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 36 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	62.5%	1264.5 / inf	954	intergenic (‑301/+173)	ykgR/ykgP	uncharacterized protein/pseudogene, oxidoreductase family
*	CP009273	297,897	0	C	T	62.1%	1462.7 / inf	1160	E130K (GAG→AAG)	paoA	PaoABC aldehyde oxidoreductase, 2Fe‑2S subunit
*	CP009273	580,748	0	G	T	35.5%	688.2 / inf	609	T114T (ACC→ACA)	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,742	0	C	T	34.4%	692.4 / inf	590	T116T (ACG→ACA)	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,784	0	G	A	32.9%	797.1 / inf	600	V102V (GTC→GTT)	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,758	0	T	G	32.6%	903.3 / inf	576	N111T (AAC→ACC) ‡	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,796	0	A	C	32.4%	924.7 / inf	615	G98G (GGT→GGG)	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,716	0	T	C	32.3%	932.0 / inf	524	Q125R (CAA→CGA) ‡	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,793	0	G	C	32.2%	991.8 / inf	612	G99G (GGC→GGG)	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,762	0	T	C	32.2%	1016.9 / inf	574	S110G (AGT→GGT) ‡	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,715	0	T	A	32.2%	760.6 / inf	527	Q125H (CAA→CAT) ‡	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,727	0	G	A	32.1%	726.4 / inf	527	H121H (CAC→CAT)	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,760	0	A	C	32.1%	931.7 / inf	579	S110R (AGT→AGG) ‡	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,805	0	G	A	31.9%	894.6 / inf	614	G95G (GGC→GGT) ‡	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,807	0	C	T	31.9%	875.6 / inf	614	G95S (GGC→AGC) ‡	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,799	0	T	C	31.8%	1133.9 / inf	621	R97R (CGA→CGG)	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,757	0	G	A	31.7%	842.9 / inf	584	N111N (AAC→AAT) ‡	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,802	0	G	A	31.7%	885.2 / inf	620	S96S (AGC→AGT)	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,730	0	T	C	31.6%	982.0 / inf	535	R120R (AGA→AGG)	ompT	DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
*	CP009273	580,806	0	C	T	31.6%	907.1 / inf	614	G95D (GGC→GAC) ‡	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	231 (0.520)	40 (0.120)	29/220	23.9	18.1%	intergenic (+100/‑47)	lysY/lysZ	tRNA‑Lys/tRNA‑Lys
	?	CP009273	777267 =	192 (0.590)					intergenic (+159/‑274)	lysQ/nadA	tRNA‑Lys/quinolinate synthase, subunit A
*	?	CP009273	= 776472	264 (0.600)	26 (0.080)	17/224	31.0	11.7%	intergenic (+98/‑52)	lysW/valZ	tRNA‑Lys/tRNA‑Val
	?	CP009273	777265 =	195 (0.590)					intergenic (+157/‑276)	lysQ/nadA	tRNA‑Lys/quinolinate synthase, subunit A
*	?	CP009273	= 4285798	336 (0.760)	16 (0.050)	15/220	31.9	5.2%	noncoding (76/530 nt)	RIP321 (repetitive extragenic palindromic) element; contains 9 REP sequences	RIP321 (repetitive extragenic palindromic) element; contains 9 REP sequences
	?	CP009273	4286251 =	331 (1.010)					noncoding (529/530 nt)	RIP321 (repetitive extragenic palindromic) element; contains 9 REP sequences	RIP321 (repetitive extragenic palindromic) element; contains 9 REP sequences
*	?	CP009273	921313 =	370 (0.830)	32 (0.100)	12/206	32.6	12.3%	intergenic (+317/+27)	clpA/serW	ATPase and specificity subunit of ClpA‑ClpP ATP‑dependent serine protease, chaperone activity/tRNA‑Ser
	?	CP009273	= 1092450	203 (0.660)					intergenic (+165/+571)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
*	?	CP009273	= 1161581	358 (0.810)	22 (0.060)	21/268	32.8	6.0%	coding (41/1305 nt)	ndh	respiratory NADH dehydrogenase 2/cupric reductase
	?	CP009273	1162077 =	371 (0.930)					coding (537/1305 nt)	ndh	respiratory NADH dehydrogenase 2/cupric reductase
*	?	CP009273	= 1282540	257 (0.580)	28 (0.070)	19/258	33.1	10.5%	noncoding (153/171 nt)	rttR	rtT sRNA, processed from tyrT transcript
	?	CP009273	1283013 =	254 (0.660)					noncoding (66/85 nt)	tyrT	tRNA‑Tyr
*	?	CP009273	921313 =	370 (0.830)	16 (0.050)	11/206	33.4	8.3%	intergenic (+317/+27)	clpA/serW	ATPase and specificity subunit of ClpA‑ClpP ATP‑dependent serine protease, chaperone activity/tRNA‑Ser
	?	CP009273	= 1092631	99 (0.320)					intergenic (+346/+390)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
*	?	CP009273	776825 =	228 (0.510)	46 (0.100) +G	23/296	34.0	13.2%	noncoding (1/76 nt)	lysZ	tRNA‑Lys
	?	CP009273	= 2514486	379 (0.850)					noncoding (214/1345 nt)	IS186	repeat region
*	?	CP009273	= 2811027	431 (0.970)	26 (0.070)	17/256	34.1	7.9%	intergenic (‑165/+116)	yqaB/argQ	fructose‑1‑P and 6‑phosphogluconate phosphatase/tRNA‑Arg
	?	CP009273	2811575 =	238 (0.630)					noncoding (59/77 nt)	argY	tRNA‑Arg
*	?	CP009273	= 1282362	300 (0.680)	20 (0.050)	16/258	35.0	7.2%	intergenic (+380/+160)	narI/rttR	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
	?	CP009273	1283013 =	254 (0.660)					noncoding (66/85 nt)	tyrT	tRNA‑Tyr