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 159 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	66.7%	3.8 / 19.4	24	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	357,880	0	T	C	63.6%	3.2 / 21.4	22	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	718,659	0	T	A	56.7%	14.6 / 40.5	30	D601V (GAT→GTT)	speF	ornithine decarboxylase isozyme, inducible
*	NC_000913	1,560,778	0	T	C	53.1%	17.0 / 39.7	32	E51G (GAA→GGA)	ddpB	D,D‑dipeptide ABC transporter permease
*	NC_000913	4,043,030	0	A	G	52.6%	11.5 / 22.6	19	N206D (AAT→GAT)	srkA	Cpx stress response Thr/Ser protein kinase; MazF antagonist protein
*	NC_000913	718,669	0	C	T	50.0%	20.2 / 15.2	28	E598K (GAA→AAA)	speF	ornithine decarboxylase isozyme, inducible
*	NC_000913	300,745	0	T	G	47.2%	48.4 / 13.3	36	T64P (ACC→CCC)	paoC	PaoABC aldehyde oxidoreductase, Moco‑containing subunit
*	NC_000913	3,206,435	0	C	T	46.0%	42.7 / 33.1	50	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	366,526	0	T	G	45.5%	36.8 / 14.1	33	T329P (ACC→CCC)	lacI	lactose‑inducible lac operon transcriptional repressor
*	NC_000913	4,555,106	0	C	A	45.0%	62.2 / 10.8	40	N177K (AAC→AAA)	uxuR	fructuronate‑inducible hexuronate regulon transcriptional repressor; autorepressor
*	NC_000913	941,713	0	T	G	44.9%	68.0 / 17.3	49	V252G (GTG→GGG)	dmsA	dimethyl sulfoxide reductase, anaerobic, subunit A
*	NC_000913	300,711	0	G	C	44.7%	43.5 / 20.3	38	P75R (CCG→CGG)	paoC	PaoABC aldehyde oxidoreductase, Moco‑containing subunit
*	NC_000913	2,578,143	0	A	C	43.8%	65.6 / 20.7	48	L79V (TTA→GTA)	maeB	malic enzyme: putative oxidoreductase/phosphotransacetylase
*	NC_000913	1,574,051	0	G	T	43.2%	55.9 / 14.5	37	V384V (GTC→GTA)	pqqL	putative periplasmic M16 family zinc metalloendopeptidase
*	NC_000913	3,812,792	0	C	A	42.5%	70.6 / 22.9	47	T21N (ACC→AAC)	dfp	fused 4'‑phosphopantothenoylcysteine decarboxylase/phosphopantothenoylcysteine synthetase, FMN‑binding
*	NC_000913	3,665,702	0	C	A	42.3%	70.1 / 29.4	52	A37S (GCG→TCG)	gadX	acid resistance regulon transcriptional activator; autoactivator
*	NC_000913	1,506,020	0	C	A	41.9%	57.6 / 16.9	43	G21C (GGC→TGC)	ydcO	BenE family inner membrane putative transporter
*	NC_000913	4,573,496	0	A	G	41.9%	53.8 / 22.3	43	pseudogene (1083/1503 nt)	yjiT	pseudogene
*	NC_000913	354,288	0	T	G	41.8%	96.7 / 12.5	55	V528G (GTG→GGG)	prpE	propionate‑‑CoA ligase
*	NC_000913	2,903,692	0	C	A	41.7%	55.5 / 32.2	48	intergenic (+318/+1055)	ygcE/queE	putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis

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	39 (0.820)	8 (0.190)	8/266	5.3	20.8%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	26 (0.610)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	1207790 =	38 (0.800)	4 (0.090)	4/266	7.3	11.6%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	27 (0.640)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related