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 297 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	48.6%	31.2 / 19.4	37	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	1,478,324	0	T	G	46.3%	76.1 / 23.8	55	G33G (GGT→GGG)	ynbB	putative CDP‑diglyceride synthase
*	NC_000913	4,112,578	0	T	G	45.6%	65.2 / 15.0	47	G88G (GGT→GGG)	yiiR	DUF805 family putative inner membrane protein
*	NC_000913	3,261,055	0	A	C	44.4%	98.1 / 12.1	63	V455G (GTG→GGG)	tdcE	pyruvate formate‑lyase 4/2‑ketobutyrate formate‑lyase
*	NC_000913	29,486	0	C	A	44.3%	75.7 / 38.2	61	intergenic (+291/‑165)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	29,496	0	T	A	44.3%	63.5 / 33.9	61	intergenic (+301/‑155)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	646,747	0	T	G	44.3%	100.7 / 13.1	61	T255P (ACC→CCC)	citG	2‑(5''‑triphosphoribosyl)‑3'‑dephosphocoenzyme‑A synthase
*	NC_000913	599,576	0	T	G	43.8%	110.0 / 18.9	64	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	4,327,934	0	A	G	43.4%	63.6 / 23.6	53	D267G (GAT→GGT)	crfC	clamp‑binding sister replication fork colocalization protein, dynamin‑related
*	NC_000913	3,001,164	0	A	C	42.9%	67.8 / 16.9	42	T274P (ACC→CCC)	xdhA	xanthine dehydrogenase, molybdenum binding subunit
*	NC_000913	4,258,974	0	T	G	42.0%	84.4 / 12.3	50	G411G (GGT→GGG)	dinF	oxidative stress resistance protein; putative MATE family efflux pump; UV and mitomycin C inducible protein
*	NC_000913	802,118	0	A	C	41.9%	100.2 / 11.8	62	T78P (ACC→CCC)	ybhI	putative DASS family tricarboxylate or dicarboxylate transporter
*	NC_000913	29,468	0	T	A	41.8%	83.4 / 26.7	56	intergenic (+273/‑183)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	1,222,596	0	G	A	41.8%	75.8 / 39.0	67	F13F (TTC→TTT)	ymgD	uncharacterized protein
*	NC_000913	1,622,816	0	G	A	41.0%	31.8 / 35.3	40	intergenic (+75/+144)	yneM/dgcZ	inner membrane‑associated protein/diguanylate cyclase, zinc‑sensing
*	NC_000913	3,270,455	0	G	T	40.8%	69.1 / 19.3	49	intergenic (+853/+170)	yhaC/garK	pentapetide repeats‑related protein/glycerate kinase I
*	NC_000913	646,777	0	G	T	40.7%	82.5 / 24.4	54	Q245K (CAA→AAA)	citG	2‑(5''‑triphosphoribosyl)‑3'‑dephosphocoenzyme‑A synthase
*	NC_000913	1,312,213	0	G	A	40.7%	74.9 / 33.4	59	L12F (CTT→TTT)	yciA	acyl‑CoA esterase
*	NC_000913	3,508,662	0	T	A	40.6%	98.8 / 22.5	64	E384D (GAA→GAT)	yhfW	phosphopentomutase‑related metalloenzyme superfamily protein
*	NC_000913	17,000	0	C	T	40.0%	60.1 / 17.0	45	intergenic (‑40/‑489)	mokC/nhaA	regulatory protein for HokC, overlaps CDS of hokC/sodium‑proton antiporter

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	= 1207805	64 (1.010)	14 (0.250)	14/266	5.5	21.2%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	47 (0.830)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	1207790 =	55 (0.870)	13 (0.230)	13/266	5.9	20.9%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	49 (0.870)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 4542690	76 (1.200)	5 (0.080)	5/280	10.3	7.1%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	59 (0.990)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	4542682 =	80 (1.260)	4 (0.070)	4/280	11.0	5.6%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	60 (1.010)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)