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 258 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	353,591	0	T	C	52.9%	7.0 / 21.7	17	K271E (AAA→GAA)	cynR	transcriptional regulator CynR
*	NZ_CP009273	4,036,353	0	C	T	51.2%	21.7 / 50.9	43	F193F (TTC→TTT)	srkA	stress response kinase SrkA
*	NZ_CP009273	383,643	0	T	G	43.8%	76.6 / 11.9	64	G131G (GGT→GGG)	tauD	taurine dioxygenase
*	NZ_CP009273	807,177	0	T	G	41.9%	75.3 / 11.6	63	V67G (GTG→GGG)	bioC	malonyl‑ACP O‑methyltransferase BioC
*	NZ_CP009273	4,091,435	0	T	G	40.3%	131.9 / 13.8	78	intergenic (+77/‑183)	sodA/kdgT	superoxide dismutase [Mn]/2‑keto‑3‑deoxygluconate transporter
*	NZ_CP009273	2,089,571	0	A	G	40.0%	112.8 / 23.8	75	I83V (ATT→GTT)	hisF	imidazole glycerol phosphate synthase subunit HisF
*	NZ_CP009273	4,036,390	0	A	G	39.2%	80.0 / 10.3	51	N206D (AAT→GAT)	srkA	stress response kinase SrkA
*	NZ_CP009273	4,091,453	0	C	T	38.4%	122.8 / 18.2	75	intergenic (+95/‑165)	sodA/kdgT	superoxide dismutase [Mn]/2‑keto‑3‑deoxygluconate transporter
*	NZ_CP009273	115,935	0	A	T	37.5%	85.1 / 22.0	56	L56F (TTA→TTT)	ampE	beta‑lactamase regulator AmpE
*	NZ_CP009273	2,476,733	0	G	A	36.7%	163.4 / 30.0	90	S29L (TCA→TTA)	emrK	multidrug efflux MFS transporter periplasmic adaptor subunit EmrK
*	NZ_CP009273	3,659,062	0	C	A	36.3%	154.1 / 34.5	91	A37S (GCG→TCG)	gadX	acid resistance transcriptional activator GadX
*	NZ_CP009273	3,415,158	0	C	G	35.9%	142.7 / 15.0	78	L159V (CTG→GTG)	yhdY	amino acid ABC transporter permease
*	NZ_CP009273	4,570,451	0	C	T	35.9%	139.5 / 36.2	79	E277K (GAA→AAA)	hsdS	type I restriction‑modification system specificity subunit
*	NZ_CP009273	4,594,167	0	C	T	35.4%	73.3 / 16.1	48	S64F (TCT→TTT)	bglJ	DNA‑binding transcriptional activator BglJ
*	NZ_CP009273	5,159	0	G	A	35.3%	135.5 / 36.0	85	intergenic (+139/‑75)	thrC/yaaX	threonine synthase/DUF2502 domain‑containing protein
*	NZ_CP009273	3,415,172	0	A	T	35.1%	135.1 / 21.2	77	L163F (TTA→TTT)	yhdY	amino acid ABC transporter permease
*	NZ_CP009273	1,819,313	0	G	A	34.6%	92.0 / 20.3	52	intergenic (‑119/+84)	ves/spy	environmental stress‑induced protein Ves/ATP‑independent periplasmic protein‑refolding chaperone Spy
*	NZ_CP009273	3,856,024	0	C	G	34.6%	35.7 / 20.0	55	pseudogene (940/1617 nt)	BW25113_RS19145	PTS sugar transporter subunit IIB
*	NZ_CP009273	1,759,042	0	T	A	34.2%	135.1 / 27.0	73	intergenic (‑399/+149)	sufA/ydiH	Fe‑S cluster assembly scaffold SufA/YdiH family protein
*	NZ_CP009273	1,995,392	0	G	A	33.9%	96.0 / 18.7	60	intergenic (‑122/+199)	fliA/fliC	RNA polymerase sigma factor FliA/H48 family flagellin FliC

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	4532499 =	94 (1.080)	17 (0.200)	17/478	8.0	16.2%	intergenic (+49/‑433)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP009273	4532813 =	85 (1.010)					intergenic (+363/‑119)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
*	?	NZ_CP009273	= 4532507	94 (1.080)	11 (0.130)	11/478	10.4	11.1%	intergenic (+57/‑425)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP009273	= 4532803	85 (1.010)					intergenic (+353/‑129)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA