breseq  version 0.35.4  revision f352f80f4bc9 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	454,919	0	G	T	58.8%	6.1 / 17.5	17	intergenic (+130/‑214)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	3,455,677	0	A	T	56.0%	‑2.4 / 21.4	25	N34Y (AAT→TAT)	gspC	Type II secretion system protein GspC
*	NC_000913	2,177,221	0	T	G	54.5%	3.5 / 22.8	22	intergenic (‑17/+291)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	580,759	0	G	C	53.3%	6.1 / 19.4	18	intergenic (‑314/‑75)	ylcI/nohD	DLP12 prophage; DUF3950 domain‑containing protein YlcI/DLP12 prophage; putative DNA‑packaging protein NohD
*	NC_000913	708,004	0	C	A	53.3%	2.8 / 11.9	17	intergenic (+247/‑330)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	4,604,344	0	C	G	48.0%	17.0 / 12.7	33	S62C (TCT→TGT)	bglJ	DNA‑binding transcriptional regulator BglJ
*	NC_000913	2,177,228	0	C	T	46.7%	‑1.3 / 12.8	22	intergenic (‑24/+284)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	2,177,255	0	G	T	42.9%	12.1 / 10.6	28	intergenic (‑51/+257)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	1,425,558	0	T	G	41.0%	28.5 / 15.8	39	V61G (GTT→GGT)	ynaK	Rac prophage; ParB‑like nuclease domain‑containing protein YnaK
*	NC_000913	1,425,560	0	A	T	41.0%	32.1 / 17.3	39	M62L (ATG→TTG)	ynaK	Rac prophage; ParB‑like nuclease domain‑containing protein YnaK
*	NC_000913	2,463,545	0	T	A	39.3%	32.8 / 10.1	28	D178E (GAT→GAA)	yfdF	protein YfdF
*	NC_000913	556,412	0	C	A	35.1%	46.8 / 10.2	37	G48C (GGC→TGC)	ybcI	conserved inner membrane protein YbcI
*	NC_000913	931,029	0	G	C	33.3%	59.0 / 14.6	39	intergenic (‑67/+56)	cydD/trxB	glutathione/L‑cysteine ABC exporter subunit CydD/thioredoxin reductase
*	NC_000913	3,933,222	0	G	T	32.6%	62.6 / 13.6	43	intergenic (+38/‑129)	kup/rbsD	K(+):H(+) symporter Kup/D‑ribose pyranase
*	NC_000913	4,395,508	0	A	G	32.4%	49.3 / 12.4	35	G481G (GGA→GGG)	nnr	NAD(P)HX epimerase/NAD(P)HX dehydratase
*	NC_000913	411,595	0	G	C	31.9%	70.1 / 11.7	48	A296G (GCT→GGT)	araJ	putative transport protein AraJ
*	NC_000913	3,004,946	0	G	T	31.2%	61.9 / 11.4	49	Q281K (CAA→AAA)	ygeV	putative sigma(54)‑dependent transcriptional regulator YgeV
*	NC_000913	4,296,060	0	C	T	30.9%	112.7 / 72.1	82	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO

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	1207790 =	60 (1.340)	9 (0.230)	9/224	2.1	18.3%	coding (290/630 nt)	ycfK	e14 prophage; protein StfP
	?	NC_000913	1209619 =	28 (0.710)					pseudogene (37/537 nt)	stfE	e14 prophage; putative side tail fiber protein fragment
*	?	NC_000913	= 1207805	53 (1.180)	4 (0.100)	4/224	3.7	9.8%	coding (305/630 nt)	ycfK	e14 prophage; protein StfP
	?	NC_000913	= 1209602	27 (0.690)					pseudogene (54/537 nt)	stfE	e14 prophage; putative side tail fiber protein fragment