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 675 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,174,626	0	G	A	46.0%	67.8 / 41.2	74	F180F (TTC→TTT)	ycfT	inner membrane protein
*	NC_000913	1,376,505	0	A	C	45.2%	119.7 / 22.7	73	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
*	NC_000913	535,918	0	A	G	42.5%	112.3 / 28.6	80	E70G (GAG→GGG)	hyi	hydroxypyruvate isomerase
*	NC_000913	3,508,657	0	A	G	42.5%	120.1 / 23.6	81	F386S (TTC→TCC)	yhfW	phosphopentomutase‑related metalloenzyme superfamily protein
*	NC_000913	3,862,638	0	T	C	41.8%	78.2 / 12.0	55	pseudogene (966/1617 nt)	glvC	pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component
*	NC_000913	786,855	0	A	C	41.6%	191.2 / 35.3	115	G247G (GGT→GGG)	gpmA	phosphoglyceromutase 1
*	NC_000913	1,174,605	0	T	C	41.0%	112.1 / 30.7	78	G187G (GGA→GGG)	ycfT	inner membrane protein
*	NC_000913	2,984,441	0	A	C	40.9%	113.4 / 17.4	67	G384G (GGT→GGG)	yqeF	short chain acyltransferase
*	NC_000913	3,508,662	0	T	A	40.7%	131.8 / 38.6	83	E384D (GAA→GAT)	yhfW	phosphopentomutase‑related metalloenzyme superfamily protein
*	NC_000913	1,621,118	0	A	C	40.7%	161.1 / 25.2	91	V7G (GTG→GGG)	eamA	cysteine and O‑acetyl‑L‑serine efflux system
*	NC_000913	3,133,302	0	T	G	40.6%	126.3 / 11.5	69	H219P (CAC→CCC)	yghS	putative ATP‑binding protein
*	NC_000913	925,900	0	A	G	40.3%	133.8 / 17.5	78	noncoding (72/88 nt)	serW	tRNA‑Ser
*	NC_000913	2,511,772	0	A	C	40.0%	113.5 / 23.5	72	V312G (GTG→GGG)	mntH	manganese/divalent cation transporter
*	NC_000913	4,604,344	0	C	T	39.7%	90.9 / 30.9	68	S62F (TCT→TTT)	bglJ	bgl operon transcriptional activator
*	NC_000913	4,488,209	0	G	T	39.5%	142.7 / 30.1	81	G298C (GGC→TGC)	lptG	lipopolysaccharide export ABC permease
*	NC_000913	1,825,061	0	G	A	39.1%	133.8 / 58.1	87	intergenic (‑124/+79)	ves/spy	cold‑ and stress‑inducible protein/periplasmic ATP‑independent protein refolding chaperone, stress‑induced
*	NC_000913	1,222,233	0	G	A	39.0%	116.9 / 41.8	82	pseudogene (60/75 nt)	ycgH	pseudogene; putative ATP‑binding component of a transport system
*	NC_000913	925,912	0	G	C	38.9%	144.6 / 34.4	74	noncoding (60/88 nt)	serW	tRNA‑Ser
*	NC_000913	2,903,692	0	C	A	38.6%	137.3 / 55.7	83	intergenic (+318/+1055)	ygcE/queE	putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis
*	NC_000913	1,487,153	0	C	A	38.2%	119.3 / 24.7	55	intergenic (+190/‑82)	hrpA/ydcF	putative ATP‑dependent helicase/DUF218 superfamily protein, SAM‑binding

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 =	120 (1.270)	7 (0.080)	7/280	14.3	6.1%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	102 (1.150)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	= 4542690	120 (1.270)	4 (0.050)	4/280	16.6	3.6%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	102 (1.150)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)