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 446 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,880	0	T	C	55.3%	21.5 / 47.7	38	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	3,350,844	0	A	C	51.5%	73.5 / 116.2	68	L728V (TTA→GTA)	arcB	aerobic respiration control sensor histidine protein kinase, cognate to two‑component response regulators ArcA and RssB
*	NC_000913	4,378,802	0	A	C	51.4%	97.8 / 132.4	73	V48G (GTA→GGA)	ampC	penicillin‑binding protein; beta‑lactamase, intrinsically weak
*	NC_000913	2,326,450	0	T	G	51.0%	82.6 / 100.4	51	G114G (GGT→GGG)	atoB	acetyl‑CoA acetyltransferase
*	NC_000913	3,206,435	0	C	T	47.4%	46.4 / 66.2	76	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	3,350,853	0	A	C	46.9%	103.3 / 10.8	67	S725A (TCA→GCA)	arcB	aerobic respiration control sensor histidine protein kinase, cognate to two‑component response regulators ArcA and RssB
*	NC_000913	231,694	0	C	T	46.5%	34.5 / 26.4	43	F191F (TTC→TTT)	yafD	endo/exonuclease/phosphatase family protein
*	NC_000913	357,875	0	A	T	46.2%	34.9 / 16.1	39	N272K (AAT→AAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	436,516	0	C	A	44.6%	75.7 / 35.6	65	Q295K (CAA→AAA)	thiL	thiamine monophosphate kinase
*	NC_000913	1,535,785	0	A	G	43.6%	83.3 / 12.2	55	F25S (TTC→TCC)	yddE	PhzC‑PhzF family protein
*	NC_000913	925,900	0	A	G	43.3%	94.8 / 12.4	62	noncoding (72/88 nt)	serW	tRNA‑Ser
*	NC_000913	354,288	0	T	G	42.4%	97.0 / 14.5	59	V528G (GTG→GGG)	prpE	propionate‑‑CoA ligase
*	NC_000913	993,917	0	A	C	41.4%	107.3 / 17.6	59	V43G (GTG→GGG)	ssuB	aliphatic sulfonate ABC transporter ATPase
*	NC_000913	2,252,646	0	T	G	41.2%	127.0 / 13.3	68	V316G (GTA→GGA)	yeiI	putative kinase
*	NC_000913	357,873	0	C	T	41.0%	32.0 / 18.9	39	S273N (AGC→AAC)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	1,435,727	0	G	A	40.9%	96.2 / 41.7	66	intergenic (‑108/+33)	uspF/ompN	stress‑induced protein, ATP‑binding protein/outer membrane pore protein N, non‑specific
*	NC_000913	213,341	0	A	G	40.5%	122.6 / 18.1	74	G337G (GGA→GGG)	tilS	tRNA(Ile)‑lysidine synthetase
*	NC_000913	29,496	0	T	A	40.4%	74.3 / 28.7	53	intergenic (+301/‑155)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	3,443,277	0	A	C	40.4%	114.2 / 13.3	57	V274G (GTA→GGA)	secY	preprotein translocase membrane subunit
*	NC_000913	345,328	0	C	A	40.3%	113.9 / 36.4	73	intergenic (+337/‑76)	yahL/yahM	uncharacterized protein/uncharacterized protein

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 =	70 (0.980)	3 (0.040)	3/280	12.9	4.4%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	66 (0.980)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)