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 259 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,480,371	0	T	G	52.1%	52.6 / 73.1	48	G390G (GGT→GGG)	dsdA	D‑serine dehydratase
*	NC_000913	4,538,109	0	A	C	49.1%	71.6 / 21.9	58	G219G (GGT→GGG)	nanM	N‑acetylneuraminic acid mutarotase
*	NC_000913	4,332,791	0	A	C	46.0%	104.8 / 17.8	63	V161G (GTG→GGG)	basS	sensory histidine kinase in two‑component regulatory system with BasR
*	NC_000913	1,415,806	0	G	T	44.7%	59.1 / 16.6	38	N527K (AAC→AAA)	recE	Rac prophage; exonuclease VIII, 5' to 3' specific dsDNA exonuclease
*	NC_000913	4,111,747	0	G	T	44.4%	84.6 / 29.3	54	N156K (AAC→AAA)	yiiQ	DUF1454 family putative periplasmic protein
*	NC_000913	4,381,728	0	A	C	44.4%	83.1 / 11.1	54	G197G (GGT→GGG)	frdA	anaerobic fumarate reductase catalytic and NAD/flavoprotein subunit
*	NC_000913	2,958,771	0	A	T	44.2%	69.2 / 30.3	52	D38E (GAT→GAA)	ptrA	protease III
*	NC_000913	4,302,658	0	T	G	44.0%	60.5 / 12.5	50	T141P (ACC→CCC)	mdtO	membrane translocase (MDR) of MdtNOP efflux pump, PET family
*	NC_000913	5,159	0	G	A	43.2%	52.0 / 21.1	45	intergenic (+139/‑75)	thrC/yaaX	L‑threonine synthase/DUF2502 family putative periplasmic protein
*	NC_000913	925,900	0	A	G	43.1%	81.3 / 12.9	51	noncoding (72/88 nt)	serW	tRNA‑Ser
*	NC_000913	1,222,233	0	G	A	42.9%	27.9 / 12.2	28	pseudogene (60/75 nt)	ycgH	pseudogene; putative ATP‑binding component of a transport system
*	NC_000913	1,567,738	0	A	T	42.4%	40.9 / 17.7	34	V362V (GTT→GTA)	yddW	liprotein, glycosyl hydrolase homolog
*	NC_000913	2,511,772	0	A	C	42.2%	82.9 / 10.5	45	V312G (GTG→GGG)	mntH	manganese/divalent cation transporter
*	NC_000913	29,496	0	T	A	42.0%	78.5 / 26.3	50	intergenic (+301/‑155)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	3,206,435	0	C	T	41.9%	46.1 / 23.6	43	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	1,487,163	0	C	T	41.7%	61.3 / 23.3	48	intergenic (+200/‑72)	hrpA/ydcF	putative ATP‑dependent helicase/DUF218 superfamily protein, SAM‑binding
*	NC_000913	4,394,579	0	G	C	41.3%	80.0 / 22.2	47	G172R (GGC→CGC)	nnr	bifunctional NAD(P)H‑hydrate repair enzyme; C‑terminal domain ADP‑dependent (S)‑NAD(P)H‑hydrate dehydratase and N‑terminal domain NAD(P)H‑hydrate epimerase
*	NC_000913	1,383,722	0	G	A	41.2%	57.8 / 21.9	51	F80F (TTC→TTT)	ycjW	LacI family putative transcriptional repressor
*	NC_000913	1,376,505	0	A	C	41.1%	107.1 / 10.4	56	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
*	NC_000913	1,312,210	0	C	A	40.5%	83.0 / 22.1	42	V13F (GTT→TTT)	yciA	acyl‑CoA esterase

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	30 (0.510)	12 (0.230)	11/266	5.4	28.0%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	35 (0.670)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	1207790 =	26 (0.440)	11 (0.210)	11/266	5.4	26.1%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	39 (0.750)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	4542682 =	58 (0.990)	3 (0.050)	3/280	9.9	5.0%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	59 (1.070)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)