BRESEQ :: Marginal Predictions

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 50 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	297,897	0	C	T	51.6%	532.0 / inf	1742	E130K (GAG→AAG)	paoA	PaoABC aldehyde oxidoreductase, 2Fe‑2S subunit
*	CP009273	309,254	0	G	A	49.4%	178.1 / inf	1366	intergenic (‑301/+173)	ykgR/ykgP	uncharacterized protein/pseudogene, oxidoreductase family
*	CP009273	580,748	0	G	T	43.4%	271.8 / inf	572	T114T (ACC→ACA)	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,742	0	C	T	42.8%	243.5 / inf	541	T116T (ACG→ACA)	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,814	0	T	G	41.3%	413.7 / inf	574	T92T (ACA→ACC)	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,784	0	G	A	41.2%	323.0 / inf	577	V102V (GTC→GTT)	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,793	0	G	C	41.0%	493.9 / inf	583	G99G (GGC→GGG)	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,802	0	G	A	40.8%	367.3 / inf	582	S96S (AGC→AGT)	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,796	0	A	C	40.6%	437.6 / inf	586	G98G (GGT→GGG)	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,806	0	C	T	40.4%	396.2 / inf	589	G95D (GGC→GAC) ‡	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,799	0	T	C	40.2%	597.1 / inf	587	R97R (CGA→CGG)	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,807	0	C	T	40.2%	418.5 / inf	589	G95S (GGC→AGC) ‡	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,805	0	G	A	40.1%	435.5 / inf	589	G95G (GGC→GGT) ‡	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,762	0	T	C	39.5%	609.8 / inf	543	S110G (AGT→GGT) ‡	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,757	0	G	A	39.3%	409.6 / inf	543	N111N (AAC→AAT) ‡	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,758	0	T	G	39.2%	492.1 / inf	550	N111T (AAC→ACC) ‡	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,760	0	A	C	39.1%	483.3 / inf	548	S110R (AGT→AGG) ‡	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,826	0	A	T	35.7%	586.4 / inf	513	A88A (GCT→GCA)	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,727	0	G	A	34.7%	510.4 / inf	450	H121H (CAC→CAT)	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,730	0	T	C	34.4%	702.3 / inf	453	R120R (AGA→AGG)	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)

Marginal new junction evidence (lowest skew 10 of 149 shown)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	= 776778	221 (0.540)	31 (0.100)	23/218	21.0	15.8%	intergenic (+100/‑47)	lysY/lysZ	tRNA‑Lys/tRNA‑Lys
*	?	CP009273	777267 =	169 (0.560)	31 (0.100)	23/218	21.0	15.8%	intergenic (+159/‑274)	lysQ/nadA	tRNA‑Lys/quinolinate synthase, subunit A
*	?	CP009273	1203246 =	353 (0.860)	33 (0.090)	30/264	21.5	10.1%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
*	?	CP009273	1205075 =	275 (0.750)	33 (0.090)	30/264	21.5	10.1%	pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	CP009273	= 1203261	346 (0.840)	45 (0.120)	29/264	21.9	13.4%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
*	?	CP009273	= 1205058	272 (0.740)	45 (0.120)	29/264	21.9	13.4%	pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	CP009273	= 4285798	250 (0.610)	23 (0.080)	21/218	22.0	8.9%	noncoding (76/530 nt)	RIP321 (repetitive extragenic palindromic) element; contains 9 REP sequences	RIP321 (repetitive extragenic palindromic) element; contains 9 REP sequences
*	?	CP009273	4286251 =	289 (0.960)	23 (0.080)	21/218	22.0	8.9%	noncoding (529/530 nt)	RIP321 (repetitive extragenic palindromic) element; contains 9 REP sequences	RIP321 (repetitive extragenic palindromic) element; contains 9 REP sequences
*	?	CP009273	= 1282362	269 (0.660)	20 (0.060)	18/256	26.5	8.4%	intergenic (+380/+160)	narI/rttR	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
*	?	CP009273	1283013 =	202 (0.570)	20 (0.060)	18/256	26.5	8.4%	noncoding (66/85 nt)	tyrT	tRNA‑Tyr
*	?	CP009273	= 776472	204 (0.500)	13 (0.040)	12/222	27.5	7.4%	intergenic (+98/‑52)	lysW/valZ	tRNA‑Lys/tRNA‑Val
*	?	CP009273	777265 =	171 (0.560)	13 (0.040)	12/222	27.5	7.4%	intergenic (+157/‑276)	lysQ/nadA	tRNA‑Lys/quinolinate synthase, subunit A
*	?	CP009273	= 1282540	238 (0.580)	21 (0.060)	16/256	27.7	9.3%	noncoding (153/171 nt)	rttR	rtT sRNA, processed from tyrT transcript
*	?	CP009273	1283013 =	202 (0.570)	21 (0.060)	16/256	27.7	9.3%	noncoding (66/85 nt)	tyrT	tRNA‑Tyr
*	?	CP009273	= 776778	221 (0.540)	21 (0.060)	16/256	27.7	9.8%	intergenic (+100/‑47)	lysY/lysZ	tRNA‑Lys/tRNA‑Lys
*	?	CP009273	777111 =	196 (0.550)	21 (0.060)	16/256	27.7	9.8%	intergenic (+3/‑430)	lysQ/nadA	tRNA‑Lys/quinolinate synthase, subunit A
*	?	CP009273	= 776778	221 (0.540)	20 (0.060)	15/256	28.2	8.5%	intergenic (+100/‑47)	lysY/lysZ	tRNA‑Lys/tRNA‑Lys
*	?	CP009273	2514690 =	237 (0.670)	20 (0.060)	15/256	28.2	8.5%	noncoding (418/1345 nt)	IS186	repeat region
*	?	CP009273	= 776738	221 (0.540)	18 (0.050)	17/280	28.8	7.6%	intergenic (+60/‑87)	lysY/lysZ	tRNA‑Lys/tRNA‑Lys
*	?	CP009273	777227 =	231 (0.600)	18 (0.050)	17/280	28.8	7.6%	intergenic (+119/‑314)	lysQ/nadA	tRNA‑Lys/quinolinate synthase, subunit A