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 31 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	40.2%	404.0 / 64.0	244	intergenic (+38/‑145)	narI/ychS	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/predicted protein
*	AP012306	1,944,288	0	A	C	37.9%	413.6 / 69.3	232	G361G (GGT→GGG)	menE	o‑succinylbenzoate‑CoA ligase
*	AP012306	1,226,557	0	A	G	30.3%	318.4 / 92.3	178	G55G (GGA→GGG)	ydcU	predicted spermidine/putrescine transporter subunit
*	AP012306	341,377	0	T	G	30.0%	180.3 / 30.5	111	G60G (GGT→GGG)	ribD	fused diaminohydroxyphosphoribosylaminopyrimidin e deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase
*	AP012306	2,714,555	0	T	G	28.8%	606.8 / 31.5	282	T175P (ACC→CCC)	ygjV	conserved inner membrane protein
*	AP012306	2,680,345	0	A	C	27.3%	433.8 / 40.2	195	T184P (ACC→CCC)	ttdA	L‑tartrate dehydratase, alpha subunit
*	AP012306	644,417	0	G	A	27.1%	1063.9 / inf	580	intergenic (+32/‑401)	lysQ/nadA	tRNA‑Lys/quinolinate synthase, subunit A
*	AP012306	3,527,368	0	A	C	26.9%	603.4 / 56.4	250	L140F (TTA→TTC)	rhaS	DNA‑binding transcriptional activator, L‑rhamnose‑binding
*	AP012306	3,590,367	0	A	C	24.5%	783.1 / 50.6	298	T30P (ACC→CCC)	fabR	DNA‑binding transcriptional repressor
*	AP012306	406,677	0	A	G	24.3%	456.4 / 25.3	181	K294E (AAA→GAA)	hemH	ferrochelatase
*	AP012306	2,326,979	0	A	C	24.3%	522.8 / 14.5	214	intergenic (‑5/+68)	gshA/yqaA	gamma‑glutamate‑cysteine ligase/conserved inner membrane protein
*	AP012306	202,417	0	T	G	24.3%	556.5 / 27.8	241	V409G (GTA→GGA)	tilS	tRNA(Ile)‑lysidine synthetase
*	AP012306	2,376,612	0	T	G	24.2%	505.0 / 21.5	190	V326G (GTA→GGA)	ygbN	predicted transporter
*	AP012306	3,938,887	0	C	T	24.2%	644.7 / 136.7	277	S44F (TCT→TTT)	bglJ	DNA‑binding transcriptional regulator
*	AP012306	2,558,071	0	A	C	24.0%	626.6 / 30.8	254	V302G (GTA→GGA)	visC	predicted oxidoreductase, FAD/NAD(P)‑binding domain
*	AP012306	935,054	0	G	T	23.8%	296.0 / 39.3	101	intergenic (+24/‑1406)	putP/ycdO	proline:sodium symporter/conserved protein
*	AP012306	800,675	0	A	C	23.8%	608.5 / 29.8	241	T192P (ACC→CCC)	lolA	chaperone for lipoproteins
*	AP012306	1,854,851	0	A	C	23.8%	669.4 / 58.6	261	T25P (ACC→CCC)	yejH	predicted ATP‑dependet helicase
*	AP012306	2,857,911	0	A	C	23.4%	559.6 / 18.6	210	K180N (AAA→AAC)	aaeR	predicted DNA‑binding transcriptional regulator, efflux system
*	AP012306	3,716,932	0	T	A	23.2%	589.2 / 133.7	237	intergenic (‑348/‑45)	acs/nrfA	bifunctional acetyl‑CoA synthetase/nitrite reductase, formate‑dependent, cytochrome

Marginal new junction evidence (lowest skew 10 of 206 shown)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	AP012306	= 997497	292 (0.910)	15 (0.050)	15/268	10.0	5.4%	coding (41/1305 nt)	ndh	respiratory NADH dehydrogenase 2/cupric reductase
	?	AP012306	997993 =	262 (0.910)					coding (537/1305 nt)	ndh	respiratory NADH dehydrogenase 2/cupric reductase
*	?	AP012306	= 215364	NA (NA)	15 (0.050)	13/288	10.9	NA	noncoding (745/2905 nt)	rrlH	23S ribosomal RNA (rrlH)
	?	AP012306	= 215372	NA (NA)					noncoding (753/2905 nt)	rrlH	23S ribosomal RNA (rrlH)
*	?	AP012306	= 1092512	363 (1.130)	13 (0.050)	10/258	11.2	4.3%	intergenic (+100/+3)	ychS/tpr	predicted protein/predicted protamine‑like protein
	?	AP012306	1092985 =	270 (0.970)					noncoding (66/85 nt)	tyrT	tRNA‑Tyr
*	?	AP012306	= 546605	224 (0.700)	11 (0.030)	11/294	11.5	4.7%	coding (1695/2583 nt)	leuS	leucyl‑tRNA synthetase
	?	AP012306	= 546618	224 (0.710)					coding (1682/2583 nt)	leuS	leucyl‑tRNA synthetase
*	?	AP012306	= 1092334	290 (0.900)	10 (0.040)	8/258	11.9	3.7%	coding (198/276 nt)	ychS	predicted protein
	?	AP012306	1092985 =	270 (0.970)					noncoding (66/85 nt)	tyrT	tRNA‑Tyr
*	?	AP012306	= 2684153	331 (1.030)	9 (0.030)	9/288	12.0	2.7%	coding (40/216 nt)	rpsU	30S ribosomal subunit protein S21
	?	AP012306	= 2684161	318 (1.030)					coding (48/216 nt)	rpsU	30S ribosomal subunit protein S21
*	?	AP012306	591499 =	327 (1.020)	7 (0.020)	7/274	12.5	2.3%	coding (1293/2199 nt)	speF	ornithine decarboxylase isozyme, inducible
	?	AP012306	591511 =	290 (0.980)					coding (1281/2199 nt)	speF	ornithine decarboxylase isozyme, inducible
*	?	AP012306	3838276 =	407 (1.270)	6 (0.020)	6/268	12.8	1.6%	intergenic (+79/‑101)	rnr/rlmB	exoribonuclease R, RNase R/23S rRNA (Gm2251)‑methyltransferase
	?	AP012306	3838337 =	385 (1.340)					intergenic (+140/‑40)	rnr/rlmB	exoribonuclease R, RNase R/23S rRNA (Gm2251)‑methyltransferase
*	?	AP012306	= 3600658	NA (NA)	29 (0.090)	7/292	12.8	NA	noncoding (2805/2904 nt)	rrlB	23S ribosomal RNA (rrlB)
	?	AP012306	= 3642045	NA (NA)					noncoding (2790/2904 nt)	rrlE	23S ribosomal RNA (rrlE)
*	?	AP012306	= 2275835	NA (NA)	7 (0.020)	7/290	12.8	NA	noncoding (950/1542 nt)	rrsG	16S ribosomal RNA (rrnG)
	?	AP012306	= 2275847	NA (NA)					noncoding (938/1542 nt)	rrsG	16S ribosomal RNA (rrnG)