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 98 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,177,245	0	G	T	59.6%	8.7 / 14.0	53	intergenic (‑41/+267)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	2,177,234	0	C	A	55.3%	‑6.5 / 23.7	53	intergenic (‑30/+278)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	4,378,981	0	C	G	50.0%	‑4.3 / 14.9	28	intergenic (‑37/+26)	ampC/frdD	beta‑lactamase/fumarate reductase membrane protein FrdD
*	NC_000913	3,815,809	0	G	C	45.0%	42.5 / 31.1	40	intergenic (‑41/+54)	pyrE/rph	orotate phosphoribosyltransferase/truncated RNase PH
*	NC_000913	3,004,946	0	G	T	44.8%	58.3 / 31.3	67	Q281K (CAA→AAA)	ygeV	putative sigma(54)‑dependent transcriptional regulator YgeV
*	NC_000913	1,879,846	0	T	G	44.2%	27.2 / 22.7	43	T35P (ACG→CCG)	yeaR	DUF1971 domain‑containing protein YeaR
*	NC_000913	729,383	0	T	G	44.1%	0.1 / 12.6	34	intergenic (+43/‑200)	ybfA/rhsC	DUF2517 domain‑containing protein YbfA/rhs element protein RhsC
*	NC_000913	4,283,228	0	T	G	43.8%	‑2.5 / 11.2	36	intergenic (‑153/+25)	yjcF/actP	pentapeptide repeat‑containing protein YjcF/acetate/glycolate:cation symporter
*	NC_000913	4,220,007	0	T	G	43.2%	17.4 / 14.5	37	V471G (GTG→GGG)	aceK	isocitrate dehydrogenase kinase/phosphatase
*	NC_000913	3,828,980	0	A	C	42.5%	11.6 / 11.1	47	Q12H (CAA→CAC)	xanP	xanthine:H(+) symporter XanP
*	NC_000913	3,455,680	0	G	T	40.5%	53.6 / 11.6	43	V35L (GTG→TTG)	gspC	Type II secretion system protein GspC
*	NC_000913	1,425,560	0	A	T	39.7%	55.2 / 34.7	61	M62L (ATG→TTG)	ynaK	Rac prophage; ParB‑like nuclease domain‑containing protein YnaK
*	NC_000913	2,470,472	0	G	T	39.3%	16.8 / 14.1	29	intergenic (+10/+605)	yfdI/yfdK	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase/CPS‑53 (KpLE1) prophage; putative tail fiber assembly protein YfdK
*	NC_000913	1,708,326	0	G	T	38.9%	76.5 / 13.5	56	E470* (GAA→TAA)	rsxC	SoxR [2Fe‑2S] reducing system protein RsxC
*	NC_000913	2,177,228	0	C	G	38.5%	29.0 / 22.8	52	intergenic (‑24/+284)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	707,981	0	C	G	38.2%	41.5 / 12.5	45	intergenic (+224/‑353)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	4,220,016	0	A	T	37.8%	27.3 / 19.7	38	Y474F (TAT→TTT)	aceK	isocitrate dehydrogenase kinase/phosphatase
*	NC_000913	1,592,972	0	C	A	37.7%	135.0 / 11.1	79	pseudogene (5115/5422 nt)	yneO	AIDA‑I family autotransporter YneO
*	NC_000913	2,930,955	0	A	C	37.5%	56.3 / 12.0	48	intergenic (+12/‑100)	sdaB/ygdG	L‑serine deaminase II/flap endonuclease
*	NC_000913	2,177,255	0	G	T	37.0%	30.5 / 29.6	56	intergenic (‑51/+257)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I

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	68 (0.880)	8 (0.110)	6/238	5.4	10.4%	intergenic (+57/‑425)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	= 4542986	75 (1.040)					intergenic (+353/‑129)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
*	?	NC_000913	1467910 =	NA (NA)	3 (0.040)	3/256	7.3	NA	noncoding (1331/1331 nt)	IS2	repeat region
	?	NC_000913	= 1469242	NA (NA)					intergenic (‑93/‑4)	insC‑2/ydbA	IS2 insertion element repressor InsA/putative outer membrane protein, N‑terminal fragment