breseq  version 0.29.0  revision 8f9c342918e4 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence (highest frequency 20 of 861 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	941,713	0	T	G	50.6%	88.1 / 138.7	83	V252G (GTG→GGG)	dmsA	dimethyl sulfoxide reductase, anaerobic, subunit A
*	NC_000913	29,496	0	T	A	48.4%	98.3 / 66.3	93	intergenic (+301/‑155)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	1,222,233	0	G	A	48.3%	46.1 / 33.0	59	pseudogene (60/75 nt)	ycgH	pseudogene; putative ATP‑binding component of a transport system
*	NC_000913	802,118	0	A	C	46.0%	112.1 / 20.7	74	T78P (ACC→CCC)	ybhI	putative DASS family tricarboxylate or dicarboxylate transporter
*	NC_000913	1,222,213	0	A	C	45.3%	106.8 / 10.4	64	pseudogene (40/75 nt)	ycgH	pseudogene; putative ATP‑binding component of a transport system
*	NC_000913	29,486	0	C	A	45.2%	145.5 / 55.2	93	intergenic (+291/‑165)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	2,624,517	0	G	T	45.1%	86.6 / 42.7	72	E492* (GAA→TAA)	ppk	polyphosphate kinase, component of RNA degradosome
*	NC_000913	4,465,787	0	G	A	44.8%	74.8 / 39.0	67	R132C (CGC→TGC)	treB	trehalose‑specific PTS enzyme: IIB and IIC component
*	NC_000913	1,825,056	0	G	A	44.4%	92.1 / 39.0	72	intergenic (‑119/+84)	ves/spy	cold‑ and stress‑inducible protein/periplasmic ATP‑independent protein refolding chaperone, stress‑induced
*	NC_000913	2,040,075	0	C	G	43.8%	96.1 / 38.3	90	L200V (CTG→GTG)	yedY	membrane‑anchored, periplasmic TMAO, DMSO reductase
*	NC_000913	941,715	0	A	G	43.5%	130.0 / 11.6	86	T253A (ACT→GCT)	dmsA	dimethyl sulfoxide reductase, anaerobic, subunit A
*	NC_000913	4,287,710	0	G	A	43.4%	77.6 / 48.9	77	intergenic (‑339/‑54)	acs/nrfA	acetyl‑CoA synthetase/nitrite reductase, formate‑dependent, cytochrome
*	NC_000913	2,434,861	0	G	T	43.2%	120.5 / 48.7	88	P259Q (CCA→CAA)	truA	tRNA pseudouridine(38‑40) synthase
*	NC_000913	4,258,974	0	T	G	43.2%	169.5 / 22.1	95	G411G (GGT→GGG)	dinF	oxidative stress resistance protein; putative MATE family efflux pump; UV and mitomycin C inducible protein
*	NC_000913	3,133,302	0	T	G	43.1%	126.1 / 16.4	72	H219P (CAC→CCC)	yghS	putative ATP‑binding protein
*	NC_000913	2,434,882	0	T	G	42.9%	157.4 / 25.7	91	Y252S (TAC→TCC)	truA	tRNA pseudouridine(38‑40) synthase
*	NC_000913	4,378,802	0	A	C	42.6%	118.3 / 19.0	68	V48G (GTA→GGA)	ampC	penicillin‑binding protein; beta‑lactamase, intrinsically weak
*	NC_000913	993,913	0	G	C	42.5%	142.2 / 37.4	80	G44G (GGC→GGG)	ssuB	aliphatic sulfonate ABC transporter ATPase
*	NC_000913	2,984,441	0	A	C	42.4%	171.9 / 10.7	85	G384G (GGT→GGG)	yqeF	short chain acyltransferase
*	NC_000913	1,097,581	0	A	G	42.3%	141.8 / 26.8	78	noncoding (72/88 nt)	serX	tRNA‑Ser

Marginal new junction evidence (sorted from low to high skew)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	4542682 =	111 (1.180)	4 (0.050)	4/280	16.7	3.7%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	106 (1.200)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	= 4542690	111 (1.180)	3 (0.030)	3/280	17.7	2.8%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	105 (1.190)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)