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	36,124	0	G	A	62.5%	115.9 / 244.8	238	A143V (GCT→GTT)	tpn	IS431mec transposase
*	CP000730	36,087	0	A	G	62.2%	196.5 / 302.2	301	C155C (TGT→TGC)	tpn	IS431mec transposase
*	CP000730	35,970	0	T	C	58.6%	129.4 / 251.7	216	E194E (GAA→GAG)	tpn	IS431mec transposase
*	CP000730	36,413	0	C	T	58.0%	81.1 / 284.0	238	V47I (GTC→ATC)	tpn	IS431mec transposase
*	CP000730	76,295	0	T	C	56.2%	93.0 / inf	301	intergenic (+353/‑781)	USA300HOU_0072/USA300HOU_0075	universal stress protein/lysophospholipase
*	CP000730	76,322	0	G	A	55.8%	61.2 / inf	280	intergenic (+380/‑754)	USA300HOU_0072/USA300HOU_0075	universal stress protein/lysophospholipase
*	CP000730	36,269	0	C	T	55.0%	3.9 / inf	375	A95T (GCA→ACA)	tpn	IS431mec transposase
*	CP000730	36,315	0	G	A	54.8%	80.1 / inf	410	Y79Y (TAC→TAT)	tpn	IS431mec transposase
*	CP000730	36,444	0	C	T	53.6%	‑3.3 / 205.7	153	R36R (AGG→AGA)	tpn	IS431mec transposase
*	CP000730	76,353	0	G	A	53.1%	28.8 / 299.2	226	intergenic (+411/‑723)	USA300HOU_0072/USA300HOU_0075	universal stress protein/lysophospholipase
*	CP000730	512,643	0	A	G	48.5%	0.4 / 94.5	68	intergenic (+711/‑150)	recR/rrs1	recombination protein RecR/16S ribosomal RNA
*	CP000730	1,929,861	0	T	C	48.0%	‑1.5 / 67.4	50	intergenic (‑944/‑224)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,842	0	T	.	46.9%	91.6 / 92.7	49	intergenic (‑925/‑243)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,843	0	A	.	46.9%	91.9 / 92.7	50	intergenic (‑926/‑242)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,867	0	G	T	46.2%	34.8 / 66.8	52	intergenic (‑950/‑218)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,848	0	C	A	45.1%	31.1 / 64.3	52	intergenic (‑931/‑237)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,870	0	A	C	45.1%	‑0.4 / 86.5	52	intergenic (‑953/‑215)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,875	0	T	C	45.1%	8.7 / 66.5	51	intergenic (‑958/‑210)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,873	0	C	A	44.2%	32.3 / 66.3	52	intergenic (‑956/‑212)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,872	0	G	A	43.4%	19.0 / 63.1	53	intergenic (‑955/‑213)	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	= 127847	28 (0.820)	5 (0.160)	5/248	4.1	16.2%	intergenic (+67/+262)	lctP/spa	LctP family L‑lactate permease/immunoglobulin G binding protein A
	?	CP000730	= 127871	26 (0.830)					intergenic (+91/+238)	lctP/spa	LctP family L‑lactate permease/immunoglobulin G binding protein A
*	?	CP000730	= 826356	28 (0.820)	3 (0.100)	3/246	5.0	11.2%	intergenic (+92/+78)	tagO/yvyE	hypothetical membrane protein/hypothetical membrane protein
	?	CP000730	= 826419	22 (0.710)					intergenic (+155/+15)	tagO/yvyE	hypothetical membrane protein/hypothetical membrane protein
*	?	CP000730	1623534 =	34 (0.990)	3 (0.100)	3/248	5.1	8.7%	intergenic (+19/+64)	graE/malA	AraC family transcriptional regulator/alpha‑glucosidase
	?	CP000730	1623587 =	32 (1.020)					intergenic (+72/+11)	graE/malA	AraC family transcriptional regulator/alpha‑glucosidase