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 343 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	29,496	0	T	A	50.0%	65.3 / 38.6	60	intergenic (+301/‑155)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	357,880	0	T	C	50.0%	36.8 / 16.0	40	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	3,705,661	0	T	C	50.0%	39.9 / 18.8	48	I44V (ATC→GTC)	dppB	dipeptide/heme ABC transporter permease
*	NC_000913	3,705,653	0	T	G	48.9%	46.1 / 17.2	47	P46P (CCA→CCC)	dppB	dipeptide/heme ABC transporter permease
*	NC_000913	2,578,143	0	A	C	48.2%	70.0 / 24.1	56	L79V (TTA→GTA)	maeB	malic enzyme: putative oxidoreductase/phosphotransacetylase
*	NC_000913	3,177,748	0	C	A	47.5%	53.3 / 40.1	59	E55* (GAG→TAG)	nudF	ADP‑ribose pyrophosphatase
*	NC_000913	436,516	0	C	A	46.2%	61.1 / 25.9	53	Q295K (CAA→AAA)	thiL	thiamine monophosphate kinase
*	NC_000913	2,001,918	0	A	C	45.8%	99.9 / 35.0	72	intergenic (‑129/+192)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin)
*	NC_000913	366,526	0	T	G	44.8%	80.4 / 26.3	58	T329P (ACC→CCC)	lacI	lactose‑inducible lac operon transcriptional repressor
*	NC_000913	4,538,109	0	A	C	44.6%	95.1 / 16.3	57	G219G (GGT→GGG)	nanM	N‑acetylneuraminic acid mutarotase
*	NC_000913	1,224,007	0	C	A	44.0%	84.4 / 25.3	50	intergenic (+100/+272)	ycgI/minE	pseudogene/cell division topological specificity factor
*	NC_000913	1,755,871	0	T	A	42.9%	79.6 / 32.8	56	G58G (GGT→GGA)	pykF	pyruvate kinase I
*	NC_000913	29,486	0	C	A	42.6%	85.3 / 39.1	61	intergenic (+291/‑165)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	2,421,443	0	A	C	42.6%	112.9 / 12.2	61	Y40S (TAC→TCC)	folX	D‑erythro‑7,8‑dihydroneopterin triphosphate 2'‑epimerase and dihydroneopterin aldolase
*	NC_000913	1,487,163	0	C	T	42.6%	58.5 / 34.0	54	intergenic (+200/‑72)	hrpA/ydcF	putative ATP‑dependent helicase/DUF218 superfamily protein, SAM‑binding
*	NC_000913	646,747	0	T	G	42.4%	115.2 / 11.4	66	T255P (ACC→CCC)	citG	2‑(5''‑triphosphoribosyl)‑3'‑dephosphocoenzyme‑A synthase
*	NC_000913	213,341	0	A	G	42.3%	67.4 / 18.2	52	G337G (GGA→GGG)	tilS	tRNA(Ile)‑lysidine synthetase
*	NC_000913	1,097,581	0	A	G	42.3%	85.3 / 17.4	52	noncoding (72/88 nt)	serX	tRNA‑Ser
*	NC_000913	3,231,104	0	C	A	42.0%	65.9 / 24.8	50	A739A (GCC→GCA)	ygjK	alpha‑glucosidase
*	NC_000913	2,434,882	0	T	G	41.5%	123.0 / 13.1	65	Y252S (TAC→TCC)	truA	tRNA pseudouridine(38‑40) synthase

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	= 1207805	55 (0.890)	15 (0.270)	14/266	5.5	24.6%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	43 (0.780)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	1207790 =	52 (0.840)	11 (0.200)	10/266	7.1	19.8%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	43 (0.780)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related