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 61 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,929,842	0	T	.	75.7%	405.5 / 207.6	184	intergenic (‑925/‑243)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,861	0	T	C	75.6%	352.2 / 92.3	183	intergenic (‑944/‑224)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,843	0	A	.	74.5%	399.7 / 212.4	185	intergenic (‑926/‑242)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,867	0	G	T	74.3%	297.6 / 133.1	188	intergenic (‑950/‑218)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,870	0	A	C	74.2%	367.4 / 106.1	187	intergenic (‑953/‑215)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,872	0	G	A	74.2%	283.3 / 126.7	188	intergenic (‑955/‑213)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,873	0	C	A	74.1%	279.5 / 130.0	188	intergenic (‑956/‑212)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,848	0	C	A	73.4%	279.7 / 137.2	189	intergenic (‑931/‑237)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,875	0	T	C	73.3%	326.4 / 115.2	191	intergenic (‑958/‑210)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,866	0	G	T	70.8%	227.0 / 139.1	188	intergenic (‑949/‑219)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,812	0	G	A	68.8%	140.4 / 101.2	126	intergenic (‑895/‑273)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	2,314,215	0	C	T	67.7%	68.1 / 53.7	67	S352N (AGT→AAT)	rhbC	MFS family major facilitator transporter
*	CP000730	1,929,918	0	A	G	63.5%	151.3 / 145.3	156	intergenic (‑1001/‑167)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,917	0	C	T	63.1%	132.9 / 150.5	157	intergenic (‑1000/‑168)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	76,295	0	T	C	62.9%	551.8 / inf	746	intergenic (+353/‑781)	USA300HOU_0072/USA300HOU_0075	universal stress protein/lysophospholipase
*	CP000730	1,929,928	0	T	A	62.9%	110.2 / 162.4	141	intergenic (‑1011/‑157)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,930	0	T	A	62.6%	109.6 / 159.2	141	intergenic (‑1013/‑155)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	36,087	0	A	G	62.2%	737.2 / inf	994	C155C (TGT→TGC)	tpn	IS431mec transposase
*	CP000730	1,929,925	0	T	A	62.1%	108.6 / 160.0	141	intergenic (‑1008/‑160)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	35,970	0	T	C	61.9%	549.8 / inf	740	E194E (GAA→GAG)	tpn	IS431mec transposase

Marginal new junction evidence (sorted from low to high skew)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	52495 =	94 (1.500)	109 (1.760) +T	6/278	4.5	58.6%	intergenic (+105/‑568)	USA300HOU_0043/USA300HOU_0044	hypothetical membrane protein/possible transcriptional regulator
	?	CP000730	= 52988	61 (0.980)					intergenic (+598/‑75)	USA300HOU_0043/USA300HOU_0044	hypothetical membrane protein/possible transcriptional regulator
*	?	CP000730	= 2618806	68 (1.090)	3 (0.050)	3/264	5.7	4.5%	coding (462/1809 nt)	pgcA	bifunctional phosphoglucomutase/phosphomannomutase
	?	CP000730	= 2618808	62 (1.050)					coding (464/1809 nt)	pgcA	bifunctional phosphoglucomutase/phosphomannomutase