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 338 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	599,576	0	T	G	54.9%	45.1 / 82.5	51	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	4,258,974	0	T	G	52.8%	57.2 / 84.1	53	G411G (GGT→GGG)	dinF	oxidative stress resistance protein; putative MATE family efflux pump; UV and mitomycin C inducible protein
*	NC_000913	357,890	0	C	A	47.1%	31.9 / 16.3	34	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	2,248,431	0	A	C	46.4%	90.5 / 27.4	70	G34G (GGT→GGG)	lysP	lysine transporter
*	NC_000913	3,206,435	0	C	T	46.3%	51.3 / 52.5	67	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	436,516	0	C	A	44.7%	102.9 / 35.5	77	Q295K (CAA→AAA)	thiL	thiamine monophosphate kinase
*	NC_000913	298,960	0	A	C	44.4%	79.1 / 17.8	54	Y659D (TAT→GAT)	paoC	PaoABC aldehyde oxidoreductase, Moco‑containing subunit
*	NC_000913	869,107	0	A	G	43.9%	55.0 / 10.9	41	I530V (ATT→GTT)	gsiA	glutathione ABC transporter ATPase
*	NC_000913	3,508,657	0	A	G	43.4%	63.6 / 12.8	54	F386S (TTC→TCC)	yhfW	phosphopentomutase‑related metalloenzyme superfamily protein
*	NC_000913	4,279,468	0	C	G	43.3%	97.4 / 20.1	60	G330G (GGC→GGG)	ghxP	guanine/hypoxanthine permease, high affinity; guanine/hypoxanthine:H+ symporter
*	NC_000913	2,337,723	0	A	C	43.2%	61.0 / 12.9	44	G566G (GGT→GGG)	gyrA	DNA gyrase (type II topoisomerase), subunit A
*	NC_000913	4,107,878	0	T	G	42.4%	82.6 / 21.7	61	G109G (GGT→GGG)	pfkA	6‑phosphofructokinase I
*	NC_000913	993,913	0	G	C	42.3%	93.8 / 11.7	52	G44G (GGC→GGG)	ssuB	aliphatic sulfonate ABC transporter ATPase
*	NC_000913	5,159	0	G	A	42.1%	62.8 / 29.1	57	intergenic (+139/‑75)	thrC/yaaX	L‑threonine synthase/DUF2502 family putative periplasmic protein
*	NC_000913	446,976	0	A	C	41.9%	90.4 / 20.9	62	W244G (TGG→GGG)	cyoE	protoheme IX farnesyltransferase
*	NC_000913	2,147,733	0	T	G	41.9%	122.0 / 17.5	75	G20G (GGT→GGG)	yegD	Hsp70 chaperone family protein
*	NC_000913	1,755,871	0	T	A	41.5%	90.2 / 38.7	65	G58G (GGT→GGA)	pykF	pyruvate kinase I
*	NC_000913	1,621,118	0	A	C	41.4%	104.5 / 19.4	70	V7G (GTG→GGG)	eamA	cysteine and O‑acetyl‑L‑serine efflux system
*	NC_000913	1,174,610	0	A	C	41.3%	102.5 / 14.8	64	W186G (TGG→GGG)	ycfT	inner membrane protein
*	NC_000913	2,483,268	0	T	A	41.3%	76.1 / 28.3	64	L24F (TTA→TTT)	emrK	multidrug resistance efflux pump membrane fusion protein

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	67 (0.980)	13 (0.210)	12/266	7.0	19.3%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	49 (0.810)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	1207790 =	61 (0.900)	6 (0.100)	6/266	10.1	10.1%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	52 (0.860)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1209618	62 (0.910)	11 (0.180)	3/268	12.4	15.4%	pseudogene (2/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
	?	NC_000913	2471897 =	65 (1.060)					pseudogene (226/579 nt)	yfdL	pseudogene, CPS‑53 (KpLE1) prophage;Phage or Prophage Related