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 233 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	52.5%	5.3 / 44.9	40	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	2,903,692	0	C	A	48.6%	65.2 / 58.6	70	intergenic (+318/+1055)	ygcE/queE	putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis
*	NC_000913	357,880	0	T	C	47.5%	40.3 / 10.9	40	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	1,622,815	0	C	A	46.0%	39.3 / 21.2	38	intergenic (+74/+145)	yneM/dgcZ	inner membrane‑associated protein/diguanylate cyclase, zinc‑sensing
*	NC_000913	2,040,075	0	C	G	45.8%	49.2 / 18.3	49	L200V (CTG→GTG)	yedY	membrane‑anchored, periplasmic TMAO, DMSO reductase
*	NC_000913	3,206,435	0	C	T	45.2%	84.2 / 58.7	85	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	689,514	0	A	C	45.0%	53.3 / 10.6	40	G456G (GGT→GGG)	lnt	apolipoprotein N‑acyltransferase
*	NC_000913	1,622,816	0	G	A	42.1%	21.1 / 40.5	38	intergenic (+75/+144)	yneM/dgcZ	inner membrane‑associated protein/diguanylate cyclase, zinc‑sensing
*	NC_000913	2,001,918	0	A	C	41.1%	88.8 / 12.4	57	intergenic (‑129/+192)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin)
*	NC_000913	29,496	0	T	A	40.8%	103.7 / 38.6	71	intergenic (+301/‑155)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	599,576	0	T	G	40.0%	92.4 / 10.9	55	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	4,536,197	0	A	T	40.0%	64.6 / 51.6	55	intergenic (+166/+417)	yjhR/nanS	pseudogene, helicase family; putative frameshift suppressor/9‑O‑acetyl N‑acetylneuraminic acid esterase
*	NC_000913	2,676,106	0	C	A	39.3%	69.5 / 26.1	58	L240F (TTG→TTT)	yphD	putative sugar ABC transporter permease
*	NC_000913	29,486	0	C	A	39.1%	113.3 / 35.3	69	intergenic (+291/‑165)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	4,580,634	0	C	T	38.6%	86.0 / 18.2	59	E277K (GAA→AAA)	hsdS	specificity determinant for hsdM and hsdR
*	NC_000913	5,159	0	G	A	38.3%	75.2 / 25.3	60	intergenic (+139/‑75)	thrC/yaaX	L‑threonine synthase/DUF2502 family putative periplasmic protein
*	NC_000913	3,443,277	0	A	C	38.2%	148.8 / 11.8	76	V274G (GTA→GGA)	secY	preprotein translocase membrane subunit
*	NC_000913	357,875	0	A	T	38.1%	54.3 / 14.0	43	N272K (AAT→AAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	1,413,735	0	A	T	38.0%	68.3 / 30.8	51	Y2* (TAT→TAA)	ydaC	DUF1187 family protein, Rac prophage; putative double‑strand break reduction protein
*	NC_000913	2,628,598	0	G	A	37.5%	80.4 / 23.6	56	S114L (TCA→TTA)	yfgF	cyclic‑di‑GMP phosphodiesterase, anaerobic

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	4542682 =	96 (1.360)	9 (0.140)	9/280	6.4	9.4%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	83 (1.250)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)