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	36,087	0	A	G	60.0%	671.8 / inf	1005	C155C (TGT→TGC)	tpn	IS431mec transposase
*	CP000730	36,124	0	G	A	59.3%	344.3 / inf	790	A143V (GCT→GTT)	tpn	IS431mec transposase
*	CP000730	76,295	0	T	C	57.5%	429.8 / inf	945	intergenic (+353/‑781)	USA300HOU_0072/USA300HOU_0075	universal stress protein/lysophospholipase
*	CP000730	36,315	0	G	A	57.4%	379.4 / inf	1374	Y79Y (TAC→TAT)	tpn	IS431mec transposase
*	CP000730	36,269	0	C	T	56.3%	126.6 / inf	1268	A95T (GCA→ACA)	tpn	IS431mec transposase
*	CP000730	76,322	0	G	A	55.5%	225.4 / inf	858	intergenic (+380/‑754)	USA300HOU_0072/USA300HOU_0075	universal stress protein/lysophospholipase
*	CP000730	35,970	0	T	C	55.1%	275.1 / inf	657	E194E (GAA→GAG)	tpn	IS431mec transposase
*	CP000730	76,353	0	G	A	52.1%	83.8 / inf	685	intergenic (+411/‑723)	USA300HOU_0072/USA300HOU_0075	universal stress protein/lysophospholipase
*	CP000730	1,929,861	0	T	C	51.4%	38.5 / 215.7	177	intergenic (‑944/‑224)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	36,413	0	C	T	51.2%	41.2 / inf	696	V47I (GTC→ATC)	tpn	IS431mec transposase
*	CP000730	1,929,867	0	G	T	50.3%	45.9 / 309.6	181	intergenic (‑950/‑218)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	2,291,785	0	A	G	50.0%	0.8 / 18.5	16	H325R (CAC→CGC)	USA300HOU_2155	transposase
*	CP000730	1,929,848	0	C	A	49.2%	66.0 / 254.0	185	intergenic (‑931/‑237)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,866	0	G	T	49.2%	51.3 / 254.1	182	intergenic (‑949/‑219)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,875	0	T	C	48.9%	9.3 / 256.7	186	intergenic (‑958/‑210)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,842	0	T	.	48.9%	316.4 / inf	184	intergenic (‑925/‑243)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,870	0	A	C	48.4%	41.0 / inf	188	intergenic (‑953/‑215)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,872	0	G	A	48.4%	34.0 / 236.2	188	intergenic (‑955/‑213)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,873	0	C	A	48.4%	67.6 / 266.0	188	intergenic (‑956/‑212)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
*	CP000730	1,929,843	0	A	.	48.4%	313.8 / inf	187	intergenic (‑926/‑242)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein

Marginal new junction evidence (lowest skew 10 of 124 shown)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	= 515130	NA (NA)	14 (0.140)	13/254	10.4	NA	noncoding (425/2921 nt)	rrl1	23S ribosomal RNA
	?	CP000730	= 515141	NA (NA)					noncoding (436/2921 nt)	rrl1	23S ribosomal RNA
*	?	CP000730	715303 =	129 (1.180)	12 (0.120)	11/240	10.8	9.2%	intergenic (+61/+56)	tagD/pbp4	glycerol‑3‑phosphate cytidylyltransferase/penicillin‑binding protein 4
	?	CP000730	715350 =	121 (1.240)					intergenic (+108/+9)	tagD/pbp4	glycerol‑3‑phosphate cytidylyltransferase/penicillin‑binding protein 4
*	?	CP000730	1878597 =	99 (0.910)	12 (0.130)	10/232	11.0	11.8%	intergenic (+56/+61)	ytfP/fmtB1	possible flavoprotein/cell surface anchored protein
	?	CP000730	1878652 =	93 (0.990)					intergenic (+111/+6)	ytfP/fmtB1	possible flavoprotein/cell surface anchored protein
*	?	CP000730	= 2753848	127 (1.170)	7 (0.090) +34 bp	7/200	11.2	7.2%	intergenic (+129/+59)	USA300HOU_2608/USA300HOU_2609	possible transcriptional regulator/possible metallo‑beta‑lactamase
	?	CP000730	2754851 =	117 (1.070)					intergenic (‑258/+6)	USA300HOU_2609/betT	possible metallo‑beta‑lactamase/BCCT family betaine/carnitine/choline transporter
*	?	CP000730	1205383 =	105 (0.960)	85 (0.960) +25 bp	8/218	11.5	55.9%	intergenic (+519/‑305)	yfiE/lspA	possible lactoylglutathione lyase/A8 family signal peptidase II
	?	CP000730	2478476 =	60 (0.550)					intergenic (+363/+708)	USA300HOU_2340/htrB	hypothetical membrane protein/hemin ABC superfamily ATP binding cassette transporter, ABC protein
*	?	CP000730	1205383 =	105 (0.960)	79 (0.890) +25 bp	8/218	11.5	57.0%	intergenic (+519/‑305)	yfiE/lspA	possible lactoylglutathione lyase/A8 family signal peptidase II
	?	CP000730	1426741 =	42 (0.390)					intergenic (‑472/+500)	pstS/yitL	phosphate ABC superfamily ATP binding cassette transporter, binding protein/hypothetical protein
*	?	CP000730	= 517640	NA (NA)	15 (0.140)	11/256	11.5	NA	intergenic (+14/‑61)	rrl1/rrf1	23S ribosomal RNA/5S ribosomal RNA
	?	CP000730	= 517643	NA (NA)					intergenic (+17/‑58)	rrl1/rrf1	23S ribosomal RNA/5S ribosomal RNA
*	?	CP000730	197371 =	106 (0.970)	10 (0.100)	10/254	11.9	9.0%	coding (396/975 nt)	USA300HOU_0186	possible ABC superfamily ATP‑binding cassette transporter, binding protein
	?	CP000730	= 197367	103 (1.000)					coding (392/975 nt)	USA300HOU_0186	possible ABC superfamily ATP‑binding cassette transporter, binding protein
*	?	CP000730	= 2317464	123 (1.130)	6 (0.070) +28 bp	6/212	12.4	5.7%	intergenic (+117/+1999)	rhbC/asp23	possible Iuc family aerobactin synthesis protein/alkaline shock protein 23
	?	CP000730	2319448 =	129 (1.180)					intergenic (+2101/+15)	rhbC/asp23	possible Iuc family aerobactin synthesis protein/alkaline shock protein 23
*	?	CP000730	= 1205323	92 (0.840)	99 (0.910)	10/268	12.4	50.1%	intergenic (+459/‑365)	yfiE/lspA	possible lactoylglutathione lyase/A8 family signal peptidase II
	?	CP000730	1205383 =	105 (0.960)					intergenic (+519/‑305)	yfiE/lspA	possible lactoylglutathione lyase/A8 family signal peptidase II