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	1,011,323	+T	intergenic (‑258/+192)	PP_0871 ← / ← SBRG_Ecoli_galM	glycine betaine/carnitine/choline ABC transporter permease/SBRG_Ecoli_galM
RA	1,167,912	+A	coding (725/1344 nt)	oprB‑I →	carbohydrate‑selective porin
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	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	30731	30773	43	2 [1]	[1] 2	PP_0026	cobalt/cadmium/zinc exporter
*	*	÷	NC_002947	49328	49395	68	3 [1]	[0] 2	[czcA‑I]	[czcA‑I]
*	*	÷	NC_002947	51694	51803	110	2 [1]	[1] 2	czcC‑I	cobalt‑zinc‑cadmium resistance protein
*	*	÷	NC_002947	139775	139801	27	2 [1]	[1] 2	kinB	alginate biosynthesis sensor protein KinB
*	*	÷	NC_002947	170798	170846	49	2 [1]	[0] 2	[PP_0159]	[PP_0159]
*	*	÷	NC_002947	316010	316043	34	2 [1]	[1] 3	cysQ/PP_0262	3'(2'),5'‑bisphosphate nucleotidase CysQ/hypothetical protein
*	*	÷	NC_002947	352798	352865	68	3 [1]	[1] 2	hisF	imidazole glycerol phosphate synthase subunit HisF
*	*	÷	NC_002947	353014	353109	96	2 [1]	[1] 2	[hisF]	[hisF]
*	*	÷	NC_002947	445072	445130	59	3 [1]	[1] 2	PP_0367/PP_0368	hypothetical protein/acyl‑CoA dehydrogenase
*	*	÷	NC_002947	478305	478336	32	4 [1]	[1] 2	PP_0393/cca	2‑amino‑4‑hydroxy‑6‑ hydroxymethyldihydropteridine pyrophosphokinase/multifunctional tRNA nucleotidyltransferase/2',3'‑cyclic phosphodiesterase/2' nucleotidase/phosphatase
*	*	÷	NC_002947	499218	499257	40	2 [0]	[1] 2	uhpA/PP_0411	two‑component system response regulator UhpA/polyamine ABC transporter ATP‑binding protein
*	*	÷	NC_002947	524149	524202	54	2 [1]	[1] 2	tyrS/PP_16SC	tyrosine‑‑tRNA ligase/16S ribosomal RNA
*	*	÷	NC_002947	544740	544767	28	3 [0]	[1] 3	rpoC	DNA‑directed RNA polymerase subunit beta'
*	*	÷	NC_002947	614267	614345	79	2 [0]	[1] 2	dxs/ispA	1‑deoxyxylulose‑5‑phosphate synthase/farnesyl diphosphate synthase
*	*	÷	NC_002947	668084	668095	12	2 [1]	[0] 2	yfhM/PP_0571	lipoprotein/membrane protein
*	*	÷	NC_002947	681207	681333	127	2 [1]	[0] 2	[PP_0583]–[PP_0584]	[PP_0583],[PP_0584]
*	*	÷	NC_002947	697079	697158	80	2 [1]	[1] 3	mmsA‑I/PP_16SD	methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA
*	*	÷	NC_002947	796835	796932	98	3 [1]	[1] 3	PP_0681/PP_0682	hypothetical protein/inner membrane protein
*	*	÷	NC_002947	883865	883872	8	2 [0]	[1] 3	PP_0766/PP_0767	hypothetical protein/LuxR family transcriptional regulator
*	*	÷	NC_002947	915056	915131	76	2 [1]	[0] 2	fruA/PP_0796	PTS fructose transporter subunit IIBC/hypothetical protein
*	*	÷	NC_002947	975212	975230	19	3 [0]	[1] 3	ycfJ/suhB	flagella biosyntheis regulator/bifunctional inositol monophosphatase/glycerol‑2‑phosphatase
*	*	÷	NC_002947	1003303	1003327	25	2 [1]	[1] 2	speC/PP_0865	ornithine decarboxylase/ECF subfamily RNA polymerase sigma‑24 factor
*	*	÷	NC_002947	1099400	1099423	24	2 [1]	[1] 2	hpf	ribosome hibernation promoting factor
*	*	÷	NC_002947	1119859	1119890	32	2 [1]	[1] 2	rlmF/valS	ribosomal RNA large subunit methyltransferase F/valine‑‑tRNA ligase
*	*	÷	NC_002947	1131565	1131583	19	7 [0]	[1] 6	tdcG‑II/gcvP‑I	L‑serine dehydratase/glycine dehydrogenase
*	*	÷	NC_002947	1215730	1215801	72	2 [1]	[1] 2	[ytnA]	[ytnA]
*	*	÷	NC_002947	1230223	1230298	76	3 [0]	[1] 2	gltJ	glutamate/aspartate ABC transporter permease
*	*	÷	NC_002947	1237822	1237910	89	3 [1]	[1] 2	[glpR]	[glpR]
*	*	÷	NC_002947	1388205	1388213	9	3 [0]	[1] 2	PP_1204	lipoprotein
*	*	÷	NC_002947	1414064	1414072	9	3 [0]	[0] 2	PP_1230/nadA	hypothetical protein/quinolinate synthase iron‑sulfur cluster subunit
*	*	÷	NC_002947	1448093	1448173	81	3 [1]	[1] 2	ghrB/PP_1262	2‑ketoaldonate reductase/hydroxypyruvate/glyoxylate reductase/LysR family transcriptional regulator
*	*	÷	NC_002947	1504381	1504498	118	3 [1]	[1] 2	trpS/zapE	tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein
*	*	÷	NC_002947	1511871	1511906	36	3 [1]	[1] 2	petC/sspA	ubiquinol‑‑cytochrome c reductase cytochrome c1 subunit/stringent starvation protein A
*	*	÷	NC_002947	1536774	1536803	30	2 [1]	[1] 3	PP_1344	hypothetical protein
*	*	÷	NC_002947	1570587	1570608	22	2 [1]	[1] 2	pitB/PP_1374	phosphate transporter/hypothetical protein
*	*	÷	NC_002947	1597566	1597621	56	3 [1]	[1] 2	PP_1397	hypothetical protein
*	*	÷	NC_002947	1620680	1620732	53	2 [1]	[1] 2	PP_1415	membrane protein
*	*	÷	NC_002947	1644562	1644579	18	2 [1]	[0] 3	czcR‑III/PP_1439	response regulator/hypothetical protein
*	*	÷	NC_002947	1935340	1935437	98	2 [1]	[1] 3	[apeB]	[apeB]
*	*	÷	NC_002947	1989663	1989687	25	2 [1]	[1] 2	PP_1776	bifunctional mannose‑6‑phosphate isomerase/mannose‑1‑phosphate guanylyltransferase
*	*	÷	NC_002947	2002179	2002208	30	2 [1]	[0] 2	rfbA	dTDP‑glucose pyrophosphorylase
*	*	÷	NC_002947	2043345	2043480	136	2 [1]	[1] 2	rffE	UDP‑N‑acetylglucosamine‑2‑epimerase
*	*	÷	NC_002947	2068189	2068206	18	3 [1]	[1] 4	PP_1838/PP_1839	membrane protein/hypothetical protein
*	*	÷	NC_002947	2104932	2104996	65	2 [1]	[1] 7	PP_1875/PP_1876	two‑component system sensor histidine kinase/response regulator/AAA family ATP/GTP‑binding protein
*	*	÷	NC_002947	2131071	2131105	35	2 [0]	[1] 2	PP_1887	hypothetical protein
*	*	÷	NC_002947	2201976	2202025	50	3 [1]	[1] 2	[PP_1941]–[PP_1942]	[PP_1941],[PP_1942]
*	*	÷	NC_002947	2204276	2204324	49	2 [1]	[1] 2	PP_1944	aminomethyltransferase
*	*	÷	NC_002947	2225062	2225083	22	3 [1]	[1] 2	[PP_1959]	[PP_1959]
*	*	÷	NC_002947	2246251	2246350	100	2 [1]	[1] 2	gltX/PP_t25	glutamate‑‑tRNA ligase/tRNA‑Ala
*	*	÷	NC_002947	2300823	2300857	35	2 [1]	[0] 3	PP_5496/PP_2023	hypothetical protein/glutathione S‑transferase family protein
*	*	÷	NC_002947	2343047	2343115	69	2 [1]	[0] 2	[ybhD]	[ybhD]
*	*	÷	NC_002947	2405499	2405528	30	2 [1]	[1] 2	evgA/dgt	two‑component system response regulator/deoxyguanosinetriphosphate triphosphohydrolase‑like protein
*	*	÷	NC_002947	2434910	2434914	5	5 [1]	[1] 2	PP_2129/PP_2130	hypothetical protein/lytic transglycosylase
*	*	÷	NC_002947	2479127	2479160	34	2 [1]	[0] 3	PP_2167/tal	PhoD‑like phosphatase/transaldolase
*	*	÷	NC_002947	2601632	2601688	57	2 [1]	[0] 2	PP_2273	DNA polymerase I
*	*	÷	NC_002947	2605581	2605609	29	2 [1]	[1] 2	PP_2279	head‑to‑tail joining protein
*	*	÷	NC_002947	2672992	2673077	86	4 [1]	[0] 2	prpF/prpD	aconitate isomerase/2‑methylcitrate dehydratase
*	*	÷	NC_002947	2717721	2717778	58	2 [1]	[1] 2	metH	cobalamin‑dependent methionine synthase
*	*	÷	NC_002947	2842042	2842159	118	2 [1]	[1] 3	sad‑I/PP_2489	NAD+‑dependent succinate semialdehyde dehydrogenase/xenobiotic reductase
*	*	÷	NC_002947	3058143	3058243	101	2 [1]	[1] 2	[PP_2664]–[agmR]	[PP_2664],[agmR]
*	*	÷	NC_002947	3376368	3376387	20	3 [0]	[0] 2	PP_2968	high‑affinity nickel/cobalt transporter
*	*	÷	NC_002947	3377041	3377098	58	2 [1]	[0] 2	[csoR]	[csoR]
*	*	÷	NC_002947	3377797	3377836	40	2 [1]	[1] 2	[PP_2971]	[PP_2971]
*	*	÷	NC_002947	3438354	3438394	41	2 [1]	[1] 2	PP_3050	hypothetical protein
*	*	÷	NC_002947	3506100	3506144	45	2 [1]	[0] 4	PP_5566/PP_5567	hypothetical protein/hypothetical protein
*	*	÷	NC_002947	3583364	3583452	89	2 [1]	[0] 2	PP_3158/PP_5589	hypothetical protein/rhs repeat‑associated core domain‑containing protein
*	*	÷	NC_002947	4155018	4155071	54	5 [1]	[0] 2	PP_3654/PP_3655	leucine‑responsive regulatory protein/cytosine/purine/uracil/thiamine/allantoin permease family protein
*	*	÷	NC_002947	4197981	4198011	31	2 [1]	[1] 2	PP_5613/PP_5614	hypothetical protein/hypothetical protein
*	*	÷	NC_002947	4206118	4206138	21	2 [1]	[0] 2	PP_3690/PP_3691	hypothetical protein/DNA helicase‑related protein
*	*	÷	NC_002947	4215273	4215291	19	2 [0]	[0] 2	PP_3692	hypothetical protein
*	*	÷	NC_002947	4217169	4217238	70	2 [1]	[1] 3	PP_3694	hypothetical protein
*	*	÷	NC_002947	4225162	4225210	49	3 [1]	[1] 2	PP_3699	hypothetical protein
*	*	÷	NC_002947	4316343	4316489	147	2 [1]	[1] 2	PP_3784	hypothetical protein
*	*	÷	NC_002947	4321137	4321202	66	2 [1]	[1] 2	PP_3788	non‑ribosomal peptide synthetase
*	*	÷	NC_002947	4345070	4345083	14	2 [0]	[0] 2	ribAB‑II/PP_3814	3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein
*	*	÷	NC_002947	4358174	4358184	11	2 [1]	[0] 2	yrpB	2‑nitropropane dioxygenase
*	*	÷	NC_002947	4488419	4488437	19	3 [1]	[0] 3	PP_3975	hypothetical protein
*	*	÷	NC_002947	4504660	4504720	61	2 [1]	[1] 2	PP_3988	hypothetical protein
*	*	÷	NC_002947	4535001	4535044	44	2 [1]	[0] 3	PP_4018/topB	acetyltransferase/DNA topoisomerase III
*	*	÷	NC_002947	4538610	4538635	26	2 [0]	[1] 2	PP_4020/cpo	oxidoreductase/non‑heme chloroperoxidase
*	*	÷	NC_002947	4645973	4646057	85	2 [1]	[1] 2	gabP‑IV	gamma‑aminobutyrate permease
*	*	÷	NC_002947	4678524	4678566	43	2 [1]	[1] 3	PP_4137	outer membrane siderophore receptor
*	*	÷	NC_002947	4680290	4680392	103	2 [1]	[1] 2	[PP_4137]	[PP_4137]
*	*	÷	NC_002947	4722657	4722675	19	2 [1]	[1] 2	fabB	3‑oxoacyl‑ACP synthase
*	*	÷	NC_002947	4745820	4745866	47	2 [0]	[1] 2	gltA/yeiW	citrate synthase/putative oxidoreductase
*	*	÷	NC_002947	4813154	4813272	119	41 [0]	[1] 2	PP_4234/dsbD‑II	bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
*	*	÷	NC_002947	4847856	4847907	52	2 [1]	[1] 2	ccoP‑II/PP_4259	cbb3‑type cytochrome c oxidase subunit/iron‑sulfur cluster‑binding protein
*	*	÷	NC_002947	4857448	4857461	14	16 [0]	[0] 2	recR/ybaB	recombination protein RecR/nucleoid‑associated broad specificity regulator
*	*	÷	NC_002947	4875663	4875696	34	2 [1]	[1] 2	xdhB/xdhC	xanthine dehydrogenase subunit XdhB/xanthine dehydrogenase accessory factor
*	*	÷	NC_002947	4894572	4894629	58	2 [1]	[0] 2	hyi/glxR	hydroxypyruvate isomerase/2‑hydroxy‑3‑oxopropionate reductase
*	*	÷	NC_002947	4955952	4955992	41	2 [1]	[1] 2	fliL/fliK	flagellar protein FliL/flagellar hook‑length control protein FliK
*	*	÷	NC_002947	5005497	5005535	39	2 [0]	[1] 2	[PP_4407]	[PP_4407]
*	*	÷	NC_002947	5018640	5018682	43	2 [1]	[1] 2	PP_4418	hypothetical protein
*	*	÷	NC_002947	5035068	5035144	77	2 [1]	[1] 2	PP_4433	amino acid MFS transporter
*	*	÷	NC_002947	5055647	5055737	91	3 [1]	[1] 3	PP_5687	MFS transporter
*	*	÷	NC_002947	5065386	5065456	71	2 [1]	[1] 2	PP_4458	opine ABC transporter substrate‑binding protein
*	*	÷	NC_002947	5083658	5083669	12	2 [1]	[1] 2	mgtE	magnesium transporter
*	*	÷	NC_002947	5102228	5102282	55	2 [1]	[1] 2	PP_mr66/acsA‑I	P6/acetyl‑CoA synthetase
*	*	÷	NC_002947	5179349	5179402	54	2 [0]	[1] 2	fadD‑II	long‑chain‑fatty acid‑‑CoA ligase
*	*	÷	NC_002947	5196405	5196430	26	3 [0]	[1] 2	[cysK]	[cysK]
*	*	÷	NC_002947	5197704	5197767	64	2 [0]	[1] 2	PP_4572/PP_4573	hypothetical protein/AAA family ATPase
*	*	÷	NC_002947	5265839	5265895	57	2 [1]	[1] 3	PP_4637	5‑methyltetrahydropteroyltriglutamate‑ homocysteine S‑methyltransferase family protein
*	*	÷	NC_002947	5349443	5349484	42	2 [1]	[0] 2	pgi‑II/acsA‑II	glucose 6‑phosphate isomerase/acetyl‑CoA synthetase
*	*	÷	NC_002947	5490110	5490189	80	2 [1]	[1] 2	purH/purD	bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase/phosphoribosylamine‑‑glycine ligase
*	*	÷	NC_002947	5511548	5511592	45	3 [1]	[0] 2	PP_4839/cycA	iron‑regulated membrane protein/D‑alanine/beta‑alanine/D‑serine/glycine permease
*	*	÷	NC_002947	5542016	5542078	63	2 [1]	[1] 3	[nadE]	[nadE]
*	*	÷	NC_002947	5599118	5599159	42	2 [0]	[1] 2	PP_4921/thiC	NCS1 family transporter/phosphomethylpyrimidine synthase
*	*	÷	NC_002947	5645280	5645296	17	3 [1]	[0] 2	PP_4950/PP_4951	hypothetical protein/EmrB/QacA family drug resistance transporter
*	*	÷	NC_002947	5657966	5657977	12	5 [0]	[1] 2	PP_4961/PP_4962	lipoprotein/hypothetical protein
*	*	÷	NC_002947	5686427	5686445	19	4 [1]	[0] 4	PP_4986/PP_4987	hemolysin III family channel protein/putative Chemotaxis protein
*	*	÷	NC_002947	5756982	5756999	18	2 [1]	[0] 2	thiI/glnA	tRNA sulfurtransferase/glutamine synthetase
*	*	÷	NC_002947	5902725	5902788	64	2 [1]	[1] 2	PP_5172/PP_5173	hypothetical protein/RND family transporter
*	*	÷	NC_002947	5908768	5908794	27	2 [1]	[0] 3	PP_5176/spuH	hypothetical protein/spermidine/putrescine ABC transporter permease
*	*	÷	NC_002947	5910464	5910555	92	2 [1]	[1] 2	spuG	spermidine/putrescine ABC transporter permease
*	*	÷	NC_002947	5973451	5973486	36	2 [1]	[1] 3	PP_5723	hypothetical protein
*	*	÷	NC_002947	6002161	6002200	40	2 [1]	[1] 3	PP_5252/PP_5253	hypothetical protein/arylesterase
*	*	÷	NC_002947	6103328	6103417	90	2 [1]	[0] 2	PP_5350	RpiR family transcriptional regulator
*	*	÷	NC_002947	6136167	6136193	27	2 [1]	[1] 2	copB‑II	copper resistance protein B
*	*	÷	NC_002947	6173417	6173460	44	3 [1]	[1] 3	PP_5407	TnsD‑like transposition protein

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	198881 =	13 (0.580)	3 (0.150) +AGCGTCGTTGTAAAC	3/234	1.3	32.6%	coding (4387/26049 nt)	PP_0168	putative surface adhesion protein
	?	NC_002947	= 211440	1 (0.040)					coding (16946/26049 nt)	PP_0168	putative surface adhesion protein
*	?	NC_002947	= 652785	29 (1.290)	39 (2.040)	11/224	0.4	76.0%	coding (1961/1962 nt)	ctpL	methyl‑accepting chemotaxis protein CtpL
	?	NC_002947	= 4813153	0 (0.000)					intergenic (‑268/‑287)	PP_4234/dsbD‑II	bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
*	?	NC_002947	1015848 =	2 (0.090)	6 (0.270)	6/262	0.9	54.6%	intergenic (‑75/‑693)	SBRG_Ecoli_galE/prfC	SBRG_Ecoli_galE/peptide chain release factor 3
	?	NC_002947	5066251 =	8 (0.360)					intergenic (‑421/‑70)	PP_4458/PP_4459	opine ABC transporter substrate‑binding protein/transposase
*	?	NC_002947	= 1015854	2 (0.090)	15 (0.690)	13/254	0.3	69.9%	intergenic (‑81/‑687)	SBRG_Ecoli_galE/prfC	SBRG_Ecoli_galE/peptide chain release factor 3
	?	NC_002947	= 5067412	11 (0.510)					coding (1092/1098 nt)	PP_4459	transposase
*	?	NC_002947	= 1424533	1 (0.040)	10 (0.590)	4/200	0.9	69.5%	intergenic (‑67/+70)	PP_1242/PP_1244	hypothetical protein/hypothetical protein
	?	NC_002947	= 1424563	8 (0.470)					intergenic (‑97/+40)	PP_1242/PP_1244	hypothetical protein/hypothetical protein
*	?	NC_002947	2477094 =	7 (0.310)	6 (0.380)	5/186	0.7	70.9%	intergenic (+6/+143)	PP_2166/PP_2167	anti‑anti‑sigma factor/PhoD‑like phosphatase
	?	NC_002947	2477218 =	0 (0.000)					intergenic (+130/+19)	PP_2166/PP_2167	anti‑anti‑sigma factor/PhoD‑like phosphatase
*	?	NC_002947	= 4813152	0 (0.000)	11 (0.490)	5/264	1.0	34.4%	intergenic (‑267/‑288)	PP_4234/dsbD‑II	bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
	?	NC_002947	= 5993975	42 (1.870)					intergenic (+264/‑282)	kefB‑III/PP_mr64	glutathione‑regulated potassium/H+ antiporter/C4 ncRNA
*	?	NC_002947	= 4988800	8 (0.360)	3 (0.180)	3/200	1.1	31.5%	intergenic (‑253/+69)	flgB/cheR	flagellar basal‑body rod protein FlgB/chemotaxis protein methyltransferase
	?	NC_002947	= 5465626	7 (0.410)					intergenic (+10/‑207)	holA/PP_4797	DNA polymerase III subunit delta/hypothetical protein