breseq  version 0.33.1  revision 8505477f25b3 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
*	USA300TCH1516_ALE	512,643	0	A	G	57.1%	43.9 / 85.6	70	intergenic (+711/‑6052)	recR/speA_2	Recombination protein RecR/Arginine decarboxylase
*	USA300TCH1516_ALE	111,512	0	A	G	30.2%	76.5 / 39.0	53	S194S (TCA→TCG)	USA300HOU_RS00520	putative lipoprotein
*	USA300TCH1516_ALE	111,516	0	C	A	26.0%	110.4 / 34.0	50	Q196K (CAA→AAA)	USA300HOU_RS00520	putative lipoprotein

Marginal new junction evidence (sorted from low to high skew)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 2850830	28 (0.860)	3 (0.100)	3/268	3.8	10.3%	intergenic (+29/+90)	pcp/USA300HOU_RS14605	Pyrrolidone‑carboxylate peptidase/hypothetical protein
	?	USA300TCH1516_ALE	= 2850851	27 (0.910)					intergenic (+50/+69)	pcp/USA300HOU_RS14605	Pyrrolidone‑carboxylate peptidase/hypothetical protein
*	?	CP000731	= 1526	145 (0.830)	5 (0.010) +TTG	5/290	24.6	1.2%	intergenic (+311/‑545)	repA/USA300HOU_pUSA300HOUMR0003	replication protein A/hypothetical protein
	?	NC_012417	= 997	692 (0.900)					intergenic (+9/+6)	USA300HOU_RS14890/USA300HOU_RS15665	replication protein/hypothetical protein