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
JC	1,851,535	+TAC	coding (579/2241 nt)	relA →	ATP:GTP 3'‑pyrophosphotransferase
RA	4,741,273	+C	intergenic (+464/+288)	gltA → / ← yeiW	citrate synthase/putative oxidoreductase
RA	4,741,275	A→G	intergenic (+466/+286)	gltA → / ← yeiW	citrate synthase/putative oxidoreductase
RA	4,741,277	C→T	intergenic (+468/+284)	gltA → / ← yeiW	citrate synthase/putative oxidoreductase
RA	4,741,280	C→T	intergenic (+471/+281)	gltA → / ← yeiW	citrate synthase/putative oxidoreductase
RA	4,741,283	C→G	intergenic (+474/+278)	gltA → / ← yeiW	citrate synthase/putative oxidoreductase
RA	4,741,285	2 bp→CT	intergenic (+476/+275)	gltA → / ← yeiW	citrate synthase/putative oxidoreductase

Unassigned missing coverage evidence
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_002947	171363–172964	173334–172972	9–1972	2 [1]	[1] 2	PP_16SA–[PP_23SA]	PP_16SA,[PP_23SA]
*	*	÷	NC_002947	176685–178394	181673–178402	9–4989	2 [1]	[1] 2	PP_16SB–[PP_r01]	PP_16SB,PP_23SB,[PP_r01]
*	*	÷	NC_002947	361115	361117	3	2 [0]	[0] 2	PP_0300	metallopeptidase
*	*	÷	NC_002947	522765	522798	34	2 [1]	[1] 2	PP_0435/tyrS	M23/M37 family peptidase/tyrosine‑‑tRNA ligase
*	*	÷	NC_002947	573960	573965	6	3 [1]	[0] 2	PP_0487	membrane protein
*	*	÷	NC_002947	1131777	1131780	4	2 [0]	[0] 2	PP_0992	hypothetical protein
*	*	÷	NC_002947	1147052	1147124	73	3 [1]	[1] 2	PP_1006	heme receptor
*	*	÷	NC_002947	1278967	1279022	56	2 [1]	[1] 2	PP_1117	hypothetical protein
*	*	÷	NC_002947	1412792	1412826	35	3 [1]	[0] 2	PP_1234	permease
*	*	÷	NC_002947	1419159	1419206	48	3 [1]	[1] 2	PP_1241/PP_1242	hypothetical protein/hypothetical protein
*	*	÷	NC_002947	1708141	1708147	7	2 [0]	[0] 2	PP_1502	OmpA family protein
*	*	÷	NC_002947	1747087	1747097	11	3 [0]	[1] 3	PP_1546	hypothetical protein
*	*	÷	NC_002947	2004288	2004319	32	5 [1]	[1] 3	PP_1787	hypothetical protein
*	*	÷	NC_002947	2064277	2064355	79	2 [1]	[1] 3	PP_1841	cytochrome c family protein
*	*	÷	NC_002947	2117619	2117665	47	2 [0]	[1] 2	PP_1884	hypothetical protein
*	*	÷	NC_002947	2195323	2195415	93	3 [1]	[0] 2	PP_1940	methyl‑accepting chemotaxis transducer
*	*	÷	NC_002947	2219068	2219118	51	2 [1]	[1] 3	PP_1959	hypothetical protein
*	*	÷	NC_002947	2343545	2343598	54	2 [1]	[1] 2	PP_2059	hypothetical protein
*	*	÷	NC_002947	2350252	2350291	40	2 [1]	[1] 2	PP_2065	multidrug RND transporter
*	*	÷	NC_002947	2380269	2380294	26	2 [0]	[0] 2	PP_2088/oprF	RNA polymerase sigma factor SigX/porin F
*	*	÷	NC_002947	2536095	2536175	81	2 [1]	[1] 2	[mrpC]–[mrpAB]	[mrpC],[mrpAB]
*	*	÷	NC_002947	2588489	2588522	34	2 [0]	[1] 2	PP_2266	DNA‑directed RNA polymerase
*	*	÷	NC_002947	2597863	2597894	32	2 [0]	[1] 2	PP_2276	exonuclease
*	*	÷	NC_002947	2620113	2620146	34	2 [1]	[0] 2	PP_2293	DNA maturase B
*	*	÷	NC_002947	2633454	2633499	46	2 [0]	[1] 2	hupB/PP_2304	DNA binding regulator subunit beta B/peptidyl‑prolyl cis‑trans isomerase D
*	*	÷	NC_002947	2791583	2791640	58	3 [1]	[1] 2	[sstT]	[sstT]
*	*	÷	NC_002947	2831524	2831599	76	2 [1]	[1] 2	[PP_2484]	[PP_2484]
*	*	÷	NC_002947	2836291	2836298	8	2 [0]	[0] 2	sad‑I	NAD+‑dependent succinate semialdehyde dehydrogenase
*	*	÷	NC_002947	2877483	2877512	30	3 [1]	[1] 3	PP_2531/PP_2532	5‑nucleotidase/hypothetical protein
*	*	÷	NC_002947	2882782	2882851	70	2 [1]	[1] 2	PP_2538	hypothetical protein
*	*	÷	NC_002947	2985826	2985951	126	2 [1]	[0] 2	PP_2612	membrane protein
*	*	÷	NC_002947	3009227	3009313	87	2 [1]	[1] 2	PP_2628/PP_2631	ABC transporter ATP‑binding protein/cellulose biosynthesis protein BcsF/YhjT
*	*	÷	NC_002947	3055024	3055056	33	3 [1]	[1] 2	PP_2667	ABC transporter permease
*	*	÷	NC_002947	3061705	3061727	23	2 [1]	[1] 2	qedH‑I	quinoprotein ethanol dehydrogenase
*	*	÷	NC_002947	3070729	3070742	14	3 [1]	[1] 3	aldB‑II/pqqD‑II	aldehyde dehydrogenase/coenzyme PQQ synthesis protein D
*	*	÷	NC_002947	3137538	3137570	33	3 [1]	[1] 2	PP_2753	ABC transporter ATP‑binding protein
*	*	÷	NC_002947	3157684	3157714	31	2 [1]	[1] 2	PP_2773	hypothetical protein
*	*	÷	NC_002947	3172036	3172047	12	2 [1]	[0] 2	PP_2784	short‑chain dehydrogenase/reductase family oxidoreductase
*	*	÷	NC_002947	3177627	3177755	129	2 [1]	[1] 2	PP_2788	MerR family transcriptional regulator
*	*	÷	NC_002947	3194668	3194703	36	2 [0]	[1] 3	PP_2802	amino acid permease family protein
*	*	÷	NC_002947	3226971	3226995	25	2 [0]	[0] 2	PP_2827/PP_2828	alcohol dehydrogenase/hypothetical protein
*	*	÷	NC_002947	3244055	3244177	123	2 [1]	[0] 4	PP_2839	hypothetical protein
*	*	÷	NC_002947	3297577	3297744	168	2 [1]	[0] 2	[PP_2900]	[PP_2900]
*	*	÷	NC_002947	3338698	3338702	5	2 [0]	[0] 2	PP_2935	membrane protein
*	*	÷	NC_002947	3349067	3349109	43	2 [1]	[1] 3	PP_2944	sensor histidine kinase
*	*	÷	NC_002947	3351602	3351652	51	2 [1]	[1] 2	arfB/PP_2947	peptidyl‑tRNA hydrolase/transcriptional regulator MvaT
*	*	÷	NC_002947	3386063	3386128	66	2 [1]	[1] 3	[PP_2987]	[PP_2987]
*	*	÷	NC_002947	3400054	3400099	46	2 [1]	[1] 3	[PP_3005]–[PP_3006]	[PP_3005],[PP_3006]
*	*	÷	NC_002947	3449928	3449949	22	4 [1]	[1] 3	PP_3067	hypothetical protein
*	*	÷	NC_002947	3517759	3517760	2	2 [0]	[0] 2	PP_5578/PP_3109	hypothetical protein/hypothetical protein
*	*	÷	NC_002947	3569591	3569687	97	2 [1]	[1] 2	sad‑II	NAD+‑dependent succinate semialdehyde dehydrogenase
*	*	÷	NC_002947	3662075	3662149	75	2 [1]	[1] 2	PP_3226	acyl‑CoA dehydrogenase‑related protein
*	*	÷	NC_002947	3664100	3664154	55	3 [1]	[1] 2	[PP_3228]	[PP_3228]
*	*	÷	NC_002947	3736062	3736066	5	2 [0]	[1] 2	PP_3302	RND family transporter
*	*	÷	NC_002947	3756486	3756577	92	2 [0]	[1] 2	PP_3319	GGDEF domain‑containing sensory box protein
*	*	÷	NC_002947	3764725	3764771	47	2 [0]	[1] 2	PP_3326/PP_3328	hypothetical protein/ring‑cleaving dioxygenase
*	*	÷	NC_002947	3872311	3872366	56	2 [1]	[1] 3	PP_3420	sensor histidine kinase
*	*	÷	NC_002947	3898779	3898832	54	2 [1]	[1] 3	PP_3441	hypothetical protein
*	*	÷	NC_002947	3939846	3939864	19	2 [1]	[1] 3	csgG	curli production assembly/transport protein CsgG
*	*	÷	NC_002947	3959518	3959531	14	2 [1]	[1] 2	mnxG	manganese‑oxidizing multicopper oxidase
*	*	÷	NC_002947	4197292	4197325	34	3 [1]	[0] 2	PP_5620	hypothetical protein
*	*	÷	NC_002947	4203249	4203289	41	3 [1]	[1] 3	PP_3691	DNA helicase‑related protein
*	*	÷	NC_002947	4295982	4296022	41	3 [1]	[1] 2	PP_3765	H‑NS family protein MvaT
*	*	÷	NC_002947	4353222	4353236	15	2 [1]	[1] 2	yrpB	2‑nitropropane dioxygenase
*	*	÷	NC_002947	4376476	4376513	38	3 [1]	[0] 2	PP_3852	BNR domain‑containing protein
*	*	÷	NC_002947	4484563	4484599	37	2 [0]	[0] 2	PP_3976/PP_3977	isochorismatase family hydrolase/hypothetical protein
*	*	÷	NC_002947	4493364	4495604–4493385	22–2241	3 [1]	[1] 2	PP_3984–[PP_3986]	PP_3984,PP_3985,[PP_3986]
*	*	÷	NC_002947	4621120	4621190	71	2 [1]	[1] 2	PP_5654	phosphotriesterase
*	*	÷	NC_002947	4676119	4676160	42	2 [0]	[0] 3	chrR/PP_4139	chromate reductase/hypothetical protein
*	*	÷	NC_002947	4808205	4808252	48	5 [0]	[1] 2	PP_4234/dsbD‑II	bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
*	*	÷	NC_002947	4943061	4943141	81	2 [1]	[1] 3	PP_4350	class V NifS/IscS family aminotransferase
*	*	÷	NC_002947	5006792	5006859	68	2 [1]	[1] 2	PP_4410	hypothetical protein
*	*	÷	NC_002947	5069944	5070006	63	3 [1]	[0] 2	PP_4465/PP_4466	porin/TauD/TfdA family dioxygenase
*	*	÷	NC_002947	5116242	5116345	104	2 [1]	[1] 2	PP_4501	septation protein A
*	*	÷	NC_002947	5194211	5194272	62	3 [1]	[1] 2	PP_4574	hypothetical protein

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	105504 =	4 (0.310)	3 (0.240)	3/258	1.3	35.8%	coding (298/720 nt)	cynT	carbonic anhydrase
	?	NC_002947	105533 =	7 (0.570)					coding (327/720 nt)	cynT	carbonic anhydrase
*	?	NC_002947	= 174906	NA (NA)	3 (0.240)	3/264	1.4	NA	noncoding (1704/2902 nt)	PP_23SA	23S ribosomal RNA
	?	NC_002947	= 174936	NA (NA)					noncoding (1734/2902 nt)	PP_23SA	23S ribosomal RNA
*	?	NC_002947	413997 =	15 (1.150)	7 (0.670)	6/218	0.6	50.1%	intergenic (+14/‑189)	glnE/waaF	glutamate‑ammonia‑ligase adenylyltransferase/ADP‑heptose:LPS heptosyltransferase II
	?	NC_002947	414083 =	2 (0.190)					intergenic (+100/‑103)	glnE/waaF	glutamate‑ammonia‑ligase adenylyltransferase/ADP‑heptose:LPS heptosyltransferase II
*	?	NC_002947	= 469835	15 (1.150)	4 (0.310)	4/268	1.1	21.8%	coding (1125/3744 nt)	PP_0386	sensory box protein
	?	NC_002947	= 469886	14 (1.100)					coding (1074/3744 nt)	PP_0386	sensory box protein
*	?	NC_002947	= 652785	8 (0.610)	4 (0.360)	4/234	1.0	53.9%	coding (1961/1962 nt)	ctpL	methyl‑accepting chemotaxis protein CtpL
	?	NC_002947	= 4808204	0 (0.000)					intergenic (‑268/‑287)	PP_4234/dsbD‑II	bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
*	?	NC_002947	= 914680	15 (1.150)	4 (0.310)	4/268	1.1	21.8%	coding (1388/1743 nt)	fruA	PTS fructose transporter subunit IIBC
	?	NC_002947	= 914721	14 (1.100)					coding (1429/1743 nt)	fruA	PTS fructose transporter subunit IIBC
*	?	NC_002947	1499443 =	8 (0.610)	3 (0.280)	3/228	1.2	30.5%	intergenic (+13/‑153)	trpS/zapE	tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein
	?	NC_002947	1499526 =	7 (0.640)					intergenic (+96/‑70)	trpS/zapE	tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein
*	?	NC_002947	= 1731232	5 (0.380)	4 (0.390)	4/218	0.9	40.0%	intergenic (‑103/+88)	dapE/PP_1526	succinyl‑diaminopimelate desuccinylase/beta‑(1‑3)‑glucosyl transferase
	?	NC_002947	= 1731268	8 (0.770)					intergenic (‑139/+52)	dapE/PP_1526	succinyl‑diaminopimelate desuccinylase/beta‑(1‑3)‑glucosyl transferase
*	?	NC_002947	1838059 =	13 (1.000)	4 (0.320)	4/266	1.1	26.1%	coding (636/672 nt)	PP_1642	hypothetical protein
	?	NC_002947	1838090 =	10 (0.790)					coding (667/672 nt)	PP_1642	hypothetical protein
*	?	NC_002947	= 2060084	14 (1.070)	4 (0.320)	4/266	1.1	21.9%	coding (588/939 nt)	PP_1836	ZIP family metal transporter
	?	NC_002947	= 2060113	15 (1.180)					coding (559/939 nt)	PP_1836	ZIP family metal transporter
*	?	NC_002947	2247118 =	7 (0.540)	3 (0.240)	3/262	1.3	26.4%	coding (2524/3297 nt)	PP_1983	PAS/PAC/GAF sensor‑containing diguanylate cyclase/phosphodiesterase
	?	NC_002947	2247154 =	10 (0.800)					coding (2488/3297 nt)	PP_1983	PAS/PAC/GAF sensor‑containing diguanylate cyclase/phosphodiesterase
*	?	NC_002947	2679659 =	9 (0.690)	3 (0.240)	3/264	1.4	22.5%	coding (357/1155 nt)	PP_2349	CBS domain‑containing protein
	?	NC_002947	2679701 =	12 (0.950)					coding (399/1155 nt)	PP_2349	CBS domain‑containing protein
*	?	NC_002947	2937810 =	NA (NA)	7 (0.560)	6/264	0.8	NA	coding (1288/1329 nt)	PP_2570	transposase
	?	NC_002947	2937843 =	NA (NA)					coding (1255/1329 nt)	PP_2570	transposase
*	?	NC_002947	= 2974787	5 (0.380)	4 (0.320)	4/260	1.1	40.5%	coding (677/777 nt)	PP_2601	IclR family transcriptional regulator
	?	NC_002947	= 2974812	7 (0.570)					coding (702/777 nt)	PP_2601	IclR family transcriptional regulator
*	?	NC_002947	= 4586100	4 (0.310)	4 (0.420)	4/198	0.8	53.7%	intergenic (+139/+78)	PP_4061/PP_4063	hypothetical protein/long‑chain fatty acid‑‑CoA ligase
	?	NC_002947	= 4586128	4 (0.420)					intergenic (+167/+50)	PP_4061/PP_4063	hypothetical protein/long‑chain fatty acid‑‑CoA ligase
*	?	NC_002947	4893598 =	18 (1.380)	4 (0.380)	4/220	0.9	25.4%	intergenic (+28/‑180)	pyk/PP_4302	pyruvate kinase/urea transporter
	?	NC_002947	4893677 =	9 (0.860)					intergenic (+107/‑101)	pyk/PP_4302	pyruvate kinase/urea transporter
*	?	NC_002947	5111564 =	17 (1.300)	4 (0.320)	4/260	1.1	21.0%	coding (896/1068 nt)	rluB	23S rRNA pseudouridylate synthase B
	?	NC_002947	5111604 =	14 (1.130)					coding (856/1068 nt)	rluB	23S rRNA pseudouridylate synthase B
*	?	NC_002947	= 5180858	12 (0.920)	5 (0.390)	5/272	1.0	29.5%	coding (177/537 nt)	def‑II	peptide deformylase
	?	NC_002947	= 5180880	12 (0.930)					coding (155/537 nt)	def‑II	peptide deformylase
*	?	NC_002947	5201627 =	11 (0.840)	4 (0.420)	4/200	0.8	42.0%	intergenic (‑65/‑115)	PP_4582/PP_4583	membrane protein/putative Peptidase
	?	NC_002947	5201722 =	3 (0.320)					intergenic (‑160/‑20)	PP_4582/PP_4583	membrane protein/putative Peptidase
*	?	NC_002947	= 5210282	12 (0.920)	5 (0.430)	5/242	0.8	26.6%	intergenic (‑100/+78)	rnd/PP_4592	ribonuclease D/metal dependent hydrolase
	?	NC_002947	= 5210341	17 (1.480)					intergenic (‑159/+19)	rnd/PP_4592	ribonuclease D/metal dependent hydrolase
*	?	NC_002947	5257895 =	12 (0.920)	5 (0.410)	4/256	1.1	24.9%	intergenic (‑46/+98)	PP_4634/PP_4635	alpha/beta family hydrolase/trans‑2‑enoyl‑CoA reductase
	?	NC_002947	5257986 =	19 (1.560)					intergenic (‑137/+7)	PP_4634/PP_4635	alpha/beta family hydrolase/trans‑2‑enoyl‑CoA reductase
*	?	NC_002947	5288442 =	9 (0.690)	4 (0.390)	4/214	0.9	39.9%	intergenic (‑75/+109)	PP_4660/mdaB	LysR family transcriptional regulator/drug activity modulator B
	?	NC_002947	5288536 =	5 (0.490)					intergenic (‑169/+15)	PP_4660/mdaB	LysR family transcriptional regulator/drug activity modulator B
*	?	NC_002947	= 5864480	14 (1.070)	5 (0.410)	4/258	1.1	32.1%	coding (1727/2253 nt)	cadA‑III	cadmium translocating P‑type ATPase
	?	NC_002947	= 5864515	8 (0.650)					coding (1692/2253 nt)	cadA‑III	cadmium translocating P‑type ATPase
*	?	NC_002947	6000959 =	22 (1.690)	4 (0.390)	4/214	0.9	20.9%	intergenic (+10/+99)	PP_5256/amaA	cyclic nucleotide‑binding protein/L‑pipecolate oxidase
	?	NC_002947	6001053 =	13 (1.280)					intergenic (+104/+5)	PP_5256/amaA	cyclic nucleotide‑binding protein/L‑pipecolate oxidase
*	?	NC_002947	6060487 =	7 (0.540)	6 (0.510)	5/246	0.8	41.0%	intergenic (+67/+114)	PP_5311/PP_5312	signal transduction protein/hypothetical protein
	?	NC_002947	6060574 =	11 (0.940)					intergenic (+154/+27)	PP_5311/PP_5312	signal transduction protein/hypothetical protein
*	?	NC_002947	= 6060500	7 (0.540)	6 (0.510)	5/246	0.8	41.0%	intergenic (+80/+101)	PP_5311/PP_5312	signal transduction protein/hypothetical protein
	?	NC_002947	= 6060559	11 (0.940)					intergenic (+139/+42)	PP_5311/PP_5312	signal transduction protein/hypothetical protein