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 422 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	298,960	0	A	C	50.7%	76.2 / 113.7	70	Y659D (TAT→GAT)	paoC	PaoABC aldehyde oxidoreductase, Moco‑containing subunit
*	NC_000913	2,326,450	0	T	G	43.6%	133.2 / 14.6	78	G114G (GGT→GGG)	atoB	acetyl‑CoA acetyltransferase
*	NC_000913	1,153,573	0	T	G	43.4%	96.4 / 50.1	76	Y92D (TAC→GAC)	pabC	4‑amino‑4‑deoxychorismate lyase component of para‑aminobenzoate synthase multienzyme complex
*	NC_000913	298,920	0	A	C	43.3%	94.6 / 19.0	67	V672G (GTG→GGG)	paoC	PaoABC aldehyde oxidoreductase, Moco‑containing subunit
*	NC_000913	436,516	0	C	A	42.0%	109.8 / 37.6	81	Q295K (CAA→AAA)	thiL	thiamine monophosphate kinase
*	NC_000913	3,492,834	0	T	G	41.9%	118.6 / 21.3	76	G89G (GGT→GGG)	tsgA	putative transporter
*	NC_000913	298,953	0	A	C	41.8%	89.5 / 19.0	67	V661G (GTG→GGG)	paoC	PaoABC aldehyde oxidoreductase, Moco‑containing subunit
*	NC_000913	2,162,120	0	T	G	40.5%	119.4 / 14.0	74	G219G (GGT→GGG)	iceT	putative citrate/iron‑citrate/zinc‑citrate efflux transporter
*	NC_000913	73,581	0	A	C	40.4%	97.0 / 16.4	57	V314G (GTA→GGA)	thiP	thiamine/thiamine pyrophosphate ABC transporter permease
*	NC_000913	1,376,505	0	A	C	39.7%	123.0 / 19.8	75	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
*	NC_000913	1,174,605	0	T	C	39.2%	127.0 / 11.4	79	G187G (GGA→GGG)	ycfT	inner membrane protein
*	NC_000913	354,288	0	T	G	39.0%	163.0 / 33.0	100	V528G (GTG→GGG)	prpE	propionate‑‑CoA ligase
*	NC_000913	354,282	0	T	G	39.0%	161.5 / 12.6	95	V526G (GTT→GGT)	prpE	propionate‑‑CoA ligase
*	NC_000913	1,312,213	0	G	A	38.8%	109.4 / 47.5	81	L12F (CTT→TTT)	yciA	acyl‑CoA esterase
*	NC_000913	1,842,914	0	A	G	38.2%	81.5 / 12.2	57	M182V (ATG→GTG)	gdhA	glutamate dehydrogenase, NADP‑specific
*	NC_000913	941,713	0	T	G	38.2%	120.8 / 20.5	77	V252G (GTG→GGG)	dmsA	dimethyl sulfoxide reductase, anaerobic, subunit A
*	NC_000913	2,984,441	0	A	C	38.2%	144.1 / 22.9	77	G384G (GGT→GGG)	yqeF	short chain acyltransferase
*	NC_000913	3,206,435	0	C	T	37.4%	125.2 / 39.4	84	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	2,481,804	0	G	A	37.0%	146.1 / 34.1	92	P125S (CCA→TCA)	emrY	putative multidrug efflux system
*	NC_000913	29,496	0	T	A	36.9%	143.7 / 36.5	84	intergenic (+301/‑155)	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	1207790 =	73 (0.830)	15 (0.190)	15/266	8.7	20.2%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	53 (0.670)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1207805	71 (0.800)	7 (0.090)	7/266	13.0	10.7%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	53 (0.670)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	4065076 =	68 (0.770)	3 (0.030)	3/296	17.3	4.3%	coding (691/1404 nt)	yihO	putative sulphoquinovose importer
	?	NC_000913	4065092 =	67 (0.760)					coding (675/1404 nt)	yihO	putative sulphoquinovose importer