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 27 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,206,435	0	C	T	44.4%	23.9 / 32.1	36	intergenic (‑179/‑28)	ttdR/ttdA	DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha
*	NC_000913	4,604,344	0	C	T	39.7%	60.7 / 40.5	59	S62F (TCT→TTT)	bglJ	DNA‑binding transcriptional regulator BglJ
*	NC_000913	1,825,061	0	G	A	36.1%	53.2 / 16.1	36	intergenic (‑124/+79)	ves/spy	HutD family protein Ves/ATP‑independent periplasmic chaperone
*	NC_000913	4,568,504	0	T	G	32.9%	146.1 / 14.2	86	T6P (ACC→CCC)	mdtM	multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter
*	NC_000913	3,556,207	0	T	C	32.4%	47.0 / 15.3	34	S215G (AGT→GGT)	rtcA	RNA 3'‑terminal phosphate cyclase
*	NC_000913	3,206,444	0	T	A	31.4%	59.2 / 16.2	35	intergenic (‑188/‑19)	ttdR/ttdA	DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha
*	NC_000913	4,111,747	0	G	T	30.0%	100.7 / 20.8	40	N156K (AAC→AAA)	yiiQ	DUF1454 domain‑containing protein YiiQ
*	NC_000913	2,628,625	0	A	C	29.8%	85.7 / 16.5	47	V105G (GTC→GGC)	pdeF	cyclic di‑GMP phosphodiesterase PdeF
*	NC_000913	445,558	0	A	C	27.7%	88.4 / 18.3	47	V370G (GTA→GGA)	yajR	putative major facilitator superfamily transport protein YajR
*	NC_000913	2,667,126	0	A	C	27.1%	138.2 / 17.4	70	Y241D (TAT→GAT)	hcaT	putative 3‑phenylpropionate transporter
*	NC_000913	650,809	0	T	G	26.2%	126.7 / 18.8	65	T350P (ACC→CCC)	citC	citrate lyase synthetase
*	NC_000913	2,326,450	0	T	G	26.0%	137.8 / 41.3	73	G114G (GGT→GGG)	atoB	acetyl‑CoA acetyltransferase
*	NC_000913	4,429,984	0	T	G	26.0%	153.0 / 25.6	73	L41V (TTG→GTG)	cycA	serine/alanine/glycine/cycloserine:H(+)symporter
*	NC_000913	4,111,752	0	T	C	26.0%	98.8 / 11.3	50	K155E (AAA→GAA)	yiiQ	DUF1454 domain‑containing protein YiiQ
*	NC_000913	2,001,918	0	A	C	25.5%	106.0 / 13.2	51	intergenic (‑129/+192)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein
*	NC_000913	4,098,155	0	A	C	25.0%	173.6 / 11.2	80	L140F (TTA→TTC)	rhaS	DNA‑binding transcriptional activator RhaS
*	NC_000913	3,740,909	0	T	G	24.7%	158.2 / 16.8	73	V402G (GTG→GGG)	avtA	valine‑‑pyruvate aminotransferase
*	NC_000913	376,401	0	T	G	23.4%	131.8 / 13.3	64	L315V (TTG→GTG)	mhpT	3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter
*	NC_000913	1,315,936	0	T	A	21.7%	114.8 / 10.4	46	K34* (AAA→TAA)	yciG	protein YciG
*	NC_000913	372,640	0	T	G	21.4%	122.8 / 12.9	56	L176V (TTA→GTA)	mhpD	2‑hydroxypentadienoate hydratase

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	71 (0.870)	16 (0.210)	16/258	3.2	17.7%	intergenic (+57/‑425)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	= 4542986	82 (1.070)					intergenic (+353/‑129)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
*	?	NC_000913	4542682 =	75 (0.920)	13 (0.170)	13/258	3.8	14.6%	intergenic (+49/‑433)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	4542996 =	82 (1.070)					intergenic (+363/‑119)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
*	?	NC_000913	= 1574322	68 (0.840)	3 (0.040) +CAG	3/268	7.6	4.3%	coding (881/2796 nt)	pqqL	putative zinc peptidase
	?	NC_000913	1574323 =	68 (0.830)					coding (880/2796 nt)	pqqL	putative zinc peptidase
*	?	NC_000913	= 3176701	76 (0.930)	3 (0.040)	3/274	7.7	3.1%	coding (133/828 nt)	cpdA	cAMP phosphodiesterase
	?	NC_000913	3179280 =	113 (1.390)					coding (1166/1482 nt)	tolC	outer membrane channel TolC
*	?	NC_000913	73391 =	54 (0.660)	3 (0.040)	3/276	7.8	4.5%	coding (1131/1611 nt)	thiP	thiamine ABC transporter membrane subunit
	?	NC_000913	4626793 =	74 (0.910)					coding (882/1383 nt)	radA	DNA recombination protein