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 22 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,087,406	0	A	C	53.3%	1.1 / 21.5	15	W285G (TGG→GGG)	yeeY	putative DNA‑binding transcriptional regulator YeeY
*	NC_000913	4,296,060	0	C	T	45.7%	21.2 / 94.8	70	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
*	NC_000913	4,414,906	0	T	G	43.5%	11.1 / 24.9	23	V211G (GTG→GGG)	aidB	putative acyl‑CoA dehydrogenase AidB
*	NC_000913	310,934	0	A	C	40.0%	36.0 / 16.0	30	F135V (TTC→GTC)	ecpR	DNA‑binding transcriptional dual regulator MatA
*	NC_000913	821,440	0	C	T	40.0%	45.2 / 39.3	50	F216F (TTC→TTT)	ybhM	Bax1‑I family protein YbhM
*	NC_000913	1,374,975	0	G	T	38.9%	21.9 / 10.4	18	V5L (GTA→TTA)	ycjQ	putative zinc‑binding dehydrogenase YcjQ
*	NC_000913	1,384,788	0	T	G	35.7%	11.5 / 11.2	14	G224G (GGT→GGG)	ycjX	DUF463 domain‑containing protein YcjX
*	NC_000913	2,699,051	0	T	G	35.7%	9.2 / 10.2	14	V98G (GTC→GGC)	yfhH	putative DNA‑binding transcriptional regulator YfhH
*	NC_000913	3,563,481	0	T	G	35.0%	56.3 / 34.1	40	V490G (GTG→GGG)	glpD	aerobic glycerol 3‑phosphate dehydrogenase
*	NC_000913	2,160,604	0	A	C	33.3%	30.8 / 10.5	21	Y740S (TAC→TCC)	mdtC	multidrug efflux pump RND permease subunit MdtC
*	NC_000913	2,349,621	0	A	C	33.3%	37.8 / 24.9	30	intergenic (‑149/‑66)	inaA/yfaH	putative lipopolysaccharide kinase InaA/putative uncharacterized protein YfaH
*	NC_000913	1,603,796	0	G	C	30.0%	29.3 / 15.5	20	G260R (GGT→CGT)	lsrC	Autoinducer‑2 ABC transporter membrane subunit LsrC
*	NC_000913	1,603,808	0	G	A	28.6%	24.9 / 10.5	21	G264S (GGT→AGT)	lsrC	Autoinducer‑2 ABC transporter membrane subunit LsrC
*	NC_000913	395,288	0	A	T	28.0%	50.0 / 18.1	25	F334I (TTC→ATC)	ampH	peptidoglycan DD‑carboxypeptidase/peptidoglycan DD‑endopeptidase
*	NC_000913	151,656	0	T	G	27.3%	111.6 / 30.0	55	A192A (GCA→GCC)	yadL	putative fimbrial protein YadL
*	NC_000913	1,203,112	0	T	G	26.0%	108.0 / 23.9	50	V30G (GTT→GGT)	ymfT	e14 prophage; putative DNA‑binding transcriptional regulator YmfT
*	NC_000913	395,291	0	C	G	25.9%	48.5 / 18.9	27	G333R (GGT→CGT)	ampH	peptidoglycan DD‑carboxypeptidase/peptidoglycan DD‑endopeptidase
*	NC_000913	3,233,922	0	G	T	23.9%	95.6 / 13.6	46	Q75K (CAA→AAA)	higA	antitoxin/DNA‑binding transcriptional repressor HigA
*	NC_000913	1,374,034	0	G	.	22.2%	42.2 / 11.9	18	coding (813/882 nt)	ycjO	putative ABC transporter membrane subunit YcjO
*	NC_000913	3,196,811	0	A	C	21.9%	98.0 / 19.1	41	V944G (GTG→GGG)	glnE	fused glutamine synthetase deadenylase/glutamine synthetase adenylyltransferase

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 =	37 (0.740)	9 (0.210)	9/116	1.4	17.0%	intergenic (+49/‑433)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	4542996 =	56 (1.290)					intergenic (+363/‑119)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
*	?	NC_000913	= 1603798	21 (0.420)	5 (0.100)	4/134	2.9	19.2%	coding (780/1029 nt)	lsrC	Autoinducer‑2 ABC transporter membrane subunit LsrC
	?	NC_000913	1603802 =	21 (0.420)					coding (784/1029 nt)	lsrC	Autoinducer‑2 ABC transporter membrane subunit LsrC
*	?	NC_000913	257908 =	NA (NA)	8 (0.160)	4/134	2.9	10.0%	noncoding (768/768 nt)	IS1	repeat region
	?	NC_000913	486122 =	72 (1.440)					coding (362/648 nt)	acrR	DNA‑binding transcriptional repressor AcrR