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 82 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,725,384	0	A	G	70.5%	146.0 / 77.7	95	intergenic (‑66/+29)	glyQ/ysaB	glycine‑‑tRNA ligase subunit alpha/putative lipoprotein YsaB
*	NC_000913	4,182,820	0	C	T	68.7%	84.5 / 60.2	68	H526Y (CAC→TAC)	rpoB	RNA polymerase subunit beta
*	NC_000913	3,018,785	0	T	.	63.9%	34.6 / 120.4	64	coding (2726/3099 nt)	ygfK	putative oxidoreductase, Fe‑S subunit
*	NC_000913	2,177,221	0	T	G	59.1%	7.2 / 41.2	44	intergenic (‑17/+291)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	2,470,427	0	C	A	57.6%	0.5 / 24.5	33	Q433K (CAA→AAA)	yfdI	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase
*	NC_000913	2,177,245	0	G	T	55.3%	‑5.5 / 23.9	48	intergenic (‑41/+267)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	454,873	0	C	G	55.0%	‑4.9 / 12.7	22	intergenic (+84/‑260)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	454,866	0	G	T	52.4%	3.1 / 16.9	21	intergenic (+77/‑267)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	454,919	0	G	T	52.4%	13.6 / 23.0	26	intergenic (+130/‑214)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	3,998,023	0	A	C	52.2%	6.4 / 22.9	23	Q14P (CAG→CCG)	uvrD	ssDNA translocase and dsDNA helicase ‑ DNA helicase II
*	NC_000913	2,177,234	0	C	A	50.0%	15.0 / 11.8	42	intergenic (‑30/+278)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	3,004,946	0	G	T	48.9%	25.0 / 28.5	47	Q281K (CAA→AAA)	ygeV	putative sigma(54)‑dependent transcriptional regulator YgeV
*	NC_000913	707,976	0	T	G	48.8%	13.8 / 18.3	44	intergenic (+219/‑358)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	3,828,980	0	A	C	47.4%	5.2 / 10.8	38	Q12H (CAA→CAC)	xanP	xanthine:H(+) symporter XanP
*	NC_000913	707,981	0	C	G	46.9%	32.8 / 15.2	47	intergenic (+224/‑353)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	454,926	0	G	A	46.7%	‑0.7 / 13.2	26	intergenic (+137/‑207)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	298,557	0	A	C	45.0%	3.0 / 12.8	42	L57R (CTC→CGC)	paoD	molybdenum cofactor insertion chaperone for PaoABC
*	NC_000913	708,004	0	C	A	44.7%	48.6 / 15.7	52	intergenic (+247/‑330)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	4,220,016	0	A	T	42.9%	24.9 / 14.0	28	Y474F (TAT→TTT)	aceK	isocitrate dehydrogenase kinase/phosphatase
*	NC_000913	3,455,671	0	A	T	41.7%	26.6 / 27.4	48	I32F (ATT→TTT)	gspC	Type II secretion system protein GspC

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	151060 =	63 (0.930)	4 (0.060)	4/244	6.1	5.9%	coding (540/597 nt)	yadK	putative fimbrial protein YadK
	?	NC_000913	= 1989747	67 (1.040)					coding (67/1212 nt)	tyrP	tyrosine:H(+) symporter