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 386 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,206,435	0	C	T	55.8%	10.9 / 65.5	53	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	2,781,645	0	A	C	50.0%	69.8 / 15.2	56	V361G (GTT→GGT)	ypjA	adhesin‑like autotransporter
*	NC_000913	4,378,802	0	A	C	49.0%	73.9 / 12.4	51	V48G (GTA→GGA)	ampC	penicillin‑binding protein; beta‑lactamase, intrinsically weak
*	NC_000913	1,376,505	0	A	C	46.7%	58.9 / 17.4	45	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
*	NC_000913	2,921,177	0	A	C	46.0%	80.5 / 12.1	50	G308G (GGT→GGG)	gudP	putative D‑glucarate transporter
*	NC_000913	4,538,109	0	A	C	45.6%	93.1 / 25.3	68	G219G (GGT→GGG)	nanM	N‑acetylneuraminic acid mutarotase
*	NC_000913	1,825,056	0	G	A	45.3%	70.9 / 38.6	64	intergenic (‑119/+84)	ves/spy	cold‑ and stress‑inducible protein/periplasmic ATP‑independent protein refolding chaperone, stress‑induced
*	NC_000913	993,917	0	A	C	45.3%	73.3 / 12.2	53	V43G (GTG→GGG)	ssuB	aliphatic sulfonate ABC transporter ATPase
*	NC_000913	993,913	0	G	C	44.4%	80.0 / 18.6	54	G44G (GGC→GGG)	ssuB	aliphatic sulfonate ABC transporter ATPase
*	NC_000913	2,903,692	0	C	A	44.3%	83.4 / 44.4	61	intergenic (+318/+1055)	ygcE/queE	putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis
*	NC_000913	3,177,748	0	C	A	43.5%	63.2 / 35.2	62	E55* (GAG→TAG)	nudF	ADP‑ribose pyrophosphatase
*	NC_000913	3,131,440	0	T	C	43.2%	50.2 / 10.1	37	G323G (GGA→GGG)	yghQ	putative inner membrane polysaccharide flippase
*	NC_000913	599,576	0	T	G	42.9%	82.1 / 27.8	56	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	3,665,702	0	C	A	42.5%	145.6 / 68.1	113	A37S (GCG→TCG)	gadX	acid resistance regulon transcriptional activator; autoactivator
*	NC_000913	1,435,727	0	G	A	42.3%	102.9 / 51.5	78	intergenic (‑108/+33)	uspF/ompN	stress‑induced protein, ATP‑binding protein/outer membrane pore protein N, non‑specific
*	NC_000913	1,755,871	0	T	A	41.8%	93.6 / 34.3	67	G58G (GGT→GGA)	pykF	pyruvate kinase I
*	NC_000913	2,252,660	0	G	T	41.4%	91.5 / 32.7	58	E321* (GAA→TAA)	yeiI	putative kinase
*	NC_000913	385,797	0	T	G	41.2%	122.2 / 16.5	69	V189G (GTG→GGG)	tauA	taurine ABC transporter periplasmic binding protein
*	NC_000913	907,602	0	A	C	40.4%	98.9 / 10.4	52	G227G (GGT→GGG)	ybjT	putative NAD‑dependent oxidoreductase
*	NC_000913	786,855	0	A	C	40.3%	109.1 / 12.0	62	G247G (GGT→GGG)	gpmA	phosphoglyceromutase 1

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	82 (1.220)	4 (0.060)	4/280	11.8	4.8%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	81 (1.280)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)