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 388 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,903,692	0	C	A	50.0%	67.3 / 44.3	64	intergenic (+318/+1055)	ygcE/queE	putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis
*	NC_000913	4,287,719	0	T	A	48.0%	74.4 / 58.5	77	intergenic (‑348/‑45)	acs/nrfA	acetyl‑CoA synthetase/nitrite reductase, formate‑dependent, cytochrome
*	NC_000913	2,386,862	0	G	A	47.1%	32.8 / 52.4	51	intergenic (+31/‑72)	yfbL/yfbM	putative M28A family peptidase/DUF1877 family protein
*	NC_000913	1,506,038	0	A	C	45.8%	89.9 / 10.2	59	F15V (TTT→GTT)	ydcO	BenE family inner membrane putative transporter
*	NC_000913	3,578,301	0	A	C	45.5%	96.4 / 10.4	57	G142G (GGT→GGG)	gntR	d‑gluconate inducible gluconate regulon transcriptional repressor
*	NC_000913	3,133,302	0	T	G	45.3%	94.2 / 10.4	65	H219P (CAC→CCC)	yghS	putative ATP‑binding protein
*	NC_000913	3,206,435	0	C	T	44.9%	66.9 / 47.2	69	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	1,376,505	0	A	C	44.8%	98.0 / 12.7	58	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
*	NC_000913	4,538,109	0	A	C	44.4%	96.2 / 18.5	63	G219G (GGT→GGG)	nanM	N‑acetylneuraminic acid mutarotase
*	NC_000913	910,914	0	A	G	43.9%	77.8 / 11.1	57	S46P (TCC→CCC)	poxB	pyruvate dehydrogenase, thiamine triphosphate‑binding, FAD‑binding
*	NC_000913	2,903,715	0	G	A	43.5%	64.0 / 50.1	62	intergenic (+341/+1032)	ygcE/queE	putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis
*	NC_000913	2,903,686	0	G	T	42.6%	98.4 / 31.5	70	intergenic (+312/+1061)	ygcE/queE	putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis
*	NC_000913	1,097,581	0	A	G	42.6%	101.9 / 20.1	63	noncoding (72/88 nt)	serX	tRNA‑Ser
*	NC_000913	2,343,821	0	C	A	42.4%	87.6 / 32.5	59	A117S (GCT→TCT)	yfaL	adhesin
*	NC_000913	213,341	0	A	G	41.7%	99.1 / 17.3	60	G337G (GGA→GGG)	tilS	tRNA(Ile)‑lysidine synthetase
*	NC_000913	3,862,661	0	T	G	41.5%	29.2 / 20.7	55	pseudogene (943/1617 nt)	glvC	pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component
*	NC_000913	599,576	0	T	G	41.0%	99.5 / 23.9	61	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	3,578,287	0	T	C	41.0%	105.8 / 11.7	61	E147G (GAA→GGA)	gntR	d‑gluconate inducible gluconate regulon transcriptional repressor
*	NC_000913	73,413	0	A	C	40.4%	105.4 / 13.2	58	V370G (GTG→GGG)	thiP	thiamine/thiamine pyrophosphate ABC transporter permease
*	NC_000913	941,713	0	T	G	40.4%	84.5 / 22.9	57	V252G (GTG→GGG)	dmsA	dimethyl sulfoxide reductase, anaerobic, subunit A

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	925901 =	45 (0.630)	10 (0.140) +C	9/296	10.1	20.5%	noncoding (71/88 nt)	serW	tRNA‑Ser
	?	NC_000913	= 1097399	33 (0.460)					intergenic (+570/+166)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
*	?	NC_000913	= 4542690	80 (1.120)	6 (0.090)	6/280	11.4	7.3%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	77 (1.140)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	4542682 =	83 (1.160)	6 (0.090)	6/280	11.4	7.2%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	77 (1.140)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	1207790 =	64 (0.890)	4 (0.060)	4/266	12.3	6.6%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	56 (0.880)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related