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 21 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	45.5%	60.8 / 69.2	88	S62F (TCT→TTT)	bglJ	DNA‑binding transcriptional regulator BglJ
*	NC_000913	650,809	0	T	G	39.6%	67.1 / 15.8	48	T350P (ACC→CCC)	citC	citrate lyase synthetase
*	NC_000913	4,568,504	0	T	G	35.4%	178.4 / 22.5	112	T6P (ACC→CCC)	mdtM	multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter
*	NC_000913	2,001,918	0	A	C	34.9%	99.8 / 26.3	63	intergenic (‑129/+192)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein
*	NC_000913	4,111,747	0	G	T	34.3%	69.4 / 23.6	35	N156K (AAC→AAA)	yiiQ	DUF1454 domain‑containing protein YiiQ
*	NC_000913	4,209,827	0	T	G	34.2%	48.6 / 15.9	41	noncoding (54/76 nt)	gltV	tRNA‑Glu
*	NC_000913	501,575	0	A	C	29.3%	73.2 / 15.7	41	V555G (GTG→GGG)	ybaL	putative transporter YbaL
*	NC_000913	888,014	0	T	G	29.2%	120.7 / 15.6	65	noncoding (44/81 nt)	rybB	small regulatory RNA RybB
*	NC_000913	2,302,034	0	C	T	27.6%	152.1 / 68.7	98	A240A (GCG→GCA)	napA	periplasmic nitrate reductase subunit NapA
*	NC_000913	1,068,173	0	T	G	26.9%	164.7 / 18.0	78	G31G (GGT→GGG)	ymdF	conserved protein YmdF
*	NC_000913	2,406,304	0	A	T	26.1%	187.6 / 72.5	92	I113N (ATC→AAC)	lrhA	DNA‑binding transcriptional dual regulator LrhA
*	NC_000913	4,296,060	0	C	T	25.4%	123.9 / 43.3	71	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
*	NC_000913	4,568,512	0	C	A	25.3%	212.6 / 28.7	83	R3L (CGT→CTT)	mdtM	multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter
*	NC_000913	29,496	0	T	A	24.1%	133.1 / 16.6	54	intergenic (+301/‑155)	dapB/carA	4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha
*	NC_000913	501,564	0	A	C	23.9%	97.9 / 14.2	46	*559E (TAA→GAA)	ybaL	putative transporter YbaL
*	NC_000913	1,679,688	0	T	G	23.2%	123.1 / 11.2	56	G44G (GGT→GGG)	ydgI	putative arginine:ornithine antiporter
*	NC_000913	3,206,435	0	C	T	23.1%	72.1 / 12.4	39	intergenic (‑179/‑28)	ttdR/ttdA	DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha
*	NC_000913	3,740,909	0	T	G	23.1%	126.1 / 12.9	65	V402G (GTG→GGG)	avtA	valine‑‑pyruvate aminotransferase
*	NC_000913	753,125	0	T	A	22.4%	120.6 / 11.8	49	intergenic (‑330/+60)	ybgD/gltA	putative fimbrial protein YbgD/citrate synthase
*	NC_000913	2,326,450	0	T	G	21.3%	106.2 / 12.4	47	G114G (GGT→GGG)	atoB	acetyl‑CoA acetyltransferase

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 =	66 (0.790)	16 (0.210)	15/258	3.1	21.1%	intergenic (+49/‑433)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	4542996 =	58 (0.740)					intergenic (+363/‑119)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
*	?	NC_000913	= 4542690	60 (0.720)	9 (0.120)	9/258	4.5	13.7%	intergenic (+57/‑425)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	= 4542986	57 (0.730)					intergenic (+353/‑129)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
*	?	NC_000913	= 4617670	79 (0.950)	3 (0.040)	3/274	7.0	3.7%	coding (348/780 nt)	deoC	deoxyribose‑phosphate aldolase
	?	NC_000913	4617676 =	76 (0.920)					coding (354/780 nt)	deoC	deoxyribose‑phosphate aldolase
*	?	NC_000913	= 2811074	69 (0.830)	4 (0.050)	3/272	7.0	5.8%	coding (305/531 nt)	mprA	DNA‑binding transcriptional repressor MprA
	?	NC_000913	= 2811131	63 (0.770)					coding (362/531 nt)	mprA	DNA‑binding transcriptional repressor MprA
*	?	NC_000913	= 2726339	NA (NA)	3 (0.040)	3/274	7.0	NA	noncoding (2846/2904 nt)	rrlG	23S ribosomal RNA
	?	NC_000913	2726343 =	NA (NA)					noncoding (2842/2904 nt)	rrlG	23S ribosomal RNA