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 525 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	599,576	0	T	G	51.3%	104.0 / 131.0	77	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	357,880	0	T	C	49.2%	62.5 / 28.0	67	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	646,747	0	T	G	46.0%	100.6 / 19.0	74	T255P (ACC→CCC)	citG	2‑(5''‑triphosphoribosyl)‑3'‑dephosphocoenzyme‑A synthase
*	NC_000913	2,434,882	0	T	G	45.6%	114.8 / 25.7	80	Y252S (TAC→TCC)	truA	tRNA pseudouridine(38‑40) synthase
*	NC_000913	354,288	0	T	G	44.3%	113.9 / 17.6	70	V528G (GTG→GGG)	prpE	propionate‑‑CoA ligase
*	NC_000913	3,640,981	0	C	T	44.2%	94.1 / 50.0	86	F40F (TTC→TTT)	dtpB	dipeptide and tripeptide permease B
*	NC_000913	4,378,802	0	A	C	43.7%	147.6 / 20.4	88	V48G (GTA→GGA)	ampC	penicillin‑binding protein; beta‑lactamase, intrinsically weak
*	NC_000913	2,001,918	0	A	C	43.7%	121.1 / 12.4	71	intergenic (‑129/+192)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin)
*	NC_000913	357,890	0	C	A	43.1%	63.8 / 34.7	65	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	29,496	0	T	A	43.0%	118.2 / 50.9	86	intergenic (+301/‑155)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	718,669	0	C	T	42.6%	85.4 / 32.7	68	E598K (GAA→AAA)	speF	ornithine decarboxylase isozyme, inducible
*	NC_000913	1,376,505	0	A	C	42.6%	115.5 / 19.0	68	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
*	NC_000913	2,903,692	0	C	A	42.5%	122.9 / 55.8	88	intergenic (+318/+1055)	ygcE/queE	putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis
*	NC_000913	2,386,862	0	G	A	41.9%	63.1 / 51.4	63	intergenic (+31/‑72)	yfbL/yfbM	putative M28A family peptidase/DUF1877 family protein
*	NC_000913	3,206,435	0	C	T	41.9%	86.6 / 45.9	74	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	718,659	0	T	A	41.4%	96.0 / 34.4	70	D601V (GAT→GTT)	speF	ornithine decarboxylase isozyme, inducible
*	NC_000913	29,486	0	C	A	41.2%	129.9 / 51.8	80	intergenic (+291/‑165)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	366,526	0	T	G	40.7%	152.0 / 20.8	81	T329P (ACC→CCC)	lacI	lactose‑inducible lac operon transcriptional repressor
*	NC_000913	835,912	0	C	G	40.3%	92.1 / 14.4	67	A222G (GCG→GGG)	ybiB	putative family 3 glycosyltransferase
*	NC_000913	4,573,500	0	A	G	40.3%	102.3 / 23.0	68	pseudogene (1087/1503 nt)	yjiT	pseudogene

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	= 4542690	117 (1.360)	11 (0.140)	10/280	9.8	9.1%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	109 (1.350)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	4542682 =	116 (1.350)	5 (0.060)	5/280	12.7	4.4%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	109 (1.350)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)