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 26 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,087,406	0	A	C	58.3%	‑6.1 / 14.2	12	W285G (TGG→GGG)	yeeY	putative DNA‑binding transcriptional regulator YeeY
*	NC_000913	395,288	0	A	T	44.0%	9.4 / 36.1	25	F334I (TTC→ATC)	ampH	peptidoglycan DD‑carboxypeptidase/peptidoglycan DD‑endopeptidase
*	NC_000913	4,296,060	0	C	T	44.0%	35.1 / 98.7	75	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
*	NC_000913	310,934	0	A	C	42.9%	28.6 / 22.3	28	F135V (TTC→GTC)	ecpR	DNA‑binding transcriptional dual regulator MatA
*	NC_000913	1,374,038	0	T	C	42.9%	17.1 / 38.3	35	F273L (TTC→CTC) ‡	ycjO	putative ABC transporter membrane subunit YcjO
*	NC_000913	3,017,405	0	A	C	42.1%	17.2 / 10.9	19	D449A (GAC→GCC)	ygfK	putative oxidoreductase, Fe‑S subunit
*	NC_000913	1,374,034	0	G	.	41.4%	48.9 / 49.8	29	coding (813/882 nt)	ycjO	putative ABC transporter membrane subunit YcjO
*	NC_000913	1,374,039	0	T	G	40.5%	22.7 / 53.1	37	F273C (TTC→TGC) ‡	ycjO	putative ABC transporter membrane subunit YcjO
*	NC_000913	1,374,040	0	C	T	40.5%	13.9 / 42.8	37	F273F (TTC→TTT) ‡	ycjO	putative ABC transporter membrane subunit YcjO
*	NC_000913	1,875,838	0	A	C	40.0%	23.7 / 12.5	20	T56P (ACC→CCC)	nimT	2‑nitroimidazole exporter
*	NC_000913	1,374,036	0	T	G	39.4%	25.3 / 43.1	33	L272R (CTC→CGC)	ycjO	putative ABC transporter membrane subunit YcjO
*	NC_000913	2,280,704	0	A	C	38.9%	20.1 / 13.2	18	T25P (ACC→CCC)	radD	putative DNA repair helicase RadD
*	NC_000913	1,958,932	0	G	C	37.5%	20.6 / 11.5	16	A112G (GCT→GGT)	cutC	protein CutC
*	NC_000913	4,414,906	0	T	G	37.0%	29.4 / 26.1	27	V211G (GTG→GGG)	aidB	putative acyl‑CoA dehydrogenase AidB
*	NC_000913	1,702,245	0	A	C	34.6%	49.5 / 10.3	26	T5P (ACC→CCC)	add	adenosine deaminase
*	NC_000913	395,291	0	C	G	34.5%	31.4 / 33.9	29	G333R (GGT→CGT)	ampH	peptidoglycan DD‑carboxypeptidase/peptidoglycan DD‑endopeptidase
*	NC_000913	794,976	0	T	C	34.4%	45.1 / 10.9	32	intergenic (+54/‑113)	acrZ/modA	multidrug efflux pump accessory protein AcrZ/molybdate ABC transporter periplasmic binding protein
*	NC_000913	1,927,854	0	A	C	34.4%	54.3 / 14.0	32	V329G (GTG→GGG)	ptrB	oligopeptidase B
*	NC_000913	395,294	0	C	G	31.8%	31.1 / 20.9	22	G332R (GGC→CGC)	ampH	peptidoglycan DD‑carboxypeptidase/peptidoglycan DD‑endopeptidase
*	NC_000913	2,710,279	0	A	C	31.2%	60.5 / 18.0	32	intergenic (‑115/‑141)	rseD/nadB	rpoE leader peptide/L‑aspartate oxidase

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	4542682 =	52 (1.020)	5 (0.110)	5/110	2.0	9.8%	intergenic (+49/‑433)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	4542996 =	47 (1.080)					intergenic (+363/‑119)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
*	?	NC_000913	= 4542690	52 (1.020)	4 (0.090)	4/110	2.3	8.0%	intergenic (+57/‑425)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	= 4542986	47 (1.080)					intergenic (+353/‑129)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
*	?	NC_000913	= 1603798	34 (0.670)	6 (0.120)	5/128	2.3	15.0%	coding (780/1029 nt)	lsrC	Autoinducer‑2 ABC transporter membrane subunit LsrC
	?	NC_000913	1603802 =	34 (0.670)					coding (784/1029 nt)	lsrC	Autoinducer‑2 ABC transporter membrane subunit LsrC