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 173 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	512,643	0	A	G	44.1%	14.1 / 65.4	60	intergenic (+711/‑6052)	recR/speA_2	Recombination protein RecR/Arginine decarboxylase
*	USA300TCH1516_ALE	277,427	0	G	C	43.5%	6.6 / 30.4	23	A84A (GCG→GCC)	USA300HOU_RS01215	hypothetical protein
*	USA300TCH1516_ALE	277,467	0	C	T	42.1%	6.8 / 15.9	19	L98F (CTT→TTT)	USA300HOU_RS01215	hypothetical protein
*	USA300TCH1516_ALE	1,584,183	0	T	C	41.2%	7.8 / 35.5	34	L510L (CTA→CTG)	USA300HOU_RS07765	hypothetical protein
*	USA300TCH1516_ALE	1,584,189	0	C	T	41.2%	18.5 / 31.6	34	L508L (TTG→TTA)	USA300HOU_RS07765	hypothetical protein
*	USA300TCH1516_ALE	1,584,147	0	G	A	37.5%	30.1 / 20.5	32	S522S (AGC→AGT)	USA300HOU_RS07765	hypothetical protein
*	USA300TCH1516_ALE	1,584,153	0	C	T	37.5%	26.1 / 24.9	32	K520K (AAG→AAA)	USA300HOU_RS07765	hypothetical protein
*	USA300TCH1516_ALE	386,762	0	T	A	36.5%	54.9 / 41.8	53	intergenic (‑152/‑60)	licR/slyA_1	putative licABCH operon regulator/Transcriptional regulator SlyA
*	USA300TCH1516_ALE	111,516	0	C	A	36.2%	62.3 / 43.9	47	Q196K (CAA→AAA)	USA300HOU_RS00520	putative lipoprotein
*	USA300TCH1516_ALE	658,055	0	A	T	35.3%	13.6 / 11.4	17	L157F (TTA→TTT)	USA300HOU_RS03150	hypothetical protein
*	USA300TCH1516_ALE	1,584,144	0	T	C	34.3%	26.6 / 28.0	35	R523R (AGA→AGG)	USA300HOU_RS07765	hypothetical protein
*	USA300TCH1516_ALE	1,584,156	0	A	T	34.3%	38.8 / 30.1	35	S519S (TCT→TCA)	USA300HOU_RS07765	hypothetical protein
*	USA300TCH1516_ALE	1,584,159	0	C	A	34.3%	41.4 / 27.7	35	P518P (CCG→CCT)	USA300HOU_RS07765	hypothetical protein
*	USA300TCH1516_ALE	1,584,162	0	C	T	34.3%	35.5 / 25.3	35	L517L (TTG→TTA)	USA300HOU_RS07765	hypothetical protein
*	USA300TCH1516_ALE	111,512	0	A	G	33.3%	43.4 / 37.3	48	S194S (TCA→TCG)	USA300HOU_RS00520	putative lipoprotein
*	USA300TCH1516_ALE	1,584,174	0	G	A	33.3%	38.1 / 22.3	36	N513N (AAC→AAT)	USA300HOU_RS07765	hypothetical protein
*	USA300TCH1516_ALE	2,705,742	0	C	T	33.3%	35.6 / 24.9	36	A31T (GCG→ACG)	crtQ	4,4'‑diaponeurosporenoate glycosyltransferase
*	USA300TCH1516_ALE	620,218	0	G	T	31.2%	50.3 / 18.3	33	V261L (GTA→TTA)	sdrE	Serine‑aspartate repeat‑containing protein E
*	USA300TCH1516_ALE	620,223	0	C	T	31.2%	38.7 / 19.3	33	N262N (AAC→AAT)	sdrE	Serine‑aspartate repeat‑containing protein E
*	USA300TCH1516_ALE	1,284,248	0	T	A	31.2%	33.3 / 26.1	32	S271S (TCT→TCA)	polC_1	DNA polymerase III PolC‑type

Marginal new junction evidence (lowest skew 10 of 13 shown)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 800928	37 (1.040)	7 (0.210)	6/266	2.3	17.9%	intergenic (+62/‑289)	hisC_1/USA300HOU_RS03915	Histidinol‑phosphate aminotransferase/Putative 5'(3')‑deoxyribonucleotidase
	?	USA300TCH1516_ALE	801948 =	29 (0.850)					intergenic (+189/+435)	USA300HOU_RS03915/USA300HOU_RS03920	Putative 5'(3')‑deoxyribonucleotidase/Putative lipid kinase
*	?	USA300TCH1516_ALE	= 2731894	28 (0.840)	5 (0.150) +ATTATAAACA	4/242	2.7	15.2%	intergenic (‑22/‑111)	USA300HOU_RS14060/cocE	hypothetical protein/Cocaine esterase
	?	USA300TCH1516_ALE	2731895 =	30 (0.840)					intergenic (‑23/‑110)	USA300HOU_RS14060/cocE	hypothetical protein/Cocaine esterase
*	?	USA300TCH1516_ALE	2278955 =	38 (1.060)	4 (0.150) +34 bp	3/212	2.8	11.8%	coding (3578/3882 nt)	ebh_3	Extracellular matrix‑binding protein ebh
	?	USA300TCH1516_ALE	= 2278980	41 (1.150)					coding (3553/3882 nt)	ebh_3	Extracellular matrix‑binding protein ebh
*	?	USA300TCH1516_ALE	= 672536	46 (1.290)	3 (0.100)	3/234	3.0	7.9%	intergenic (+138/‑241)	nth_1/btuF	Endonuclease III/Vitamin B12‑binding protein
	?	USA300TCH1516_ALE	672603 =	32 (1.070)					intergenic (+205/‑174)	nth_1/btuF	Endonuclease III/Vitamin B12‑binding protein
*	?	USA300TCH1516_ALE	= 895801	29 (0.810)	3 (0.100)	3/246	3.2	9.5%	coding (822/822 nt)	metQ_2	Methionine‑binding lipoprotein MetQ
	?	USA300TCH1516_ALE	909758 =	32 (1.020)					intergenic (‑681/‑353)	USA300HOU_RS04500/csbD_1	hypothetical protein/Stress response protein CsbD
*	?	USA300TCH1516_ALE	895785 =	26 (0.730)	8 (0.260)	3/246	3.2	22.6%	coding (806/822 nt)	metQ_2	Methionine‑binding lipoprotein MetQ
	?	USA300TCH1516_ALE	= 909740	32 (1.020)					intergenic (‑663/‑371)	USA300HOU_RS04500/csbD_1	hypothetical protein/Stress response protein CsbD
*	?	USA300TCH1516_ALE	= 2144160	31 (0.870)	4 (0.120) +TGGTTTATCT	3/260	3.3	12.2%	coding (484/1254 nt)	USA300HOU_RS10940	hypothetical protein
	?	USA300TCH1516_ALE	2144165 =	31 (0.870)					coding (479/1254 nt)	USA300HOU_RS10940	hypothetical protein
*	?	USA300TCH1516_ALE	2080223 =	19 (0.530)	3 (0.090)	3/264	3.4	14.0%	intergenic (‑131/+133)	ytrA/USA300HOU_RS10505	HTH‑type transcriptional repressor YtrA/hypothetical protein
	?	USA300TCH1516_ALE	= 2080217	19 (0.560)					intergenic (‑125/+139)	ytrA/USA300HOU_RS10505	HTH‑type transcriptional repressor YtrA/hypothetical protein
*	?	USA300TCH1516_ALE	= 2635582	50 (1.400)	4 (0.110) +TCT	3/274	3.5	7.7%	coding (366/3057 nt)	fnbA_2	Fibronectin‑binding protein A
	?	USA300TCH1516_ALE	2635601 =	48 (1.340)					coding (347/3057 nt)	fnbA_2	Fibronectin‑binding protein A
*	?	USA300TCH1516_ALE	= 2376100	37 (1.040)	5 (0.140)	3/280	3.5	10.8%	intergenic (‑77/‑110)	topB/USA300HOU_RS12205	DNA topoisomerase 3/hypothetical protein
	?	USA300TCH1516_ALE	2376113 =	46 (1.290)					intergenic (‑90/‑97)	topB/USA300HOU_RS12205	DNA topoisomerase 3/hypothetical protein