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	49,791	G→A	intergenic (+160/‑32)	kefC → / → folA	glutathione‑regulated potassium‑efflux system protein KefC/type 3 dihydrofolate reductase
RA	1,613,627	T→A	V84E (GTG→GAG)	marR →	multiple antibiotic resistance transcriptional regulator MarR
MC JC	2,399,465	Δ7 bp	coding (650‑656/939 nt)	lrhA ←	transcriptional regulator LrhA
MC JC	3,631,242	Δ66 bp	coding (241‑306/1500 nt)	pitA →	inorganic phosphate transporter PitA

Unassigned missing coverage evidence
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NZ_CP009273	356976	357570	595	2 [0]	[0] 4	lacA	galactoside O‑acetyltransferase
*	*	÷	NZ_CP009273	380426	380467	42	2 [1]	[1] 2	BW25113_RS01880/tauA	PIG‑L family deacetylase/taurine ABC transporter substrate‑binding protein
*	*	÷	NZ_CP009273	385384	385416	33	2 [1]	[1] 2	hemB/BW25113_RS01915	porphobilinogen synthase/outer membrane autotransporter barrel domain‑containing protein
*	*	÷	NZ_CP009273	428529	428554	26	2 [0]	[1] 3	nrdR	transcriptional regulator NrdR
*	*	÷	NZ_CP009273	613496	613526	31	3 [1]	[0] 2	entF/wzz(fepE)	enterobactin non‑ribosomal peptide synthetase EntF/LPS O‑antigen length regulator Wzz(fepE)
*	*	÷	NZ_CP009273	651479	651500	22	2 [1]	[1] 2	dcuC/pagP	anaerobic C4‑dicarboxylate transporter DcuC/lipid IV(A) palmitoyltransferase PagP
*	*	÷	NZ_CP009273	703464	703521	58	2 [1]	[1] 2	glnS/chiP	glutamine‑‑tRNA ligase/chitoporin
*	*	÷	NZ_CP009273	724884	724894	11	3 [1]	[0] 4	ybfA/rhsC	YbfA family protein/rhs element protein RhsC
*	*	÷	NZ_CP009273	733482	733509	28	2 [0]	[1] 3	BW25113_RS03650/ybfD	ISAs1 family transposase/ISAs1 family transposase
*	*	÷	NZ_CP009273	902983	903047	65	4 [1]	[1] 2	ybjT	SDR family oxidoreductase
*	*	÷	NZ_CP009273	950041	950059	19	2 [0]	[1] 3	focA/ycaO	formate transporter FocA/30S ribosomal protein S12 methylthiotransferase accessory factor YcaO
*	*	÷	NZ_CP009273	982534	982577	44	3 [1]	[1] 3	ompF/asnS	porin OmpF/asparagine‑‑tRNA ligase
*	*	÷	NZ_CP009273	982691	982741	51	3 [1]	[1] 2	ompF/asnS	porin OmpF/asparagine‑‑tRNA ligase
*	*	÷	NZ_CP009273	982919	982958	40	2 [0]	[1] 2	ompF/asnS	porin OmpF/asparagine‑‑tRNA ligase
*	*	÷	NZ_CP009273	983061	983070	10	2 [1]	[0] 4	asnS	asparagine‑‑tRNA ligase
*	*	÷	NZ_CP009273	1088102	1088130	29	2 [1]	[1] 3	pgaA/dgcT	poly‑beta‑1,6 N‑acetyl‑D‑glucosamine export porin PgaA/GGDEF domain‑containing protein
*	*	÷	NZ_CP009273	1172301	1172357	57	3 [1]	[1] 2	lolD	lipoprotein‑releasing ABC transporter ATP‑binding protein LolD
*	*	÷	NZ_CP009273	1184942	1184959	18	2 [0]	[1] 2	phoQ	two‑component system sensor histidine kinase PhoQ
*	*	÷	NZ_CP009273	1193061	1193083	23	2 [1]	[1] 2	BW25113_RS05920	hypothetical protein
*	*	÷	NZ_CP009273	1207675	1207691	17	4 [0]	[0] 5	iraM/BW25113_RS25985	anti‑adapter protein IraM/protein YmgK
*	*	÷	NZ_CP009273	1228934	1228942	9	3 [1]	[1] 2	nhaB	Na(+)/H(+) antiporter NhaB
*	*	÷	NZ_CP009273	1258706	1258784	79	3 [1]	[0] 6	lolB	lipoprotein insertase outer membrane protein LolB
*	*	÷	NZ_CP009273	1324129	1324151	23	2 [1]	[1] 4	sohB	protease SohB
*	*	÷	NZ_CP009273	1338988	1338990	3	2 [0]	[0] 2	ymiD	protein YmiD
*	*	÷	NZ_CP009273	1346015	1346061	47	2 [1]	[0] 2	[ycjD]	[ycjD]
*	*	÷	NZ_CP009273	1361224	1361236	13	2 [1]	[1] 4	pspF	phage shock protein operon transcriptional activator
*	*	÷	NZ_CP009273	1363718	1363754	37	3 [1]	[1] 2	pspD	phage shock protein PspD
*	*	÷	NZ_CP009273	1415759	1415783	25	2 [0]	[1] 3	ydaU	YdaU family protein
*	*	÷	NZ_CP009273	1459394	1459516	123	2 [1]	[1] 2	BW25113_RS25580	BW25113_RS25580
*	*	÷	NZ_CP009273	1521365	1521384	20	3 [1]	[1] 2	yncH	YncH family protein
*	*	÷	NZ_CP009273	1540297	1540372	76	2 [1]	[1] 2	yddL/yddG	porin/aromatic amino acid efflux DMT transporter YddG
*	*	÷	NZ_CP009273	1560574	1560652	79	3 [1]	[1] 4	dosC	diguanylate cyclase DosC
*	*	÷	NZ_CP009273	1572066	1572105	40	2 [1]	[1] 2	yddA	ABC transporter ATP‑binding protein/permease
*	*	÷	NZ_CP009273	1576961	1577049	89	2 [1]	[0] 3	ydeN/ydeO	sulfatase/acid stress response transcriptional regulator YdeO
*	*	÷	NZ_CP009273	1592526	1592543	18	2 [0]	[1] 3	BW25113_RS07915/lsrK	ECSE_1600 family autotransporter/autoinducer‑2 kinase
*	*	÷	NZ_CP009273	1729823	1729853	31	2 [0]	[1] 3	sodB	superoxide dismutase [Fe]
*	*	÷	NZ_CP009273	1826254	1826281	28	2 [0]	[1] 2	astC/xthA	succinylornithine/acetylornithine transaminase/exodeoxyribonuclease III
*	*	÷	NZ_CP009273	1830925	1830925	1	2 [0]	[0] 3	ynjB	ABC transporter substrate‑binding protein
*	*	÷	NZ_CP009273	1847216	1847226	11	2 [0]	[1] 3	ydjE	MFS transporter
*	*	÷	NZ_CP009273	1848410	1848429	20	2 [1]	[1] 2	ydjF	DeoR/GlpR family DNA‑binding transcription regulator
*	*	÷	NZ_CP009273	1864658	1864678	21	2 [1]	[1] 2	cdgI	GGDEF domain‑containing protein
*	*	÷	NZ_CP009273	2096858	2096879	22	4 [1]	[1] 2	[wbbL]–[wbbK]	[wbbL],[wbbK]
*	*	÷	NZ_CP009273	2101613	2101623	11	2 [0]	[0] 2	glf	UDP‑galactopyranose mutase
*	*	÷	NZ_CP009273	2101895	2101916	22	2 [1]	[1] 2	wzx	O16 family O‑antigen flippase
*	*	÷	NZ_CP009273	2170689	2170764	76	2 [1]	[1] 2	gatY/fbaB	tagatose‑bisphosphate aldolase subunit GatY/class I fructose‑bisphosphate aldolase
*	*	÷	NZ_CP009273	2463182	2463192	11	4 [0]	[0] 2	BW25113_RS12270	hypothetical protein
*	*	÷	NZ_CP009273	2622990	2623030	41	3 [1]	[1] 2	yfgG/yfgH	YfgG family protein/glycine zipper 2TM domain‑containing protein
*	*	÷	NZ_CP009273	2897180	2897243	64	2 [1]	[1] 2	ygcE/queE	FGGY‑family carbohydrate kinase/7‑carboxy‑7‑deazaguanine synthase QueE
*	*	÷	NZ_CP009273	2986924	2986952	29	2 [1]	[1] 3	ygeH/BW25113_RS14840	HilA family transcriptional regulator YgeH/hypothetical protein
*	*	÷	NZ_CP009273	2988558	2988641	84	2 [1]	[1] 3	BW25113_RS14850/BW25113_RS26010	response regulator transcription factor/hypothetical protein
*	*	÷	NZ_CP009273	2999279	2999304	26	2 [1]	[1] 2	ygeV/ygeW	sigma‑54‑dependent Fis family transcriptional regulator/knotted carbamoyltransferase YgeW
*	*	÷	NZ_CP009273	3129899	3129918	20	2 [0]	[1] 2	pitB/gss	inorganic phosphate transporter PitB/bifunctional glutathionylspermidine amidase/synthase
*	*	÷	NZ_CP009273	3178634	3178649	16	2 [0]	[0] 2	ubiK/ygiL	ubiquinone biosynthesis accessory factor UbiK/fimbrial‑like protein
*	*	÷	NZ_CP009273	3262601	3262632	32	2 [1]	[1] 3	yhaC	YhaC family protein
*	*	÷	NZ_CP009273	3280620	3280634	15	2 [1]	[1] 2	agaI/yraH	galactosamine‑6‑phosphate isomerase/fimbrial protein
*	*	÷	NZ_CP009273	3463406	3463433	28	2 [0]	[1] 2	chiA/tuf	bifunctional chitinase/lysozyme/elongation factor Tu
*	*	÷	NZ_CP009273	3647059	3647077	19	5 [1]	[0] 3	BW25113_RS18165/slp	hypothetical protein/outer membrane lipoprotein Slp
*	*	÷	NZ_CP009273	3837241	3837296	56	3 [1]	[1] 2	adeQ/adeD	adenine permease AdeQ/adenine deaminase
*	*	÷	NZ_CP009273	4241449	4241450	2	3 [0]	[0] 3	BW25113_RS20970	SopA family protein
*	*	÷	NZ_CP009273	4466835	4466882	48	2 [0]	[0] 2	BW25113_RS22080	hypothetical protein

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	15391 =	NA (NA)	19 (1.010)	14/156	0.3	95.2%	intergenic (+93/‑54)	dnaJ/BW25113_RS00080	molecular chaperone DnaJ/IS4‑like element IS421 family transposase
	?	NZ_CP009273	= 454255	1 (0.050)					intergenic (+99/‑89)	clpX/lon	ATP‑dependent protease ATP‑binding subunit ClpX/endopeptidase La
*	?	NZ_CP009273	360104 =	NA (NA)	28 (1.410)	16/164	0.2	40.6%	intergenic (‑35/+251)	lacZ/BW25113_RS23320	beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein
	?	NZ_CP009273	= 360286	41 (2.070)					intergenic (‑217/+69)	lacZ/BW25113_RS23320	beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein
*	?	NZ_CP009273	454243 =	3 (0.150)	21 (1.100)	14/158	0.3	87.9%	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 =	0 (0.000)	8 (0.500)	8/132	0.5	94.1%	coding (290/630 nt)	BW25113_RS05990	hypothetical protein
	?	NZ_CP009273	1205075 =	1 (0.060)					coding (40/540 nt)	BW25113_RS06005	phage tail protein
*	?	NZ_CP009273	= 1203261	0 (0.000)	7 (0.440)	6/132	0.7	93.3%	coding (305/630 nt)	BW25113_RS05990	hypothetical protein
	?	NZ_CP009273	= 1205058	1 (0.060)					coding (57/540 nt)	BW25113_RS06005	phage tail protein
*	?	NZ_CP009273	= 1391494	NA (NA)	8 (0.410)	6/162	1.0	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	= 1972751	0 (0.000)	21 (1.060)	12/164	0.4	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 =	1 (0.050)	11 (0.620)	8/146	0.6	81.8%	intergenic (+49/‑433)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP009273	4532813 =	4 (0.230)					intergenic (+363/‑119)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
*	?	NZ_CP009273	= 4532507	1 (0.050)	7 (0.400)	6/146	0.8	74.1%	intergenic (+57/‑425)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP009273	= 4532803	4 (0.230)					intergenic (+353/‑129)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA