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 633 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,604,344	0	C	T	46.9%	48.5 / 45.7	65	S62F (TCT→TTT)	bglJ	bgl operon transcriptional activator
*	NC_000913	3,155,639	0	T	G	44.6%	100.1 / 22.7	66	G95G (GGT→GGG)	yqhD	aldehyde reductase, NADPH‑dependent
*	NC_000913	4,604,350	0	C	T	44.4%	64.5 / 34.5	65	S64F (TCT→TTT)	bglJ	bgl operon transcriptional activator
*	NC_000913	357,890	0	C	A	43.6%	35.1 / 20.6	39	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	599,576	0	T	G	43.2%	95.6 / 39.0	81	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	3,350,853	0	A	C	42.7%	111.5 / 19.2	75	S725A (TCA→GCA)	arcB	aerobic respiration control sensor histidine protein kinase, cognate to two‑component response regulators ArcA and RssB
*	NC_000913	599,579	0	T	G	42.5%	131.2 / 13.6	81	V289G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	3,206,435	0	C	T	42.3%	79.3 / 59.1	78	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	1,376,505	0	A	C	42.0%	120.1 / 19.8	69	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
*	NC_000913	4,042,993	0	C	T	42.0%	62.3 / 19.5	51	F193F (TTC→TTT)	srkA	Cpx stress response Thr/Ser protein kinase; MazF antagonist protein
*	NC_000913	3,751,537	0	A	C	42.0%	137.7 / 13.1	81	V111G (GTT→GGT)	yiaT	putative outer membrane protein
*	NC_000913	2,678,039	0	T	G	41.7%	98.4 / 15.2	60	N108T (AAC→ACC)	yphE	putative sugar ABC transporter ATPase
*	NC_000913	3,578,301	0	A	C	41.3%	111.7 / 12.0	63	G142G (GGT→GGG)	gntR	d‑gluconate inducible gluconate regulon transcriptional repressor
*	NC_000913	1,356,201	0	T	G	40.9%	108.4 / 19.1	66	T304P (ACC→CCC)	sapA	antimicrobial peptide transport ABC transporter periplasmic binding protein
*	NC_000913	3,508,657	0	A	G	40.6%	111.0 / 16.4	69	F386S (TTC→TCC)	yhfW	phosphopentomutase‑related metalloenzyme superfamily protein
*	NC_000913	3,350,844	0	A	C	40.0%	123.6 / 19.4	75	L728V (TTA→GTA)	arcB	aerobic respiration control sensor histidine protein kinase, cognate to two‑component response regulators ArcA and RssB
*	NC_000913	1,676,805	0	T	G	39.8%	108.2 / 21.5	83	T367P (ACC→CCC)	pntA	pyridine nucleotide transhydrogenase, alpha subunit
*	NC_000913	2,851,654	0	T	G	39.8%	133.2 / 29.7	84	G218G (GGT→GGG)	hypB	GTP hydrolase involved in nickel liganding into hydrogenases
*	NC_000913	3,508,662	0	T	A	39.7%	118.0 / 33.3	73	E384D (GAA→GAT)	yhfW	phosphopentomutase‑related metalloenzyme superfamily protein
*	NC_000913	2,921,173	0	T	C	39.7%	100.6 / 16.6	63	I310V (ATT→GTT)	gudP	putative D‑glucarate transporter

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	93 (1.050)	9 (0.110)	9/266	11.2	11.3%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	58 (0.740)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	1207790 =	91 (1.030)	6 (0.080)	6/266	13.1	7.9%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	59 (0.750)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	4542682 =	125 (1.420)	6 (0.070)	6/280	13.7	5.1%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	108 (1.300)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	= 4542690	124 (1.400)	5 (0.060)	5/280	14.4	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	106 (1.280)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)