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 383 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	64.9%	1.6 / 27.5	37	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	357,880	0	T	C	56.1%	19.5 / 47.7	41	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	357,875	0	A	T	50.0%	24.5 / 25.1	42	N272K (AAT→AAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	993,917	0	A	C	48.3%	80.5 / 21.2	58	V43G (GTG→GGG)	ssuB	aliphatic sulfonate ABC transporter ATPase
*	NC_000913	993,913	0	G	C	47.5%	95.7 / 22.3	60	G44G (GGC→GGG)	ssuB	aliphatic sulfonate ABC transporter ATPase
*	NC_000913	2,678,039	0	T	G	47.1%	104.3 / 19.6	68	N108T (AAC→ACC)	yphE	putative sugar ABC transporter ATPase
*	NC_000913	4,538,109	0	A	C	47.1%	105.4 / 17.9	68	G219G (GGT→GGG)	nanM	N‑acetylneuraminic acid mutarotase
*	NC_000913	1,079,468	0	A	G	46.8%	61.6 / 11.0	47	D55G (GAT→GGT)	putP	proline:sodium symporter
*	NC_000913	2,337,723	0	A	C	46.0%	78.2 / 19.6	51	G566G (GGT→GGG)	gyrA	DNA gyrase (type II topoisomerase), subunit A
*	NC_000913	1,604,237	0	C	T	45.6%	62.0 / 23.2	57	S64L (TCG→TTG)	lsrD	autoinducer 2 import system permease protein
*	NC_000913	3,443,277	0	A	C	44.9%	106.9 / 25.4	69	V274G (GTA→GGA)	secY	preprotein translocase membrane subunit
*	NC_000913	1,755,871	0	T	A	44.4%	68.3 / 45.5	63	G58G (GGT→GGA)	pykF	pyruvate kinase I
*	NC_000913	1,222,596	0	G	A	44.2%	50.3 / 37.8	53	F13F (TTC→TTT)	ymgD	uncharacterized protein
*	NC_000913	3,206,435	0	C	T	43.6%	64.7 / 26.5	55	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	1,510,395	0	C	A	42.9%	77.4 / 30.1	64	S131R (AGC→AGA)	ydcR	putative DNA‑binding transcriptional regulator and putative aminotransferase
*	NC_000913	2,481,804	0	G	A	42.6%	86.7 / 30.0	68	P125S (CCA→TCA)	emrY	putative multidrug efflux system
*	NC_000913	354,288	0	T	G	42.6%	92.8 / 16.2	61	V528G (GTG→GGG)	prpE	propionate‑‑CoA ligase
*	NC_000913	357,873	0	C	T	41.5%	28.6 / 19.6	42	S273N (AGC→AAC)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	1,153,573	0	T	G	41.0%	63.0 / 18.7	39	Y92D (TAC→GAC)	pabC	4‑amino‑4‑deoxychorismate lyase component of para‑aminobenzoate synthase multienzyme complex
*	NC_000913	1,755,862	0	C	A	40.7%	97.8 / 28.9	59	S55R (AGC→AGA)	pykF	pyruvate kinase I

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	= 4542690	75 (1.120)	7 (0.110)	7/280	9.8	8.9%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	72 (1.140)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	4542682 =	76 (1.130)	6 (0.100)	6/280	10.4	7.7%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	72 (1.140)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)