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 46 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	4,548,694	0	T	C	73.9%	36.9 / 10.6	23	E217G (GAA→GGA)	iadA	beta‑aspartyl‑peptidase
*	NZ_CP009273	473,861	0	G	T	73.3%	36.9 / 57.6	60	G71G (GGC→GGA)	pdeB	cyclic‑guanylate‑specific phosphodiesterase PdeB
*	NZ_CP009273	521,261	1	.	C	68.0%	50.5 / 24.2	25	coding (2545/4281 nt)	rhsD	rhs element protein RhsD
*	NZ_CP009273	4,594,161	0	C	T	58.3%	‑1.3 / 37.3	36	S62F (TCT→TTT)	bglJ	DNA‑binding transcriptional activator BglJ
*	NZ_CP009273	4,594,167	0	C	T	58.3%	7.1 / 40.2	36	S64F (TCT→TTT)	bglJ	DNA‑binding transcriptional activator BglJ
*	NZ_CP009273	1,698,298	0	G	T	57.9%	13.1 / 28.0	19	H90N (CAT→AAT)	ydgJ	oxidoreductase
*	NZ_CP009273	1,698,302	0	A	C	55.6%	10.1 / 12.4	18	G88G (GGT→GGG)	ydgJ	oxidoreductase
*	NZ_CP009273	687,319	0	T	A	53.8%	2.6 / 16.9	13	intergenic (‑79/+11)	corC/ybeY	CNNM family magnesium/cobalt transport protein CorC/rRNA maturation RNase YbeY
*	NZ_CP009273	1,558,373	0	C	T	52.9%	6.4 / 17.4	17	E540K (GAG→AAG)	dosP	oxygen‑sensing cyclic‑di‑GMP phosphodiesterase
*	NZ_CP009273	1,819,318	0	G	A	52.2%	6.4 / 30.3	23	intergenic (‑124/+79)	ves/spy	environmental stress‑induced protein Ves/ATP‑independent periplasmic protein‑refolding chaperone Spy
*	NZ_CP009273	3,199,794	0	C	T	47.8%	11.4 / 15.3	23	intergenic (‑179/‑28)	ttdR/ttdA	DNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha
*	NZ_CP009273	4,086,494	0	T	G	46.9%	15.6 / 13.2	32	Y102S (TAC→TCC)	rhaM	L‑rhamnose mutarotase
*	NZ_CP009273	1,819,313	0	G	A	45.5%	11.0 / 11.5	22	intergenic (‑119/+84)	ves/spy	environmental stress‑induced protein Ves/ATP‑independent periplasmic protein‑refolding chaperone Spy
*	NZ_CP009273	4,086,499	0	C	A	45.2%	25.8 / 14.9	31	V100V (GTG→GTT)	rhaM	L‑rhamnose mutarotase
*	NZ_CP009273	4,558,329	0	C	A	44.0%	33.5 / 11.9	25	R3L (CGT→CTT)	mdtM	multidrug efflux MFS transporter MdtM
*	NZ_CP009273	3,436,636	0	A	C	42.3%	11.6 / 11.8	26	V274G (GTA→GGA)	secY	preprotein translocase subunit SecY
*	NZ_CP009273	278,791	0	T	C	42.1%	17.2 / 40.2	38	L268P (CTC→CCC)	yagE	2‑keto‑3‑deoxygluconate aldolase
*	NZ_CP009273	3,734,269	0	T	G	41.0%	47.2 / 24.8	61	V402G (GTG→GGG)	avtA	valine‑‑pyruvate transaminase
*	NZ_CP009273	4,440,600	0	T	G	39.5%	30.5 / 12.8	43	G274G (GGT→GGG)	ytfQ	galactofuranose ABC transporter substrate‑binding protein YtfQ
*	NZ_CP009273	3,953,261	0	T	G	38.1%	36.8 / 10.2	42	intergenic (‑88/+111)	ppiC/BW25113_RS25790	peptidylprolyl isomerase PpiC/type II toxin‑antitoxin system PemK/MazF family toxin

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	1203246 =	31 (0.880)	3 (0.110)	3/132	2.3	13.4%	coding (290/630 nt)	BW25113_RS05990	hypothetical protein
	?	NZ_CP009273	1205075 =	14 (0.490)					coding (40/540 nt)	BW25113_RS06005	phage tail protein
*	?	NZ_CP009273	4583141 =	19 (0.540)	3 (0.100)	3/142	2.4	15.6%	intergenic (+12/+37)	tsr/lgoT	methyl‑accepting chemotaxis protein/MFS transporter
	?	NZ_CP009273	4583171 =	16 (0.520)					intergenic (+42/+7)	tsr/lgoT	methyl‑accepting chemotaxis protein/MFS transporter
*	?	NZ_CP009273	= 3609927	60 (1.700)	3 (0.090)	3/148	2.5	6.2%	coding (386/834 nt)	nikC	nickel ABC transporter permease subunit NikC
	?	NZ_CP009273	= 3610020	37 (1.160)					coding (479/834 nt)	nikC	nickel ABC transporter permease subunit NikC
*	?	NZ_CP009273	1242342 =	24 (0.680)	3 (0.090)	3/160	2.6	10.8%	coding (491/1698 nt)	treA	alpha,alpha‑trehalase
	?	NZ_CP009273	1242352 =	26 (0.760)					coding (481/1698 nt)	treA	alpha,alpha‑trehalase