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

Marginal read alignment evidence (highest frequency 20 of 225 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	579,502	0	A	G	65.8%	34.5 / 37.0	41	N31N (AAT→AAC)	ybcV	DUF1398 domain‑containing protein YbcV
*	NC_000913	579,457	0	A	G	64.1%	31.2 / 37.0	39	I46I (ATT→ATC)	ybcV	DUF1398 domain‑containing protein YbcV
*	NC_000913	579,540	0	T	C	62.2%	38.5 / 40.3	45	N19D (AAC→GAC)	ybcV	DUF1398 domain‑containing protein YbcV
*	NC_000913	579,651	0	C	T	61.2%	27.6 / 53.2	50	intergenic (‑57/‑229)	ybcV/ybcW	DUF1398 domain‑containing protein YbcV/uncharacterized protein YbcW
*	NC_000913	578,729	0	A	G	61.0%	46.9 / 60.2	60	A55A (GCT→GCC)	borD	prophage lipoprotein BorD
*	NC_000913	579,671	0	T	C	59.6%	32.5 / 57.0	52	intergenic (‑77/‑209)	ybcV/ybcW	DUF1398 domain‑containing protein YbcV/uncharacterized protein YbcW
*	NC_000913	579,385	0	A	G	58.1%	17.1 / 49.6	43	N70N (AAT→AAC)	ybcV	DUF1398 domain‑containing protein YbcV
*	NC_000913	578,571	0	C	T	56.2%	7.6 / 62.5	48	intergenic (+3/+29)	rzpD/borD	putative prophage endopeptidase RzpD/prophage lipoprotein BorD
*	NC_000913	1,636,503	0	T	C	55.6%	6.1 / 49.5	45	intergenic (‑136/‑253)	nohA/ynfO	putative prophage DNA‑packaging protein NohA/DUF3950 domain‑containing protein YnfO
*	NC_000913	579,717	0	A	C	55.4%	30.5 / 62.5	56	intergenic (‑123/‑163)	ybcV/ybcW	DUF1398 domain‑containing protein YbcV/uncharacterized protein YbcW
*	NC_000913	578,574	0	A	C	55.1%	‑1.0 / 65.2	49	intergenic (+6/+26)	rzpD/borD	putative prophage endopeptidase RzpD/prophage lipoprotein BorD
*	NC_000913	578,605	0	T	G	54.9%	9.8 / 61.9	51	K97Q (AAA→CAA)	borD	prophage lipoprotein BorD
*	NC_000913	580,115	0	C	T	53.6%	‑0.9 / 102.1	69	intergenic (+29/+136)	ybcW/ylcI	uncharacterized protein YbcW/DUF3950 domain‑containing protein YlcI
*	NC_000913	1,636,484	0	C	T	52.3%	‑0.4 / 59.4	45	intergenic (‑117/‑272)	nohA/ynfO	putative prophage DNA‑packaging protein NohA/DUF3950 domain‑containing protein YnfO
*	NC_000913	579,004	0	C	T	52.2%	‑4.9 / 65.1	46	intergenic (‑111/+180)	borD/ybcV	prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV
*	NC_000913	579,285	0	T	C	52.2%	4.5 / 59.8	46	I104V (ATT→GTT)	ybcV	DUF1398 domain‑containing protein YbcV
*	NC_000913	580,119	0	A	G	52.1%	8.2 / 96.2	71	intergenic (+33/+132)	ybcW/ylcI	uncharacterized protein YbcW/DUF3950 domain‑containing protein YlcI
*	NC_000913	580,120	0	C	T	52.1%	‑6.5 / 101.5	71	intergenic (+34/+131)	ybcW/ylcI	uncharacterized protein YbcW/DUF3950 domain‑containing protein YlcI
*	NC_000913	1,429,732	0	G	A	50.7%	‑1.0 / 198.7	142	K228K (AAG→AAA)	stfR	putative prophage side tail fiber protein StfR
*	NC_000913	1,429,724	0	A	G	50.4%	9.1 / 206.5	143	T226A (ACC→GCC)	stfR	putative prophage side tail fiber protein StfR

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	257908 =	NA (NA)	9 (0.200)	8/486	2.5	15.8%	noncoding (768/768 nt)	IS1	repeat region
	?	NC_000913	1596913 =	48 (1.080)					intergenic (‑4471/+1704)	hipB/lsrK	antitoxin/DNA‑binding transcriptional repressor HipB/autoinducer‑2 kinase
*	?	NC_000913	= 1596921	44 (0.990)	6 (0.140)	6/486	2.9	12.0%	intergenic (‑4479/+1696)	hipB/lsrK	antitoxin/DNA‑binding transcriptional repressor HipB/autoinducer‑2 kinase
	?	NC_000913	= 1979270	NA (NA)					noncoding (1/768 nt)	IS1	repeat region
*	?	NC_000913	257908 =	NA (NA)	3 (0.070)	3/486	3.8	NA	noncoding (768/768 nt)	IS1	repeat region
	?	NC_000913	1396001 =	NA (NA)					intergenic (‑79/‑111)	ynaI/insH4	small conductance mechanosensitive channel YnaI/IS5 family transposase and trans‑activator