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 865 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,206,435	0	C	T	58.0%	‑1.1 / 97.8	81	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	599,576	0	T	G	52.8%	85.7 / 152.5	89	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	599,579	0	T	G	50.6%	146.4 / 159.4	89	V289G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	29,496	0	T	A	49.4%	87.6 / 65.9	89	intergenic (+301/‑155)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	1,755,862	0	C	A	49.2%	82.5 / 43.9	63	S55R (AGC→AGA)	pykF	pyruvate kinase I
*	NC_000913	354,288	0	T	G	47.5%	108.6 / 27.6	80	V528G (GTG→GGG)	prpE	propionate‑‑CoA ligase
*	NC_000913	1,222,233	0	G	A	47.2%	50.7 / 29.4	53	pseudogene (60/75 nt)	ycgH	pseudogene; putative ATP‑binding component of a transport system
*	NC_000913	1,755,871	0	T	A	46.3%	64.9 / 54.6	67	G58G (GGT→GGA)	pykF	pyruvate kinase I
*	NC_000913	354,282	0	T	G	44.9%	114.6 / 15.8	78	V526G (GTT→GGT)	prpE	propionate‑‑CoA ligase
*	NC_000913	29,486	0	C	A	44.7%	137.1 / 47.3	85	intergenic (+291/‑165)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	941,713	0	T	G	44.1%	92.6 / 29.5	68	V252G (GTG→GGG)	dmsA	dimethyl sulfoxide reductase, anaerobic, subunit A
*	NC_000913	2,547,772	0	T	G	43.8%	142.0 / 19.2	89	V367G (GTA→GGA)	murP	N‑acetylmuramic acid permease, EIIBC component, PTS system
*	NC_000913	2,921,177	0	A	C	43.4%	125.2 / 13.8	77	G308G (GGT→GGG)	gudP	putative D‑glucarate transporter
*	NC_000913	2,984,441	0	A	C	43.4%	127.0 / 41.3	83	G384G (GGT→GGG)	yqeF	short chain acyltransferase
*	NC_000913	3,350,844	0	A	C	43.3%	178.4 / 18.7	97	L728V (TTA→GTA)	arcB	aerobic respiration control sensor histidine protein kinase, cognate to two‑component response regulators ArcA and RssB
*	NC_000913	3,206,452	0	C	A	42.9%	105.2 / 49.8	84	intergenic (‑196/‑11)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	826,942	0	A	C	42.4%	85.9 / 13.6	59	V104G (GTG→GGG)	ybhS	putative ABC transporter permease
*	NC_000913	357,890	0	C	A	41.9%	51.1 / 21.0	43	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	3,206,446	0	C	A	41.5%	84.8 / 34.9	83	intergenic (‑190/‑17)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	1,133,857	0	A	G	41.3%	106.2 / 22.2	75	Q19R (CAG→CGG)	flgF	flagellar component of cell‑proximal portion of basal‑body rod

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	1207790 =	68 (0.730)	14 (0.170)	14/266	10.1	16.2%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	84 (1.010)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1207805	67 (0.720)	10 (0.120)	10/266	12.2	12.2%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	84 (1.010)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related