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 37 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	60.0%	‑5.5 / 14.1	35	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	59.3%	‑1.6 / 12.7	38	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	58.8%	11.0 / 15.1	34	intergenic (‑51/+257)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	707,984	0	C	G	56.5%	12.3 / 30.7	24	intergenic (+227/‑350)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	4,613,297	0	A	T	55.0%	‑4.8 / 12.3	20	Y296F (TAT→TTT)	yjjU	putative patatin‑like phospholipase YjjU
*	NC_000913	707,976	0	T	G	50.0%	6.9 / 10.5	24	intergenic (+219/‑358)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	3,004,946	0	G	T	50.0%	3.7 / 25.0	36	Q281K (CAA→AAA)	ygeV	putative sigma(54)‑dependent transcriptional regulator YgeV
*	NC_000913	3,455,677	0	A	T	48.6%	18.3 / 18.7	35	N34Y (AAT→TAT)	gspC	Type II secretion system protein GspC
*	NC_000913	931,029	0	G	C	48.4%	21.4 / 23.1	31	intergenic (‑67/+56)	cydD/trxB	glutathione/L‑cysteine ABC exporter subunit CydD/thioredoxin reductase
*	NC_000913	1,879,846	0	T	G	47.1%	7.7 / 20.7	34	T35P (ACG→CCG)	yeaR	DUF1971 domain‑containing protein YeaR
*	NC_000913	2,171,831	0	T	G	46.9%	13.3 / 11.8	32	intergenic (‑104/+2)	gatR/gatD	DNA‑binding transcriptional repressor GatR, N‑terminal fragment/galactitol‑1‑phosphate 5‑dehydrogenase
*	NC_000913	2,470,431	0	G	A	41.7%	17.4 / 15.1	32	R434K (AGA→AAA)	yfdI	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase
*	NC_000913	2,470,405	0	T	G	41.4%	29.6 / 11.1	29	V425V (GTT→GTG)	yfdI	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase
*	NC_000913	4,439,033	0	T	G	40.5%	41.4 / 15.9	37	N77T (AAC→ACC)	ytfJ	protein YtfJ
*	NC_000913	2,177,221	0	T	G	37.8%	23.6 / 12.2	37	intergenic (‑17/+291)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	3,455,680	0	G	T	37.8%	34.8 / 11.6	37	V35L (GTG→TTG)	gspC	Type II secretion system protein GspC
*	NC_000913	2,177,272	0	T	A	37.0%	27.9 / 15.8	46	intergenic (‑68/+240)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	3,955,616	0	T	G	36.1%	37.1 / 18.1	37	F96V (TTT→GTT)	ilvA	threonine deaminase
*	NC_000913	361,307	0	A	T	35.0%	52.4 / 13.8	40	I185K (ATA→AAA)	lacA	galactoside O‑acetyltransferase
*	NC_000913	1,757,197	0	C	A	34.8%	119.3 / 14.0	66	intergenic (+87/‑224)	pykF/lpp	pyruvate kinase I/murein lipoprotein

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	= 1207805	60 (1.110)	9 (0.190)	9/224	3.0	16.8%	coding (305/630 nt)	ycfK	e14 prophage; protein StfP
	?	NC_000913	= 1209602	37 (0.780)					pseudogene (54/537 nt)	stfE	e14 prophage; putative side tail fiber protein fragment
*	?	NC_000913	1207790 =	60 (1.110)	9 (0.190)	9/224	3.0	16.8%	coding (290/630 nt)	ycfK	e14 prophage; protein StfP
	?	NC_000913	1209619 =	37 (0.780)					pseudogene (37/537 nt)	stfE	e14 prophage; putative side tail fiber protein fragment
*	?	NC_000913	2392618 =	41 (0.760)	4 (0.080)	4/236	4.9	9.6%	coding (424/1530 nt)	nuoM	NADH:quinone oxidoreductase subunit M
	?	NC_000913	= 2392614	38 (0.760)					coding (428/1530 nt)	nuoM	NADH:quinone oxidoreductase subunit M
*	?	NC_000913	= 274941	NA (NA)	3 (0.060)	3/256	5.8	NA	noncoding (209/1195 nt)	IS5	repeat region
	?	NC_000913	274945 =	NA (NA)					noncoding (205/1195 nt)	IS5	repeat region