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 60 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	4,558,321	0	T	G	73.3%	1.1 / 14.8	30	T6P (ACC→CCC)	mdtM	multidrug efflux MFS transporter MdtM
*	NZ_CP009273	4,558,329	0	C	A	70.8%	4.6 / 18.5	24	R3L (CGT→CTT)	mdtM	multidrug efflux MFS transporter MdtM
*	NZ_CP009273	1,816,473	0	A	C	66.7%	3.4 / 10.7	15	V14G (GTA→GGA)	osmE	osmotically‑inducible lipoprotein OsmE
*	NZ_CP009273	4,558,343	0	C	A	66.7%	‑5.7 / 16.8	21	intergenic (‑7/‑472)	mdtM/BW25113_RS25845	multidrug efflux MFS transporter MdtM/Rpn family recombination‑promoting nuclease/putative transposase
*	NZ_CP009273	1,673,569	0	A	C	63.2%	5.4 / 15.0	19	T296P (ACC→CCC)	ydgH	DUF1471 family protein YdgH
*	NZ_CP009273	937,169	0	T	G	62.5%	0.2 / 11.6	16	V252G (GTG→GGG)	dmsA	dimethylsulfoxide reductase subunit A
*	NZ_CP009273	937,171	0	A	G	62.5%	0.5 / 11.9	16	T253A (ACT→GCT)	dmsA	dimethylsulfoxide reductase subunit A
*	NZ_CP009273	4,558,339	0	C	A	61.9%	‑3.3 / 16.6	21	intergenic (‑3/‑476)	mdtM/BW25113_RS25845	multidrug efflux MFS transporter MdtM/Rpn family recombination‑promoting nuclease/putative transposase
*	NZ_CP009273	1,377,991	0	A	C	61.5%	4.8 / 10.7	13	G76G (GGT→GGG)	ycjW	LacI family DNA‑binding transcriptional regulator
*	NZ_CP009273	1,377,967	0	C	A	60.0%	‑0.3 / 13.6	10	L84F (TTG→TTT)	ycjW	LacI family DNA‑binding transcriptional regulator
*	NZ_CP009273	2,290,243	0	T	G	58.3%	5.1 / 10.7	12	L87F (TTA→TTC)	ccmB	heme exporter protein CcmB
*	NZ_CP009273	1,906,007	0	T	G	57.9%	10.1 / 20.0	19	H276P (CAC→CCC)	htpX	protease HtpX
*	NZ_CP009273	172,920	0	C	A	57.1%	2.9 / 11.6	14	P443T (CCG→ACG)	clcA	H(+)/Cl(‑) exchange transporter ClcA
*	NZ_CP009273	684,970	0	A	C	57.1%	0.6 / 12.1	14	G456G (GGT→GGG)	lnt	apolipoprotein N‑acyltransferase
*	NZ_CP009273	1,622,316	0	T	G	57.1%	5.8 / 11.2	14	G181G (GGT→GGG)	ydfG	bifunctional NADP‑dependent 3‑hydroxy acid dehydrogenase/3‑hydroxypropionate dehydrogenase YdfG
*	NZ_CP009273	4,594,161	0	C	T	57.1%	5.2 / 42.9	35	S62F (TCT→TTT)	bglJ	DNA‑binding transcriptional activator BglJ
*	NZ_CP009273	4,464,532	0	T	G	56.6%	33.6 / 43.1	54	*198G (TGA→GGA)	bdcR	TetR/AcrR family transcriptional regulator
*	NZ_CP009273	1,152,727	0	T	G	56.2%	12.2 / 18.8	16	G165G (GGT→GGG)	ycfH	metal‑dependent hydrolase
*	NZ_CP009273	2,247,828	0	C	A	55.6%	9.1 / 21.5	18	V280F (GTT→TTT)	rihB	ribosylpyrimidine nucleosidase
*	NZ_CP009273	3,806,452	0	T	C	55.6%	‑0.1 / 11.3	18	L121P (CTC→CCC)	coaBC	bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate‑‑cysteine ligase CoaBC

Marginal new junction evidence (sorted from low to high skew)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	4278944 =	30 (1.290)	3 (0.140)	3/152	1.8	10.8%	coding (1253/1437 nt)	nrfA	ammonia‑forming nitrite reductase cytochrome c552 subunit
	?	NZ_CP009273	4279020 =	23 (1.110)					coding (1329/1437 nt)	nrfA	ammonia‑forming nitrite reductase cytochrome c552 subunit
*	?	NZ_CP009273	2416916 =	21 (0.900)	3 (0.140)	3/154	1.8	15.8%	coding (103/891 nt)	rpnB	recombination‑promoting nuclease RpnB
	?	NZ_CP009273	2416950 =	13 (0.620)					coding (69/891 nt)	rpnB	recombination‑promoting nuclease RpnB
*	?	NZ_CP009273	3816618 =	51 (2.200)	3 (0.130)	3/164	1.9	6.7%	coding (859/2109 nt)	spoT	bifunctional GTP diphosphokinase/guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase
	?	NZ_CP009273	3816703 =	34 (1.520)					coding (944/2109 nt)	spoT	bifunctional GTP diphosphokinase/guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase