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 66 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,231,407	0	G	A	78.7%	180.2 / 49.6	95	E18K (GAA→AAA)	prpC	possible PP2C protein phosphatase
*	CP000730	1,000,948	0	C	T	77.0%	106.7 / 32.5	61	T11I (ACA→ATA)	spxA	possible glutaredoxin
*	CP000730	567,389	0	A	T	72.3%	142.4 / 69.2	83	Q95L (CAA→CTA)	ctsR	CtsR family transcriptional regulator
*	CP000730	1,744,443	0	C	A	67.1%	73.8 / 85.2	79	V77F (GTT→TTT)	apt	adenine phosphoribosyltransferase
*	CP000730	1,929,842	0	T	.	66.3%	257.1 / 281.3	185	intergenic (‑925/‑243)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,843	0	A	.	66.0%	246.2 / 284.0	185	intergenic (‑926/‑242)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,861	0	T	C	65.8%	220.7 / 163.0	185	intergenic (‑944/‑224)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,848	0	C	A	64.9%	154.4 / 230.9	189	intergenic (‑931/‑237)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,867	0	G	T	62.9%	118.0 / 248.3	194	intergenic (‑950/‑218)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,873	0	C	A	62.9%	128.5 / 256.9	194	intergenic (‑956/‑212)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,870	0	A	C	62.7%	288.6 / 190.1	194	intergenic (‑953/‑215)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,872	0	G	A	62.7%	160.3 / 207.4	194	intergenic (‑955/‑213)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,875	0	T	C	62.2%	183.2 / 199.3	196	intergenic (‑958/‑210)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,866	0	G	T	61.9%	92.6 / 262.5	194	intergenic (‑949/‑219)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	35,970	0	T	C	60.0%	604.4 / inf	852	E194E (GAA→GAG)	tpn	IS431mec transposase
*	CP000730	76,295	0	T	C	59.5%	644.8 / inf	990	intergenic (+353/‑781)	USA300HOU_0072/USA300HOU_0075	universal stress protein/lysophospholipase
*	CP000730	36,315	0	G	A	59.4%	806.9 / inf	1629	Y79Y (TAC→TAT)	tpn	IS431mec transposase
*	CP000730	36,269	0	C	T	59.4%	468.1 / inf	1440	A95T (GCA→ACA)	tpn	IS431mec transposase
*	CP000730	36,087	0	A	G	58.5%	752.8 / inf	1190	C155C (TGT→TGC)	tpn	IS431mec transposase
*	CP000730	76,322	0	G	A	58.3%	487.5 / inf	944	intergenic (+380/‑754)	USA300HOU_0072/USA300HOU_0075	universal stress protein/lysophospholipase

Marginal new junction evidence (lowest skew 10 of 24 shown)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	52495 =	40 (0.440)	132 (1.460) +T	6/276	11.8	67.2%	intergenic (+105/‑568)	USA300HOU_0043/USA300HOU_0044	hypothetical membrane protein/possible transcriptional regulator
	?	CP000730	= 52988	90 (0.990)					intergenic (+598/‑75)	USA300HOU_0043/USA300HOU_0044	hypothetical membrane protein/possible transcriptional regulator
*	?	CP000730	2082519 =	77 (0.850)	5 (0.060)	5/260	11.9	6.7%	intergenic (+160/+465)	USA300HOU_1940/mapW2	aminotransferase/cell surface protein MapW2
	?	CP000730	2082566 =	68 (0.800)					intergenic (+207/+418)	USA300HOU_1940/mapW2	aminotransferase/cell surface protein MapW2
*	?	CP000730	1217678 =	69 (0.760)	5 (0.060)	4/246	12.2	8.3%	intergenic (+7/‑430)	USA300HOU_1144/USA300HOU_1145	hypothetical protein/possible 3‑demethylubiquinone‑9 3‑methyltransferase
	?	CP000730	1217746 =	49 (0.610)					intergenic (+75/‑362)	USA300HOU_1144/USA300HOU_1145	hypothetical protein/possible 3‑demethylubiquinone‑9 3‑methyltransferase
*	?	CP000730	2041611 =	80 (0.880)	4 (0.050)	4/256	12.5	5.3%	coding (36/147 nt)	USA300HOU_1899	hypothetical protein
	?	CP000730	2041657 =	68 (0.810)					intergenic (‑11/+29)	USA300HOU_1899/gatB2	hypothetical protein/glutamyl‑tRNA(Gln) amidotransferase subunit B
*	?	CP000730	= 462756	120 (1.320)	5 (0.060)	4/260	12.6	4.7%	intergenic (+15/+88)	USA300HOU_0436/USA300HOU_0437	hypothetical protein/hypothetical protein
	?	CP000730	= 462805	91 (1.070)					intergenic (+64/+39)	USA300HOU_0436/USA300HOU_0437	hypothetical protein/hypothetical protein
*	?	CP000730	2388283 =	98 (1.080)	4 (0.050)	3/244	12.9	4.5%	intergenic (+18/+84)	USA300HOU_2247/USA300HOU_2248	MFS family major facilitator transporter/hypothetical protein
	?	CP000730	2388362 =	82 (1.030)					intergenic (+97/+5)	USA300HOU_2247/USA300HOU_2248	MFS family major facilitator transporter/hypothetical protein
*	?	CP000730	1910817 =	57 (0.630)	10 (0.110)	4/268	12.9	17.4%	intergenic (+350/+1733)	sigS/ytbE	camphor resistance protein/possible aldo/keto reductase
	?	CP000730	2317562 =	40 (0.460)					intergenic (+215/+1901)	rhbC/asp23	possible Iuc family aerobactin synthesis protein/alkaline shock protein 23
*	?	CP000730	1910735 =	40 (0.440)	11 (0.130)	4/268	12.9	19.0%	intergenic (+268/+1815)	sigS/ytbE	camphor resistance protein/possible aldo/keto reductase
	?	CP000730	1910822 =	55 (0.630)					intergenic (+355/+1728)	sigS/ytbE	camphor resistance protein/possible aldo/keto reductase
*	?	CP000730	= 1804958	26 (0.290)	11 (0.130)	4/268	12.9	21.1%	intergenic (+1930/+395)	cycA/pykA	APC family amino acid‑polyamine‑organocation transporter/pyruvate kinase
	?	CP000730	1910822 =	57 (0.650)					intergenic (+355/+1728)	sigS/ytbE	camphor resistance protein/possible aldo/keto reductase
*	?	CP000730	1417767 =	92 (1.010)	3 (0.040)	3/254	13.2	3.5%	coding (152/831 nt)	oppD	oligopeptide ABC superfamily ATP binding cassette transporter, membrane protein
	?	CP000730	1417824 =	83 (1.000)					coding (95/831 nt)	oppD	oligopeptide ABC superfamily ATP binding cassette transporter, membrane protein