breseq  version 0.39.0   mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence (highest frequency 20 of 39 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	729,710	0	T	G	36.5%	40.5 / 10.7	52	V43G (GTG→GGG)	rhsC	rhs element protein RhsC
*	NC_000913	4,622,250	0	A	G	36.0%	77.1 / 13.2	51	E161G (GAG→GGG)	yjjJ	toxin YjjJ
*	NC_000913	1,825,061	0	G	A	35.0%	57.6 / 19.2	40	intergenic (‑124/+79)	ves/spy	HutD family protein Ves/ATP‑independent periplasmic chaperone
*	NC_000913	1,346,653	0	C	A	33.3%	23.2 / 10.2	30	L30F (TTG→TTT)	pdeR	cyclic di‑GMP phosphodiesterase PdeR
*	NC_000913	3,788,061	0	T	G	33.3%	127.9 / 13.9	91	G408G (GGT→GGG)	envC	murein hydrolase activator EnvC
*	NC_000913	811,721	0	T	G	32.8%	145.7 / 13.4	120	V67G (GTG→GGG)	bioC	malonyl‑acyl carrier protein methyltransferase
*	NC_000913	2,851,654	0	T	G	30.8%	114.8 / 11.3	68	G218G (GGT→GGG)	hypB	hydrogenase isoenzymes nickel incorporation protein HypB
*	NC_000913	144,160	0	C	T	30.6%	76.0 / 18.0	49	F153F (TTC→TTT)	yadH	putative ABC transporter membrane subunit YadH
*	NC_000913	4,286,478	0	A	C	30.1%	130.8 / 17.7	95	G298G (GGT→GGG)	acs	acetyl‑CoA synthetase (AMP‑forming)
*	NC_000913	1,825,056	0	G	A	29.7%	68.0 / 10.5	37	intergenic (‑119/+84)	ves/spy	HutD family protein Ves/ATP‑independent periplasmic chaperone
*	NC_000913	1,360,780	0	T	A	28.9%	78.1 / 10.6	45	L43F (TTA→TTT)	puuA	glutamate‑putrescine ligase
*	NC_000913	2,337,723	0	A	C	28.6%	103.9 / 13.4	74	G566G (GGT→GGG)	gyrA	DNA gyrase subunit A
*	NC_000913	3,556,207	0	T	C	28.2%	145.4 / 13.3	71	S215G (AGT→GGT)	rtcA	RNA 3'‑terminal phosphate cyclase
*	NC_000913	2,878,947	0	C	T	27.4%	102.4 / 16.8	63	E276K (GAA→AAA)	cas1	multifunctional nuclease Cas1
*	NC_000913	2,828,506	0	T	G	27.4%	115.7 / 12.0	89	V257G (GTG→GGG)	srlD	sorbitol‑6‑phosphate 2‑dehydrogenase
*	NC_000913	288,382	0	A	C	27.4%	170.7 / 13.4	98	T532P (ACC→CCC)	yagH	putative xylosidase/arabinosidase
*	NC_000913	1,825,031	0	C	T	27.0%	68.6 / 11.7	37	intergenic (‑94/+109)	ves/spy	HutD family protein Ves/ATP‑independent periplasmic chaperone
*	NC_000913	3,177,531	0	A	C	27.0%	123.6 / 11.2	64	V127G (GTG→GGG)	nudF	ADP‑sugar pyrophosphatase
*	NC_000913	2,185,199	0	T	G	26.2%	138.6 / 12.9	82	T35P (ACC→CCC)	thiM	hydroxyethylthiazole kinase
*	NC_000913	3,357,015	0	T	C	25.6%	216.9 / 82.3	122	L764P (CTG→CCG)	gltB	glutamate synthase subunit GltB

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	= 2421268	53 (0.760)	6 (0.090)	6/490	3.6	10.2%	coding (648/648 nt)	yfcG	disulfide bond oxidoreductase YfcG
	?	NC_000913	= 3131340	NA (NA)					noncoding (1195/1195 nt)	IS5	repeat region
*	?	NC_000913	= 2344409	27 (0.390)	5 (0.070)	5/482	3.8	15.8%	intergenic (‑240/+185)	yfaL/ypaB	putative autotransporter adhesin YfaL/protein YpaB
	?	NC_000913	= 3131340	NA (NA)					noncoding (1195/1195 nt)	IS5	repeat region
*	?	NC_000913	= 2290113	NA (NA)	4 (0.060)	4/490	4.1	6.8%	noncoding (1/1195 nt)	IS5	repeat region
	?	NC_000913	2421265 =	55 (0.790)					coding (645/648 nt)	yfcG	disulfide bond oxidoreductase YfcG