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 528 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,880	0	T	C	58.5%	26.3 / 52.9	41	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	357,890	0	C	A	55.3%	22.4 / 67.9	47	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	2,984,441	0	A	C	51.4%	85.6 / 127.6	70	G384G (GGT→GGG)	yqeF	short chain acyltransferase
*	NC_000913	213,341	0	A	G	50.0%	67.6 / 25.1	66	G337G (GGA→GGG)	tilS	tRNA(Ile)‑lysidine synthetase
*	NC_000913	357,873	0	C	T	48.9%	32.9 / 27.3	45	S273N (AGC→AAC)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	3,640,981	0	C	T	48.2%	46.0 / 35.6	56	F40F (TTC→TTT)	dtpB	dipeptide and tripeptide permease B
*	NC_000913	501,575	0	A	C	47.0%	106.1 / 11.2	66	V555G (GTG→GGG)	ybaL	inner membrane putative NAD(P)‑binding transporter
*	NC_000913	354,288	0	T	G	46.8%	121.6 / 23.1	79	V528G (GTG→GGG)	prpE	propionate‑‑CoA ligase
*	NC_000913	1,574,051	0	G	T	46.2%	80.6 / 28.2	52	V384V (GTC→GTA)	pqqL	putative periplasmic M16 family zinc metalloendopeptidase
*	NC_000913	2,349,145	0	A	C	45.6%	90.2 / 15.0	57	F110V (TTC→GTC)	inaA	acid‑inducible Kdo/WaaP family putative kinase
*	NC_000913	3,029,965	0	A	C	44.6%	82.3 / 21.9	56	L323V (TTA→GTA)	ygfT	putative oxidoreductase, Fe‑S subunit/nucleotide‑binding subunit
*	NC_000913	357,875	0	A	T	44.4%	54.4 / 18.9	45	N272K (AAT→AAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	599,576	0	T	G	44.0%	112.4 / 38.5	76	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	4,161,142	0	C	A	43.5%	89.7 / 31.3	62	Q7K (CAA→AAA)	fabR	transcriptional repressor of fabA and fabB
*	NC_000913	3,423,294	0	T	C	43.4%	116.9 / 31.9	83	intergenic (+100/+129)	yhdZ/rrfF	putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon
*	NC_000913	941,713	0	T	G	43.1%	100.0 / 26.0	67	V252G (GTG→GGG)	dmsA	dimethyl sulfoxide reductase, anaerobic, subunit A
*	NC_000913	29,496	0	T	A	43.0%	114.0 / 38.6	79	intergenic (+301/‑155)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	2,846,674	0	T	G	42.9%	90.5 / 14.3	65	T247P (ACC→CCC)	hycD	hydrogenase 3, membrane subunit
*	NC_000913	298,960	0	A	C	42.6%	80.8 / 26.0	55	Y659D (TAT→GAT)	paoC	PaoABC aldehyde oxidoreductase, Moco‑containing subunit
*	NC_000913	3,177,531	0	A	C	42.4%	105.3 / 10.3	59	V127G (GTG→GGG)	nudF	ADP‑ribose pyrophosphatase

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	= 781446	0 (0.000)	26 (0.410)	19/258	4.4	46.9%	intergenic (+2/‑131)	lysZ/lysQ	tRNA‑Lys/tRNA‑Lys
	?	NC_000913	2521487 =	59 (0.940)					intergenic (+159/+106)	lysV/xapR	tRNA‑Lys/transcriptional activator of xapAB
*	?	NC_000913	= 4542690	86 (1.180)	17 (0.250)	17/280	5.5	17.5%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	79 (1.150)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	4542682 =	81 (1.110)	19 (0.280)	17/280	5.5	19.7%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	79 (1.150)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)