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	111,512	0	A	G	44.8%	19.3 / 77.5	58	S194S (TCA→TCG)	USA300HOU_RS00520	putative lipoprotein
*	USA300TCH1516_ALE	111,516	0	C	A	44.6%	43.9 / 72.1	56	Q196K (CAA→AAA)	USA300HOU_RS00520	putative lipoprotein
*	USA300TCH1516_ALE	512,643	0	A	G	32.9%	92.4 / 76.5	79	intergenic (+711/‑6052)	recR/speA_2	Recombination protein RecR/Arginine decarboxylase
*	USA300TCH1516_ALE	77,356	0	A	T	22.2%	47.2 / 15.5	27	N94I (AAC→ATC)	USA300HOU_RS00350	Monoacylglycerol lipase

Marginal new junction evidence (sorted from low to high skew)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000731	= 4399	104 (0.950)	4 (0.010)	3/258	11.2	0.76%	intergenic (+364/‑101)	USA300HOU_pUSA300HOUMR0006/cadR	hypothetical protein/cadmium binding protein
	?	NC_012417	= 1963	946 (1.020)					intergenic (+196/+130)	USA300HOU_RS14895/USA300HOU_RS14900	hypothetical protein/hypothetical protein
*	?	CP000731	= 2352	105 (0.950)	4 (0.010)	3/258	11.2	0.76%	intergenic (+132/+36)	USA300HOU_pUSA300HOUMR0003/USA300HOU_pUSA300HOUMR0004	hypothetical protein/hypothetical protein
	?	NC_012417	= 1963	946 (1.020)					intergenic (+196/+130)	USA300HOU_RS14895/USA300HOU_RS14900	hypothetical protein/hypothetical protein
*	?	NC_012417	= 2937	983 (0.970)	10 (0.010)	6/270	40.3	1.1%	intergenic (‑263/–)	USA300HOU_RS14900/–	hypothetical protein/–
	?	NC_012417	= 2949	895 (0.920)					intergenic (‑275/–)	USA300HOU_RS14900/–	hypothetical protein/–
*	?	NC_012417	= 1974	1031 (1.020)	4 (0.000)	3/258	42.5	0.42%	intergenic (+207/+119)	USA300HOU_RS14895/USA300HOU_RS14900	hypothetical protein/hypothetical protein
	?	NC_012417	= 2041	954 (1.030)					intergenic (+274/+52)	USA300HOU_RS14895/USA300HOU_RS14900	hypothetical protein/hypothetical protein