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	1,879,830	0	T	C	46.8%	9.9 / 223.4	154	Y40C (TAC→TGC)	yeaR	DUF1971 domain‑containing protein YeaR
*	NC_000913	3,745,397	0	A	C	37.7%	96.5 / 22.6	61	L198F (TTA→TTC)	yiaN	2,3‑diketo‑L‑gulonate:Na(+) symporter ‑ membrane subunit
*	NC_000913	4,568,504	0	T	G	34.8%	225.7 / 23.5	119	T6P (ACC→CCC)	mdtM	multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter
*	NC_000913	3,943,488	0	T	G	33.3%	52.3 / 11.9	37	noncoding (54/76 nt)	gltU	tRNA‑Glu
*	NC_000913	4,213,778	0	A	C	32.9%	130.8 / 18.8	73	F116V (TTC→GTC)	yjaB	putative N‑acetyltransferase YjaB
*	NC_000913	4,604,344	0	C	T	31.6%	110.9 / 32.0	77	S62F (TCT→TTT)	bglJ	DNA‑binding transcriptional regulator BglJ
*	NC_000913	3,844,219	0	T	G	30.3%	221.5 / 30.5	99	F86V (TTT→GTT)	adeD	adenine deaminase
*	NC_000913	4,296,060	0	C	T	28.8%	206.0 / 85.5	118	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
*	NC_000913	937,942	0	A	C	28.8%	140.8 / 18.0	73	T191P (ACC→CCC)	lolA	outer membrane lipoprotein carrier protein
*	NC_000913	650,809	0	T	G	27.1%	156.7 / 14.8	70	T350P (ACC→CCC)	citC	citrate lyase synthetase
*	NC_000913	3,556,205	0	A	C	26.7%	108.1 / 10.1	45	S215R (AGT→AGG) ‡	rtcA	RNA 3'‑terminal phosphate cyclase
*	NC_000913	3,740,909	0	T	G	26.3%	175.1 / 18.7	76	V402G (GTG→GGG)	avtA	valine‑‑pyruvate aminotransferase
*	NC_000913	3,404,215	0	T	G	26.2%	157.0 / 19.8	65	G244G (GGT→GGG)	yhdH	acrylyl‑CoA reductase
*	NC_000913	3,206,435	0	C	T	26.1%	92.5 / 15.1	46	intergenic (‑179/‑28)	ttdR/ttdA	DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha
*	NC_000913	3,556,207	0	T	C	26.1%	91.5 / 10.1	46	S215G (AGT→GGT) ‡	rtcA	RNA 3'‑terminal phosphate cyclase
*	NC_000913	1,068,173	0	T	G	25.8%	159.1 / 16.7	66	G31G (GGT→GGG)	ymdF	conserved protein YmdF
*	NC_000913	729,648	0	T	G	25.0%	150.2 / 12.1	64	G22G (GGT→GGG)	rhsC	rhs element protein RhsC
*	NC_000913	4,213,761	0	A	C	24.1%	223.5 / 19.5	87	G121G (GGT→GGG)	yjaB	putative N‑acetyltransferase YjaB
*	NC_000913	646,747	0	T	G	23.8%	98.2 / 17.3	42	T255P (ACC→CCC)	citG	triphosphoribosyl‑dephospho‑CoA synthase
*	NC_000913	4,111,747	0	G	T	23.7%	103.7 / 12.7	38	N156K (AAC→AAA)	yiiQ	DUF1454 domain‑containing protein YiiQ

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	14 (0.150)	13 (0.150)	13/260	4.3	32.1%	intergenic (+57/‑425)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	= 4542986	42 (0.490)					intergenic (+353/‑129)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
*	?	NC_000913	4542682 =	18 (0.200)	11 (0.130)	9/260	5.5	26.6%	intergenic (+49/‑433)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	4542996 =	44 (0.510)					intergenic (+363/‑119)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
*	?	NC_000913	375124 =	NA (NA)	3 (0.050)	3/194	6.9	NA	intergenic (+243/‑335)	mhpE/mhpT	4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter
	?	NC_000913	377530 =	NA (NA)					intergenic (+219/+5)	yaiL/frmB	DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB