breseq  version 0.39.0   mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence (highest frequency 20 of 230 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,304,522	0	G	T	68.2%	59.4 / 50.2	66	intergenic (+129/+586)	eco/mqo	serine protease inhibitor ecotin/malate:quinone oxidoreductase
*	NC_000913	2,304,523	0	G	C	68.2%	72.4 / 52.6	66	intergenic (+130/+585)	eco/mqo	serine protease inhibitor ecotin/malate:quinone oxidoreductase
*	NC_000913	2,304,537	0	A	G	55.7%	‑3.2 / 67.9	61	intergenic (+144/+571)	eco/mqo	serine protease inhibitor ecotin/malate:quinone oxidoreductase
*	NC_000913	4,040,623	0	G	A	55.4%	5.5 / 206.3	148	noncoding (107/120 nt)	rrfA	5S ribosomal RNA
*	NC_000913	2,304,540	0	C	T	54.8%	‑1.0 / 79.7	62	intergenic (+147/+568)	eco/mqo	serine protease inhibitor ecotin/malate:quinone oxidoreductase
*	NC_000913	2,304,549	0	C	T	49.1%	20.2 / 74.9	59	intergenic (+156/+559)	eco/mqo	serine protease inhibitor ecotin/malate:quinone oxidoreductase
*	NC_000913	4,166,856	0	G	A	43.3%	21.1 / 35.1	30	noncoding (198/1542 nt)	rrsB	16S ribosomal RNA
*	NC_000913	2,151,686	0	G	T	40.6%	14.0 / 11.0	32	intergenic (+40/+25)	yegJ/pphC	DUF2314 domain‑containing protein YegJ/protein‑serine/threonine phosphatase PphC
*	NC_000913	4,296,268	0	T	C	39.7%	48.4 / 77.9	69	intergenic (+474/+168)	gltP/yjcO	glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
*	NC_000913	2,326,450	0	T	G	36.3%	208.7 / 21.9	113	G114G (GGT→GGG)	atoB	acetyl‑CoA acetyltransferase
*	NC_000913	4,033,612	0	T	G	35.4%	246.6 / 18.4	128	G156G (GGT→GGG)	trkH	K(+) transporter TrkH
*	NC_000913	1,435,727	0	G	A	34.8%	120.6 / 27.4	66	intergenic (‑108/+33)	uspF/ompN	universal stress protein F/outer membrane porin N
*	NC_000913	3,177,748	0	C	A	34.8%	131.1 / 37.7	89	E55* (GAG→TAG)	nudF	ADP‑sugar pyrophosphatase
*	NC_000913	2,483,268	0	T	A	34.8%	80.6 / 20.4	46	L24F (TTA→TTT)	emrK	tripartite efflux pump membrane fusion protein EmrK
*	NC_000913	445,558	0	A	C	34.3%	151.3 / 11.7	106	V370G (GTA→GGA)	yajR	putative transport protein YajR
*	NC_000913	1,074,816	0	T	G	32.6%	152.7 / 21.2	94	V192G (GTA→GGA)	rutR	DNA‑binding transcriptional dual regulator RutR
*	NC_000913	1,435,715	0	G	A	32.3%	114.8 / 22.9	65	intergenic (‑96/+45)	uspF/ompN	universal stress protein F/outer membrane porin N
*	NC_000913	581,380	0	C	G	32.2%	294.1 / 248.5	202	intergenic (+1/‑154)	nohD/tfaD	putative DNA‑packaging protein NohD/putative tail fiber assembly protein TfaD
*	NC_000913	2,664,896	0	T	G	32.0%	194.4 / 13.7	97	G169G (GGT→GGG)	yfhR	putative peptidase
*	NC_000913	4,604,344	0	C	T	31.9%	155.9 / 33.3	92	S62F (TCT→TTT)	bglJ	DNA‑binding transcriptional regulator BglJ

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	31 (0.230)	23 (0.180)	22/456	4.0	37.5%	intergenic (+57/‑425)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	= 4542986	47 (0.360)					intergenic (+353/‑129)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
*	?	NC_000913	4542682 =	32 (0.240)	25 (0.190)	22/456	4.0	37.9%	intergenic (+49/‑433)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	4542996 =	51 (0.390)					intergenic (+363/‑119)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
*	?	NC_000913	= 3972942	144 (1.070)	3 (0.020)	3/462	8.6	1.9%	coding (421/1068 nt)	rffG	dTDP‑glucose 4,6‑dehydratase 2
	?	NC_000913	= 3973277	164 (1.250)					coding (756/1068 nt)	rffG	dTDP‑glucose 4,6‑dehydratase 2