BRESEQ :: Mutation Predictions

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	49,884	C→T	P21L (CCG→CTG)	folA →	type 3 dihydrofolate reductase
MC JC	2,399,465	Δ7 bp	coding (650‑656/939 nt)	lrhA ←	transcriptional regulator LrhA
RA	4,171,725	G→C	D185H (GAC→CAC)	rpoB →	DNA‑directed RNA polymerase subunit beta

Unassigned missing coverage evidence
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NZ_CP009273	153614	153698	85	2 [1]	[1] 2	yadN/folK	fimbrial protein/2‑amino‑4‑hydroxy‑6‑ hydroxymethyldihydropteridine diphosphokinase
*	*	÷	NZ_CP009273	255901	255919	19	2 [0]	[1] 2	phoE/proB	phosphoporin PhoE/glutamate 5‑kinase
*	*	÷	NZ_CP009273	356981	357567	587	2 [0]	[0] 2	lacA	galactoside O‑acetyltransferase
*	*	÷	NZ_CP009273	674902	674918	17	4 [0]	[1] 2	ybeT/ybeU	tetratricopeptide repeat protein/DUF1266 domain‑containing protein
*	*	÷	NZ_CP009273	712149	712159	11	2 [1]	[1] 2	BW25113_RS03565/BW25113_RS03570	DUF2625 domain‑containing protein/winged helix‑turn‑helix domain‑containing protein
*	*	÷	NZ_CP009273	1423670	1423680	11	2 [1]	[0] 2	stfR	prophage tail fiber N‑terminal domain‑containing protein
*	*	÷	NZ_CP009273	1539242	1539288	47	2 [0]	[1] 3	BW25113_RS07710	leucine‑rich repeat domain‑containing protein
*	*	÷	NZ_CP009273	1566586	1566607	22	2 [1]	[0] 2	gadB/pqqL	glutamate decarboxylase/insulinase family protein
*	*	÷	NZ_CP009273	1633012	1633073	62	3 [1]	[1] 3	cspI/rzpQ	cold shock protein CspI/DUF2514 domain‑containing protein
*	*	÷	NZ_CP009273	1633170	1633269	100	2 [1]	[0] 3	cspI/rzpQ	cold shock protein CspI/DUF2514 domain‑containing protein
*	*	÷	NZ_CP009273	1748986	1749077	92	2 [1]	[1] 2	ydhY/fumD	ferredoxin‑like protein/fumarate hydratase FumD
*	*	÷	NZ_CP009273	1765193	1765197	5	2 [1]	[0] 2	ydiL	YdiL family protein
*	*	÷	NZ_CP009273	1783818	1783895	78	2 [1]	[1] 3	[hemP]	[hemP]
*	*	÷	NZ_CP009273	1940474	1940525	52	4 [1]	[1] 4	[yebB]	[yebB]
*	*	÷	NZ_CP009273	1990581	1990596	16	2 [1]	[0] 2	yecC	L‑cystine ABC transporter ATP‑binding protein YecC
*	*	÷	NZ_CP009273	2027336	2027407	72	2 [1]	[0] 2	drpB/ompC	cell division protein DrpB/porin OmpC
*	*	÷	NZ_CP009273	2062034	2062036	3	2 [1]	[0] 2	BW25113_RS10415/BW25113_RS24005	IS5‑like element IS5 family transposase/TonB‑dependent receptor plug domain‑containing protein
*	*	÷	NZ_CP009273	2062087	2062119	33	2 [0]	[1] 2	[BW25113_RS24005]	[BW25113_RS24005]
*	*	÷	NZ_CP009273	2300371	2300381	11	2 [0]	[0] 4	mqo/yojI	malate dehydrogenase (quinone)/microcin J25 efflux ABC transporter YojI
*	*	÷	NZ_CP009273	2370467	2370477	11	2 [0]	[1] 2	menH	2‑succinyl‑6‑hydroxy‑2, 4‑cyclohexadiene‑1‑carboxylate synthase
*	*	÷	NZ_CP009273	2463867	2463878	12	2 [1]	[0] 3	BW25113_RS12270	hypothetical protein
*	*	÷	NZ_CP009273	3629063	3629885	823	39 [0]	[1] 2	[yhiM]–[yhiN]	[yhiM],[yhiN]
*	*	÷	NZ_CP009273	3629971	3630345	375	2 [1]	[0] 2	yhiN	NAD(P)/FAD‑dependent oxidoreductase
*	*	÷	NZ_CP009273	3630482	3631216	735	2 [1]	[0] 2	[yhiN]–[pitA]	[yhiN],[pitA]
*	*	÷	NZ_CP009273	3631296	3631875	580	2 [0]	[1] 2	pitA	inorganic phosphate transporter PitA
*	*	÷	NZ_CP009273	3631958	3632048	91	2 [1]	[1] 2	pitA	inorganic phosphate transporter PitA
*	*	÷	NZ_CP009273	3632125	3632186	62	2 [1]	[1] 2	pitA	inorganic phosphate transporter PitA
*	*	÷	NZ_CP009273	3632277	3632641	365	2 [1]	[1] 3	[pitA]	[pitA]
*	*	÷	NZ_CP009273	3632700	3633050	351	3 [1]	[1] 2	[uspB]	[uspB]
*	*	÷	NZ_CP009273	3633090	3635486	2397	2 [1]	[1] 2	uspA–[dtpB]	uspA,BW25113_RS26225,BW25113_RS26230,[dtpB]
*	*	÷	NZ_CP009273	3635503	3636790	1288	2 [1]	[1] 2	[dtpB]–[prlC]	[dtpB],rsmJ,[prlC]
*	*	÷	NZ_CP009273	3636793	3637741	949	2 [1]	[1] 2	prlC	oligopeptidase A
*	*	÷	NZ_CP009273	3637821	3638059	239	2 [1]	[1] 2	prlC	oligopeptidase A
*	*	÷	NZ_CP009273	3638098	3638164	67	2 [1]	[1] 2	prlC	oligopeptidase A
*	*	÷	NZ_CP009273	3638255	3639067	813	2 [1]	[0] 2	[prlC]–[rlmJ]	[prlC],[rlmJ]
*	*	÷	NZ_CP009273	3639109	3640413	1305	2 [0]	[1] 2	[rlmJ]–[gorA]	[rlmJ],[gorA]
*	*	÷	NZ_CP009273	3640436	3641483	1048	2 [1]	[1] 2	[gorA]–dinQ	[gorA],dinQ
*	*	÷	NZ_CP009273	3641550	3641927	378	2 [1]	[1] 2	[arsR]	[arsR]
*	*	÷	NZ_CP009273	3641958	3642584	627	2 [1]	[1] 2	[arsR]–[arsB]	[arsR],[arsB]
*	*	÷	NZ_CP009273	3642675	3643995	1321	2 [1]	[1] 2	[arsB]–[arsC]	[arsB],[arsC]
*	*	÷	NZ_CP009273	3644068	3644222	155	2 [1]	[1] 2	arsC/BW25113_RS18155	glutaredoxin‑dependent arsenate reductase/hypothetical protein
*	*	÷	NZ_CP009273	3644285	3644514	230	2 [1]	[0] 2	arsC/BW25113_RS18155	glutaredoxin‑dependent arsenate reductase/hypothetical protein
*	*	÷	NZ_CP009273	3644560	3646512–3645396	837–1953	2 [0]	[1] 2	BW25113_RS18155–[BW25113_RS18160]	BW25113_RS18155,[BW25113_RS18160]
*	*	÷	NZ_CP009273	4466660	4466682	23	3 [1]	[1] 3	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)	17 (0.860)	11/166	0.5	38.6%	intergenic (‑35/+251)	lacZ/BW25113_RS23320	beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein
*	?	NZ_CP009273	= 360286	27 (1.360)	17 (0.860)	11/166	0.5	38.6%	intergenic (‑217/+69)	lacZ/BW25113_RS23320	beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein
*	?	NZ_CP009273	2282398 =	NA (NA)	39 (1.960)	17/166	0.2	100%	pseudogene (3/2532 nt)	yejO	autotransporter YejO
*	?	NZ_CP009273	= 3629062	0 (0.000)	39 (1.960)	17/166	0.2	100%	coding (862/1053 nt)	yhiM	DUF2776 domain‑containing protein
*	?	NZ_CP009273	4532499 =	3 (0.150)	14 (0.790)	11/148	0.4	78.5%	intergenic (+49/‑433)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
*	?	NZ_CP009273	4532813 =	5 (0.280)	14 (0.790)	11/148	0.4	78.5%	intergenic (+363/‑119)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA