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	48.1%	70.9 / 98.7	108	S62F (TCT→TTT)	bglJ	DNA‑binding transcriptional regulator BglJ
*	NC_000913	501,575	0	A	C	36.6%	56.9 / 24.1	41	V555G (GTG→GGG)	ybaL	putative transporter YbaL
*	NC_000913	4,209,827	0	T	G	34.3%	43.2 / 11.0	35	noncoding (54/76 nt)	gltV	tRNA‑Glu
*	NC_000913	4,568,504	0	T	G	32.8%	250.9 / 24.3	129	T6P (ACC→CCC)	mdtM	multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter
*	NC_000913	3,275,611	0	A	C	32.1%	109.5 / 10.2	56	E110D (GAA→GAC)	garD	galactarate dehydratase
*	NC_000913	3,206,435	0	C	T	30.6%	76.8 / 28.4	49	intergenic (‑179/‑28)	ttdR/ttdA	DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha
*	NC_000913	445,558	0	A	C	29.5%	78.7 / 22.0	44	V370G (GTA→GGA)	yajR	putative major facilitator superfamily transport protein YajR
*	NC_000913	501,572	0	A	C	29.3%	75.3 / 12.0	41	V556G (GTG→GGG)	ybaL	putative transporter YbaL
*	NC_000913	2,001,918	0	A	C	28.8%	124.5 / 17.3	59	intergenic (‑129/+192)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein
*	NC_000913	4,429,984	0	T	G	28.6%	155.7 / 31.4	77	L41V (TTG→GTG)	cycA	serine/alanine/glycine/cycloserine:H(+)symporter
*	NC_000913	4,032,731	0	T	G	28.3%	115.1 / 18.5	60	G80G (GGT→GGG)	yigZ	IMPACT family member YigZ
*	NC_000913	4,101,507	0	T	G	27.8%	148.1 / 18.9	72	intergenic (+77/‑183)	sodA/kdgT	superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter
*	NC_000913	4,111,747	0	G	T	27.1%	133.8 / 21.8	48	N156K (AAC→AAA)	yiiQ	DUF1454 domain‑containing protein YiiQ
*	NC_000913	786,855	0	A	C	26.0%	108.1 / 15.8	50	G247G (GGT→GGG)	gpmA	2,3‑bisphosphoglycerate‑dependent phosphoglycerate mutase
*	NC_000913	4,296,060	0	C	T	26.0%	200.7 / 64.6	100	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
*	NC_000913	646,747	0	T	G	25.5%	100.2 / 17.4	47	T255P (ACC→CCC)	citG	triphosphoribosyl‑dephospho‑CoA synthase
*	NC_000913	3,350,853	0	A	C	24.6%	133.2 / 14.1	57	S725A (TCA→GCA)	arcB	sensory histidine kinase ArcB
*	NC_000913	3,556,207	0	T	C	24.4%	87.8 / 13.4	45	S215G (AGT→GGT)	rtcA	RNA 3'‑terminal phosphate cyclase
*	NC_000913	501,564	0	A	C	24.4%	84.9 / 18.4	41	*559E (TAA→GAA)	ybaL	putative transporter YbaL
*	NC_000913	1,825,061	0	G	A	24.4%	92.4 / 10.8	41	intergenic (‑124/+79)	ves/spy	HutD family protein Ves/ATP‑independent periplasmic chaperone

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 =	100 (0.990)	7 (0.070)	7/258	5.6	7.3%	intergenic (+49/‑433)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	4542996 =	84 (0.890)					intergenic (+363/‑119)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
*	?	NC_000913	3652036 =	NA (NA)	8 (0.080)	6/276	6.2	4.3%	noncoding (1195/1195 nt)	IS5	repeat region
	?	NC_000913	3766503 =	176 (1.740)					coding (167/843 nt)	yibA	putative lyase containing HEAT‑repeat
*	?	NC_000913	= 4542690	87 (0.860)	5 (0.050)	5/258	6.4	5.7%	intergenic (+57/‑425)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	= 4542986	84 (0.890)					intergenic (+353/‑129)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
*	?	NC_000913	1118245 =	77 (0.760)	3 (0.030)	3/266	7.5	3.9%	coding (232/576 nt)	yceI	protein YceI
	?	NC_000913	= 1118241	74 (0.760)					coding (236/576 nt)	yceI	protein YceI