breseq  version 0.35.4  revision f352f80f4bc9 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence (highest frequency 20 of 26 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP025533	2,084,510	0	T	A	50.3%	‑3.4 / inf	297	intergenic (‑12/+189)	dapA/CYL77_09945	4‑hydroxy‑tetrahydrodipicolinate synthase/thymidylate synthase (FAD)
*	CP025533	2,084,508	0	G	T	50.0%	26.0 / inf	298	intergenic (‑10/+191)	dapA/CYL77_09945	4‑hydroxy‑tetrahydrodipicolinate synthase/thymidylate synthase (FAD)
*	CP025533	2,084,509	0	G	T	50.0%	33.0 / inf	298	intergenic (‑11/+190)	dapA/CYL77_09945	4‑hydroxy‑tetrahydrodipicolinate synthase/thymidylate synthase (FAD)
*	CP025533	2,420,733	0	C	T	48.1%	260.1 / inf	235	P464S (CCA→TCA)	CYL77_11475	HNH endonuclease
*	CP025533	2,420,723	0	G	A	47.7%	277.6 / inf	242	V460V (GTG→GTA)	CYL77_11475	HNH endonuclease
*	CP025533	2,420,717	0	A	C	47.5%	317.2 / inf	242	G458G (GGA→GGC)	CYL77_11475	HNH endonuclease
*	CP025533	2,420,726	0	G	T	47.5%	333.0 / inf	242	G461G (GGG→GGT)	CYL77_11475	HNH endonuclease
*	CP025533	2,420,739	0	G	A	47.2%	277.1 / inf	229	G466S (GGT→AGT)	CYL77_11475	HNH endonuclease
*	CP025533	2,420,708	0	T	C	47.1%	285.8 / inf	240	P455P (CCT→CCC)	CYL77_11475	HNH endonuclease
*	CP025533	2,420,738	0	G	A	47.0%	282.9 / inf	230	V465V (GTG→GTA) ‡	CYL77_11475	HNH endonuclease
*	CP025533	2,420,737	0	T	C	46.9%	281.4 / inf	230	V465A (GTG→GCG) ‡	CYL77_11475	HNH endonuclease
*	CP025533	2,420,710	0	C	T	46.9%	278.8 / inf	240	A456V (GCT→GTT)	CYL77_11475	HNH endonuclease
*	CP025533	2,086,244	0	T	G	45.5%	70.0 / inf	248	G2G (GGA→GGC)	CYL77_09950	4‑hydroxy‑tetrahydrodipicolinate reductase
*	CP025533	2,420,781	0	A	C	42.0%	396.9 / inf	219	S480R (AGT→CGT)	CYL77_11475	HNH endonuclease
*	CP025533	2,420,786	0	G	C	41.0%	435.2 / inf	222	S481S (TCG→TCC)	CYL77_11475	HNH endonuclease
*	CP025533	2,420,810	0	A	G	39.6%	392.3 / 301.1	230	K489K (AAA→AAG)	CYL77_11475	HNH endonuclease
*	CP025533	2,420,828	0	C	G	39.1%	459.4 / inf	235	P495P (CCC→CCG)	CYL77_11475	HNH endonuclease
*	CP025533	985,647	0	A	C	38.6%	346.6 / 308.7	202	P272P (CCA→CCC)	CYL77_04730	HNH endonuclease
*	CP025533	985,671	0	A	C	34.2%	410.5 / 265.3	203	R280R (CGA→CGC)	CYL77_04730	HNH endonuclease
*	CP025533	985,522	0	T	G	32.2%	255.5 / 187.3	152	S231A (TCA→GCA)	CYL77_04730	HNH endonuclease

Marginal new junction evidence (sorted from low to high skew)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP025533	= 1777777	73 (0.530)	5 (0.050)	5/340	17.8	6.9%	intergenic (‑3/+31)	CYL77_08485/CYL77_08490	tRNA‑Gly/tRNA‑Val
	?	CP025533	1777992 =	84 (0.890)					intergenic (‑4/‑344)	CYL77_08495/CYL77_08500	tRNA‑Gly/tRNA‑Val
*	?	CP025533	= 497710	105 (0.760)	6 (0.060)	5/346	18.1	7.8%	intergenic (+2/‑251)	CYL77_02460/CYL77_02465	tRNA‑Thr/tRNA‑Thr
	?	CP025533	498036 =	69 (0.720)					intergenic (+3/‑36)	CYL77_02465/CYL77_02470	tRNA‑Thr/tRNA‑Met
*	?	CP025533	= 2166721	114 (0.830)	3 (0.020)	3/494	25.9	2.6%	intergenic (‑375/+163)	CYL77_10310/CYL77_10315	3‑carboxy‑cis,cis‑muconate cycloisomerase/hypothetical protein
	?	CP025533	2352056 =	NA (NA)					intergenic (+230/+6)	CYL77_11115/CYL77_11120	permease/IS30 family transposase ISCg2