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

Marginal read alignment evidence (highest frequency 20 of 83 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,684,749	0	A	C	39.3%	81.3 / 16.8	61	D164A (GAC→GCC)	tus	DNA replication terminus site‑binding protein
*	NC_000913	2,326,450	0	T	G	37.2%	119.8 / 16.0	79	G114G (GGT→GGG)	atoB	acetyl‑CoA acetyltransferase
*	NC_000913	2,386,862	0	G	A	34.4%	40.2 / 13.3	32	intergenic (+31/‑72)	yfbL/yfbM	putative peptidase YfbL/DUF1877 domain‑containing protein YfbM
*	NC_000913	4,056,115	0	A	C	33.7%	160.1 / 27.0	95	G75G (GGT→GGG)	glnL	protein histidine kinase NtrB
*	NC_000913	2,434,882	0	T	G	33.3%	130.1 / 16.5	79	Y252S (TAC→TCC)	truA	tRNA pseudouridine(38‑40) synthase
*	NC_000913	4,604,344	0	C	T	33.3%	54.5 / 13.8	39	S62F (TCT→TTT)	bglJ	DNA‑binding transcriptional regulator BglJ
*	NC_000913	1,825,056	0	G	A	32.6%	69.5 / 14.8	43	intergenic (‑119/+84)	ves/spy	HutD family protein Ves/ATP‑independent periplasmic chaperone
*	NC_000913	1,997,114	0	T	G	32.4%	101.3 / 12.6	69	D234A (GAC→GCC)	tcyN	cystine ABC transporter ATP binding subunit
*	NC_000913	2,228,275	0	T	C	31.7%	78.6 / 10.3	60	intergenic (‑1005/‑707)	yohF/yohP	putative oxidoreductase YohF/putative membrane protein YohP
*	NC_000913	1,322,428	0	G	A	31.4%	79.3 / 14.3	51	F173F (TTC→TTT)	trpE	anthranilate synthase subunit TrpE
*	NC_000913	4,336,901	0	T	A	31.4%	69.7 / 20.5	51	Y44F (TAT→TTT)	adiC	arginine:agmatine antiporter
*	NC_000913	1,074,816	0	T	G	31.1%	129.4 / 12.2	74	V192G (GTA→GGA)	rutR	DNA‑binding transcriptional dual regulator RutR
*	NC_000913	2,001,636	0	A	C	30.8%	138.4 / 11.0	78	L52V (TTA→GTA)	fliA	RNA polymerase sigma factor FliA
*	NC_000913	4,604,350	0	C	T	30.8%	62.1 / 10.1	39	S64F (TCT→TTT)	bglJ	DNA‑binding transcriptional regulator BglJ
*	NC_000913	3,864,099	0	C	A	30.6%	66.0 / 13.5	49	R67R (CGC→CGA)	yidP	putative DNA‑binding transcriptional regulator YidP
*	NC_000913	1,159,837	0	A	G	30.0%	77.8 / 10.8	50	I572T (ATC→ACC)	fhuE	ferric coprogen/ferric rhodotorulic acid outer membrane transporter
*	NC_000913	4,296,268	0	T	C	30.0%	51.2 / 25.2	40	intergenic (+474/+168)	gltP/yjcO	glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
*	NC_000913	766,716	0	G	T	28.9%	55.2 / 10.2	46	A245S (GCG→TCG)	mngA	2‑O‑alpha‑mannosyl‑D‑glycerate specific PTS enzyme II
*	NC_000913	4,457,105	0	A	G	28.7%	160.4 / 30.2	94	I441V (ATC→GTC)	mpl	UDP‑N‑acetylmuramate‑‑L‑alanyl‑gamma‑D‑glutamyl‑ meso‑2,6‑diaminoheptanedioate ligase
*	NC_000913	2,833,533	0	T	G	28.7%	179.3 / 11.1	101	V353G (GTG→GGG)	norV	anaerobic nitric oxide reductase flavorubredoxin

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	4295835 =	111 (1.260)	4 (0.050) +GTTG	4/478	5.8	4.3%	intergenic (+41/+601)	gltP/yjcO	glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
	?	NC_000913	= 4628846	69 (0.790)					intergenic (+299/+9)	nadR/ettA	DNA‑binding transcriptional repressor/NMN adenylyltransferase NadR/energy‑dependent translational throttle protein EttA
*	?	NC_000913	3207387 =	135 (1.540)	3 (0.030)	3/476	6.2	2.3%	coding (17/606 nt)	ttdB	L(+)‑tartrate dehydratase subunit beta
	?	NC_000913	3207672 =	121 (1.410)					coding (302/606 nt)	ttdB	L(+)‑tartrate dehydratase subunit beta
*	?	NC_000913	1604822 =	78 (0.890)	3 (0.030)	3/476	6.2	3.5%	coding (776/993 nt)	lsrD	Autoinducer‑2 ABC transporter membrane subunit LsrD
	?	NC_000913	= 1620648	90 (1.050)					coding (490/900 nt)	eamA	cysteine/O‑acetylserine exporter EamA
*	?	NC_000913	214421 =	104 (1.180)	3 (0.040)	3/474	6.2	4.5%	coding (131/546 nt)	yaeQ	uncharacterized protein YaeQ
	?	NC_000913	526533 =	26 (0.300)					coding (3273/4281 nt)	rhsD	protein RhsD