breseq  version 0.33.1  revision 8505477f25b3 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence (highest frequency 20 of 148 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,862,664	0	C	G	53.8%	‑3.1 / 30.5	42	pseudogene (940/1617 nt)	glvC	pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component
*	NC_000913	433,649	0	T	G	46.4%	20.0 / 19.8	60	G65G (GGT→GGG)	ribD	fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase
*	NC_000913	3,745,019	0	C	G	43.6%	29.7 / 15.9	39	G72G (GGC→GGG)	yiaN	2,3‑diketo‑L‑gulonate TRAP transporter large permease protein
*	NC_000913	3,505,088	0	C	T	42.1%	41.1 / 15.0	38	S311S (TCG→TCA)	yhfS	FNR‑regulated pyridoxal phosphate‑dependent aminotransferase family protein
*	NC_000913	1,554,013	0	A	C	38.6%	51.9 / 11.7	44	W553G (TGG→GGG)	maeA	malate dehydrogenase, decarboxylating, NAD‑requiring; malic enzyme
*	NC_000913	3,930,718	0	T	G	36.8%	126.2 / 12.2	58	T126P (ACC→CCC)	ravA	hexameric AAA+ MoxR family ATPase, putative molecular chaperone
*	NC_000913	4,429,990	0	A	T	35.0%	64.1 / 17.0	40	M43L (ATG→TTG)	cycA	D‑alanine/D‑serine/glycine transporter
*	NC_000913	827,507	0	T	G	34.4%	132.3 / 12.1	61	D492A (GAC→GCC)	ybhF	putative ABC transporter ATPase
*	NC_000913	2,296,764	0	T	G	34.3%	151.1 / 16.1	67	L87F (TTA→TTC)	ccmB	heme export ABC transporter permease
*	NC_000913	657,676	0	A	C	32.9%	155.4 / 16.2	70	V88G (GTG→GGG)	flc	fluoride efflux channel, dual topology membrane protein
*	NC_000913	3,731,713	0	G	A	32.8%	109.0 / 21.5	61	E195K (GAA→AAA)	xylF	D‑xylose transporter subunit
*	NC_000913	4,622,250	0	A	G	32.7%	112.7 / 19.4	55	E161G (GAG→GGG)	yjjJ	putative protein kinase
*	NC_000913	3,757,668	0	C	T	32.6%	67.1 / 18.7	43	A54T (GCA→ACA)	yiaY	L‑threonine dehydrogenase
*	NC_000913	825,235	0	T	A	32.3%	81.5 / 19.0	64	M292L (ATG→TTG)	ybhR	putative ABC transporter permease
*	NC_000913	2,615,733	0	T	A	32.1%	121.5 / 19.7	56	Y50F (TAT→TTT)	yfgO	putative UPF0118 family inner membrane permease
*	NC_000913	3,862,667	0	G	A	31.8%	57.5 / 10.5	44	pseudogene (937/1617 nt)	glvC	pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component
*	NC_000913	1,383,722	0	G	A	31.8%	112.4 / 24.9	63	F80F (TTC→TTT)	ycjW	LacI family putative transcriptional repressor
*	NC_000913	3,731,724	0	G	A	31.7%	118.0 / 19.5	60	L198L (TTG→TTA)	xylF	D‑xylose transporter subunit
*	NC_000913	4,101,536	0	C	A	31.7%	159.0 / 16.0	60	intergenic (+106/‑154)	sodA/kdgT	superoxide dismutase, Mn/2‑keto‑3‑deoxy‑D‑gluconate transporter
*	NC_000913	1,933,409	0	T	C	31.6%	182.4 / 10.0	79	E399G (GAA→GGA)	edd	6‑phosphogluconate dehydratase

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	4345644 =	109 (0.960)	5 (0.050)	5/292	8.2	4.9%	intergenic (‑86/+36)	yjdF/fumB	DUF2238 family inner membrane protein/anaerobic class I fumarate hydratase (fumarase B)
	?	NC_000913	4345664 =	98 (0.990)					intergenic (‑106/+16)	yjdF/fumB	DUF2238 family inner membrane protein/anaerobic class I fumarate hydratase (fumarase B)
*	?	NC_000913	= 1804091	156 (1.380)	4 (0.040)	4/312	9.1	2.5%	pseudogene (574/1476 nt)	arpB	pseudogene, ankyrin repeats
	?	NC_000913	= 1804275	165 (1.550)					pseudogene (758/1476 nt)	arpB	pseudogene, ankyrin repeats
*	?	NC_000913	= 3741913	98 (0.870)	3 (0.030)	3/306	9.6	2.4%	coding (620/849 nt)	yiaJ	transcriptional repressor for the yiaKLMNO‑lyxK‑sgbHUE operon
	?	NC_000913	= 3742213	150 (1.440)					coding (320/849 nt)	yiaJ	transcriptional repressor for the yiaKLMNO‑lyxK‑sgbHUE operon