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

Marginal read alignment evidence
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,604,344	0	C	T	55.4%	9.4 / 76.4	56	S62F (TCT→TTT)	bglJ	DNA‑binding transcriptional regulator BglJ
*	NC_000913	1,550,663	0	A	C	37.9%	32.9 / 11.8	29	N68T (AAC→ACC)	fdnH	formate dehydrogenase N subunit beta
*	NC_000913	4,568,504	0	T	G	36.5%	121.9 / 16.9	85	T6P (ACC→CCC)	mdtM	multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter
*	NC_000913	3,206,435	0	C	T	34.9%	57.1 / 26.8	43	intergenic (‑179/‑28)	ttdR/ttdA	DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha
*	NC_000913	1,825,061	0	G	A	34.3%	59.1 / 12.2	35	intergenic (‑124/+79)	ves/spy	HutD family protein Ves/ATP‑independent periplasmic chaperone
*	NC_000913	753,125	0	T	A	33.3%	131.9 / 39.4	75	intergenic (‑330/+60)	ybgD/gltA	putative fimbrial protein YbgD/citrate synthase
*	NC_000913	4,101,507	0	T	G	33.3%	57.4 / 12.1	42	intergenic (+77/‑183)	sodA/kdgT	superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter
*	NC_000913	3,206,444	0	T	A	31.8%	70.7 / 14.8	44	intergenic (‑188/‑19)	ttdR/ttdA	DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha
*	NC_000913	4,628,649	0	A	C	31.1%	71.1 / 15.6	45	intergenic (+102/+206)	nadR/ettA	DNA‑binding transcriptional repressor/NMN adenylyltransferase NadR/energy‑dependent translational throttle protein EttA
*	NC_000913	445,558	0	A	C	30.9%	60.0 / 20.9	42	V370G (GTA→GGA)	yajR	putative major facilitator superfamily transport protein YajR
*	NC_000913	2,326,450	0	T	G	27.3%	67.8 / 27.4	44	G114G (GGT→GGG)	atoB	acetyl‑CoA acetyltransferase
*	NC_000913	4,429,984	0	T	G	25.6%	80.6 / 11.7	43	L41V (TTG→GTG)	cycA	serine/alanine/glycine/cycloserine:H(+)symporter
*	NC_000913	753,105	0	A	T	25.3%	212.8 / 26.7	87	intergenic (‑310/+80)	ybgD/gltA	putative fimbrial protein YbgD/citrate synthase
*	NC_000913	501,564	0	A	C	25.0%	67.3 / 11.0	36	*559E (TAA→GAA)	ybaL	putative transporter YbaL
*	NC_000913	2,001,918	0	A	C	24.5%	105.4 / 16.0	53	intergenic (‑129/+192)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein
*	NC_000913	4,296,060	0	C	T	23.1%	170.1 / 42.9	78	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
*	NC_000913	753,114	0	G	T	22.1%	211.1 / 14.8	77	intergenic (‑319/+71)	ybgD/gltA	putative fimbrial protein YbgD/citrate 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	94 (1.340)	13 (0.200)	13/258	3.0	14.5%	intergenic (+57/‑425)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	= 4542986	65 (0.990)					intergenic (+353/‑129)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
*	?	NC_000913	= 1397238	NA (NA)	13 (0.190)	9/276	4.2	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	= 1207805	85 (1.210)	4 (0.060)	4/244	5.6	5.7%	coding (305/630 nt)	ycfK	e14 prophage; protein StfP
	?	NC_000913	= 1209602	57 (0.920)					pseudogene (54/537 nt)	stfE	e14 prophage; putative side tail fiber protein fragment
*	?	NC_000913	4542682 =	98 (1.400)	4 (0.060)	4/258	5.8	4.8%	intergenic (+49/‑433)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	4542996 =	66 (1.010)					intergenic (+363/‑119)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit