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 480 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,376,505	0	A	C	52.6%	74.6 / 103.8	57	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
*	NC_000913	29,486	0	C	A	51.2%	91.9 / 162.9	86	intergenic (+291/‑165)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	3,206,435	0	C	T	50.9%	40.5 / 86.7	53	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	1,487,163	0	C	T	50.0%	58.2 / 39.5	68	intergenic (+200/‑72)	hrpA/ydcF	putative ATP‑dependent helicase/DUF218 superfamily protein, SAM‑binding
*	NC_000913	1,535,785	0	A	G	47.1%	83.7 / 24.0	68	F25S (TTC→TCC)	yddE	PhzC‑PhzF family protein
*	NC_000913	29,496	0	T	A	45.7%	109.4 / 64.1	94	intergenic (+301/‑155)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	3,585,086	0	A	C	45.6%	105.8 / 21.8	69	Y580D (TAC→GAC)	ggt	gamma‑glutamyltranspeptidase
*	NC_000913	17,041	0	G	C	45.0%	100.8 / 28.6	61	intergenic (‑81/‑448)	mokC/nhaA	regulatory protein for HokC, overlaps CDS of hokC/sodium‑proton antiporter
*	NC_000913	357,890	0	C	A	43.1%	60.0 / 26.8	52	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	1,504,799	0	A	G	42.4%	81.4 / 32.0	68	G361G (GGA→GGG)	insQ	IS609 transposase B
*	NC_000913	2,835,219	0	A	C	42.2%	107.1 / 22.5	64	V736G (GTT→GGT)	hypF	carbamoyl phosphate phosphatase and [NiFe] hydrogenase maturation protein
*	NC_000913	1,487,157	0	C	A	42.0%	103.1 / 32.5	69	intergenic (+194/‑78)	hrpA/ydcF	putative ATP‑dependent helicase/DUF218 superfamily protein, SAM‑binding
*	NC_000913	2,984,441	0	A	C	41.9%	116.7 / 13.1	62	G384G (GGT→GGG)	yqeF	short chain acyltransferase
*	NC_000913	3,556,200	0	G	A	41.8%	89.1 / 33.5	67	S217F (TCC→TTC)	rtcA	RNA 3'‑terminal phosphate cyclase
*	NC_000913	1,506,038	0	A	C	41.6%	152.8 / 11.7	77	F15V (TTT→GTT)	ydcO	BenE family inner membrane putative transporter
*	NC_000913	1,487,150	0	G	A	41.4%	94.0 / 29.6	72	intergenic (+187/‑85)	hrpA/ydcF	putative ATP‑dependent helicase/DUF218 superfamily protein, SAM‑binding
*	NC_000913	599,576	0	T	G	41.4%	148.8 / 38.3	87	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	4,258,974	0	T	G	41.2%	117.4 / 12.1	68	G411G (GGT→GGG)	dinF	oxidative stress resistance protein; putative MATE family efflux pump; UV and mitomycin C inducible protein
*	NC_000913	4,536,197	0	A	T	41.1%	96.8 / 64.7	73	intergenic (+166/+417)	yjhR/nanS	pseudogene, helicase family; putative frameshift suppressor/9‑O‑acetyl N‑acetylneuraminic acid esterase
*	NC_000913	2,958,771	0	A	T	41.0%	100.0 / 27.3	61	D38E (GAT→GAA)	ptrA	protease III

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	62 (0.800)	10 (0.150)	8/266	10.7	15.8%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	51 (0.740)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	1207790 =	60 (0.780)	8 (0.120)	8/266	10.7	13.0%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	54 (0.780)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related