G→T	6.3%	intergenic (+17/‑115)	aroH → / → ydiE	3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, tryptophan repressible/hemin uptake protein HemP homolog
RA	1,789,499	A→C	7.7%	intergenic (+18/‑114)	aroH → / → ydiE	3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, tryptophan repressible/hemin uptake protein HemP homolog
RA	1,789,500	C→A	6.9%	intergenic (+19/‑113)	aroH → / → ydiE	3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, tryptophan repressible/hemin uptake protein HemP homolog
RA	1,790,787	C→T	5.6%	S153N (AGC→AAC)	ydiU ←	UPF0061 family protein
RA	1,795,227	A→T	9.5%	intergenic (‑75/+26)	btuC ← / ← ihfA	vitamin B12 ABC transporter permease/integration host factor (IHF), DNA‑binding protein, alpha subunit
RA	1,795,228	G→C	9.5%	intergenic (‑76/+25)	btuC ← / ← ihfA	vitamin B12 ABC transporter permease/integration host factor (IHF), DNA‑binding protein, alpha subunit
RA	1,795,229	A→T	9.4%	intergenic (‑77/+24)	btuC ← / ← ihfA	vitamin B12 ABC transporter permease/integration host factor (IHF), DNA‑binding protein, alpha subunit
RA	1,799,370	Δ1 bp	6.0%	intergenic (‑100/+23)	pheM ← / ← rplT	phenylalanyl‑tRNA synthetase operon leader peptide/50S ribosomal subunit protein L20
RA	1,799,374:1	+T	6.0%	intergenic (‑104/+19)	pheM ← / ← rplT	phenylalanyl‑tRNA synthetase operon leader peptide/50S ribosomal subunit protein L20
RA	1,807,316	G→A	7.4%	intergenic (+17/‑84)	pfkB → / → ydiZ	6‑phosphofructokinase II/uncharacterized protein
RA	1,807,317	C→T	7.5%	intergenic (+18/‑83)	pfkB → / → ydiZ	6‑phosphofructokinase II/uncharacterized protein
RA	1,807,318	A→G	7.4%	intergenic (+19/‑82)	pfkB → / → ydiZ	6‑phosphofructokinase II/uncharacterized protein
RA	1,807,319	T→C	7.5%	intergenic (+20/‑81)	pfkB → / → ydiZ	6‑phosphofructokinase II/uncharacterized protein
RA	1,816,192	G→A	6.5%	intergenic (+64/+194)	katE → / ← chbG	catalase HPII, heme d‑containing/chito‑oligosaccharide deacetylase
RA	1,816,193	C→A	5.2%	intergenic (+65/+193)	katE → / ← chbG	catalase HPII, heme d‑containing/chito‑oligosaccharide deacetylase
RA	1,822,071	G→A	9.3%	I62I (ATC→ATT) ‡	osmE ←	osmotically‑inducible lipoprotein
RA	1,822,072	A→T	9.4%	I62N (ATC→AAC) ‡	osmE ←	osmotically‑inducible lipoprotein
RA	1,822,073	T→C	9.5%	I62V (ATC→GTC) ‡	osmE ←	osmotically‑inducible lipoprotein
RA	1,825,939	T→A	6.5%	intergenic (‑314/+16)	spy ← / ← astE	periplasmic ATP‑independent protein refolding chaperone, stress‑induced/succinylglutamate desuccinylase
RA	1,830,060	G→C	5.3%	R236G (CGC→GGC)	astA ←	arginine succinyltransferase
RA	1,830,061	G→T	5.3%	A235A (GCC→GCA)	astA ←	arginine succinyltransferase
RA	1,864,758	G→A	5.6%	intergenic (+24/+24)	yeaD → / ← yeaE	D‑hexose‑6‑phosphate epimerase‑like protein/aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent
RA	1,864,763	A→T	5.4%	intergenic (+29/+19)	yeaD → / ← yeaE	D‑hexose‑6‑phosphate epimerase‑like protein/aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent
RA	1,889,916	C→T	5.1%	intergenic (‑170/+35)	fadD ← / ← yeaY	acyl‑CoA synthetase (long‑chain‑fatty‑acid‑‑CoA ligase)/Slp family lipoprotein, RpoE‑regulated
RA	1,889,917	C→G	5.2%	intergenic (‑171/+34)	fadD ← / ← yeaY	acyl‑CoA synthetase (long‑chain‑fatty‑acid‑‑CoA ligase)/Slp family lipoprotein, RpoE‑regulated
RA	1,889,918	A→G	5.2%	intergenic (‑172/+33)	fadD ← / ← yeaY	acyl‑CoA synthetase (long‑chain‑fatty‑acid‑‑CoA ligase)/Slp family lipoprotein, RpoE‑regulated
RA	1,929,012	C→T	9.3%	intergenic (‑173/+36)	ptrB ← / ← yebE	protease II/DUF533 family inner membrane protein
RA	1,929,016	A→G	8.2%	intergenic (‑177/+32)	ptrB ← / ← yebE	protease II/DUF533 family inner membrane protein
RA	1,929,018	A→T	7.8%	intergenic (‑179/+30)	ptrB ← / ← yebE	protease II/DUF533 family inner membrane protein
RA	1,929,020	T→A	8.3%	intergenic (‑181/+28)	ptrB ← / ← yebE	protease II/DUF533 family inner membrane protein
RA	1,929,022	A→T	8.3%	intergenic (‑183/+26)	ptrB ← / ← yebE	protease II/DUF533 family inner membrane protein
RA	1,929,024	C→T	8.2%	intergenic (‑185/+24)	ptrB ← / ← yebE	protease II/DUF533 family inner membrane protein
RA	1,929,028	A→G	8.1%	intergenic (‑189/+20)	ptrB ← / ← yebE	protease II/DUF533 family inner membrane protein
RA	1,932,095	T→A	6.2%	intergenic (+36/+20)	purT → / ← eda	phosphoribosylglycinamide formyltransferase 2/KHG/KDPG aldolase; 2‑dehydro‑3‑deoxy‑phosphogluconate/4‑hydroxy‑2‑ oxoglutarate aldolase
RA	1,944,234	A→C	6.2%	intergenic (+35/+112)	znuB → / ← ruvB	zinc ABC transporter permease/ATP‑dependent DNA helicase, component of RuvABC resolvasome
RA	1,944,240	T→G	7.1%	intergenic (+41/+106)	znuB → / ← ruvB	zinc ABC transporter permease/ATP‑dependent DNA helicase, component of RuvABC resolvasome
MC JC	1,978,503	Δ776 bp	100%		insB1–insA	insB1, insA
JC JC	1,979,486	IS5 (+) +4 bp	100%	intergenic (‑271/‑264)	insA ← / → uspC	IS1 repressor TnpA/universal stress protein
RA	1,982,500	T→C	5.3%	intergenic (‑113/+54)	otsB ← / ← araH	trehalose‑6‑phosphate phosphatase, biosynthetic/L‑arabinose ABC transporter permease
RA	1,985,112	C→G	6.8%	intergenic (‑43/+27)	araG ← / ← araF	L‑arabinose ABC transporter ATPase/L‑arabinose ABC transporter periplasmic binding protein
RA	1,987,857	C→T	6.8%	intergenic (‑99/+16)	yecJ ← / ← azuC	DUF2766 family protein/acid‑inducible small membrane‑associated protein
RA	1,987,858	G→C	6.3%	intergenic (‑100/+15)	yecJ ← / ← azuC	DUF2766 family protein/acid‑inducible small membrane‑associated protein
RA	1,987,859	G→C	6.4%	intergenic (‑101/+14)	yecJ ← / ← azuC	DUF2766 family protein/acid‑inducible small membrane‑associated protein
RA	1,987,860	A→G	6.9%	intergenic (‑102/+13)	yecJ ← / ← azuC	DUF2766 family protein/acid‑inducible small membrane‑associated protein
RA	1,990,922	C→T	8.9%	intergenic (+30/+32)	tyrP → / ← yecA	tyrosine transporter/UPF0149 family protein
RA	1,990,926	A→C	9.0%	intergenic (+34/+28)	tyrP → / ← yecA	tyrosine transporter/UPF0149 family protein
RA	1,990,927	A→G	9.1%	intergenic (+35/+27)	tyrP → / ← yecA	tyrosine transporter/UPF0149 family protein
RA	1,990,932	C→T	9.0%	intergenic (+40/+22)	tyrP → / ← yecA	tyrosine transporter/UPF0149 family protein
RA	1,990,933	G→T	8.5%	intergenic (+41/+21)	tyrP → / ← yecA	tyrosine transporter/UPF0149 family protein
RA	1,990,937	A→G	9.6%	intergenic (+45/+17)	tyrP → / ← yecA	tyrosine transporter/UPF0149 family protein
RA	1,999,231	T→A	8.7%	T84S (ACT→TCT)	dcyD ←	D‑cysteine desulfhydrase, PLP‑dependent
RA	2,044,721	G→A	6.2%	intergenic (+97/‑217)	asnT → / → yeeJ	tRNA‑Asn/putative adhesin
RA	2,044,725	T→A	5.9%	intergenic (+101/‑213)	asnT → / → yeeJ	tRNA‑Asn/putative adhesin
RA	2,044,727	T→A	6.1%	intergenic (+103/‑211)	asnT → / → yeeJ	tRNA‑Asn/putative adhesin
RA	2,044,729	T→A	5.8%	intergenic (+105/‑209)	asnT → / → yeeJ	tRNA‑Asn/putative adhesin
RA	2,044,733	T→C	6.0%	intergenic (+109/‑205)	asnT → / → yeeJ	tRNA‑Asn/putative adhesin
RA	2,059,946	T→A	5.1%	intergenic (+20/+18)	asnU → / ← cbl	tRNA‑Asn/ssuEADCB/tauABCD operon transcriptional activator
RA	2,059,948	T→A	5.2%	intergenic (+22/+16)	asnU → / ← cbl	tRNA‑Asn/ssuEADCB/tauABCD operon transcriptional activator
RA	2,079,004	G→C	5.7%	intergenic (+73/+28)	yoeF → / ← yeeX	pseudogene, CP4‑44 putative prophage remnant;Phage or Prophage Related/UPF0265 family protein
RA	2,081,688	A→T	7.7%	I287N (ATT→AAT)	dacD ←	D‑alanyl‑D‑alanine carboxypeptidase; penicillin‑binding protein 6b
RA	2,085,662	C→T	5.8%	intergenic (‑137/+42)	yeeE ← / ← plaP	UPF0394 family inner membrane protein/putrescine importer, low affinity
RA	2,085,664	A→G	6.0%	intergenic (‑139/+40)	yeeE ← / ← plaP	UPF0394 family inner membrane protein/putrescine importer, low affinity
RA	2,085,669	T→A	5.6%	intergenic (‑144/+35)	yeeE ← / ← plaP	UPF0394 family inner membrane protein/putrescine importer, low affinity
RA	2,085,670	T→A	6.6%	intergenic (‑145/+34)	yeeE ← / ← plaP	UPF0394 family inner membrane protein/putrescine importer, low affinity
RA	2,085,675	C→T	6.4%	intergenic (‑150/+29)	yeeE ← / ← plaP	UPF0394 family inner membrane protein/putrescine importer, low affinity
RA	2,085,677	A→G	6.4%	intergenic (‑152/+27)	yeeE ← / ← plaP	UPF0394 family inner membrane protein/putrescine importer, low affinity
RA	2,115,847	G→T	7.7%	A17E (GCG→GAG)	wcaM ←	colanic acid biosynthesis protein
RA	2,115,849	C→G	6.8%	S16S (TCG→TCC) ‡	wcaM ←	colanic acid biosynthesis protein
RA	2,115,851	A→C	7.4%	S16A (TCG→GCG) ‡	wcaM ←	colanic acid biosynthesis protein
RA	2,121,583	Δ1 bp	6.2%	intergenic (‑29/+26)	wcaJ ← / ← cpsG	colanic biosynthesis UDP‑glucose lipid carrier transferase/phosphomannomutase
RA	2,121,586	G→C	6.9%	intergenic (‑32/+23)	wcaJ ← / ← cpsG	colanic biosynthesis UDP‑glucose lipid carrier transferase/phosphomannomutase
RA	2,121,588:1	+C	6.5%	intergenic (‑34/+21)	wcaJ ← / ← cpsG	colanic biosynthesis UDP‑glucose lipid carrier transferase/phosphomannomutase
RA	2,139,709	G→A	6.6%	intergenic (+224/+50)	yegH → / ← asmA	inner membrane protein/suppressor of OmpF assembly mutants; putative outer membrane protein assembly factor; inner membrane‑anchored periplasmic protein
RA	2,139,710	C→A	5.9%	intergenic (+225/+49)	yegH → / ← asmA	inner membrane protein/suppressor of OmpF assembly mutants; putative outer membrane protein assembly factor; inner membrane‑anchored periplasmic protein
RA	2,139,716	T→G	6.4%	intergenic (+231/+43)	yegH → / ← asmA	inner membrane protein/suppressor of OmpF assembly mutants; putative outer membrane protein assembly factor; inner membrane‑anchored periplasmic protein
RA	2,139,718	T→A	6.4%	intergenic (+233/+41)	yegH → / ← asmA	inner membrane protein/suppressor of OmpF assembly mutants; putative outer membrane protein assembly factor; inner membrane‑anchored periplasmic protein
RA	2,139,720	C→A	6.5%	intergenic (+235/+39)	yegH → / ← asmA	inner membrane protein/suppressor of OmpF assembly mutants; putative outer membrane protein assembly factor; inner membrane‑anchored periplasmic protein
RA	2,139,726	T→G	5.5%	intergenic (+241/+33)	yegH → / ← asmA	inner membrane protein/suppressor of OmpF assembly mutants; putative outer membrane protein assembly factor; inner membrane‑anchored periplasmic protein
RA	2,139,727	T→C	5.5%	intergenic (+242/+32)	yegH → / ← asmA	inner membrane protein/suppressor of OmpF assembly mutants; putative outer membrane protein assembly factor; inner membrane‑anchored periplasmic protein
RA	2,142,505	G→C	5.3%	R148R (CGC→CGG)	udk ←	uridine/cytidine kinase
RA	2,153,396	C→A	6.7%	noncoding (88/143 nt) V5F (GTC→TTC)	sibA → ibsA ←	sRNA antisense regulator of toxic IbsA protein toxic membrane protein
RA	2,153,398	T→C	5.9%	noncoding (90/143 nt) H4R (CAC→CGC) ‡	sibA → ibsA ←	sRNA antisense regulator of toxic IbsA protein toxic membrane protein
RA	2,153,399	G→A	5.8%	noncoding (91/143 nt) H4Y (CAC→TAC) ‡	sibA → ibsA ←	sRNA antisense regulator of toxic IbsA protein toxic membrane protein
RA	2,153,401	T→G	5.6%	noncoding (93/143 nt) K3T (AAG→ACG)	sibA → ibsA ←	sRNA antisense regulator of toxic IbsA protein toxic membrane protein
RA	2,153,763	T→C	6.4%	noncoding (120/136 nt)	sibB →	sRNA antisense regulator of toxic IbsB protein
RA	2,153,766	T→G	7.0%	noncoding (123/136 nt)	sibB →	sRNA antisense regulator of toxic IbsB protein
RA	2,153,767	C→A	6.2%	noncoding (124/136 nt)	sibB →	sRNA antisense regulator of toxic IbsB protein
RA	2,153,770	G→A	6.6%	noncoding (127/136 nt)	sibB →	sRNA antisense regulator of toxic IbsB protein
RA	2,154,604	C→G	5.4%	R197G (CGG→GGG)	mdtA →	multidrug efflux system, subunit A
RA	2,173,151	C→T	5.5%	pseudogene (212/442 nt)	gatC ←	pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC
RA	2,173,153	A→T	5.9%	pseudogene (210/442 nt)	gatC ←	pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC
RA	2,173,155	A→G	5.5%	pseudogene (208/442 nt)	gatC ←	pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC
RA	2,173,361	Δ2 bp	100%	pseudogene (1‑2/442 nt)	gatC ←	pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC
RA	2,252,810	T→G	5.5%	intergenic (+22/+85)	yeiI → / ← nupX	putative kinase/nucleoside permease
RA	2,252,812	A→T	5.1%	intergenic (+24/+83)	yeiI → / ← nupX	putative kinase/nucleoside permease
RA	2,252,814	C→A	5.2%	intergenic (+26/+81)	yeiI → / ← nupX	putative kinase/nucleoside permease
RA	2,254,348	A→C	5.2%	V280G (GTT→GGT)	rihB ←	ribonucleoside hydrolase 2
RA	2,259,549	A→T	6.4%	intergenic (‑253/+170)	psuK ← / ← fruA	pseudouridine kinase/fused fructose‑specific PTS enzymes: IIBcomponent/IIC components
RA	2,259,550	A→T	7.0%	intergenic (‑254/+169)	psuK ← / ← fruA	pseudouridine kinase/fused fructose‑specific PTS enzymes: IIBcomponent/IIC components
RA	2,259,553	A→T	6.5%	intergenic (‑257/+166)	psuK ← / ← fruA	pseudouridine kinase/fused fructose‑specific PTS enzymes: IIBcomponent/IIC components
RA	2,259,554	A→T	7.0%	intergenic (‑258/+165)	psuK ← / ← fruA	pseudouridine kinase/fused fructose‑specific PTS enzymes: IIBcomponent/IIC components
RA	2,263,235	C→T	6.2%	W87* (TGG→TGA) ‡	fruB ←	fused fructose‑specific PTS enzymes: IIA component/HPr component
RA	2,263,236	C→G	6.4%	W87S (TGG→TCG) ‡	fruB ←	fused fructose‑specific PTS enzymes: IIA component/HPr component
RA	2,263,237	A→G	6.6%	W87R (TGG→CGG) ‡	fruB ←	fused fructose‑specific PTS enzymes: IIA component/HPr component
RA	2,270,602	T→C	8.5%	intergenic (+57/‑124)	mepS → / → rtn	murein DD‑endopeptidase, space‑maker hydrolase, mutational suppressor of prc thermosensitivity, outer membrane lipoprotein, weak murein LD‑carboxypeptidase/resistance protein for phages lambda and N4, putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	2,270,605	G→A	8.5%	intergenic (+60/‑121)	mepS → / → rtn	murein DD‑endopeptidase, space‑maker hydrolase, mutational suppressor of prc thermosensitivity, outer membrane lipoprotein, weak murein LD‑carboxypeptidase/resistance protein for phages lambda and N4, putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA	2,279,422	A→G	5.3%	A113A (GCT→GCC)	bcr ←	bicyclomycin/cysteine/sulfonamide efflux transporter
RA	2,282,449	A→G	5.7%	intergenic (+57/‑68)	yejH → / → rplY	putative ATP‑dependent DNA or RNA helicase/50S ribosomal subunit protein L25
RA	2,282,452	C→T	5.5%	intergenic (+60/‑65)	yejH → / → rplY	putative ATP‑dependent DNA or RNA helicase/50S ribosomal subunit protein L25
RA	2,286,311	C→G	5.8%	intergenic (+24/+79)	proL → / ← yejO	tRNA‑Pro/pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system
RA	2,286,313	T→A	6.6%	intergenic (+26/+77)	proL → / ← yejO	tRNA‑Pro/pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system
RA	2,286,315	C→G	5.7%	intergenic (+28/+75)	proL → / ← yejO	tRNA‑Pro/pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system
RA	2,290,448	A→G	5.1%	intergenic (‑268/‑52)	yejO ← / → narP	pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system/response regulator in two‑component regulatory system with NarQ
RA	2,290,449	C→G	5.1%	intergenic (‑269/‑51)	yejO ← / → narP	pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system/response regulator in two‑component regulatory system with NarQ
RA	2,290,450	C→T	5.1%	intergenic (‑270/‑50)	yejO ← / → narP	pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system/response regulator in two‑component regulatory system with NarQ
RA	2,319,581	A→G	9.6%	V99A (GTG→GCG) ‡	rcsC ←	hybrid sensory kinase in two‑component regulatory system with RcsB and YojN
RA	2,319,582	C→G	9.5%	V99L (GTG→CTG) ‡	rcsC ←	hybrid sensory kinase in two‑component regulatory system with RcsB and YojN
RA	2,319,585	C→G	10.1%	D98H (GAT→CAT)	rcsC ←	hybrid sensory kinase in two‑component regulatory system with RcsB and YojN
RA	2,319,586	C→T	9.5%	A97A (GCG→GCA)	rcsC ←	hybrid sensory kinase in two‑component regulatory system with RcsB and YojN
RA	2,347,167	G→A	5.4%	intergenic (+17/‑217)	nrdA → / → nrdB	ribonucleoside‑diphosphate reductase 1, alpha subunit/ribonucleoside‑diphosphate reductase 1, beta subunit, ferritin‑like protein
RA	2,347,168	C→A	5.1%	intergenic (+18/‑216)	nrdA → / → nrdB	ribonucleoside‑diphosphate reductase 1, alpha subunit/ribonucleoside‑diphosphate reductase 1, beta subunit, ferritin‑like protein
RA	2,347,174	A→T	5.1%	intergenic (+24/‑210)	nrdA → / → nrdB	ribonucleoside‑diphosphate reductase 1, alpha subunit/ribonucleoside‑diphosphate reductase 1, beta subunit, ferritin‑like protein
RA	2,347,181	T→G	5.1%	intergenic (+31/‑203)	nrdA → / → nrdB	ribonucleoside‑diphosphate reductase 1, alpha subunit/ribonucleoside‑diphosphate reductase 1, beta subunit, ferritin‑like protein
RA	2,347,182	T→C	5.2%	intergenic (+32/‑202)	nrdA → / → nrdB	ribonucleoside‑diphosphate reductase 1, alpha subunit/ribonucleoside‑diphosphate reductase 1, beta subunit, ferritin‑like protein
RA	2,356,734	G→C	6.7%	intergenic (+23/‑170)	glpC → / → yfaD	anaerobic sn‑glycerol‑3‑phosphate dehydrogenase, C subunit, 4Fe‑4S iron‑sulfur cluster/transposase_31 family protein
RA	2,356,737	T→C	7.0%	intergenic (+26/‑167)	glpC → / → yfaD	anaerobic sn‑glycerol‑3‑phosphate dehydrogenase, C subunit, 4Fe‑4S iron‑sulfur cluster/transposase_31 family protein
RA	2,356,738	G→A	6.9%	intergenic (+27/‑166)	glpC → / → yfaD	anaerobic sn‑glycerol‑3‑phosphate dehydrogenase, C subunit, 4Fe‑4S iron‑sulfur cluster/transposase_31 family protein
RA	2,356,741	G→C	7.0%	intergenic (+30/‑163)	glpC → / → yfaD	anaerobic sn‑glycerol‑3‑phosphate dehydrogenase, C subunit, 4Fe‑4S iron‑sulfur cluster/transposase_31 family protein
RA	2,357,665	G→A	7.6%	G254G (GGG→GGA)	yfaD →	transposase_31 family protein
RA	2,364,995	T→G	8.9%	intergenic (+16/+23)	nudI → / ← ais	nucleoside triphosphatase/putative LPS core heptose(II)‑phosphate phosphatase
RA	2,364,998	C→A	9.4%	intergenic (+19/+20)	nudI → / ← ais	nucleoside triphosphatase/putative LPS core heptose(II)‑phosphate phosphatase
RA	2,366,010:1	+T	5.5%	coding (83/1140 nt)	arnB →	uridine 5'‑(beta‑1‑threo‑pentapyranosyl‑4‑ulose diphosphate) aminotransferase, PLP‑dependent
RA	2,366,015	Δ1 bp	5.4%	coding (88/1140 nt)	arnB →	uridine 5'‑(beta‑1‑threo‑pentapyranosyl‑4‑ulose diphosphate) aminotransferase, PLP‑dependent
RA	2,391,414	C→G	6.5%	R31P (CGA→CCA)	nuoN ←	NADH:ubiquinone oxidoreductase, membrane subunit N
RA	2,391,417	C→G	7.3%	W30S (TGG→TCG)	nuoN ←	NADH:ubiquinone oxidoreductase, membrane subunit N
RA	2,399,828	T→G	5.4%	H113P (CAT→CCT)	nuoG ←	NADH:ubiquinone oxidoreductase, chain G
RA	2,399,878	C→G	5.0%	M96I (ATG→ATC)	nuoG ←	NADH:ubiquinone oxidoreductase, chain G
RA	2,407,890	Δ1 bp	5.6%	coding (330/1218 nt)	alaA →	glutamate‑pyruvate aminotransferase; glutamic‑pyruvic transaminase (GPT); alanine transaminase
RA	2,407,898	A→C	7.1%	Q113P (CAG→CCG) ‡	alaA →	glutamate‑pyruvate aminotransferase; glutamic‑pyruvic transaminase (GPT); alanine transaminase
RA	2,407,899	G→T	7.3%	Q113H (CAG→CAT) ‡	alaA →	glutamate‑pyruvate aminotransferase; glutamic‑pyruvic transaminase (GPT); alanine transaminase
RA	2,413,009	T→A	5.5%	K42* (AAG→TAG)	yfbV ←	UPF0208 family inner membrane protein
RA	2,428,039	A→T	5.8%	intergenic (‑248/+18)	argT ← / ← ubiX	lysine/arginine/ornithine transporter subunit/3‑octaprenyl‑4‑hydroxybenzoate carboxy‑lyase
RA	2,438,862	A→G	5.1%	T305A (ACG→GCG)	flk →	putative flagella assembly protein
RA	2,449,615	C→G	5.2%	G145G (GGG→GGC) ‡	yfcO ←	DUF2544 family putative outer membrane protein
RA	2,449,616	C→G	5.8%	G145A (GGG→GCG) ‡	yfcO ←	DUF2544 family putative outer membrane protein
RA	2,449,624	Δ1 bp	5.2%	coding (426/822 nt)	yfcO ←	DUF2544 family putative outer membrane protein
RA	2,462,677	A→T	6.8%	intergenic (+31/‑335)	fadL → / → yfdF	long‑chain fatty acid outer membrane transporter/uncharacterized protein
RA	2,462,678	T→A	6.9%	intergenic (+32/‑334)	fadL → / → yfdF	long‑chain fatty acid outer membrane transporter/uncharacterized protein
RA	2,462,679	A→T	6.6%	intergenic (+33/‑333)	fadL → / → yfdF	long‑chain fatty acid outer membrane transporter/uncharacterized protein
RA	2,464,228	C→A	7.7%	intergenic (+158/+24)	yfdF → / ← mlaA	uncharacterized protein/ABC transporter maintaining OM lipid asymmetry, OM lipoprotein component
RA	2,470,480	A→T	6.0%	intergenic (+18/‑335)	gtrS → / → tfaS	serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage/pseudogene, CPS‑53 (KpLE1) prophage; tail fiber assembly protein fragment;Phage or Prophage Related
RA	2,470,482	C→A	7.9%	intergenic (+20/‑333)	gtrS → / → tfaS	serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage/pseudogene, CPS‑53 (KpLE1) prophage; tail fiber assembly protein fragment;Phage or Prophage Related
RA	2,470,483	A→T	5.3%	intergenic (+21/‑332)	gtrS → / → tfaS	serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage/pseudogene, CPS‑53 (KpLE1) prophage; tail fiber assembly protein fragment;Phage or Prophage Related
RA	2,474,878	T→C	5.3%	intergenic (+22/‑106)	yfdQ → / → yfdR	CPS‑53 (KpLE1) prophage; uncharacterized protein/CPS‑53 (KpLE1) prophage; conserved protein
RA	2,477,014	C→A	8.6%	A206S (GCA→TCA)	dsdC ←	dsd operon activator; autorepressor
RA	2,503,518	G→T	8.7%	A323D (GCC→GAC) ‡	fryA ←	putative PTS enzyme: Hpr, enzyme I and IIA components
RA	2,503,519	C→T	7.0%	A323T (GCC→ACC) ‡	fryA ←	putative PTS enzyme: Hpr, enzyme I and IIA components
RA	2,503,522	A→G	7.1%	Y322H (TAT→CAT)	fryA ←	putative PTS enzyme: Hpr, enzyme I and IIA components
RA	2,503,523	A→C	7.6%	R321R (CGT→CGG)	fryA ←	putative PTS enzyme: Hpr, enzyme I and IIA components
RA	2,512,728	C→A	5.7%	intergenic (‑22/‑314)	mntH ← / → nupC	manganese/divalent cation transporter/nucleoside (except guanosine) transporter
RA	2,521,346	A→T	5.0%	intergenic (+18/+247)	lysV → / ← xapR	tRNA‑Lys/transcriptional activator of xapAB
RA	2,560,326	A→G	5.2%	T24A (ACA→GCA)	yffL →	CPZ‑55 prophage; uncharacterized protein
RA	2,560,330	G→T	5.7%	C25F (TGC→TTC)	yffL →	CPZ‑55 prophage; uncharacterized protein
RA	2,592,990	A→C	8.6%	intergenic (+28/+82)	ypfN → / ← ypfH	putative membrane protein, UPF0370 family/palmitoyl‑CoA esterase activity, uncertain physiological substrate
RA	2,593,004	C→T	7.6%	intergenic (+42/+68)	ypfN → / ← ypfH	putative membrane protein, UPF0370 family/palmitoyl‑CoA esterase activity, uncertain physiological substrate
RA	2,611,517	A→G	5.0%	S21G (AGC→GGC)	hyfJ →	putative processing element hydrogenase 4
RA	2,620,216	C→T	7.5%	intergenic (‑56/+30)	uraA ← / ← upp	uracil permease/uracil phosphoribosyltransferase
RA	2,620,218	T→A	7.1%	intergenic (‑58/+28)	uraA ← / ← upp	uracil permease/uracil phosphoribosyltransferase
RA	2,620,220	A→G	7.1%	intergenic (‑60/+26)	uraA ← / ← upp	uracil permease/uracil phosphoribosyltransferase
RA	2,648,446	Δ1 bp	7.3%	coding (3842/4962 nt)	yfhM ←	bacterial alpha2‑macroglobulin colonization factor ECAM; anti‑host protease defense factor; periplasmic inner membrane‑anchored lipoprotein
RA	2,648,452	C→A	8.5%	G1279V (GGT→GTT)	yfhM ←	bacterial alpha2‑macroglobulin colonization factor ECAM; anti‑host protease defense factor; periplasmic inner membrane‑anchored lipoprotein
RA	2,648,455	C→G	8.3%	R1278P (CGG→CCG)	yfhM ←	bacterial alpha2‑macroglobulin colonization factor ECAM; anti‑host protease defense factor; periplasmic inner membrane‑anchored lipoprotein
RA	2,648,458	T→G	9.6%	N1277T (AAC→ACC)	yfhM ←	bacterial alpha2‑macroglobulin colonization factor ECAM; anti‑host protease defense factor; periplasmic inner membrane‑anchored lipoprotein
RA	2,648,463:1	+A	8.3%	coding (3825/4962 nt)	yfhM ←	bacterial alpha2‑macroglobulin colonization factor ECAM; anti‑host protease defense factor; periplasmic inner membrane‑anchored lipoprotein
RA	2,654,142	T→A	5.6%	noncoding (288/304 nt)	ryfA →	novel sRNA, function unknown
RA	2,654,143	T→A	5.1%	noncoding (289/304 nt)	ryfA →	novel sRNA, function unknown
RA	2,673,783	G→A	6.0%	intergenic (+15/+33)	yphA → / ← yphB	DoxX family inner membrane protein/mutarotase superfamily protein, YphB family
RA	2,673,784	C→A	7.9%	intergenic (+16/+32)	yphA → / ← yphB	DoxX family inner membrane protein/mutarotase superfamily protein, YphB family
RA	2,681,967	T→C	6.4%	Y260C (TAC→TGC)	yphG ←	DUF4380 domain‑containing TPR repeat protein
RA	2,681,969	C→G	6.3%	Q259H (CAG→CAC) ‡	yphG ←	DUF4380 domain‑containing TPR repeat protein
RA	2,681,971	G→A	6.2%	Q259* (CAG→TAG) ‡	yphG ←	DUF4380 domain‑containing TPR repeat protein
RA	2,700,862	G→A	5.5%	P46L (CCG→CTG) ‡	acpS ←	holo‑[acyl‑carrier‑protein] synthase 1
RA	2,700,863	G→C	5.3%	P46A (CCG→GCG) ‡	acpS ←	holo‑[acyl‑carrier‑protein] synthase 1
RA	2,700,865	T→A	5.1%	Q45L (CAG→CTG)	acpS ←	holo‑[acyl‑carrier‑protein] synthase 1
RA	2,700,867	G→C	5.8%	H44Q (CAC→CAG) ‡	acpS ←	holo‑[acyl‑carrier‑protein] synthase 1
RA	2,700,868	T→C	5.8%	H44R (CAC→CGC) ‡	acpS ←	holo‑[acyl‑carrier‑protein] synthase 1
RA	2,704,304	A→G	5.5%	intergenic (‑241/+31)	rnc ← / ← lepB	RNase III/leader peptidase (signal peptidase I)
RA	2,704,306	A→T	5.4%	intergenic (‑243/+29)	rnc ← / ← lepB	RNase III/leader peptidase (signal peptidase I)
RA	2,704,308	C→T	5.6%	intergenic (‑245/+27)	rnc ← / ← lepB	RNase III/leader peptidase (signal peptidase I)
RA	2,724,097	T→A	5.2%	intergenic (+15/‑31)	pssA → / → yfiM	phosphatidylserine synthase; CDP‑diacylglycerol‑serine O‑phosphatidyltransferase/putative lipoprotein
RA	2,724,099	T→G	5.2%	intergenic (+17/‑29)	pssA → / → yfiM	phosphatidylserine synthase; CDP‑diacylglycerol‑serine O‑phosphatidyltransferase/putative lipoprotein
RA	2,724,413	A→T	5.3%	S96C (AGC→TGC)	yfiM →	putative lipoprotein
RA	2,725,837	T→A	5.1%	intergenic (‑91/+232)	kgtP ← / ← rrfG	alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon
RA	2,731,580	C→T	5.3%	intergenic (‑423/+20)	rrsG ← / ← clpB	16S ribosomal RNA of rrnG operon/protein disaggregation chaperone
RA	2,731,581	G→T	5.0%	intergenic (‑424/+19)	rrsG ← / ← clpB	16S ribosomal RNA of rrnG operon/protein disaggregation chaperone
RA	2,731,582	A→C	5.6%	intergenic (‑425/+18)	rrsG ← / ← clpB	16S ribosomal RNA of rrnG operon/protein disaggregation chaperone
RA	2,731,583	A→G	5.1%	intergenic (‑426/+17)	rrsG ← / ← clpB	16S ribosomal RNA of rrnG operon/protein disaggregation chaperone
RA	2,733,927	G→T	5.6%	P83T (CCA→ACA)	clpB ←	protein disaggregation chaperone
RA	2,742,796	A→C	5.1%	E138D (GAA→GAC)	yfiN →	putative membrane‑anchored diguanylate cyclase
RA	2,744,282	G→T	5.2%	S83R (AGC→AGA)	rplS ←	50S ribosomal subunit protein L19
RA	2,756,017	A→C	6.3%	intergenic (+639/‑142)	smpB → / → intA	tmRNA‑binding trans‑translation protein/CP4‑57 prophage; integrase
RA	2,768,609	T→C	9.5%	intergenic (+36/‑56)	yfjP → / → yfjQ	CP4‑57 prophage; 50S ribosome‑binding GTPase family protein/CP4‑57 prophage; uncharacterized protein
RA	2,768,614	A→C	9.8%	intergenic (+41/‑51)	yfjP → / → yfjQ	CP4‑57 prophage; 50S ribosome‑binding GTPase family protein/CP4‑57 prophage; uncharacterized protein
RA	2,768,615	G→T	9.0%	intergenic (+42/‑50)	yfjP → / → yfjQ	CP4‑57 prophage; 50S ribosome‑binding GTPase family protein/CP4‑57 prophage; uncharacterized protein
RA	2,768,620	G→A	9.4%	intergenic (+47/‑45)	yfjP → / → yfjQ	CP4‑57 prophage; 50S ribosome‑binding GTPase family protein/CP4‑57 prophage; uncharacterized protein
RA	2,800,515	C→A	5.0%	intergenic (+40/‑208)	ygaM → / → nrdH	putative membrane‑anchored DUF883 family ribosome‑binding protein/hydrogen donor for NrdEF electron transport system; glutaredoxin‑like protein
RA	2,800,519	T→G	5.4%	intergenic (+44/‑204)	ygaM → / → nrdH	putative membrane‑anchored DUF883 family ribosome‑binding protein/hydrogen donor for NrdEF electron transport system; glutaredoxin‑like protein
RA	2,801,056	A→T	5.7%	N31I (AAT→ATT)	nrdI →	NrdEF cluster assembly flavodoxin
RA	2,807,091	T→C	7.7%	intergenic (+17/‑41)	proW → / → proX	glycine betaine/proline ABC transporter permease/glycine betaine/proline ABC transporter periplasmic binding protein; cold shock protein
RA	2,807,093	A→T	7.6%	intergenic (+19/‑39)	proW → / → proX	glycine betaine/proline ABC transporter permease/glycine betaine/proline ABC transporter periplasmic binding protein; cold shock protein
RA	2,807,095	G→A	7.6%	intergenic (+21/‑37)	proW → / → proX	glycine betaine/proline ABC transporter permease/glycine betaine/proline ABC transporter periplasmic binding protein; cold shock protein
RA	2,815,730	C→T	23.8%	S237N (AGC→AAC)	gshA ←	glutamate‑cysteine ligase
RA	2,818,049	T→A	7.6%	intergenic (‑189/+10)	argQ ← / ← argZ	tRNA‑Arg/tRNA‑Arg
RA	2,822,679	A→C	6.3%	intergenic (‑40/+29)	recX ← / ← recA	regulatory protein for RecA/DNA recombination and repair protein; ssDNA‑dependent ATPase; synaptase; ssDNA and dsDNA binding protein; ATP‑dependent homologous DNA strand exchanger; recombinase A; LexA autocleavage cofactor
RA	2,828,533	A→T	5.1%	intergenic (+17/‑88)	srlD → / → srlM	sorbitol‑6‑phosphate dehydrogenase/sorbitol=responsive srl operon transcriptional activator
RA	2,828,537	A→T	5.8%	intergenic (+21/‑84)	srlD → / → srlM	sorbitol‑6‑phosphate dehydrogenase/sorbitol=responsive srl operon transcriptional activator
RA	2,838,222	A→T	5.9%	intergenic (‑117/+32)	hydN ← / ← ascG	formate dehydrogenase‑H, [4Fe‑4S] ferredoxin subunit/asc operon transcriptional repressor; prpBC operon repressor
RA	2,838,231	A→T	5.7%	intergenic (‑126/+23)	hydN ← / ← ascG	formate dehydrogenase‑H, [4Fe‑4S] ferredoxin subunit/asc operon transcriptional repressor; prpBC operon repressor
RA	2,839,321	C→G	7.8%	intergenic (‑57/‑203)	ascG ← / → ascF	asc operon transcriptional repressor; prpBC operon repressor/cellobiose/arbutin/salicin‑specific PTS enzymes, IIB and IC components
RA	2,839,323	T→A	7.2%	intergenic (‑59/‑201)	ascG ← / → ascF	asc operon transcriptional repressor; prpBC operon repressor/cellobiose/arbutin/salicin‑specific PTS enzymes, IIB and IC components
RA	2,839,324	T→A	7.2%	intergenic (‑60/‑200)	ascG ← / → ascF	asc operon transcriptional repressor; prpBC operon repressor/cellobiose/arbutin/salicin‑specific PTS enzymes, IIB and IC components
RA	2,839,326	C→G	7.7%	intergenic (‑62/‑198)	ascG ← / → ascF	asc operon transcriptional repressor; prpBC operon repressor/cellobiose/arbutin/salicin‑specific PTS enzymes, IIB and IC components
RA	2,894,852	T→G	5.2%	intergenic (+81/+67)	ygcP → / ← ygcQ	putative antiterminator regulatory protein/putative flavoprotein
RA	2,911,007	G→A	7.2%	R29C (CGT→TGT)	mazF ←	mRNA interferase toxin, antitoxin is MazE
RA	2,911,008	A→T	6.6%	H28Q (CAT→CAA) ‡	mazF ←	mRNA interferase toxin, antitoxin is MazE
RA	2,911,009	T→C	7.2%	H28R (CAT→CGT) ‡	mazF ←	mRNA interferase toxin, antitoxin is MazE
RA	2,918,017	C→T	5.8%	intergenic (+204/+28)	barA → / ← gudD	hybrid sensory histidine kinase, in two‑component regulatory system with UvrY/D‑glucarate dehydratase 1
RA	2,918,019	G→T	5.8%	intergenic (+206/+26)	barA → / ← gudD	hybrid sensory histidine kinase, in two‑component regulatory system with UvrY/D‑glucarate dehydratase 1
RA	2,918,020	A→C	6.4%	intergenic (+207/+25)	barA → / ← gudD	hybrid sensory histidine kinase, in two‑component regulatory system with UvrY/D‑glucarate dehydratase 1
RA	2,918,022	A→G	5.9%	intergenic (+209/+23)	barA → / ← gudD	hybrid sensory histidine kinase, in two‑component regulatory system with UvrY/D‑glucarate dehydratase 1
RA	2,931,836	T→G	5.4%	intergenic (+26/+29)	ygdG → / ← fucO	Ssb‑binding protein, misidentified as ExoIX/L‑1,2‑propanediol oxidoreductase
RA	2,961,248	A→T	6.1%	L394Q (CTG→CAG)	recC ←	exonuclease V (RecBCD complex), gamma chain
RA	2,961,251	A→T	6.6%	L393Q (CTG→CAG)	recC ←	exonuclease V (RecBCD complex), gamma chain
RA	2,976,754	T→G	5.9%	R52R (CGT→CGG)	galR →	galactose‑inducible d‑galactose regulon transcriptional repressor; autorepressor
RA	2,976,758	C→T	6.4%	L54L (CTG→TTG)	galR →	galactose‑inducible d‑galactose regulon transcriptional repressor; autorepressor
RA	2,980,742	A→G	5.4%	intergenic (‑107/+22)	ygeA ← / ← araE	Asp/Glu_racemase family protein/arabinose transporter
RA	2,980,744	A→T	5.7%	intergenic (‑109/+20)	ygeA ← / ← araE	Asp/Glu_racemase family protein/arabinose transporter
RA	2,980,746	C→T	5.6%	intergenic (‑111/+18)	ygeA ← / ← araE	Asp/Glu_racemase family protein/arabinose transporter
RA	2,987,103	C→T	5.7%	intergenic (+27/‑433)	yqeG → / → yqeH	putative transporter/putative LuxR family transcriptional regulator
RA	2,987,104	T→A	5.7%	intergenic (+28/‑432)	yqeG → / → yqeH	putative transporter/putative LuxR family transcriptional regulator
RA	2,987,105	A→G	5.6%	intergenic (+29/‑431)	yqeG → / → yqeH	putative transporter/putative LuxR family transcriptional regulator
RA	3,020,510	G→T	6.9%	intergenic (+21/‑30)	ssnA → / → ygfM	putative chlorohydrolase/aminohydrolase/putative oxidoreductase
RA	3,020,511	C→G	7.8%	intergenic (+22/‑29)	ssnA → / → ygfM	putative chlorohydrolase/aminohydrolase/putative oxidoreductase
RA	3,020,512	A→C	6.5%	intergenic (+23/‑28)	ssnA → / → ygfM	putative chlorohydrolase/aminohydrolase/putative oxidoreductase
RA	3,045,124	T→C	7.0%	intergenic (+23/+34)	bglA → / ← ygfF	6‑phospho‑beta‑glucosidase A/putative NAD(P)‑dependent oxidoreductase
RA	3,045,126	C→A	6.8%	intergenic (+25/+32)	bglA → / ← ygfF	6‑phospho‑beta‑glucosidase A/putative NAD(P)‑dependent oxidoreductase
RA	3,045,127	T→G	7.9%	intergenic (+26/+31)	bglA → / ← ygfF	6‑phospho‑beta‑glucosidase A/putative NAD(P)‑dependent oxidoreductase
RA	3,045,129	G→A	7.4%	intergenic (+28/+29)	bglA → / ← ygfF	6‑phospho‑beta‑glucosidase A/putative NAD(P)‑dependent oxidoreductase
RA	3,066,308	A→T	6.1%	I289N (ATT→AAT) ‡	ygfI ←	putative DNA‑binding transcriptional regulator
RA	3,066,309	T→A	6.5%	I289F (ATT→TTT) ‡	ygfI ←	putative DNA‑binding transcriptional regulator
RA	3,066,310	A→T	6.5%	H288Q (CAT→CAA)	ygfI ←	putative DNA‑binding transcriptional regulator
RA	3,079,615	C→T	5.9%	intergenic (‑285/+29)	cmtB ← / ← tktA	putative mannitol‑specific enzyme IIA component of PTS/transketolase 1, thiamine triphosphate‑binding
RA	3,079,616	G→T	5.7%	intergenic (‑286/+28)	cmtB ← / ← tktA	putative mannitol‑specific enzyme IIA component of PTS/transketolase 1, thiamine triphosphate‑binding
RA	3,079,617	A→C	5.7%	intergenic (‑287/+27)	cmtB ← / ← tktA	putative mannitol‑specific enzyme IIA component of PTS/transketolase 1, thiamine triphosphate‑binding
RA	3,079,618	A→G	5.7%	intergenic (‑288/+26)	cmtB ← / ← tktA	putative mannitol‑specific enzyme IIA component of PTS/transketolase 1, thiamine triphosphate‑binding
RA	3,140,351	C→T	5.8%	R150H (CGC→CAC) ‡	hybE ←	hydrogenase 2‑specific chaperone
RA	3,140,352	G→C	5.8%	R150G (CGC→GGC) ‡	hybE ←	hydrogenase 2‑specific chaperone
RA	3,140,353	A→G	5.9%	R149R (CGT→CGC)	hybE ←	hydrogenase 2‑specific chaperone
RA	3,156,590	C→A	6.9%	intergenic (+72/‑33)	yqhD → / → dkgA	aldehyde reductase, NADPH‑dependent/2,5‑diketo‑D‑gluconate reductase A
RA	3,156,591	T→G	7.0%	intergenic (+73/‑32)	yqhD → / → dkgA	aldehyde reductase, NADPH‑dependent/2,5‑diketo‑D‑gluconate reductase A
RA	3,171,857	A→T	5.3%	intergenic (+24/+22)	qseC → / ← ygiZ	quorum sensing sensory histidine kinase in two‑component regulatory system with QseB/inner membrane protein
RA	3,181,603	C→T	5.3%	intergenic (+22/+16)	ygiC → / ← ygiD	ATP‑Grasp family ATPase/4,5‑ DOPA‑extradiol‑dioxygenase
RA	3,183,345:1	+T	5.8%	intergenic (+22/+468)	zupT → / ← ribB	zinc transporter/3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase
RA	3,183,350	Δ1 bp	5.7%	intergenic (+27/+463)	zupT → / ← ribB	zinc transporter/3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase
RA	3,202,009	A→T	6.7%	Q40L (CAG→CTG)	cca →	fused tRNA nucleotidyl transferase/2'3'‑cyclic phosphodiesterase/2'nucleotidase and phosphatase
RA	3,202,685	A→G	5.6%	E265E (GAA→GAG)	cca →	fused tRNA nucleotidyl transferase/2'3'‑cyclic phosphodiesterase/2'nucleotidase and phosphatase
RA	3,233,153	A→T	5.7%	K497* (AAA→TAA) ‡	fadH →	2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked
RA	3,233,154	A→T	5.1%	K497I (AAA→ATA) ‡	fadH →	2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked
RA	3,233,155	A→T	5.2%	K497N (AAA→AAT) ‡	fadH →	2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked
RA	3,233,708	A→G	6.9%	intergenic (+25/+20)	fadH → / ← higA	2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked/antitoxinof the HigB‑HigA toxin‑antitoxin system
RA	3,233,710	C→T	5.9%	intergenic (+27/+18)	fadH → / ← higA	2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked/antitoxinof the HigB‑HigA toxin‑antitoxin system
RA	3,241,781	C→T	5.6%	intergenic (‑37/+46)	ygjV ← / ← uxaA	Imp‑YgjV family inner membrane protein/altronate hydrolase
RA	3,241,786	C→T	5.6%	intergenic (‑42/+41)	ygjV ← / ← uxaA	Imp‑YgjV family inner membrane protein/altronate hydrolase
RA	3,241,788	T→A	5.4%	intergenic (‑44/+39)	ygjV ← / ← uxaA	Imp‑YgjV family inner membrane protein/altronate hydrolase
RA	3,241,790	A→G	5.4%	intergenic (‑46/+37)	ygjV ← / ← uxaA	Imp‑YgjV family inner membrane protein/altronate hydrolase
RA	3,241,795	A→G	5.6%	intergenic (‑51/+32)	ygjV ← / ← uxaA	Imp‑YgjV family inner membrane protein/altronate hydrolase
RA	3,250,990	A→T	5.1%	intergenic (+36/‑34)	yqjF → / → yqjG	putative quinol oxidase subunit/putative S‑transferase
RA	3,256,441	T→G	9.0%	T71P (ACG→CCG)	yhaM ←	putative L‑serine dehydratase alpha chain
RA	3,256,442	G→C	8.1%	G70G (GGC→GGG) ‡	yhaM ←	putative L‑serine dehydratase alpha chain
RA	3,256,443	C→A	8.1%	G70V (GGC→GTC) ‡	yhaM ←	putative L‑serine dehydratase alpha chain
RA	3,256,450	C→T	7.6%	V68I (GTT→ATT)	yhaM ←	putative L‑serine dehydratase alpha chain
RA	3,263,500	G→A	9.5%	P54L (CCG→CTG) ‡	tdcD ←	propionate kinase/acetate kinase C, anaerobic
RA	3,263,501	G→C	9.8%	P54A (CCG→GCG) ‡	tdcD ←	propionate kinase/acetate kinase C, anaerobic
RA	3,263,502	T→C	9.2%	A53A (GCA→GCG)	tdcD ←	propionate kinase/acetate kinase C, anaerobic
RA	3,281,719	C→A	5.6%	intergenic (+94/‑257)	agaA → / → agaS	pseudogene, N‑acetylgalactosamine‑6‑phosphate deacetylase fragment; putative N‑acetylgalactosamine‑6‑phosphate deacetylase/tagatose‑6‑phosphate ketose/aldose isomerase
RA	3,282,927	A→G	5.2%	I318V (ATC→GTC) ‡	agaS →	tagatose‑6‑phosphate ketose/aldose isomerase
RA	3,282,928	T→A	5.3%	I318N (ATC→AAC) ‡	agaS →	tagatose‑6‑phosphate ketose/aldose isomerase
RA	3,282,929	C→T	5.3%	I318I (ATC→ATT) ‡	agaS →	tagatose‑6‑phosphate ketose/aldose isomerase
RA	3,288,032	C→A	6.0%	intergenic (+22/‑58)	yraH → / → yraI	putative fimbrial‑like adhesin protein/putative periplasmic pilin chaperone
RA	3,288,033	T→G	5.9%	intergenic (+23/‑57)	yraH → / → yraI	putative fimbrial‑like adhesin protein/putative periplasmic pilin chaperone
RA	3,316,740	A→G	7.8%	S263P (TCT→CCT)	nusA ←	transcription termination/antitermination L factor
RA	3,334,704	G→C	6.5%	intergenic (+23/‑205)	ispB → / → sfsB	octaprenyl diphosphate synthase/malPQ operon transcriptional activator
RA	3,368,982	G→C	5.3%	intergenic (+28/+32)	yhcG → / ← yhcH	DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily/DUF386 family protein, cupin superfamily
RA	3,370,703	G→A	6.1%	P112S (CCG→TCG)	nanE ←	putative N‑acetylmannosamine‑6‑P epimerase
RA	3,370,704	A→C	7.6%	R111R (CGT→CGG)	nanE ←	putative N‑acetylmannosamine‑6‑P epimerase
RA	3,370,708	G→C	6.5%	P110R (CCG→CGG) ‡	nanE ←	putative N‑acetylmannosamine‑6‑P epimerase
RA	3,370,709	G→C	6.5%	P110A (CCG→GCG) ‡	nanE ←	putative N‑acetylmannosamine‑6‑P epimerase
RA	3,370,713	G→T	7.2%	D108E (GAC→GAA) ‡	nanE ←	putative N‑acetylmannosamine‑6‑P epimerase
RA	3,370,714	T→C	6.7%	D108G (GAC→GGC) ‡	nanE ←	putative N‑acetylmannosamine‑6‑P epimerase
RA	3,392,189	T→G	5.1%	intergenic (‑161/+269)	tldD ← / ← yhdP	putative peptidase/DUF3971‑AsmA2 domains protein
RA	3,392,320	A→C	5.5%	intergenic (‑292/+138)	tldD ← / ← yhdP	putative peptidase/DUF3971‑AsmA2 domains protein
RA	3,397,961	T→G	5.6%	S140R (AGC→CGC)	yhdE ←	dTTP/UTP pyrophosphatase; m(5)UTP/m(5)CTP/pseudo‑UTP pyrophosphatase
RA	3,397,965	G→T	5.6%	V138V (GTC→GTA) ‡	yhdE ←	dTTP/UTP pyrophosphatase; m(5)UTP/m(5)CTP/pseudo‑UTP pyrophosphatase
RA	3,397,967	C→T	5.6%	V138I (GTC→ATC) ‡	yhdE ←	dTTP/UTP pyrophosphatase; m(5)UTP/m(5)CTP/pseudo‑UTP pyrophosphatase
RA	3,397,968	A→G	5.6%	Y137Y (TAT→TAC) ‡	yhdE ←	dTTP/UTP pyrophosphatase; m(5)UTP/m(5)CTP/pseudo‑UTP pyrophosphatase
RA	3,397,970	A→C	6.2%	Y137D (TAT→GAT) ‡	yhdE ←	dTTP/UTP pyrophosphatase; m(5)UTP/m(5)CTP/pseudo‑UTP pyrophosphatase
RA	3,397,974	C→A	5.4%	A135A (GCG→GCT)	yhdE ←	dTTP/UTP pyrophosphatase; m(5)UTP/m(5)CTP/pseudo‑UTP pyrophosphatase
RA	3,430,942	A→C	5.5%	F158L (TTT→TTG)	tsaC ←	tRNA(ANN) t(6)A37 threonylcarbamoyladenosine modification protein, threonine‑dependent ADP‑forming ATPase
RA	3,448,276	T→A	6.3%	intergenic (‑127/+38)	rplN ← / ← rpsQ	50S ribosomal subunit protein L14/30S ribosomal subunit protein S17
RA	3,458,110	C→A	100%	T578T (ACC→ACA)	gspD →	general secretory pathway component, cryptic
RA	3,482,325	G→A	100%	R346H (CGC→CAC)	yheS →	ABC‑F family protein predicted regulatory ATPase
RA	3,510,359	C→A	5.5%	L206F (TTG→TTT)	yhfX ←	putative pyridoxal 5'‑phosphate binding protein
RA	3,510,363	A→G	6.9%	V205A (GTT→GCT) ‡	yhfX ←	putative pyridoxal 5'‑phosphate binding protein
RA	3,510,364	C→T	5.8%	V205I (GTT→ATT) ‡	yhfX ←	putative pyridoxal 5'‑phosphate binding protein
RA	3,510,368	T→G	6.5%	G203G (GGA→GGC)	yhfX ←	putative pyridoxal 5'‑phosphate binding protein
RA	3,528,479	T→G	6.6%	Y671D (TAC→GAC) ‡	yrfF →	putative RcsCDB‑response attenuator, inner membrane protein
RA	3,528,480	A→T	7.1%	Y671F (TAC→TTC) ‡	yrfF →	putative RcsCDB‑response attenuator, inner membrane protein
RA	3,528,481	C→A	6.3%	Y671* (TAC→TAA) ‡	yrfF →	putative RcsCDB‑response attenuator, inner membrane protein
RA	3,530,671	A→C	5.1%	intergenic (+19/+44)	hslO → / ← yhgE	heat shock protein Hsp33/DUF4153 family putative inner membrane protein
RA	3,530,672	G→C	5.5%	intergenic (+20/+43)	hslO → / ← yhgE	heat shock protein Hsp33/DUF4153 family putative inner membrane protein
RA	3,530,673	G→C	5.8%	intergenic (+21/+42)	hslO → / ← yhgE	heat shock protein Hsp33/DUF4153 family putative inner membrane protein
RA	3,530,674	G→T	6.1%	intergenic (+22/+41)	hslO → / ← yhgE	heat shock protein Hsp33/DUF4153 family putative inner membrane protein
RA	3,539,815	A→T	6.6%	intergenic (+109/‑348)	yhgF → / → feoA	putative transcriptional accessory protein/ferrous iron transporter, protein A
RA	3,539,816	T→A	6.5%	intergenic (+110/‑347)	yhgF → / → feoA	putative transcriptional accessory protein/ferrous iron transporter, protein A
RA	3,539,817	A→T	5.9%	intergenic (+111/‑346)	yhgF → / → feoA	putative transcriptional accessory protein/ferrous iron transporter, protein A
RA	3,560,455:1	+G	100%	intergenic (‑2/+1)	glpR ← / ← glpR	pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon
RA	3,566,218	C→G	5.4%	G122R (GGT→CGT)	glgP ←	glycogen phosphorylase
RA	3,570,878	A→G	5.1%	W148R (TGG→CGG)	glgX ←	glycogen debranching enzyme
RA	3,570,880	G→C	5.2%	P147R (CCG→CGG)	glgX ←	glycogen debranching enzyme
RA	3,570,884	T→C	5.2%	T146A (ACG→GCG)	glgX ←	glycogen debranching enzyme
RA	3,570,885	G→A	5.1%	R145R (CGC→CGT)	glgX ←	glycogen debranching enzyme
RA	3,570,889	G→C	5.4%	P144R (CCG→CGG)	glgX ←	glycogen debranching enzyme
RA	3,570,891	C→T	5.3%	P143P (CCG→CCA)	glgX ←	glycogen debranching enzyme
RA	3,599,756	A→G	5.5%	intergenic (‑98/+173)	livJ ← / ← rpoH	branched‑chain amino acid ABC transporter periplasmic binding protein/RNA polymerase, sigma 32 (sigma H) factor
RA	3,599,759	C→T	5.4%	intergenic (‑101/+170)	livJ ← / ← rpoH	branched‑chain amino acid ABC transporter periplasmic binding protein/RNA polymerase, sigma 32 (sigma H) factor
RA	3,599,760	T→G	6.0%	intergenic (‑102/+169)	livJ ← / ← rpoH	branched‑chain amino acid ABC transporter periplasmic binding protein/RNA polymerase, sigma 32 (sigma H) factor
RA	3,600,988	T→A	6.6%	intergenic (‑205/+40)	rpoH ← / ← ftsX	RNA polymerase, sigma 32 (sigma H) factor/putative ABC transporter permease
RA	3,600,990	C→T	6.7%	intergenic (‑207/+38)	rpoH ← / ← ftsX	RNA polymerase, sigma 32 (sigma H) factor/putative ABC transporter permease
RA	3,600,993	A→G	6.5%	intergenic (‑210/+35)	rpoH ← / ← ftsX	RNA polymerase, sigma 32 (sigma H) factor/putative ABC transporter permease
RA	3,600,994	A→T	6.7%	intergenic (‑211/+34)	rpoH ← / ← ftsX	RNA polymerase, sigma 32 (sigma H) factor/putative ABC transporter permease
RA	3,600,995	C→T	6.2%	intergenic (‑212/+33)	rpoH ← / ← ftsX	RNA polymerase, sigma 32 (sigma H) factor/putative ABC transporter permease
RA	3,600,998	A→G	6.2%	intergenic (‑215/+30)	rpoH ← / ← ftsX	RNA polymerase, sigma 32 (sigma H) factor/putative ABC transporter permease
RA	3,601,000	T→A	6.1%	intergenic (‑217/+28)	rpoH ← / ← ftsX	RNA polymerase, sigma 32 (sigma H) factor/putative ABC transporter permease
RA	3,614,830	G→A	8.1%	Q388Q (CAG→CAA)	nikA →	nickel/heme ABC transporter periplasmic binding protein
RA	3,614,831	A→T	7.9%	I389F (ATT→TTT) ‡	nikA →	nickel/heme ABC transporter periplasmic binding protein
RA	3,614,832	T→C	8.2%	I389T (ATT→ACT) ‡	nikA →	nickel/heme ABC transporter periplasmic binding protein
RA	3,616,399	T→G	5.9%	V73G (GTG→GGG)	nikC →	nickel ABC transporter permease
RA	3,648,128	G→T	5.0%	noncoding (66/84 nt)	agrA →	inactive antisense sRNA
RA	3,648,129	C→T	5.1%	noncoding (67/84 nt)	agrA →	inactive antisense sRNA
RA	3,648,130	A→T	6.4%	noncoding (68/84 nt)	agrA →	inactive antisense sRNA
RA	3,657,599	T→A	7.4%	intergenic (+32/+387)	hdeD → / ← arrS	acid‑resistance membrane protein/antisense sRNA ArrS, function unknown
RA	3,657,601	G→C	7.3%	intergenic (+34/+385)	hdeD → / ← arrS	acid‑resistance membrane protein/antisense sRNA ArrS, function unknown
RA	3,657,603	T→A	8.1%	intergenic (+36/+383)	hdeD → / ← arrS	acid‑resistance membrane protein/antisense sRNA ArrS, function unknown
RA	3,702,835	G→A	5.9%	L12L (CTG→TTG)	dppF ←	dipeptide/heme ABC transporter ATPas
RA	3,702,837	G→C	6.0%	P11R (CCG→CGG)	dppF ←	dipeptide/heme ABC transporter ATPas
RA	3,702,839	T→C	6.3%	Q10Q (CAA→CAG)	dppF ←	dipeptide/heme ABC transporter ATPas
RA	3,728,215	T→A	5.9%	K386I (AAA→ATA)	xylB ←	xylulokinase
RA	3,728,217	A→T	5.4%	I385I (ATT→ATA) ‡	xylB ←	xylulokinase
RA	3,728,219	T→A	5.5%	I385F (ATT→TTT) ‡	xylB ←	xylulokinase
RA	3,748,108	T→A	6.1%	F342Y (TTC→TAC)	lyxK →	L‑xylulose kinase
RA	3,748,110	C→A	6.2%	L343M (CTG→ATG) ‡	lyxK →	L‑xylulose kinase
RA	3,748,111	T→G	5.4%	L343R (CTG→CGG) ‡	lyxK →	L‑xylulose kinase
RA	3,748,113	T→A	6.0%	Y344N (TAC→AAC)	lyxK →	L‑xylulose kinase
RA	3,757,939	Δ1 bp	5.2%	intergenic (‑112/+78)	yiaY ← / ← selB	L‑threonine dehydrogenase/selenocysteinyl‑tRNA‑specific translation factor
RA	3,757,942	C→A	7.3%	intergenic (‑115/+75)	yiaY ← / ← selB	L‑threonine dehydrogenase/selenocysteinyl‑tRNA‑specific translation factor
RA	3,757,947:1	+T	5.1%	intergenic (‑120/+70)	yiaY ← / ← selB	L‑threonine dehydrogenase/selenocysteinyl‑tRNA‑specific translation factor
RA	3,760,788	C→G	5.5%	A154A (GCG→GCC)	selA ←	selenocysteine synthase
RA	3,760,792	T→G	6.3%	N153T (AAT→ACT)	selA ←	selenocysteine synthase
RA	3,792,765	C→T	6.9%	intergenic (‑214/+61)	kbl ← / ← yibB	glycine C‑acetyltransferase/YibB family protein, function unknown
RA	3,792,766	A→T	6.0%	intergenic (‑215/+60)	kbl ← / ← yibB	glycine C‑acetyltransferase/YibB family protein, function unknown
RA	3,792,767	A→T	5.9%	intergenic (‑216/+59)	kbl ← / ← yibB	glycine C‑acetyltransferase/YibB family protein, function unknown
RA	3,792,768	A→G	6.2%	intergenic (‑217/+58)	kbl ← / ← yibB	glycine C‑acetyltransferase/YibB family protein, function unknown
RA	3,798,234	A→T	6.2%	intergenic (+27/+5)	waaL → / ← waaU	O‑antigen ligase/lipopolysaccharide core biosynthesis
RA	3,798,235	A→T	7.1%	intergenic (+28/+4)	waaL → / ← waaU	O‑antigen ligase/lipopolysaccharide core biosynthesis
RA	3,809,354	A→G	6.5%	E272G (GAA→GGA)	waaA →	3‑deoxy‑D‑manno‑octulosonic‑acid transferase (KDO transferase)
RA	3,809,356	C→A	6.2%	R273S (CGC→AGC)	waaA →	3‑deoxy‑D‑manno‑octulosonic‑acid transferase (KDO transferase)
RA	3,809,359	T→G	6.3%	F274V (TTC→GTC) ‡	waaA →	3‑deoxy‑D‑manno‑octulosonic‑acid transferase (KDO transferase)
RA	3,809,361	C→T	5.8%	F274F (TTC→TTT) ‡	waaA →	3‑deoxy‑D‑manno‑octulosonic‑acid transferase (KDO transferase)
MC JC	3,815,859	Δ82 bp	100%		[rph]–[rph]	[rph], [rph]
RA	3,880,374	A→T	5.6%	L283Q (CTG→CAG) ‡	recF ←	gap repair protein
RA	3,880,375	G→T	5.6%	L283M (CTG→ATG) ‡	recF ←	gap repair protein
RA	3,880,380	A→C	5.7%	L281* (TTA→TGA) ‡	recF ←	gap repair protein
RA	3,880,381	A→T	5.7%	L281I (TTA→ATA) ‡	recF ←	gap repair protein
RA	3,888,212	Δ1 bp	6.6%	intergenic (+20/‑223)	mnmE → / → tnaC	tRNA U34 5‑methylaminomethyl‑2‑thiouridine modification GTPase/tryptophanase leader peptide
RA	3,888,219	T→A	6.4%	intergenic (+27/‑216)	mnmE → / → tnaC	tRNA U34 5‑methylaminomethyl‑2‑thiouridine modification GTPase/tryptophanase leader peptide
RA	3,888,224:1	+A	6.6%	intergenic (+32/‑211)	mnmE → / → tnaC	tRNA U34 5‑methylaminomethyl‑2‑thiouridine modification GTPase/tryptophanase leader peptide
RA	3,891,504	T→A	5.6%	intergenic (+21/‑111)	tnaB → / → mdtL	tryptophan transporter of low affinity/multidrug efflux system protein
RA	3,891,506	C→G	5.6%	intergenic (+23/‑109)	tnaB → / → mdtL	tryptophan transporter of low affinity/multidrug efflux system protein
RA	3,906,267	G→T	5.4%	H101N (CAT→AAT)	bglG ←	transcriptional antiterminator of the bgl operon
RA	3,906,826	T→C	9.4%	intergenic (‑259/+27)	bglG ← / ← phoU	transcriptional antiterminator of the bgl operon/negative regulator of PhoR/PhoB two‑component regulator
RA	3,906,828	A→T	9.0%	intergenic (‑261/+25)	bglG ← / ← phoU	transcriptional antiterminator of the bgl operon/negative regulator of PhoR/PhoB two‑component regulator
RA	3,906,830	G→A	9.0%	intergenic (‑263/+23)	bglG ← / ← phoU	transcriptional antiterminator of the bgl operon/negative regulator of PhoR/PhoB two‑component regulator
RA	3,918,291	C→T	7.2%	intergenic (‑26/+25)	atpG ← / ← atpA	F1 sector of membrane‑bound ATP synthase, gamma subunit/F1 sector of membrane‑bound ATP synthase, alpha subunit
RA	3,918,296	C→T	7.3%	intergenic (‑31/+20)	atpG ← / ← atpA	F1 sector of membrane‑bound ATP synthase, gamma subunit/F1 sector of membrane‑bound ATP synthase, alpha subunit
RA	3,918,299	A→G	7.1%	intergenic (‑34/+17)	atpG ← / ← atpA	F1 sector of membrane‑bound ATP synthase, gamma subunit/F1 sector of membrane‑bound ATP synthase, alpha subunit
RA	3,918,304	A→G	7.2%	intergenic (‑39/+12)	atpG ← / ← atpA	F1 sector of membrane‑bound ATP synthase, gamma subunit/F1 sector of membrane‑bound ATP synthase, alpha subunit
RA	3,947,051	A→C	6.2%	intergenic (+19/+77)	trpT → / ← hdfR	tRNA‑Trp/flhDC operon transcriptional repressor
RA	3,947,332	A→T	6.4%	A212A (GCT→GCA)	hdfR ←	flhDC operon transcriptional repressor
RA	3,947,335	A→T	7.0%	S211S (TCT→TCA)	hdfR ←	flhDC operon transcriptional repressor
RA	3,966,768	G→T	6.3%	E118* (GAA→TAA) ‡	rho →	transcription termination factor
RA	3,966,769	A→T	6.3%	E118V (GAA→GTA) ‡	rho →	transcription termination factor
RA	3,966,770	A→C	6.5%	E118D (GAA→GAC) ‡	rho →	transcription termination factor
RA	3,980,726	G→A	5.7%	intergenic (+30/‑161)	wecG → / → yifK	UDP‑N‑acetyl‑D‑mannosaminuronic acid transferase/putative APC family amino acid transporter
RA	3,980,727	T→C	5.7%	intergenic (+31/‑160)	wecG → / → yifK	UDP‑N‑acetyl‑D‑mannosaminuronic acid transferase/putative APC family amino acid transporter
RA	3,995,720	G→C	5.2%	P46P (CCG→CCC)	yigA →	DUF484 family protein
RA	4,015,333	A→T	5.8%	intergenic (+19/+21)	metE → / ← ysgA	5‑methyltetrahydropteroyltriglutamate‑ homocysteine S‑methyltransferase/putative carboxymethylenebutenolidase
RA	4,049,986	G→T	9.8%	noncoding (88/109 nt)	spf →	Spot 42 sRNA antisense regulator of galK translation, Hfq‑dependent
RA	4,049,989	A→C	5.8%	noncoding (91/109 nt)	spf →	Spot 42 sRNA antisense regulator of galK translation, Hfq‑dependent
RA	4,051,259	G→T	6.3%	noncoding (224/245 nt)	csrC →	CsrC sRNA sequesters CsrA, a carbon flux regulator
RA	4,051,262	A→C	6.3%	noncoding (227/245 nt)	csrC →	CsrC sRNA sequesters CsrA, a carbon flux regulator
RA	4,070,413	T→G	6.8%	intergenic (‑12/+102)	yihR ← / ← yihS	putative sulphoquinovose mutarotase/sulphoquinovose isomerase
RA	4,074,842	C→T	5.7%	H58H (CAC→CAT)	yihW →	putative transcriptional regulator for sulphoquinovose utilization
RA	4,088,091	G→C	9.0%	intergenic (+34/+16)	yiiG → / ← frvR	DUF3829 family lipoprotein/putative frv operon regulator; contains a PTS EIIA domain
RA	4,092,780	C→A	5.2%	G15V (GGC→GTC)	frvA ←	putative enzyme IIA component of PTS
RA	4,095,842	A→C	5.9%	G47G (GGT→GGG)	rhaA ←	L‑rhamnose isomerase
RA	4,103,527	T→A	5.2%	intergenic (+31/+75)	yiiM → / ← cpxA	6‑N‑hydroxylaminopurine resistance protein/sensory histidine kinase in two‑component regulatory system with CpxR
RA	4,126,129	A→T	6.1%	S228T (TCC→ACC)	priA ←	Primosome factor n' (replication factor Y)
RA	4,126,130	A→T	6.6%	G227G (GGT→GGA)	priA ←	Primosome factor n' (replication factor Y)
RA	4,132,424	T→A	7.3%	intergenic (+157/‑192)	metL → / → metF	Bifunctional aspartokinase/homoserine dehydrogenase 2/5,10‑methylenetetrahydrofolate reductase
RA	4,132,428	T→A	7.3%	intergenic (+161/‑188)	metL → / → metF	Bifunctional aspartokinase/homoserine dehydrogenase 2/5,10‑methylenetetrahydrofolate reductase
RA	4,132,429	T→A	7.3%	intergenic (+162/‑187)	metL → / → metF	Bifunctional aspartokinase/homoserine dehydrogenase 2/5,10‑methylenetetrahydrofolate reductase
RA	4,132,430	T→A	7.8%	intergenic (+163/‑186)	metL → / → metF	Bifunctional aspartokinase/homoserine dehydrogenase 2/5,10‑methylenetetrahydrofolate reductase
RA	4,132,434	T→A	6.5%	intergenic (+167/‑182)	metL → / → metF	Bifunctional aspartokinase/homoserine dehydrogenase 2/5,10‑methylenetetrahydrofolate reductase
RA	4,136,033	G→A	6.6%	intergenic (+18/‑75)	katG → / → yijE	catalase‑peroxidase HPI, heme b‑containing/EamA‑like transporter family protein
RA	4,136,038	T→C	6.7%	intergenic (+23/‑70)	katG → / → yijE	catalase‑peroxidase HPI, heme b‑containing/EamA‑like transporter family protein
RA	4,136,039	T→A	6.6%	intergenic (+24/‑69)	katG → / → yijE	catalase‑peroxidase HPI, heme b‑containing/EamA‑like transporter family protein
RA	4,136,042	T→A	6.7%	intergenic (+27/‑66)	katG → / → yijE	catalase‑peroxidase HPI, heme b‑containing/EamA‑like transporter family protein
RA	4,136,043	G→A	6.5%	intergenic (+28/‑65)	katG → / → yijE	catalase‑peroxidase HPI, heme b‑containing/EamA‑like transporter family protein
RA	4,136,048	T→C	6.6%	intergenic (+33/‑60)	katG → / → yijE	catalase‑peroxidase HPI, heme b‑containing/EamA‑like transporter family protein
RA	4,241,067	C→T	6.3%	S396S (TCG→TCA)	xylE ←	D‑xylose transporter
RA	4,245,108	T→G	6.1%	intergenic (‑33/+121)	malF ← / ← malE	maltose transporter subunit/maltose transporter subunit
RA	4,245,110	T→G	6.2%	intergenic (‑35/+119)	malF ← / ← malE	maltose transporter subunit/maltose transporter subunit
RA	4,245,111	C→A	6.7%	intergenic (‑36/+118)	malF ← / ← malE	maltose transporter subunit/maltose transporter subunit
RA	4,245,113	C→A	6.5%	intergenic (‑38/+116)	malF ← / ← malE	maltose transporter subunit/maltose transporter subunit
RA	4,262,250	G→C	5.4%	G194G (GGG→GGC)	dusA →	tRNA‑dihydrouridine synthase A
RA	4,262,255	G→C	6.5%	S196T (AGC→ACC)	dusA →	tRNA‑dihydrouridine synthase A
RA	4,281,677	T→A	5.2%	intergenic (+48/+106)	yjcE → / ← yjcF	putative cation/proton antiporter/pentapeptide repeats protein
RA	4,281,678	C→A	5.8%	intergenic (+49/+105)	yjcE → / ← yjcF	putative cation/proton antiporter/pentapeptide repeats protein
RA	4,281,679	T→G	5.4%	intergenic (+50/+104)	yjcE → / ← yjcF	putative cation/proton antiporter/pentapeptide repeats protein
RA	4,281,680	T→A	5.3%	intergenic (+51/+103)	yjcE → / ← yjcF	putative cation/proton antiporter/pentapeptide repeats protein
RA	4,296,060	C→T	40.5%	intergenic (+266/+376)	gltP → / ← yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA	4,296,380:1	+CG	100%	intergenic (+586/+56)	gltP → / ← yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA	4,307,294	A→T	9.0%	L169Q (CTG→CAG)	alsK ←	D‑allose kinase
RA	4,307,298	G→A	8.9%	P168S (CCC→TCC)	alsK ←	D‑allose kinase
RA	4,314,233	A→T	5.1%	intergenic (+36/+111)	yjdP → / ← phnP	putative periplasmic protein/5‑phospho‑alpha‑D‑ribosyl 1,2‑cyclic phosphate phosphodiesterase
RA	4,317,977	A→G	5.1%	intergenic (‑82/+29)	phnL ← / ← phnK	ribophosphonate triphosphate synthase subunit; putative ABC transporter‑related ATPase/carbon‑phosphorus lyase complex subunit, putative ATP transporter ATP‑binding protein
RA	4,317,978	A→C	5.6%	intergenic (‑83/+28)	phnL ← / ← phnK	ribophosphonate triphosphate synthase subunit; putative ABC transporter‑related ATPase/carbon‑phosphorus lyase complex subunit, putative ATP transporter ATP‑binding protein
RA	4,317,984	T→A	5.1%	intergenic (‑89/+22)	phnL ← / ← phnK	ribophosphonate triphosphate synthase subunit; putative ABC transporter‑related ATPase/carbon‑phosphorus lyase complex subunit, putative ATP transporter ATP‑binding protein
RA	4,317,991	G→T	5.1%	intergenic (‑96/+15)	phnL ← / ← phnK	ribophosphonate triphosphate synthase subunit; putative ABC transporter‑related ATPase/carbon‑phosphorus lyase complex subunit, putative ATP transporter ATP‑binding protein
RA	4,317,992	C→T	5.4%	intergenic (‑97/+14)	phnL ← / ← phnK	ribophosphonate triphosphate synthase subunit; putative ABC transporter‑related ATPase/carbon‑phosphorus lyase complex subunit, putative ATP transporter ATP‑binding protein
RA	4,332,868	G→T	6.4%	R135R (CGC→CGA)	basS ←	sensory histidine kinase in two‑component regulatory system with BasR
RA	4,332,871	A→C	7.9%	S134R (AGT→AGG)	basS ←	sensory histidine kinase in two‑component regulatory system with BasR
RA	4,336,974	A→T	6.7%	S20T (TCG→ACG)	adiC ←	arginine:agmatine antiporter
RA	4,336,979	A→C	6.0%	M18R (ATG→AGG)	adiC ←	arginine:agmatine antiporter
RA	4,336,981	C→G	6.0%	L17L (CTG→CTC) ‡	adiC ←	arginine:agmatine antiporter
RA	4,336,983	G→T	6.6%	L17M (CTG→ATG) ‡	adiC ←	arginine:agmatine antiporter
RA	4,336,988	A→T	6.1%	V15D (GTC→GAC)	adiC ←	arginine:agmatine antiporter
RA	4,353,170	G→A	6.0%	intergenic (+89/+30)	ghoT → / ← lysU	toxin of GhoTS toxin‑antitoxin pair; membrane‑lytic protein; stimulator of persister cell formation/lysine tRNA synthetase, inducible
RA	4,353,171	C→G	5.6%	intergenic (+90/+29)	ghoT → / ← lysU	toxin of GhoTS toxin‑antitoxin pair; membrane‑lytic protein; stimulator of persister cell formation/lysine tRNA synthetase, inducible
RA	4,353,172	C→G	6.6%	intergenic (+91/+28)	ghoT → / ← lysU	toxin of GhoTS toxin‑antitoxin pair; membrane‑lytic protein; stimulator of persister cell formation/lysine tRNA synthetase, inducible
RA	4,353,173	T→C	6.1%	intergenic (+92/+27)	ghoT → / ← lysU	toxin of GhoTS toxin‑antitoxin pair; membrane‑lytic protein; stimulator of persister cell formation/lysine tRNA synthetase, inducible
RA	4,365,452	G→T	6.2%	intergenic (‑96/+20)	cutA ← / ← dcuA	divalent‑cation tolerance protein, copper sensitivity/C4‑dicarboxylate antiporter
RA	4,365,453	A→C	7.4%	intergenic (‑97/+19)	cutA ← / ← dcuA	divalent‑cation tolerance protein, copper sensitivity/C4‑dicarboxylate antiporter
RA	4,366,854	T→G	6.4%	intergenic (‑81/+37)	dcuA ← / ← aspA	C4‑dicarboxylate antiporter/aspartate ammonia‑lyase
RA	4,366,855	C→A	7.3%	intergenic (‑82/+36)	dcuA ← / ← aspA	C4‑dicarboxylate antiporter/aspartate ammonia‑lyase
RA	4,388,931	T→G	7.4%	D147A (GAC→GCC)	mscM ←	mechanosensitive channel protein, miniconductance
RA	4,390,401	C→A	7.2%	intergenic (‑41/+56)	psd ← / ← rsgA	phosphatidylserine decarboxylase/ribosome small subunit‑dependent GTPase A
RA	4,390,403	A→G	7.5%	intergenic (‑43/+54)	psd ← / ← rsgA	phosphatidylserine decarboxylase/ribosome small subunit‑dependent GTPase A
RA	4,390,404	C→T	7.4%	intergenic (‑44/+53)	psd ← / ← rsgA	phosphatidylserine decarboxylase/ribosome small subunit‑dependent GTPase A
RA	4,390,406	T→G	7.4%	intergenic (‑46/+51)	psd ← / ← rsgA	phosphatidylserine decarboxylase/ribosome small subunit‑dependent GTPase A
RA	4,407,947	G→A	5.3%	E432K (GAA→AAA)	rnr →	exoribonuclease R, RNase R
RA	4,414,234	G→C	7.0%	intergenic (+43/‑41)	yjfC → / → aidB	ATP‑Grasp family ATPase/DNA alkylation damage repair protein; flavin‑containing DNA binding protein, weak isovaleryl CoA dehydrogenase
RA	4,414,240	A→T	6.6%	intergenic (+49/‑35)	yjfC → / → aidB	ATP‑Grasp family ATPase/DNA alkylation damage repair protein; flavin‑containing DNA binding protein, weak isovaleryl CoA dehydrogenase
RA	4,414,241	C→A	5.8%	intergenic (+50/‑34)	yjfC → / → aidB	ATP‑Grasp family ATPase/DNA alkylation damage repair protein; flavin‑containing DNA binding protein, weak isovaleryl CoA dehydrogenase
RA	4,414,242	T→G	6.7%	intergenic (+51/‑33)	yjfC → / → aidB	ATP‑Grasp family ATPase/DNA alkylation damage repair protein; flavin‑containing DNA binding protein, weak isovaleryl CoA dehydrogenase
RA	4,414,243	A→T	7.0%	intergenic (+52/‑32)	yjfC → / → aidB	ATP‑Grasp family ATPase/DNA alkylation damage repair protein; flavin‑containing DNA binding protein, weak isovaleryl CoA dehydrogenase
RA	4,414,249	G→C	6.6%	intergenic (+58/‑26)	yjfC → / → aidB	ATP‑Grasp family ATPase/DNA alkylation damage repair protein; flavin‑containing DNA binding protein, weak isovaleryl CoA dehydrogenase
RA	4,473,927	C→A	100%	A43S (GCC→TCC)	bdcA ←	c‑di‑GMP‑binding biofilm dispersal mediator protein
RA	4,510,334	G→T	6.3%	intergenic (+201/+356)	yjhV → / ← fecE	pseudogene, KpLE2 phage‑like element/ferric citrate ABC transporter ATPase
RA	4,510,335	C→G	6.2%	intergenic (+202/+355)	yjhV → / ← fecE	pseudogene, KpLE2 phage‑like element/ferric citrate ABC transporter ATPase
RA	4,510,336	A→C	6.6%	intergenic (+203/+354)	yjhV → / ← fecE	pseudogene, KpLE2 phage‑like element/ferric citrate ABC transporter ATPase
RA	4,519,311	A→G	5.7%	intergenic (+87/+27)	insB1 → / ← yjhU	IS1 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related/putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element
RA	4,519,313	C→A	5.3%	intergenic (+89/+25)	insB1 → / ← yjhU	IS1 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related/putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element
RA	4,519,314	T→G	5.4%	intergenic (+90/+24)	insB1 → / ← yjhU	IS1 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related/putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element
RA	4,519,316	C→T	5.6%	intergenic (+92/+22)	insB1 → / ← yjhU	IS1 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related/putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element
RA	4,520,500	Δ1 bp	6.0%	intergenic (‑176/+171)	yjhU ← / ← yjhF	putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter
RA	4,520,504:1	+T	5.2%	intergenic (‑180/+167)	yjhU ← / ← yjhF	putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter
RA	4,523,472	A→C	5.4%	F208C (TTC→TGC)	yjhG ←	putative dehydratase
RA	4,551,422	T→A	6.3%	intergenic (‑126/‑214)	gntP ← / → uxuA	fructuronate transporter/mannonate hydrolase
RA	4,591,498	T→A	8.9%	intergenic (‑219/‑159)	yjiY ← / → tsr	putative transporter/methyl‑accepting chemotaxis protein I, serine sensor receptor
RA	4,591,499	C→T	8.8%	intergenic (‑220/‑158)	yjiY ← / → tsr	putative transporter/methyl‑accepting chemotaxis protein I, serine sensor receptor
RA	4,591,500	A→G	9.2%	intergenic (‑221/‑157)	yjiY ← / → tsr	putative transporter/methyl‑accepting chemotaxis protein I, serine sensor receptor
RA	4,591,501	T→A	10.0%	intergenic (‑222/‑156)	yjiY ← / → tsr	putative transporter/methyl‑accepting chemotaxis protein I, serine sensor receptor
RA	4,608,604	C→G	5.1%	I140M (ATC→ATG)	rimI →	ribosomal‑protein‑S18‑alanine N‑acetyltransferase
RA	4,608,607	C→G	5.7%	I141M (ATC→ATG)	rimI →	ribosomal‑protein‑S18‑alanine N‑acetyltransferase
RA	4,612,329	A→G	6.1%	intergenic (+40/‑82)	ytjA → / → yjjU	uncharacterized protein/putative patatin‑like family phospholipase
RA	4,612,330	G→C	6.5%	intergenic (+41/‑81)	ytjA → / → yjjU	uncharacterized protein/putative patatin‑like family phospholipase
RA	4,612,331	C→T	6.0%	intergenic (+42/‑80)	ytjA → / → yjjU	uncharacterized protein/putative patatin‑like family phospholipase
RA	4,627,180	T→G	5.4%	G423G (GGT→GGG)	radA →	DNA repair protein
RA	4,627,810	G→T	14.5%	A166S (GCT→TCT)	nadR →	trifunctional protein: nicotinamide mononucleotide adenylyltransferase, ribosylnicotinamide kinase, transcriptional repressor
RA	4,627,828	C→A	12.4%	P172T (CCG→ACG)	nadR →	trifunctional protein: nicotinamide mononucleotide adenylyltransferase, ribosylnicotinamide kinase, transcriptional repressor

Unassigned missing coverage evidence
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	448619	450690	2072	60 [59]	[59] 60	[cyoC]–[cyoA]	[cyoC],cyoB,[cyoA]
*	*	÷	NC_000913	2403904	2404681	778	60 [59]	[59] 61	nuoB–[nuoA]	nuoB,[nuoA]

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 4421	111 (1.040)	6 (0.060)	6/268	NT	5.4%	coding (688/1287 nt)	thrC	L‑threonine synthase
	?	NC_000913	= 4450	105 (1.020)					coding (717/1287 nt)	thrC	L‑threonine synthase
*	?	NC_000913	= 193453	91 (0.850)	5 (0.050)	4/258	NT	5.3%	intergenic (+24/‑68)	frr/dxr	ribosome recycling factor/1‑deoxy‑D‑xylulose 5‑phosphate reductoisomerase
	?	NC_000913	= 193478	93 (0.940)					intergenic (+49/‑43)	frr/dxr	ribosome recycling factor/1‑deoxy‑D‑xylulose 5‑phosphate reductoisomerase
*	?	NC_000913	= 211775	90 (0.840)	5 (0.050)	4/268	NT	5.3%	coding (2097/2142 nt)	ldcC	lysine decarboxylase 2, constitutive
	?	NC_000913	= 211799	91 (0.890)					coding (2121/2142 nt)	ldcC	lysine decarboxylase 2, constitutive
*	?	NC_000913	257908 =	NA (NA)	6 (0.060)	6/278	NT	17.1%	noncoding (768/768 nt)	IS1	repeat region
	?	NC_000913	1293015 =	29 (0.270)					intergenic (‑93/‑512)	hns/tdk	global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
*	?	NC_000913	271017 =	NA (NA)	7 (0.070)	6/264	NT	NA	noncoding (477/1221 nt)	IS30	repeat region
	?	NC_000913	271039 =	NA (NA)					noncoding (499/1221 nt)	IS30	repeat region
*	?	NC_000913	274347 =	NA (NA)	4 (0.040)	4/264	NT	NA	noncoding (803/1195 nt)	IS5	repeat region
	?	NC_000913	274410 =	NA (NA)					noncoding (740/1195 nt)	IS5	repeat region
*	?	NC_000913	274620 =	NA (NA)	7 (0.070)	6/260	NT	NA	noncoding (530/1195 nt)	IS5	repeat region
	?	NC_000913	274663 =	NA (NA)					noncoding (487/1195 nt)	IS5	repeat region
*	?	NC_000913	= 274695	NA (NA)	6 (0.060)	4/270	NT	NA	noncoding (455/1195 nt)	IS5	repeat region
	?	NC_000913	= 274727	NA (NA)					noncoding (423/1195 nt)	IS5	repeat region
*	?	NC_000913	315563 =	NA (NA)	3 (0.030)	3/258	NT	NA	noncoding (335/1255 nt)	IS3	repeat region
	?	NC_000913	315599 =	NA (NA)					noncoding (371/1255 nt)	IS3	repeat region
*	?	NC_000913	= 315572	NA (NA)	7 (0.070)	5/258	NT	NA	noncoding (344/1255 nt)	IS3	repeat region
	?	NC_000913	= 315588	NA (NA)					noncoding (360/1255 nt)	IS3	repeat region
*	?	NC_000913	381663 =	NA (NA)	8 (0.080)	6/264	NT	NA	noncoding (404/1331 nt)	IS2	repeat region
	?	NC_000913	381703 =	NA (NA)					noncoding (444/1331 nt)	IS2	repeat region
*	?	NC_000913	= 381669	NA (NA)	4 (0.040)	3/264	NT	NA	noncoding (410/1331 nt)	IS2	repeat region
	?	NC_000913	= 381695	NA (NA)					noncoding (436/1331 nt)	IS2	repeat region
*	?	NC_000913	381681 =	NA (NA)	4 (0.040)	3/260	NT	NA	noncoding (422/1331 nt)	IS2	repeat region
	?	NC_000913	381753 =	NA (NA)					noncoding (494/1331 nt)	IS2	repeat region
*	?	NC_000913	= 381689	NA (NA)	4 (0.040)	4/260	NT	NA	noncoding (430/1331 nt)	IS2	repeat region
	?	NC_000913	= 381743	NA (NA)					noncoding (484/1331 nt)	IS2	repeat region
*	?	NC_000913	526459 =	NA (NA)	4 (0.040)	4/268	NT	100%	coding (3199/4281 nt)	rhsD	Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
	?	NC_000913	526482 =	0 (0.000)					coding (3222/4281 nt)	rhsD	Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
*	?	NC_000913	= 535514	94 (0.880)	6 (0.060)	6/254	NT	6.4%	coding (1599/1782 nt)	gcl	glyoxylate carboligase
	?	NC_000913	= 535539	89 (0.910)					coding (1624/1782 nt)	gcl	glyoxylate carboligase
*	?	NC_000913	= 552400	120 (1.130)	6 (0.060)	5/264	NT	5.0%	coding (195/1068 nt)	purK	N5‑carboxyaminoimidazole ribonucleotide synthase
	?	NC_000913	= 552430	113 (1.120)					coding (165/1068 nt)	purK	N5‑carboxyaminoimidazole ribonucleotide synthase
*	?	NC_000913	= 580768	77 (0.720)	5 (0.050)	5/246	NT	6.0%	intergenic (‑323/‑66)	ylcI/nohD	DUF3950 family protein, DLP12 prophage/DLP12 prophage; DNA packaging protein
	?	NC_000913	= 580793	88 (0.930)					intergenic (‑348/‑41)	ylcI/nohD	DUF3950 family protein, DLP12 prophage/DLP12 prophage; DNA packaging protein
*	?	NC_000913	696863 =	26 (0.240)	11 (0.110) +GAAGAAACAATC	9/254	NT	17.0%	intergenic (‑33/+2)	glnW/glnU	tRNA‑Gln/tRNA‑Gln
	?	NC_000913	= 697134	92 (0.860)					intergenic (‑1/+379)	metT/asnB	tRNA‑Met/asparagine synthetase B
*	?	NC_000913	878637 =	130 (1.220)	9 (0.090)	8/258	NT	7.3%	intergenic (+6/‑105)	bssR/yliI	repressor of biofilm formation by indole transport regulation/soluble aldose sugar dehydrogenase
	?	NC_000913	878662 =	107 (1.080)					intergenic (+31/‑80)	bssR/yliI	repressor of biofilm formation by indole transport regulation/soluble aldose sugar dehydrogenase
*	?	NC_000913	1110890 =	121 (1.140)	6 (0.060)	5/262	NT	5.3%	coding (28/2544 nt)	opgH	OPG biosynthetic ACP‑dependent transmembrane UDP‑glucose beta‑1,2 glycosyltransferase; nutrient‑dependent cell size regulator, FtsZ assembly antagonist
	?	NC_000913	1110927 =	102 (1.020)					coding (65/2544 nt)	opgH	OPG biosynthetic ACP‑dependent transmembrane UDP‑glucose beta‑1,2 glycosyltransferase; nutrient‑dependent cell size regulator, FtsZ assembly antagonist
*	?	NC_000913	1207790 =	31 (0.290)	51 (0.540)	45/246	NT	59.5%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	42 (0.450)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1207805	30 (0.280)	50 (0.530)	43/246	NT	59.3%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	42 (0.450)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	1294420 =	NA (NA)	3 (0.030)	3/268	NT	NA	intergenic (+276/+6)	tdk/insZ	thymidine kinase/deoxyuridine kinase/pseudogene, transposase homolog
	?	NC_000913	1294445 =	NA (NA)					noncoding (961/980 nt)	ISZ	repeat region
*	?	NC_000913	1396537 =	NA (NA)	9 (0.090)	6/266	NT	6.9%	noncoding (494/1195 nt)	IS5	repeat region
	?	NC_000913	= 1428270	127 (1.190)					noncoding (525/1196 nt)	IS5	repeat region
*	?	NC_000913	= 1456149	95 (0.890)	6 (0.060)	4/266	NT	6.0%	coding (225/498 nt)	paaD	ring 1,2‑phenylacetyl‑CoA epoxidase subunit
	?	NC_000913	= 1456169	96 (0.940)					coding (245/498 nt)	paaD	ring 1,2‑phenylacetyl‑CoA epoxidase subunit
*	?	NC_000913	1463439 =	123 (1.150)	9 (0.090)	5/264	NT	7.4%	intergenic (+1/‑100)	paaK/paaX	phenylacetyl‑CoA ligase/transcriptional repressor of phenylacetic acid degradation paa operon, phenylacetyl‑CoA inducer
	?	NC_000913	1463490 =	109 (1.080)					intergenic (+52/‑49)	paaK/paaX	phenylacetyl‑CoA ligase/transcriptional repressor of phenylacetic acid degradation paa operon, phenylacetyl‑CoA inducer
*	?	NC_000913	1510110 =	97 (0.910)	5 (0.050)	4/264	NT	5.3%	coding (108/1407 nt)	ydcR	putative DNA‑binding transcriptional regulator and putative aminotransferase
	?	NC_000913	1510142 =	86 (0.850)					coding (140/1407 nt)	ydcR	putative DNA‑binding transcriptional regulator and putative aminotransferase
*	?	NC_000913	1611571 =	70 (0.660)	4 (0.040)	3/270	NT	5.5%	coding (284/948 nt)	yneF	putative membrane‑bound diguanylate cyclase
	?	NC_000913	1611609 =	69 (0.670)					coding (246/948 nt)	yneF	putative membrane‑bound diguanylate cyclase
*	?	NC_000913	= 1953511	89 (0.830)	6 (0.060)	3/268	NT	6.1%	coding (70/972 nt)	cmoB	tRNA (cmo5U34)‑carboxymethyltransferase, carboxy‑SAM‑dependent
	?	NC_000913	= 1953539	100 (0.970)					coding (98/972 nt)	cmoB	tRNA (cmo5U34)‑carboxymethyltransferase, carboxy‑SAM‑dependent
*	?	NC_000913	= 2227439	109 (1.020)	6 (0.060)	4/270	NT	5.4%	pseudogene (1171/1287 nt)	mdtQ	pseudogene; putative channel/filament proteins
	?	NC_000913	= 2227471	105 (1.010)					pseudogene (1139/1287 nt)	mdtQ	pseudogene; putative channel/filament proteins
*	?	NC_000913	3108915 =	80 (0.750)	5 (0.050)	4/272	NT	6.1%	coding (241/2136 nt)	speC	ornithine decarboxylase, constitutive
	?	NC_000913	3108959 =	77 (0.740)					coding (197/2136 nt)	speC	ornithine decarboxylase, constitutive
*	?	NC_000913	3255217 =	NA (NA)	5 (0.050)	4/264	NT	NA	noncoding (1/103 nt)	REP236 (repetitive extragenic palindromic) element; contains 2 REP sequences	REP236 (repetitive extragenic palindromic) element; contains 2 REP sequences
	?	NC_000913	3255247 =	NA (NA)					noncoding (31/103 nt)	REP236 (repetitive extragenic palindromic) element; contains 2 REP sequences	REP236 (repetitive extragenic palindromic) element; contains 2 REP sequences
*	?	NC_000913	3277819 =	NA (NA)	4 (0.040)	4/262	NT	NA	noncoding (1/29 nt)	REP238 (repetitive extragenic palindromic) element; contains 1 REP sequences	REP238 (repetitive extragenic palindromic) element; contains 1 REP sequences
	?	NC_000913	3277844 =	NA (NA)					noncoding (26/29 nt)	REP238 (repetitive extragenic palindromic) element; contains 1 REP sequences	REP238 (repetitive extragenic palindromic) element; contains 1 REP sequences
*	?	NC_000913	3336923 =	NA (NA)	3 (0.030)	3/266	NT	NA	noncoding (5/34 nt)	REP244 (repetitive extragenic palindromic) element; contains 1 REP sequences	REP244 (repetitive extragenic palindromic) element; contains 1 REP sequences
	?	NC_000913	3336953 =	NA (NA)					intergenic (‑150/+10)	ibaG/mlaB	acid stress protein; putative BolA family transcriptional regulator/ABC transporter maintaining OM lipid asymmetry, cytoplasmic STAS component
*	?	NC_000913	= 3519887	70 (0.660)	4 (0.040)	3/264	NT	5.4%	coding (817/1239 nt)	hofQ	DNA catabolic putative fimbrial transporter
	?	NC_000913	= 3519903	74 (0.730)					coding (801/1239 nt)	hofQ	DNA catabolic putative fimbrial transporter
*	?	NC_000913	3594944 =	94 (0.880)	7 (0.070)	4/272	NT	7.3%	coding (537/1278 nt)	livM	branched‑chain amino acid ABC transporter permease
	?	NC_000913	3594982 =	87 (0.830)					coding (499/1278 nt)	livM	branched‑chain amino acid ABC transporter permease
*	?	NC_000913	= 3620350	NA (NA)	4 (0.040)	3/266	NT	100%	coding (1159/4236 nt)	rhsB	Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
	?	NC_000913	= 3620425	0 (0.000)					coding (1234/4236 nt)	rhsB	Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
*	?	NC_000913	= 3625632	NA (NA)	4 (0.040)	4/266	NT	NA	noncoding (44/82 nt)	RIP260 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site	RIP260 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site
	?	NC_000913	= 3625670	NA (NA)					noncoding (82/82 nt)	RIP260 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site	RIP260 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site
*	?	NC_000913	3736715 =	125 (1.170)	7 (0.070)	7/266	NT	5.8%	coding (463/825 nt)	bax	putative glucosaminidase
	?	NC_000913	3736730 =	109 (1.070)					coding (448/825 nt)	bax	putative glucosaminidase
*	?	NC_000913	3839241 =	110 (1.030)	6 (0.060)	3/266	NT	5.4%	coding (753/819 nt)	nlpA	cytoplasmic membrane lipoprotein‑28
	?	NC_000913	3839282 =	104 (1.020)					coding (712/819 nt)	nlpA	cytoplasmic membrane lipoprotein‑28
*	?	NC_000913	= 3998044	98 (0.920)	7 (0.070)	4/264	NT	6.7%	coding (62/2163 nt)	uvrD	DNA‑dependent ATPase I and helicase II
	?	NC_000913	= 3998069	101 (1.000)					coding (87/2163 nt)	uvrD	DNA‑dependent ATPase I and helicase II
*	?	NC_000913	= 4081273	110 (1.030)	7 (0.070)	6/260	NT	6.3%	coding (588/636 nt)	fdoI	formate dehydrogenase‑O, cytochrome b556 subunit
	?	NC_000913	= 4081294	107 (1.070)					coding (567/636 nt)	fdoI	formate dehydrogenase‑O, cytochrome b556 subunit
*	?	NC_000913	= 4168341	53 (0.500)	3 (0.030)	3/258	NT	5.4%	intergenic (+141/‑31)	rrsB/gltT	16S ribosomal RNA of rrnB operon/tRNA‑Glu
	?	NC_000913	= 4168363	55 (0.560)					intergenic (+163/‑9)	rrsB/gltT	16S ribosomal RNA of rrnB operon/tRNA‑Glu
*	?	NC_000913	= 4369155	73 (0.680)	4 (0.040)	4/258	NT	5.1%	intergenic (+15/+1)	fxsA/yjeH	suppressor of F exclusion of phage T7/putative transporter
	?	NC_000913	= 4369174	81 (0.820)					coding (1239/1257 nt)	yjeH	putative transporter