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 666 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,443,277	0	A	C	46.8%	111.5 / 36.1	79	V274G (GTA→GGA)	secY	preprotein translocase membrane subunit
*	NC_000913	907,602	0	A	C	46.8%	84.6 / 22.2	62	G227G (GGT→GGG)	ybjT	putative NAD‑dependent oxidoreductase
*	NC_000913	802,118	0	A	C	46.8%	105.5 / 15.0	77	T78P (ACC→CCC)	ybhI	putative DASS family tricarboxylate or dicarboxylate transporter
*	NC_000913	925,900	0	A	G	45.8%	101.8 / 25.6	72	noncoding (72/88 nt)	serW	tRNA‑Ser
*	NC_000913	1,491,098	0	A	C	44.7%	99.5 / 10.5	76	Y66S (TAC→TCC)	cybB	cytochrome b561
*	NC_000913	73,581	0	A	C	44.6%	110.4 / 21.3	65	V314G (GTA→GGA)	thiP	thiamine/thiamine pyrophosphate ABC transporter permease
*	NC_000913	354,288	0	T	G	44.4%	103.7 / 24.2	72	V528G (GTG→GGG)	prpE	propionate‑‑CoA ligase
*	NC_000913	29,486	0	C	A	44.1%	105.1 / 46.2	69	intergenic (+291/‑165)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	1,755,871	0	T	A	43.9%	83.9 / 43.9	67	G58G (GGT→GGA)	pykF	pyruvate kinase I
*	NC_000913	4,258,974	0	T	G	43.3%	100.0 / 19.5	62	G411G (GGT→GGG)	dinF	oxidative stress resistance protein; putative MATE family efflux pump; UV and mitomycin C inducible protein
*	NC_000913	4,457,105	0	A	G	42.9%	86.6 / 27.4	70	I441V (ATC→GTC)	mpl	UDP‑N‑acetylmuramate:L‑alanyl‑gamma‑D‑glutamyl‑ meso‑diaminopimelate ligase
*	NC_000913	29,496	0	T	A	42.2%	94.1 / 39.5	71	intergenic (+301/‑155)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	3,155,639	0	T	G	42.2%	134.5 / 11.1	71	G95G (GGT→GGG)	yqhD	aldehyde reductase, NADPH‑dependent
*	NC_000913	941,713	0	T	G	42.0%	104.7 / 37.0	69	V252G (GTG→GGG)	dmsA	dimethyl sulfoxide reductase, anaerobic, subunit A
*	NC_000913	2,511,772	0	A	C	41.9%	146.3 / 14.1	74	V312G (GTG→GGG)	mntH	manganese/divalent cation transporter
*	NC_000913	2,984,441	0	A	C	41.5%	92.4 / 17.5	55	G384G (GGT→GGG)	yqeF	short chain acyltransferase
*	NC_000913	1,097,581	0	A	G	41.3%	136.3 / 26.6	75	noncoding (72/88 nt)	serX	tRNA‑Ser
*	NC_000913	4,573,500	0	A	G	41.2%	104.7 / 23.2	69	pseudogene (1087/1503 nt)	yjiT	pseudogene
*	NC_000913	1,982,523	0	A	G	41.1%	81.9 / 27.6	56	intergenic (‑136/+31)	otsB/araH	trehalose‑6‑phosphate phosphatase, biosynthetic/L‑arabinose ABC transporter permease
*	NC_000913	1,982,529	0	C	A	41.1%	98.3 / 35.9	56	intergenic (‑142/+25)	otsB/araH	trehalose‑6‑phosphate phosphatase, biosynthetic/L‑arabinose ABC transporter permease

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 =	108 (1.410)	6 (0.080)	6/280	12.3	6.0%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	88 (1.220)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	2631147 =	70 (0.910)	3 (0.040)	3/280	14.6	4.3%	coding (1389/1578 nt)	guaA	GMP synthetase (glutamine aminotransferase)
	?	NC_000913	= 2649434	69 (0.960)					coding (2854/4962 nt)	yfhM	bacterial alpha2‑macroglobulin colonization factor ECAM; anti‑host protease defense factor; periplasmic inner membrane‑anchored lipoprotein