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	2,470,427	0	C	A	62.5%	12.3 / 37.8	43	Q433K (CAA→AAA)	yfdI	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase
*	NC_000913	2,177,234	0	C	A	62.1%	‑5.0 / 18.4	41	intergenic (‑30/+278)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	2,177,255	0	G	T	54.9%	‑4.0 / 34.9	51	intergenic (‑51/+257)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	708,004	0	C	A	52.9%	15.5 / 39.5	38	intergenic (+247/‑330)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	1,886,834	0	T	G	52.6%	‑0.1 / 10.5	19	intergenic (+24/+30)	yeaX/rnd	carnitine monooxygenase subunit YeaX/RNase D
*	NC_000913	2,449,194	0	A	C	52.2%	‑5.1 / 12.4	28	intergenic (+37/+34)	smrB/yfcO	putative endonuclease SmrB/DUF2544 domain‑containing protein YfcO
*	NC_000913	1,080,903	0	A	C	52.0%	8.4 / 22.4	27	intergenic (+90/‑453)	putP/efeU	proline:Na(+) symporter/inactive ferrous iron permease EfeU, N‑terminal fragment
*	NC_000913	2,470,411	0	A	T	48.8%	26.3 / 25.7	43	L427F (TTA→TTT)	yfdI	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase
*	NC_000913	3,004,946	0	G	T	47.5%	18.4 / 41.8	63	Q281K (CAA→AAA)	ygeV	putative sigma(54)‑dependent transcriptional regulator YgeV
*	NC_000913	2,470,431	0	G	T	46.9%	19.4 / 15.3	43	R434I (AGA→ATA)	yfdI	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase
*	NC_000913	2,139,598	0	T	G	44.2%	16.7 / 12.2	47	intergenic (+113/+161)	yegH/asmA	inner membrane protein YegH/putative assembly protein AsmA
*	NC_000913	2,177,221	0	T	G	43.5%	37.2 / 15.1	46	intergenic (‑17/+291)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	1,879,846	0	T	G	43.4%	41.1 / 18.3	53	T35P (ACG→CCG)	yeaR	DUF1971 domain‑containing protein YeaR
*	NC_000913	2,177,245	0	G	T	43.2%	18.5 / 11.8	46	intergenic (‑41/+267)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	2,570,475	0	A	C	41.5%	31.2 / 14.0	41	L426R (CTG→CGG)	eutE	putative aldehyde dehydrogenase, ethanolamine utilization protein
*	NC_000913	50,123	0	G	T	41.2%	26.4 / 14.1	34	E101* (GAA→TAA)	folA	dihydrofolate reductase
*	NC_000913	2,177,228	0	C	G	40.6%	21.1 / 18.6	44	intergenic (‑24/+284)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	707,984	0	C	G	40.5%	38.9 / 11.2	39	intergenic (+227/‑350)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	361,305	0	T	G	40.0%	33.8 / 16.8	40	N186H (AAC→CAC)	lacA	galactoside O‑acetyltransferase
*	NC_000913	1,224,912	0	T	G	40.0%	40.1 / 15.4	40	V150V (GTA→GTC)	minD	Z‑ring positioning protein MinD

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 =	90 (1.270)	17 (0.270)	12/224	2.9	19.9%	coding (290/630 nt)	ycfK	e14 prophage; protein StfP
	?	NC_000913	1209619 =	58 (0.930)					pseudogene (37/537 nt)	stfE	e14 prophage; putative side tail fiber protein fragment
*	?	NC_000913	= 1207805	79 (1.110)	6 (0.100)	6/224	4.8	8.6%	coding (305/630 nt)	ycfK	e14 prophage; protein StfP
	?	NC_000913	= 1209602	58 (0.930)					pseudogene (54/537 nt)	stfE	e14 prophage; putative side tail fiber protein fragment
*	?	NC_000913	409404 =	73 (1.030)	3 (0.040)	3/256	6.9	4.4%	coding (616/912 nt)	rdgC	nucleoid‑associated protein RdgC
	?	NC_000913	4004331 =	56 (0.790)					coding (367/468 nt)	yigI	putative thioesterase YigI