breseq  version 0.27.1  revision 87c22d663cc3 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	1,196,220	C→T	H366H (CAC→CAT)	icd →	isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase
RA	1,196,232	C→T	T370T (ACC→ACT)	icd →	isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase
RA	1,196,245	T→C	L375L (TTA→CTA)	icd →	isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase
RA	1,196,247	A→G	L375L (TTA→TTG)	icd →	isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase
RA	1,196,277	C→T	N385N (AAC→AAT)	icd →	isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase
RA	1,529,175	T→C	pseudogene (1274/2037 nt)	rhsE →	pseudogene, Rhs family
RA	1,529,180	T→C	pseudogene (1279/2037 nt)	rhsE →	pseudogene, Rhs family
RA	1,529,185	C→T	pseudogene (1284/2037 nt)	rhsE →	pseudogene, Rhs family
RA	1,529,203	C→A	pseudogene (1302/2037 nt)	rhsE →	pseudogene, Rhs family
RA	1,529,218	C→T	pseudogene (1317/2037 nt)	rhsE →	pseudogene, Rhs family
RA	1,621,022	C→A	R39L (CGC→CTC)	eamA ←	cysteine and O‑acetyl‑L‑serine efflux system
JC JC	1,907,562	IS1 (+) +9 bp	coding (22‑30/144 nt)	yobF ←	DUF2527 family heat‑induced protein
MC JC	1,978,503	Δ776 bp		insB1–insA	insB1, insA
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	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]
RA	4,187,633	A→C	N762H (AAC→CAC)	rpoC →	RNA polymerase, beta prime 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	1196280	1211471	15192	39 [36]	[38] 40	[icd]–[icdC]	25 genes [icd], ymfD, ymfE, lit, intE, xisE, ymfI, ymfJ, cohE, croE, ymfL, ymfM, oweE, aaaE, ymfR, beeE, jayE, ymfQ, stfP, tfaP, tfaE, stfE, pinE, mcrA, [icdC]
*	*	÷	NC_000913	3423834–3424233	3424521–3424238	6–688	39 [38]	[38] 39	[rrlD]	[rrlD]

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 1299498	0 (0.000)	123 (1.490)	113/592	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)					intergenic (+1453/‑484)	ychE/oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein