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 23 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,532,856	0	T	G	50.0%	10.5 / 57.2	39	D347E (GAT→GAG)	ydcC	H repeat‑associated putative transposase YdcC
*	NC_000913	4,101,514	0	G	T	38.3%	107.3 / 40.0	60	intergenic (+84/‑176)	sodA/kdgT	superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter
*	NC_000913	4,604,344	0	C	T	36.1%	80.2 / 35.7	72	S62F (TCT→TTT)	bglJ	DNA‑binding transcriptional regulator BglJ
*	NC_000913	4,568,504	0	T	G	34.4%	162.2 / 15.6	95	T6P (ACC→CCC)	mdtM	multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter
*	NC_000913	1,208,042	1	.	G	33.3%	90.1 / 140.1	87	coding (542/630 nt)	ycfK	e14 prophage; protein StfP
*	NC_000913	4,101,507	0	T	G	32.3%	114.5 / 12.8	65	intergenic (+77/‑183)	sodA/kdgT	superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter
*	NC_000913	888,014	0	T	G	29.8%	84.6 / 11.5	47	noncoding (44/81 nt)	rybB	small regulatory RNA RybB
*	NC_000913	2,667,126	0	A	C	29.6%	104.2 / 10.5	54	Y241D (TAT→GAT)	hcaT	putative 3‑phenylpropionate transporter
*	NC_000913	372,640	0	T	G	29.5%	122.4 / 17.5	61	L176V (TTA→GTA)	mhpD	2‑hydroxypentadienoate hydratase
*	NC_000913	2,001,918	0	A	C	27.7%	95.9 / 11.5	47	intergenic (‑129/+192)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein
*	NC_000913	753,125	0	T	A	27.3%	98.8 / 14.5	44	intergenic (‑330/+60)	ybgD/gltA	putative fimbrial protein YbgD/citrate synthase
*	NC_000913	4,101,536	0	C	A	26.8%	136.6 / 12.6	56	intergenic (+106/‑154)	sodA/kdgT	superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter
*	NC_000913	3,844,219	0	T	G	26.6%	188.5 / 26.6	94	F86V (TTT→GTT)	adeD	adenine deaminase
*	NC_000913	2,326,450	0	T	G	26.4%	145.1 / 31.2	72	G114G (GGT→GGG)	atoB	acetyl‑CoA acetyltransferase
*	NC_000913	239,282	0	G	T	26.3%	128.2 / 38.9	57	pseudogene (93/189 nt)	yafF	putative uncharacterized protein YafF
*	NC_000913	3,401,459	0	T	C	26.2%	126.7 / 14.8	65	D625G (GAT→GGT)	csrD	regulator of CsrB and CsrC decay
*	NC_000913	3,206,435	0	C	T	26.0%	84.1 / 18.5	50	intergenic (‑179/‑28)	ttdR/ttdA	DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha
*	NC_000913	4,296,060	0	C	T	25.3%	152.0 / 52.0	83	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
*	NC_000913	650,809	0	T	G	23.9%	145.3 / 13.4	67	T350P (ACC→CCC)	citC	citrate lyase synthetase
*	NC_000913	646,747	0	T	G	23.2%	125.5 / 17.7	56	T255P (ACC→CCC)	citG	triphosphoribosyl‑dephospho‑CoA synthase

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	67 (0.780)	8 (0.100)	8/258	5.3	10.8%	intergenic (+57/‑425)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	= 4542986	70 (0.870)					intergenic (+353/‑129)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
*	?	NC_000913	4542682 =	73 (0.850)	5 (0.060)	5/258	6.4	6.7%	intergenic (+49/‑433)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	4542996 =	70 (0.870)					intergenic (+363/‑119)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
*	?	NC_000913	626648 =	93 (1.080)	4 (0.050)	3/268	7.6	4.2%	coding (579/1611 nt)	entE	2,3‑dihydroxybenzoate‑AMP ligase
	?	NC_000913	= 626644	90 (1.070)					coding (575/1611 nt)	entE	2,3‑dihydroxybenzoate‑AMP ligase
*	?	NC_000913	= 2719833	100 (1.160)	4 (0.050)	3/272	7.7	4.0%	coding (611/699 nt)	yfiP	conserved protein YfiP
	?	NC_000913	= 2719931	92 (1.080)					intergenic (+10/‑22)	yfiP/patZ	conserved protein YfiP/peptidyl‑lysine acetyltransferase