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 26 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	309,254	0	G	A	62.3%	1198.6 / inf	908	intergenic (‑301/+173)	ykgR/ykgP	uncharacterized protein/pseudogene, oxidoreductase family
*	CP009273	297,897	0	C	T	61.9%	1463.5 / inf	1154	E130K (GAG→AAG)	paoA	PaoABC aldehyde oxidoreductase, 2Fe‑2S subunit
*	CP009273	2,222,669	0	T	A	24.6%	449.8 / 63.0	233	intergenic (+125/+248)	yohP/dusC	uncharacterized protein/tRNA‑dihydrouridine synthase C
*	CP009273	580,748	0	G	T	23.5%	1046.8 / inf	473	T114T (ACC→ACA)	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	2,222,683	0	T	A	23.4%	489.4 / 50.5	233	intergenic (+139/+234)	yohP/dusC	uncharacterized protein/tRNA‑dihydrouridine synthase C
*	CP009273	580,757	0	G	A	22.5%	1025.0 / inf	458	N111N (AAC→AAT) ‡	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,742	0	C	T	22.3%	1042.6 / inf	471	T116T (ACG→ACA)	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,807	0	C	T	22.3%	1031.0 / inf	455	G95S (GGC→AGC) ‡	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,758	0	T	G	22.2%	1069.7 / 315.9	460	N111T (AAC→ACC) ‡	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,762	0	T	C	22.2%	1251.6 / inf	464	S110G (AGT→GGT) ‡	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,784	0	G	A	22.2%	1023.5 / inf	461	V102V (GTC→GTT)	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,760	0	A	C	22.1%	1101.6 / inf	466	S110R (AGT→AGG) ‡	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,802	0	G	A	22.1%	1012.6 / inf	457	S96S (AGC→AGT)	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,805	0	G	A	22.1%	1052.8 / inf	458	G95G (GGC→GGT) ‡	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,806	0	C	T	22.1%	1041.9 / inf	455	G95D (GGC→GAC) ‡	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,799	0	T	C	22.0%	1293.6 / 316.2	473	R97R (CGA→CGG)	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,796	0	A	C	22.0%	1121.9 / 313.9	471	G98G (GGT→GGG)	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,814	0	T	G	21.8%	1128.3 / 316.6	467	T92T (ACA→ACC)	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	1,815,284	0	G	T	21.6%	561.1 / 19.6	258	S63Y (TCC→TAC)	chbC	N,N'‑diacetylchitobiose‑specific enzyme IIC component of PTS
*	CP009273	580,793	0	G	C	21.3%	1255.6 / inf	475	G99G (GGC→GGG)	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)

Marginal new junction evidence (lowest skew 10 of 83 shown)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	= 776778	226 (0.580)	32 (0.110)	26/222	20.5	16.6%	intergenic (+100/‑47)	lysY/lysZ	tRNA‑Lys/tRNA‑Lys
	?	CP009273	777267 =	154 (0.540)					intergenic (+159/‑274)	lysQ/nadA	tRNA‑Lys/quinolinate synthase, subunit A
*	?	CP009273	= 4285798	305 (0.780)	16 (0.060)	16/222	25.7	5.7%	noncoding (76/530 nt)	RIP321 (repetitive extragenic palindromic) element; contains 9 REP sequences	RIP321 (repetitive extragenic palindromic) element; contains 9 REP sequences
	?	CP009273	4286251 =	301 (1.050)					noncoding (529/530 nt)	RIP321 (repetitive extragenic palindromic) element; contains 9 REP sequences	RIP321 (repetitive extragenic palindromic) element; contains 9 REP sequences
*	?	CP009273	= 1282362	325 (0.840)	22 (0.070)	18/260	27.5	7.7%	intergenic (+380/+160)	narI/rttR	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
	?	CP009273	1283013 =	247 (0.730)					noncoding (66/85 nt)	tyrT	tRNA‑Tyr
*	?	CP009273	777033 =	235 (0.600)	35 (0.090) +G	22/298	28.0	11.8%	noncoding (1/76 nt)	lysQ	tRNA‑Lys
	?	CP009273	= 2514487	290 (0.750)					noncoding (215/1345 nt)	IS186	repeat region
*	?	CP009273	= 777144	273 (0.700)	8 (0.030)	8/192	28.5	4.6%	intergenic (+36/‑397)	lysQ/nadA	tRNA‑Lys/quinolinate synthase, subunit A
	?	CP009273	777301 =	155 (0.630)					intergenic (+193/‑240)	lysQ/nadA	tRNA‑Lys/quinolinate synthase, subunit A
*	?	CP009273	= 2871271	639 (1.640)	14 (0.040)	13/242	29.2	2.9%	intergenic (+294/+657)	iap/ygbF	aminopeptidase in alkaline phosphatase isozyme conversion/CRISPR adaptation ssRNA endonuclease
	?	CP009273	2871823 =	433 (1.380)					intergenic (+846/+105)	iap/ygbF	aminopeptidase in alkaline phosphatase isozyme conversion/CRISPR adaptation ssRNA endonuclease
*	?	CP009273	= 1282540	249 (0.640)	19 (0.060)	15/260	29.3	7.6%	noncoding (153/171 nt)	rttR	rtT sRNA, processed from tyrT transcript
	?	CP009273	1283013 =	247 (0.730)					noncoding (66/85 nt)	tyrT	tRNA‑Tyr
*	?	CP009273	= 776678	205 (0.530)	28 (0.080)	14/264	30.2	12.6%	noncoding (76/76 nt)	lysY	tRNA‑Lys
	?	CP009273	777265 =	209 (0.610)					intergenic (+157/‑276)	lysQ/nadA	tRNA‑Lys/quinolinate synthase, subunit A
*	?	CP009273	= 2871131	510 (1.310)	17 (0.050)	14/278	31.1	3.4%	intergenic (+154/+797)	iap/ygbF	aminopeptidase in alkaline phosphatase isozyme conversion/CRISPR adaptation ssRNA endonuclease
	?	CP009273	2871622 =	487 (1.350)					intergenic (+645/+306)	iap/ygbF	aminopeptidase in alkaline phosphatase isozyme conversion/CRISPR adaptation ssRNA endonuclease
*	?	CP009273	= 2811716	275 (0.710)	17 (0.050)	12/260	31.2	6.9%	intergenic (‑83/+116)	argY/argV	tRNA‑Arg/tRNA‑Arg
	?	CP009273	2811851 =	221 (0.660)					noncoding (58/77 nt)	argV	tRNA‑Arg