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
MC JC	257,908	Δ776 bp		[crl]	[crl]
RA	264,098	G→T	L50L (CTC→CTA)	ykfH ←	uncharacterized protein
RA	275,065	G→A	T18I (ACC→ATC)	insH1 ←	IS5 transposase and trans‑activator
RA	389,925	(T)6→7	intergenic (‑198/‑326)	hemB ← / → yaiT	5‑aminolevulinate dehydratase (porphobilinogen synthase)/pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein
RA	482,230	G→A	P725L (CCG→CTG)	acrB ←	multidrug efflux system protein
RA	1,158,559	C→T	Q231* (CAG→TAG)	ptsG →	fused glucose‑specific PTS enzymes: IIB component/IIC component
RA	1,197,502	C→T	G11R (GGA→AGA)	ymfD ←	e14 prophage; putative SAM‑dependent methyltransferase
RA	1,544,022	1 bp→AA	coding (39/1389 nt)	narU ←	nitrate/nitrite transporter
RA	1,549,573	C→A	H725N (CAT→AAT)	fdnG →	formate dehydrogenase‑N, alpha subunit, nitrate‑inducible
RA	1,726,372	A→T	D117V (GAT→GTT)	nemR →	transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated
RA	1,774,576	G→A	G263E (GGG→GAG)	ydiB →	quinate/shikimate 5‑dehydrogenase, NAD(P)‑binding
MC JC	1,978,503	Δ776 bp		insB1–insA	insB1, insA
RA	2,106,741	A→T	S162S (TCT→TCA)	wbbH ←	O‑antigen polymerase
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	2,679,525	G→T	A1074D (GCT→GAT)	yphG ←	DUF4380 domain‑containing TPR repeat protein
RA	2,795,396	C→A	Q382K (CAG→AAG)	gabP →	gamma‑aminobutyrate transporter
RA	2,817,170	C→A	E112* (GAA→TAA)	yqaB ←	fructose‑1‑P and 6‑phosphogluconate phosphatase
RA	2,976,684	G→T	S29I (AGC→ATC)	galR →	galactose‑inducible d‑galactose regulon transcriptional repressor; autorepressor
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	4,187,572	G→T	M747I (ATG→ATT)	rpoC →	RNA polymerase, beta prime subunit
RA	4,296,363	+GC	intergenic (+587/+55)	gltP → / ← yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA	4,546,943	C→A	S622R (AGC→AGA)	fimD →	fimbrial usher outer membrane porin protein; FimCD chaperone‑usher
RA	4,604,698	C→A	A186E (GCA→GAA)	bglJ →	bgl operon transcriptional activator

Unassigned missing coverage evidence
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913_3_hsa_tpiA	3423746–3424234	3424576–3424238	5–831	45 [44]	[44] 45	[rrfD]–[rrlD]	[rrfD],[rrlD]

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_hsa_tpiA	= 1299498	0 (0.000)	92 (1.040)	74/272	0.2	100%	intergenic (+253/‑1684)	ychE/oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
	?	NC_000913_3_hsa_tpiA	1300698 =	0 (0.000)					intergenic (+1453/‑484)	ychE/oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein