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 23 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	AP012306	1,091,992	0	T	G	39.5%	549.5 / 80.5	319	intergenic (+38/‑145)	narI/ychS	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/predicted protein
*	AP012306	341,377	0	T	G	33.1%	201.0 / 26.3	131	G60G (GGT→GGG)	ribD	fused diaminohydroxyphosphoribosylaminopyrimidin e deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase
*	AP012306	3,527,368	0	A	C	29.3%	574.7 / 41.4	232	L140F (TTA→TTC)	rhaS	DNA‑binding transcriptional activator, L‑rhamnose‑binding
*	AP012306	1,944,288	0	A	C	28.9%	616.6 / 47.8	263	G361G (GGT→GGG)	menE	o‑succinylbenzoate‑CoA ligase
*	AP012306	644,417	0	G	A	27.9%	841.3 / inf	484	intergenic (+32/‑401)	lysQ/nadA	tRNA‑Lys/quinolinate synthase, subunit A
*	AP012306	3,938,887	0	C	T	26.8%	434.3 / 115.2	209	S44F (TCT→TTT)	bglJ	DNA‑binding transcriptional regulator
*	AP012306	1,421,147	0	T	G	26.6%	528.5 / 10.6	253	T79P (ACC→CCC)	ydhB	predicted DNA‑binding transcriptional regulator
*	AP012306	1,226,557	0	A	G	26.0%	365.6 / 75.4	173	G55G (GGA→GGG)	ydcU	predicted spermidine/putrescine transporter subunit
*	AP012306	3,324,433	0	T	A	24.1%	512.0 / 85.2	207	intergenic (+2/+52)	yieF/yieG	chromate reductase, Class I, flavoprotein/predicted inner membrane protein
*	AP012306	1,854,851	0	A	C	24.0%	732.3 / 42.2	272	T25P (ACC→CCC)	yejH	predicted ATP‑dependet helicase
*	AP012306	800,675	0	A	C	23.3%	582.1 / 26.5	223	T192P (ACC→CCC)	lolA	chaperone for lipoproteins
*	AP012306	2,376,612	0	T	G	23.3%	544.9 / 26.8	206	V326G (GTA→GGA)	ygbN	predicted transporter
*	AP012306	1,074,619	0	T	C	22.4%	335.3 / 100.9	179	S29G (AGC→GGC)	ldrA	toxic polypeptide, small
*	AP012306	3,182,861	0	A	C	21.7%	339.6 / 16.9	129	L198F (TTA→TTC)	yiaN	predicted transporter
*	AP012306	2,212,753	0	A	C	21.5%	540.9 / 39.9	191	Y241D (TAT→GAT)	hcaT	predicted 3‑phenylpropionic transporter
*	AP012306	3,116,354	0	T	G	21.2%	454.9 / 12.1	179	T307P (ACC→CCC)	yhjG	predicted outer membrane biogenesis protein
*	AP012306	1,128,412	0	T	G	21.1%	779.0 / 50.7	285	V29G (GTG→GGG)	yciO	conserved protein
*	AP012306	3,282,076	0	T	G	20.8%	570.6 / 16.7	231	intergenic (‑79/+27)	ilvB/ivbL	acetolactate synthase I, large subunit/ilvB operon leader peptide
*	AP012306	2,680,345	0	A	C	20.7%	568.6 / 14.9	215	T184P (ACC→CCC)	ttdA	L‑tartrate dehydratase, alpha subunit
*	AP012306	3,590,367	0	A	C	20.4%	756.7 / 22.2	264	T30P (ACC→CCC)	fabR	DNA‑binding transcriptional repressor

Marginal new junction evidence (lowest skew 10 of 100 shown)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	AP012306	644102 =	510 (1.660)	27 (0.090) +G	10/296	19.8	6.3%	noncoding (1/76 nt)	lysZ	tRNA‑Lys
	?	AP012306	= 2073541	302 (0.980)					intergenic (+1/‑46)	valX/valY	tRNA‑Val/tRNA‑Val
*	?	AP012306	= 236382	317 (1.030)	10 (0.040)	8/266	19.9	3.5%	intergenic (+59/‑117)	yafL/yafM	predicted lipoprotein and C40 family peptidase/conserved protein
	?	AP012306	237024 =	262 (0.960)					intergenic (+28/‑2736)	yafM/dinB	conserved protein/DNA polymerase IV
*	?	AP012306	= 3600650	NA (NA)	40 (0.130) +AAAGG	9/288	20.1	NA	noncoding (2797/2904 nt)	rrlB	23S ribosomal RNA (rrlB)
	?	AP012306	= 3642048	NA (NA)					noncoding (2793/2904 nt)	rrlE	23S ribosomal RNA (rrlE)
*	?	AP012306	= 3600658	NA (NA)	26 (0.090)	9/292	20.2	NA	noncoding (2805/2904 nt)	rrlB	23S ribosomal RNA (rrlB)
	?	AP012306	= 3642045	NA (NA)					noncoding (2790/2904 nt)	rrlE	23S ribosomal RNA (rrlE)
*	?	AP012306	= 1092512	400 (1.300)	12 (0.050)	7/258	20.2	3.6%	intergenic (+100/+3)	ychS/tpr	predicted protein/predicted protamine‑like protein
	?	AP012306	1092985 =	304 (1.150)					noncoding (66/85 nt)	tyrT	tRNA‑Tyr
*	?	AP012306	644102 =	511 (1.670)	25 (0.080) +GG	8/294	20.8	5.7%	noncoding (1/76 nt)	lysZ	tRNA‑Lys
	?	AP012306	= 2073420	331 (1.080)					noncoding (76/76 nt)	valU	tRNA‑Val
*	?	AP012306	3774746 =	334 (1.090)	5 (0.020)	5/258	21.4	1.7%	intergenic (‑86/+36)	yjdF/fumB	conserved inner membrane protein/anaerobic class I fumarate hydratase
	?	AP012306	3774766 =	280 (1.060)					intergenic (‑106/+16)	yjdF/fumB	conserved inner membrane protein/anaerobic class I fumarate hydratase
*	?	AP012306	= 1092334	337 (1.100)	5 (0.020)	5/258	21.4	1.7%	coding (198/276 nt)	ychS	predicted protein
	?	AP012306	1092985 =	304 (1.150)					noncoding (66/85 nt)	tyrT	tRNA‑Tyr
*	?	AP012306	= 3725357	179 (0.580)	6 (0.020)	6/284	21.6	3.4%	intergenic (+350/+181)	gltP/yjcO	glutamate/aspartate:proton symporter/conserved protein
	?	AP012306	= 3725373	166 (0.570)					intergenic (+366/+165)	gltP/yjcO	glutamate/aspartate:proton symporter/conserved protein
*	?	AP012306	= 3725131	239 (0.780)	6 (0.020)	6/284	21.6	3.0%	intergenic (+124/+407)	gltP/yjcO	glutamate/aspartate:proton symporter/conserved protein
	?	AP012306	= 3725373	166 (0.570)					intergenic (+366/+165)	gltP/yjcO	glutamate/aspartate:proton symporter/conserved protein