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 346 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	646,747	0	T	G	52.2%	65.4 / 110.9	67	T255P (ACC→CCC)	citG	2‑(5''‑triphosphoribosyl)‑3'‑dephosphocoenzyme‑A synthase
*	NC_000913	1,413,735	0	A	T	51.6%	52.0 / 109.7	62	Y2* (TAT→TAA)	ydaC	DUF1187 family protein, Rac prophage; putative double‑strand break reduction protein
*	NC_000913	3,355,457	0	A	C	49.1%	85.5 / 20.3	60	T245P (ACC→CCC)	gltB	glutamate synthase, large subunit
*	NC_000913	4,378,802	0	A	C	49.0%	72.8 / 14.5	51	V48G (GTA→GGA)	ampC	penicillin‑binding protein; beta‑lactamase, intrinsically weak
*	NC_000913	357,890	0	C	A	47.8%	37.9 / 30.7	46	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	2,228,275	0	T	C	44.8%	54.1 / 13.3	58	pseudogene (335/1287 nt)	mdtQ	pseudogene; putative channel/filament proteins
*	NC_000913	213,341	0	A	G	44.6%	80.1 / 14.2	57	G337G (GGA→GGG)	tilS	tRNA(Ile)‑lysidine synthetase
*	NC_000913	357,880	0	T	C	44.0%	61.1 / 13.9	50	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	3,443,277	0	A	C	44.0%	72.3 / 18.6	50	V274G (GTA→GGA)	secY	preprotein translocase membrane subunit
*	NC_000913	2,326,450	0	T	G	43.4%	90.3 / 15.9	53	G114G (GGT→GGG)	atoB	acetyl‑CoA acetyltransferase
*	NC_000913	3,864,099	0	C	A	43.4%	73.9 / 22.1	53	R67R (CGC→CGA)	yidP	UTRA domain‑containing GntR family putative transcriptional regulator
*	NC_000913	3,423,290	0	A	C	43.3%	76.1 / 23.3	60	intergenic (+96/+133)	yhdZ/rrfF	putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon
*	NC_000913	1,413,751	0	A	C	43.1%	84.3 / 25.4	58	N59K (AAT→AAG)	ralR	Rac prophage; restriction alleviation protein
*	NC_000913	2,903,692	0	C	A	43.1%	79.6 / 42.2	58	intergenic (+318/+1055)	ygcE/queE	putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis
*	NC_000913	3,423,287	0	G	C	43.1%	72.3 / 30.6	59	intergenic (+93/+136)	yhdZ/rrfF	putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon
*	NC_000913	1,859,685	0	A	C	42.9%	78.8 / 17.9	57	V182G (GTA→GGA)	ydjK	putative MFS sugar transporter, membrane protein
*	NC_000913	646,765	0	G	T	42.4%	77.3 / 37.4	60	Q249K (CAA→AAA)	citG	2‑(5''‑triphosphoribosyl)‑3'‑dephosphocoenzyme‑A synthase
*	NC_000913	307,821	0	G	T	42.1%	108.5 / 22.8	57	Y504* (TAC→TAA)	ecpC	ECP production outer membrane protein
*	NC_000913	2,001,911	0	G	A	41.8%	62.0 / 27.2	55	intergenic (‑122/+199)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin)
*	NC_000913	1,478,324	0	T	G	41.5%	121.1 / 19.4	65	G33G (GGT→GGG)	ynbB	putative CDP‑diglyceride synthase

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	1207790 =	59 (0.960)	11 (0.200)	11/266	6.4	18.5%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	44 (0.800)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1207805	61 (0.990)	7 (0.130)	7/266	8.3	12.6%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	43 (0.780)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related