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

Predicted mutations
evidence	position	mutation	annotation	gene	description
RA	28,072	C→T	G260G (GGC→GGT)	rihC →	ribonucleoside hydrolase 3
RA	40,651	A→G	S427S (TCT→TCC)	caiT ←	putative transporter
MC JC	257,908	Δ776 bp		[crl]	[crl]
RA	276,574	T→C	V417A (GTG→GCG)	mmuP →	CP4‑6 prophage, putative S‑methylmethionine transporter
RA	506,758	(T)6→7	coding (325/480 nt)	ybaK ←	Cys‑tRNA(Pro)/Cys‑tRNA(Cys) deacylase
RA	585,420	Δ1 bp	coding (214/954 nt)	ompT ←	DLP12 prophage, outer membrane protease VII, outer membrane protein 3b
RA	640,862	G→A	A370A (GCG→GCA)	ahpF →	alkyl hydroperoxide reductase, F52a subunit, FAD/NAD(P)‑binding
RA	700,790	C→T	A269T (GCT→ACT)	nagC ←	N‑acetylglucosamine‑inducible nag divergent operon transcriptional repressor
RA	701,461	(G)5→6	coding (134/1221 nt)	nagC ←	N‑acetylglucosamine‑inducible nag divergent operon transcriptional repressor
RA	705,972	(T)9→8	intergenic (+82/‑121)	nagE → / → glnS	N‑acetyl glucosamine specific PTS enzyme IIC, IIB, and IIA components/glutamyl‑tRNA synthetase
RA	942,993	A→G	T679A (ACG→GCG)	dmsA →	dimethyl sulfoxide reductase, anaerobic, subunit A
RA	1,021,908	C→A	R659L (CGC→CTC)	yccS ←	putative transporter, FUSC superfamily inner membrane protein
RA	1,209,825	(A)6→7	coding (141/555 nt)	pinE →	e14 prophage, site‑specific DNA recombinase
RA	1,277,435	C→T	A62T (GCG→ACG)	narX ←	sensory histidine kinase in two‑component regulatory system with NarL
MC JC	1,299,499	Δ1,199 bp	intergenic (+254/‑485)	ychE → / → oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
RA	1,351,196	G→A	intergenic (‑157/+211)	fabI ← / ← ycjD	enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent/DUF559 family endonuclease‑related protein
RA	1,458,617	A→G	A118A (GCA→GCG)	paaG →	1,2‑epoxyphenylacetyl‑CoA isomerase, oxepin‑CoA‑forming
RA	1,461,176	A→G	D95G (GAC→GGC)	paaJ →	3‑oxoadipyl‑CoA/3‑oxo‑5,6‑dehydrosuberyl‑CoA thiolase
RA	1,488,515	(G)5→6	coding (284/1440 nt)	aldA →	aldehyde dehydrogenase A, NAD‑linked
RA	1,595,427	A→G	pseudogene (2561/3861 nt)	yneO ←	pseudogene, AidA homolog
RA	1,613,082	T→C	D57G (GAC→GGC)	glsB ←	glutaminase 2
RA	1,840,240	G→A	W258* (TGG→TGA)	ynjE →	molybdopterin synthase sulfurtransferase
RA	1,904,586	T→C	V231A (GTC→GCC)	manZ →	mannose‑specific enzyme IID component of PTS
RA	1,907,616	C→T	intergenic (‑25/+645)	yobF ← / ← yebO	DUF2527 family heat‑induced protein/putative inner membrane protein
RA	1,910,043	A→C	V19V (GTT→GTG)	kdgR ←	KDG regulon transcriptional repressor
MC JC	1,978,503	Δ776 bp		insB1–insA	insB1, insA
RA	2,024,017	C→T	T17I (ACC→ATC)	rcsA →	transcriptional regulator of colanic acid capsular biosynthesis
RA	2,035,112	T→C	pseudogene (400/531 nt)	yedS →	pseudogene, outer membrane protein homology, putative outer membrane protein
RA	2,073,094	T→C	L519P (CTG→CCG)	flu →	CP4‑44 prophage, antigen 43 (Ag43) phase‑variable biofilm formation autotransporter
RA	2,173,363	Δ2 bp	intergenic (‑1/+1)	gatC ← / ← gatC	pseudogene, galactitol‑specific enzyme IIC component of PTS,transport, Transport of small molecules: Carbohydrates, organic acids, alcohols, PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS,transport, Transport of small molecules: Carbohydrates, organic acids, alcohols, PTS system galactitol‑specific enzyme IIC
RA	2,401,103	G→A	T151T (ACC→ACT)	nuoF ←	NADH:ubiquinone oxidoreductase, chain F
RA	2,457,127	A→T	M678K (ATG→AAG)	fadJ ←	enoyl‑CoA hydratase/epimerase and isomerase/3‑hydroxyacyl‑CoA dehydrogenase
RA	2,567,794	C→T	G105D (GGC→GAC)	eutH ←	ethanolamine transporter
RA	2,624,129	C→T	F362F (TTC→TTT)	ppk →	polyphosphate kinase, component of RNA degradosome
RA	2,763,869	(T)7→8	coding (1285/1617 nt)	yfjL ←	CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein
RA	2,765,794	(C)7→6	intergenic (‑18/‑124)	yfjM ← / → rnlA	CP4‑57 prophage, uncharacterized protein/CP4‑57 prophage, RNase LS
RA	2,823,930	G→A	S139S (AGC→AGT)	pncC ←	nicotinamide‑nucleotide amidohydrolase, NMN amidohydrolase
RA	2,827,065	T→C	L225P (CTG→CCG)	srlE →	glucitol/sorbitol‑specific enzyme IIB component of PTS
RA	2,842,591	T→C	L151L (TTA→TTG)	hycI ←	protease involved in processing C‑terminal end of HycE
RA	2,873,023	T→C	L105L (CTA→CTG)	ygbE ←	DUF3561 family inner membrane protein
RA	2,937,802	A→G	D112G (GAC→GGC)	fucK →	L‑fuculokinase
RA	2,960,862	T→C	T523A (ACC→GCC)	recC ←	exonuclease V (RecBCD complex), gamma chain
RA	3,124,562	(T)5→6	coding (898/1224 nt)	glcF ←	glycolate oxidase 4Fe‑4S iron‑sulfur cluster subunit
RA	3,139,583	G→A	R286H (CGT→CAT)	yghU →	putative S‑transferase
RA	3,238,707	C→T	A43V (GCC→GTC)	alx →	putative membrane‑bound redox modulator
RA	3,256,941	G→A	A357V (GCC→GTC)	yhaO ←	putative transporter
RA	3,315,163	G→A	G284G (GGC→GGT)	infB ←	translation initiation factor IF‑2
RA	3,366,953	G→A	G10R (GGA→AGA)	yhcF →	putative transcriptional regulator
RA	3,457,094	A→G	I240V (ATC→GTC)	gspD →	general secretory pathway component, cryptic
RA	3,560,455	+G	intergenic (‑2/+1)	glpR ← / ← glpR	pseudogene, DNA‑binding transcriptional repressor,regulator, Energy metabolism, carbon: Anaerobic respiration, repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor,regulator, Energy metabolism, carbon: Anaerobic respiration, repressor of the glp operon
RA	3,791,004	A→G	G114G (GGT→GGC)	tdh ←	L‑threonine 3‑dehydrogenase, NAD(P)‑binding
RA	3,815,811	Δ1 bp	intergenic (‑43/+23)	pyrE ← / ← rph	orotate phosphoribosyltransferase/ribonuclease PH (defective),enzyme, Degradation of RNA, RNase PH
RA	3,901,765	G→A	G152G (GGC→GGT)	bglH ←	carbohydrate‑specific outer membrane porin, cryptic
RA	3,936,381	C→T	T35M (ACG→ATG)	rbsB →	D‑ribose ABC transporter periplasmic binding protein, ribose chemotaxis receptor
RA	3,946,742	C→T	noncoding (43/120 nt)	rrfC →	5S ribosomal RNA of rrnC operon
RA	3,969,883	A→T	N285Y (AAT→TAT)	wzzE →	Entobacterial Common Antigen (ECA) polysaccharide chain length modulation protein
RA	4,078,169	C→T	R241C (CGT→TGT)	yiiD →	GNAT family putative N‑acetyltransferase
RA	4,160,278	G→A	S171S (AGC→AGT)	sthA ←	pyridine nucleotide transhydrogenase, soluble
RA	4,281,472	A→G	E498G (GAG→GGG)	yjcE →	putative cation/proton antiporter
RA	4,296,381	+GC	intergenic (+587/+55)	gltP → / ← yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA	4,385,906	T→C	L68P (CTC→CCC)	yjeO →	inner membrane protein
RA	4,415,887	(G)6→7	coding (1613/1626 nt)	aidB →	DNA alkylation damage repair protein, flavin‑containing DNA binding protein, weak isovaleryl CoA dehydrogenase
RA	4,442,061	A→G	V39A (GTA→GCA)	msrA ←	methionine sulfoxide reductase A
RA	4,490,935	A→G	L69L (TTG→CTG)	idnR ←	transcriptional repressor, 5‑gluconate‑binding
RA	4,538,491	C→T	G92D (GGC→GAC)	nanM ←	N‑acetylneuraminic acid mutarotase
RA	4,574,259	A→G	pseudogene (341/2937 nt)	yjiV →	pseudogene, conserved hypothetical protein

Unassigned missing coverage evidence
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	84045	84091	47	2 [1]	[0] 4	leuL/leuO	leu operon leader peptide/global transcription factor
*	*	÷	NC_000913	563833	563856	24	2 [1]	[1] 2	[sfmF]–[sfmZ]	[sfmF], [sfmZ]
*	*	÷	NC_000913	662719	662780	62	2 [1]	[0] 2	[dacA]	[dacA]
*	*	÷	NC_000913	700696	700727	32	3 [1]	[0] 2	nagC	N‑acetylglucosamine‑inducible nag divergent operon transcriptional repressor
*	*	÷	NC_000913	708040	708059	20	2 [1]	[1] 3	glnS/chiP	glutamyl‑tRNA synthetase/chitoporin, uptake of chitosugars
*	*	÷	NC_000913	770856	770866	11	2 [0]	[0] 2	mngB/cydA	alpha‑mannosidase/cytochrome d terminal oxidase, subunit I
*	*	÷	NC_000913	807347	810359	3013	3 [0]	[0] 3	ybhB–[bioB]	ybhB, bioA, [bioB]
*	*	÷	NC_000913	1176926	1176943	18	2 [0]	[0] 2	lolD	outer membrane‑specific lipoprotein transporter subunit
*	*	÷	NC_000913	1318333	1318355	23	3 [1]	[0] 2	trpB	tryptophan synthase, beta subunit
*	*	÷	NC_000913	1640990	1641027	38	2 [0]	[1] 2	essQ/cspB	Qin prophage, putative S lysis protein/Qin prophage, cold shock protein
*	*	÷	NC_000913	1697553	1697570	18	3 [0]	[0] 2	hdhA	7‑alpha‑hydroxysteroid dehydrogenase, NAD‑dependent
*	*	÷	NC_000913	1816158	1816169	12	4 [0]	[0] 2	katE/chbG	catalase HPII, heme d‑containing/chito‑oligosaccharide deacetylase
*	*	÷	NC_000913	2033850	2033927	78	2 [1]	[0] 2	rseX/yedS	sRNA antisense regulator of ompA and ompC translation, Hfq‑dependent/pseudogene, outer membrane protein homology, putative outer membrane protein
*	*	÷	NC_000913	2056699	2056789	91	2 [0]	[0] 3	amn/yeeN	AMP nucleosidase/UPF0082 family protein
*	*	÷	NC_000913	2306848	2306903	56	2 [0]	[1] 7	mqo/yojI	malate dehydrogenase, FAD/NAD(P)‑binding domain/microcin J25 efflux ABC transporter permease/ATPase
*	*	÷	NC_000913	2446976	2446981	6	2 [0]	[0] 4	aroC	chorismate synthase
*	*	÷	NC_000913	2455869	2455874	6	4 [0]	[0] 2	yfcV/sixA	putative fimbrial‑like adhesin protein/phosphohistidine phosphatase
*	*	÷	NC_000913	2470199	2470272	74	2 [1]	[0] 2	gtrS	serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
*	*	÷	NC_000913	2536215	2536241	27	3 [1]	[0] 2	crr	glucose‑specific enzyme IIA component of PTS
*	*	÷	NC_000913	2536309	2536438	130	2 [0]	[1] 2	[crr]–[pdxK]	[crr], [pdxK]
*	*	÷	NC_000913	2563386	2563418	33	2 [0]	[0] 2	yffP/yffQ	CPZ‑55 prophage, uncharacterized protein/CPZ‑55 prophage, uncharacterized protein
*	*	÷	NC_000913	2774389	2774391	3	2 [1]	[0] 2	yfjW	CP4‑57 prophage, putative inner membrane protein
*	*	÷	NC_000913	2857138	2859608	2471	4 [0]	[0] 2	mutS	methyl‑directed mismatch repair protein
*	*	÷	NC_000913	2922539	2922543	5	2 [0]	[1] 4	yqcA	short‑chain flavodoxin, FMN‑binding
*	*	÷	NC_000913	3024155	3024170	16	3 [1]	[1] 4	xdhD	putative hypoxanthine oxidase, molybdopterin‑binding/Fe‑S binding
*	*	÷	NC_000913	3252745	3252775	31	2 [1]	[0] 2	yhaH/yhaI	DUF805 family inner membrane protein/DUF805 family inner membrane protein
*	*	÷	NC_000913	3256505	3256574	70	2 [0]	[0] 2	yhaM	putative L‑serine dehydratase alpha chain
*	*	÷	NC_000913	3368365	3368403	39	3 [1]	[1] 2	yhcG	DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily
*	*	÷	NC_000913	3423782–3424234	3424517–3424238	5–736	2 [1]	[0] 2	[rrfD]–[rrlD]	[rrfD], [rrlD]
*	*	÷	NC_000913	3455447	3455487	41	2 [0]	[1] 2	gspA/gspC	general secretory pathway component, cryptic/general secretory pathway component, cryptic
*	*	÷	NC_000913	3469938	3470024	87	3 [1]	[1] 2	chiA/tufA	periplasmic endochitinase/translation elongation factor EF‑Tu 1
*	*	÷	NC_000913	3602671	3602677	7	2 [0]	[0] 2	ftsE	cell division ATP‑binding protein
*	*	÷	NC_000913	3751949	3751981	33	2 [1]	[0] 5	yiaT/yiaU	putative outer membrane protein/putative DNA‑binding transcriptional regulator
*	*	÷	NC_000913	3793444	3793456	13	3 [1]	[0] 3	yibB	YibB family protein, function unknown
*	*	÷	NC_000913	3793696	3793745	50	2 [0]	[1] 6	yibB/hldD	YibB family protein, function unknown/ADP‑L‑glycero‑D‑mannoheptose‑6‑epimerase, NAD(P)‑binding
*	*	÷	NC_000913	3799495	3799498	4	2 [0]	[0] 2	waaZ	lipopolysaccharide KdoIII transferase, lipopolysaccharide core biosynthesis protein
*	*	÷	NC_000913	3994691	3994712	22	3 [1]	[1] 4	yifL	putative lipoprotein
*	*	÷	NC_000913	4044068	4044115	48	2 [0]	[0] 8	dsbA/yihF	periplasmic protein disulfide isomerase I/DUF945 family protein