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	242,170	T→C	G41G (GGA→GGG)	dpaA ←	peptidoglycan meso‑diaminopimelic acid protein amidase
RA	1,613,576	A→C	D67A (GAC→GCC)	marR →	multiple antibiotic resistance transcriptional regulator MarR
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	2 [0]	[0] 5	lacA	galactoside O‑acetyltransferase
*	*	÷	NZ_CP009273	376327	376364	38	2 [1]	[1] 2	BW25113_RS01855	transferase
*	*	÷	NZ_CP009273	519379	519388	10	2 [0]	[1] 2	rhsD	rhs element protein RhsD
*	*	÷	NZ_CP009273	610481	610496	16	3 [1]	[1] 4	entF	enterobactin non‑ribosomal peptide synthetase EntF
*	*	÷	NZ_CP009273	724885	724928	44	2 [1]	[1] 2	ybfA/rhsC	YbfA family protein/rhs element protein RhsC
*	*	÷	NZ_CP009273	824156	824166	11	5 [1]	[0] 3	ybhF	ATP‑binding cassette domain‑containing protein
*	*	÷	NZ_CP009273	902978	903053	76	3 [1]	[1] 2	ybjT	SDR family oxidoreductase
*	*	÷	NZ_CP009273	929553	929616	64	2 [1]	[0] 2	ftsK	DNA translocase FtsK
*	*	÷	NZ_CP009273	929666	929676	11	2 [0]	[1] 3	ftsK	DNA translocase FtsK
*	*	÷	NZ_CP009273	1079803	1079816	14	6 [1]	[0] 2	efeB	iron uptake transporter deferrochelatase/peroxidase subunit
*	*	÷	NZ_CP009273	1086740	1086749	10	2 [1]	[1] 4	pgaA	poly‑beta‑1,6 N‑acetyl‑D‑glucosamine export porin PgaA
*	*	÷	NZ_CP009273	1111270	1111285	16	4 [1]	[1] 4	lpxL	kdo(2)‑lipid IV(A) lauroyltransferase
*	*	÷	NZ_CP009273	1206642	1206672	31	2 [1]	[1] 2	mcrA/BW25113_RS23640	5‑methylcytosine‑specific endonuclease McrA/isocitrate/isopropylmalate family dehydrogenase
*	*	÷	NZ_CP009273	1211827	1211885	59	2 [1]	[1] 2	ariR	biofilm/acid‑resistance regulator AriR
*	*	÷	NZ_CP009273	1216588	1216613	26	3 [1]	[1] 2	BW25113_RS25990	autotransporter outer membrane beta‑barrel domain‑containing protein
*	*	÷	NZ_CP009273	1303459	1303469	11	3 [0]	[1] 3	kch	voltage‑gated potassium channel protein
*	*	÷	NZ_CP009273	1308186	1308210	25	2 [0]	[0] 2	BW25113_RS25555/ompW	YkgJ family cysteine cluster protein/outer membrane protein OmpW
*	*	÷	NZ_CP009273	1366958	1366977	20	2 [1]	[1] 2	ycjN	ABC transporter substrate‑binding protein
*	*	÷	NZ_CP009273	1635258	1635285	28	2 [1]	[0] 6	ynfU/cspB	putative zinc‑binding protein YnfU/cold shock‑like protein CspB
*	*	÷	NZ_CP009273	1719909	1719930	22	2 [1]	[1] 2	ydhF/ydhL	aldo/keto reductase family oxidoreductase/DUF1289 domain‑containing protein
*	*	÷	NZ_CP009273	1722108	1722111	4	2 [0]	[1] 8	gloA	lactoylglutathione lyase
*	*	÷	NZ_CP009273	1731261	1731335	75	4 [1]	[1] 2	ydhP	MFS transporter
*	*	÷	NZ_CP009273	1818686	1818739	54	2 [1]	[1] 3	ves	environmental stress‑induced protein Ves
*	*	÷	NZ_CP009273	1888048	1888056	9	2 [0]	[1] 2	yoaB/yoaC	RidA family protein/DUF1889 family protein
*	*	÷	NZ_CP009273	2019151	2019180	30	2 [1]	[1] 3	yedP	mannosyl‑3‑phosphoglycerate phosphatase‑related protein
*	*	÷	NZ_CP009273	2112161	2112182	22	3 [1]	[1] 2	wzxC	colanic acid undecaprenyl disphosphate flippase WzxC
*	*	÷	NZ_CP009273	2211902	2211987	86	2 [1]	[1] 2	yehY	glycine betaine ABC transporter permease YehY
*	*	÷	NZ_CP009273	2300314	2300356	43	2 [1]	[1] 2	mqo/yojI	malate dehydrogenase (quinone)/microcin J25 efflux ABC transporter YojI
*	*	÷	NZ_CP009273	2400642	2400650	9	2 [1]	[0] 2	lrhA/alaA	transcriptional regulator LrhA/alanine transaminase AlaA
*	*	÷	NZ_CP009273	2462967	2463035	69	3 [1]	[1] 2	BW25113_RS12270	hypothetical protein
*	*	÷	NZ_CP009273	2554352	2554368	17	3 [1]	[0] 3	BW25113_RS12740/BW25113_RS12745	hypothetical protein/hypothetical protein
*	*	÷	NZ_CP009273	2701336	2701359	24	4 [0]	[1] 3	rseB	sigma‑E factor regulatory protein RseB
*	*	÷	NZ_CP009273	3151420	3151466	47	3 [1]	[1] 2	yqhG	YbjP/YqhG family protein
*	*	÷	NZ_CP009273	3629247	3629458	212	26 [0]	[1] 2	[yhiM]	[yhiM]
*	*	÷	NZ_CP009273	3629586	3633481	3896	2 [1]	[1] 2	[yhiN]–[uspA]	[yhiN],pitA,uspB,[uspA]
*	*	÷	NZ_CP009273	3633561	3634122	562	2 [1]	[0] 2	[uspA]–BW25113_RS26230	[uspA],BW25113_RS26225,BW25113_RS26230
*	*	÷	NZ_CP009273	3634203	3634238	36	2 [0]	[0] 2	[dtpB]	[dtpB]
*	*	÷	NZ_CP009273	3634288	3634416	129	2 [0]	[0] 2	dtpB	dipeptide/tripeptide permease DtpB
*	*	÷	NZ_CP009273	3634556	3636558	2003	2 [0]	[1] 2	[dtpB]–[prlC]	[dtpB],rsmJ,[prlC]
*	*	÷	NZ_CP009273	3636632	3637414	783	2 [1]	[1] 2	prlC	oligopeptidase A
*	*	÷	NZ_CP009273	3637421	3639636	2216	2 [1]	[1] 2	[prlC]–rlmJ	[prlC],rlmJ
*	*	÷	NZ_CP009273	3639808	3640299	492	2 [0]	[0] 2	gorA	glutathione‑disulfide reductase
*	*	÷	NZ_CP009273	3640369	3640372	4	2 [0]	[0] 2	gorA	glutathione‑disulfide reductase
*	*	÷	NZ_CP009273	3640418	3640449	32	2 [0]	[1] 2	gorA	glutathione‑disulfide reductase
*	*	÷	NZ_CP009273	3640529	3640819	291	2 [1]	[1] 2	gorA	glutathione‑disulfide reductase
*	*	÷	NZ_CP009273	3640866	3640913	48	2 [1]	[0] 2	gorA	glutathione‑disulfide reductase
*	*	÷	NZ_CP009273	3640982	3641264	283	2 [0]	[1] 2	[gorA]–dinQ	[gorA],dinQ
*	*	÷	NZ_CP009273	3641315	3643827	2513	2 [1]	[1] 2	arsR–[arsC]	arsR,arsB,[arsC]
*	*	÷	NZ_CP009273	3643900	3646527–3645398	1499–2628	2 [1]	[0] 2	[arsC]–BW25113_RS18160	[arsC],BW25113_RS18155,BW25113_RS18160
*	*	÷	NZ_CP009273	4305557	4305575	19	2 [1]	[1] 4	phnN	ribose 1,5‑bisphosphokinase

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	360104 =	NA (NA)	43 (2.660)	26/168	0.0	NA	intergenic (‑35/+251)	lacZ/BW25113_RS23320	beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein
*	?	NZ_CP009273	= 360286	NA (NA)	43 (2.660)	26/168	0.0	NA	intergenic (‑217/+69)	lacZ/BW25113_RS23320	beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein
*	?	NZ_CP009273	= 1391494	NA (NA)	12 (0.750)	9/166	0.5	92.4%	intergenic (+145/‑128)	BW25113_RS06980/ynaJ	IS5‑like element IS5 family transposase/DUF2534 family protein
*	?	NZ_CP009273	1972747 =	1 (0.060)	12 (0.750)	9/166	0.5	92.4%	intergenic (‑293/‑487)	flhD/uspC	flagellar transcriptional regulator FlhD/universal stress protein UspC
*	?	NZ_CP009273	= 1972751	0 (0.000)	12 (0.740)	11/168	0.3	100%	intergenic (‑297/‑483)	flhD/uspC	flagellar transcriptional regulator FlhD/universal stress protein UspC
*	?	NZ_CP009273	= 2283592	NA (NA)	12 (0.740)	11/168	0.3	100%	intergenic (‑68/‑387)	BW25113_RS11435/narP	IS5‑like element IS5 family transposase/nitrate/nitrite response regulator protein NarP
*	?	NZ_CP009273	2282398 =	NA (NA)	19 (1.180)	12/168	0.3	100%	pseudogene (3/2532 nt)	yejO	autotransporter YejO
*	?	NZ_CP009273	3512437 =	0 (0.000)	19 (1.180)	12/168	0.3	100%	intergenic (‑14/+387)	aroK/hofQ	shikimate kinase AroK/DNA uptake porin HofQ
*	?	NZ_CP009273	= 2283591	NA (NA)	22 (1.380)	11/166	0.3	95.7%	intergenic (‑67/‑388)	BW25113_RS11435/narP	IS5‑like element IS5 family transposase/nitrate/nitrite response regulator protein NarP
*	?	NZ_CP009273	= 3512441	1 (0.060)	22 (1.380)	11/166	0.3	95.7%	intergenic (‑18/+383)	aroK/hofQ	shikimate kinase AroK/DNA uptake porin HofQ
*	?	NZ_CP009273	= 3629246	0 (0.000)	26 (1.610)	15/168	0.2	100%	coding (1046/1053 nt)	yhiM	DUF2776 domain‑containing protein
*	?	NZ_CP009273	3645396 =	NA (NA)	26 (1.610)	15/168	0.2	100%	pseudogene (746/747 nt)	BW25113_RS18155	hypothetical protein
*	?	NZ_CP009273	= 4532507	11 (0.680)	9 (0.620)	8/150	0.5	48.9%	intergenic (+57/‑425)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
*	?	NZ_CP009273	= 4532803	9 (0.620)	9 (0.620)	8/150	0.5	48.9%	intergenic (+353/‑129)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA