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	49,905	T→G	L28R (CTC→CGC)	folA →	type 3 dihydrofolate reductase
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

Unassigned missing coverage evidence
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NZ_CP009273	356976	357567	592	2 [1]	[0] 2	lacA	galactoside O‑acetyltransferase
*	*	÷	NZ_CP009273	428524	428565	42	2 [0]	[1] 2	nrdR	transcriptional regulator NrdR
*	*	÷	NZ_CP009273	602511	602592	82	2 [1]	[1] 2	ybdK	YbdK family carboxylate‑amine ligase
*	*	÷	NZ_CP009273	772559	772615	57	2 [1]	[1] 3	tolA	cell envelope integrity protein TolA
*	*	÷	NZ_CP009273	856575	856607	33	2 [1]	[1] 2	ybiW	glycyl radical protein
*	*	÷	NZ_CP009273	903024	903048	25	2 [1]	[1] 2	ybjT	SDR family oxidoreductase
*	*	÷	NZ_CP009273	950036	950056	21	2 [1]	[0] 2	focA/ycaO	formate transporter FocA/30S ribosomal protein S12 methylthiotransferase accessory factor YcaO
*	*	÷	NZ_CP009273	964316	964319	4	3 [1]	[0] 2	lpxK	tetraacyldisaccharide 4'‑kinase
*	*	÷	NZ_CP009273	1108894	1108899	6	2 [0]	[1] 3	mdoH/yceK	glucans biosynthesis glucosyltransferase MdoH/YceK/YidQ family lipoprotein
*	*	÷	NZ_CP009273	1205059	1205074	16	10 [0]	[0] 11	BW25113_RS06005	phage tail protein
*	*	÷	NZ_CP009273	1633174	1633192	19	2 [1]	[1] 3	cspI/rzpQ	cold shock protein CspI/DUF2514 domain‑containing protein
*	*	÷	NZ_CP009273	2566390	2566396	7	4 [1]	[1] 2	pta	phosphate acetyltransferase
*	*	÷	NZ_CP009273	3629137	3629343	207	2 [1]	[1] 2	[yhiM]	[yhiM]
*	*	÷	NZ_CP009273	3629405	3629507	103	2 [1]	[1] 2	yhiM/yhiN	DUF2776 domain‑containing protein/NAD(P)/FAD‑dependent oxidoreductase
*	*	÷	NZ_CP009273	3629584	3629650	67	3 [1]	[1] 2	yhiN	NAD(P)/FAD‑dependent oxidoreductase
*	*	÷	NZ_CP009273	3630276	3630415	140	2 [1]	[1] 2	yhiN	NAD(P)/FAD‑dependent oxidoreductase
*	*	÷	NZ_CP009273	3630719	3630903	185	2 [1]	[1] 2	[yhiN]	[yhiN]
*	*	÷	NZ_CP009273	3631217	3631372	156	2 [1]	[0] 2	pitA	inorganic phosphate transporter PitA
*	*	÷	NZ_CP009273	3631427	3631642	216	2 [0]	[1] 2	pitA	inorganic phosphate transporter PitA
*	*	÷	NZ_CP009273	3631775	3631867	93	2 [1]	[1] 3	pitA	inorganic phosphate transporter PitA
*	*	÷	NZ_CP009273	3631958	3632034	77	3 [1]	[1] 2	pitA	inorganic phosphate transporter PitA
*	*	÷	NZ_CP009273	3632125	3632231	107	2 [1]	[1] 3	pitA	inorganic phosphate transporter PitA
*	*	÷	NZ_CP009273	3632636	3632645	10	2 [1]	[1] 2	pitA/uspB	inorganic phosphate transporter PitA/universal stress protein UspB
*	*	÷	NZ_CP009273	3632805	3632892	88	2 [1]	[1] 3	uspB	universal stress protein UspB
*	*	÷	NZ_CP009273	3632960	3632996	37	3 [1]	[1] 2	uspB	universal stress protein UspB
*	*	÷	NZ_CP009273	3633074	3633153	80	2 [1]	[1] 2	[uspB]	[uspB]
*	*	÷	NZ_CP009273	3633244	3633369	126	2 [1]	[0] 2	uspB/uspA	universal stress protein UspB/universal stress protein UspA
*	*	÷	NZ_CP009273	3633695	3633785	91	2 [1]	[1] 2	uspA	universal stress protein UspA
*	*	÷	NZ_CP009273	3633847	3633908	62	2 [1]	[0] 2	[uspA]	[uspA]
*	*	÷	NZ_CP009273	3634067	3634117	51	2 [1]	[0] 2	BW25113_RS26230/dtpB	protein YriB/dipeptide/tripeptide permease DtpB
*	*	÷	NZ_CP009273	3634272	3634669	398	2 [1]	[1] 2	dtpB	dipeptide/tripeptide permease DtpB
*	*	÷	NZ_CP009273	3634909	3634999	91	2 [1]	[1] 2	dtpB	dipeptide/tripeptide permease DtpB
*	*	÷	NZ_CP009273	3635965	3636096	132	3 [1]	[1] 2	rsmJ	16S rRNA (guanine(1516)‑N(2))‑methyltransferase RsmJ
*	*	÷	NZ_CP009273	3636261	3636352	92	2 [1]	[1] 2	rsmJ	16S rRNA (guanine(1516)‑N(2))‑methyltransferase RsmJ
*	*	÷	NZ_CP009273	3636554	3637117	564	2 [1]	[1] 3	prlC	oligopeptidase A
*	*	÷	NZ_CP009273	3637208	3637313	106	2 [0]	[0] 3	prlC	oligopeptidase A
*	*	÷	NZ_CP009273	3637787	3637974	188	2 [1]	[1] 2	prlC	oligopeptidase A
*	*	÷	NZ_CP009273	3638418	3638493	76	2 [1]	[1] 2	prlC	oligopeptidase A
*	*	÷	NZ_CP009273	3638679	3638903	225	2 [1]	[1] 2	[rlmJ]	[rlmJ]
*	*	÷	NZ_CP009273	3639092	3639274	183	2 [1]	[1] 2	rlmJ	23S rRNA (adenine(2030)‑N(6))‑methyltransferase
*	*	÷	NZ_CP009273	3639473	3639835	363	2 [1]	[1] 2	[rlmJ]–[gorA]	[rlmJ],[gorA]
*	*	÷	NZ_CP009273	3639919	3640133	215	2 [1]	[0] 2	gorA	glutathione‑disulfide reductase
*	*	÷	NZ_CP009273	3640218	3640606	389	2 [0]	[1] 3	gorA	glutathione‑disulfide reductase
*	*	÷	NZ_CP009273	3640696	3640841	146	3 [1]	[1] 2	gorA	glutathione‑disulfide reductase
*	*	÷	NZ_CP009273	3640932	3641038	107	2 [1]	[0] 2	[gorA]	[gorA]
*	*	÷	NZ_CP009273	3641111	3641348	238	2 [0]	[1] 2	[dinQ]	[dinQ]
*	*	÷	NZ_CP009273	3641454	3641531	78	2 [0]	[1] 2	dinQ/arsR	hypothetical protein/As(III)‑sensing metalloregulatory transcriptional repressor ArsR
*	*	÷	NZ_CP009273	3641671	3641830	160	2 [1]	[1] 2	dinQ/arsR	hypothetical protein/As(III)‑sensing metalloregulatory transcriptional repressor ArsR
*	*	÷	NZ_CP009273	3642083	3642157	75	2 [0]	[1] 2	arsR	As(III)‑sensing metalloregulatory transcriptional repressor ArsR
*	*	÷	NZ_CP009273	3642513	3642601	89	2 [1]	[1] 2	arsB	arsenite/antimonite:H(+) antiporter ArsB
*	*	÷	NZ_CP009273	3642795	3642957	163	2 [1]	[1] 2	arsB	arsenite/antimonite:H(+) antiporter ArsB
*	*	÷	NZ_CP009273	3643140	3643166	27	2 [0]	[0] 2	arsB	arsenite/antimonite:H(+) antiporter ArsB
*	*	÷	NZ_CP009273	3643330	3643363	34	2 [1]	[1] 2	arsB	arsenite/antimonite:H(+) antiporter ArsB
*	*	÷	NZ_CP009273	3643890	3643952	63	2 [1]	[1] 2	arsC	glutaredoxin‑dependent arsenate reductase
*	*	÷	NZ_CP009273	3644229	3644319	91	2 [0]	[1] 2	arsC/BW25113_RS18155	glutaredoxin‑dependent arsenate reductase/hypothetical protein
*	*	÷	NZ_CP009273	3644350	3644555	206	2 [1]	[1] 2	arsC/BW25113_RS18155	glutaredoxin‑dependent arsenate reductase/hypothetical protein
*	*	÷	NZ_CP009273	3644930	3645089	160	2 [0]	[1] 3	BW25113_RS18155	hypothetical protein
*	*	÷	NZ_CP009273	3645177	3646509–3645391	215–1333	3 [1]	[1] 2	[BW25113_RS18155]–[BW25113_RS18160]	[BW25113_RS18155],[BW25113_RS18160]

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	15391 =	NA (NA)	15 (0.650)	12/164	0.5	72.4%	intergenic (+93/‑54)	dnaJ/BW25113_RS00080	molecular chaperone DnaJ/IS4‑like element IS421 family transposase
	?	NZ_CP009273	= 454255	6 (0.250)					intergenic (+99/‑89)	clpX/lon	ATP‑dependent protease ATP‑binding subunit ClpX/endopeptidase La
*	?	NZ_CP009273	360104 =	NA (NA)	29 (1.190)	17/172	0.2	48.3%	intergenic (‑35/+251)	lacZ/BW25113_RS23320	beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein
	?	NZ_CP009273	= 360286	31 (1.270)					intergenic (‑217/+69)	lacZ/BW25113_RS23320	beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein
*	?	NZ_CP009273	454243 =	1 (0.040)	19 (0.810)	14/166	0.4	95.2%	intergenic (+87/‑101)	clpX/lon	ATP‑dependent protease ATP‑binding subunit ClpX/endopeptidase La
	?	NZ_CP009273	= 604803	NA (NA)					intergenic (+170/+112)	BW25113_RS03025/entD	IS4‑like element IS421 family transposase/enterobactin synthase subunit EntD
*	?	NZ_CP009273	1203246 =	3 (0.120)	8 (0.400)	7/140	0.8	86.8%	coding (290/630 nt)	BW25113_RS05990	hypothetical protein
	?	NZ_CP009273	1205075 =	0 (0.000)					coding (40/540 nt)	BW25113_RS06005	phage tail protein
*	?	NZ_CP009273	= 1203261	3 (0.120)	8 (0.400)	8/140	0.7	86.8%	coding (305/630 nt)	BW25113_RS05990	hypothetical protein
	?	NZ_CP009273	= 1205058	0 (0.000)					coding (57/540 nt)	BW25113_RS06005	phage tail protein
*	?	NZ_CP009273	= 1391494	NA (NA)	14 (0.580)	8/170	0.9	93.4%	intergenic (+145/‑128)	BW25113_RS06980/ynaJ	IS5‑like element IS5 family transposase/DUF2534 family protein
	?	NZ_CP009273	1972747 =	1 (0.040)					intergenic (‑293/‑487)	flhD/uspC	flagellar transcriptional regulator FlhD/universal stress protein UspC
*	?	NZ_CP009273	= 1972751	0 (0.000)	22 (0.900)	17/172	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	= 3629105	1 (0.040)	29 (1.210)	17/170	0.2	96.7%	coding (905/1053 nt)	yhiM	DUF2776 domain‑containing protein
	?	NZ_CP009273	3645397 =	NA (NA)					pseudogene (747/747 nt)	BW25113_RS18155	hypothetical protein
*	?	NZ_CP009273	4532499 =	11 (0.450)	11 (0.510)	7/154	0.9	35.6%	intergenic (+49/‑433)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP009273	4532813 =	30 (1.380)					intergenic (+363/‑119)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
*	?	NZ_CP009273	= 4532507	11 (0.450)	16 (0.740)	14/154	0.3	44.5%	intergenic (+57/‑425)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP009273	= 4532803	30 (1.380)					intergenic (+353/‑129)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA