breseq  version 0.35.4  revision f352f80f4bc9 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence (highest frequency 20 of 28 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,604,344	0	C	T	36.8%	113.1 / 51.7	87	S62F (TCT→TTT)	bglJ	DNA‑binding transcriptional regulator BglJ
*	NC_000913	3,206,435	0	C	T	36.5%	76.5 / 45.2	63	intergenic (‑179/‑28)	ttdR/ttdA	DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha
*	NC_000913	888,014	0	T	G	35.8%	98.5 / 21.8	67	noncoding (44/81 nt)	rybB	small regulatory RNA RybB
*	NC_000913	4,568,504	0	T	G	35.4%	143.8 / 22.2	102	T6P (ACC→CCC)	mdtM	multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter
*	NC_000913	1,825,061	0	G	A	31.6%	65.6 / 14.4	38	intergenic (‑124/+79)	ves/spy	HutD family protein Ves/ATP‑independent periplasmic chaperone
*	NC_000913	501,575	0	A	C	31.1%	67.9 / 23.4	45	V555G (GTG→GGG)	ybaL	putative transporter YbaL
*	NC_000913	2,326,450	0	T	G	30.4%	119.4 / 49.7	79	G114G (GGT→GGG)	atoB	acetyl‑CoA acetyltransferase
*	NC_000913	3,206,444	0	T	A	30.0%	101.7 / 25.9	60	intergenic (‑188/‑19)	ttdR/ttdA	DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha
*	NC_000913	4,111,747	0	G	T	30.0%	154.0 / 36.5	60	N156K (AAC→AAA)	yiiQ	DUF1454 domain‑containing protein YiiQ
*	NC_000913	29,496	0	T	A	29.8%	116.0 / 26.4	57	intergenic (+301/‑155)	dapB/carA	4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha
*	NC_000913	501,572	0	A	C	29.5%	79.6 / 10.6	44	V556G (GTG→GGG)	ybaL	putative transporter YbaL
*	NC_000913	650,809	0	T	G	28.8%	103.6 / 13.8	59	T350P (ACC→CCC)	citC	citrate lyase synthetase
*	NC_000913	2,001,918	0	A	C	28.8%	134.4 / 26.6	73	intergenic (‑129/+192)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein
*	NC_000913	753,125	0	T	A	28.4%	145.0 / 27.1	67	intergenic (‑330/+60)	ybgD/gltA	putative fimbrial protein YbgD/citrate synthase
*	NC_000913	3,943,488	0	T	G	26.3%	94.2 / 15.3	57	noncoding (54/76 nt)	gltU	tRNA‑Glu
*	NC_000913	4,101,507	0	T	G	25.3%	185.6 / 13.3	92	intergenic (+77/‑183)	sodA/kdgT	superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter
*	NC_000913	1,218,414	0	A	C	25.0%	135.2 / 10.7	68	T363P (ACC→CCC)	pdeG	putative c‑di‑GMP phosphodiesterase PdeG
*	NC_000913	3,745,397	0	A	C	25.0%	106.5 / 10.4	64	L198F (TTA→TTC)	yiaN	2,3‑diketo‑L‑gulonate:Na(+) symporter ‑ membrane subunit
*	NC_000913	1,565,621	0	T	G	24.7%	161.6 / 16.2	85	N38T (AAC→ACC)	dosP	oxygen‑sensing c‑di‑GMP phosphodiesterase DosP
*	NC_000913	2,094,899	0	A	C	24.0%	148.4 / 12.2	75	Y122S (TAC→TCC)	hisH	imidazole glycerol phosphate synthase subunit HisH

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 =	104 (0.990)	11 (0.110)	10/258	5.9	11.1%	intergenic (+49/‑433)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	4542996 =	80 (0.810)					intergenic (+363/‑119)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
*	?	NC_000913	= 4542690	99 (0.940)	9 (0.090)	9/258	6.3	9.4%	intergenic (+57/‑425)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	= 4542986	80 (0.810)					intergenic (+353/‑129)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
*	?	NC_000913	= 1397238	NA (NA)	9 (0.090)	5/276	8.3	100%	noncoding (1195/1195 nt)	IS5	repeat region
	?	NC_000913	= 1978494	0 (0.000)					intergenic (‑297/+24)	flhD/insB‑5	DNA‑binding transcriptional dual regulator FlhD/IS1 protein InsB
*	?	NC_000913	= 3891943	135 (1.280)	3 (0.030)	3/272	9.4	2.2%	coding (329/1176 nt)	mdtL	efflux pump MdtL
	?	NC_000913	3891947 =	137 (1.320)					coding (333/1176 nt)	mdtL	efflux pump MdtL