breseq  version 0.29.0  revision 8f9c342918e4 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence (highest frequency 20 of 263 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	718,690	0	T	G	52.2%	48.5 / 74.5	47	T591P (ACC→CCC)	speF	ornithine decarboxylase isozyme, inducible
*	NC_000913	436,516	0	C	A	51.8%	39.0 / 75.4	55	Q295K (CAA→AAA)	thiL	thiamine monophosphate kinase
*	NC_000913	1,510,395	0	C	A	49.1%	56.3 / 39.2	57	S131R (AGC→AGA)	ydcR	putative DNA‑binding transcriptional regulator and putative aminotransferase
*	NC_000913	357,890	0	C	A	48.5%	20.8 / 16.7	33	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	354,288	0	T	G	48.2%	80.7 / 11.9	56	V528G (GTG→GGG)	prpE	propionate‑‑CoA ligase
*	NC_000913	2,678,039	0	T	G	47.5%	94.4 / 15.5	62	N108T (AAC→ACC)	yphE	putative sugar ABC transporter ATPase
*	NC_000913	3,845,823	0	G	T	47.4%	53.5 / 13.5	39	R449S (CGC→AGC)	uhpT	hexose phosphate transporter
*	NC_000913	2,676,106	0	C	A	46.0%	54.7 / 32.9	63	L240F (TTG→TTT)	yphD	putative sugar ABC transporter permease
*	NC_000913	3,001,164	0	A	C	46.0%	73.5 / 20.5	50	T274P (ACC→CCC)	xdhA	xanthine dehydrogenase, molybdenum binding subunit
*	NC_000913	1,535,785	0	A	G	45.9%	80.7 / 15.0	61	F25S (TTC→TCC)	yddE	PhzC‑PhzF family protein
*	NC_000913	3,717,014	0	T	G	45.6%	87.6 / 13.3	57	G156G (GGT→GGG)	yiaD	multicopy suppressor of bamB; outer membrane lipoprotein
*	NC_000913	993,913	0	G	C	44.2%	89.4 / 11.6	52	G44G (GGC→GGG)	ssuB	aliphatic sulfonate ABC transporter ATPase
*	NC_000913	1,969,794	0	A	C	43.9%	101.7 / 11.5	57	G397G (GGT→GGG)	tap	methyl‑accepting protein IV
*	NC_000913	718,669	0	C	T	43.8%	52.7 / 21.0	48	E598K (GAA→AAA)	speF	ornithine decarboxylase isozyme, inducible
*	NC_000913	1,079,468	0	A	G	43.6%	80.1 / 12.5	55	D55G (GAT→GGT)	putP	proline:sodium symporter
*	NC_000913	3,285,853	0	G	T	43.4%	66.6 / 27.7	53	A126S (GCC→TCC)	agaD	N‑acetylgalactosamine‑specific enzyme IID component of PTS
*	NC_000913	1,825,056	0	G	A	43.2%	39.2 / 14.0	37	intergenic (‑119/+84)	ves/spy	cold‑ and stress‑inducible protein/periplasmic ATP‑independent protein refolding chaperone, stress‑induced
*	NC_000913	1,413,735	0	A	T	42.9%	75.4 / 29.8	56	Y2* (TAT→TAA)	ydaC	DUF1187 family protein, Rac prophage; putative double‑strand break reduction protein
*	NC_000913	4,040,772	0	C	G	42.5%	47.3 / 12.6	40	intergenic (+136/+134)	rrfA/mobB	5S ribosomal RNA of rrnA operon/molybdopterin‑guanine dinucleotide biosynthesis protein B
*	NC_000913	1,825,061	0	G	A	42.1%	43.0 / 15.7	38	intergenic (‑124/+79)	ves/spy	cold‑ and stress‑inducible protein/periplasmic ATP‑independent protein refolding chaperone, stress‑induced

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	60 (1.010)	4 (0.070)	4/280	10.4	6.3%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	62 (1.120)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)