breseq  version 0.35.4  revision f352f80f4bc9 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence	position	mutation	annotation	gene	description
RA	222,965	(A)8→7	coding (133/576 nt)	gmhB →	D,D‑heptose 1,7‑bisphosphate phosphatase
MC JC	257,908	Δ776 bp		[crl]	[crl]
JC JC	1,237,329	IS2 (+) +5 bp	intergenic (‑88/‑238)	ycgB ← / → dadA	SpoVR family stationary phase protein/D‑amino acid dehydrogenase
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	2,019,460	G→A	V359I (GTC→ATC)	fliK →	flagellar hook‑length control protein
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
JC JC	2,375,828	IS186 (+) +4 bp	coding (132‑135/963 nt)	menC ←	O‑succinylbenzoyl‑CoA synthase
RA	2,904,212	G→A	intergenic (+838/+535)	ygcE → / ← queE	putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis
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
JC JC	3,890,075	IS5 (–) +4 bp	coding (1346‑1349/1416 nt)	tnaA →	tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent
RA	4,296,381	+GC	intergenic (+587/+55)	gltP → / ← yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA	4,406,129	T→C	intergenic (+144/‑61)	purA → / → nsrR	adenylosuccinate synthetase/nitric oxide‑sensitive repressor for NO regulon
RA	4,633,785	C→A	intergenic (‑40/‑12)	yjjX ← / → ytjC	non‑canonical purine NTP phosphatase, ITPase/XTPase/phosphatase
JC JC	4,640,551	IS1 (–) +9 bp	intergenic (+9/‑383)	yjjY → / → yjtD	uncharacterized protein/putative methyltransferase

Unassigned missing coverage evidence
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	772999	774196	1198	30 [29]	[29] 30	[cydA]–[cydX]	[cydA],cydB,[cydX]
*	*	÷	NC_000913	1037687	1039317	1631	30 [29]	[29] 30	cbdA–[cbdB]	cbdA,[cbdB]
*	*	÷	NC_000913	1166047	1167400	1354	30 [29]	[29] 34	ndh	ndh
*	*	÷	NC_000913	3423704–3424556	3424556	1–853	30 [29]	[28] 30	[rrfD]–[rrlD]	[rrfD],[rrlD]