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 90 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	707,981	0	C	G	55.9%	11.6 / 42.9	50	intergenic (+224/‑353)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	4,378,973	0	G	C	55.9%	1.5 / 15.4	34	intergenic (‑29/+34)	ampC/frdD	beta‑lactamase/fumarate reductase membrane protein FrdD
*	NC_000913	454,919	0	G	T	54.0%	30.5 / 47.8	40	intergenic (+130/‑214)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	707,976	0	T	G	54.0%	7.6 / 42.3	50	intergenic (+219/‑358)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	454,873	0	C	G	52.9%	‑4.5 / 23.0	36	intergenic (+84/‑260)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	454,934	0	A	C	52.8%	10.1 / 33.4	36	intergenic (+145/‑199)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	707,992	0	C	A	52.6%	13.6 / 35.1	54	intergenic (+235/‑342)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	454,933	0	T	A	51.4%	2.6 / 27.9	36	intergenic (+144/‑200)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	708,004	0	C	A	50.0%	43.3 / 13.9	55	intergenic (+247/‑330)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	2,177,245	0	G	T	50.0%	12.5 / 14.8	45	intergenic (‑41/+267)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	1,708,326	0	G	T	47.5%	63.8 / 21.0	59	E470* (GAA→TAA)	rsxC	SoxR [2Fe‑2S] reducing system protein RsxC
*	NC_000913	2,177,221	0	T	G	46.0%	20.6 / 17.3	37	intergenic (‑17/+291)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	2,177,255	0	G	T	43.6%	42.9 / 25.0	55	intergenic (‑51/+257)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	454,926	0	G	C	42.9%	8.4 / 14.1	36	intergenic (+137/‑207)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	1,636,447	0	C	G	42.1%	45.6 / 12.4	42	intergenic (‑80/‑309)	nohA/ynfO	Qin prophage; putative prophage DNA‑packaging protein NohA/Qin prophage; protein YnfO
*	NC_000913	707,984	0	C	G	41.2%	37.7 / 17.3	51	intergenic (+227/‑350)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	3,004,946	0	G	T	41.1%	35.8 / 30.9	57	Q281K (CAA→AAA)	ygeV	putative sigma(54)‑dependent transcriptional regulator YgeV
*	NC_000913	4,220,007	0	T	G	41.0%	22.2 / 16.9	39	V471G (GTG→GGG)	aceK	isocitrate dehydrogenase kinase/phosphatase
*	NC_000913	2,139,594	0	A	C	39.2%	21.4 / 11.7	51	intergenic (+109/+165)	yegH/asmA	inner membrane protein YegH/putative assembly protein AsmA
*	NC_000913	4,604,344	0	C	G	38.9%	56.0 / 12.0	50	S62C (TCT→TGT)	bglJ	DNA‑binding transcriptional regulator BglJ

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	4542682 =	63 (0.840)	12 (0.170)	8/236	4.8	15.5%	intergenic (+49/‑433)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	4542996 =	72 (1.030)					intergenic (+363/‑119)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
*	?	NC_000913	381258 =	NA (NA)	14 (0.190)	7/252	5.4	NA	pseudogene (3/417 nt)	yaiX	putative acyltransferase, N‑terminal fragment
	?	NC_000913	= 382589	NA (NA)					noncoding (1330/1331 nt)	IS2	repeat region
*	?	NC_000913	4498181 =	NA (NA)	17 (0.230)	7/254	5.5	NA	noncoding (1/1331 nt)	IS2	repeat region
	?	NC_000913	= 4499512	NA (NA)					intergenic (+12/+81)	insD‑6/yjgX	KpLE2 phage‑like element; IS2 insertion element protein InsB/KpLE2 phage‑like element; putative phosphoethanolamine transferase YjgX, N‑terminal fragment