breseq  version 0.35.4  revision f352f80f4bc9 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,604,344	0	C	T	42.4%	20.0 / 21.6	33	S62F (TCT→TTT)	bglJ	DNA‑binding transcriptional regulator BglJ
*	NC_000913	3,206,435	0	C	T	33.3%	39.6 / 19.5	33	intergenic (‑179/‑28)	ttdR/ttdA	DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha
*	NC_000913	4,111,747	0	G	T	33.3%	55.2 / 14.3	27	N156K (AAC→AAA)	yiiQ	DUF1454 domain‑containing protein YiiQ
*	NC_000913	753,125	0	T	A	31.7%	72.3 / 13.4	41	intergenic (‑330/+60)	ybgD/gltA	putative fimbrial protein YbgD/citrate synthase
*	NC_000913	1,068,173	0	T	G	29.6%	111.3 / 16.2	54	G31G (GGT→GGG)	ymdF	conserved protein YmdF
*	NC_000913	3,608,719	0	G	A	29.6%	35.7 / 10.2	27	intergenic (+70/+32)	zntA/tusA	Zn(2(+))/Cd(2(+))/Pb(2(+)) exporting P‑type ATPase/sulfur transfer protein TusA
*	NC_000913	3,206,444	0	T	A	29.4%	57.0 / 11.0	34	intergenic (‑188/‑19)	ttdR/ttdA	DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha
*	NC_000913	29,496	0	T	A	25.0%	110.5 / 15.6	48	intergenic (+301/‑155)	dapB/carA	4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha

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	= 258675	NA (NA)	5 (0.110)	5/278	3.9	12.8%	noncoding (1/768 nt)	IS1	repeat region
	?	NC_000913	= 293764	34 (0.740)					coding (155/699 nt)	yagL	CP4‑6 prophage; resolvase‑like catalytic domain‑containing protein YagL
*	?	NC_000913	= 291401	NA (NA)	3 (0.070)	3/276	4.8	8.2%	noncoding (1/768 nt)	IS1	repeat region
	?	NC_000913	= 293764	34 (0.740)					coding (155/699 nt)	yagL	CP4‑6 prophage; resolvase‑like catalytic domain‑containing protein YagL