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

Marginal read alignment evidence (highest frequency 20 of 299 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	51.1%	31.8 / 77.7	47	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	3,206,435	0	C	T	50.9%	34.1 / 89.4	55	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	4,381,728	0	A	C	46.7%	87.7 / 14.8	60	G197G (GGT→GGG)	frdA	anaerobic fumarate reductase catalytic and NAD/flavoprotein subunit
*	NC_000913	2,434,882	0	T	G	45.3%	80.6 / 10.7	53	Y252S (TAC→TCC)	truA	tRNA pseudouridine(38‑40) synthase
*	NC_000913	29,496	0	T	A	44.8%	71.7 / 32.8	58	intergenic (+301/‑155)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	1,014,009	0	G	T	44.4%	65.9 / 25.7	54	D251Y (GAT→TAT)	pqiB	paraquat‑inducible, SoxRS‑regulated MCE domain protein
*	NC_000913	1,621,118	0	A	C	44.4%	77.0 / 12.6	54	V7G (GTG→GGG)	eamA	cysteine and O‑acetyl‑L‑serine efflux system
*	NC_000913	75,079	0	C	T	43.8%	74.0 / 33.9	64	L134L (CTG→CTA)	thiB	thiamine/thiamine pyrophosphate/thiamine monophosphate ABC transporter periplasmic binding protein
*	NC_000913	3,465,167	0	G	T	43.6%	72.7 / 28.9	55	C29F (TGT→TTT)	gspM	general secretory pathway component, cryptic
*	NC_000913	298,960	0	A	C	43.5%	102.4 / 14.4	62	Y659D (TAT→GAT)	paoC	PaoABC aldehyde oxidoreductase, Moco‑containing subunit
*	NC_000913	436,516	0	C	A	43.5%	55.5 / 21.5	46	Q295K (CAA→AAA)	thiL	thiamine monophosphate kinase
*	NC_000913	3,850,007	0	G	A	43.1%	59.7 / 23.1	51	P44S (CCG→TCG)	uhpB	sensory histidine kinase in two‑component regulatory sytem with UhpA
*	NC_000913	1,014,023	0	T	G	43.1%	85.5 / 14.3	58	G255G (GGT→GGG)	pqiB	paraquat‑inducible, SoxRS‑regulated MCE domain protein
*	NC_000913	2,984,441	0	A	C	43.1%	103.5 / 13.9	58	G384G (GGT→GGG)	yqeF	short chain acyltransferase
*	NC_000913	1,222,596	0	G	A	42.6%	64.1 / 37.9	61	F13F (TTC→TTT)	ymgD	uncharacterized protein
*	NC_000913	3,443,277	0	A	C	42.2%	112.7 / 13.2	64	V274G (GTA→GGA)	secY	preprotein translocase membrane subunit
*	NC_000913	3,508,662	0	T	A	41.7%	98.3 / 21.8	61	E384D (GAA→GAT)	yhfW	phosphopentomutase‑related metalloenzyme superfamily protein
*	NC_000913	4,238,049	0	A	G	40.9%	110.2 / 13.1	67	E139G (GAA→GGA)	yjbH	DUF940 family extracellular polysaccharide protein
*	NC_000913	436,497	0	A	C	40.8%	74.9 / 11.5	53	V288V (GTA→GTC)	thiL	thiamine monophosphate kinase
*	NC_000913	366,526	0	T	G	40.7%	100.9 / 12.3	59	T329P (ACC→CCC)	lacI	lactose‑inducible lac operon transcriptional repressor

Marginal new junction evidence (sorted from low to high skew)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 1207805	48 (0.730)	11 (0.190)	11/266	6.9	21.8%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	36 (0.610)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	925901 =	69 (1.040)	9 (0.140) +C	8/296	9.3	14.8%	noncoding (71/88 nt)	serW	tRNA‑Ser
	?	NC_000913	= 1097399	35 (0.530)					intergenic (+570/+166)	ycdU/serX	putative inner membrane protein/tRNA‑Ser