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
*	CP000730	512,643	0	A	G	48.1%	19.3 / 183.1	129	intergenic (+711/‑150)	recR/rrs1	recombination protein RecR/16S ribosomal RNA
*	CP000730	111,512	0	A	G	44.8%	40.2 / 125.2	96	S194S (TCA→TCG)	USA300HOU_0110	possible staphylococcal tandem lipoprotein
*	CP000730	111,516	0	C	A	44.2%	82.0 / 118.7	96	Q196K (CAA→AAA)	USA300HOU_0110	possible staphylococcal tandem lipoprotein
*	CP000730	110,660	0	T	A	27.5%	120.3 / 58.2	69	I173I (ATT→ATA)	USA300HOU_0109	staphylococcal tandem lipoprotein
*	CP000730	110,651	0	C	T	22.2%	130.2 / 33.1	63	D170D (GAC→GAT)	USA300HOU_0109	staphylococcal tandem lipoprotein

Marginal new junction evidence (sorted from low to high skew)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	365029 =	72 (1.130)	8 (0.140)	7/248	7.9	10.2%	intergenic (+39/+66)	nupC/USA300HOU_0334	possible CNT family concentrative nucleoside transporter/SSS family solute:sodium (Na+) symporter
	?	CP000730	365083 =	75 (1.300)					intergenic (+93/+12)	nupC/USA300HOU_0334	possible CNT family concentrative nucleoside transporter/SSS family solute:sodium (Na+) symporter
*	?	CP000730	329202 =	83 (1.310)	6 (0.100)	6/252	8.5	7.7%	intergenic (+70/+73)	USA300HOU_0295/USA300HOU_0296	hypothetical membrane protein/hypothetical protein
	?	CP000730	329255 =	66 (1.120)					intergenic (+123/+20)	USA300HOU_0295/USA300HOU_0296	hypothetical membrane protein/hypothetical protein
*	?	CP000730	= 2476453	44 (0.690)	3 (0.050)	3/248	10.4	7.3%	intergenic (‑198/+42)	tcaA/tcaR	teicoplanin resistance protein TcaA/transcriptional regulator TcaR
	?	CP000730	= 2476476	36 (0.620)					intergenic (‑221/+19)	tcaA/tcaR	teicoplanin resistance protein TcaA/transcriptional regulator TcaR
*	?	CP000730	2830190 =	51 (0.800)	3 (0.050)	3/250	10.5	6.3%	intergenic (+18/+173)	icaC/USA300HOU_2670	intercellular adhesion protein C/hypothetical protein
	?	CP000730	2830247 =	42 (0.720)					intergenic (+75/+116)	icaC/USA300HOU_2670	intercellular adhesion protein C/hypothetical protein
*	?	CP000730	= 686561	67 (1.060)	3 (0.050)	3/250	10.5	4.5%	coding (962/1359 nt)	ydcQ	FtsK/SpoIIIE family cell division protein
	?	CP000730	= 686641	65 (1.110)					coding (882/1359 nt)	ydcQ	FtsK/SpoIIIE family cell division protein
*	?	CP000730	= 970911	55 (0.870)	3 (0.050)	3/254	10.6	4.9%	intergenic (+257/‑72)	fahA/USA300HOU_0928	fumarylacetoacetase/hypothetical membrane protein
	?	CP000730	= 970942	65 (1.100)					intergenic (+288/‑41)	fahA/USA300HOU_0928	fumarylacetoacetase/hypothetical membrane protein
*	?	CP000730	= 1465231	67 (1.060)	3 (0.050)	3/258	10.7	4.7%	intergenic (‑75/+125)	dfrB/thyA	dihydrofolate reductase/thymidylate synthase
	?	CP000730	= 1465259	59 (0.980)					intergenic (‑103/+97)	dfrB/thyA	dihydrofolate reductase/thymidylate synthase
*	?	CP000730	769469 =	61 (0.960)	3 (0.050)	3/258	10.7	4.6%	intergenic (+56/‑237)	norA/USA300HOU_0719	MFS family major facilitator transporter/hypothetical protein
	?	CP000730	769512 =	66 (1.100)					intergenic (+99/‑194)	norA/USA300HOU_0719	MFS family major facilitator transporter/hypothetical protein
*	?	CP000730	= 16077	60 (0.940)	3 (0.050)	3/266	11.0	4.5%	intergenic (+307/‑56)	azlD/metX	possible membrane protein/possible homoserine O‑acetyltransferase
	?	CP000730	= 16108	70 (1.130)					intergenic (+338/‑25)	azlD/metX	possible membrane protein/possible homoserine O‑acetyltransferase