BRESEQ :: Mutation Predictions

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	1,484,303	T→G	V125G (GTC→GGC)	yhdX →	amino acid ABC transporter permease
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	4,743,195	+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	97567	97627	61	3 [1]	[1] 3	[PP_0090]–[PP_0091]	[PP_0090],[PP_0091]
*	*	÷	NC_002947	148231	148249	19	3 [1]	[1] 2	PP_0140	hypothetical protein
*	*	÷	NC_002947	171379–172965	176295–172970	6–4917	2 [1]	[1] 2	PP_16SA–[PP_5SA]	PP_16SA,PP_23SA,[PP_5SA]
*	*	÷	NC_002947	176665–178395	181690–178400	6–5026	2 [0]	[1] 2	PP_16SB–[PP_r01]	PP_16SB,PP_23SB,[PP_r01]
*	*	÷	NC_002947	220535	220629	95	2 [1]	[1] 3	[PP_0168]	[PP_0168]
*	*	÷	NC_002947	284564	284608	45	2 [1]	[1] 2	betT‑II/atsK	choline/carnitine/betaine transporter/alpha‑ketoglutarate‑dependent sulfonate dioxygenase
*	*	÷	NC_002947	336208	336263	56	2 [1]	[0] 2	PP_0278/PP_0279	hypothetical protein/hypothetical protein
*	*	÷	NC_002947	353084	353103	20	2 [1]	[1] 2	hisF/cbcV	imidazole glycerol phosphate synthase subunit HisF/choline/betaine/carnitine ABC transporter ATP binding protein
*	*	÷	NC_002947	380856	380878	23	2 [1]	[1] 3	gbcB/PP_0317	glycine‑betaine dioxygenase subunit/methyl‑accepting chemotaxis transducer
*	*	÷	NC_002947	445117	445139	23	2 [0]	[1] 2	PP_0367/PP_0368	hypothetical protein/acyl‑CoA dehydrogenase
*	*	÷	NC_002947	478322	478323	2	4 [0]	[0] 2	PP_0393/cca	2‑amino‑4‑hydroxy‑6‑ hydroxymethyldihydropteridine pyrophosphokinase/multifunctional tRNA nucleotidyltransferase/2',3'‑cyclic phosphodiesterase/2' nucleotidase/phosphatase
*	*	÷	NC_002947	486362	486404	43	2 [1]	[1] 2	apaG/rsmA	Co(2+)/Mg(2+) efflux protein/ribosomal RNA small subunit methyltransferase A
*	*	÷	NC_002947	499201	499236	36	2 [1]	[0] 3	uhpA/PP_0411	two‑component system response regulator UhpA/polyamine ABC transporter ATP‑binding protein
*	*	÷	NC_002947	524143	524224	82	3 [0]	[1] 2	tyrS/PP_16SC	tyrosine‑‑tRNA ligase/16S ribosomal RNA
*	*	÷	NC_002947	614283	614385	103	2 [0]	[1] 2	[ispA]	[ispA]
*	*	÷	NC_002947	668082	668095	14	4 [0]	[1] 4	yfhM/PP_0571	lipoprotein/membrane protein
*	*	÷	NC_002947	681281	681320	40	2 [1]	[1] 2	PP_0583/PP_0584	AraC family transcriptional regulator/methyl‑accepting chemotaxis transducer
*	*	÷	NC_002947	954714	954734	21	2 [1]	[1] 2	cyoE	protoheme IX farnesyltransferase
*	*	÷	NC_002947	975193	975228	36	2 [0]	[1] 3	ycfJ/suhB	flagella biosyntheis regulator/bifunctional inositol monophosphatase/glycerol‑2‑phosphatase
*	*	÷	NC_002947	1114920	1114935	16	2 [0]	[0] 3	rlmF/valS	ribosomal RNA large subunit methyltransferase F/valine‑‑tRNA ligase
*	*	÷	NC_002947	1156335	1156387	53	3 [1]	[1] 2	PP_1013/yihS	sensor histidine kinase/aldose‑ketose isomerase
*	*	÷	NC_002947	1276104	1276134	31	2 [0]	[1] 2	PP_5464	hypothetical protein
*	*	÷	NC_002947	1311729	1311784	56	3 [0]	[0] 3	PP_1144/rapA	membrane protein/RNA polymerase‑associated protein RapA
*	*	÷	NC_002947	1403565	1403610	46	2 [1]	[1] 2	PP_1227/PP_1228	membrane protein/methyl‑accepting chemotaxis transducer
*	*	÷	NC_002947	1409117	1409133	17	2 [1]	[0] 2	PP_1230/nadA	hypothetical protein/quinolinate synthase iron‑sulfur cluster subunit
*	*	÷	NC_002947	1443099	1443162	64	2 [1]	[1] 3	ghrB/PP_1262	2‑ketoaldonate reductase/hydroxypyruvate/glyoxylate reductase/LysR family transcriptional regulator
*	*	÷	NC_002947	1464203	1464219	17	2 [0]	[0] 3	algX	alginate biosynthesis protein AlgX
*	*	÷	NC_002947	1531833	1531873	41	2 [0]	[1] 2	PP_1344	hypothetical protein
*	*	÷	NC_002947	1592617	1592688	72	2 [1]	[1] 5	PP_1397	hypothetical protein
*	*	÷	NC_002947	1615727	1615755	29	2 [1]	[1] 2	PP_1415	membrane protein
*	*	÷	NC_002947	1659895	1659913	19	2 [1]	[0] 2	PP_1452/nudL	MutT/nudix family protein/NUDIX hydrolase
*	*	÷	NC_002947	1676922	1676995	74	2 [0]	[1] 2	thrC	threonine synthase
*	*	÷	NC_002947	1704662	1704689	28	2 [1]	[0] 2	[PP_1499]	[PP_1499]
*	*	÷	NC_002947	1712094	1712227	134	2 [1]	[1] 2	ppc/adk	phosphoenolpyruvate carboxylase/adenylate kinase
*	*	÷	NC_002947	1780119	1780130	12	7 [0]	[1] 2	PP_1587/dapC	NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase
*	*	÷	NC_002947	1898696	1898746	51	2 [1]	[1] 2	PP_t16/PP_t17	tRNA‑Asp/tRNA‑Val
*	*	÷	NC_002947	1921561	1921607	47	3 [1]	[0] 2	[PP_1720]	[PP_1720]
*	*	÷	NC_002947	1930384	1930491	108	2 [1]	[1] 3	[apeB]	[apeB]
*	*	÷	NC_002947	1947820	1947842	23	2 [1]	[0] 2	PP_1748/PP_1749	hypothetical protein/acetyltransferase
*	*	÷	NC_002947	2040275	2040351	77	2 [0]	[1] 3	[rffE]	[rffE]
*	*	÷	NC_002947	2065075	2065162	88	2 [1]	[0] 2	[PP_1838]	[PP_1838]
*	*	÷	NC_002947	2101947	2101975	29	2 [1]	[1] 2	PP_1875/PP_1876	two‑component system sensor histidine kinase/response regulator/AAA family ATP/GTP‑binding protein
*	*	÷	NC_002947	2197504	2197524	21	3 [1]	[1] 2	PP_1940	methyl‑accepting chemotaxis transducer
*	*	÷	NC_002947	2201479	2201636	158	2 [1]	[1] 2	PP_1944	aminomethyltransferase
*	*	÷	NC_002947	2209727	2209830	104	2 [1]	[1] 2	[PP_1951]	[PP_1951]
*	*	÷	NC_002947	2214269	2214303	35	2 [1]	[1] 2	PP_1955	cytochrome P450 family protein
*	*	÷	NC_002947	2243226	2243296	71	2 [1]	[1] 2	gltX/PP_t25	glutamate‑‑tRNA ligase/tRNA‑Ala
*	*	÷	NC_002947	2273203	2273212	10	2 [1]	[1] 3	PP_2002/PP_t31	oxidoreductase/tRNA‑Val
*	*	÷	NC_002947	2297780	2297859	80	2 [1]	[1] 2	[PP_2023]	[PP_2023]
*	*	÷	NC_002947	2476115	2476118	4	7 [0]	[0] 2	PP_2167/tal	PhoD‑like phosphatase/transaldolase
*	*	÷	NC_002947	2617298	2617355	58	3 [1]	[1] 2	PP_2287	internal core protein
*	*	÷	NC_002947	2666001	2666009	9	3 [0]	[1] 2	prpC/acnA‑II	methylcitrate synthase/aconitate hydratase
*	*	÷	NC_002947	2839131	2839156	26	2 [0]	[1] 2	sad‑I/PP_2489	NAD+‑dependent succinate semialdehyde dehydrogenase/xenobiotic reductase
*	*	÷	NC_002947	3055090	3055199	110	5 [1]	[0] 2	[PP_2664]	[PP_2664]
*	*	÷	NC_002947	3056670	3056726	57	2 [1]	[1] 2	PP_2666/PP_2667	hypothetical protein/ABC transporter permease
*	*	÷	NC_002947	3087817	3087836	20	2 [1]	[1] 2	PP_2694	aldehyde dehydrogenase family protein
*	*	÷	NC_002947	3432137	3432155	19	2 [1]	[1] 2	PP_3045	ATP‑dependent protease ClpP
*	*	÷	NC_002947	3518080	3518115	36	3 [1]	[1] 2	PP_5576/PP_5578	hypothetical protein/hypothetical protein
*	*	÷	NC_002947	3579360	3579426	67	2 [1]	[1] 2	[PP_3157]	[PP_3157]
*	*	÷	NC_002947	3778329	3778374	46	2 [1]	[1] 2	PP_3338/PP_3339	cytochrome bd‑type quinol oxidase/hypothetical protein
*	*	÷	NC_002947	3847647	3847715	69	3 [0]	[1] 3	[PP_3395]	[PP_3395]
*	*	÷	NC_002947	3890427	3890491	65	2 [1]	[1] 2	PP_3431	ThiJ/PfpI family protein
*	*	÷	NC_002947	4152011	4152101	91	2 [1]	[1] 2	PP_3654/PP_3655	leucine‑responsive regulatory protein/cytosine/purine/uracil/thiamine/allantoin permease family protein
*	*	÷	NC_002947	4210424	4210514	91	2 [1]	[1] 2	PP_3692	hypothetical protein
*	*	÷	NC_002947	4311475	4311493	19	2 [0]	[1] 2	PP_3781	oxygen‑independent coproporphyrinogen III oxidase family protein
*	*	÷	NC_002947	4340458	4340476	19	3 [1]	[1] 2	PP_3812/PP_5632	lipase/allo‑isoleucine metabolism protein
*	*	÷	NC_002947	4342007	4342055	49	2 [1]	[1] 3	ribAB‑II/PP_3814	3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein
*	*	÷	NC_002947	4346259	4346303	45	2 [0]	[1] 3	PP_3817/PP_3818	polyamine ABC transporter ATP‑binding protein/phosphate‑binding protein
*	*	÷	NC_002947	4355138	4355164	27	2 [1]	[0] 4	yrpB	2‑nitropropane dioxygenase
*	*	÷	NC_002947	4505724	4505764	41	3 [1]	[1] 2	xanP/tusD	xanthine permease/sulfur transfer protein complex subunit TusD
*	*	÷	NC_002947	4531976	4532021	46	2 [0]	[1] 2	PP_4018/topB	acetyltransferase/DNA topoisomerase III
*	*	÷	NC_002947	4553936	4553990	55	2 [1]	[0] 3	pydA/rutR	NADP‑dependent dihydropyrimidine dehydrogenase subunit PreA/transcriptional regulator, TetR family
*	*	÷	NC_002947	4588016	4588047	32	2 [1]	[1] 2	PP_4061/PP_4063	hypothetical protein/long‑chain fatty acid‑‑CoA ligase
*	*	÷	NC_002947	4677237	4677350	114	3 [1]	[1] 3	[PP_4137]	[PP_4137]
*	*	÷	NC_002947	4719244	4719358	115	2 [1]	[1] 2	fabA	3R‑3‑hydroxydecanoyl‑ACP dehydratase
*	*	÷	NC_002947	4742755	4742827	73	2 [1]	[1] 2	gltA/yeiW	citrate synthase/putative oxidoreductase
*	*	÷	NC_002947	4798572	4798635	64	3 [0]	[1] 2	[PP_4224]	[PP_4224]
*	*	÷	NC_002947	4810147	4810182	36	12 [0]	[1] 2	PP_4234/dsbD‑II	bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
*	*	÷	NC_002947	4844852	4844881	30	3 [1]	[1] 2	ccoP‑II/PP_4259	cbb3‑type cytochrome c oxidase subunit/iron‑sulfur cluster‑binding protein
*	*	÷	NC_002947	4854421	4854444	24	7 [0]	[0] 2	recR/ybaB	recombination protein RecR/nucleoid‑associated broad specificity regulator
*	*	÷	NC_002947	4898392	4898413	22	2 [1]	[1] 2	PP_4304/sbp‑I	VIC family cation transporter/sulfate ABC transporter substrate‑binding protein
*	*	÷	NC_002947	4952909	4952965	57	2 [1]	[1] 2	fliL/fliK	flagellar protein FliL/flagellar hook‑length control protein FliK
*	*	÷	NC_002947	5020906	5020952	47	2 [1]	[1] 3	gabD‑II/PP_4423	succinate‑semialdehyde dehydrogenase/hypothetical protein
*	*	÷	NC_002947	5052989	5053042	54	2 [1]	[1] 3	[PP_5687]	[PP_5687]
*	*	÷	NC_002947	5074475	5074490	16	2 [1]	[1] 2	PP_5689	hypothetical protein
*	*	÷	NC_002947	5098216	5098277	62	2 [0]	[1] 2	argT	lysine/arginine/ornithine ABC transporter substrate‑binding protein
*	*	÷	NC_002947	5099218	5099219	2	2 [0]	[0] 2	PP_mr66/acsA‑I	P6/acetyl‑CoA synthetase
*	*	÷	NC_002947	5101510	5101551	42	2 [1]	[1] 2	acsA‑I/PP_4488	acetyl‑CoA synthetase/hypothetical protein
*	*	÷	NC_002947	5164571	5164591	21	2 [0]	[1] 4	PP_4544/PP_4545	hypothetical protein/beta‑ketodecanoyl‑ACP synthase
*	*	÷	NC_002947	5175216	5175236	21	2 [0]	[1] 2	fadD‑I/fadD‑II	long‑chain‑fatty acid‑‑CoA ligase/long‑chain‑fatty acid‑‑CoA ligase
*	*	÷	NC_002947	5194715	5194739	25	4 [1]	[1] 6	PP_4572/PP_4573	hypothetical protein/AAA family ATPase
*	*	÷	NC_002947	5201619	5201648	30	3 [0]	[1] 2	PP_4579/PP_4580	LysR family transcriptional regulator/hypothetical protein
*	*	÷	NC_002947	5259830	5259862	33	2 [1]	[0] 2	PP_4634/PP_4635	alpha/beta family hydrolase/trans‑2‑enoyl‑CoA reductase
*	*	÷	NC_002947	5282915	5282934	20	2 [1]	[1] 4	trmA/pcaG	tRNA/tmRNA (uridine(54)‑C5)‑methyltransferase TrmA/protocatechuate 3,4‑dioxygenase subunit alpha
*	*	÷	NC_002947	5290395	5290418	24	2 [0]	[1] 2	PP_4660/mdaB	LysR family transcriptional regulator/drug activity modulator B
*	*	÷	NC_002947	5301350	5301371	22	4 [1]	[0] 2	recD	multifunctional ATP‑dependent DNA helicase/dsDNA/ssDNA exonuclease/ssDNA endonuclease
*	*	÷	NC_002947	5384420	5384437	18	2 [0]	[0] 2	smpB/pdhR	SsrA‑binding protein/DNA‑binding transcriptional regulator LldR
*	*	÷	NC_002947	5487089	5487170	82	2 [1]	[1] 2	purH/purD	bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase/phosphoribosylamine‑‑glycine ligase
*	*	÷	NC_002947	5538993	5539027	35	2 [1]	[1] 2	[nadE]	[nadE]
*	*	÷	NC_002947	5657576	5657626	51	2 [1]	[0] 3	epd/tktA	D‑erythrose 4‑phosphate dehydrogenase/transketolase A
*	*	÷	NC_002947	5673589	5673626	38	2 [1]	[1] 2	PP_4978/PP_4979	hypothetical protein/substrate‑binding protein
*	*	÷	NC_002947	5700726	5700779	54	3 [1]	[1] 2	hslU/PP_5002	protease HslVU ATPase subunit/hypothetical protein
*	*	÷	NC_002947	5742446	5742508	63	2 [0]	[1] 2	[PP_5037]	[PP_5037]
*	*	÷	NC_002947	5776676	5776694	19	2 [0]	[0] 2	betB	NAD‑dependent betaine aldehyde dehydrogenase
*	*	÷	NC_002947	5788462	5788496	35	2 [1]	[1] 2	PP_5068/trxC	hypothetical protein/thioredoxin
*	*	÷	NC_002947	5899715	5899788	74	2 [1]	[1] 2	PP_5172/PP_5173	hypothetical protein/RND family transporter
*	*	÷	NC_002947	5905115	5905161	47	2 [1]	[1] 2	PP_5175/PP_5176	HlyD family secretion protein/hypothetical protein
*	*	÷	NC_002947	5905722	5905767	46	3 [1]	[0] 2	[PP_5176]	[PP_5176]
*	*	÷	NC_002947	5945602	5945635	34	2 [1]	[1] 2	PP_5210/PP_5211	alcohol dehydrogenase/ChaC‑related protein
*	*	÷	NC_002947	6011119	6011123	5	3 [0]	[1] 2	norM/PP_5263	multidrug resistance protein NorM/GGDEF domain‑containing protein
*	*	÷	NC_002947	6021243	6021254	12	4 [0]	[1] 2	dadX/dadA‑II	alanine racemase/D‑amino acid:quinone oxidoreductase
*	*	÷	NC_002947	6034823	6034839	17	2 [0]	[1] 2	dppA‑IV/PP_5284	dipeptide transport protein/hypothetical protein
*	*	÷	NC_002947	6079829	6079838	10	3 [0]	[1] 2	PP_5329/PP_5330	phosphate ABC transporter substrate‑binding protein/MFS transporter
*	*	÷	NC_002947	6082910	6082969	60	2 [1]	[0] 2	[PP_5332]	[PP_5332]
*	*	÷	NC_002947	6100150	6100159	10	2 [0]	[0] 2	PP_5730/PP_5350	hypothetical protein/RpiR family transcriptional regulator
*	*	÷	NC_002947	6183852	6183858	7	12 [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)	12 (0.710)	9/264	0.5	100%	intergenic (–/+146)	–/parB	–/chromosome‑partitioning protein
*	?	NC_002947	= 6183851	0 (0.000)	12 (0.710)	9/264	0.5	100%	intergenic (‑3/–)	atpI/–	ATP synthase protein I/–
*	?	NC_002947	699484 =	6 (0.360)	3 (0.220)	3/210	1.1	26.4%	noncoding (51/77 nt)	PP_t05	tRNA‑Ile
*	?	NC_002947	5312903 =	12 (0.900)	3 (0.220)	3/210	1.1	26.4%	intergenic (‑34/+63)	PP_t51/PP_t50	tRNA‑Ala/tRNA‑Ile
*	?	NC_002947	= 2474080	4 (0.240)	3 (0.190)	3/250	1.3	31.9%	intergenic (+19/+130)	PP_2166/PP_2167	anti‑anti‑sigma factor/PhoD‑like phosphatase
*	?	NC_002947	2474278 =	9 (0.570)	3 (0.190)	3/250	1.3	31.9%	coding (1783/1851 nt)	PP_2167	PhoD‑like phosphatase
*	?	NC_002947	3368518 =	9 (0.540)	11 (0.650)	11/264	0.3	66.7%	intergenic (+219/‑142)	PP_2962/PP_2964	alcohol dehydrogenase/transposase
*	?	NC_002947	4459337 =	2 (0.120)	11 (0.650)	11/264	0.3	66.7%	coding (9/696 nt)	pcaI	3‑oxoadipate CoA‑transferase subunit A
*	?	NC_002947	= 3385530	15 (0.890)	19 (1.130)	13/264	0.2	71.7%	coding (501/546 nt)	PP_2985	hypothetical protein
*	?	NC_002947	= 4459341	0 (0.000)	19 (1.130)	13/264	0.2	71.7%	coding (13/696 nt)	pcaI	3‑oxoadipate CoA‑transferase subunit A
*	?	NC_002947	= 4810146	0 (0.000)	8 (0.560)	4/224	1.0	30.8%	intergenic (‑288/‑267)	PP_4234/dsbD‑II	bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
*	?	NC_002947	= 5990927	36 (2.520)	8 (0.560)	4/224	1.0	30.8%	intergenic (+243/‑303)	kefB‑III/PP_mr64	glutathione‑regulated potassium/H+ antiporter/C4 ncRNA