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 468 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,678,039	0	T	G	49.1%	71.0 / 10.6	54	N108T (AAC→ACC)	yphE	putative sugar ABC transporter ATPase
*	NC_000913	802,118	0	A	C	45.6%	89.7 / 23.2	68	T78P (ACC→CCC)	ybhI	putative DASS family tricarboxylate or dicarboxylate transporter
*	NC_000913	3,206,435	0	C	T	44.4%	30.7 / 33.6	45	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	4,604,350	0	C	T	43.5%	57.3 / 35.1	62	S64F (TCT→TTT)	bglJ	bgl operon transcriptional activator
*	NC_000913	2,326,450	0	T	G	42.6%	109.8 / 19.3	68	G114G (GGT→GGG)	atoB	acetyl‑CoA acetyltransferase
*	NC_000913	1,157,271	0	T	G	42.4%	92.2 / 15.9	60	G165G (GGT→GGG)	ycfH	putative DNase
*	NC_000913	1,776,263	0	T	G	42.2%	90.3 / 16.4	65	V226G (GTG→GGG)	ydiF	putative acetyl‑CoA:acetoacetyl‑CoA transferase: alpha subunit/beta subunit
*	NC_000913	2,434,882	0	T	G	42.1%	120.3 / 15.7	77	Y252S (TAC→TCC)	truA	tRNA pseudouridine(38‑40) synthase
*	NC_000913	2,151,686	0	G	T	41.5%	48.5 / 25.4	66	intergenic (+40/+25)	yegJ/yegK	uncharacterized protein/ser/thr phosphatase‑related protein
*	NC_000913	436,516	0	C	A	41.5%	66.0 / 27.7	54	Q295K (CAA→AAA)	thiL	thiamine monophosphate kinase
*	NC_000913	354,288	0	T	G	41.2%	123.7 / 34.7	80	V528G (GTG→GGG)	prpE	propionate‑‑CoA ligase
*	NC_000913	3,261,055	0	A	C	41.2%	109.4 / 13.6	68	V455G (GTG→GGG)	tdcE	pyruvate formate‑lyase 4/2‑ketobutyrate formate‑lyase
*	NC_000913	2,678,043	0	C	T	41.1%	59.7 / 25.6	56	E107K (GAA→AAA)	yphE	putative sugar ABC transporter ATPase
*	NC_000913	1,764,785	0	T	A	40.7%	75.1 / 30.9	59	intergenic (‑399/+149)	sufA/ydiH	Fe‑S cluster assembly protein/uncharacterized protein
*	NC_000913	2,185,199	0	T	G	40.5%	106.5 / 26.7	75	T35P (ACC→CCC)	thiM	hydoxyethylthiazole kinase
*	NC_000913	213,341	0	A	G	40.0%	113.2 / 23.2	70	G337G (GGA→GGG)	tilS	tRNA(Ile)‑lysidine synthetase
*	NC_000913	4,604,344	0	C	T	40.0%	69.4 / 29.8	62	S62F (TCT→TTT)	bglJ	bgl operon transcriptional activator
*	NC_000913	29,486	0	C	A	39.7%	100.5 / 43.0	73	intergenic (+291/‑165)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	2,664,896	0	T	G	39.4%	102.5 / 17.1	70	G169G (GGT→GGG)	yfhR	putative S9 family prolyl oligopeptidase
*	NC_000913	786,855	0	A	C	39.3%	155.4 / 15.4	87	G247G (GGT→GGG)	gpmA	phosphoglyceromutase 1

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	= 2817942	92 (1.130)	40 (0.570)	25/258	4.2	50.1%	intergenic (‑82/+117)	argQ/argZ	tRNA‑Arg/tRNA‑Arg
	?	NC_000913	2818492 =	0 (0.000)					noncoding (58/77 nt)	argV	tRNA‑Arg
*	?	NC_000913	= 2818357	0 (0.000)	36 (0.510)	17/258	6.6	100%	intergenic (‑83/+116)	argY/argV	tRNA‑Arg/tRNA‑Arg
	?	NC_000913	2818492 =	0 (0.000)					noncoding (58/77 nt)	argV	tRNA‑Arg
*	?	NC_000913	4542682 =	102 (1.250)	6 (0.080)	5/280	13.5	6.2%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	85 (1.110)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	= 4542690	98 (1.200)	3 (0.040)	3/280	15.1	3.3%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	85 (1.110)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)