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 36 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,021,824	0	T	G	53.3%	‑4.1 / 18.2	15	G533G (GGT→GGG)	ubiB	ubiquinone biosynthesis protein UbiB
*	NC_000913	2,087,406	0	A	C	52.6%	4.8 / 28.3	19	W285G (TGG→GGG)	yeeY	putative DNA‑binding transcriptional regulator YeeY
*	NC_000913	4,296,060	0	C	T	49.4%	6.1 / 110.8	77	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
*	NC_000913	3,812,386	0	C	A	41.7%	7.1 / 22.1	24	L58F (TTG→TTT)	yicR	RadC‑like JAB domain‑containing protein YicR
*	NC_000913	2,318,354	0	A	C	40.0%	27.2 / 18.3	30	V508G (GTG→GGG)	rcsC	sensory histidine kinase RcsC
*	NC_000913	4,414,906	0	T	G	39.3%	27.3 / 24.5	28	V211G (GTG→GGG)	aidB	putative acyl‑CoA dehydrogenase AidB
*	NC_000913	395,288	0	A	T	38.5%	17.2 / 36.0	26	F334I (TTC→ATC)	ampH	peptidoglycan DD‑carboxypeptidase/peptidoglycan DD‑endopeptidase
*	NC_000913	395,291	0	C	G	38.5%	11.4 / 35.7	26	G333R (GGT→CGT)	ampH	peptidoglycan DD‑carboxypeptidase/peptidoglycan DD‑endopeptidase
*	NC_000913	395,294	0	C	G	37.5%	8.7 / 30.3	24	G332R (GGC→CGC)	ampH	peptidoglycan DD‑carboxypeptidase/peptidoglycan DD‑endopeptidase
*	NC_000913	4,020,316	0	A	C	36.7%	39.8 / 19.1	30	T31P (ACC→CCC)	ubiB	ubiquinone biosynthesis protein UbiB
*	NC_000913	2,280,704	0	A	C	36.4%	49.5 / 17.2	33	T25P (ACC→CCC)	radD	putative DNA repair helicase RadD
*	NC_000913	4,333,728	0	C	A	35.7%	36.3 / 15.7	28	V75L (GTA→TTA)	basR	DNA‑binding transcriptional dual regulator BasR
*	NC_000913	821,440	0	C	T	34.2%	48.4 / 19.9	41	F216F (TTC→TTT)	ybhM	Bax1‑I family protein YbhM
*	NC_000913	514,159	0	T	G	32.3%	46.3 / 14.1	31	V56G (GTG→GGG)	cueR	DNA‑binding transcriptional dual regulator CueR
*	NC_000913	4,342,974	0	A	C	31.2%	57.3 / 13.0	32	N355T (AAC→ACC)	melA	alpha‑galactosidase
*	NC_000913	3,479,276	0	G	T	30.8%	47.6 / 10.9	26	Y444* (TAC→TAA)	kefB	K(+) : H(+) antiporter KefB
*	NC_000913	1,232,468	0	A	G	30.3%	44.1 / 11.3	33	intergenic (+14/+32)	umuC/dsbB	DNA polymerase V catalytic protein/protein thiol:quinone oxidoreductase DsbB
*	NC_000913	4,358,391	0	T	G	30.2%	102.7 / 22.6	53	N76T (AAC→ACC)	cadA	lysine decarboxylase 1
*	NC_000913	3,233,922	0	G	T	30.0%	63.2 / 16.0	40	Q75K (CAA→AAA)	higA	antitoxin/DNA‑binding transcriptional repressor HigA
*	NC_000913	2,656,936	0	T	G	29.0%	60.4 / 12.3	31	T50P (ACC→CCC)	fdx	reduced ferredoxin

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	42 (0.760)	10 (0.210)	7/110	1.9	18.3%	intergenic (+57/‑425)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	= 4542986	53 (1.120)					intergenic (+353/‑129)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
*	?	NC_000913	4542682 =	42 (0.760)	5 (0.110)	5/110	2.5	10.1%	intergenic (+49/‑433)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	4542996 =	53 (1.120)					intergenic (+363/‑119)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit