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 359 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,111,747	0	G	T	54.2%	55.3 / 106.0	59	N156K (AAC→AAA)	yiiQ	DUF1454 family putative periplasmic protein
*	NC_000913	1,356,201	0	T	G	54.2%	54.3 / 70.6	49	T304P (ACC→CCC)	sapA	antimicrobial peptide transport ABC transporter periplasmic binding protein
*	NC_000913	354,282	0	T	G	51.8%	67.9 / 84.7	54	V526G (GTT→GGT)	prpE	propionate‑‑CoA ligase
*	NC_000913	3,601,170	0	G	C	51.4%	42.6 / 68.8	35	A306G (GCA→GGA)	ftsX	putative ABC transporter permease
*	NC_000913	4,107,866	0	T	G	51.4%	32.4 / 54.6	35	G105G (GGT→GGG)	pfkA	6‑phosphofructokinase I
*	NC_000913	29,496	0	T	A	51.1%	37.6 / 74.6	45	intergenic (+301/‑155)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	2,096,090	0	A	G	51.0%	54.8 / 80.0	51	I83V (ATT→GTT)	hisF	imidazole glycerol phosphate synthase, catalytic subunit with HisH
*	NC_000913	29,486	0	C	A	48.9%	47.5 / 34.5	45	intergenic (+291/‑165)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	599,576	0	T	G	48.1%	109.8 / 33.3	79	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	2,859,104	0	T	G	46.5%	40.4 / 17.7	43	M671R (ATG→AGG)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	354,288	0	T	G	46.3%	73.4 / 14.3	54	V528G (GTG→GGG)	prpE	propionate‑‑CoA ligase
*	NC_000913	2,846,674	0	T	G	45.9%	89.5 / 14.4	62	T247P (ACC→CCC)	hycD	hydrogenase 3, membrane subunit
*	NC_000913	3,601,176	0	T	C	45.7%	34.2 / 17.1	35	E304G (GAA→GGA)	ftsX	putative ABC transporter permease
*	NC_000913	589,934	0	T	G	44.1%	37.8 / 19.0	34	T341P (ACC→CCC)	nfrA	bacteriophage N4 receptor, outer membrane subunit
*	NC_000913	925,900	0	A	G	44.0%	130.0 / 25.3	84	noncoding (72/88 nt)	serW	tRNA‑Ser
*	NC_000913	1,825,056	0	G	A	43.8%	73.4 / 41.1	64	intergenic (‑119/+84)	ves/spy	cold‑ and stress‑inducible protein/periplasmic ATP‑independent protein refolding chaperone, stress‑induced
*	NC_000913	2,185,199	0	T	G	43.8%	60.4 / 18.7	48	T35P (ACC→CCC)	thiM	hydoxyethylthiazole kinase
*	NC_000913	4,258,974	0	T	G	43.3%	90.5 / 10.5	61	G411G (GGT→GGG)	dinF	oxidative stress resistance protein; putative MATE family efflux pump; UV and mitomycin C inducible protein
*	NC_000913	1,825,061	0	G	A	43.3%	89.9 / 32.5	67	intergenic (‑124/+79)	ves/spy	cold‑ and stress‑inducible protein/periplasmic ATP‑independent protein refolding chaperone, stress‑induced
*	NC_000913	3,747,132	0	G	A	43.1%	56.3 / 26.6	60	A17T (GCC→ACC)	lyxK	L‑xylulose kinase

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	1207790 =	68 (1.110)	12 (0.220)	12/266	5.7	18.5%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	45 (0.820)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1207805	68 (1.110)	7 (0.130)	7/266	8.0	11.8%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	44 (0.810)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related