breseq  version 0.33.1  revision 8505477f25b3 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence (highest frequency 20 of 54 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	36,269	0	C	T	62.3%	455.5 / inf	951	A95T (GCA→ACA)	tpn	IS431mec transposase
*	CP000730	36,315	0	G	A	61.7%	519.8 / inf	1006	Y79Y (TAC→TAT)	tpn	IS431mec transposase
*	CP000730	76,295	0	T	C	59.5%	327.4 / inf	666	intergenic (+353/‑781)	USA300HOU_0072/USA300HOU_0075	universal stress protein/lysophospholipase
*	CP000730	76,322	0	G	A	58.4%	218.4 / inf	616	intergenic (+380/‑754)	USA300HOU_0072/USA300HOU_0075	universal stress protein/lysophospholipase
*	CP000730	36,087	0	A	G	56.4%	366.3 / inf	848	C155C (TGT→TGC)	tpn	IS431mec transposase
*	CP000730	36,124	0	G	A	56.0%	149.7 / inf	631	A143V (GCT→GTT)	tpn	IS431mec transposase
*	CP000730	36,413	0	C	T	55.0%	60.2 / inf	570	V47I (GTC→ATC)	tpn	IS431mec transposase
*	CP000730	35,970	0	T	C	54.3%	243.5 / inf	590	E194E (GAA→GAG)	tpn	IS431mec transposase
*	CP000730	76,353	0	G	A	53.8%	69.8 / inf	482	intergenic (+411/‑723)	USA300HOU_0072/USA300HOU_0075	universal stress protein/lysophospholipase
*	CP000730	36,444	0	C	T	50.4%	88.0 / inf	391	R36R (AGG→AGA)	tpn	IS431mec transposase
*	CP000730	1,929,861	0	T	C	50.0%	12.2 / 166.6	132	intergenic (‑944/‑224)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	35,876	0	C	T	49.2%	90.8 / 157.1	130	intergenic (+107/+1)	rlmH/tpn	hypothetical protein/IS431mec transposase
*	CP000730	1,929,875	0	T	C	48.5%	‑1.2 / 184.2	135	intergenic (‑958/‑210)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,870	0	A	C	48.2%	9.6 / 223.3	139	intergenic (‑953/‑215)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,872	0	G	A	47.8%	35.6 / 165.1	138	intergenic (‑955/‑213)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,843	0	A	.	47.8%	221.2 / 264.6	138	intergenic (‑926/‑242)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,848	0	C	A	47.1%	62.6 / 189.0	140	intergenic (‑931/‑237)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,873	0	C	A	47.1%	56.8 / 187.8	138	intergenic (‑956/‑212)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,867	0	G	T	46.8%	65.9 / 187.3	139	intergenic (‑950/‑218)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,842	0	T	.	46.7%	243.1 / 259.4	137	intergenic (‑925/‑243)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein

Marginal new junction evidence (lowest skew 10 of 104 shown)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	= 234750	98 (1.220)	9 (0.120)	9/248	8.6	9.1%	intergenic (+48/+217)	USA300HOU_0211/USA300HOU_0212	hypothetical protein/oligopeptide ABC superfamily ATP binding cassette transporter, ABC protein
	?	CP000730	= 234763	89 (1.200)					intergenic (+61/+204)	USA300HOU_0211/USA300HOU_0212	hypothetical protein/oligopeptide ABC superfamily ATP binding cassette transporter, ABC protein
*	?	CP000730	1205383 =	84 (1.050)	36 (0.550) +25 bp	6/218	9.2	41.5%	intergenic (+519/‑305)	yfiE/lspA	possible lactoylglutathione lyase/A8 family signal peptidase II
	?	CP000730	2478476 =	41 (0.510)					intergenic (+363/+708)	USA300HOU_2340/htrB	hypothetical membrane protein/hemin ABC superfamily ATP binding cassette transporter, ABC protein
*	?	CP000730	1885475 =	74 (0.920)	8 (0.110)	7/252	9.8	10.1%	intergenic (‑257/+69)	fmtB1/USA300HOU_1748	cell surface anchored protein/possible rhodanese domain sulfurtransferase
	?	CP000730	1885505 =	73 (0.970)					intergenic (‑287/+39)	fmtB1/USA300HOU_1748	cell surface anchored protein/possible rhodanese domain sulfurtransferase
*	?	CP000730	1205383 =	84 (1.050)	28 (0.430) +25 bp	5/218	9.8	35.5%	intergenic (+519/‑305)	yfiE/lspA	possible lactoylglutathione lyase/A8 family signal peptidase II
	?	CP000730	1426741 =	41 (0.510)					intergenic (‑472/+500)	pstS/yitL	phosphate ABC superfamily ATP binding cassette transporter, binding protein/hypothetical protein
*	?	CP000730	1072165 =	102 (1.270)	7 (0.090)	7/260	10.0	6.6%	intergenic (‑637/+168)	iraE/folD	possible chitinase/bifunctional methylenetetrahydrofolate dehydrogenase (NADP(+))/methenyltetrahydrofolate cyclohydrolase
	?	CP000730	2699372 =	100 (1.280)					intergenic (+276/‑15)	copA/merP	P‑ATPase superfamily P‑type ATPase copper (Cu2+) transporter/MerTP family mercury (Hg2+) permease, binding protein MerP
*	?	CP000730	= 2731894	80 (1.070)	9 (0.120) +ATTATAAACA	5/230	10.3	10.3%	coding (55/99 nt)	USA300HOU_2589	hypothetical protein
	?	CP000730	2731895 =	84 (1.050)					coding (54/99 nt)	USA300HOU_2589	hypothetical protein
*	?	CP000730	= 1750776	70 (0.870)	6 (0.080)	6/250	10.3	8.2%	coding (366/1140 nt)	tgt	queuine tRNA‑ribosyltransferase
	?	CP000730	= 1750789	69 (0.920)					coding (353/1140 nt)	tgt	queuine tRNA‑ribosyltransferase
*	?	CP000730	1245321 =	66 (0.820)	6 (0.080)	6/250	10.3	9.1%	coding (146/156 nt)	USA300HOU_1168	hypothetical protein
	?	CP000730	1245355 =	58 (0.780)					intergenic (+24/‑83)	USA300HOU_1168/hmrB	hypothetical protein/possible acyl carrier protein HmrB
*	?	CP000730	533277 =	93 (1.160)	6 (0.080)	6/250	10.3	6.4%	intergenic (+2848/‑2877)	veg/rplY	hypothetical protein/ribosomal protein L25
	?	CP000730	= 533297	88 (1.180)					intergenic (+2868/‑2857)	veg/rplY	hypothetical protein/ribosomal protein L25
*	?	CP000730	1456948 =	80 (1.000)	17 (0.220) +GTTTT	6/258	10.6	19.2%	intergenic (‑62/‑182)	USA300HOU_1352/arlR	hypothetical protein/IS200 transposase
	?	CP000730	= 1918540	69 (0.860)					intergenic (‑219/+240)	pckA/USA300HOU_1780	transposase/hypothetical protein