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	35,970	0	T	C	61.5%	331.4 / inf	370	E194E (GAA→GAG)	tpn	IS431mec transposase
*	CP000730	36,315	0	G	A	59.3%	266.5 / inf	554	Y79Y (TAC→TAT)	tpn	IS431mec transposase
*	CP000730	1,929,861	0	T	C	59.2%	59.4 / 84.6	76	intergenic (‑944/‑224)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	36,087	0	A	G	58.5%	346.4 / inf	599	C155C (TGT→TGC)	tpn	IS431mec transposase
*	CP000730	1,929,867	0	G	T	58.4%	31.9 / 109.0	77	intergenic (‑950/‑218)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,870	0	A	C	57.7%	92.4 / 89.5	78	intergenic (‑953/‑215)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,872	0	G	A	57.7%	36.4 / 95.8	78	intergenic (‑955/‑213)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,873	0	C	A	57.7%	24.3 / 114.3	78	intergenic (‑956/‑212)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,866	0	G	T	57.3%	13.8 / 118.1	77	intergenic (‑949/‑219)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,875	0	T	C	57.0%	52.4 / 92.4	79	intergenic (‑958/‑210)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	36,413	0	C	T	56.8%	119.8 / inf	303	V47I (GTC→ATC)	tpn	IS431mec transposase
*	CP000730	36,124	0	G	A	56.2%	88.2 / inf	445	A143V (GCT→GTT)	tpn	IS431mec transposase
*	CP000730	36,269	0	C	T	55.7%	38.5 / inf	522	A95T (GCA→ACA)	tpn	IS431mec transposase
*	CP000730	1,929,848	0	C	A	54.9%	13.6 / 129.0	82	intergenic (‑931/‑237)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	76,295	0	T	C	54.3%	116.3 / inf	393	intergenic (+353/‑781)	USA300HOU_0072/USA300HOU_0075	universal stress protein/lysophospholipase
*	CP000730	1,929,842	0	T	.	52.9%	161.8 / 212.6	85	intergenic (‑925/‑243)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	76,322	0	G	A	52.5%	26.2 / inf	380	intergenic (+380/‑754)	USA300HOU_0072/USA300HOU_0075	universal stress protein/lysophospholipase
*	CP000730	1,929,843	0	A	.	52.3%	158.2 / 215.6	86	intergenic (‑926/‑242)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,862	1	.	T	51.3%	160.3 / 159.6	76	intergenic (‑945/‑223)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,865	0	A	C	50.6%	36.6 / 113.8	77	intergenic (‑948/‑220)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein

Marginal new junction evidence (sorted from low to high skew)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	2085296 =	65 (1.270)	8 (0.170)	7/252	3.2	15.5%	intergenic (‑558/‑400)	mapW2/USA300HOU_1944	cell surface protein MapW2/hypothetical protein
	?	CP000730	= 2128343	29 (0.630)					intergenic (+57/+1062)	int/hlgB	bacteriophage integrase/possible leukocidin subunit
*	?	CP000730	2457361 =	64 (1.250)	4 (0.090)	3/254	4.9	7.8%	intergenic (+40/+90)	USA300HOU_2317/USA300HOU_2318	hypothetical protein/hypothetical protein
	?	CP000730	2457434 =	37 (0.800)					intergenic (+113/+17)	USA300HOU_2317/USA300HOU_2318	hypothetical protein/hypothetical protein
*	?	CP000730	= 800928	53 (1.040)	3 (0.060)	3/266	5.1	6.1%	intergenic (+62/‑289)	hisC1/USA300HOU_0748	histidinol‑phosphate transaminase/hypothetical protein
	?	CP000730	801948 =	42 (0.870)					intergenic (+189/+435)	USA300HOU_0748/dgkA1	hypothetical protein/possible diacylglycerol kinase
*	?	CP000730	1502317 =	57 (1.120)	3 (0.060)	3/270	5.2	5.3%	intergenic (‑294/+104)	ebh/norB	extracellular matrix binding protein/MFS family major facilitator transporter
	?	CP000730	1502366 =	52 (1.060)					intergenic (‑343/+55)	ebh/norB	extracellular matrix binding protein/MFS family major facilitator transporter