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	1,484,303	T→G	V125G (GTC→GGC)	yhdX →	amino acid ABC transporter permease
JC	1,843,229	(GCGCCAGTTCGTGGC)1→2	coding (1607/2754 nt)	gacS ←	sensor protein GacS
MC JC	1,930,434	Δ63 bp		[apeB]	[apeB]
RA	3,823,901	+T	coding (1248/1293 nt)	kguT ←	2‑ketogluconate transporter, putative
RA	3,824,415	A→G	I245T (ATC→ACC)	kguT ←	2‑ketogluconate transporter, putative
MC JC	3,827,335	Δ51 bp	coding (626‑676/1020 nt)	ptxS ←	2‑ketogluconate utilization repressor
RA	4,160,437	A→C	S161R (AGC→CGC)	PP_3661 →	membrane protein
RA	4,743,195	+C	intergenic (+464/+288)	gltA → / ← yeiW	citrate synthase/putative oxidoreductase
RA	4,743,197	A→G	intergenic (+466/+286)	gltA → / ← yeiW	citrate synthase/putative oxidoreductase
RA	4,743,199	C→T	intergenic (+468/+284)	gltA → / ← yeiW	citrate synthase/putative oxidoreductase
RA	4,743,202	C→T	intergenic (+471/+281)	gltA → / ← yeiW	citrate synthase/putative oxidoreductase
RA	4,743,205	C→G	intergenic (+474/+278)	gltA → / ← yeiW	citrate synthase/putative oxidoreductase
RA	4,743,207	2 bp→CT	intergenic (+476/+275)	gltA → / ← yeiW	citrate synthase/putative oxidoreductase
RA	4,743,221	C→T	intergenic (+490/+262)	gltA → / ← yeiW	citrate synthase/putative oxidoreductase
RA	4,743,223	A→C	intergenic (+492/+260)	gltA → / ← yeiW	citrate synthase/putative oxidoreductase
RA	4,743,226	2 bp→GC	intergenic (+495/+256)	gltA → / ← yeiW	citrate synthase/putative oxidoreductase

Unassigned missing coverage evidence
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_002947	19502	19566	65	2 [1]	[1] 3	PP_0015	transposon protein
*	*	÷	NC_002947	20797	20933	137	2 [1]	[1] 2	PP_0016	hypothetical protein
*	*	÷	NC_002947	22872	22959	88	2 [0]	[1] 2	PP_0017/PP_0018	transcriptional regulator/hypothetical protein
*	*	÷	NC_002947	23343	23377	35	2 [1]	[1] 3	PP_0018	hypothetical protein
*	*	÷	NC_002947	23813	23929	117	3 [1]	[1] 2	PP_0018	hypothetical protein
*	*	÷	NC_002947	34709	34722	14	2 [1]	[0] 2	czrSA	metal‑sensor histidine kinase
*	*	÷	NC_002947	35314	35366	53	2 [1]	[1] 2	PP_0031	hypothetical protein
*	*	÷	NC_002947	43411	43449	39	2 [1]	[1] 2	[PP_0040]	[PP_0040]
*	*	÷	NC_002947	97568	97611	44	2 [1]	[1] 5	[PP_0090]–[PP_0091]	[PP_0090],[PP_0091]
*	*	÷	NC_002947	170836	170848	13	2 [0]	[1] 2	PP_0159/PP_16SA	family III CoA‑transferase/16S ribosomal RNA
*	*	÷	NC_002947	171390–176316	176316	1–4927	2 [1]	[1] 2	[PP_16SA]–[PP_5SA]	[PP_16SA],PP_23SA,[PP_5SA]
*	*	÷	NC_002947	176645–181722	181722	1–5078	2 [1]	[1] 2	PP_16SB–[PP_r01]	PP_16SB,PP_23SB,[PP_r01]
*	*	÷	NC_002947	353059	353115	57	2 [1]	[1] 2	hisF/cbcV	imidazole glycerol phosphate synthase subunit HisF/choline/betaine/carnitine ABC transporter ATP binding protein
*	*	÷	NC_002947	524170	524205	36	2 [1]	[1] 3	tyrS/PP_16SC	tyrosine‑‑tRNA ligase/16S ribosomal RNA
*	*	÷	NC_002947	536776	536854	79	2 [1]	[1] 2	rplJ	50S ribosomal protein L10
*	*	÷	NC_002947	614283	614321	39	2 [1]	[1] 3	dxs/ispA	1‑deoxyxylulose‑5‑phosphate synthase/farnesyl diphosphate synthase
*	*	÷	NC_002947	681289	681307	19	2 [1]	[0] 2	PP_0583/PP_0584	AraC family transcriptional regulator/methyl‑accepting chemotaxis transducer
*	*	÷	NC_002947	718452	718476	25	2 [1]	[1] 2	thiO/PP_0613	FAD‑dependent glycine/D‑amino acid oxidase/amidase family protein
*	*	÷	NC_002947	883871	883889	19	2 [0]	[1] 2	PP_0766/PP_0767	hypothetical protein/LuxR family transcriptional regulator
*	*	÷	NC_002947	955141	955159	19	2 [1]	[0] 2	cyoE/alaC	protoheme IX farnesyltransferase/aminotransferase
*	*	÷	NC_002947	1114923	1114941	19	3 [0]	[0] 2	rlmF/valS	ribosomal RNA large subunit methyltransferase F/valine‑‑tRNA ligase
*	*	÷	NC_002947	1156332	1156359	28	2 [1]	[0] 2	PP_1013/yihS	sensor histidine kinase/aldose‑ketose isomerase
*	*	÷	NC_002947	1367700	1367749	50	2 [1]	[1] 3	PP_1193	membrane protein
*	*	÷	NC_002947	1419584	1419591	8	2 [0]	[0] 2	PP_1242/PP_1244	hypothetical protein/hypothetical protein
*	*	÷	NC_002947	1499473	1499498	26	3 [1]	[1] 2	trpS/zapE	tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein
*	*	÷	NC_002947	1592635	1592672	38	2 [1]	[0] 4	PP_1397	hypothetical protein
*	*	÷	NC_002947	1639610	1639660	51	3 [1]	[1] 6	czcR‑III/PP_1439	response regulator/hypothetical protein
*	*	÷	NC_002947	1921576	1921607	32	3 [1]	[1] 4	PP_1720/PP_1721	alcohol dehydrogenase/phosphoserine phosphatase
*	*	÷	NC_002947	1970805	1970823	19	2 [1]	[0] 2	mtnA/PP_mr25	methylthioribose‑1‑phosphate isomerase/gyrA regulatory region
*	*	÷	NC_002947	2003395	2003516	122	2 [1]	[1] 2	PP_1786	glycosyl transferase
*	*	÷	NC_002947	2006704	2006782	79	2 [1]	[1] 2	[PP_1789]–[PP_1790]	[PP_1789],[PP_1790]
*	*	÷	NC_002947	2187079	2187211	133	2 [0]	[1] 2	PP_1936	membrane protein
*	*	÷	NC_002947	2187937	2187961	25	3 [0]	[1] 2	PP_1936	membrane protein
*	*	÷	NC_002947	2188196	2188207	12	2 [0]	[1] 2	PP_1936	membrane protein
*	*	÷	NC_002947	2192366	2192409	44	2 [1]	[0] 3	PP_1937	helicase
*	*	÷	NC_002947	2203387	2203444	58	2 [1]	[0] 2	PP_1946	short‑chain dehydrogenase/reductase family oxidoreductase
*	*	÷	NC_002947	2222641	2222692	52	2 [1]	[0] 2	PP_1960	hypothetical protein
*	*	÷	NC_002947	2297796	2297823	28	8 [0]	[1] 2	PP_5496/PP_2023	hypothetical protein/glutathione S‑transferase family protein
*	*	÷	NC_002947	3055154	3055211	58	4 [0]	[1] 2	[PP_2664]–[agmR]	[PP_2664],[agmR]
*	*	÷	NC_002947	3468792	3468817	26	2 [0]	[0] 3	PP_3081/PP_5560	hypothetical protein/hypothetical protein
*	*	÷	NC_002947	3778314	3778379	66	2 [0]	[0] 2	PP_3338/PP_3339	cytochrome bd‑type quinol oxidase/hypothetical protein
*	*	÷	NC_002947	3953052	3953070	19	2 [1]	[0] 2	PP_3486/PP_3487	cytochrome c/hypothetical protein
*	*	÷	NC_002947	4051876	4051888	13	3 [0]	[1] 2	quiA/oprB‑III	quinate dehydrogenase/carbohydrate‑selective porin
*	*	÷	NC_002947	4081443	4081473	31	2 [1]	[1] 5	sdaC/amaC	serine:H+ symport permease/D‑lysine aminotransferase
*	*	÷	NC_002947	4172144	4172157	14	2 [1]	[0] 2	katG/PP_3669	catalase‑peroxidase/LysR family transcriptional regulator
*	*	÷	NC_002947	4184621	4184695	75	4 [1]	[1] 2	PP_3680	hypothetical protein
*	*	÷	NC_002947	4206232	4206333	102	2 [1]	[1] 2	PP_3691	DNA helicase‑related protein
*	*	÷	NC_002947	4212977	4212993	17	2 [1]	[1] 3	PP_5621	hypothetical protein
*	*	÷	NC_002947	4214257	4214402	146	2 [1]	[1] 2	PP_3694	hypothetical protein
*	*	÷	NC_002947	4223436	4223532	97	2 [1]	[1] 2	PP_3700	chromosome partitioning ATPase
*	*	÷	NC_002947	4226551	4226598	48	2 [0]	[1] 2	PP_3703/PP_3704	hypothetical protein/hypothetical protein
*	*	÷	NC_002947	4229540	4229627	88	2 [1]	[1] 2	PP_3706	hypothetical protein
*	*	÷	NC_002947	4355149	4355164	16	2 [1]	[1] 6	yrpB	2‑nitropropane dioxygenase
*	*	÷	NC_002947	4677277	4677338	62	4 [1]	[1] 2	PP_4137/chrR	outer membrane siderophore receptor/chromate reductase
*	*	÷	NC_002947	4742773	4742824	52	2 [0]	[1] 2	gltA/yeiW	citrate synthase/putative oxidoreductase
*	*	÷	NC_002947	4798556	4798590	35	2 [1]	[0] 3	pvdH/PP_4224	diaminobutyrate‑2‑oxoglutarate transaminase/sensor histidine kinase
*	*	÷	NC_002947	4810147	4810175	29	20 [0]	[0] 10	PP_4234/dsbD‑II	bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
*	*	÷	NC_002947	4844864	4844868	5	2 [1]	[0] 2	ccoP‑II/PP_4259	cbb3‑type cytochrome c oxidase subunit/iron‑sulfur cluster‑binding protein
*	*	÷	NC_002947	4854421	4854447	27	5 [0]	[1] 2	recR/ybaB	recombination protein RecR/nucleoid‑associated broad specificity regulator
*	*	÷	NC_002947	4952923	4952960	38	2 [1]	[1] 2	fliL/fliK	flagellar protein FliL/flagellar hook‑length control protein FliK
*	*	÷	NC_002947	5029647	5029732	86	3 [1]	[1] 3	[ocd]–[PP_4432]	[ocd],[PP_4432]
*	*	÷	NC_002947	5030388	5030417	30	2 [1]	[1] 2	PP_4432	Xaa‑Pro aminopeptidase
*	*	÷	NC_002947	5058733	5058846	114	2 [1]	[1] 2	ooxA	opine oxidase subunit A
*	*	÷	NC_002947	5065530	5065615	86	2 [1]	[1] 2	PP_4460/PP_4461	LysR family transcriptional regulator/MFS transporter
*	*	÷	NC_002947	5068031	5068054	24	3 [1]	[1] 2	PP_4463	carbon‑nitrogen hydrolase family protein
*	*	÷	NC_002947	5069713	5069733	21	2 [1]	[1] 2	PP_4464/PP_4465	LysR family transcriptional regulator/porin
*	*	÷	NC_002947	5070666	5070785	120	2 [1]	[1] 2	PP_4465	porin
*	*	÷	NC_002947	5099205	5099219	15	2 [1]	[0] 2	PP_mr66/acsA‑I	P6/acetyl‑CoA synthetase
*	*	÷	NC_002947	5201613	5201658	46	2 [0]	[1] 2	PP_4579/PP_4580	LysR family transcriptional regulator/hypothetical protein
*	*	÷	NC_002947	5258830	5258845	16	2 [1]	[1] 2	PP_5703/PP_4634	type III effector protein HopJ/alpha/beta family hydrolase
*	*	÷	NC_002947	5487097	5487128	32	3 [1]	[1] 2	purH/purD	bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase/phosphoribosylamine‑‑glycine ligase
*	*	÷	NC_002947	5508537	5508565	29	4 [0]	[1] 2	PP_4839/cycA	iron‑regulated membrane protein/D‑alanine/beta‑alanine/D‑serine/glycine permease
*	*	÷	NC_002947	6100358	6100390	33	7 [0]	[0] 2	PP_5350	RpiR family transcriptional regulator
*	*	÷	NC_002947	6162520	6162564	45	2 [0]	[1] 2	PP_5740	hypothetical protein
*	*	÷	NC_002947	6163716	6163722	7	2 [1]	[0] 2	PP_5403	hypothetical protein
*	*	÷	NC_002947	6183852	6183858	7	21 [0]	[0] NA	atpI/–	ATP synthase protein I/–

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	1 =	0 (0.000)	21 (0.540)	16/264	0.6	100%	intergenic (–/+146)	–/parB	–/chromosome‑partitioning protein
	?	NC_002947	= 6183851	0 (0.000)					intergenic (‑3/–)	atpI/–	ATP synthase protein I/–
*	?	NC_002947	= 652786	35 (0.900)	23 (0.590)	7/264	1.5	56.8%	coding (1960/1962 nt)	ctpL	methyl‑accepting chemotaxis protein CtpL
	?	NC_002947	= 4810125	0 (0.000)					intergenic (‑267/‑288)	PP_4234/dsbD‑II	bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
*	?	NC_002947	= 652786	35 (0.900)	6 (0.210)	4/194	1.7	31.8%	coding (1960/1962 nt)	ctpL	methyl‑accepting chemotaxis protein CtpL
	?	NC_002947	4810176 =	0 (0.000)					intergenic (‑318/‑237)	PP_4234/dsbD‑II	bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
*	?	NC_002947	1617825 =	20 (0.520)	12 (0.350)	9/234	1.1	43.9%	intergenic (‑38/+135)	PP_1417/PP_1418	tricarboxylate transport protein TctB/tricarboxylate transport protein TctC
	?	NC_002947	1617914 =	13 (0.380)					intergenic (‑127/+46)	PP_1417/PP_1418	tricarboxylate transport protein TctB/tricarboxylate transport protein TctC
*	?	NC_002947	1843211 =	4 (0.100)	3 (0.080) +CGAACTT	3/250	2.3	44.2%	coding (1625/2754 nt)	gacS	sensor protein GacS
	?	NC_002947	= 1843218	4 (0.100)					coding (1618/2754 nt)	gacS	sensor protein GacS
*	?	NC_002947	2474067 =	5 (0.130)	3 (0.110)	3/186	1.9	34.2%	intergenic (+6/+143)	PP_2166/PP_2167	anti‑anti‑sigma factor/PhoD‑like phosphatase
	?	NC_002947	2474191 =	8 (0.290)					intergenic (+130/+19)	PP_2166/PP_2167	anti‑anti‑sigma factor/PhoD‑like phosphatase
*	?	NC_002947	= 2474080	5 (0.130)	3 (0.080)	3/250	2.3	21.6%	intergenic (+19/+130)	PP_2166/PP_2167	anti‑anti‑sigma factor/PhoD‑like phosphatase
	?	NC_002947	2474278 =	17 (0.460)					coding (1783/1851 nt)	PP_2167	PhoD‑like phosphatase
*	?	NC_002947	= 4810146	0 (0.000)	12 (0.360)	7/224	1.3	38.1%	intergenic (‑288/‑267)	PP_4234/dsbD‑II	bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
	?	NC_002947	= 5990927	39 (1.190)					intergenic (+243/‑303)	kefB‑III/PP_mr64	glutathione‑regulated potassium/H+ antiporter/C4 ncRNA