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

Marginal read alignment evidence (highest frequency 20 of 94 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,208,132	0	G	A	67.9%	34.0 / 45.8	54	intergenic (‑600/‑15)	purH/rrsE	bifunctional AICAR transformylase/IMP cyclohydrolase/16S ribosomal RNA
*	NC_000913	1,636,484	0	C	T	60.6%	16.3 / 34.2	33	intergenic (‑117/‑272)	nohA/ynfO	putative prophage DNA‑packaging protein NohA/DUF3950 domain‑containing protein YnfO
*	NC_000913	1,636,503	0	T	C	57.1%	1.8 / 45.5	36	intergenic (‑136/‑253)	nohA/ynfO	putative prophage DNA‑packaging protein NohA/DUF3950 domain‑containing protein YnfO
*	NC_000913	1,636,455	0	G	A	56.7%	‑4.4 / 40.6	30	intergenic (‑88/‑301)	nohA/ynfO	putative prophage DNA‑packaging protein NohA/DUF3950 domain‑containing protein YnfO
*	NC_000913	579,540	0	T	C	56.4%	13.0 / 47.9	39	N19D (AAC→GAC)	ybcV	DUF1398 domain‑containing protein YbcV
*	NC_000913	1,636,145	0	T	C	55.2%	‑4.9 / 39.3	29	T75A (ACA→GCA)	nohA	putative prophage DNA‑packaging protein NohA
*	NC_000913	579,502	0	A	G	54.8%	‑5.3 / 58.9	43	N31N (AAT→AAC)	ybcV	DUF1398 domain‑containing protein YbcV
*	NC_000913	579,385	0	A	G	52.6%	‑3.7 / 52.3	38	N70N (AAT→AAC)	ybcV	DUF1398 domain‑containing protein YbcV
*	NC_000913	1,636,128	0	C	T	51.4%	8.7 / 52.2	35	G80G (GGG→GGA)	nohA	putative prophage DNA‑packaging protein NohA
*	NC_000913	579,271	0	G	A	51.2%	‑6.0 / 61.7	41	H108H (CAC→CAT)	ybcV	DUF1398 domain‑containing protein YbcV
*	NC_000913	1,636,074	0	C	T	51.0%	6.2 / 67.4	49	E98E (GAG→GAA)	nohA	putative prophage DNA‑packaging protein NohA
*	NC_000913	579,004	0	C	T	50.0%	‑3.8 / 60.2	43	intergenic (‑111/+180)	borD/ybcV	prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV
*	NC_000913	579,099	0	A	.	50.0%	88.6 / 95.1	48	intergenic (‑206/+85)	borD/ybcV	prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV
*	NC_000913	1,636,068	0	T	C	50.0%	10.4 / 79.2	50	K100K (AAA→AAG)	nohA	putative prophage DNA‑packaging protein NohA
*	NC_000913	579,285	0	T	C	48.8%	‑2.8 / 57.1	41	I104V (ATT→GTT)	ybcV	DUF1398 domain‑containing protein YbcV
*	NC_000913	1,423,338	0	G	C	47.7%	52.7 / 78.1	45	intergenic (+26/‑62)	ydaW/rzoR	putative uncharacterized protein YdaW/putative prophage outer membrane lipoprotein RzoR
*	NC_000913	1,423,404	0	G	T	47.7%	32.4 / 57.7	44	R2L (CGA→CTA)	rzoR	putative prophage outer membrane lipoprotein RzoR
*	NC_000913	578,809	0	T	C	47.7%	0.6 / 93.5	65	T29A (ACA→GCA)	borD	prophage lipoprotein BorD
*	NC_000913	578,811	0	T	G	47.7%	9.3 / 91.9	65	Q28P (CAG→CCG)	borD	prophage lipoprotein BorD
*	NC_000913	1,636,413	0	C	A	47.6%	9.9 / 17.6	21	intergenic (‑46/‑343)	nohA/ynfO	putative prophage DNA‑packaging protein NohA/DUF3950 domain‑containing protein YnfO

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	= 4542690	17 (0.380)	3 (0.070)	3/464	2.5	14.9%	intergenic (+57/‑425)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	= 4542986	18 (0.420)					intergenic (+353/‑129)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit