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]
JC	1,673,557	Δ120 bp	intergenic (‑56/‑237)	mdtJ ← / → tqsA	multidrug efflux system transporter/pheromone AI‑2 transporter
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
RA	3,815,883	+C	pseudogene (667/669 nt)	rph ←	ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH
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	1673516	1676631	3116	353 [348]	[347] 352	tqsA–[pntA]	tqsA, pntB, [pntA]
*	*	÷	NC_000913	3423664–3424234	3424615–3424238	5–952	352 [348]	[349] 355	rrfD–[rrlD]	rrfD, [rrlD]

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	1207790 =	67 (0.130)	376 (0.830)	192/268	0.2	85.5%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	68 (0.150)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1207805	70 (0.140)	407 (0.900)	210/268	0.0	86.2%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	68 (0.150)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1299498	0 (0.000)	566 (1.140)	242/292	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
*	?	NC_000913	3583428 =	NA (NA)	309 (0.610)	176/298	2.5	48.5%	noncoding (1/768 nt)	IS1	repeat region
	?	NC_000913	= 4542049	328 (0.650)					coding (13/597 nt)	fimE	tyrosine recombinase/inversion of on/off regulator of fimA
*	?	NC_000913	= 3815858	244 (0.480)	256 (0.540)	170/280	2.0	53.7%	pseudogene (24/48 nt)	rph	ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH
	?	NC_000913	3815941 =	214 (0.450)					pseudogene (609/669 nt)	rph	ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH
*	?	NC_000913	4542682 =	295 (0.580)	264 (0.550)	162/282	3.0	47.3%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	311 (0.650)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	= 4542690	295 (0.580)	286 (0.600)	165/282	2.6	49.3%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	311 (0.650)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)