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 58 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,929,861	0	T	C	66.7%	162.2 / 97.3	131	intergenic (‑944/‑224)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,867	0	G	T	64.9%	103.1 / 131.2	134	intergenic (‑950/‑218)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,870	0	A	C	64.2%	170.2 / 112.8	135	intergenic (‑953/‑215)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,872	0	G	A	64.2%	108.6 / 128.2	136	intergenic (‑955/‑213)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,873	0	C	A	63.7%	100.0 / 132.3	136	intergenic (‑956/‑212)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,875	0	T	C	63.4%	142.3 / 115.3	135	intergenic (‑958/‑210)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,917	0	C	T	63.2%	108.7 / 133.5	137	intergenic (‑1000/‑168)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,843	0	A	.	63.2%	124.1 / 239.9	135	intergenic (‑926/‑242)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,842	0	T	.	62.7%	116.6 / 246.3	135	intergenic (‑925/‑243)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,918	0	A	G	62.6%	132.4 / 123.6	139	intergenic (‑1001/‑167)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,848	0	C	A	62.3%	91.7 / 147.1	139	intergenic (‑931/‑237)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,866	0	G	T	60.5%	50.9 / 137.9	134	intergenic (‑949/‑219)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	35,970	0	T	C	60.3%	416.4 / inf	574	E194E (GAA→GAG)	tpn	IS431mec transposase
*	CP000730	36,124	0	G	A	59.6%	277.8 / inf	579	A143V (GCT→GTT)	tpn	IS431mec transposase
*	CP000730	36,269	0	C	T	59.6%	226.4 / inf	724	A95T (GCA→ACA)	tpn	IS431mec transposase
*	CP000730	36,087	0	A	G	59.5%	511.0 / inf	782	C155C (TGT→TGC)	tpn	IS431mec transposase
*	CP000730	76,180	0	C	T	58.5%	70.9 / 126.1	124	intergenic (+238/‑896)	USA300HOU_0072/USA300HOU_0075	universal stress protein/lysophospholipase
*	CP000730	1,929,928	0	T	A	58.4%	61.5 / 149.2	125	intergenic (‑1011/‑157)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,925	0	T	A	58.1%	64.0 / 147.0	125	intergenic (‑1008/‑160)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,930	0	T	A	58.1%	66.6 / 144.9	125	intergenic (‑1013/‑155)	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	= 2464733	70 (1.190)	3 (0.060)	3/258	6.9	4.5%	intergenic (+29/+19)	gltS/fni	ESS family glutamate:sodium (Na+) symporter/isopentenyl‑diphosphate delta‑isomerase
	?	CP000730	= 2464737	66 (1.280)					intergenic (+33/+15)	gltS/fni	ESS family glutamate:sodium (Na+) symporter/isopentenyl‑diphosphate delta‑isomerase
*	?	CP000730	52495 =	70 (1.190)	85 (1.460) +T	3/292	7.5	59.2%	intergenic (+105/‑568)	USA300HOU_0043/USA300HOU_0044	hypothetical membrane protein/possible transcriptional regulator
	?	CP000730	= 52988	48 (0.820)					intergenic (+598/‑75)	USA300HOU_0043/USA300HOU_0044	hypothetical membrane protein/possible transcriptional regulator