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 62 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,177,221	0	T	G	58.8%	‑4.0 / 25.1	34	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	53.3%	‑4.1 / 14.3	15	intergenic (+280/+456)	ycdU/serX	uncharacterized protein YcdU/tRNA‑Ser
*	NC_000913	4,378,973	0	G	C	50.0%	‑5.9 / 10.9	24	intergenic (‑29/+34)	ampC/frdD	beta‑lactamase/fumarate reductase membrane protein FrdD
*	NC_000913	1,879,848	0	C	G	47.2%	39.4 / 13.2	39	G34A (GGA→GCA)	yeaR	DUF1971 domain‑containing protein YeaR
*	NC_000913	2,177,228	0	C	G	45.0%	‑6.4 / 14.7	32	intergenic (‑24/+284)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	669,355	0	G	T	43.3%	19.4 / 16.5	30	Q185K (CAA→AAA)	cobC	putative adenosylcobalamin phosphatase/alpha‑ribazole phosphatase
*	NC_000913	3,455,680	0	G	T	42.2%	37.9 / 20.5	45	V35L (GTG→TTG)	gspC	Type II secretion system protein GspC
*	NC_000913	4,220,007	0	T	G	40.9%	9.4 / 10.7	22	V471G (GTG→GGG)	aceK	isocitrate dehydrogenase kinase/phosphatase
*	NC_000913	2,470,411	0	A	T	39.5%	31.1 / 15.8	38	L427F (TTA→TTT)	yfdI	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase
*	NC_000913	707,984	0	C	G	39.4%	36.8 / 11.1	34	intergenic (+227/‑350)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	3,004,946	0	G	T	38.6%	36.8 / 17.4	44	Q281K (CAA→AAA)	ygeV	putative sigma(54)‑dependent transcriptional regulator YgeV
*	NC_000913	1,879,846	0	T	G	38.5%	32.2 / 12.8	39	T35P (ACG→CCG)	yeaR	DUF1971 domain‑containing protein YeaR
*	NC_000913	2,177,255	0	G	T	38.5%	16.4 / 16.9	39	intergenic (‑51/+257)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	2,470,416	0	A	T	38.2%	35.7 / 11.7	34	Y429F (TAT→TTT)	yfdI	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase
*	NC_000913	446,660	0	C	A	38.2%	51.0 / 11.6	55	D3Y (GAT→TAT)	yajR	putative major facilitator superfamily transport protein YajR
*	NC_000913	1,297,119	0	C	G	36.5%	76.4 / 18.0	67	E335Q (GAA→CAA)	adhE	aldehyde‑alcohol dehydrogenase
*	NC_000913	238,535	0	G	T	36.4%	71.7 / 14.2	69	H68N (CAT→AAT)	ykfM	uncharacterized protein YkfM
*	NC_000913	2,470,405	0	T	G	35.1%	39.7 / 10.2	37	V425V (GTT→GTG)	yfdI	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase
*	NC_000913	1,331,188	0	T	G	34.6%	69.8 / 11.7	55	S47R (AGT→AGG)	topA	DNA topoisomerase 1
*	NC_000913	2,872,863	0	G	C	33.3%	88.0 / 14.6	48	intergenic (‑43/+151)	ftsB/ygbE	cell division protein FtsB/conserved inner membrane protein YgbE

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 =	76 (1.160)	9 (0.160)	9/224	3.3	13.2%	coding (290/630 nt)	ycfK	e14 prophage; protein StfP
	?	NC_000913	1209619 =	52 (0.910)					pseudogene (37/537 nt)	stfE	e14 prophage; putative side tail fiber protein fragment
*	?	NC_000913	= 1207805	69 (1.050)	8 (0.140)	7/224	3.9	12.6%	coding (305/630 nt)	ycfK	e14 prophage; protein StfP
	?	NC_000913	= 1209602	51 (0.890)					pseudogene (54/537 nt)	stfE	e14 prophage; putative side tail fiber protein fragment
*	?	NC_000913	1467910 =	NA (NA)	6 (0.090)	6/256	4.8	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	= 2070275	NA (NA)	9 (0.140)	5/250	5.1	NA	intergenic (‑95/‑2)	insC‑3/yoeA	CP4‑44 prophage; IS2 insertion element repressor InsA/CP4‑44 prophage; TonB‑dependent receptor plug domain‑containing protein YoeA
	?	NC_000913	2996364 =	NA (NA)					noncoding (1328/1331 nt)	IS2	repeat region