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 564 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	56.7%	1.2 / 35.4	30	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	599,576	0	T	G	50.0%	64.2 / 38.2	66	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	3,508,662	0	T	A	45.0%	80.5 / 28.0	62	E384D (GAA→GAT)	yhfW	phosphopentomutase‑related metalloenzyme superfamily protein
*	NC_000913	3,177,531	0	A	C	44.9%	133.3 / 18.9	91	V127G (GTG→GGG)	nudF	ADP‑ribose pyrophosphatase
*	NC_000913	2,678,039	0	T	G	44.1%	85.5 / 15.0	62	N108T (AAC→ACC)	yphE	putative sugar ABC transporter ATPase
*	NC_000913	3,508,657	0	A	G	43.5%	88.5 / 14.9	62	F386S (TTC→TCC)	yhfW	phosphopentomutase‑related metalloenzyme superfamily protein
*	NC_000913	17,050	0	A	C	43.1%	106.0 / 13.9	73	intergenic (‑90/‑439)	mokC/nhaA	regulatory protein for HokC, overlaps CDS of hokC/sodium‑proton antiporter
*	NC_000913	3,026,941	0	A	C	40.5%	126.0 / 16.2	79	E392D (GAA→GAC)	guaD	guanine deaminase
*	NC_000913	3,812,792	0	C	A	40.3%	128.8 / 32.1	72	T21N (ACC→AAC)	dfp	fused 4'‑phosphopantothenoylcysteine decarboxylase/phosphopantothenoylcysteine synthetase, FMN‑binding
*	NC_000913	4,378,802	0	A	C	40.0%	89.8 / 21.1	55	V48G (GTA→GGA)	ampC	penicillin‑binding protein; beta‑lactamase, intrinsically weak
*	NC_000913	1,080,837	0	G	T	39.4%	105.6 / 32.6	71	intergenic (+24/‑519)	putP/efeU	proline:sodium symporter/ferrous iron permease (pseudogene)
*	NC_000913	599,579	0	T	G	39.4%	106.3 / 11.5	66	V289G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	1,435,727	0	G	A	39.2%	109.8 / 55.4	79	intergenic (‑108/+33)	uspF/ompN	stress‑induced protein, ATP‑binding protein/outer membrane pore protein N, non‑specific
*	NC_000913	3,556,207	0	T	C	39.2%	111.6 / 22.8	74	S215G (AGT→GGT)	rtcA	RNA 3'‑terminal phosphate cyclase
*	NC_000913	4,457,105	0	A	G	39.2%	105.3 / 27.4	74	I441V (ATC→GTC)	mpl	UDP‑N‑acetylmuramate:L‑alanyl‑gamma‑D‑glutamyl‑ meso‑diaminopimelate ligase
*	NC_000913	2,168,966	0	A	C	38.2%	104.4 / 17.8	69	I85I (ATA→ATC)	yegS	phosphatidylglycerol kinase, metal‑dependent
*	NC_000913	3,350,844	0	A	C	38.2%	121.4 / 18.0	68	L728V (TTA→GTA)	arcB	aerobic respiration control sensor histidine protein kinase, cognate to two‑component response regulators ArcA and RssB
*	NC_000913	2,326,450	0	T	G	38.2%	102.9 / 13.4	56	G114G (GGT→GGG)	atoB	acetyl‑CoA acetyltransferase
*	NC_000913	4,604,344	0	C	T	38.2%	73.3 / 23.9	55	S62F (TCT→TTT)	bglJ	bgl operon transcriptional activator
*	NC_000913	4,604,350	0	C	T	38.2%	70.6 / 26.0	55	S64F (TCT→TTT)	bglJ	bgl operon transcriptional activator

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	71 (0.880)	14 (0.200)	14/266	8.0	19.1%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	55 (0.770)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	1207790 =	74 (0.920)	8 (0.110)	8/266	11.0	11.4%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	58 (0.810)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related