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 696 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	501,575	0	A	C	55.4%	62.2 / 88.9	56	V555G (GTG→GGG)	ybaL	inner membrane putative NAD(P)‑binding transporter
*	NC_000913	357,880	0	T	C	54.1%	47.4 / 91.5	61	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	501,564	0	A	C	53.6%	66.0 / 92.7	56	*559E (TAA→GAA)	ybaL	inner membrane putative NAD(P)‑binding transporter
*	NC_000913	2,326,450	0	T	G	53.5%	88.5 / 126.2	72	G114G (GGT→GGG)	atoB	acetyl‑CoA acetyltransferase
*	NC_000913	357,890	0	C	A	51.7%	38.8 / 104.1	60	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	3,206,435	0	C	T	51.1%	51.8 / 142.4	88	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	1,376,505	0	A	C	48.3%	83.6 / 16.5	58	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
*	NC_000913	40,515	0	G	T	47.5%	132.3 / 71.5	121	Q473K (CAA→AAA)	caiT	putative transporter
*	NC_000913	1,271,827	0	A	T	47.3%	63.2 / 61.7	74	V8E (GTA→GAA)	chaA	calcium/sodium:proton antiporter
*	NC_000913	599,576	0	T	G	46.7%	124.9 / 27.0	75	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	3,443,277	0	A	C	46.6%	149.1 / 27.3	88	V274G (GTA→GGA)	secY	preprotein translocase membrane subunit
*	NC_000913	354,288	0	T	G	45.8%	121.4 / 29.8	83	V528G (GTG→GGG)	prpE	propionate‑‑CoA ligase
*	NC_000913	646,747	0	T	G	45.3%	100.8 / 20.4	64	T255P (ACC→CCC)	citG	2‑(5''‑triphosphoribosyl)‑3'‑dephosphocoenzyme‑A synthase
*	NC_000913	1,764,785	0	T	A	45.2%	70.8 / 41.2	62	intergenic (‑399/+149)	sufA/ydiH	Fe‑S cluster assembly protein/uncharacterized protein
*	NC_000913	4,604,344	0	C	T	44.9%	82.6 / 41.6	78	S62F (TCT→TTT)	bglJ	bgl operon transcriptional activator
*	NC_000913	3,177,748	0	C	A	44.3%	137.7 / 58.0	97	E55* (GAG→TAG)	nudF	ADP‑ribose pyrophosphatase
*	NC_000913	573,403	0	T	C	44.2%	52.2 / 14.9	43	P11P (CCT→CCC)	rusA	DLP12 prophage; endonuclease RUS
*	NC_000913	1,245,234	0	G	T	44.1%	104.1 / 35.2	68	L25F (TTG→TTT)	ycgY	uncharacterized protein
*	NC_000913	1,621,118	0	A	C	43.6%	76.7 / 10.1	55	V7G (GTG→GGG)	eamA	cysteine and O‑acetyl‑L‑serine efflux system
*	NC_000913	1,576,069	0	T	C	43.3%	80.5 / 32.8	68	G517G (GGA→GGG)	yddB	putative TonB‑dependent outer membrane receptor

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	2482743 =	77 (0.970)	23 (0.290)	22/298	3.8	25.1%	coding (597/1164 nt)	emrK	multidrug resistance efflux pump membrane fusion protein
	?	NC_000913	= 3628995	60 (0.760)					coding (544/2736 nt)	rbbA	ribosome‑associated ATPase: ATP‑binding protein/ATP‑binding membrane protein
*	?	NC_000913	= 4542690	111 (1.400)	5 (0.070)	5/280	8.6	4.3%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	116 (1.560)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	4542682 =	110 (1.390)	5 (0.070)	5/280	8.6	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 =	116 (1.560)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)