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	167,843	+T	coding (360/2244 nt)	fhuA →	ferrichrome outer membrane transporter
MC JC	257,908	Δ776 bp		[crl]	[crl]
RA	909,422	G→A	A543V (GCC→GTC)	poxB ←	pyruvate dehydrogenase, thiamine triphosphate‑binding, FAD‑binding
JC JC	911,086	IS2 (–) +5 bp	intergenic (‑37/+92)	poxB ← / ← hcr	pyruvate dehydrogenase, thiamine triphosphate‑binding, FAD‑binding/HCP oxidoreductase, NADH‑dependent
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
JC JC	1,979,486	IS5 (+) +4 bp	intergenic (‑271/‑264)	insA ← / → uspC	IS1 repressor TnpA/universal stress 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	2,720,868	(CGCTGG)2→3	coding (916/2661 nt)	pka →	protein lysine acetyltransferase
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
RA	3,768,131	A→T	pseudogene (911/945 nt)	rhsJ →	Rhs‑family protein
RA	3,964,929	C→T	E234E (GAG→GAA)	rhlB ←	ATP‑dependent RNA helicase
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	123036	127554	4519	35 [33]	[33] 37	[aceE]–[aceF]	[aceE],[aceF]
*	*	÷	NC_000913	3423749–3424234	3424601–3424238	5–853	35 [34]	[33] 35	[rrfD]–[rrlD]	[rrfD],[rrlD]
*	*	÷	NC_000913	3619345–3621083	3688673	67591–69329	35 [32]	[1] 80	[rhsB]–[bcsC]	[rhsB],yhhH,yrhC,yhhI,yhhJ,rbbA,yhiI,yhiJ,yhiL,yhiL,yhiM,yhiN,pitA,uspB,uspA,dtpB,rsmJ,prlC,rlmJ,gor,dinQ,agrA,agrB,arsR,arsB,arsC,yhiS,insH1,yhiS,slp,dctR,yhiD,hdeB,hdeA,hdeD,arrS,gadE,mdtE,mdtF,gadW,gadY,gadX,gadA,yhjA,treF,yhjB,yhjC,yhjD,yhjE,yhjG,yhjH,kdgK,yhjJ,dctA,yhjK,[bcsC]

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	1213105 =	24 (0.250)	44 (0.460)	42/274	1.9	64.7%	coding (3/405 nt)	ycgX	DUF1398 family protein
	?	NC_000913	1467910 =	NA (NA)					noncoding (1331/1331 nt)	IS2	repeat region
*	?	NC_000913	= 1213109	23 (0.240)	48 (0.500)	40/274	2.1	67.6%	intergenic (‑2/+219)	ycgX/bluR	DUF1398 family protein/repressor of blue light‑responsive genes
	?	NC_000913	= 1469240	NA (NA)					noncoding (1/1331 nt)	IS2	repeat region
*	?	NC_000913	3688674 =	1 (0.010)	79 (0.830)	63/272	0.5	61.5%	coding (500/3474 nt)	bcsC	cellulose synthase subunit
	?	NC_000913	= 4506221	98 (1.030)					coding (935/1119 nt)	yjhC	GFO/IDH/MOCA family putative oxidoreductase. NAD(P)‑dependent