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 525 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,443,277	0	A	C	53.2%	68.5 / 100.6	62	V274G (GTA→GGA)	secY	preprotein translocase membrane subunit
*	NC_000913	1,097,581	0	A	G	50.0%	73.3 / 20.6	58	noncoding (72/88 nt)	serX	tRNA‑Ser
*	NC_000913	2,781,645	0	A	C	50.0%	90.5 / 23.5	76	V361G (GTT→GGT)	ypjA	adhesin‑like autotransporter
*	NC_000913	4,604,350	0	C	T	49.3%	54.9 / 42.1	69	S64F (TCT→TTT)	bglJ	bgl operon transcriptional activator
*	NC_000913	730,750	0	A	C	48.9%	57.1 / 13.7	47	T390P (ACC→CCC)	rhsC	Rhs protein with putative toxin domain; putative neighboring cell growth inhibitor
*	NC_000913	2,434,861	0	G	T	47.4%	58.1 / 35.1	57	P259Q (CCA→CAA)	truA	tRNA pseudouridine(38‑40) synthase
*	NC_000913	3,640,981	0	C	T	47.1%	38.6 / 39.0	51	F40F (TTC→TTT)	dtpB	dipeptide and tripeptide permease B
*	NC_000913	4,604,344	0	C	T	47.1%	55.3 / 45.3	69	S62F (TCT→TTT)	bglJ	bgl operon transcriptional activator
*	NC_000913	3,508,657	0	A	G	46.2%	66.7 / 15.3	52	F386S (TTC→TCC)	yhfW	phosphopentomutase‑related metalloenzyme superfamily protein
*	NC_000913	2,984,718	0	G	C	45.7%	92.5 / 38.3	71	P292R (CCG→CGG)	yqeF	short chain acyltransferase
*	NC_000913	599,576	0	T	G	45.2%	89.1 / 25.9	63	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	436,516	0	C	A	45.1%	62.7 / 26.8	51	Q295K (CAA→AAA)	thiL	thiamine monophosphate kinase
*	NC_000913	730,748	0	T	C	44.7%	53.4 / 13.4	47	I389T (ATC→ACC)	rhsC	Rhs protein with putative toxin domain; putative neighboring cell growth inhibitor
*	NC_000913	3,423,297	0	G	C	44.1%	108.4 / 31.6	68	intergenic (+103/+126)	yhdZ/rrfF	putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon
*	NC_000913	3,508,662	0	T	A	43.6%	77.3 / 29.7	55	E384D (GAA→GAT)	yhfW	phosphopentomutase‑related metalloenzyme superfamily protein
*	NC_000913	357,890	0	C	A	43.5%	42.5 / 27.5	46	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	925,900	0	A	G	43.4%	80.5 / 13.9	53	noncoding (72/88 nt)	serW	tRNA‑Ser
*	NC_000913	2,642,689	0	T	G	43.1%	83.7 / 12.0	58	A52A (GCA→GCC)	rodZ	MreB assembly cytoskeletal protein
*	NC_000913	2,434,882	0	T	G	42.6%	94.4 / 19.3	62	Y252S (TAC→TCC)	truA	tRNA pseudouridine(38‑40) synthase
*	NC_000913	3,270,455	0	G	T	42.5%	46.3 / 20.2	47	intergenic (+853/+170)	yhaC/garK	pentapetide repeats‑related protein/glycerate kinase I

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	= 4542690	87 (1.230)	4 (0.060)	4/280	12.8	4.7%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	79 (1.180)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	4542682 =	85 (1.200)	3 (0.040)	3/280	13.6	3.6%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	80 (1.200)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)