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 52 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,177,228	0	C	G	64.0%	6.5 / 10.9	32	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	60.0%	‑2.0 / 12.6	31	intergenic (‑30/+278)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	454,919	0	G	T	58.8%	1.5 / 11.5	20	intergenic (+130/‑214)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	2,177,221	0	T	G	58.1%	‑4.2 / 21.0	31	intergenic (‑17/+291)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	1,097,109	0	A	T	57.1%	‑5.1 / 10.7	15	intergenic (+280/+456)	ycdU/serX	uncharacterized protein YcdU/tRNA‑Ser
*	NC_000913	1,636,442	0	C	G	55.6%	3.2 / 18.1	19	intergenic (‑75/‑314)	nohA/ynfO	Qin prophage; putative prophage DNA‑packaging protein NohA/Qin prophage; protein YnfO
*	NC_000913	1,879,848	0	C	G	55.6%	11.4 / 35.0	29	G34A (GGA→GCA)	yeaR	DUF1971 domain‑containing protein YeaR
*	NC_000913	2,470,472	0	G	T	50.0%	13.5 / 11.6	24	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	1,879,846	0	T	G	48.3%	10.0 / 11.8	29	T35P (ACG→CCG)	yeaR	DUF1971 domain‑containing protein YeaR
*	NC_000913	3,455,677	0	A	T	44.9%	30.1 / 26.1	49	N34Y (AAT→TAT)	gspC	Type II secretion system protein GspC
*	NC_000913	2,470,405	0	T	G	44.7%	35.0 / 21.0	38	V425V (GTT→GTG)	yfdI	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase
*	NC_000913	2,177,255	0	G	T	44.7%	14.8 / 28.4	47	intergenic (‑51/+257)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	1,879,875	0	C	A	44.1%	50.1 / 10.3	38	G25V (GGA→GTA)	yeaR	DUF1971 domain‑containing protein YeaR
*	NC_000913	3,004,946	0	G	T	42.6%	50.7 / 21.6	54	Q281K (CAA→AAA)	ygeV	putative sigma(54)‑dependent transcriptional regulator YgeV
*	NC_000913	50,118	0	T	G	41.0%	41.1 / 15.8	39	V99G (GTT→GGT)	folA	dihydrofolate reductase
*	NC_000913	3,455,671	0	A	T	40.8%	29.8 / 24.2	49	I32F (ATT→TTT)	gspC	Type II secretion system protein GspC
*	NC_000913	2,470,411	0	A	T	40.5%	32.0 / 22.2	37	L427F (TTA→TTT)	yfdI	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase
*	NC_000913	2,930,955	0	A	C	39.6%	44.9 / 14.2	49	intergenic (+12/‑100)	sdaB/ygdG	L‑serine deaminase II/flap endonuclease
*	NC_000913	3,455,680	0	G	T	39.6%	28.6 / 23.7	48	V35L (GTG→TTG)	gspC	Type II secretion system protein GspC
*	NC_000913	3,815,809	0	G	C	37.5%	32.2 / 12.1	24	intergenic (‑41/+54)	pyrE/rph	orotate phosphoribosyltransferase/truncated RNase PH

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	1467910 =	NA (NA)	11 (0.180)	9/256	3.5	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
*	?	NC_000913	= 1207805	49 (0.800)	6 (0.110)	6/224	4.0	15.2%	coding (305/630 nt)	ycfK	e14 prophage; protein StfP
	?	NC_000913	= 1209602	24 (0.450)					pseudogene (54/537 nt)	stfE	e14 prophage; putative side tail fiber protein fragment
*	?	NC_000913	= 2070269	NA (NA)	3 (0.050)	3/252	5.9	NA	noncoding (3/1331 nt)	IS2	repeat region
	?	NC_000913	= 3187430	NA (NA)					intergenic (+15/‑2)	insD‑5/yqiG	IS2 insertion element protein InsB/putative outer membrane usher protein YqiG