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

Marginal read alignment evidence (highest frequency 20 of 216 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	579,811	0	C	T	65.0%	33.2 / 34.8	40	intergenic (‑217/‑69)	ybcV/ybcW	DUF1398 domain‑containing protein YbcV/uncharacterized protein YbcW
*	NC_000913	578,571	0	C	T	64.4%	27.2 / 44.4	45	intergenic (+3/+29)	rzpD/borD	putative prophage endopeptidase RzpD/prophage lipoprotein BorD
*	NC_000913	578,605	0	T	G	64.4%	46.8 / 43.0	45	K97Q (AAA→CAA)	borD	prophage lipoprotein BorD
*	NC_000913	578,574	0	A	C	63.6%	36.1 / 37.1	45	intergenic (+6/+26)	rzpD/borD	putative prophage endopeptidase RzpD/prophage lipoprotein BorD
*	NC_000913	579,717	0	A	C	60.0%	22.0 / 27.4	30	intergenic (‑123/‑163)	ybcV/ybcW	DUF1398 domain‑containing protein YbcV/uncharacterized protein YbcW
*	NC_000913	579,099	0	A	.	58.5%	4.0 / 111.2	53	intergenic (‑206/+85)	borD/ybcV	prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV
*	NC_000913	579,004	0	C	T	58.2%	28.8 / 60.9	55	intergenic (‑111/+180)	borD/ybcV	prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV
*	NC_000913	579,651	0	C	T	55.9%	12.7 / 36.0	35	intergenic (‑57/‑229)	ybcV/ybcW	DUF1398 domain‑containing protein YbcV/uncharacterized protein YbcW
*	NC_000913	579,671	0	T	C	55.2%	7.8 / 32.3	30	intergenic (‑77/‑209)	ybcV/ybcW	DUF1398 domain‑containing protein YbcV/uncharacterized protein YbcW
*	NC_000913	580,302	0	C	T	54.8%	14.0 / 79.1	62	R48R (AGG→AGA)	ylcI	DUF3950 domain‑containing protein YlcI
*	NC_000913	579,127	0	T	C	53.7%	9.7 / 73.0	54	intergenic (‑234/+57)	borD/ybcV	prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV
*	NC_000913	1,634,724	0	G	A	53.5%	7.1 / 54.8	43	F54F (TTC→TTT)	tfaQ	putative tail fiber assembly protein TfaQ
*	NC_000913	578,427	0	G	C	53.3%	3.7 / 128.6	75	T107T (ACG→ACC)  R34P (CGG→CCG)	rzpD rzoD	putative prophage endopeptidase RzpD putative prophage lysis lipoprotein RzoD
*	NC_000913	1,634,578	0	T	C	53.1%	10.5 / 62.8	49	E103G (GAA→GGA)	tfaQ	putative tail fiber assembly protein TfaQ
*	NC_000913	1,429,714	0	A	C	52.9%	10.8 / 168.4	119	A222A (GCA→GCC)	stfR	putative prophage side tail fiber protein StfR
*	NC_000913	579,134	0	T	C	52.8%	‑0.4 / 72.1	53	intergenic (‑241/+50)	borD/ybcV	prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV
*	NC_000913	1,634,597	0	C	A	52.8%	13.6 / 81.6	53	V97F (GTT→TTT)	tfaQ	putative tail fiber assembly protein TfaQ
*	NC_000913	1,429,708	0	A	G	52.1%	2.0 / 172.9	120	T220T (ACA→ACG)	stfR	putative prophage side tail fiber protein StfR
*	NC_000913	1,634,676	0	A	G	51.8%	13.4 / 70.6	56	D70D (GAT→GAC)	tfaQ	putative tail fiber assembly protein TfaQ
*	NC_000913	1,429,702	0	A	C	51.7%	2.2 / 168.2	116	A218A (GCA→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	3113622 =	35 (0.900)	3 (0.080)	3/490	3.7	7.9%	coding (731/810 nt)	pppA	prepilin peptidase
	?	NC_000913	= 3584195	NA (NA)					noncoding (768/768 nt)	IS1	repeat region
*	?	NC_000913	381368 =	NA (NA)	3 (0.080)	3/482	3.7	NA	noncoding (109/1331 nt)	IS2	repeat region
	?	NC_000913	381615 =	NA (NA)					noncoding (356/1331 nt)	IS2	repeat region