breseq  version 0.29.0  revision 8f9c342918e4 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence	position	mutation	annotation	gene	description
RA	2,374	G→T	A680S (GCG→TCG)	thrA →	Bifunctional aspartokinase/homoserine dehydrogenase 1
MC JC	257,908	Δ776 bp		[crl]	[crl]
RA	1,903,497	T→C	I139T (ATC→ACC)	manY →	mannose‑specific enzyme IIC component of PTS
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
MC JC	2,801,966	Δ11,843 bp		[nrdE]–[emrB]	[nrdE], nrdF, proV, proW, proX, ygaY, ygaY, ygaZ, ygaH, mprA, emrA, [emrB]
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	3,683,736	Δ1 bp	coding (1883/1989 nt)	yhjK ←	cyclic‑di‑GMP phosphodiesterase
RA	3,815,810	Δ1 bp	intergenic (‑42/+24)	pyrE ← / ← rph	orotate phosphoribosyltransferase/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	3423744–3424234	3424572–3424238	5–829	16 [14]	[14] 16	[rrfD]–[rrlD]	[rrfD], [rrlD]

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	1207790 =	6 (0.160)	29 (0.880)	25/266	0.6	84.9%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	5 (0.150)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1207805	6 (0.160)	23 (0.700)	22/266	0.8	81.6%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	5 (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)	53 (1.470)	48/290	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	= 3966715	8 (0.220)	25 (0.690) +GAT	25/286	0.7	75.9%	coding (299/1260 nt)	rho	transcription termination factor
	?	NC_000913	3966716 =	8 (0.220)					coding (300/1260 nt)	rho	transcription termination factor
*	?	NC_000913	4542682 =	45 (1.220)	11 (0.320)	11/280	3.0	20.9%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	41 (1.180)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)