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 641 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	354,288	0	T	G	51.3%	93.0 / 130.1	76	V528G (GTG→GGG)	prpE	propionate‑‑CoA ligase
*	NC_000913	3,508,657	0	A	G	46.2%	77.7 / 22.2	65	F386S (TTC→TCC)	yhfW	phosphopentomutase‑related metalloenzyme superfamily protein
*	NC_000913	1,604,237	0	C	T	46.0%	65.4 / 30.2	64	S64L (TCG→TTG)	lsrD	autoinducer 2 import system permease protein
*	NC_000913	993,913	0	G	C	44.4%	88.0 / 25.6	54	G44G (GGC→GGG)	ssuB	aliphatic sulfonate ABC transporter ATPase
*	NC_000913	3,261,055	0	A	C	44.2%	126.4 / 24.7	77	V455G (GTG→GGG)	tdcE	pyruvate formate‑lyase 4/2‑ketobutyrate formate‑lyase
*	NC_000913	3,508,662	0	T	A	43.9%	83.6 / 34.3	66	E384D (GAA→GAT)	yhfW	phosphopentomutase‑related metalloenzyme superfamily protein
*	NC_000913	4,378,802	0	A	C	43.3%	110.9 / 24.2	67	V48G (GTA→GGA)	ampC	penicillin‑binding protein; beta‑lactamase, intrinsically weak
*	NC_000913	354,282	0	T	G	43.1%	117.0 / 12.0	73	V526G (GTT→GGT)	prpE	propionate‑‑CoA ligase
*	NC_000913	2,547,772	0	T	G	42.9%	101.8 / 15.1	64	V367G (GTA→GGA)	murP	N‑acetylmuramic acid permease, EIIBC component, PTS system
*	NC_000913	3,026,941	0	A	C	42.1%	89.4 / 10.5	57	E392D (GAA→GAC)	guaD	guanine deaminase
*	NC_000913	1,969,794	0	A	C	41.7%	102.0 / 16.3	62	G397G (GGT→GGG)	tap	methyl‑accepting protein IV
*	NC_000913	3,585,086	0	A	C	41.6%	132.2 / 29.1	78	Y580D (TAC→GAC)	ggt	gamma‑glutamyltranspeptidase
*	NC_000913	1,222,596	0	G	A	41.1%	82.5 / 43.9	73	F13F (TTC→TTT)	ymgD	uncharacterized protein
*	NC_000913	2,151,592	0	G	T	41.1%	89.3 / 39.6	56	L136F (TTG→TTT)	yegJ	uncharacterized protein
*	NC_000913	925,900	0	A	G	40.8%	116.1 / 18.0	72	noncoding (72/88 nt)	serW	tRNA‑Ser
*	NC_000913	1,825,056	0	G	A	40.8%	104.3 / 35.6	71	intergenic (‑119/+84)	ves/spy	cold‑ and stress‑inducible protein/periplasmic ATP‑independent protein refolding chaperone, stress‑induced
*	NC_000913	354,318	0	T	G	40.6%	133.5 / 11.5	69	V538G (GTG→GGG)	prpE	propionate‑‑CoA ligase
*	NC_000913	4,302,658	0	T	G	40.6%	123.1 / 10.8	69	T141P (ACC→CCC)	mdtO	membrane translocase (MDR) of MdtNOP efflux pump, PET family
*	NC_000913	941,713	0	T	G	40.5%	131.3 / 26.3	74	V252G (GTG→GGG)	dmsA	dimethyl sulfoxide reductase, anaerobic, subunit A
*	NC_000913	606,619	0	T	C	40.3%	84.7 / 21.9	62	G255G (GGA→GGG)	ybdK	weak gamma‑glutamyl:cysteine ligase

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	63 (0.780)	15 (0.210)	14/266	8.4	25.2%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	33 (0.460)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	1207790 =	61 (0.750)	15 (0.210)	14/266	8.4	25.3%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	34 (0.470)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related