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
MC JC	257,908	Δ776 bp		[crl]	[crl]
JC JC	458,790	IS186 (–) +6 bp :: Δ1 bp	intergenic (+90/‑93)	clpX → / → lon	ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La
RA	1,196,305	C→T	R395C (CGT→TGT)	icd →	isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase
JC JC	1,293,032	IS1 (–) +8 bp	intergenic (‑110/‑488)	hns ← / → tdk	global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
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	1,619,080	Δ35 bp	intergenic (‑172/‑6)	marC ← / → marR	UPF0056 family inner membrane protein/transcriptional repressor of multiple antibiotic resistance
MC JC	1,978,503	Δ776 bp		insB1–insA	insB1, insA
JC JC	1,979,486	IS5 (+) +4 bp	intergenic (‑271/‑264)	insA ← / → uspC	IS1 repressor TnpA/universal stress protein
RA	2,132,787	A→C	I204S (ATC→AGC)	wcaA ←	putative glycosyl transferase
RA	2,173,363	Δ2 bp	intergenic (‑1/+1)	gatC ← / ← gatC	pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC
RA	2,414,037	A→C	T190P (ACC→CCC)	ackA →	acetate kinase A and propionate kinase 2
RA	3,560,455	+G	intergenic (‑2/+1)	glpR ← / ← glpR	pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon
MC JC	3,815,859	Δ82 bp		[rph]–[rph]	[rph], [rph]
MC JC	4,001,645	Δ5 bp	coding (220‑224/951 nt)	corA →	magnesium/nickel/cobalt transporter
JC	4,049,991	Δ12 bp	noncoding (93‑104/109 nt)	spf →	Spot 42 sRNA antisense regulator of galK translation, Hfq‑dependent
RA	4,184,543	C→A	P1100Q (CCG→CAG)	rpoB →	RNA polymerase, beta subunit
RA	4,296,381	+GC	intergenic (+587/+55)	gltP → / ← yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein

Unassigned missing coverage evidence
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	3423754–3424521	3424521	1–768	14 [12]	[12] 13	[rrfD]–[rrlD]	[rrfD],[rrlD]
*	*	÷	NC_000913	4233759	4235424	1666	13 [10]	[12] 13	[pgi]	[pgi]