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 420 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,624,517	0	G	T	49.1%	63.4 / 36.1	59	E492* (GAA→TAA)	ppk	polyphosphate kinase, component of RNA degradosome
*	NC_000913	2,326,450	0	T	G	48.4%	91.7 / 23.3	65	G114G (GGT→GGG)	atoB	acetyl‑CoA acetyltransferase
*	NC_000913	3,850,007	0	G	A	45.1%	54.3 / 23.3	51	P44S (CCG→TCG)	uhpB	sensory histidine kinase in two‑component regulatory sytem with UhpA
*	NC_000913	628,652	0	T	G	44.8%	78.7 / 13.3	58	G34G (GGT→GGG)	entA	2,3‑dihydro‑2,3‑dihydroxybenzoate dehydrogenase
*	NC_000913	357,890	0	C	A	44.4%	43.9 / 23.5	45	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	3,423,287	0	G	C	44.0%	73.2 / 26.2	51	intergenic (+93/+136)	yhdZ/rrfF	putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon
*	NC_000913	2,984,441	0	A	C	43.6%	95.1 / 14.8	56	G384G (GGT→GGG)	yqeF	short chain acyltransferase
*	NC_000913	2,228,222	0	T	G	43.5%	110.7 / 13.0	69	pseudogene (388/1287 nt)	mdtQ	pseudogene; putative channel/filament proteins
*	NC_000913	436,504	0	A	C	43.2%	124.2 / 32.6	83	T291P (ACC→CCC)	thiL	thiamine monophosphate kinase
*	NC_000913	1,622,816	0	G	A	43.1%	38.4 / 57.7	58	intergenic (+75/+144)	yneM/dgcZ	inner membrane‑associated protein/diguanylate cyclase, zinc‑sensing
*	NC_000913	3,206,435	0	C	T	42.9%	76.5 / 46.3	71	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	4,536,197	0	A	T	42.9%	69.3 / 58.5	63	intergenic (+166/+417)	yjhR/nanS	pseudogene, helicase family; putative frameshift suppressor/9‑O‑acetyl N‑acetylneuraminic acid esterase
*	NC_000913	3,743,657	0	A	C	42.2%	104.6 / 29.6	64	T309P (ACC→CCC)	yiaK	2,3‑diketo‑L‑gulonate reductase, NADH‑dependent
*	NC_000913	4,378,802	0	A	C	41.9%	110.0 / 15.4	62	V48G (GTA→GGA)	ampC	penicillin‑binding protein; beta‑lactamase, intrinsically weak
*	NC_000913	987,494	0	T	G	41.8%	104.7 / 12.9	55	intergenic (‑512/+91)	ompF/asnS	outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
*	NC_000913	3,508,662	0	T	A	41.8%	78.3 / 20.2	55	E384D (GAA→GAT)	yhfW	phosphopentomutase‑related metalloenzyme superfamily protein
*	NC_000913	503,820	0	T	C	41.5%	55.1 / 12.6	41	K293E (AAA→GAA)	fsr	putative fosmidomycin efflux system protein
*	NC_000913	2,571,036	0	T	G	41.2%	121.7 / 12.9	69	N239T (AAC→ACC)	eutE	aldehyde oxidoreductase, ethanolamine utilization protein
*	NC_000913	15,410	0	T	G	40.8%	86.8 / 13.6	49	intergenic (+112/‑35)	dnaJ/insL1	chaperone Hsp40, DnaK co‑chaperone/IS186 transposase
*	NC_000913	3,578,287	0	T	C	40.8%	71.5 / 13.3	49	E147G (GAA→GGA)	gntR	d‑gluconate inducible gluconate regulon 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	4542682 =	86 (1.260)	4 (0.060)	4/280	12.2	4.7%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	82 (1.280)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)