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	302,732	IS2 (–) +5 bp	intergenic (‑159/‑255)	paoA ← / → yagU	PaoABC aldehyde oxidoreductase, 2Fe‑2S subunit/DUF1440 family inner membrane acid resistance protein
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	L375M (TTA→CTG)	icd →	isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase
RA	1,196,247	A→G	L375M (TTA→CTG)	icd →	isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase
RA	1,514,951	G→T	A64S (GCC→TCC)	ydcV →	putative ABC transporter permease
RA	1,610,724	T→C	intergenic (‑44/+183)	uxaB ← / ← yneF	altronate oxidoreductase, NAD‑dependent/putative membrane‑bound diguanylate cyclase
MC JC	1,867,235	Δ4 bp	coding (328‑331/1935 nt)	yeaG →	protein kinase, endogenous substrate unidentified; autokinase
RA	1,881,844	T→G	intergenic (‑35/‑68)	dmlR ← / → dmlA	transcriptional activator of dmlA/D‑malate oxidase, NAD‑dependent; putative tartrate dehydrogenase
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	2,416,674	C→A	S643Y (TCT→TAT)	pta →	phosphate acetyltransferase
JC	2,860,769	Δ20 bp	coding (447‑466/768 nt)	ygbI ←	DeoR family putative transcriptional regulator
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	3,815,810	G→T	intergenic (‑42/+24)	pyrE ← / ← rph	orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH
RA	3,951,538	Δ1 bp	pseudogene (979/984 nt)	ilvG →	pseudogene, acetolactate synthase 2 large subunit, valine‑insensitive; acetolactate synthase II, large subunit, cryptic, interrupted
RA	3,991,184	G→T	R11I (AGA→ATA)	cyaA →	adenylate cyclase
RA	4,001,885	G→T	D154Y (GAC→TAC)	corA →	magnesium/nickel/cobalt transporter
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	1196256	1211579	15324	62 [58]	[58] 59	[icd]–icdC	[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

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 1299498	0 (0.000)	105 (0.810)	72/540	0.4	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