breseq  version 0.27.1  revision 87c22d663cc3 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence (highest frequency 20 of 688 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	786,855	0	A	C	57.7%	99.3 / 121.7	78	G247G (GGT→GGG)	gpmA	phosphoglyceromutase 1
*	NC_000913	2,434,882	0	T	G	50.7%	100.3 / 130.0	72	Y252S (TAC→TCC)	truA	tRNA pseudouridine(38‑40) synthase
*	NC_000913	4,258,974	0	T	G	49.4%	137.7 / 12.5	85	G411G (GGT→GGG)	dinF	oxidative stress resistance protein; putative MATE family efflux pump; UV and mitomycin C inducible protein
*	NC_000913	657,676	0	A	C	49.2%	78.6 / 27.6	67	V88G (GTG→GGG)	flc	fluoride efflux channel, dual topology membrane protein
*	NC_000913	357,890	0	C	A	48.9%	37.4 / 24.9	47	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	1,097,581	0	A	G	48.8%	109.4 / 25.3	80	noncoding (72/88 nt)	serX	tRNA‑Ser
*	NC_000913	3,206,435	0	C	T	48.1%	72.1 / 49.7	81	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	1,604,237	0	C	T	46.4%	96.0 / 25.4	84	S64L (TCG→TTG)	lsrD	autoinducer 2 import system permease protein
*	NC_000913	29,496	0	T	A	46.0%	124.8 / 44.8	87	intergenic (+301/‑155)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	3,585,086	0	A	C	45.6%	115.1 / 18.1	68	Y580D (TAC→GAC)	ggt	gamma‑glutamyltranspeptidase
*	NC_000913	29,486	0	C	A	45.4%	121.1 / 45.4	86	intergenic (+291/‑165)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	2,903,692	0	C	A	45.2%	110.3 / 70.1	84	intergenic (+318/+1055)	ygcE/queE	putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis
*	NC_000913	802,118	0	A	C	44.9%	186.6 / 21.8	107	T78P (ACC→CCC)	ybhI	putative DASS family tricarboxylate or dicarboxylate transporter
*	NC_000913	827,507	0	T	G	44.6%	164.5 / 18.7	92	D492A (GAC→GCC)	ybhF	putative ABC transporter ATPase
*	NC_000913	40,515	0	G	T	44.3%	93.2 / 33.6	80	Q473K (CAA→AAA)	caiT	putative transporter
*	NC_000913	3,508,662	0	T	A	44.2%	120.3 / 36.4	77	E384D (GAA→GAT)	yhfW	phosphopentomutase‑related metalloenzyme superfamily protein
*	NC_000913	3,862,638	0	T	C	44.0%	115.3 / 14.9	75	pseudogene (966/1617 nt)	glvC	pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component
*	NC_000913	3,601,560	0	A	C	43.9%	114.3 / 11.5	66	V176G (GTG→GGG)	ftsX	putative ABC transporter permease
*	NC_000913	941,713	0	T	G	43.8%	123.0 / 26.8	73	V252G (GTG→GGG)	dmsA	dimethyl sulfoxide reductase, anaerobic, subunit A
*	NC_000913	4,171,882	0	C	G	43.8%	71.0 / 23.7	48	intergenic (+126/‑175)	rrfB/murB	5S ribosomal RNA of rrnB operon/UDP‑N‑acetylenolpyruvoylglucosamine reductase, FAD‑binding

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	925901 =	74 (0.850)	22 (0.250) +C	17/298	9.0	26.2%	noncoding (71/88 nt)	serW	tRNA‑Ser
	?	NC_000913	= 1097399	51 (0.580)					intergenic (+570/+166)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
*	?	NC_000913	1411899 =	97 (1.110)	5 (0.070)	5/248	13.4	5.7%	coding (50/936 nt)	ttcA	tRNA s(2)C32 thioltransferase, iron sulfur cluster protein
	?	NC_000913	= 1434958	86 (1.190)					pseudogene (51/51 nt)	ttcC	pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related
*	?	NC_000913	4542682 =	111 (1.270)	6 (0.070)	6/282	14.1	5.5%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	103 (1.250)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)