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	51.1%	‑1.8 / 130.3	88	intergenic (+711/‑150)	recR/rrs1	recombination protein RecR/16S ribosomal RNA
*	CP000730	111,512	0	A	G	31.5%	70.9 / 40.4	54	S194S (TCA→TCG)	USA300HOU_0110	possible staphylococcal tandem lipoprotein
*	CP000730	111,516	0	C	A	29.6%	93.6 / 39.8	54	Q196K (CAA→AAA)	USA300HOU_0110	possible staphylococcal tandem lipoprotein
*	CP000730	2,504,889	0	G	A	29.1%	120.1 / 49.8	89	intergenic (+193/+211)	USA300HOU_2365/gltT	hypothetical protein/DAACS family dicarboxylate/amino acid:sodium (Na+) or proton (H+) symporter
*	CP000730	2,504,894	0	C	T	23.5%	132.5 / 38.6	85	intergenic (+198/+206)	USA300HOU_2365/gltT	hypothetical protein/DAACS family dicarboxylate/amino acid:sodium (Na+) or proton (H+) symporter

Marginal new junction evidence (lowest skew 10 of 13 shown)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	1929559 =	54 (1.420)	4 (0.110)	4/264	5.6	7.2%	intergenic (‑642/‑526)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
	?	CP000730	1929585 =	52 (1.430)					intergenic (‑668/‑500)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	?	CP000730	= 1292768	33 (0.870)	4 (0.110)	4/262	5.6	11.9%	intergenic (+322/‑64)	infB/rbfA	translation initiation factor IF‑2/ribosome‑binding factor A
	?	CP000730	= 1292797	28 (0.780)					intergenic (+351/‑35)	infB/rbfA	translation initiation factor IF‑2/ribosome‑binding factor A
*	?	CP000730	= 225539	37 (0.970)	4 (0.110)	4/262	5.6	9.7%	coding (626/897 nt)	murQ	possible sugar phosphate isomerase
	?	CP000730	= 225543	39 (1.080)					coding (630/897 nt)	murQ	possible sugar phosphate isomerase
*	?	CP000730	= 2201286	45 (1.180)	3 (0.090)	3/252	6.0	7.3%	intergenic (+16/+353)	kdpE/cshA	KDP operon transcriptional regulator/ATP‑dependent RNA helicase
	?	CP000730	= 2201313	35 (1.010)					intergenic (+43/+326)	kdpE/cshA	KDP operon transcriptional regulator/ATP‑dependent RNA helicase
*	?	CP000730	1325375 =	31 (0.820)	3 (0.080)	3/258	6.1	8.3%	coding (132/543 nt)	glpP	glycerol uptake operon antiterminator
	?	CP000730	1325473 =	37 (1.040)					coding (230/543 nt)	glpP	glycerol uptake operon antiterminator
*	?	CP000730	811555 =	42 (1.100)	4 (0.110)	3/256	6.1	8.6%	intergenic (+160/‑117)	USA300HOU_0757/USA300HOU_0758	hypothetical protein/hypothetical protein
	?	CP000730	2220727 =	46 (1.300)					intergenic (‑378/+184)	USA300HOU_2091/atpC	hypothetical protein/F‑ATPase superfamily proton(H+)‑ or sodium (Na+)‑translocating F‑type ATPase epsilon subunit
*	?	CP000730	811555 =	42 (1.100)	4 (0.110)	3/262	6.2	8.8%	intergenic (+160/‑117)	USA300HOU_0757/USA300HOU_0758	hypothetical protein/hypothetical protein
	?	CP000730	= 2664960	43 (1.190)					intergenic (+195/‑283)	pat/USA300HOU_2519	acetyltransferase/hypothetical protein
*	?	CP000730	811555 =	42 (1.100)	4 (0.110)	3/262	6.2	10.3%	intergenic (+160/‑117)	USA300HOU_0757/USA300HOU_0758	hypothetical protein/hypothetical protein
	?	CP000730	= 1903651	30 (0.830)					intergenic (+105/+190)	arsC2/gad	arsenate reductase (glutaredoxin)/possible mannosyl‑glycoprotein endo‑beta‑N‑glucosaminidase
*	?	CP000730	811555 =	42 (1.100)	4 (0.110)	3/262	6.2	11.8%	intergenic (+160/‑117)	USA300HOU_0757/USA300HOU_0758	hypothetical protein/hypothetical protein
	?	CP000730	= 891954	20 (0.550)					intergenic (+21/‑370)	USA300HOU_0844/yusF	hypothetical protein/TOPRIM domain topiosmerase/primase
*	?	CP000730	811555 =	42 (1.100)	4 (0.110)	3/262	6.2	10.1%	intergenic (+160/‑117)	USA300HOU_0757/USA300HOU_0758	hypothetical protein/hypothetical protein
	?	CP000730	= 848296	31 (0.860)					intergenic (+301/+73)	trxB1/USA300HOU_0793	thioredoxin‑disulfide reductase/hypothetical protein