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]
MC JC	1,299,499	Δ1,199 bp	intergenic (+254/‑485)	ychE → / → oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
MC JC	1,978,503	Δ776 bp		insB1–insA	insB1, insA
RA	2,132,787	A→C	I204S (ATC→AGC)	wcaA ←	putative glycosyl transferase
RA	2,509,495	C→G	intergenic (‑71/‑133)	glk ← / → yfeO	glucokinase/putative ion channel protein
RA	3,088,093	T→A	intergenic (+235/‑189)	metK → / → galP	S‑adenosylmethionine synthetase/D‑galactose transporter
MC JC	3,815,858	Δ82 bp		[rph]–[rph]	[rph], [rph]
MC 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

Unassigned missing coverage evidence
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	2533752	2536357	2606	22 [21]	[21] 23	ptsH–crr	ptsH, ptsI, crr
*	*	÷	NC_000913	3762326–3764073	3765214–3764075	3–2889	22 [21]	[21] 23	rhsA	Rhs protein with putative toxin 55 domain, putative polysaccharide synthesis/export protein, putative neighboring cell growth inhibitor

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	257908 =	NA (NA)	45 (0.830)	38/282	0.4	93.8%	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	3 (0.060)					intergenic (‑117/‑488)	hns/tdk	global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
*	?	NC_000913	1207790 =	11 (0.200)	50 (1.050)	46/250	0.0	88.7%	coding (290/630 nt)	stfP	e14 prophage, uncharacterized protein
	?	NC_000913	1209619 =	3 (0.060)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related
*	?	NC_000913	= 1207805	8 (0.150)	37 (0.770)	29/250	0.7	88.0%	coding (305/630 nt)	stfP	e14 prophage, uncharacterized protein
	?	NC_000913	= 1209602	3 (0.060)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related
*	?	NC_000913	1293032 =	2 (0.040)	71 (1.310)	56/282	0.0	97.3%	intergenic (‑110/‑495)	hns/tdk	global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
	?	NC_000913	= 1979270	NA (NA)					intergenic (‑55/‑483)	insA/uspC	IS1 repressor TnpA/universal stress protein
*	?	NC_000913	1979486 =	2 (0.040)	102 (1.890)	66/282	0.0	98.1%	intergenic (‑271/‑267)	insA/uspC	IS1 repressor TnpA/universal stress protein
	?	NC_000913	2101749 =	NA (NA)					intergenic (‑5/+146)	wbbL/insH1	pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator
*	?	NC_000913	= 1979489	1 (0.020)	64 (1.190)	45/282	0.1	98.5%	intergenic (‑274/‑264)	insA/uspC	IS1 repressor TnpA/universal stress protein
	?	NC_000913	= 2290111	NA (NA)					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	2024155 =	3 (0.060)	60 (1.110)	49/282	0.1	95.2%	coding (188/624 nt)	rcsA	transcriptional regulator of colanic acid capsular biosynthesis
	?	NC_000913	2101749 =	NA (NA)					intergenic (‑5/+146)	wbbL/insH1	pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator
*	?	NC_000913	= 2024158	2 (0.040)	79 (1.460)	55/282	0.0	97.5%	coding (191/624 nt)	rcsA	transcriptional regulator of colanic acid capsular biosynthesis
	?	NC_000913	= 2290111	NA (NA)					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	2288917 =	NA (NA)	50 (0.930)	44/282	0.2	98.0%	intergenic (‑5/+146)	yejO/insH1	pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system/IS5 transposase and trans‑activator
	?	NC_000913	3526447 =	1 (0.020)					intergenic (‑300/‑20)	nudE/yrfF	adenosine nucleotide hydrolase, Ap3A/Ap2A/ADP‑ribose/NADH hydrolase/putative RcsCDB‑response attenuator, inner membrane protein
*	?	NC_000913	= 2290110	NA (NA)	42 (0.780)	32/280	0.7	95.5%	intergenic (‑31/+2)	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	= 3526451	2 (0.040)					intergenic (‑304/‑16)	nudE/yrfF	adenosine nucleotide hydrolase, Ap3A/Ap2A/ADP‑ribose/NADH hydrolase/putative RcsCDB‑response attenuator, inner membrane protein
*	?	NC_000913	3845530 =	32 (0.590)	45 (0.900)	40/262	0.2	56.7%	coding (1568/1767 nt)	adeD	cryptic adenine deaminase
	?	NC_000913	= 3992759	39 (0.780)					coding (1608/2547 nt)	cyaA	adenylate cyclase