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 53 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	65.5%	‑1.6 / 10.3	33	intergenic (‑41/+267)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	3,750,798	0	T	G	61.5%	‑6.7 / 13.9	27	intergenic (+17/+330)	sgbE/yiaT	L‑ribulose‑5‑phosphate 4‑epimerase SgbE/outer membrane protein YiaT
*	NC_000913	2,177,234	0	C	A	58.3%	0.9 / 21.0	35	intergenic (‑30/+278)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	454,933	0	T	A	56.5%	‑4.9 / 15.5	23	intergenic (+144/‑200)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	4,283,226	0	G	C	56.5%	‑3.8 / 17.1	23	intergenic (‑151/+27)	yjcF/actP	pentapeptide repeat‑containing protein YjcF/acetate/glycolate:cation symporter
*	NC_000913	3,407,970	0	C	G	55.0%	6.5 / 26.6	22	L122V (CTT→GTT)	panF	pantothenate:Na(+) symporter
*	NC_000913	707,981	0	C	G	52.4%	14.3 / 30.8	25	intergenic (+224/‑353)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	2,470,427	0	C	A	47.4%	35.8 / 13.9	43	Q433K (CAA→AAA)	yfdI	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase
*	NC_000913	50,123	0	G	T	45.5%	15.0 / 10.7	22	E101* (GAA→TAA)	folA	dihydrofolate reductase
*	NC_000913	361,305	0	T	G	42.9%	23.9 / 14.1	35	N186H (AAC→CAC)	lacA	galactoside O‑acetyltransferase
*	NC_000913	931,029	0	G	C	42.6%	58.0 / 26.1	54	intergenic (‑67/+56)	cydD/trxB	glutathione/L‑cysteine ABC exporter subunit CydD/thioredoxin reductase
*	NC_000913	3,454,069	0	G	T	40.4%	59.5 / 11.2	57	Q444K (CAA→AAA)	gspA	Type II secretion system protein GspA
*	NC_000913	1,879,848	0	C	G	40.0%	49.1 / 11.0	36	G34A (GGA→GCA)	yeaR	DUF1971 domain‑containing protein YeaR
*	NC_000913	2,185,429	0	T	G	40.0%	42.9 / 22.4	40	intergenic (‑128/+95)	thiM/rcnR	hydroxyethylthiazole kinase/DNA‑binding transcriptional repressor RcnR
*	NC_000913	707,989	0	C	T	38.9%	16.6 / 11.4	27	intergenic (+232/‑345)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	4,050,007	0	A	T	37.8%	39.4 / 14.3	37	noncoding (109/109 nt)	spf	small regulatory RNA Spot 42
*	NC_000913	186,145	0	C	A	37.5%	35.2 / 10.1	32	A836S (GCC→TCC)	glnD	PII uridylyltransferase/uridylyl removing enzyme
*	NC_000913	2,177,255	0	G	T	36.8%	36.1 / 15.6	38	intergenic (‑51/+257)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	3,815,809	0	G	C	36.0%	34.9 / 16.9	25	intergenic (‑41/+54)	pyrE/rph	orotate phosphoribosyltransferase/truncated RNase PH
*	NC_000913	4,220,016	0	A	T	35.9%	44.8 / 15.9	39	Y474F (TAT→TTT)	aceK	isocitrate dehydrogenase kinase/phosphatase

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	4498181 =	NA (NA)	20 (0.360)	11/256	3.1	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
*	?	NC_000913	381258 =	NA (NA)	18 (0.320)	11/254	3.1	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	= 4086380	66 (1.170)	3 (0.050)	3/254	6.0	4.2%	coding (365/834 nt)	fdhD	sulfurtransferase for molybdenum cofactor sulfuration
	?	NC_000913	4086394 =	72 (1.290)					coding (379/834 nt)	fdhD	sulfurtransferase for molybdenum cofactor sulfuration