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 410 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,326,450	0	T	G	58.3%	35.2 / 67.1	48	G114G (GGT→GGG)	atoB	acetyl‑CoA acetyltransferase
*	NC_000913	357,890	0	C	A	51.6%	0.7 / 32.6	31	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	357,880	0	T	C	50.0%	20.4 / 11.6	31	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	357,875	0	A	T	48.4%	28.3 / 12.6	32	N272K (AAT→AAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	802,118	0	A	C	47.6%	61.1 / 17.9	63	T78P (ACC→CCC)	ybhI	putative DASS family tricarboxylate or dicarboxylate transporter
*	NC_000913	646,747	0	T	G	44.1%	86.2 / 14.9	59	T255P (ACC→CCC)	citG	2‑(5''‑triphosphoribosyl)‑3'‑dephosphocoenzyme‑A synthase
*	NC_000913	786,855	0	A	C	43.9%	85.8 / 12.9	59	G247G (GGT→GGG)	gpmA	phosphoglyceromutase 1
*	NC_000913	2,185,199	0	T	G	43.8%	116.9 / 31.0	90	T35P (ACC→CCC)	thiM	hydoxyethylthiazole kinase
*	NC_000913	2,040,081	0	T	A	43.6%	47.8 / 32.0	55	Y202N (TAT→AAT)	yedY	membrane‑anchored, periplasmic TMAO, DMSO reductase
*	NC_000913	599,576	0	T	G	43.1%	86.0 / 34.2	67	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	753,125	0	T	A	42.5%	53.8 / 26.9	47	intergenic (‑330/+60)	ybgD/gltA	putative fimbrial‑like adhesin protein/citrate synthase
*	NC_000913	357,873	0	C	T	41.9%	21.4 / 14.9	31	S273N (AGC→AAC)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	1,080,837	0	G	T	41.7%	61.0 / 29.2	60	intergenic (+24/‑519)	putP/efeU	proline:sodium symporter/ferrous iron permease (pseudogene)
*	NC_000913	599,579	0	T	G	40.9%	104.7 / 15.3	67	V289G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	2,040,075	0	C	G	40.8%	50.6 / 22.0	55	L200V (CTG→GTG)	yedY	membrane‑anchored, periplasmic TMAO, DMSO reductase
*	NC_000913	3,042,604	0	A	C	40.7%	78.9 / 14.8	54	V182G (GTG→GGG)	yqfA	hemolysin III family HylIII inner membrane protein
*	NC_000913	802,111	0	G	T	39.1%	74.9 / 24.9	64	A75A (GCG→GCT)	ybhI	putative DASS family tricarboxylate or dicarboxylate transporter
*	NC_000913	29,496	0	T	A	39.0%	85.2 / 34.2	59	intergenic (+301/‑155)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	4,378,802	0	A	C	39.0%	98.4 / 22.9	59	V48G (GTA→GGA)	ampC	penicillin‑binding protein; beta‑lactamase, intrinsically weak
*	NC_000913	29,486	0	C	A	38.3%	83.6 / 30.4	61	intergenic (+291/‑165)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase

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	88 (1.140)	3 (0.040)	3/280	14.1	3.5%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	85 (1.170)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	4542682 =	94 (1.220)	3 (0.040)	3/280	14.1	3.3%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	85 (1.170)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)