breseq  version 0.39.0   mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence (highest frequency 20 of 90 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	579,004	0	C	T	75.6%	58.7 / 22.4	41	intergenic (‑111/+180)	borD/ybcV	prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV
*	NC_000913	578,831	0	T	C	75.0%	99.8 / 30.9	56	T21T (ACA→ACG)	borD	prophage lipoprotein BorD
*	NC_000913	1,636,413	0	C	A	73.0%	61.7 / 46.5	74	intergenic (‑46/‑343)	nohA/ynfO	putative prophage DNA‑packaging protein NohA/DUF3950 domain‑containing protein YnfO
*	NC_000913	1,636,423	0	T	C	72.2%	53.6 / 43.1	72	intergenic (‑56/‑333)	nohA/ynfO	putative prophage DNA‑packaging protein NohA/DUF3950 domain‑containing protein YnfO
*	NC_000913	579,651	0	C	T	71.8%	61.4 / 23.9	39	intergenic (‑57/‑229)	ybcV/ybcW	DUF1398 domain‑containing protein YbcV/uncharacterized protein YbcW
*	NC_000913	1,636,455	0	G	A	71.8%	70.7 / 56.2	78	intergenic (‑88/‑301)	nohA/ynfO	putative prophage DNA‑packaging protein NohA/DUF3950 domain‑containing protein YnfO
*	NC_000913	578,811	0	T	G	71.7%	100.0 / 42.5	61	Q28P (CAG→CCG)	borD	prophage lipoprotein BorD
*	NC_000913	1,636,503	0	T	C	71.3%	95.1 / 60.3	88	intergenic (‑136/‑253)	nohA/ynfO	putative prophage DNA‑packaging protein NohA/DUF3950 domain‑containing protein YnfO
*	NC_000913	1,636,484	0	C	T	71.2%	89.7 / 50.5	81	intergenic (‑117/‑272)	nohA/ynfO	putative prophage DNA‑packaging protein NohA/DUF3950 domain‑containing protein YnfO
*	NC_000913	578,809	0	T	C	71.0%	90.4 / 39.1	62	T29A (ACA→GCA)	borD	prophage lipoprotein BorD
*	NC_000913	579,134	0	T	C	71.0%	40.2 / 20.1	32	intergenic (‑241/+50)	borD/ybcV	prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV
*	NC_000913	579,385	0	A	G	71.0%	36.9 / 20.2	32	N70N (AAT→AAC)	ybcV	DUF1398 domain‑containing protein YbcV
*	NC_000913	579,457	0	A	G	69.4%	40.5 / 26.3	36	I46I (ATT→ATC)	ybcV	DUF1398 domain‑containing protein YbcV
*	NC_000913	579,502	0	A	G	68.8%	34.4 / 22.7	32	N31N (AAT→AAC)	ybcV	DUF1398 domain‑containing protein YbcV
*	NC_000913	579,099	0	A	.	68.4%	40.1 / 54.7	38	intergenic (‑206/+85)	borD/ybcV	prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV
*	NC_000913	579,671	0	T	C	68.3%	48.6 / 29.7	42	intergenic (‑77/‑209)	ybcV/ybcW	DUF1398 domain‑containing protein YbcV/uncharacterized protein YbcW
*	NC_000913	580,302	0	C	T	68.2%	84.8 / 48.2	66	R48R (AGG→AGA)	ylcI	DUF3950 domain‑containing protein YlcI
*	NC_000913	579,146	0	A	G	67.7%	27.0 / 25.3	31	intergenic (‑253/+38)	borD/ybcV	prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV
*	NC_000913	579,127	0	T	C	66.7%	32.2 / 25.3	33	intergenic (‑234/+57)	borD/ybcV	prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV
*	NC_000913	579,540	0	T	C	66.7%	26.0 / 21.7	27	N19D (AAC→GAC)	ybcV	DUF1398 domain‑containing protein YbcV

Marginal new junction evidence (sorted from low to high skew)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	2173734 =	31 (0.860)	4 (0.110)	4/486	2.7	11.4%	intergenic (‑861/+548)	gatD/gatB	galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component
	?	NC_000913	= 3584195	NA (NA)					noncoding (768/768 nt)	IS1	repeat region
*	?	NC_000913	= 4491693	34 (0.940)	3 (0.080)	3/476	3.0	9.6%	coding (833/1320 nt)	idnT	L‑idonate/5‑ketogluconate/gluconate transporter
	?	NC_000913	4492415 =	23 (0.650)					coding (111/1320 nt)	idnT	L‑idonate/5‑ketogluconate/gluconate transporter