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	482,230	G→A	P725L (CCG→CTG)	acrB ←	multidrug efflux system protein
RA	1,197,502	C→T	G11R (GGA→AGA)	ymfD ←	e14 prophage; putative SAM‑dependent methyltransferase
MC JC	1,299,499	Δ1,199 bp	intergenic (+254/‑485)	ychE → / → oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
RA	1,544,022	1 bp→AA	coding (39/1389 nt)	narU ←	nitrate/nitrite transporter
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	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	4,111,596	G→A	L179L (CTG→TTG)	yiiQ ←	DUF1454 family putative periplasmic protein
RA	4,296,297	+GC	intergenic (+587/+55)	gltP → / ← yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA	4,604,632	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_pae_tpiA	366233	366393	161	8 [7]	[7] 8	[lacZ]	[lacZ]

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	446776 =	28 (0.970)	7 (0.260)	7/266	2.4	21.2%	intergenic (‑110/+39)	yajR/cyoE	putative transporter/protoheme IX farnesyltransferase
	?	NC_000913_3_pae_tpiA	446800 =	26 (0.970)					intergenic (‑134/+15)	yajR/cyoE	putative transporter/protoheme IX farnesyltransferase
*	?	NC_000913_3_pae_tpiA	1207790 =	4 (0.140)	21 (0.820)	20/254	0.4	86.5%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913_3_pae_tpiA	1209619 =	3 (0.120)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913_3_pae_tpiA	= 1207805	4 (0.140)	23 (0.900)	16/254	0.7	87.5%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913_3_pae_tpiA	= 1209602	3 (0.120)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913_3_pae_tpiA	= 3548549	24 (0.830)	11 (0.460) +23 bp	10/240	1.4	32.3%	coding (1522/2085 nt)	malQ	4‑alpha‑glucanotransferase (amylomaltase)
	?	NC_000913_3_pae_tpiA	3548573 =	31 (1.080)					coding (1498/2085 nt)	malQ	4‑alpha‑glucanotransferase (amylomaltase)