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 56 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,929,918	0	A	G	67.1%	182.6 / 124.9	159	intergenic (‑1001/‑167)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,867	0	G	T	66.2%	163.3 / 139.2	156	intergenic (‑950/‑218)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,861	0	T	C	66.0%	195.4 / 122.0	156	intergenic (‑944/‑224)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,873	0	C	A	66.0%	168.8 / 132.3	157	intergenic (‑956/‑212)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,875	0	T	C	66.0%	189.3 / 123.3	155	intergenic (‑958/‑210)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,917	0	C	T	65.8%	153.9 / 147.1	159	intergenic (‑1000/‑168)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,870	0	A	C	64.7%	218.9 / 125.4	159	intergenic (‑953/‑215)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,872	0	G	A	64.7%	153.2 / 138.2	158	intergenic (‑955/‑213)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	35,970	0	T	C	63.7%	474.7 / inf	549	E194E (GAA→GAG)	tpn	IS431mec transposase
*	CP000730	36,087	0	A	G	62.9%	775.1 / inf	842	C155C (TGT→TGC)	tpn	IS431mec transposase
*	CP000730	1,929,848	0	C	A	62.4%	117.8 / 181.9	165	intergenic (‑931/‑237)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,866	0	G	T	62.0%	109.7 / 152.1	156	intergenic (‑949/‑219)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	36,315	0	G	A	61.6%	391.1 / inf	835	Y79Y (TAC→TAT)	tpn	IS431mec transposase
*	CP000730	1,929,843	0	A	.	61.6%	136.1 / 298.7	165	intergenic (‑926/‑242)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,842	0	T	.	61.2%	132.7 / 301.2	165	intergenic (‑925/‑243)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,925	0	T	A	60.9%	94.0 / 157.5	139	intergenic (‑1008/‑160)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,928	0	T	A	60.9%	95.5 / 168.3	139	intergenic (‑1011/‑157)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,930	0	T	A	60.9%	91.4 / 163.1	139	intergenic (‑1013/‑155)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	36,269	0	C	T	60.5%	276.2 / inf	830	A95T (GCA→ACA)	tpn	IS431mec transposase
*	CP000730	36,124	0	G	A	58.9%	331.5 / inf	639	A143V (GCT→GTT)	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 =	44 (0.820)	89 (1.680) +T	5/294	4.9	60.3%	intergenic (+105/‑568)	USA300HOU_0043/USA300HOU_0044	hypothetical membrane protein/possible transcriptional regulator
	?	CP000730	= 52988	74 (1.380)					intergenic (+598/‑75)	USA300HOU_0043/USA300HOU_0044	hypothetical membrane protein/possible transcriptional regulator
*	?	CP000730	52489 =	44 (0.820)	10 (0.210)	3/266	5.4	16.1%	intergenic (+99/‑574)	USA300HOU_0043/USA300HOU_0044	hypothetical membrane protein/possible transcriptional regulator
	?	CP000730	= 52983	65 (1.350)					intergenic (+593/‑80)	USA300HOU_0043/USA300HOU_0044	hypothetical membrane protein/possible transcriptional regulator