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 227 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	76,322	0	G	A	66.1%	227.0 / 266.0	312	intergenic (+380/‑754)	USA300HOU_0072/USA300HOU_0075	universal stress protein/lysophospholipase
*	CP000730	76,295	0	T	C	62.5%	233.5 / 289.7	340	intergenic (+353/‑781)	USA300HOU_0072/USA300HOU_0075	universal stress protein/lysophospholipase
*	CP000730	76,353	0	G	A	59.2%	103.2 / 258.5	243	intergenic (+411/‑723)	USA300HOU_0072/USA300HOU_0075	universal stress protein/lysophospholipase
*	CP000730	36,087	0	A	G	59.0%	267.5 / inf	422	C155C (TGT→TGC)	tpn	IS431mec transposase
*	CP000730	36,269	0	C	T	58.3%	84.0 / inf	420	A95T (GCA→ACA)	tpn	IS431mec transposase
*	CP000730	36,124	0	G	A	58.2%	105.9 / inf	288	A143V (GCT→GTT)	tpn	IS431mec transposase
*	CP000730	1,929,861	0	T	C	57.9%	47.9 / 72.3	76	intergenic (‑944/‑224)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,870	0	A	C	57.1%	64.1 / 83.5	77	intergenic (‑953/‑215)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	35,970	0	T	C	56.6%	168.0 / inf	311	E194E (GAA→GAG)	tpn	IS431mec transposase
*	CP000730	1,929,867	0	G	T	56.4%	2.9 / 110.5	78	intergenic (‑950/‑218)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	36,315	0	G	A	55.9%	77.6 / inf	441	Y79Y (TAC→TAT)	tpn	IS431mec transposase
*	CP000730	1,929,866	0	G	T	55.8%	1.6 / 108.9	78	intergenic (‑949/‑219)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,872	0	G	A	55.7%	8.2 / 95.8	79	intergenic (‑955/‑213)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,873	0	C	A	54.3%	‑5.8 / 120.6	81	intergenic (‑956/‑212)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,848	0	C	A	53.0%	‑3.8 / 120.1	83	intergenic (‑931/‑237)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	36,413	0	C	T	52.8%	14.7 / inf	252	V47I (GTC→ATC)	tpn	IS431mec transposase
*	CP000730	1,929,842	0	T	.	51.8%	137.2 / 203.0	85	intergenic (‑925/‑243)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,843	0	A	.	51.8%	131.6 / 200.6	85	intergenic (‑926/‑242)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,875	0	T	C	51.8%	17.1 / 97.7	85	intergenic (‑958/‑210)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,917	0	C	T	49.2%	2.5 / 75.7	63	intergenic (‑1000/‑168)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein

Marginal new junction evidence (lowest skew 10 of 12 shown)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	= 800928	37 (1.030)	7 (0.210)	6/266	2.3	17.7%	intergenic (+62/‑289)	hisC1/USA300HOU_0748	histidinol‑phosphate transaminase/hypothetical protein
	?	CP000730	801948 =	30 (0.880)					intergenic (+189/+435)	USA300HOU_0748/dgkA1	hypothetical protein/possible diacylglycerol kinase
*	?	CP000730	= 2731894	28 (0.830)	5 (0.150) +ATTATAAACA	4/242	2.7	15.2%	coding (55/99 nt)	USA300HOU_2589	hypothetical protein
	?	CP000730	2731895 =	30 (0.840)					coding (54/99 nt)	USA300HOU_2589	hypothetical protein
*	?	CP000730	2278955 =	39 (1.090)	4 (0.150) +34 bp	3/212	2.8	11.7%	intergenic (+623/+7409)	mtlD/glmM	mannitol‑1‑phosphate 5‑dehydrogenase/phosphoglucosamine mutase
	?	CP000730	= 2278980	41 (1.140)					intergenic (+648/+7384)	mtlD/glmM	mannitol‑1‑phosphate 5‑dehydrogenase/phosphoglucosamine mutase
*	?	CP000730	= 672536	46 (1.280)	3 (0.100)	3/234	3.0	7.9%	intergenic (+138/‑241)	USA300HOU_0614/yvrC	deoxyribonuclease (pyrimidine dimer)/iron (Fe3+) ABC superfamily ATP binding cassette transporter, binding protein
	?	CP000730	672603 =	32 (1.070)					intergenic (+205/‑174)	USA300HOU_0614/yvrC	deoxyribonuclease (pyrimidine dimer)/iron (Fe3+) ABC superfamily ATP binding cassette transporter, binding protein
*	?	CP000730	= 895801	29 (0.810)	3 (0.100)	3/246	3.2	9.5%	coding (822/822 nt)	metQ	ABC superfamily ATP binding cassette transporter, binding protein
	?	CP000730	909758 =	32 (1.020)					intergenic (‑681/‑353)	ear/USA300HOU_0868	Ear protein/hypothetical protein
*	?	CP000730	895785 =	26 (0.720)	8 (0.250)	3/246	3.2	22.6%	coding (806/822 nt)	metQ	ABC superfamily ATP binding cassette transporter, binding protein
	?	CP000730	= 909740	32 (1.020)					intergenic (‑663/‑371)	ear/USA300HOU_0868	Ear protein/hypothetical protein
*	?	CP000730	= 2144160	31 (0.860)	4 (0.120) +TGGTTTATCT	3/260	3.3	12.2%	coding (484/1254 nt)	sdrH	Ser‑Asp rich fibrinogen/bone sialoprotein bindin protein SdrH
	?	CP000730	2144165 =	31 (0.860)					coding (479/1254 nt)	sdrH	Ser‑Asp rich fibrinogen/bone sialoprotein bindin protein SdrH
*	?	CP000730	2080223 =	20 (0.560)	3 (0.090)	3/264	3.4	13.4%	intergenic (‑56/+133)	bcrA/USA300HOU_1938	GntR family transcriptional regulator/hypothetical protein
	?	CP000730	= 2080217	20 (0.590)					intergenic (‑50/+139)	bcrA/USA300HOU_1938	GntR family transcriptional regulator/hypothetical protein
*	?	CP000730	= 2635582	50 (1.390)	4 (0.110) +TCT	3/274	3.5	7.7%	coding (366/3057 nt)	fnbA	fibronectin‑binding protein A
	?	CP000730	2635601 =	48 (1.340)					coding (347/3057 nt)	fnbA	fibronectin‑binding protein A
*	?	CP000730	= 2376100	37 (1.030)	5 (0.140)	3/280	3.5	10.6%	coding (45/96 nt)	USA300HOU_2236	hypothetical protein
	?	CP000730	2376113 =	47 (1.310)					coding (32/96 nt)	USA300HOU_2236	hypothetical protein