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

Predicted mutations
evidence	position	mutation	annotation	gene	description
RA	49,765	C→T	intergenic (+134/‑58)	kefC → / → folA	glutathione‑regulated potassium‑efflux system protein KefC/type 3 dihydrofolate reductase
RA	49,912	G→T	W30C (TGG→TGT)	folA →	type 3 dihydrofolate reductase
RA	214,743	A→C	Y174D (TAC→GAC)	proS ←	proline‑‑tRNA ligase
MC JC	2,399,465	Δ7 bp	coding (650‑656/939 nt)	lrhA ←	transcriptional regulator LrhA
RA	3,754,231	G→T	R127S (CGC→AGC)	selA ←	L‑seryl‑tRNA(Sec) selenium transferase
RA	4,267,454	C→T	R20C (CGC→TGC)	soxR →	redox‑sensitive transcriptional activator SoxR

Unassigned missing coverage evidence
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NZ_CP009273	356981	357569	589	3 [0]	[1] 3	lacA	galactoside O‑acetyltransferase
*	*	÷	NZ_CP009273	396670	396700	31	2 [1]	[1] 2	BW25113_RS25915/iraP	hypothetical protein/anti‑adapter protein IraP
*	*	÷	NZ_CP009273	578967	578997	31	2 [1]	[1] 2	BW25113_RS26085/appY	tail fiber assembly protein/DNA‑binding transcriptional activator AppY
*	*	÷	NZ_CP009273	716403	716491	89	2 [1]	[1] 2	BW25113_RS26090/kdpE	leader peptide SpeFL/two‑component system response regulator KdpE
*	*	÷	NZ_CP009273	724408	724461	54	2 [1]	[1] 2	kdpF/ybfA	K(+)‑transporting ATPase subunit F/YbfA family protein
*	*	÷	NZ_CP009273	837037	837050	14	2 [1]	[1] 3	fiu/mcbA	catecholate siderophore receptor Fiu/DUF1471 family periplasmic protein McbA
*	*	÷	NZ_CP009273	950171	950219	49	2 [1]	[1] 2	focA/ycaO	formate transporter FocA/30S ribosomal protein S12 methylthiotransferase accessory factor YcaO
*	*	÷	NZ_CP009273	1193193	1193262	70	2 [1]	[1] 2	BW25113_RS05920	hypothetical protein
*	*	÷	NZ_CP009273	1205776	1205806	31	2 [1]	[1] 3	[mcrA]	[mcrA]
*	*	÷	NZ_CP009273	1212091	1212113	23	2 [0]	[1] 2	[ariR]	[ariR]
*	*	÷	NZ_CP009273	1431318	1431373	56	2 [1]	[1] 3	ompN/nifJ	porin OmpN/pyruvate:ferredoxin (flavodoxin) oxidoreductase
*	*	÷	NZ_CP009273	1524310	1524340	31	2 [1]	[1] 3	BW25113_RS07645/BW25113_RS26145	RHS repeat protein/hypothetical protein
*	*	÷	NZ_CP009273	1540318	1540420	103	2 [1]	[1] 2	yddL/yddG	porin/aromatic amino acid efflux DMT transporter YddG
*	*	÷	NZ_CP009273	1567137	1567147	11	2 [0]	[1] 3	pqqL	insulinase family protein
*	*	÷	NZ_CP009273	1783818	1783881	64	3 [1]	[0] 4	[hemP]	[hemP]
*	*	÷	NZ_CP009273	1899534	1899572	39	2 [1]	[1] 2	yobD/mntP	DUF986 family protein/manganese efflux pump MntP
*	*	÷	NZ_CP009273	1972752	1972775	24	30 [0]	[1] 2	flhD/uspC	flagellar transcriptional regulator FlhD/universal stress protein UspC
*	*	÷	NZ_CP009273	2097490	2097570	81	2 [1]	[0] 2	wbbK	glycosyltransferase family 1 protein
*	*	÷	NZ_CP009273	2100145	2100208	64	2 [1]	[1] 2	wzy	O16 family O‑antigen polymerase
*	*	÷	NZ_CP009273	2449323	2449367	45	3 [1]	[1] 2	yfcV/sixA	fimbrial protein/phosphohistidine phosphatase SixA
*	*	÷	NZ_CP009273	2462860	2462908	49	2 [1]	[1] 2	BW25113_RS12270	hypothetical protein
*	*	÷	NZ_CP009273	2779386	2779392	7	2 [1]	[0] 2	BW25113_RS13825/BW25113_RS26005	tRNA‑Ile/alpha‑amylase family glycosyl hydrolase
*	*	÷	NZ_CP009273	2779430	2779464	35	2 [0]	[1] 2	BW25113_RS13825/BW25113_RS26005	tRNA‑Ile/alpha‑amylase family glycosyl hydrolase
*	*	÷	NZ_CP009273	2819106	2819145	40	3 [1]	[1] 7	mltB/srlA	lytic murein transglycosylase B/PTS glucitol/sorbitol transporter subunit IIC
*	*	÷	NZ_CP009273	3044356	3044362	7	2 [1]	[0] 5	BW25113_RS25745	protein YqfI
*	*	÷	NZ_CP009273	3178740	3178750	11	2 [0]	[0] 2	ubiK/ygiL	ubiquinone biosynthesis accessory factor UbiK/fimbrial‑like protein
*	*	÷	NZ_CP009273	3354473	3354480	8	2 [0]	[1] 3	gltD/gltF	glutamate synthase subunit GltD/DUF1120 domain‑containing protein
*	*	÷	NZ_CP009273	3406917	3406966	50	2 [0]	[1] 2	acrS/acrE	multidrug efflux transporter transcriptional repressor AcrS/multidrug efflux RND transporter periplasmic adaptor subunit AcrE
*	*	÷	NZ_CP009273	3763017	3763127	111	2 [1]	[1] 2	BW25113_RS26240	Imm57 family immunity protein
*	*	÷	NZ_CP009273	3787031	3787095	65	2 [1]	[1] 2	[yibB]	[yibB]
*	*	÷	NZ_CP009273	3798187	3798216	30	2 [1]	[0] 2	rfaS	LPS core biosynthesis protein RfaS
*	*	÷	NZ_CP009273	3798345	3798474	130	2 [1]	[1] 2	rfaS	LPS core biosynthesis protein RfaS
*	*	÷	NZ_CP009273	3979613	3979664	52	4 [1]	[1] 2	aslA/hemY	arylsulfatase AslA/protoheme IX biogenesis protein HemY
*	*	÷	NZ_CP009273	4427375	4427430	56	4 [1]	[1] 4	cysQ/BW25113_RS21900	3'(2'),5'‑bisphosphate nucleotidase CysQ/hypothetical protein

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	360104 =	NA (NA)	73 (3.940)	32/168	0.0	NA	intergenic (‑35/+251)	lacZ/BW25113_RS23320	beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein
	?	NZ_CP009273	= 360286	NA (NA)					intergenic (‑217/+69)	lacZ/BW25113_RS23320	beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein
*	?	NZ_CP009273	1203246 =	13 (0.700)	17 (1.140)	10/136	0.3	68.7%	coding (290/630 nt)	BW25113_RS05990	hypothetical protein
	?	NZ_CP009273	1205075 =	5 (0.330)					coding (40/540 nt)	BW25113_RS06005	phage tail protein
*	?	NZ_CP009273	1686630 =	5 (0.270)	13 (0.710)	3/166	1.7	72.5%	coding (479/1266 nt)	uidC	glucuronide uptake porin UidC
	?	NZ_CP009273	2095231 =	NA (NA)					intergenic (‑1/+145)	wbbL/BW25113_RS10605	N‑acetylglucosaminyl‑diphospho‑decaprenol L‑rhamnosyltransferase WbbL/IS5‑like element IS5 family transposase
*	?	NZ_CP009273	= 1686634	6 (0.320)	9 (0.490)	8/168	0.7	60.0%	coding (475/1266 nt)	uidC	glucuronide uptake porin UidC
	?	NZ_CP009273	= 2283592	NA (NA)					intergenic (‑68/‑387)	BW25113_RS11435/narP	IS5‑like element IS5 family transposase/nitrate/nitrite response regulator protein NarP
*	?	NZ_CP009273	= 1972751	0 (0.000)	30 (1.620)	14/168	0.3	100%	intergenic (‑297/‑483)	flhD/uspC	flagellar transcriptional regulator FlhD/universal stress protein UspC
	?	NZ_CP009273	= 2283592	NA (NA)					intergenic (‑68/‑387)	BW25113_RS11435/narP	IS5‑like element IS5 family transposase/nitrate/nitrite response regulator protein NarP
*	?	NZ_CP009273	4532499 =	0 (0.000)	3 (0.180)	3/150	1.5	27.3%	intergenic (+49/‑433)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP009273	4532813 =	16 (0.970)					intergenic (+363/‑119)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
*	?	NZ_CP009273	= 4532507	0 (0.000)	4 (0.240)	4/150	1.3	33.3%	intergenic (+57/‑425)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP009273	= 4532803	16 (0.970)					intergenic (+353/‑129)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA