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 519 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,206,435	0	C	T	50.7%	46.3 / 108.7	75	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	1,825,056	0	G	A	50.0%	53.2 / 40.7	58	intergenic (‑119/+84)	ves/spy	cold‑ and stress‑inducible protein/periplasmic ATP‑independent protein refolding chaperone, stress‑induced
*	NC_000913	2,678,039	0	T	G	50.0%	82.1 / 15.7	62	N108T (AAC→ACC)	yphE	putative sugar ABC transporter ATPase
*	NC_000913	2,248,431	0	A	C	49.2%	73.4 / 37.0	67	G34G (GGT→GGG)	lysP	lysine transporter
*	NC_000913	4,378,802	0	A	C	49.2%	89.0 / 25.5	67	V48G (GTA→GGA)	ampC	penicillin‑binding protein; beta‑lactamase, intrinsically weak
*	NC_000913	1,478,324	0	T	G	47.9%	96.1 / 28.5	71	G33G (GGT→GGG)	ynbB	putative CDP‑diglyceride synthase
*	NC_000913	354,288	0	T	G	46.3%	106.7 / 14.3	67	V528G (GTG→GGG)	prpE	propionate‑‑CoA ligase
*	NC_000913	1,376,505	0	A	C	45.6%	103.0 / 26.2	69	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
*	NC_000913	2,001,918	0	A	C	45.6%	111.4 / 17.5	69	intergenic (‑129/+192)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin)
*	NC_000913	2,984,441	0	A	C	43.8%	105.0 / 21.3	64	G384G (GGT→GGG)	yqeF	short chain acyltransferase
*	NC_000913	2,678,043	0	C	T	43.5%	68.2 / 27.7	62	E107K (GAA→AAA)	yphE	putative sugar ABC transporter ATPase
*	NC_000913	1,097,581	0	A	G	43.3%	104.4 / 17.5	60	noncoding (72/88 nt)	serX	tRNA‑Ser
*	NC_000913	786,855	0	A	C	42.9%	167.4 / 15.2	91	G247G (GGT→GGG)	gpmA	phosphoglyceromutase 1
*	NC_000913	925,900	0	A	G	42.9%	114.5 / 24.5	77	noncoding (72/88 nt)	serW	tRNA‑Ser
*	NC_000913	1,825,061	0	G	A	42.9%	74.9 / 40.0	63	intergenic (‑124/+79)	ves/spy	cold‑ and stress‑inducible protein/periplasmic ATP‑independent protein refolding chaperone, stress‑induced
*	NC_000913	2,386,862	0	G	A	42.9%	80.2 / 62.5	77	intergenic (+31/‑72)	yfbL/yfbM	putative M28A family peptidase/DUF1877 family protein
*	NC_000913	2,248,424	0	C	A	42.4%	79.2 / 32.7	66	V37F (GTT→TTT)	lysP	lysine transporter
*	NC_000913	3,133,302	0	T	G	42.4%	111.7 / 10.1	66	H219P (CAC→CCC)	yghS	putative ATP‑binding protein
*	NC_000913	1,222,233	0	G	A	42.2%	87.2 / 25.8	65	pseudogene (60/75 nt)	ycgH	pseudogene; putative ATP‑binding component of a transport system
*	NC_000913	15,410	0	T	G	41.8%	92.6 / 11.7	56	intergenic (+112/‑35)	dnaJ/insL1	chaperone Hsp40, DnaK co‑chaperone/IS186 transposase

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	59 (0.750)	15 (0.210)	15/266	7.5	21.2%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	59 (0.840)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	1207790 =	59 (0.750)	12 (0.170)	12/266	8.8	17.4%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	61 (0.870)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related