BRESEQ :: Mutation Predictions

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	4,110,747	G→T	intergenic (+62/+784)	cdh → / ← yiiQ	CDP‑diacylglycerol phosphotidylhydrolase/DUF1454 family putative periplasmic protein
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	366271	366409	139	9 [7]	[7] 11	[lacZ]	[lacZ]
*	*	÷	NC_000913_3_pae_tpiA	3423751–3424234	3424543–3424238	5–793	8 [7]	[7] 8	[rrfD]–[rrlD]	[rrfD],[rrlD]

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	1207790 =	24 (0.820)	8 (0.310)	8/250	2.0	25.3%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
*	?	NC_000913_3_pae_tpiA	1209619 =	26 (1.000)	8 (0.310)	8/250	2.0	25.3%	pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913_3_pae_tpiA	2304923 =	16 (0.550)	6 (0.220)	6/268	2.8	27.8%	noncoding (507/655 nt)	REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences	REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences
*	?	NC_000913_3_pae_tpiA	2304955 =	16 (0.580)	6 (0.220)	6/268	2.8	27.8%	noncoding (539/655 nt)	REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences	REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences
*	?	NC_000913_3_pae_tpiA	4542598 =	27 (0.920)	8 (0.290)	8/264	2.2	24.9%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913_3_pae_tpiA	4542912 =	23 (0.840)	8 (0.290)	8/264	2.2	24.9%	intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)