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	49,898	G→A	A26T (GCC→ACC)	folA →	type 3 dihydrofolate reductase
RA	49,910	T→G	W30G (TGG→GGG)	folA →	type 3 dihydrofolate reductase
MC JC	2,399,465	Δ7 bp	coding (650‑656/939 nt)	lrhA ←	transcriptional regulator LrhA

Unassigned missing coverage evidence
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NZ_CP009273	233664	233760	97	2 [1]	[1] 2	BW25113_RS01085/BW25113_RS01090	tRNA‑Asp/lipoprotein
*	*	÷	NZ_CP009273	234778	234793	16	2 [0]	[1] 3	BW25113_RS01095	hypothetical protein
*	*	÷	NZ_CP009273	356979	357568	590	2 [1]	[1] 2	lacA	galactoside O‑acetyltransferase
*	*	÷	NZ_CP009273	564139	564149	11	4 [1]	[0] 2	emrE/BW25113_RS25485	SMR family multidrug efflux protein EmrE/hypothetical protein
*	*	÷	NZ_CP009273	621322	621361	40	2 [1]	[1] 2	entC	isochorismate synthase EntC
*	*	÷	NZ_CP009273	647595	647650	56	2 [1]	[0] 2	citC/dpiB	[citrate (pro‑3S)‑lyase] ligase/sensor histidine kinase DpiB
*	*	÷	NZ_CP009273	674899	674945	47	2 [1]	[0] 2	ybeT/ybeU	tetratricopeptide repeat protein/DUF1266 domain‑containing protein
*	*	÷	NZ_CP009273	724884	724909	26	5 [0]	[1] 2	ybfA/rhsC	YbfA family protein/rhs element protein RhsC
*	*	÷	NZ_CP009273	950167	950252	86	2 [1]	[1] 3	focA/ycaO	formate transporter FocA/30S ribosomal protein S12 methylthiotransferase accessory factor YcaO
*	*	÷	NZ_CP009273	955680	955701	22	2 [0]	[1] 3	aroA/ycaL	3‑phosphoshikimate 1‑carboxyvinyltransferase/metallopeptidase YcaL
*	*	÷	NZ_CP009273	994698	994775	78	3 [1]	[1] 2	elfC	fimbrial biogenesis usher protein
*	*	÷	NZ_CP009273	1097437	1097446	10	2 [0]	[0] 2	csgF	curli production assembly/transport protein CsgF
*	*	÷	NZ_CP009273	1098876	1098980	105	2 [1]	[1] 3	csgD/csgB	biofilm master transcriptional regulator CsgD/curli minor subunit CsgB
*	*	÷	NZ_CP009273	1129469	1129483	15	2 [1]	[1] 2	flgF	flagellar basal‑body rod protein FlgF
*	*	÷	NZ_CP009273	1159054	1159067	14	2 [1]	[0] 2	thiK	thiamine kinase
*	*	÷	NZ_CP009273	1159817	1159828	12	2 [1]	[1] 2	nagZ	beta‑N‑acetylhexosaminidase
*	*	÷	NZ_CP009273	1161462	1161497	36	2 [1]	[1] 2	ycfP/ndh	alpha/beta hydrolase YcfP/NADH‑quinone dehydrogenase
*	*	÷	NZ_CP009273	1188059	1188124	66	3 [1]	[0] 2	[hflD]–[mnmA]	[hflD],[mnmA]
*	*	÷	NZ_CP009273	1190781	1190808	28	2 [1]	[0] 2	icd	NADP‑dependent isocitrate dehydrogenase
*	*	÷	NZ_CP009273	1192962	1193015	54	2 [1]	[1] 2	[ymfD]–[BW25113_RS05920]	[ymfD],[BW25113_RS05920]
*	*	÷	NZ_CP009273	1193235	1193257	23	2 [0]	[1] 2	BW25113_RS05920	hypothetical protein
*	*	÷	NZ_CP009273	1207978	1208005	28	3 [1]	[0] 2	[BW25113_RS25535]	[BW25113_RS25535]
*	*	÷	NZ_CP009273	1297537	1297545	9	2 [1]	[0] 3	oppB	oligopeptide ABC transporter permease OppB
*	*	÷	NZ_CP009273	1327509	1327561	53	2 [0]	[1] 2	topA	type I DNA topoisomerase
*	*	÷	NZ_CP009273	1431157	1431249	93	2 [0]	[1] 2	ompN/nifJ	porin OmpN/pyruvate:ferredoxin (flavodoxin) oxidoreductase
*	*	÷	NZ_CP009273	1470810	1470825	16	3 [1]	[1] 2	ydbD	DUF2773 domain‑containing bactofilin
*	*	÷	NZ_CP009273	1477474	1477482	9	2 [0]	[1] 2	hrpA	ATP‑dependent RNA helicase HrpA
*	*	÷	NZ_CP009273	1504622	1504685	64	3 [1]	[1] 2	ydcR	PLP‑dependent aminotransferase family protein
*	*	÷	NZ_CP009273	1509359	1509365	7	2 [1]	[0] 2	ydcV	ABC transporter permease
*	*	÷	NZ_CP009273	1521131	1521146	16	2 [1]	[1] 2	yncG/yncH	glutathione S‑transferase family protein/YncH family protein
*	*	÷	NZ_CP009273	1521911	1521955	45	2 [0]	[1] 2	yncH/BW25113_RS07645	YncH family protein/RHS repeat protein
*	*	÷	NZ_CP009273	1535814	1535824	11	2 [1]	[0] 2	narZ	nitrate reductase Z subunit alpha
*	*	÷	NZ_CP009273	1547412	1547428	17	2 [1]	[0] 4	adhP	alcohol dehydrogenase AdhP
*	*	÷	NZ_CP009273	1576929	1576969	41	2 [1]	[1] 2	ydeN/ydeO	sulfatase/acid stress response transcriptional regulator YdeO
*	*	÷	NZ_CP009273	1631946	1632002	57	2 [0]	[1] 2	gnsB	addiction module toxin, GnsA/GnsB family
*	*	÷	NZ_CP009273	1632049	1632147	99	2 [1]	[1] 3	gnsB/BW25113_RS08135	addiction module toxin, GnsA/GnsB family/hypothetical protein
*	*	÷	NZ_CP009273	1783823	1783858	36	2 [1]	[1] 2	aroH/hemP	3‑deoxy‑7‑phosphoheptulonate synthase AroH/hemin uptake protein HemP
*	*	÷	NZ_CP009273	1807458	1807564	107	2 [1]	[1] 2	BW25113_RS09050/cedA	hypothetical protein/cell division activator CedA
*	*	÷	NZ_CP009273	1978972	1978979	8	2 [0]	[1] 2	araF	arabinose ABC transporter substrate‑binding protein AraF
*	*	÷	NZ_CP009273	1989128	1989156	29	2 [1]	[1] 2	[BW25113_RS25650]	[BW25113_RS25650]
*	*	÷	NZ_CP009273	2005483	2005525	43	2 [0]	[1] 2	BW25113_RS10120	DUF5503 domain‑containing protein
*	*	÷	NZ_CP009273	2027091	2027114	24	2 [1]	[0] 4	drpB/ompC	cell division protein DrpB/porin OmpC
*	*	÷	NZ_CP009273	2185810	2185845	36	2 [1]	[1] 2	yehD/yehE	fimbrial protein/YehE family protein
*	*	÷	NZ_CP009273	2189449	2189460	12	2 [1]	[1] 2	metG	methionine‑‑tRNA ligase
*	*	÷	NZ_CP009273	2303215	2303225	11	2 [0]	[0] 3	ada	bifunctional DNA‑binding transcriptional regulator/O6‑methylguanine‑DNA methyltransferase Ada
*	*	÷	NZ_CP009273	2312874	2312897	24	2 [1]	[1] 2	rcsC	two‑component system sensor histidine kinase RcsC
*	*	÷	NZ_CP009273	2326470	2326472	3	2 [0]	[1] 2	BW25113_RS11635	alpha‑2‑macroglobulin family protein
*	*	÷	NZ_CP009273	2376501	2376526	26	2 [1]	[0] 4	elaD	deubiquitinase ElaD
*	*	÷	NZ_CP009273	2462870	2462946	77	2 [0]	[1] 2	BW25113_RS12270	hypothetical protein
*	*	÷	NZ_CP009273	2463749	2463763	15	2 [0]	[0] 2	BW25113_RS12270	hypothetical protein
*	*	÷	NZ_CP009273	2768327	2768424	98	2 [1]	[0] 2	[BW25113_RS13770]	[BW25113_RS13770]
*	*	÷	NZ_CP009273	2777865	2777880	16	2 [0]	[1] 2	BW25113_RS25705	DUF5507 domain‑containing protein
*	*	÷	NZ_CP009273	2779409	2779450	42	2 [1]	[1] 2	BW25113_RS13825/BW25113_RS26005	tRNA‑Ile/alpha‑amylase family glycosyl hydrolase
*	*	÷	NZ_CP009273	2877733	2877791	59	3 [1]	[1] 2	casA/cas3	type I‑E CRISPR‑associated protein Cse1/CasA/CRISPR‑associated helicase/endonuclease Cas3
*	*	÷	NZ_CP009273	2988532	2988647	116	2 [1]	[1] 2	BW25113_RS14850/BW25113_RS26010	response regulator transcription factor/hypothetical protein
*	*	÷	NZ_CP009273	3996307	3996311	5	2 [1]	[0] 7	BW25113_RS19825	hypothetical protein
*	*	÷	NZ_CP009273	4466875	4466929	55	2 [1]	[1] 2	BW25113_RS22080	hypothetical protein

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	360104 =	NA (NA)	34 (1.920)	24/168	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 =	5 (0.280)	5 (0.350)	4/136	1.0	62.4%	coding (290/630 nt)	BW25113_RS05990	hypothetical protein
	?	NZ_CP009273	1205075 =	2 (0.140)					coding (40/540 nt)	BW25113_RS06005	phage tail protein
*	?	NZ_CP009273	= 1203261	5 (0.280)	7 (0.490)	7/136	0.6	69.9%	coding (305/630 nt)	BW25113_RS05990	hypothetical protein
	?	NZ_CP009273	= 1205058	2 (0.140)					coding (57/540 nt)	BW25113_RS06005	phage tail protein
*	?	NZ_CP009273	= 1391494	NA (NA)	6 (0.340)	4/166	1.2	100%	intergenic (+145/‑128)	BW25113_RS06980/ynaJ	IS5‑like element IS5 family transposase/DUF2534 family protein
	?	NZ_CP009273	1972747 =	0 (0.000)					intergenic (‑293/‑487)	flhD/uspC	flagellar transcriptional regulator FlhD/universal stress protein UspC
*	?	NZ_CP009273	1613558 =	18 (1.020)	16 (0.920)	15/166	0.2	49.4%	coding (182/435 nt)	marR	multiple antibiotic resistance transcriptional regulator MarR
	?	NZ_CP009273	= 1613717	15 (0.860)					coding (341/435 nt)	marR	multiple antibiotic resistance transcriptional regulator MarR
*	?	NZ_CP009273	= 1972751	0 (0.000)	23 (1.300)	15/168	0.2	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 =	2 (0.110)	4 (0.250)	4/150	1.1	35.1%	intergenic (+49/‑433)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP009273	4532813 =	13 (0.820)					intergenic (+363/‑119)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
*	?	NZ_CP009273	= 4532507	2 (0.110)	6 (0.380)	6/150	0.8	44.8%	intergenic (+57/‑425)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP009273	= 4532803	13 (0.820)					intergenic (+353/‑129)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA