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 22 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	580,761	0	A	C	57.9%	‑3.6 / 11.9	19	intergenic (‑316/‑73)	ylcI/nohD	DLP12 prophage; DUF3950 domain‑containing protein YlcI/DLP12 prophage; putative DNA‑packaging protein NohD
*	NC_000913	2,177,228	0	C	G	57.9%	6.4 / 22.7	23	intergenic (‑24/+284)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	2,177,234	0	C	G	53.3%	8.1 / 21.8	23	intergenic (‑30/+278)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	4,220,018	0	G	T	52.6%	4.0 / 15.6	19	D475Y (GAT→TAT)	aceK	isocitrate dehydrogenase kinase/phosphatase
*	NC_000913	2,177,245	0	G	T	51.8%	0.9 / 19.5	27	intergenic (‑41/+267)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	707,976	0	T	G	50.0%	7.1 / 12.2	24	intergenic (+219/‑358)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	984,064	0	T	G	45.7%	16.2 / 10.7	35	F139V (TTT→GTT)	gloC	hydroxyacylglutathione hydrolase GloC
*	NC_000913	2,177,255	0	G	T	45.2%	7.2 / 14.9	31	intergenic (‑51/+257)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	4,220,016	0	A	T	45.0%	2.1 / 16.2	20	Y474F (TAT→TTT)	aceK	isocitrate dehydrogenase kinase/phosphatase
*	NC_000913	3,004,946	0	G	T	43.9%	31.2 / 13.0	42	Q281K (CAA→AAA)	ygeV	putative sigma(54)‑dependent transcriptional regulator YgeV
*	NC_000913	1,297,110	0	A	G	38.5%	20.8 / 11.5	32	S338P (TCC→CCC)	adhE	aldehyde‑alcohol dehydrogenase
*	NC_000913	2,736,240	0	C	A	36.0%	25.6 / 10.5	25	P32Q (CCA→CAA)	bamD	outer membrane protein assembly factor BamD
*	NC_000913	3,815,809	0	G	C	35.0%	24.6 / 13.7	20	intergenic (‑41/+54)	pyrE/rph	orotate phosphoribosyltransferase/truncated RNase PH
*	NC_000913	2,982,476	0	C	A	33.9%	95.2 / 24.8	62	intergenic (‑294/+21)	araE/kduD	arabinose:H(+) symporter/putative 2‑keto‑3‑deoxy‑D‑gluconate dehydrogenase
*	NC_000913	3,441,285	0	T	A	32.6%	50.9 / 11.9	43	N131Y (AAC→TAC)	rpsD	30S ribosomal subunit protein S4
*	NC_000913	2,642,521	0	T	G	30.9%	44.8 / 13.3	42	K108N (AAA→AAC)	rodZ	transmembrane component of cytoskeleton
*	NC_000913	361,305	0	T	G	28.9%	69.4 / 12.7	45	N186H (AAC→CAC)	lacA	galactoside O‑acetyltransferase
*	NC_000913	3,188,976	0	C	A	28.6%	74.0 / 13.6	56	pseudogene (1545/2434 nt)	yqiG	putative outer membrane usher protein YqiG
*	NC_000913	3,640,595	0	C	G	26.9%	117.6 / 11.7	53	intergenic (+50/‑267)	uspA/dtpB	universal stress global stress response regulator/dipeptide/tripeptide:H(+) symporter DtpB
*	NC_000913	3,312,733	0	C	A	21.4%	104.3 / 12.3	42	L15F (TTG→TTT)	truB	tRNA pseudouridine(55) synthase

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	381262 =	NA (NA)	4 (0.090)	3/252	4.8	NA	noncoding (3/1331 nt)	IS2	repeat region
	?	NC_000913	= 382594	NA (NA)					pseudogene (279/282 nt)	yaiX	putative acyltransferase, N‑terminal fragment