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	80516	80543	28	3 [0]	[1] 3	leuL/leuO	leu operon leader peptide/transcriptional regulator LeuO
*	*	÷	NZ_CP009273	118264	118282	19	3 [1]	[1] 2	aroP/pdhR	aromatic amino acid transporter AroP/pyruvate dehydrogenase complex transcriptional repressor PdhR
*	*	÷	NZ_CP009273	230566	230633	68	2 [1]	[1] 3	gloB	hydroxyacylglutathione hydrolase
*	*	÷	NZ_CP009273	243020	243037	18	2 [1]	[1] 2	dinJ/yafL	type II toxin‑antitoxin system antitoxin DinJ/C40 family peptidase
*	*	÷	NZ_CP009273	356976	357568	593	2 [1]	[1] 2	lacA	galactoside O‑acetyltransferase
*	*	÷	NZ_CP009273	567059	567087	29	2 [1]	[1] 2	ybcM	helix‑turn‑helix transcriptional regulator
*	*	÷	NZ_CP009273	567198	567263	66	2 [1]	[1] 3	ybcM	helix‑turn‑helix transcriptional regulator
*	*	÷	NZ_CP009273	569861	569866	6	2 [0]	[0] 2	quuD/BW25113_RS02850	antitermination protein QuuD/IS5‑like element IS5 family transposase
*	*	÷	NZ_CP009273	572333	572447	115	2 [1]	[1] 3	BW25113_RS02855/essD	porin/phage lysis protein EssD
*	*	÷	NZ_CP009273	578962	579066	105	2 [1]	[1] 2	BW25113_RS26085/appY	tail fiber assembly protein/DNA‑binding transcriptional activator AppY
*	*	÷	NZ_CP009273	579276	579301	26	3 [0]	[1] 2	appY	DNA‑binding transcriptional activator AppY
*	*	÷	NZ_CP009273	579618	579663	46	2 [0]	[1] 2	appY	DNA‑binding transcriptional activator AppY
*	*	÷	NZ_CP009273	579778	579781	4	3 [0]	[0] 2	appY	DNA‑binding transcriptional activator AppY
*	*	÷	NZ_CP009273	579867	579933	67	5 [1]	[0] 2	[appY]	[appY]
*	*	÷	NZ_CP009273	580001	580011	11	2 [0]	[0] 2	appY/ompT	DNA‑binding transcriptional activator AppY/omptin family outer membrane protease OmpT
*	*	÷	NZ_CP009273	581290	581349	60	2 [1]	[1] 2	ompT/envY	omptin family outer membrane protease OmpT/DNA‑binding transcriptional regulator EnvY
*	*	÷	NZ_CP009273	632508	632543	36	2 [0]	[1] 2	ybdO	LysR family transcriptional regulator
*	*	÷	NZ_CP009273	647490	647522	33	2 [1]	[1] 2	citC/dpiB	[citrate (pro‑3S)‑lyase] ligase/sensor histidine kinase DpiB
*	*	÷	NZ_CP009273	647613	647621	9	2 [1]	[1] 2	citC/dpiB	[citrate (pro‑3S)‑lyase] ligase/sensor histidine kinase DpiB
*	*	÷	NZ_CP009273	716332	716350	19	4 [1]	[0] 3	BW25113_RS26090/kdpE	leader peptide SpeFL/two‑component system response regulator KdpE
*	*	÷	NZ_CP009273	716523	716545	23	5 [1]	[0] 2	kdpE	two‑component system response regulator KdpE
*	*	÷	NZ_CP009273	731649	731658	10	2 [1]	[0] 2	BW25113_RS03640	hypothetical protein
*	*	÷	NZ_CP009273	731696	731829	134	2 [0]	[1] 3	BW25113_RS03640/ybfQ	hypothetical protein/ISAs1 family transposase
*	*	÷	NZ_CP009273	748531	748600	70	3 [1]	[1] 3	ybgD/gltA	fimbrial protein/citrate synthase
*	*	÷	NZ_CP009273	816157	816221	65	2 [1]	[1] 2	ybhL/ybhM	Bax inhibitor‑1/YccA family protein/Bax inhibitor‑1/YccA family protein
*	*	÷	NZ_CP009273	868426	868465	40	2 [0]	[1] 3	[pdeI]	[pdeI]
*	*	÷	NZ_CP009273	903021	903036	16	2 [0]	[1] 2	ybjT	SDR family oxidoreductase
*	*	÷	NZ_CP009273	949990	950040	51	3 [0]	[1] 3	focA/ycaO	formate transporter FocA/30S ribosomal protein S12 methylthiotransferase accessory factor YcaO
*	*	÷	NZ_CP009273	982669	982711	43	2 [0]	[1] 2	ompF/asnS	porin OmpF/asparagine‑‑tRNA ligase
*	*	÷	NZ_CP009273	993181	993231	51	2 [0]	[1] 2	ssuE/elfA	NADPH‑dependent FMN reductase/fimbrial protein
*	*	÷	NZ_CP009273	1059498	1059554	57	2 [0]	[1] 3	yccE	YccE family protein
*	*	÷	NZ_CP009273	1059599	1059658	60	3 [1]	[1] 2	yccE	YccE family protein
*	*	÷	NZ_CP009273	1059753	1059808	56	2 [1]	[0] 3	yccE	YccE family protein
*	*	÷	NZ_CP009273	1081854	1081877	24	2 [1]	[1] 2	pgaD	poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine biosynthesis protein PgaD
*	*	÷	NZ_CP009273	1144759	1144800	42	2 [1]	[1] 3	fabH	beta‑ketoacyl‑ACP synthase III
*	*	÷	NZ_CP009273	1172287	1172340	54	2 [1]	[1] 2	lolD	lipoprotein‑releasing ABC transporter ATP‑binding protein LolD
*	*	÷	NZ_CP009273	1176281	1176293	13	2 [1]	[1] 5	ycfZ	TPM domain‑containing protein
*	*	÷	NZ_CP009273	1188853	1188862	10	2 [1]	[0] 2	mnmA	tRNA 2‑thiouridine(34) synthase MnmA
*	*	÷	NZ_CP009273	1190805	1190808	4	2 [0]	[0] 2	icd	NADP‑dependent isocitrate dehydrogenase
*	*	÷	NZ_CP009273	1192318	1192337	20	2 [1]	[1] 2	[ymfD]	[ymfD]
*	*	÷	NZ_CP009273	1192630	1192721	92	2 [1]	[1] 2	ymfD	class I SAM‑dependent methyltransferase
*	*	÷	NZ_CP009273	1200831	1200863	33	2 [1]	[1] 3	BW25113_RS05965	terminase large subunit
*	*	÷	NZ_CP009273	1205052	1205052	1	2 [0]	[0] 2	BW25113_RS06005	phage tail protein
*	*	÷	NZ_CP009273	1207285	1207369	85	2 [1]	[1] 2	iraM	anti‑adapter protein IraM
*	*	÷	NZ_CP009273	1207530	1207556	27	2 [0]	[1] 2	iraM/BW25113_RS25985	anti‑adapter protein IraM/protein YmgK
*	*	÷	NZ_CP009273	1207645	1207701	57	3 [1]	[1] 3	iraM/BW25113_RS25985	anti‑adapter protein IraM/protein YmgK
*	*	÷	NZ_CP009273	1207757	1207827	71	3 [1]	[1] 3	[BW25113_RS25985]	[BW25113_RS25985]
*	*	÷	NZ_CP009273	1211116	1211138	23	2 [1]	[1] 3	bluF/ycgZ	blue light‑responsive regulator BluF/regulatory protein YcgZ
*	*	÷	NZ_CP009273	1212153	1212155	3	2 [0]	[0] 2	ariR/BW25113_RS06060	biofilm/acid‑resistance regulator AriR/hypothetical protein
*	*	÷	NZ_CP009273	1218524	1218709	186	4 [1]	[1] 3	[BW25113_RS06100]	[BW25113_RS06100]
*	*	÷	NZ_CP009273	1294882	1294926	45	2 [0]	[0] 2	BW25113_RS25865	hypothetical protein
*	*	÷	NZ_CP009273	1310507	1310531	25	2 [0]	[1] 3	yciG/trpA	general stress protein/tryptophan synthase subunit alpha
*	*	÷	NZ_CP009273	1320627	1320675	49	2 [0]	[1] 2	yciQ	DUF2207 domain‑containing protein
*	*	÷	NZ_CP009273	1377951	1377967	17	2 [0]	[1] 2	ycjW	LacI family DNA‑binding transcriptional regulator
*	*	÷	NZ_CP009273	1389964	1390010	47	2 [0]	[1] 2	ynaI	low conductance mechanosensitive channel YnaI
*	*	÷	NZ_CP009273	1427957	1428531–1428356	400–575	2 [1]	[1] 2	ydfK	ydfK
*	*	÷	NZ_CP009273	1459348	1459432	85	3 [1]	[1] 3	[BW25113_RS25580]	[BW25113_RS25580]
*	*	÷	NZ_CP009273	1521865	1521887	23	2 [0]	[0] 2	yncH/BW25113_RS07645	YncH family protein/RHS repeat protein
*	*	÷	NZ_CP009273	1521931	1521997	67	2 [0]	[1] 2	yncH/BW25113_RS07645	YncH family protein/RHS repeat protein
*	*	÷	NZ_CP009273	1524429	1524487	59	2 [0]	[1] 2	BW25113_RS26145	hypothetical protein
*	*	÷	NZ_CP009273	1539048	1539130	83	2 [1]	[1] 2	BW25113_RS07710	leucine‑rich repeat domain‑containing protein
*	*	÷	NZ_CP009273	1566584	1566620	37	2 [1]	[1] 2	gadB/pqqL	glutamate decarboxylase/insulinase family protein
*	*	÷	NZ_CP009273	1573583	1573626	44	2 [1]	[1] 2	[yddA]	[yddA]
*	*	÷	NZ_CP009273	1574802	1574817	16	4 [0]	[1] 2	ydeM	anaerobic sulfatase maturase
*	*	÷	NZ_CP009273	1576878	1576963	86	2 [1]	[0] 2	ydeN/ydeO	sulfatase/acid stress response transcriptional regulator YdeO
*	*	÷	NZ_CP009273	1580831	1580843	13	3 [1]	[0] 2	ydeP/ydeQ	acid resistance putative oxidoreductase YdeP/fimbrial protein
*	*	÷	NZ_CP009273	1631990	1632100	111	2 [0]	[1] 3	[gnsB]	[gnsB]
*	*	÷	NZ_CP009273	1685882	1685895	14	2 [1]	[0] 2	uidC	glucuronide uptake porin UidC
*	*	÷	NZ_CP009273	1748967	1749066	100	3 [0]	[1] 3	ydhY/fumD	ferredoxin‑like protein/fumarate hydratase FumD
*	*	÷	NZ_CP009273	1772983	1773007	25	3 [1]	[1] 2	ydiP	AraC family transcriptional regulator
*	*	÷	NZ_CP009273	1798623	1798636	14	2 [0]	[1] 3	espL1	type III secretion system effector EspL1
*	*	÷	NZ_CP009273	1806942	1806980	39	2 [0]	[1] 3	BW25113_RS09050	hypothetical protein
*	*	÷	NZ_CP009273	1864657	1864733	77	2 [1]	[1] 2	cdgI	GGDEF domain‑containing protein
*	*	÷	NZ_CP009273	1877364	1877430	67	3 [1]	[1] 2	[yeaV]	[yeaV]
*	*	÷	NZ_CP009273	1952498	1952515	18	2 [0]	[1] 3	torY/cutC	NapC/NirT family cytochrome c/copper homeostasis protein CutC
*	*	÷	NZ_CP009273	1973024	1973092	69	2 [1]	[1] 2	flhD/uspC	flagellar transcriptional regulator FlhD/universal stress protein UspC
*	*	÷	NZ_CP009273	1980157	1980251	95	2 [1]	[1] 3	araF/ftnB	arabinose ABC transporter substrate‑binding protein AraF/non‑heme ferritin‑like protein
*	*	÷	NZ_CP009273	2004762	2004767	6	2 [0]	[0] 2	BW25113_RS10120	DUF5503 domain‑containing protein
*	*	÷	NZ_CP009273	2027132	2027152	21	2 [1]	[0] 2	drpB/ompC	cell division protein DrpB/porin OmpC
*	*	÷	NZ_CP009273	2028931	2028960	30	2 [1]	[1] 2	ompC/hchA	porin OmpC/protein deglycase HchA
*	*	÷	NZ_CP009273	2033104	2033151	48	2 [0]	[1] 3	msrP	protein‑methionine‑sulfoxide reductase catalytic subunit MsrP
*	*	÷	NZ_CP009273	2035352	2035364	13	3 [1]	[0] 2	zinT	metal‑binding protein ZinT
*	*	÷	NZ_CP009273	2035404	2035414	11	2 [0]	[0] 2	zinT	metal‑binding protein ZinT
*	*	÷	NZ_CP009273	2051081	2051147	67	2 [1]	[1] 2	yeeN/BW25113_RS10360	YebC/PmpR family DNA‑binding transcriptional regulator/tRNA‑Asn
*	*	÷	NZ_CP009273	2052915	2052921	7	2 [1]	[1] 2	yeeO	toxic metabolite efflux MATE transporter YeeO
*	*	÷	NZ_CP009273	2096813	2096874	62	2 [1]	[1] 3	[wbbL]–[wbbK]	[wbbL],[wbbK]
*	*	÷	NZ_CP009273	2097525	2097592	68	2 [1]	[1] 2	wbbK	glycosyltransferase family 1 protein
*	*	÷	NZ_CP009273	2099570	2099625	56	2 [1]	[1] 2	wzy	O16 family O‑antigen polymerase
*	*	÷	NZ_CP009273	2100130	2100145	16	4 [1]	[0] 2	wzy	O16 family O‑antigen polymerase
*	*	÷	NZ_CP009273	2101496	2101594	99	2 [1]	[1] 2	glf	UDP‑galactopyranose mutase
*	*	÷	NZ_CP009273	2108346	2108351	6	4 [0]	[1] 3	wcaM	colanic acid biosynthesis protein WcaM
*	*	÷	NZ_CP009273	2144495	2144513	19	2 [1]	[1] 3	yegI/yegJ	protein kinase YegI/DUF2314 domain‑containing protein
*	*	÷	NZ_CP009273	2185795	2185918	124	2 [1]	[0] 3	yehD/yehE	fimbrial protein/YehE family protein
*	*	÷	NZ_CP009273	2377053	2377070	18	2 [1]	[0] 2	elaD	deubiquitinase ElaD
*	*	÷	NZ_CP009273	2380370	2380380	11	2 [1]	[0] 3	yfbL/yfbM	M28 family metallopeptidase/YfbM family protein
*	*	÷	NZ_CP009273	2449451	2449463	13	3 [1]	[1] 2	yfcV/sixA	fimbrial protein/phosphohistidine phosphatase SixA
*	*	÷	NZ_CP009273	2462836	2462886	51	2 [1]	[0] 2	BW25113_RS12270	hypothetical protein
*	*	÷	NZ_CP009273	2463160	2463189	30	2 [1]	[0] 2	BW25113_RS12270	hypothetical protein
*	*	÷	NZ_CP009273	2463562	2463727	166	3 [1]	[1] 2	BW25113_RS12270	hypothetical protein
*	*	÷	NZ_CP009273	2463818	2463873	56	2 [1]	[0] 2	BW25113_RS12270	hypothetical protein
*	*	÷	NZ_CP009273	2563818	2563833	16	3 [1]	[0] 3	eutE	aldehyde dehydrogenase EutE
*	*	÷	NZ_CP009273	2584399	2584495	97	2 [0]	[1] 2	ypfM/yffB	protein YpfM/ArsC family reductase
*	*	÷	NZ_CP009273	2753688	2753733	46	2 [0]	[1] 2	yfjI	YfjI family protein
*	*	÷	NZ_CP009273	2767048	2767069	22	2 [0]	[1] 2	BW25113_RS13770	hypothetical protein
*	*	÷	NZ_CP009273	2777555	2777644	90	3 [1]	[1] 3	BW25113_RS25705	DUF5507 domain‑containing protein
*	*	÷	NZ_CP009273	2779382	2779409	28	3 [1]	[1] 2	BW25113_RS13825/BW25113_RS26005	tRNA‑Ile/alpha‑amylase family glycosyl hydrolase
*	*	÷	NZ_CP009273	2877619	2877641	23	2 [0]	[0] 2	casA/cas3	type I‑E CRISPR‑associated protein Cse1/CasA/CRISPR‑associated helicase/endonuclease Cas3
*	*	÷	NZ_CP009273	2897091	2897132	42	2 [1]	[0] 2	ygcE/queE	FGGY‑family carbohydrate kinase/7‑carboxy‑7‑deazaguanine synthase QueE
*	*	÷	NZ_CP009273	2897880	2897904	25	3 [1]	[1] 2	ygcE/queE	FGGY‑family carbohydrate kinase/7‑carboxy‑7‑deazaguanine synthase QueE
*	*	÷	NZ_CP009273	2980506	2980617	112	2 [1]	[0] 2	yqeG/yqeH	amino acid permease/helix‑turn‑helix transcriptional regulator
*	*	÷	NZ_CP009273	2981706	2981733	28	2 [0]	[0] 3	yqeH/yqeI	helix‑turn‑helix transcriptional regulator/transcriptional regulator
*	*	÷	NZ_CP009273	2983296	2983305	10	2 [0]	[1] 2	BW25113_RS14820	hypothetical protein
*	*	÷	NZ_CP009273	2984458	2984524	67	2 [1]	[0] 2	BW25113_RS14825/ygeG	hypothetical protein/tetratricopeptide repeat protein
*	*	÷	NZ_CP009273	3112445	3112481	37	2 [1]	[0] 2	[sslE]	[sslE]
*	*	÷	NZ_CP009273	3112611	3112621	11	2 [0]	[0] 4	sslE/glcA	lipoprotein metalloprotease SslE/glycolate permease GlcA
*	*	÷	NZ_CP009273	3262523	3262555	33	2 [1]	[1] 2	yhaC	YhaC family protein
*	*	÷	NZ_CP009273	3262646	3262707	62	2 [1]	[1] 5	yhaC	YhaC family protein
*	*	÷	NZ_CP009273	3280648	3280685	38	2 [1]	[1] 2	agaI/yraH	galactosamine‑6‑phosphate isomerase/fimbrial protein
*	*	÷	NZ_CP009273	3448784	3448882	99	3 [1]	[1] 2	gspA/gspC	type II secretion system protein GspA/type II secretion system protein GspC
*	*	÷	NZ_CP009273	3617381	3617384	4	3 [0]	[1] 2	BW25113_RS18035	lyase
*	*	÷	NZ_CP009273	3627377	3627411	35	3 [1]	[0] 2	BW25113_RS18065	YhiJ/YhiL family protein
*	*	÷	NZ_CP009273	3644365	3644375	11	2 [0]	[1] 3	arsC/BW25113_RS18155	glutaredoxin‑dependent arsenate reductase/hypothetical protein
*	*	÷	NZ_CP009273	3647067	3647077	11	4 [0]	[0] 4	BW25113_RS18165/slp	hypothetical protein/outer membrane lipoprotein Slp
*	*	÷	NZ_CP009273	3751289	3751350	62	2 [1]	[1] 3	yiaY/selB	L‑threonine dehydrogenase/selenocysteine‑specific translation elongation factor
*	*	÷	NZ_CP009273	3792426	3792467	42	2 [0]	[0] 4	waaU	glycosyltransferase family 9 protein
*	*	÷	NZ_CP009273	3798122	3798132	11	2 [0]	[1] 2	rfaS	LPS core biosynthesis protein RfaS
*	*	÷	NZ_CP009273	3798371	3798396	26	2 [0]	[1] 2	rfaS	LPS core biosynthesis protein RfaS
*	*	÷	NZ_CP009273	4062689	4062701	13	2 [0]	[0] 2	yihQ/yihR	sulfoquinovosidase/aldose‑1‑epimerase
*	*	÷	NZ_CP009273	4072417	4072445	29	2 [1]	[1] 2	BW25113_RS26270/yiiE	hypothetical protein/ribbon‑helix‑helix domain‑containing protein
*	*	÷	NZ_CP009273	4225613	4225660	48	2 [1]	[0] 2	pgi/yjbE	glucose‑6‑phosphate isomerase/exopolysaccharide production protein YjbE
*	*	÷	NZ_CP009273	4487732	4487742	11	2 [0]	[0] 3	BW25113_RS22170	tyrosine‑type recombinase/integrase
*	*	÷	NZ_CP009273	4592974	4593063	90	2 [1]	[1] 2	yjjP/yjjQ	threonine/serine exporter ThrE family protein/response regulator transcription factor

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	360104 =	NA (NA)	36 (1.890)	22/160	0.1	NA	intergenic (‑35/+251)	lacZ/BW25113_RS23320	beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein
*	?	NZ_CP009273	= 360286	NA (NA)	36 (1.890)	22/160	0.1	NA	intergenic (‑217/+69)	lacZ/BW25113_RS23320	beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein
*	?	NZ_CP009273	= 1391494	NA (NA)	9 (0.480)	6/158	1.0	69.5%	intergenic (+145/‑128)	BW25113_RS06980/ynaJ	IS5‑like element IS5 family transposase/DUF2534 family protein
*	?	NZ_CP009273	1972747 =	4 (0.210)	9 (0.480)	6/158	1.0	69.5%	intergenic (‑293/‑487)	flhD/uspC	flagellar transcriptional regulator FlhD/universal stress protein UspC
*	?	NZ_CP009273	= 1972751	1 (0.050)	24 (1.260)	14/160	0.3	96.0%	intergenic (‑297/‑483)	flhD/uspC	flagellar transcriptional regulator FlhD/universal stress protein UspC
*	?	NZ_CP009273	= 2283592	NA (NA)	24 (1.260)	14/160	0.3	96.0%	intergenic (‑68/‑387)	BW25113_RS11435/narP	IS5‑like element IS5 family transposase/nitrate/nitrite response regulator protein NarP