BRESEQ :: Mutation Predictions

breseq version 0.32.0 revision 6ff6de7d1b87
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence	position	mutation	annotation	gene	description
MC JC	257,908	Δ776 bp		[crl]	[crl]
RA	418,961	Δ1 bp	coding (1073/1296 nt)	phoR →	sensory histidine kinase in two‑component regulatory system with PhoB
RA	704,083	C→A	A47E (GCG→GAG)	nagE →	N‑acetyl glucosamine specific PTS enzyme IIC, IIB, and IIA components
RA	1,157,900	+A	coding (32/1434 nt)	ptsG →	fused glucose‑specific PTS enzymes: IIB component/IIC component
RA	1,726,390	G→T	R123L (CGC→CTC)	nemR →	transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated
RA	1,756,374	G→A	G226D (GGC→GAC)	pykF →	pyruvate kinase I
MC JC	1,978,503	Δ776 bp		insB1–insA	insB1, insA
RA	2,132,787	A→C	I204S (ATC→AGC)	wcaA ←	putative glycosyl transferase
MC JC	3,815,858	Δ82 bp		[rph]–[rph]	[rph], [rph]
MC JC	3,909,311	Δ774 bp		[pstA]–[pstC]	[pstA], [pstC]
JC	4,001,644	Δ5 bp	coding (220‑224/951 nt)	corA →	magnesium/nickel/cobalt transporter
RA	4,184,542	C→A	P1100Q (CCG→CAG)	rpoB →	RNA polymerase, beta subunit
RA	4,189,512	+C	coding (4164/4224 nt)	rpoC →	RNA polymerase, beta prime subunit

Unassigned missing coverage evidence
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	3423742–3424528	3424528	1–787	22 [21]	[21] 22	[rrfD]–[rrlD]	[rrfD], [rrlD]
*	*	÷	NC_000913	4110737	4111500	764	22 [20]	[21] 22	[tpiA]	[tpiA]

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	257908 =	NA (NA)	41 (0.800)	34/284	0.5	91.1%	intergenic (+9/‑768)	crl/crl	pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers
*	?	NC_000913	= 700605	4 (0.080)	41 (0.800)	34/284	0.5	91.1%	coding (990/1221 nt)	nagC	N‑acetylglucosamine‑inducible nag divergent operon transcriptional repressor
*	?	NC_000913	257908 =	NA (NA)	46 (0.890)	37/284	0.3	95.8%	intergenic (+9/‑768)	crl/crl	pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers
*	?	NC_000913	= 1293039	2 (0.040)	46 (0.890)	37/284	0.3	95.8%	intergenic (‑117/‑488)	hns/tdk	global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
*	?	NC_000913	= 258675	NA (NA)	65 (1.260)	51/284	0.0	94.2%	intergenic (+776/‑1)	crl/crl	pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers
*	?	NC_000913	700597 =	4 (0.080)	65 (1.260)	51/284	0.0	94.2%	coding (998/1221 nt)	nagC	N‑acetylglucosamine‑inducible nag divergent operon transcriptional repressor
*	?	NC_000913	1207790 =	8 (0.160)	38 (0.830)	33/252	0.3	80.8%	coding (290/630 nt)	stfP	e14 prophage, uncharacterized protein
*	?	NC_000913	1209619 =	11 (0.240)	38 (0.830)	33/252	0.3	80.8%	pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related
*	?	NC_000913	= 1207805	9 (0.170)	40 (0.870)	35/252	0.2	80.8%	coding (305/630 nt)	stfP	e14 prophage, uncharacterized protein
*	?	NC_000913	= 1209602	11 (0.240)	40 (0.870)	35/252	0.2	80.8%	pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related
*	?	NC_000913	1293032 =	6 (0.120)	56 (1.090)	43/284	0.1	90.3%	intergenic (‑110/‑495)	hns/tdk	global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
*	?	NC_000913	= 1979270	NA (NA)	56 (1.090)	43/284	0.1	90.3%	intergenic (‑55/‑483)	insA/uspC	IS1 repressor TnpA/universal stress protein
*	?	NC_000913	= 1299498	0 (0.000)	67 (1.340)	61/276	0.0	100%	intergenic (+253/‑1684)	ychE/oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
*	?	NC_000913	1300698 =	0 (0.000)	67 (1.340)	61/276	0.0	100%	intergenic (+1453/‑484)	ychE/oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
*	?	NC_000913	1962618 =	22 (0.430)	28 (0.540)	24/284	1.4	56.0%	coding (355/393 nt)	flhE	proton seal during flagellar secretion
*	?	NC_000913	= 2290111	NA (NA)	28 (0.540)	24/284	1.4	56.0%	intergenic (‑32/+1)	insH1/yejO	IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system
*	?	NC_000913	1979486 =	2 (0.040)	68 (1.320)	40/284	0.2	97.1%	intergenic (‑271/‑267)	insA/uspC	IS1 repressor TnpA/universal stress protein
*	?	NC_000913	2101749 =	NA (NA)	68 (1.320)	40/284	0.2	97.1%	intergenic (‑5/+146)	wbbL/insH1	pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator
*	?	NC_000913	= 1979489	2 (0.040)	67 (1.300)	34/284	0.5	97.1%	intergenic (‑274/‑264)	insA/uspC	IS1 repressor TnpA/universal stress protein
*	?	NC_000913	= 2290111	NA (NA)	67 (1.300)	34/284	0.5	97.1%	intergenic (‑32/+1)	insH1/yejO	IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system