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 670 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,604,344	0	C	T	46.0%	56.4 / 38.5	63	S62F (TCT→TTT)	bglJ	bgl operon transcriptional activator
*	NC_000913	4,381,728	0	A	C	45.7%	108.1 / 23.2	81	G197G (GGT→GGG)	frdA	anaerobic fumarate reductase catalytic and NAD/flavoprotein subunit
*	NC_000913	3,556,200	0	G	A	45.6%	95.1 / 52.4	93	S217F (TCC→TTC)	rtcA	RNA 3'‑terminal phosphate cyclase
*	NC_000913	357,890	0	C	A	44.9%	48.5 / 23.5	49	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	941,713	0	T	G	44.8%	125.6 / 34.5	87	V252G (GTG→GGG)	dmsA	dimethyl sulfoxide reductase, anaerobic, subunit A
*	NC_000913	2,984,441	0	A	C	44.6%	118.6 / 14.0	65	G384G (GGT→GGG)	yqeF	short chain acyltransferase
*	NC_000913	213,341	0	A	G	44.6%	120.8 / 38.2	92	G337G (GGA→GGG)	tilS	tRNA(Ile)‑lysidine synthetase
*	NC_000913	3,556,207	0	T	C	44.0%	120.0 / 34.5	92	S215G (AGT→GGT)	rtcA	RNA 3'‑terminal phosphate cyclase
*	NC_000913	786,855	0	A	C	43.0%	161.4 / 18.7	95	G247G (GGT→GGG)	gpmA	phosphoglyceromutase 1
*	NC_000913	370,869	0	T	G	42.6%	104.9 / 35.2	68	L198W (TTG→TGG)	mhpB	2,3‑dihydroxyphenylpropionate 1,2‑dioxygenase
*	NC_000913	599,576	0	T	G	41.2%	129.7 / 34.8	81	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	1,376,505	0	A	C	41.2%	145.1 / 25.5	80	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
*	NC_000913	370,876	0	C	G	40.9%	120.9 / 31.4	66	S200R (AGC→AGG)	mhpB	2,3‑dihydroxyphenylpropionate 1,2‑dioxygenase
*	NC_000913	357,880	0	T	C	40.7%	74.5 / 16.0	54	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	3,177,748	0	C	A	40.7%	120.8 / 47.3	87	E55* (GAG→TAG)	nudF	ADP‑ribose pyrophosphatase
*	NC_000913	1,413,735	0	A	T	40.2%	132.9 / 46.2	82	Y2* (TAT→TAA)	ydaC	DUF1187 family protein, Rac prophage; putative double‑strand break reduction protein
*	NC_000913	2,001,918	0	A	C	40.2%	172.0 / 20.9	93	intergenic (‑129/+192)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin)
*	NC_000913	2,001,911	0	G	A	40.2%	135.7 / 40.4	97	intergenic (‑122/+199)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin)
*	NC_000913	1,825,061	0	G	A	40.0%	94.6 / 41.9	70	intergenic (‑124/+79)	ves/spy	cold‑ and stress‑inducible protein/periplasmic ATP‑independent protein refolding chaperone, stress‑induced
*	NC_000913	993,913	0	G	C	39.7%	137.0 / 20.8	74	G44G (GGC→GGG)	ssuB	aliphatic sulfonate ABC transporter ATPase

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 =	98 (0.980)	14 (0.150)	13/280	12.2	11.9%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	116 (1.240)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	= 4542690	100 (1.000)	8 (0.090)	8/280	15.1	7.1%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	115 (1.220)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)