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 31 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	52.2%	8.5 / 31.1	23	F135V (TTC→GTC)	ecpR	DNA‑binding transcriptional dual regulator MatA
*	NC_000913	2,280,704	0	A	C	50.0%	‑2.9 / 28.8	20	T25P (ACC→CCC)	radD	putative DNA repair helicase RadD
*	NC_000913	4,296,060	0	C	T	48.6%	2.5 / 104.0	72	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
*	NC_000913	2,560,039	0	T	G	45.8%	21.4 / 10.4	24	G394G (GGT→GGG)	intZ	CPZ‑55 prophage; putative phage integrase IntZ
*	NC_000913	2,223,410	0	T	G	41.7%	20.0 / 20.3	24	V409G (GTG→GGG)	dld	D‑lactate dehydrogenase
*	NC_000913	3,933,973	0	A	G	39.1%	15.0 / 14.0	23	K66E (AAA→GAA)	rbsA	ribose ABC transporter ATP binding subunit
*	NC_000913	821,440	0	C	T	37.0%	35.5 / 37.9	46	F216F (TTC→TTT)	ybhM	Bax1‑I family protein YbhM
*	NC_000913	408,367	0	T	G	36.4%	27.1 / 14.2	22	V64G (GTG→GGG)	ppnP	nucleoside phosphorylase PpnP
*	NC_000913	1,374,034	0	G	.	33.3%	39.7 / 26.8	21	coding (813/882 nt)	ycjO	putative ABC transporter membrane subunit YcjO
*	NC_000913	3,196,811	0	A	C	33.3%	51.5 / 21.4	33	V944G (GTG→GGG)	glnE	fused glutamine synthetase deadenylase/glutamine synthetase adenylyltransferase
*	NC_000913	2,357,894	0	C	A	32.1%	47.0 / 16.7	28	pseudogene (79/186 nt)	ypaA	protein YpaA
*	NC_000913	794,976	0	T	C	31.4%	48.1 / 17.3	36	intergenic (+54/‑113)	acrZ/modA	multidrug efflux pump accessory protein AcrZ/molybdate ABC transporter periplasmic binding protein
*	NC_000913	4,414,906	0	T	G	29.2%	41.6 / 13.0	24	V211G (GTG→GGG)	aidB	putative acyl‑CoA dehydrogenase AidB
*	NC_000913	2,794,787	0	C	T	29.0%	35.5 / 14.9	31	P179S (CCG→TCG)	gabP	4‑aminobutyrate:H(+) symporter
*	NC_000913	2,349,621	0	A	C	28.6%	35.6 / 15.5	21	intergenic (‑149/‑66)	inaA/yfaH	putative lipopolysaccharide kinase InaA/putative uncharacterized protein YfaH
*	NC_000913	1,990,872	0	T	G	28.1%	56.6 / 15.4	32	L398V (TTG→GTG)	tyrP	tyrosine:H(+) symporter
*	NC_000913	412,298	0	A	G	28.0%	40.9 / 10.3	25	S62P (TCC→CCC)	araJ	putative transport protein AraJ
*	NC_000913	1,374,036	0	T	G	28.0%	35.8 / 20.5	25	L272R (CTC→CGC)	ycjO	putative ABC transporter membrane subunit YcjO
*	NC_000913	1,374,038	0	T	C	28.0%	37.1 / 13.4	25	F273L (TTC→CTC) ‡	ycjO	putative ABC transporter membrane subunit YcjO
*	NC_000913	1,374,039	0	T	G	28.0%	38.0 / 20.5	25	F273C (TTC→TGC) ‡	ycjO	putative ABC transporter membrane subunit YcjO

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)	4 (0.070)	4/128	2.8	7.4%	noncoding (1/768 nt)	IS1	repeat region
	?	NC_000913	= 485253	50 (0.930)					coding (367/1194 nt)	acrA	multidrug efflux pump membrane fusion lipoprotein AcrA
*	?	NC_000913	= 291401	NA (NA)	4 (0.070)	4/128	2.8	5.6%	noncoding (1/768 nt)	IS1	repeat region
	?	NC_000913	= 480989	68 (1.260)					intergenic (‑281/+265)	tomB/acrB	protein that modulates Hha toxicity/multidrug efflux pump RND permease AcrB
*	?	NC_000913	= 258675	NA (NA)	6 (0.110)	4/128	2.8	6.8%	noncoding (1/768 nt)	IS1	repeat region
	?	NC_000913	= 480930	82 (1.520)					intergenic (‑222/+324)	tomB/acrB	protein that modulates Hha toxicity/multidrug efflux pump RND permease AcrB