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 567 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	366,526	0	T	G	58.5%	38.3 / 76.3	53	T329P (ACC→CCC)	lacI	lactose‑inducible lac operon transcriptional repressor
*	NC_000913	907,602	0	A	C	52.2%	62.0 / 100.1	67	G227G (GGT→GGG)	ybjT	putative NAD‑dependent oxidoreductase
*	NC_000913	2,984,441	0	A	C	51.4%	81.2 / 130.3	72	G384G (GGT→GGG)	yqeF	short chain acyltransferase
*	NC_000913	3,026,941	0	A	C	50.0%	79.4 / 24.4	66	E392D (GAA→GAC)	guaD	guanine deaminase
*	NC_000913	366,539	0	C	T	47.2%	50.4 / 26.1	53	V324V (GTG→GTA)	lacI	lactose‑inducible lac operon transcriptional repressor
*	NC_000913	646,747	0	T	G	46.3%	104.8 / 16.8	68	T255P (ACC→CCC)	citG	2‑(5''‑triphosphoribosyl)‑3'‑dephosphocoenzyme‑A synthase
*	NC_000913	366,508	0	G	T	45.5%	51.7 / 30.5	56	Q335K (CAA→AAA)	lacI	lactose‑inducible lac operon transcriptional repressor
*	NC_000913	941,713	0	T	G	45.1%	72.6 / 24.0	51	V252G (GTG→GGG)	dmsA	dimethyl sulfoxide reductase, anaerobic, subunit A
*	NC_000913	3,042,604	0	A	C	45.0%	96.1 / 16.2	60	V182G (GTG→GGG)	yqfA	hemolysin III family HylIII inner membrane protein
*	NC_000913	3,743,657	0	A	C	45.0%	72.6 / 32.3	60	T309P (ACC→CCC)	yiaK	2,3‑diketo‑L‑gulonate reductase, NADH‑dependent
*	NC_000913	2,434,882	0	T	G	44.3%	107.9 / 13.7	61	Y252S (TAC→TCC)	truA	tRNA pseudouridine(38‑40) synthase
*	NC_000913	718,659	0	T	A	44.1%	99.6 / 27.1	68	D601V (GAT→GTT)	speF	ornithine decarboxylase isozyme, inducible
*	NC_000913	3,508,662	0	T	A	43.5%	99.8 / 23.7	62	E384D (GAA→GAT)	yhfW	phosphopentomutase‑related metalloenzyme superfamily protein
*	NC_000913	366,522	0	A	C	43.1%	64.3 / 13.4	55	L330R (CTG→CGG)	lacI	lactose‑inducible lac operon transcriptional repressor
*	NC_000913	2,678,039	0	T	G	42.9%	102.5 / 11.9	56	N108T (AAC→ACC)	yphE	putative sugar ABC transporter ATPase
*	NC_000913	3,743,669	0	G	A	42.9%	60.2 / 28.7	56	E313K (GAA→AAA)	yiaK	2,3‑diketo‑L‑gulonate reductase, NADH‑dependent
*	NC_000913	987,494	0	T	G	42.6%	93.5 / 21.2	62	intergenic (‑512/+91)	ompF/asnS	outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
*	NC_000913	3,105,499	0	A	C	42.4%	116.3 / 10.9	69	Y356S (TAC→TCC)	mltC	membrane‑bound lytic murein transglycosylase C
*	NC_000913	1,504,799	0	A	G	42.3%	75.0 / 18.5	53	G361G (GGA→GGG)	insQ	IS609 transposase B
*	NC_000913	366,534	0	C	T	42.0%	65.7 / 18.4	53	R326K (AGA→AAA)	lacI	lactose‑inducible lac operon transcriptional repressor

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	= 1207805	50 (0.680)	7 (0.110)	7/266	10.4	11.0%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	69 (1.050)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	4542682 =	96 (1.300)	5 (0.070)	5/280	12.2	5.8%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	72 (1.040)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	= 4542690	88 (1.190)	4 (0.060)	4/280	12.9	5.0%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	70 (1.010)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)