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 32 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	310,934	0	A	C	51.4%	20.4 / 55.0	35	F135V (TTC→GTC)	ecpR	DNA‑binding transcriptional dual regulator MatA
*	NC_000913	2,280,704	0	A	C	47.1%	9.3 / 14.6	17	T25P (ACC→CCC)	radD	putative DNA repair helicase RadD
*	NC_000913	4,296,060	0	C	T	43.6%	34.5 / 99.7	78	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
*	NC_000913	4,020,316	0	A	C	38.7%	51.6 / 12.5	32	T31P (ACC→CCC)	ubiB	ubiquinone biosynthesis protein UbiB
*	NC_000913	1,374,034	0	G	.	38.2%	66.8 / 54.1	34	coding (813/882 nt)	ycjO	putative ABC transporter membrane subunit YcjO
*	NC_000913	1,232,468	0	A	G	37.5%	25.6 / 14.5	32	intergenic (+14/+32)	umuC/dsbB	DNA polymerase V catalytic protein/protein thiol:quinone oxidoreductase DsbB
*	NC_000913	1,374,036	0	T	G	36.1%	37.4 / 40.8	36	L272R (CTC→CGC)	ycjO	putative ABC transporter membrane subunit YcjO
*	NC_000913	1,374,038	0	T	C	36.1%	34.2 / 32.1	36	F273L (TTC→CTC) ‡	ycjO	putative ABC transporter membrane subunit YcjO
*	NC_000913	1,374,039	0	T	G	36.1%	38.1 / 41.9	36	F273C (TTC→TGC) ‡	ycjO	putative ABC transporter membrane subunit YcjO
*	NC_000913	1,374,040	0	C	T	35.1%	30.1 / 35.5	37	F273F (TTC→TTT) ‡	ycjO	putative ABC transporter membrane subunit YcjO
*	NC_000913	4,414,906	0	T	G	34.8%	28.9 / 20.4	23	V211G (GTG→GGG)	aidB	putative acyl‑CoA dehydrogenase AidB
*	NC_000913	859,054	0	G	A	32.3%	35.5 / 18.0	31	S3F (TCT→TTT)	ybiU	DUF1479 domain‑containing protein YbiU
*	NC_000913	395,291	0	C	G	32.1%	38.7 / 26.4	28	G333R (GGT→CGT)	ampH	peptidoglycan DD‑carboxypeptidase/peptidoglycan DD‑endopeptidase
*	NC_000913	395,288	0	A	T	30.8%	35.9 / 25.9	26	F334I (TTC→ATC)	ampH	peptidoglycan DD‑carboxypeptidase/peptidoglycan DD‑endopeptidase
*	NC_000913	1,632,523	0	A	C	30.8%	77.6 / 12.5	39	intergenic (‑238/‑367)	ydfJ/ynfT	putative transporter YdfJ/Qin prophage; protein YnfT
*	NC_000913	3,644,918	0	T	G	29.6%	110.6 / 12.7	56	T89P (ACC→CCC)	prlC	oligopeptidase A
*	NC_000913	821,440	0	C	T	29.4%	69.9 / 28.1	51	F216F (TTC→TTT)	ybhM	Bax1‑I family protein YbhM
*	NC_000913	3,233,922	0	G	T	28.6%	49.8 / 13.2	28	Q75K (CAA→AAA)	higA	antitoxin/DNA‑binding transcriptional repressor HigA
*	NC_000913	3,563,481	0	T	G	28.6%	68.8 / 24.0	35	V490G (GTG→GGG)	glpD	aerobic glycerol 3‑phosphate dehydrogenase
*	NC_000913	2,160,604	0	A	C	28.0%	50.8 / 10.6	25	Y740S (TAC→TCC)	mdtC	multidrug efflux pump RND permease subunit MdtC

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	= 291401	NA (NA)	6 (0.100)	5/128	2.4	8.6%	noncoding (1/768 nt)	IS1	repeat region
	?	NC_000913	= 481015	64 (1.100)					intergenic (‑307/+239)	tomB/acrB	protein that modulates Hha toxicity/multidrug efflux pump RND permease AcrB
*	?	NC_000913	516635 =	64 (1.100)	3 (0.060)	3/110	2.8	4.8%	coding (53/780 nt)	fetB	putative iron ABC exporter membrane subunit FetB
	?	NC_000913	= 516631	63 (1.260)					coding (49/780 nt)	fetB	putative iron ABC exporter membrane subunit FetB
*	?	NC_000913	= 477256	51 (0.880)	3 (0.050)	3/128	3.1	5.6%	coding (1362/1551 nt)	pdeB	c‑di‑GMP phosphodiesterase PdeB
	?	NC_000913	= 1979270	NA (NA)					noncoding (1/768 nt)	IS1	repeat region