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
RA	60,422	T→C	E948G (GAA→GGA)	rapA ←	RNA polymerase remodeling/recycling factor ATPase, RNA polymerase‑associated, ATP‑dependent RNA translocase
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	516,003	(T)5→4	coding (85/678 nt)	fetA →	iron export ABC transporter ATPase, peroxide resistance protein
RA	521,055	T→C	L214L (TTA→CTA)	ybbP →	putative ABC transporter permease
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	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	1,212,088	(C)8→9	intergenic (‑85/+615)	iraM ← / ← ycgX	RpoS stabilzer during Mg starvation, anti‑RssB factor/DUF1398 family protein
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	+A	intergenic (‑157/+211)	fabI ← / ← ycjD	enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent/DUF559 family endonuclease‑related protein
RA	1,398,875	A→G	F218L (TTC→CTC)	fnr ←	oxygen‑sensing anaerobic growth regulon transcriptional regulator FNR, autorepressor
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	1,904,586	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
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	2,073,094	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	2,624,129	C→T	F362F (TTC→TTT)	ppk →	polyphosphate kinase, component of RNA degradosome
RA	2,689,476	G→A	R11* (CGA→TGA)	yfhG ←	putative outer membrane protein modulating the QseEF response
RA	2,763,869	(T)7→8	coding (1285/1617 nt)	yfjL ←	CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein
RA	2,823,930	G→A	S139S (AGC→AGT)	pncC ←	nicotinamide‑nucleotide amidohydrolase, NMN amidohydrolase
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	3,139,583	G→A	R286H (CGT→CAT)	yghU →	putative S‑transferase
RA	3,256,941	G→A	A357V (GCC→GTC)	yhaO ←	putative transporter
RA	3,271,600	(C)5→6	coding (171/1146 nt)	garK ←	glycerate kinase I
RA	3,315,163	G→A	G284G (GGC→GGT)	infB ←	translation initiation factor IF‑2
RA	3,328,816	(A)7→8	intergenic (‑101/‑147)	greA ← / → dacB	transcript cleavage factor/D‑alanyl‑D‑alanine carboxypeptidase
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	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	4,410,053	(T)9→8	intergenic (+47/‑80)	rlmB → / → yjfI	23S rRNA mG2251 2'‑O‑ribose methyltransferase, SAM‑dependent/DUF2170 family 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
RA	4,595,843	A→G	R3R (CGT→CGC)	lgoR ←	putative transcriptional activator for L‑galactonate catabolism

Unassigned missing coverage evidence
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	237222	237270	49	3 [0]	[0] 2	aspV/yafT	tRNA‑Asp/lipoprotein
*	*	÷	NC_000913	502360	502378	19	2 [0]	[1] 2	ybaL	inner membrane putative NAD(P)‑binding transporter
*	*	÷	NC_000913	807337	807842	506	2 [1]	[1] 2	[ybhB]	[ybhB]
*	*	÷	NC_000913	807959	810363	2405	2 [1]	[0] 2	bioA–[bioB]	bioA, [bioB]
*	*	÷	NC_000913	1166581	1166593	13	3 [1]	[0] 2	ndh	respiratory NADH dehydrogenase 2/cupric reductase
*	*	÷	NC_000913	1176829	1176880	52	2 [0]	[0] 2	lolD	outer membrane‑specific lipoprotein transporter subunit
*	*	÷	NC_000913	1573741	1573766	26	3 [1]	[0] 2	pqqL	putative periplasmic M16 family zinc metalloendopeptidase
*	*	÷	NC_000913	1640993	1641020	28	2 [0]	[1] 3	essQ/cspB	Qin prophage, putative S lysis protein/Qin prophage, cold shock protein
*	*	÷	NC_000913	1923305	1923320	16	2 [1]	[1] 3	[ryeA]	[ryeA]
*	*	÷	NC_000913	2056699	2056789	91	2 [1]	[1] 3	amn/yeeN	AMP nucleosidase/UPF0082 family protein
*	*	÷	NC_000913	2211701	2211814	114	3 [1]	[1] 2	[yehS]	[yehS]
*	*	÷	NC_000913	2305074	2305093	20	2 [1]	[1] 3	eco/mqo	ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
*	*	÷	NC_000913	2857138	2859614	2477	6 [0]	[1] 3	mutS	methyl‑directed mismatch repair protein
*	*	÷	NC_000913	2877922	2877935	14	2 [0]	[0] 3	iap/ygbF	aminopeptidase in alkaline phosphatase isozyme conversion/CRISPR adaptation ssRNA endonuclease
*	*	÷	NC_000913	2903795	2903824	30	3 [0]	[0] 2	ygcE/queE	putative kinase/7‑carboxy‑7‑deazaguanine synthase, queosine biosynthesis
*	*	÷	NC_000913	2978709	2978728	20	2 [1]	[1] 2	lysA	diaminopimelate decarboxylase, PLP‑binding
*	*	÷	NC_000913	3007766	3007794	29	2 [0]	[1] 2	ygeX	2,3‑diaminopropionate ammonia lyase, PLP‑dependent
*	*	÷	NC_000913	3136568	3136627	60	3 [1]	[1] 3	pitB/gss	phosphate transporter/glutathionylspermidine amidase and glutathionylspermidine synthetase
*	*	÷	NC_000913	3281732	3281736	5	2 [0]	[0] 2	agaA/agaS	pseudogene, N‑acetylgalactosamine‑6‑phosphate deacetylase fragment, putative N‑acetylgalactosamine‑6‑phosphate deacetylase/tagatose‑6‑phosphate ketose/aldose isomerase
*	*	÷	NC_000913	3385296	3385304	9	2 [1]	[0] 2	argR/yhcN	l‑arginine‑responsive arginine metabolism regulon transcriptional regulator/cadmium and peroxide resistance protein, stress‑induced
*	*	÷	NC_000913	3413567	3413601	35	5 [1]	[0] 2	acrS/acrE	acrAB operon transcriptional repressor/cytoplasmic membrane lipoprotein
*	*	÷	NC_000913	3423798–3424230	3424524–3424239	10–727	2 [1]	[1] 2	[rrlD]	[rrlD]
*	*	÷	NC_000913	3455440	3455473	34	4 [0]	[1] 2	gspA/gspC	general secretory pathway component, cryptic/general secretory pathway component, cryptic
*	*	÷	NC_000913	3603669	3603752	84	2 [0]	[1] 2	ftsY	Signal Recognition Particle (SRP) receptor
*	*	÷	NC_000913	3793691	3793728	38	3 [1]	[1] 2	yibB/hldD	YibB family protein, function unknown/ADP‑L‑glycero‑D‑mannoheptose‑6‑epimerase, NAD(P)‑binding
*	*	÷	NC_000913	3943715–3943987	3945785–3945570	1584–2071	2 [1]	[0] 2	rrlC	23S ribosomal RNA of rrnC operon
*	*	÷	NC_000913	4240931	4240942	12	7 [1]	[0] 3	xylE	D‑xylose transporter
*	*	÷	NC_000913	4408929	4409022	94	2 [0]	[1] 2	rnr	exoribonuclease R, RNase R
*	*	÷	NC_000913	4571930	4571937	8	2 [0]	[0] 2	yjiS/yjiT	DUF1127 family protein/pseudogene

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	2996360 =	NA (NA)	4 (0.180) +C	3/218	2.1	NA	pseudogene (1/399 nt)	ygeO	pseudogene, orgA family, part of T3SS PAI ETT2 remnant
	?	NC_000913	= 2997691	NA (NA)					noncoding (1/1331 nt)	IS2	repeat region