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 613 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	941,713	0	T	G	47.8%	71.9 / 31.9	69	V252G (GTG→GGG)	dmsA	dimethyl sulfoxide reductase, anaerobic, subunit A
*	NC_000913	357,890	0	C	A	45.7%	31.7 / 16.3	35	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	345,328	0	C	A	45.2%	64.3 / 46.9	62	intergenic (+337/‑76)	yahL/yahM	uncharacterized protein/uncharacterized protein
*	NC_000913	2,001,911	0	G	A	44.8%	50.8 / 40.8	58	intergenic (‑122/+199)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin)
*	NC_000913	3,350,844	0	A	C	44.4%	84.6 / 11.9	55	L728V (TTA→GTA)	arcB	aerobic respiration control sensor histidine protein kinase, cognate to two‑component response regulators ArcA and RssB
*	NC_000913	742,106	0	A	C	43.8%	102.2 / 19.9	73	S151A (TCT→GCT)	dtpD	dipeptide and tripeptide permease D
*	NC_000913	599,576	0	T	G	43.7%	98.6 / 23.9	72	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	2,001,918	0	A	C	43.6%	76.5 / 12.3	56	intergenic (‑129/+192)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin)
*	NC_000913	3,261,055	0	A	C	43.6%	73.1 / 12.6	57	V455G (GTG→GGG)	tdcE	pyruvate formate‑lyase 4/2‑ketobutyrate formate‑lyase
*	NC_000913	1,764,785	0	T	A	43.0%	112.8 / 46.4	79	intergenic (‑399/+149)	sufA/ydiH	Fe‑S cluster assembly protein/uncharacterized protein
*	NC_000913	3,423,297	0	G	C	42.5%	120.5 / 53.3	80	intergenic (+103/+126)	yhdZ/rrfF	putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon
*	NC_000913	3,133,302	0	T	G	42.4%	108.4 / 16.3	66	H219P (CAC→CCC)	yghS	putative ATP‑binding protein
*	NC_000913	1,684,749	0	A	C	42.3%	76.8 / 11.8	53	D164A (GAC→GCC)	tus	inhibitor of replication at Ter, DNA‑binding protein
*	NC_000913	753,125	0	T	A	42.2%	127.0 / 38.6	84	intergenic (‑330/+60)	ybgD/gltA	putative fimbrial‑like adhesin protein/citrate synthase
*	NC_000913	5,159	0	G	A	41.7%	63.4 / 39.1	60	intergenic (+139/‑75)	thrC/yaaX	L‑threonine synthase/DUF2502 family putative periplasmic protein
*	NC_000913	3,206,435	0	C	T	41.7%	73.9 / 50.1	73	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	3,782,908	0	T	G	41.7%	36.9 / 15.3	51	T252P (ACC→CCC)	gpsA	glycerol‑3‑phosphate dehydrogenase (NAD+)
*	NC_000913	4,257,698	0	T	G	41.2%	122.3 / 21.5	80	V195G (GTT→GGT)	lexA	transcriptional repressor of SOS regulon
*	NC_000913	1,222,213	0	A	C	41.1%	94.9 / 10.1	56	pseudogene (40/75 nt)	ycgH	pseudogene; putative ATP‑binding component of a transport system
*	NC_000913	3,350,853	0	A	C	41.1%	86.6 / 14.7	56	S725A (TCA→GCA)	arcB	aerobic respiration control sensor histidine protein kinase, cognate to two‑component response regulators ArcA and RssB

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	78 (0.970)	11 (0.150)	10/266	9.7	15.1%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	54 (0.750)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	1207790 =	78 (0.970)	10 (0.140)	10/266	9.7	13.6%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	57 (0.790)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	4542682 =	96 (1.190)	7 (0.090)	7/280	11.9	7.6%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	81 (1.070)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	1411899 =	78 (0.970)	3 (0.050)	3/246	13.5	4.0%	coding (50/936 nt)	ttcA	tRNA s(2)C32 thioltransferase, iron sulfur cluster protein
	?	NC_000913	= 1434958	78 (1.180)					pseudogene (51/51 nt)	ttcC	pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related
*	?	NC_000913	= 4542690	97 (1.210)	4 (0.050)	4/280	14.0	4.4%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	81 (1.070)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)