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 66 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	454,873	0	C	G	56.5%	‑2.4 / 13.1	27	intergenic (+84/‑260)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	454,934	0	A	C	55.6%	‑3.4 / 14.4	27	intergenic (+145/‑199)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	2,177,245	0	G	T	54.3%	‑3.8 / 17.2	37	intergenic (‑41/+267)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	454,866	0	G	T	53.8%	‑5.0 / 14.7	26	intergenic (+77/‑267)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	707,976	0	T	G	52.8%	0.8 / 30.1	36	intergenic (+219/‑358)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	2,177,234	0	C	A	52.0%	‑4.6 / 13.8	36	intergenic (‑30/+278)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	2,470,405	0	T	G	48.6%	29.1 / 19.6	37	V425V (GTT→GTG)	yfdI	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase
*	NC_000913	2,470,411	0	A	T	46.0%	24.9 / 18.1	37	L427F (TTA→TTT)	yfdI	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase
*	NC_000913	707,981	0	C	G	45.8%	17.6 / 16.3	36	intergenic (+224/‑353)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	707,984	0	C	G	45.7%	32.2 / 12.8	36	intergenic (+227/‑350)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	454,913	0	G	C	45.5%	2.4 / 10.6	26	intergenic (+124/‑220)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	3,004,946	0	G	T	44.7%	27.1 / 54.2	76	Q281K (CAA→AAA)	ygeV	putative sigma(54)‑dependent transcriptional regulator YgeV
*	NC_000913	1,879,846	0	T	G	42.9%	22.8 / 21.4	42	T35P (ACG→CCG)	yeaR	DUF1971 domain‑containing protein YeaR
*	NC_000913	3,955,616	0	T	G	42.9%	27.6 / 12.2	35	F96V (TTT→GTT)	ilvA	threonine deaminase
*	NC_000913	4,531,219	0	C	G	41.2%	74.3 / 19.7	55	D145H (GAC→CAC)	sgcX	KpLE2 phage‑like element; putative endoglucanase with Zn‑dependent exopeptidase domain
*	NC_000913	2,594,969	0	A	C	39.0%	52.1 / 14.4	41	G297G (GGT→GGG)	tmcA	tRNA(Met) cytidine acetyltransferase
*	NC_000913	2,177,255	0	G	T	38.5%	14.3 / 18.9	39	intergenic (‑51/+257)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	3,455,677	0	A	T	38.1%	31.1 / 18.2	42	N34Y (AAT→TAT)	gspC	Type II secretion system protein GspC
*	NC_000913	707,989	0	C	T	37.5%	24.1 / 16.4	37	intergenic (+232/‑345)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	2,594,962	0	G	C	37.2%	74.4 / 10.8	44	L300V (CTG→GTG)	tmcA	tRNA(Met) cytidine acetyltransferase

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	= 50103	38 (0.580)	3 (0.050)	3/248	5.8	7.5%	coding (281/480 nt)	folA	dihydrofolate reductase
	?	NC_000913	274739 =	NA (NA)					noncoding (411/1195 nt)	IS5	repeat region