BRESEQ :: Mutation Predictions

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

Predicted mutation
evidence	position	mutation	annotation	gene	description
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	356981	357567	587	5 [0]	[0] 4	lacA	galactoside O‑acetyltransferase
*	*	÷	NZ_CP009273	508217	508237	21	3 [1]	[1] 2	ybaT	APC family permease
*	*	÷	NZ_CP009273	768230	768262	33	2 [1]	[1] 3	cydA	cytochrome ubiquinol oxidase subunit I
*	*	÷	NZ_CP009273	772580	772602	23	3 [1]	[1] 2	tolA	cell envelope integrity protein TolA
*	*	÷	NZ_CP009273	827921	827994	74	2 [1]	[1] 4	[ybiA]	[ybiA]
*	*	÷	NZ_CP009273	889233	889245	13	2 [1]	[1] 7	[potF]	[potF]
*	*	÷	NZ_CP009273	925561	925580	20	2 [0]	[1] 2	cydD	cysteine/glutathione ABC transporter permease/ATP‑binding protein CydD
*	*	÷	NZ_CP009273	1013368	1013392	25	2 [1]	[1] 3	ycbZ	Lon protease family protein
*	*	÷	NZ_CP009273	1032563	1032589	27	2 [1]	[1] 2	hyaF	hydrogenase expression/formation protein
*	*	÷	NZ_CP009273	1039731	1039763	33	2 [0]	[1] 2	etp	protein‑tyrosine‑phosphatase Etp
*	*	÷	NZ_CP009273	1137337	1137366	30	2 [1]	[0] 2	rne	ribonuclease E
*	*	÷	NZ_CP009273	1164416	1164496	81	2 [1]	[1] 2	comR/bhsA	TetR family copper‑responsive transcriptional repressor ComR/multiple stress resistance protein BhsA
*	*	÷	NZ_CP009273	1181497	1181545	49	2 [1]	[1] 3	pepT	peptidase T
*	*	÷	NZ_CP009273	1185809	1185815	7	2 [0]	[1] 2	phoP	two‑component system response regulator PhoP
*	*	÷	NZ_CP009273	1198614	1198629	16	2 [0]	[1] 2	ymfT	YdaS family helix‑turn‑helix protein
*	*	÷	NZ_CP009273	1231006	1231017	12	4 [1]	[0] 3	fadR	fatty acid metabolism transcriptional regulator FadR
*	*	÷	NZ_CP009273	1242451	1242521	71	4 [1]	[1] 2	treA	alpha,alpha‑trehalase
*	*	÷	NZ_CP009273	1251735	1251804	70	2 [1]	[1] 2	ycgV/ychF	autotransporter outer membrane beta‑barrel domain‑containing protein/redox‑regulated ATPase YchF
*	*	÷	NZ_CP009273	1253061	1253070	10	2 [1]	[1] 2	ychF	redox‑regulated ATPase YchF
*	*	÷	NZ_CP009273	1281925	1281941	17	2 [1]	[1] 2	narI	respiratory nitrate reductase subunit gamma
*	*	÷	NZ_CP009273	1301356	1301364	9	3 [1]	[1] 2	yciU	HI1450 family dsDNA‑mimic protein
*	*	÷	NZ_CP009273	1303926	1303946	21	2 [1]	[1] 3	kch	voltage‑gated potassium channel protein
*	*	÷	NZ_CP009273	1410429	1410436	8	2 [1]	[0] 2	recE	exodeoxyribonuclease VIII
*	*	÷	NZ_CP009273	1417276	1417301	26	2 [1]	[1] 3	BW25113_RS07140	DUF1627 domain‑containing protein
*	*	÷	NZ_CP009273	1450735	1450756	22	4 [1]	[0] 2	paaK	phenylacetate‑CoA oxygenase/reductase subunit PaaK
*	*	÷	NZ_CP009273	1459415	1459482	68	4 [1]	[1] 2	[BW25113_RS25580]	[BW25113_RS25580]
*	*	÷	NZ_CP009273	1507170	1507185	16	2 [1]	[1] 3	ydcT	ABC transporter ATP‑binding protein
*	*	÷	NZ_CP009273	1509354	1509370	17	2 [1]	[0] 3	ydcV	ABC transporter permease
*	*	÷	NZ_CP009273	1532105	1532201	97	3 [1]	[1] 2	narH	nitrate reductase subunit beta
*	*	÷	NZ_CP009273	1543246	1543255	10	2 [0]	[0] 2	fdnG	formate dehydrogenase‑N subunit alpha
*	*	÷	NZ_CP009273	1568074	1568108	35	2 [1]	[1] 2	pqqL	insulinase family protein
*	*	÷	NZ_CP009273	1632909	1632929	21	2 [1]	[0] 3	[cspI]	[cspI]
*	*	÷	NZ_CP009273	1654938	1654948	11	2 [1]	[1] 2	ynfF	dimethyl sulfoxide reductase subunit A
*	*	÷	NZ_CP009273	1704209	1704222	14	2 [1]	[1] 2	rsxD	electron transport complex subunit RsxD
*	*	÷	NZ_CP009273	1733878	1733893	16	2 [1]	[1] 2	punR	DNA‑binding transcriptional activator PunR
*	*	÷	NZ_CP009273	1754807	1754827	21	2 [0]	[1] 3	sufD	Fe‑S cluster assembly protein SufD
*	*	÷	NZ_CP009273	1884456	1884483	28	2 [1]	[1] 3	yeaY	Slp family lipoprotein YeaY
*	*	÷	NZ_CP009273	1901737	1901738	2	4 [1]	[0] 2	yobF	DUF2627 domain‑containing protein

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	360104 =	NA (NA)	112 (5.260)	45/168	0.0	NA	intergenic (‑35/+251)	lacZ/BW25113_RS23320	beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein
*	?	NZ_CP009273	= 360286	NA (NA)	112 (5.260)	45/168	0.0	NA	intergenic (‑217/+69)	lacZ/BW25113_RS23320	beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein
*	?	NZ_CP009273	1203246 =	14 (0.660)	6 (0.350)	6/136	0.8	38.3%	coding (290/630 nt)	BW25113_RS05990	hypothetical protein
*	?	NZ_CP009273	1205075 =	8 (0.460)	6 (0.350)	6/136	0.8	38.3%	coding (40/540 nt)	BW25113_RS06005	phage tail protein
*	?	NZ_CP009273	= 1203261	14 (0.660)	6 (0.350)	6/136	0.8	38.3%	coding (305/630 nt)	BW25113_RS05990	hypothetical protein
*	?	NZ_CP009273	= 1205058	8 (0.460)	6 (0.350)	6/136	0.8	38.3%	coding (57/540 nt)	BW25113_RS06005	phage tail protein