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	36,378	0	C	T	79.8%	445.6 / 131.4	286	L58L (TTG→TTA)	tpn	IS431mec transposase
*	CP000730	36,269	0	C	T	60.7%	114.2 / inf	306	A95T (GCA→ACA)	tpn	IS431mec transposase
*	CP000730	36,315	0	G	A	57.6%	117.4 / inf	332	Y79Y (TAC→TAT)	tpn	IS431mec transposase
*	CP000730	1,929,867	0	G	T	57.1%	‑2.9 / 65.9	42	intergenic (‑950/‑218)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,861	0	T	C	56.1%	11.5 / 48.2	42	intergenic (‑944/‑224)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,866	0	G	T	56.1%	‑5.9 / 64.6	42	intergenic (‑949/‑219)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	35,970	0	T	C	55.6%	72.1 / 229.6	188	E194E (GAA→GAG)	tpn	IS431mec transposase
*	CP000730	36,087	0	A	G	55.4%	96.0 / inf	271	C155C (TGT→TGC)	tpn	IS431mec transposase
*	CP000730	76,295	0	T	C	55.1%	92.5 / 308.8	254	intergenic (+353/‑781)	USA300HOU_0072/USA300HOU_0075	universal stress protein/lysophospholipase
*	CP000730	1,929,848	0	C	A	54.5%	‑5.5 / 61.8	44	intergenic (‑931/‑237)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,870	0	A	C	54.5%	26.7 / 52.4	44	intergenic (‑953/‑215)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,875	0	T	C	54.5%	13.7 / 49.9	44	intergenic (‑958/‑210)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	76,322	0	G	A	54.1%	61.7 / 307.2	242	intergenic (+380/‑754)	USA300HOU_0072/USA300HOU_0075	universal stress protein/lysophospholipase
*	CP000730	36,413	0	C	T	53.4%	2.0 / 248.3	189	V47I (GTC→ATC)	tpn	IS431mec transposase
*	CP000730	1,929,842	0	T	.	53.3%	‑6.2 / 97.7	45	intergenic (‑925/‑243)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,843	0	A	.	53.3%	70.0 / 99.2	46	intergenic (‑926/‑242)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,872	0	G	A	53.3%	0.7 / 58.3	45	intergenic (‑955/‑213)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,873	0	C	A	53.3%	2.8 / 74.4	45	intergenic (‑956/‑212)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	36,124	0	G	A	52.9%	36.0 / inf	227	A143V (GCT→GTT)	tpn	IS431mec transposase
*	CP000730	1,929,862	1	.	T	52.4%	78.4 / 79.4	42	intergenic (‑945/‑223)	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	= 2693372	26 (0.850)	6 (0.210)	5/254	3.5	19.2%	intergenic (+43/+34)	USA300HOU_2547/USA300HOU_2548	TetR family transcriptional regulator/hypothetical protein
	?	CP000730	= 2693412	26 (0.910)					coding (162/168 nt)	USA300HOU_2548	hypothetical protein
*	?	CP000730	= 690094	27 (0.890)	3 (0.110)	3/252	4.4	10.1%	intergenic (‑23/+12)	USA300HOU_0631/USA300HOU_0632	hypothetical membrane protein/hypothetical membrane protein
	?	CP000730	= 690115	28 (0.980)					coding (375/384 nt)	USA300HOU_0632	hypothetical membrane protein
*	?	CP000730	613921 =	30 (0.980)	3 (0.110)	3/248	4.4	9.7%	coding (2233/2844 nt)	sdrC	Ser‑Asp rich fibrinogen/bone sialoprotein‑binding protein SdrC
	?	CP000730	= 618390	28 (1.000)					coding (3492/4146 nt)	sdrD	Ser‑Asp rich fibrinogen/bone sialoprotein‑binding protein SdrD
*	?	CP000730	= 940821	22 (0.720)	3 (0.100)	3/258	4.5	13.0%	intergenic (+2/+54)	comA/USA300HOU_0905	hypothetical protein/hypothetical protein
	?	CP000730	= 940872	19 (0.650)					intergenic (+53/+3)	comA/USA300HOU_0905	hypothetical protein/hypothetical protein