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 1043 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,676,106	0	C	A	49.4%	88.2 / 57.3	81	L240F (TTG→TTT)	yphD	putative sugar ABC transporter permease
*	NC_000913	3,206,435	0	C	T	48.0%	52.2 / 62.3	75	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	5,159	0	G	A	47.9%	78.8 / 75.3	96	intergenic (+139/‑75)	thrC/yaaX	L‑threonine synthase/DUF2502 family putative periplasmic protein
*	NC_000913	2,678,039	0	T	G	47.0%	95.4 / 18.2	66	N108T (AAC→ACC)	yphE	putative sugar ABC transporter ATPase
*	NC_000913	29,496	0	T	A	46.8%	119.9 / 55.6	94	intergenic (+301/‑155)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	354,288	0	T	G	45.5%	142.2 / 37.1	88	V528G (GTG→GGG)	prpE	propionate‑‑CoA ligase
*	NC_000913	1,245,234	0	G	T	45.5%	119.4 / 62.7	99	L25F (TTG→TTT)	ycgY	uncharacterized protein
*	NC_000913	925,900	0	A	G	44.4%	115.9 / 36.2	81	noncoding (72/88 nt)	serW	tRNA‑Ser
*	NC_000913	1,621,118	0	A	C	44.4%	201.0 / 30.9	125	V7G (GTG→GGG)	eamA	cysteine and O‑acetyl‑L‑serine efflux system
*	NC_000913	4,604,344	0	C	T	43.8%	118.3 / 53.0	96	S62F (TCT→TTT)	bglJ	bgl operon transcriptional activator
*	NC_000913	501,575	0	A	C	43.3%	166.7 / 18.0	90	V555G (GTG→GGG)	ybaL	inner membrane putative NAD(P)‑binding transporter
*	NC_000913	941,713	0	T	G	43.0%	112.6 / 41.2	79	V252G (GTG→GGG)	dmsA	dimethyl sulfoxide reductase, anaerobic, subunit A
*	NC_000913	29,486	0	C	A	42.4%	131.8 / 54.2	85	intergenic (+291/‑165)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	646,747	0	T	G	42.4%	145.6 / 25.5	85	T255P (ACC→CCC)	citG	2‑(5''‑triphosphoribosyl)‑3'‑dephosphocoenzyme‑A synthase
*	NC_000913	2,984,441	0	A	C	41.9%	168.7 / 26.0	93	G384G (GGT→GGG)	yqeF	short chain acyltransferase
*	NC_000913	2,678,043	0	C	T	41.8%	80.0 / 27.7	67	E107K (GAA→AAA)	yphE	putative sugar ABC transporter ATPase
*	NC_000913	1,222,596	0	G	A	41.7%	85.6 / 43.8	72	F13F (TTC→TTT)	ymgD	uncharacterized protein
*	NC_000913	40,515	0	G	T	41.6%	136.1 / 47.1	89	Q473K (CAA→AAA)	caiT	putative transporter
*	NC_000913	535,918	0	A	G	41.6%	135.2 / 18.6	89	E70G (GAG→GGG)	hyi	hydroxypyruvate isomerase
*	NC_000913	2,892,195	0	A	T	41.4%	111.2 / 51.9	99	intergenic (‑297/‑19)	cysJ/queD	sulfite reductase, alpha subunit, flavoprotein/6‑pyruvoyl tetrahydrobiopterin synthase (PTPS)

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	1411899 =	176 (1.610)	11 (0.120)	11/246	11.9	7.0%	coding (50/936 nt)	ttcA	tRNA s(2)C32 thioltransferase, iron sulfur cluster protein
	?	NC_000913	= 1434958	145 (1.610)					pseudogene (51/51 nt)	ttcC	pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related
*	?	NC_000913	4542682 =	135 (1.240)	5 (0.050)	5/280	17.3	3.7%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	133 (1.300)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)