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 59 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,622,816	0	G	A	52.2%	6.3 / 32.1	23	intergenic (+75/+144)	yneM/dgcZ	inner membrane‑associated protein/diguanylate cyclase, zinc‑sensing
*	NC_000913	1,622,815	0	C	A	50.0%	10.8 / 15.2	22	intergenic (+74/+145)	yneM/dgcZ	inner membrane‑associated protein/diguanylate cyclase, zinc‑sensing
*	NC_000913	1,413,735	0	A	T	47.2%	32.4 / 22.2	36	Y2* (TAT→TAA)	ydaC	DUF1187 family protein, Rac prophage; putative double‑strand break reduction protein
*	NC_000913	2,248,431	0	A	C	47.2%	40.3 / 11.6	37	G34G (GGT→GGG)	lysP	lysine transporter
*	NC_000913	3,745,509	0	A	T	45.8%	43.7 / 26.7	48	T236S (ACC→TCC)	yiaN	2,3‑diketo‑L‑gulonate TRAP transporter large permease protein
*	NC_000913	29,496	0	T	A	45.5%	47.9 / 21.6	44	intergenic (+301/‑155)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	1,157,271	0	T	G	44.7%	56.7 / 10.4	39	G165G (GGT→GGG)	ycfH	putative DNase
*	NC_000913	4,536,197	0	A	T	44.4%	35.9 / 30.2	36	intergenic (+166/+417)	yjhR/nanS	pseudogene, helicase family; putative frameshift suppressor/9‑O‑acetyl N‑acetylneuraminic acid esterase
*	NC_000913	3,026,941	0	A	C	44.2%	50.1 / 16.6	43	E392D (GAA→GAC)	guaD	guanine deaminase
*	NC_000913	2,532,988	0	G	A	43.5%	19.2 / 11.1	23	G194S (GGC→AGC)	cysK	cysteine synthase A, O‑acetylserine sulfhydrolase A subunit
*	NC_000913	4,457,105	0	A	G	43.2%	40.1 / 10.5	37	I441V (ATC→GTC)	mpl	UDP‑N‑acetylmuramate:L‑alanyl‑gamma‑D‑glutamyl‑ meso‑diaminopimelate ligase
*	NC_000913	29,486	0	C	A	43.2%	54.5 / 27.1	44	intergenic (+291/‑165)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	3,665,702	0	C	A	42.1%	45.9 / 17.8	38	A37S (GCG→TCG)	gadX	acid resistance regulon transcriptional activator; autoactivator
*	NC_000913	357,890	0	C	A	41.9%	28.0 / 11.7	31	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	1,413,761	0	C	T	41.7%	46.7 / 18.5	36	G56E (GGA→GAA)	ralR	Rac prophage; restriction alleviation protein
*	NC_000913	3,745,494	0	C	T	41.5%	35.9 / 17.7	42	R231C (CGC→TGC)	yiaN	2,3‑diketo‑L‑gulonate TRAP transporter large permease protein
*	NC_000913	3,206,435	0	C	T	41.0%	43.6 / 18.7	40	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	2,676,106	0	C	A	40.7%	33.5 / 11.1	27	L240F (TTG→TTT)	yphD	putative sugar ABC transporter permease
*	NC_000913	3,601,160	0	G	A	40.7%	31.8 / 11.0	28	F309F (TTC→TTT)	ftsX	putative ABC transporter permease
*	NC_000913	2,984,718	0	G	C	40.5%	53.3 / 15.9	44	P292R (CCG→CGG)	yqeF	short chain acyltransferase

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	37 (0.930)	8 (0.220)	8/266	4.1	20.8%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	28 (0.790)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related