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 678 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,984,441	0	A	C	57.6%	46.5 / 87.5	60	G384G (GGT→GGG)	yqeF	short chain acyltransferase
*	NC_000913	3,511,923	0	A	C	46.6%	108.0 / 15.2	73	V141G (GTT→GGT)	yhfZ	putative DNA‑binding transcriptional regulator
*	NC_000913	599,576	0	T	G	46.0%	129.3 / 39.0	87	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	646,747	0	T	G	45.8%	113.8 / 15.8	72	T255P (ACC→CCC)	citG	2‑(5''‑triphosphoribosyl)‑3'‑dephosphocoenzyme‑A synthase
*	NC_000913	1,604,237	0	C	T	45.3%	85.3 / 33.5	75	S64L (TCG→TTG)	lsrD	autoinducer 2 import system permease protein
*	NC_000913	4,622,250	0	A	G	44.4%	87.8 / 25.9	72	E161G (GAG→GGG)	yjjJ	putative protein kinase
*	NC_000913	1,222,596	0	G	A	43.5%	69.5 / 47.3	69	F13F (TTC→TTT)	ymgD	uncharacterized protein
*	NC_000913	941,713	0	T	G	43.2%	124.4 / 35.5	82	V252G (GTG→GGG)	dmsA	dimethyl sulfoxide reductase, anaerobic, subunit A
*	NC_000913	599,579	0	T	G	43.0%	148.2 / 20.4	87	V289G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	925,900	0	A	G	42.5%	122.1 / 24.2	74	noncoding (72/88 nt)	serW	tRNA‑Ser
*	NC_000913	501,575	0	A	C	42.2%	129.7 / 13.9	73	V555G (GTG→GGG)	ybaL	inner membrane putative NAD(P)‑binding transporter
*	NC_000913	345,328	0	C	A	41.9%	137.5 / 58.9	86	intergenic (+337/‑76)	yahL/yahM	uncharacterized protein/uncharacterized protein
*	NC_000913	4,457,105	0	A	G	41.9%	124.9 / 31.2	86	I441V (ATC→GTC)	mpl	UDP‑N‑acetylmuramate:L‑alanyl‑gamma‑D‑glutamyl‑ meso‑diaminopimelate ligase
*	NC_000913	1,842,914	0	A	G	41.4%	68.9 / 16.2	59	M182V (ATG→GTG)	gdhA	glutamate dehydrogenase, NADP‑specific
*	NC_000913	3,717,014	0	T	G	40.6%	197.9 / 25.5	102	G156G (GGT→GGG)	yiaD	multicopy suppressor of bamB; outer membrane lipoprotein
*	NC_000913	213,341	0	A	G	40.2%	127.4 / 23.1	82	G337G (GGA→GGG)	tilS	tRNA(Ile)‑lysidine synthetase
*	NC_000913	354,288	0	T	G	40.0%	138.1 / 27.3	80	V528G (GTG→GGG)	prpE	propionate‑‑CoA ligase
*	NC_000913	2,603,342	0	A	C	40.0%	88.3 / 56.1	65	T509P (ACC→CCC)	hyfB	hydrogenase 4, membrane subunit
*	NC_000913	2,613,099	0	C	A	40.0%	95.8 / 31.3	50	V400V (GTC→GTA)	hyfR	hydrogenase‑4 transcriptional activator
*	NC_000913	646,765	0	G	T	39.7%	152.5 / 35.6	78	Q249K (CAA→AAA)	citG	2‑(5''‑triphosphoribosyl)‑3'‑dephosphocoenzyme‑A synthase

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	4542682 =	109 (1.240)	3 (0.040)	3/280	13.3	2.8%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	106 (1.280)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)