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 157 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	822,955	0	T	G	69.0%	11.3 / 36.3	43	T495P (ACC→CCC)	ybhF	ATP‑binding cassette domain‑containing protein
*	NZ_CP009273	822,963	0	T	G	68.2%	1.8 / 40.4	44	D492A (GAC→GCC)	ybhF	ATP‑binding cassette domain‑containing protein
*	NZ_CP009273	3,738,361	0	T	G	63.3%	7.9 / 17.4	30	G66G (GGT→GGG)	yiaN	2,3‑diketo‑L‑gulonate transporter large permease YiaN
*	NZ_CP009273	4,594,161	0	C	T	61.3%	5.7 / 83.0	94	S62F (TCT→TTT)	bglJ	DNA‑binding transcriptional activator BglJ
*	NZ_CP009273	2,380,362	0	C	T	61.1%	‑1.2 / 14.1	18	intergenic (+52/‑51)	yfbL/yfbM	M28 family metallopeptidase/YfbM family protein
*	NZ_CP009273	3,126,661	0	T	G	59.1%	9.2 / 25.6	22	H219P (CAC→CCC)	yghS	dTMP kinase
*	NZ_CP009273	4,594,167	0	C	T	58.5%	‑0.1 / 87.6	94	S64F (TCT→TTT)	bglJ	DNA‑binding transcriptional activator BglJ
*	NZ_CP009273	899,438	0	A	C	58.3%	33.1 / 44.5	36	G162G (GGT→GGG)	ybjP	lipoprotein
*	NZ_CP009273	2,738,448	0	A	C	58.0%	23.2 / 58.2	50	V84G (GTG→GGG)	trmD	tRNA (guanosine(37)‑N1)‑methyltransferase TrmD
*	NZ_CP009273	766,353	0	T	G	55.6%	15.6 / 22.6	18	intergenic (+286/‑561)	mngB/cydA	mannosylglycerate hydrolase/cytochrome ubiquinol oxidase subunit I
*	NZ_CP009273	822,957	0	A	G	54.5%	28.7 / 48.0	44	L494P (CTC→CCC)	ybhF	ATP‑binding cassette domain‑containing protein
*	NZ_CP009273	1,429,984	0	G	A	54.2%	‑2.9 / 25.4	24	intergenic (‑108/+33)	uspF/ompN	universal stress protein UspF/porin OmpN
*	NZ_CP009273	2,290,243	0	T	G	52.9%	39.8 / 47.5	34	L87F (TTA→TTC)	ccmB	heme exporter protein CcmB
*	NZ_CP009273	68,443	0	T	G	52.3%	53.0 / 59.9	44	G202G (GGT→GGG)	yabI	DedA family protein
*	NZ_CP009273	2,380,341	0	G	A	52.2%	0.6 / 26.1	23	intergenic (+31/‑72)	yfbL/yfbM	M28 family metallopeptidase/YfbM family protein
*	NZ_CP009273	4,142,237	0	T	G	52.2%	48.9 / 56.1	46	T264P (ACC→CCC)	ppc	phosphoenolpyruvate carboxylase
*	NZ_CP009273	1,429,975	0	G	A	51.8%	8.6 / 31.5	27	intergenic (‑99/+42)	uspF/ompN	universal stress protein UspF/porin OmpN
*	NZ_CP009273	5,159	0	G	A	51.7%	10.1 / 32.2	29	intergenic (+139/‑75)	thrC/yaaX	threonine synthase/DUF2502 domain‑containing protein
*	NZ_CP009273	5,162	0	T	A	50.0%	29.0 / 11.4	30	intergenic (+142/‑72)	thrC/yaaX	threonine synthase/DUF2502 domain‑containing protein
*	NZ_CP009273	595,032	0	T	G	50.0%	13.1 / 22.8	32	V288G (GTG→GGG)	cusA	Cu(+)/Ag(+) efflux RND transporter permease subunit CusA

Marginal new junction evidence (sorted from low to high skew)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	4532499 =	27 (0.480)	6 (0.120)	6/152	2.7	14.8%	intergenic (+49/‑433)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP009273	4532813 =	45 (0.900)					intergenic (+363/‑119)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
*	?	NZ_CP009273	= 4532507	23 (0.410)	6 (0.120)	5/152	3.0	15.7%	intergenic (+57/‑425)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP009273	= 4532803	44 (0.880)					intergenic (+353/‑129)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA