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 22 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	AC_000091	3,543,547	0	A	C	38.5%	188.8 / 35.9	104	Y102S (TAC→TCC)	yiiL	L‑rhamnose mutarotase
*	AC_000091	3,676,780	0	A	C	35.0%	155.6 / 28.4	97	intergenic (+111/‑88)	yifO/ppiC	hypothetical protein/peptidyl‑prolyl cis‑trans isomerase C
*	AC_000091	771,319	0	T	G	34.7%	175.4 / 13.5	99	intergenic (+286/‑561)	mngB/cydA	alpha‑mannosidase/cytochrome d terminal oxidase, subunit I
*	AC_000091	2,060,392	0	T	G	32.5%	237.6 / 12.3	118	Y531S (TAC→TCC)	yeeO	predicted multidrug efflux system
*	AC_000091	3,259,711	0	A	C	29.0%	199.5 / 16.6	93	V455G (GTG→GGG)	tdcE	pyruvate formate‑lyase 4/2‑ketobutyrate formate‑lyase
*	AC_000091	2,354,291	0	A	C	28.4%	250.7 / 29.2	109	intergenic (‑149/‑66)	inaA/yfaH	hypothetical protein/hypothetical protein
*	AC_000091	119,384	0	T	G	27.8%	277.5 / 18.6	115	V35G (GTG→GGG)	ampE	predicted inner membrane protein
*	AC_000091	3,350,708	0	A	C	27.8%	307.5 / 20.5	133	S725A (TCA→GCA)	arcB	hybrid sensory histidine kinase in two‑component regulatory system with ArcA
*	AC_000091	4,076,934	0	A	C	27.5%	339.2 / 33.8	150	V490G (GTG→GGG)	glpD	sn‑glycerol‑3‑phosphate dehydrogenase, aerobic, FAD/NAD(P)‑binding
*	AC_000091	2,817,030	0	G	C	27.4%	148.8 / 37.9	62	intergenic (‑100/+99)	argY/argV	tRNA‑Arg/tRNA‑Arg
*	AC_000091	2,004,055	0	A	C	27.4%	326.2 / 26.9	135	intergenic (‑129/+192)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein
*	AC_000091	4,419,586	0	T	G	26.9%	228.1 / 23.3	108	V211G (GTG→GGG)	aidB	isovaleryl CoA dehydrogenase
*	AC_000091	2,987,535	0	A	C	26.6%	297.7 / 26.0	129	P126P (CCA→CCC)	yqeI	predicted transcriptional regulator
*	AC_000091	2,708,935	0	A	C	25.8%	221.8 / 17.0	93	intergenic (‑267/‑141)	rpoE/nadB	RNA polymerase, sigma 24 (sigma E) factor/quinolinate synthase, L‑aspartate oxidase (B protein) subunit
*	AC_000091	3,962,968	0	A	C	25.0%	327.0 / 12.5	146	T307P (ACC→CCC)	yhjG	predicted outer membrane biogenesis protein
*	AC_000091	175,694	0	T	G	24.6%	296.7 / 11.0	114	G196G (GGT→GGG)	clcA	chloride channel, voltage‑gated
*	AC_000091	2,226,744	0	T	G	24.5%	194.5 / 16.7	94	V409G (GTG→GGG)	dld	D‑lactate dehydrogenase, FAD‑binding, NADH independent
*	AC_000091	4,147,012	0	A	C	24.1%	266.1 / 12.0	113	G279G (GGT→GGG)	tsgA	predicted transporter
*	AC_000091	1,163,018	0	T	G	23.6%	226.3 / 16.8	106	A37A (GCA→GCC)	fhuE	ferric‑rhodotorulic acid outer membrane transporter
*	AC_000091	2,331,120	0	T	G	23.1%	282.7 / 11.1	104	G114G (GGT→GGG)	atoB	acetyl‑CoA acetyltransferase

Marginal new junction evidence (sorted from low to high skew)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	AC_000091	= 4547370	126 (0.940)	30 (0.250)	25/160	8.3	22.3%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin
	?	AC_000091	= 4547666	96 (0.800)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin
*	?	AC_000091	4547362 =	122 (0.910)	26 (0.220)	25/160	8.3	20.2%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin
	?	AC_000091	4547676 =	96 (0.800)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin