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	111,516	0	C	A	46.2%	0.3 / 27.1	27	Q196K (CAA→AAA)	USA300HOU_RS00520	putative lipoprotein
*	USA300TCH1516_ALE	111,512	0	A	G	38.5%	17.3 / 16.5	28	S194S (TCA→TCG)	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
*	?	CP000731	= 1526	45 (0.790)	4 (0.010) +TTG	4/250	7.7	1.4%	intergenic (+311/‑545)	repA/USA300HOU_pUSA300HOUMR0003	replication protein A/hypothetical protein
	?	NC_012417	= 997	548 (0.910)					intergenic (+9/+6)	USA300HOU_RS14890/USA300HOU_RS15665	replication protein/hypothetical protein
*	?	NC_012417	= 997	548 (0.910)	5 (0.010)	5/234	31.7	0.98%	intergenic (+9/+6)	USA300HOU_RS14890/USA300HOU_RS15665	replication protein/hypothetical protein
	?	NC_012417	= 1001	510 (0.920)					intergenic (+13/+2)	USA300HOU_RS14890/USA300HOU_RS15665	replication protein/hypothetical protein
*	?	NC_012417	= 2937	607 (1.010)	3 (0.010)	3/246	34.3	0.53%	intergenic (‑263/–)	USA300HOU_RS14900/–	hypothetical protein/–
	?	NC_012417	= 2949	551 (0.950)					intergenic (‑275/–)	USA300HOU_RS14900/–	hypothetical protein/–