breseq  version 0.33.1  revision 8505477f25b3 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence	position	mutation	annotation	gene	description
RA	188,837	C→T	R316C (CGC→TGC)	PP_0165 →	GGDEF domain‑containing protein
RA	233,545	C→T	G548G (GGC→GGT)	PP_0180 →	cytochrome c family protein
RA	476,133	A→T	Q141L (CAG→CTG)	tsaD →	tRNA N6‑adenosine(37)‑threonylcarbamoyltransferase complex transferase subunit TsaD
RA	539,301	A→G	H559R (CAC→CGC)	rpoB →	DNA‑directed RNA polymerase subunit beta
RA	1,011,323	+T	intergenic (‑258/+192)	PP_0871 ← / ← SBRG_Ecoli_galM	glycine betaine/carnitine/choline ABC transporter permease/SBRG_Ecoli_galM
MC JC	1,515,811	(33-bp)2→1	pseudogene (715‑747/1851 nt)	PP_1325 ←	putative lipoprotein
RA	1,856,513	A→G	D203G (GAT→GGT)	relA →	ATP:GTP 3'‑pyrophosphotransferase
RA	2,533,181	G→A	A30A (GCG→GCA)	PP_2217 →	enoyl‑CoA hydratase
RA	4,018,201	G→A	intergenic (+144/‑36)	mvaB → / → PP_mr44	hydroxymethylglutaryl‑CoA lyase/CrcZ ncRNA
RA	4,163,459	T→G	L159R (CTG→CGG)	PP_3661 →	membrane protein
RA	4,746,222	+C	intergenic (+464/+288)	gltA → / ← yeiW	citrate synthase/putative oxidoreductase
RA	4,746,224	A→G	intergenic (+466/+286)	gltA → / ← yeiW	citrate synthase/putative oxidoreductase
RA	4,746,226	C→T	intergenic (+468/+284)	gltA → / ← yeiW	citrate synthase/putative oxidoreductase
RA	4,746,229	C→T	intergenic (+471/+281)	gltA → / ← yeiW	citrate synthase/putative oxidoreductase
RA	4,746,232	C→G	intergenic (+474/+278)	gltA → / ← yeiW	citrate synthase/putative oxidoreductase
RA	4,746,234	2 bp→CT	intergenic (+476/+275)	gltA → / ← yeiW	citrate synthase/putative oxidoreductase
RA	4,746,248	C→T	intergenic (+490/+262)	gltA → / ← yeiW	citrate synthase/putative oxidoreductase
RA	4,746,250	A→C	intergenic (+492/+260)	gltA → / ← yeiW	citrate synthase/putative oxidoreductase
RA	4,746,253	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	20790	20800	11	2 [0]	[1] 2	PP_0016	hypothetical protein
*	*	÷	NC_002947	97583	97606	24	3 [1]	[1] 2	PP_0090/PP_0091	hypothetical protein/putative lipoprotein
*	*	÷	NC_002947	170806	170858	53	2 [1]	[1] 3	[PP_0159]	[PP_0159]
*	*	÷	NC_002947	171394–172965	176278–172975	11–4885	2 [1]	[1] 2	[PP_16SA]–[PP_5SA]	[PP_16SA],PP_23SA,[PP_5SA]
*	*	÷	NC_002947	176673–178395	181704–178405	11–5032	2 [1]	[1] 2	PP_16SB–[PP_r01]	PP_16SB,PP_23SB,[PP_r01]
*	*	÷	NC_002947	315963	316030	68	2 [1]	[0] 2	[cysQ]	[cysQ]
*	*	÷	NC_002947	353099	353163	65	3 [0]	[0] 2	[cbcV]	[cbcV]
*	*	÷	NC_002947	403255	403271	17	2 [1]	[1] 2	msrA/PP_0337	peptide methionine sulfoxide reductase MsrA/sensory box protein
*	*	÷	NC_002947	524143	524231	89	4 [1]	[1] 2	tyrS/PP_16SC	tyrosine‑‑tRNA ligase/16S ribosomal RNA
*	*	÷	NC_002947	545260	545345	86	2 [1]	[1] 2	rpoC	DNA‑directed RNA polymerase subunit beta'
*	*	÷	NC_002947	558703	558710	8	3 [1]	[1] 2	rplR	50S ribosomal protein L18
*	*	÷	NC_002947	614303	614321	19	2 [0]	[0] 2	dxs/ispA	1‑deoxyxylulose‑5‑phosphate synthase/farnesyl diphosphate synthase
*	*	÷	NC_002947	668082	668156	75	5 [1]	[1] 3	yfhM/PP_0571	lipoprotein/membrane protein
*	*	÷	NC_002947	681262	681307	46	2 [1]	[1] 3	[PP_0583]	[PP_0583]
*	*	÷	NC_002947	697096	697152	57	3 [1]	[1] 2	mmsA‑I/PP_16SD	methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA
*	*	÷	NC_002947	718440	718470	31	2 [1]	[1] 2	thiO/PP_0613	FAD‑dependent glycine/D‑amino acid oxidase/amidase family protein
*	*	÷	NC_002947	796814	796888	75	2 [0]	[1] 2	PP_0681/PP_0682	hypothetical protein/inner membrane protein
*	*	÷	NC_002947	874312	874318	7	2 [0]	[0] 2	PP_0758/PP_0759	hypothetical protein/hypothetical protein
*	*	÷	NC_002947	883856	883893	38	2 [1]	[1] 2	PP_0766/PP_0767	hypothetical protein/LuxR family transcriptional regulator
*	*	÷	NC_002947	955138	955163	26	2 [0]	[1] 2	cyoE/alaC	protoheme IX farnesyltransferase/aminotransferase
*	*	÷	NC_002947	1012397	1012405	9	2 [1]	[1] 2	SBRG_Ecoli_galM	SBRG_Ecoli_galM
*	*	÷	NC_002947	1018183	1018194	12	2 [1]	[0] 2	prfC/potF‑I	peptide chain release factor 3/putrescine‑binding protein
*	*	÷	NC_002947	1161290	1161342	53	2 [1]	[1] 2	PP_1013/yihS	sensor histidine kinase/aldose‑ketose isomerase
*	*	÷	NC_002947	1259410	1259452	43	2 [0]	[1] 2	metG	methionine‑‑tRNA ligase
*	*	÷	NC_002947	1316656	1316752	97	2 [1]	[1] 2	PP_1144/rapA	membrane protein/RNA polymerase‑associated protein RapA
*	*	÷	NC_002947	1408524	1408557	34	2 [1]	[1] 3	PP_1227/PP_1228	membrane protein/methyl‑accepting chemotaxis transducer
*	*	÷	NC_002947	1414064	1414075	12	2 [0]	[1] 4	PP_1230/nadA	hypothetical protein/quinolinate synthase iron‑sulfur cluster subunit
*	*	÷	NC_002947	1448070	1448112	43	2 [1]	[1] 2	ghrB/PP_1262	2‑ketoaldonate reductase/hydroxypyruvate/glyoxylate reductase/LysR family transcriptional regulator
*	*	÷	NC_002947	1467966	1467999	34	2 [1]	[1] 2	algI/algL	alginate O‑acetylase AlgI/alginate lyase
*	*	÷	NC_002947	1511861	1511910	50	2 [1]	[1] 2	petC/sspA	ubiquinol‑‑cytochrome c reductase cytochrome c1 subunit/stringent starvation protein A
*	*	÷	NC_002947	1536736	1536768	33	2 [1]	[1] 2	PP_1344	hypothetical protein
*	*	÷	NC_002947	1549467	1549485	19	2 [0]	[1] 3	mdfA/ampG	multidrug MFS transporter/muropeptide permease AmpG
*	*	÷	NC_002947	1597584	1597630	47	2 [1]	[1] 2	PP_1397	hypothetical protein
*	*	÷	NC_002947	1620667	1620741	75	2 [1]	[1] 2	PP_1415	membrane protein
*	*	÷	NC_002947	1709617	1709633	17	2 [0]	[1] 2	[PP_1499]	[PP_1499]
*	*	÷	NC_002947	1785081	1785096	16	4 [1]	[1] 6	PP_1587/dapC	NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase
*	*	÷	NC_002947	1930719	1930742	24	2 [1]	[1] 2	PP_1725/PP_1726	hypothetical protein/ABC transporter substrate‑binding protein
*	*	÷	NC_002947	1975810	1975877	68	2 [0]	[1] 2	mtnA/PP_mr25	methylthioribose‑1‑phosphate isomerase/gyrA regulatory region
*	*	÷	NC_002947	1976441	1976473	33	2 [1]	[1] 2	gyrA	DNA gyrase subunit A
*	*	÷	NC_002947	1978858	1978911	54	2 [1]	[1] 2	gyrA/serC	DNA gyrase subunit A/3‑phosphoserine/phosphohydroxythreonine aminotransferase
*	*	÷	NC_002947	2011294	2011371	78	2 [1]	[1] 2	PP_1789	haloacid dehalogenase‑like family hydrolase
*	*	÷	NC_002947	2012192	2012256	65	2 [0]	[1] 2	PP_1790	acylneuraminate cytidylyltransferase
*	*	÷	NC_002947	2039295	2039409	115	3 [1]	[1] 3	pgi‑I/PP_5477	glucose 6‑phosphate isomerase/hypothetical protein
*	*	÷	NC_002947	2062806	2062822	17	2 [1]	[0] 5	PP_1832/PP_1833	oxidase/hypothetical protein
*	*	÷	NC_002947	2104930	2104996	67	2 [1]	[0] 3	PP_1875/PP_1876	two‑component system sensor histidine kinase/response regulator/AAA family ATP/GTP‑binding protein
*	*	÷	NC_002947	2194965	2195040	76	2 [1]	[1] 2	PP_1937	helicase
*	*	÷	NC_002947	2197505	2197538	34	2 [0]	[1] 2	PP_1937/PP_1938	helicase/hypothetical protein
*	*	÷	NC_002947	2226522	2226633	112	2 [1]	[1] 2	[PP_1960]–[PP_1961]	[PP_1960],[PP_1961]
*	*	÷	NC_002947	2238049	2238087	39	3 [1]	[1] 4	PP_1971/PP_t63	hypothetical protein/tRNA‑Asn
*	*	÷	NC_002947	2300778	2300841	64	2 [1]	[1] 2	PP_5496/PP_2023	hypothetical protein/glutathione S‑transferase family protein
*	*	÷	NC_002947	2405504	2405544	41	2 [1]	[0] 2	evgA/dgt	two‑component system response regulator/deoxyguanosinetriphosphate triphosphohydrolase‑like protein
*	*	÷	NC_002947	2434885	2434924	40	3 [1]	[0] 2	PP_2129/PP_2130	hypothetical protein/lytic transglycosylase
*	*	÷	NC_002947	2461845	2461876	32	2 [1]	[1] 2	gapB/PP_2150	glyceraldehyde‑3‑phosphate dehydrogenase/thiamine biosynthesis lipoprotein
*	*	÷	NC_002947	2479127	2479160	34	3 [1]	[1] 4	PP_2167/tal	PhoD‑like phosphatase/transaldolase
*	*	÷	NC_002947	2483376	2483469	94	2 [1]	[1] 2	PP_2172	hypothetical protein
*	*	÷	NC_002947	2598658	2598696	39	3 [1]	[1] 2	PP_5509	hypothetical protein
*	*	÷	NC_002947	2621704	2621812	109	2 [1]	[1] 2	PP_2288	tail fiber protein
*	*	÷	NC_002947	2673000	2673050	51	2 [1]	[0] 2	prpF/prpD	aconitate isomerase/2‑methylcitrate dehydratase
*	*	÷	NC_002947	2764402	2764469	68	2 [1]	[0] 3	PP_2413	GGDEF domain‑containing protein
*	*	÷	NC_002947	2842075	2842147	73	2 [1]	[1] 2	sad‑I/PP_2489	NAD+‑dependent succinate semialdehyde dehydrogenase/xenobiotic reductase
*	*	÷	NC_002947	2901602	2901609	8	2 [1]	[0] 5	PP_2550/PP_2551	transcriptional regulator/LysR family transcriptional regulator
*	*	÷	NC_002947	2927138	2927171	34	2 [1]	[1] 2	PP_2562	hypothetical protein
*	*	÷	NC_002947	3058181	3058243	63	2 [1]	[1] 3	[PP_2664]–[agmR]	[PP_2664],[agmR]
*	*	÷	NC_002947	3176734	3176829	96	2 [1]	[1] 3	PP_2784	short‑chain dehydrogenase/reductase family oxidoreductase
*	*	÷	NC_002947	3202985	3203067	83	3 [1]	[1] 2	ethA	FAD‑containing monooxygenase EthA
*	*	÷	NC_002947	3292218	3292266	49	2 [1]	[1] 2	[PP_2889]	[PP_2889]
*	*	÷	NC_002947	3324152	3324180	29	3 [1]	[0] 2	treSA/PP_2919	trehalose synthase A/LysR family transcriptional regulator
*	*	÷	NC_002947	3369161	3369223	63	3 [1]	[1] 2	PP_2960	transcriptional regulator, AraC family
*	*	÷	NC_002947	3377768	3377845	78	2 [1]	[1] 2	[PP_2971]	[PP_2971]
*	*	÷	NC_002947	3380271	3380314	44	2 [1]	[1] 2	PP_2974	sulfatase
*	*	÷	NC_002947	3471817	3471862	46	2 [1]	[0] 2	[PP_3081]	[PP_3081]
*	*	÷	NC_002947	3781336	3781390	55	2 [1]	[1] 2	PP_3338/PP_3339	cytochrome bd‑type quinol oxidase/hypothetical protein
*	*	÷	NC_002947	3850686	3850739	54	2 [1]	[0] 2	[PP_3395]	[PP_3395]
*	*	÷	NC_002947	3956084	3956102	19	2 [0]	[1] 3	PP_3486/PP_3487	cytochrome c/hypothetical protein
*	*	÷	NC_002947	4084464	4084464	1	2 [0]	[0] 2	sdaC/amaC	serine:H+ symport permease/D‑lysine aminotransferase
*	*	÷	NC_002947	4119325	4119354	30	4 [1]	[1] 5	PP_3619/ycaO	hypothetical protein/ribosomal protein S12 methylthiotransferase accessory factor
*	*	÷	NC_002947	4155040	4155158	119	3 [1]	[1] 2	PP_3654/PP_3655	leucine‑responsive regulatory protein/cytosine/purine/uracil/thiamine/allantoin permease family protein
*	*	÷	NC_002947	4175171	4175211	41	2 [0]	[1] 2	katG/PP_3669	catalase‑peroxidase/LysR family transcriptional regulator
*	*	÷	NC_002947	4205162	4205218	57	2 [0]	[1] 2	PP_3690	hypothetical protein
*	*	÷	NC_002947	4212809	4212839	31	2 [1]	[1] 2	PP_3691/PP_3692	DNA helicase‑related protein/hypothetical protein
*	*	÷	NC_002947	4316287	4316360	74	2 [1]	[1] 2	PP_3784	hypothetical protein
*	*	÷	NC_002947	4345064	4345073	10	2 [1]	[1] 2	ribAB‑II/PP_3814	3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein
*	*	÷	NC_002947	4358176	4358191	16	3 [0]	[0] 3	yrpB	2‑nitropropane dioxygenase
*	*	÷	NC_002947	4375454	4375470	17	2 [1]	[0] 2	PP_3847	LuxR family transcriptional regulator
*	*	÷	NC_002947	4535003	4535054	52	2 [1]	[1] 2	PP_4018/topB	acetyltransferase/DNA topoisomerase III
*	*	÷	NC_002947	4636420	4636531	112	3 [1]	[1] 2	PP_4094/PP_4096	hypothetical protein/hypothetical protein
*	*	÷	NC_002947	4680270	4680370	101	3 [1]	[1] 2	[PP_4137]	[PP_4137]
*	*	÷	NC_002947	4732220	4732245	26	2 [0]	[1] 3	brnQ	branched‑chain amino acid transporter
*	*	÷	NC_002947	4745810	4745852	43	2 [1]	[1] 2	gltA/yeiW	citrate synthase/putative oxidoreductase
*	*	÷	NC_002947	4801595	4801620	26	2 [1]	[1] 3	pvdH/PP_4224	diaminobutyrate‑2‑oxoglutarate transaminase/sensor histidine kinase
*	*	÷	NC_002947	4857465	4857466	2	2 [0]	[0] 2	recR/ybaB	recombination protein RecR/nucleoid‑associated broad specificity regulator
*	*	÷	NC_002947	4894547	4894650	104	2 [1]	[1] 2	[hyi]	[hyi]
*	*	÷	NC_002947	4955948	4955986	39	2 [1]	[1] 3	fliL/fliK	flagellar protein FliL/flagellar hook‑length control protein FliK
*	*	÷	NC_002947	5006327	5006437	111	2 [1]	[1] 2	PP_4407/PP_4409	gamma‑aminobutyrate transporter/site‑specific recombinase
*	*	÷	NC_002947	5019742	5019784	43	2 [1]	[1] 4	PP_4420	transposase
*	*	÷	NC_002947	5045439	5045478	40	2 [1]	[1] 2	PP_4446	group II intron‑encoding maturase
*	*	÷	NC_002947	5069801	5069876	76	2 [1]	[1] 2	PP_4461	MFS transporter
*	*	÷	NC_002947	5073870	5073888	19	3 [1]	[1] 3	PP_4465	porin
*	*	÷	NC_002947	5102184	5102246	63	2 [1]	[0] 3	PP_mr66/acsA‑I	P6/acetyl‑CoA synthetase
*	*	÷	NC_002947	5104964	5105005	42	2 [1]	[0] 4	PP_4488/phhR	hypothetical protein/sigma‑54 dependent transcriptional regulator
*	*	÷	NC_002947	5178227	5178244	18	2 [1]	[1] 2	fadD‑I/fadD‑II	long‑chain‑fatty acid‑‑CoA ligase/long‑chain‑fatty acid‑‑CoA ligase
*	*	÷	NC_002947	5197748	5197766	19	5 [1]	[1] 2	PP_4572/PP_4573	hypothetical protein/AAA family ATPase
*	*	÷	NC_002947	5204648	5204690	43	2 [1]	[1] 3	PP_4579/PP_4580	LysR family transcriptional regulator/hypothetical protein
*	*	÷	NC_002947	5261770	5261885	116	2 [0]	[1] 2	[PP_5703]	[PP_5703]
*	*	÷	NC_002947	5262887	5262918	32	2 [1]	[0] 2	PP_4634/PP_4635	alpha/beta family hydrolase/trans‑2‑enoyl‑CoA reductase
*	*	÷	NC_002947	5293391	5293500	110	2 [1]	[1] 2	[mdaB]	[mdaB]
*	*	÷	NC_002947	5329930	5329966	37	2 [1]	[1] 3	PP_4684/PP_4685	kinase‑like domain‑containing protein/hypothetical protein
*	*	÷	NC_002947	5387435	5387464	30	2 [0]	[0] 3	smpB/pdhR	SsrA‑binding protein/DNA‑binding transcriptional regulator LldR
*	*	÷	NC_002947	5463878	5463950	73	2 [0]	[1] 2	[PP_4795]	[PP_4795]
*	*	÷	NC_002947	5473604	5473635	32	3 [1]	[1] 2	mltB	membrane‑bound lytic murein transglycosylase B
*	*	÷	NC_002947	5490110	5490197	88	2 [1]	[1] 2	purH/purD	bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase/phosphoribosylamine‑‑glycine ligase
*	*	÷	NC_002947	5490844	5490899	56	3 [1]	[1] 2	purD	phosphoribosylamine‑‑glycine ligase
*	*	÷	NC_002947	5511542	5511595	54	2 [1]	[1] 3	PP_4839/cycA	iron‑regulated membrane protein/D‑alanine/beta‑alanine/D‑serine/glycine permease
*	*	÷	NC_002947	5542063	5542095	33	2 [1]	[1] 2	nadE/PP_4870	NH(3)‑dependent NAD(+) synthetase/azurin
*	*	÷	NC_002947	5599129	5599149	21	2 [0]	[0] 2	PP_4921/thiC	NCS1 family transporter/phosphomethylpyrimidine synthase
*	*	÷	NC_002947	5686422	5686456	35	3 [1]	[1] 3	PP_4986/PP_4987	hemolysin III family channel protein/putative Chemotaxis protein
*	*	÷	NC_002947	5703770	5703808	39	3 [1]	[1] 2	hslU/PP_5002	protease HslVU ATPase subunit/hypothetical protein
*	*	÷	NC_002947	5779646	5779705	60	2 [1]	[1] 2	betB	NAD‑dependent betaine aldehyde dehydrogenase
*	*	÷	NC_002947	5821895	5821910	16	2 [1]	[1] 3	PP_5092/pilT	NLP/P60 protein/twitching motility protein
*	*	÷	NC_002947	5908156	5908182	27	2 [1]	[1] 2	PP_5175/PP_5176	HlyD family secretion protein/hypothetical protein
*	*	÷	NC_002947	5989435	5989465	31	3 [1]	[0] 2	PP_5242/ycaC‑II	GAF domain‑containing sensor histidine kinase/putative hydrolase
*	*	÷	NC_002947	6011580	6011586	7	5 [0]	[1] 3	ydcJ/PP_5261	metalloprotein/LysR family transcriptional regulator
*	*	÷	NC_002947	6014154	6014168	15	2 [0]	[1] 2	norM/PP_5263	multidrug resistance protein NorM/GGDEF domain‑containing protein
*	*	÷	NC_002947	6032915	6032950	36	2 [1]	[1] 2	PP_5277/kauB	MFS transporter/4‑guanidinobutyraldehyde dehydrogenase
*	*	÷	NC_002947	6133254	6133272	19	2 [1]	[0] 2	PP_5375/PP_5376	LysR family transcriptional regulator/hypothetical protein

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	533500 =	5 (0.250)	4 (0.220)	4/238	1.1	45.7%	coding (762/1194 nt)	tufA	elongation factor Tu‑A
	?	NC_002947	= 533496	5 (0.270)					coding (758/1194 nt)	tufA	elongation factor Tu‑A
*	?	NC_002947	744925 =	NA (NA)	15 (0.750)	12/262	0.4	71.6%	intergenic (‑587/+44)	PP_0636/PP_0637	cold shock DNA‑binding domain‑containing protein/transposase
	?	NC_002947	1015813 =	6 (0.300)					intergenic (‑40/‑728)	SBRG_Ecoli_galE/prfC	SBRG_Ecoli_galE/peptide chain release factor 3
*	?	NC_002947	= 746963	NA (NA)	14 (0.700)	11/262	0.4	77.9%	intergenic (‑87/‑707)	PP_0638/PP_5448	transposase/hypothetical protein
	?	NC_002947	= 1015822	4 (0.200)					intergenic (‑49/‑719)	SBRG_Ecoli_galE/prfC	SBRG_Ecoli_galE/peptide chain release factor 3
*	?	NC_002947	1849125 =	1 (0.050)	19 (0.970)	12/254	0.3	86.4%	coding (660/2754 nt)	gacS	sensor protein GacS
	?	NC_002947	= 2184368	5 (0.260)					intergenic (+175/+93)	PP_1931/PP_5486	hypothetical protein/hypothetical protein
*	?	NC_002947	= 1849128	1 (0.050)	17 (0.860)	14/256	0.3	69.4%	coding (657/2754 nt)	gacS	sensor protein GacS
	?	NC_002947	2182694 =	14 (0.710)					intergenic (+103/‑63)	PP_5485/PP_1931	GNAT family acetyltransferase/hypothetical protein
*	?	NC_002947	= 4813173	1 (0.050)	35 (1.900)	10/240	0.4	34.8%	intergenic (‑288/‑267)	PP_4234/dsbD‑II	bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
	?	NC_002947	5993770 =	130 (7.050)					intergenic (+59/‑487)	kefB‑III/PP_mr64	glutathione‑regulated potassium/H+ antiporter/C4 ncRNA