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 174 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	535,920	0	C	T	59.5%	87.4 / ‑2.7	42	R71C (CGC→TGC)	hyi	hydroxypyruvate isomerase
*	NC_000913	2,483,268	0	T	A	50.9%	45.2 / 86.4	57	L24F (TTA→TTT)	emrK	multidrug resistance efflux pump membrane fusion protein
*	NC_000913	802,118	0	A	C	48.7%	44.8 / 12.6	39	T78P (ACC→CCC)	ybhI	putative DASS family tricarboxylate or dicarboxylate transporter
*	NC_000913	4,042,993	0	C	T	47.2%	20.9 / 16.5	36	F193F (TTC→TTT)	srkA	Cpx stress response Thr/Ser protein kinase; MazF antagonist protein
*	NC_000913	941,713	0	T	G	47.2%	73.5 / 22.2	53	V252G (GTG→GGG)	dmsA	dimethyl sulfoxide reductase, anaerobic, subunit A
*	NC_000913	4,111,747	0	G	T	45.9%	78.3 / 33.4	61	N156K (AAC→AAA)	yiiQ	DUF1454 family putative periplasmic protein
*	NC_000913	3,133,302	0	T	G	45.5%	45.8 / 13.9	44	H219P (CAC→CCC)	yghS	putative ATP‑binding protein
*	NC_000913	357,890	0	C	A	44.8%	25.9 / 14.9	29	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	2,326,450	0	T	G	44.4%	75.2 / 13.6	45	G114G (GGT→GGG)	atoB	acetyl‑CoA acetyltransferase
*	NC_000913	213,341	0	A	G	43.9%	53.0 / 11.1	41	G337G (GGA→GGG)	tilS	tRNA(Ile)‑lysidine synthetase
*	NC_000913	436,516	0	C	A	43.9%	60.2 / 17.7	41	Q295K (CAA→AAA)	thiL	thiamine monophosphate kinase
*	NC_000913	4,346,675	0	T	G	43.9%	57.5 / 12.6	41	T218P (ACC→CCC)	fumB	anaerobic class I fumarate hydratase (fumarase B)
*	NC_000913	1,133,857	0	A	G	43.2%	59.0 / 10.2	45	Q19R (CAG→CGG)	flgF	flagellar component of cell‑proximal portion of basal‑body rod
*	NC_000913	1,755,871	0	T	A	42.9%	54.3 / 20.5	42	G58G (GGT→GGA)	pykF	pyruvate kinase I
*	NC_000913	4,286,504	0	T	A	42.6%	73.2 / 24.4	54	K290* (AAA→TAA)	acs	acetyl‑CoA synthetase
*	NC_000913	357,873	0	C	T	42.3%	23.5 / 10.1	26	S273N (AGC→AAC)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	2,248,431	0	A	C	41.3%	81.8 / 14.2	46	G34G (GGT→GGG)	lysP	lysine transporter
*	NC_000913	2,617,681	0	A	C	41.3%	76.4 / 11.2	46	Y35S (TAC→TCC)	yfgD	putative oxidoreductase
*	NC_000913	987,494	0	T	G	41.2%	82.5 / 12.2	51	intergenic (‑512/+91)	ompF/asnS	outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
*	NC_000913	3,423,287	0	G	C	41.2%	47.8 / 17.3	34	intergenic (+93/+136)	yhdZ/rrfF	putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon

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 =	74 (1.490)	5 (0.110)	5/280	7.2	7.4%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	56 (1.200)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)