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 1005 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	49.1%	49.1 / 36.8	55	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	987,494	0	T	G	47.3%	163.9 / 26.2	93	intergenic (‑512/+91)	ompF/asnS	outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
*	NC_000913	689,514	0	A	C	44.9%	112.5 / 18.2	70	G456G (GGT→GGG)	lnt	apolipoprotein N‑acyltransferase
*	NC_000913	599,576	0	T	G	43.8%	185.1 / 46.1	112	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	1,478,324	0	T	G	42.5%	199.5 / 57.7	120	G33G (GGT→GGG)	ynbB	putative CDP‑diglyceride synthase
*	NC_000913	357,880	0	T	C	42.1%	82.9 / 22.2	58	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	1,356,201	0	T	G	41.9%	188.3 / 17.0	93	T304P (ACC→CCC)	sapA	antimicrobial peptide transport ABC transporter periplasmic binding protein
*	NC_000913	3,350,853	0	A	C	41.5%	176.3 / 13.3	95	S725A (TCA→GCA)	arcB	aerobic respiration control sensor histidine protein kinase, cognate to two‑component response regulators ArcA and RssB
*	NC_000913	1,376,505	0	A	C	41.3%	178.3 / 28.9	92	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
*	NC_000913	907,602	0	A	C	41.0%	162.0 / 10.8	83	G227G (GGT→GGG)	ybjT	putative NAD‑dependent oxidoreductase
*	NC_000913	2,578,143	0	A	C	40.9%	144.1 / 50.9	88	L79V (TTA→GTA)	maeB	malic enzyme: putative oxidoreductase/phosphotransacetylase
*	NC_000913	4,604,344	0	C	T	40.4%	132.9 / 53.4	104	S62F (TCT→TTT)	bglJ	bgl operon transcriptional activator
*	NC_000913	1,153,573	0	T	G	40.2%	160.5 / 74.5	102	Y92D (TAC→GAC)	pabC	4‑amino‑4‑deoxychorismate lyase component of para‑aminobenzoate synthase multienzyme complex
*	NC_000913	535,901	0	T	G	40.0%	179.8 / 15.0	96	G64G (GGT→GGG)	hyi	hydroxypyruvate isomerase
*	NC_000913	659,942	0	G	A	40.0%	126.0 / 50.3	90	A92V (GCT→GTT)	lipA	lipoate synthase
*	NC_000913	2,628,625	0	A	C	40.0%	178.0 / 17.9	95	V105G (GTC→GGC)	yfgF	cyclic‑di‑GMP phosphodiesterase, anaerobic
*	NC_000913	3,270,455	0	G	T	40.0%	178.7 / 59.1	110	intergenic (+853/+170)	yhaC/garK	pentapetide repeats‑related protein/glycerate kinase I
*	NC_000913	3,423,294	0	T	C	39.5%	201.5 / 55.1	129	intergenic (+100/+129)	yhdZ/rrfF	putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon
*	NC_000913	3,640,981	0	C	T	39.4%	123.7 / 50.5	94	F40F (TTC→TTT)	dtpB	dipeptide and tripeptide permease B
*	NC_000913	2,048,721	0	A	C	39.2%	194.7 / 21.7	107	T1262P (ACC→CCC)	yeeJ	putative adhesin

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	84 (0.670)	37 (0.330)	33/266	7.2	32.5%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	79 (0.710)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	1207790 =	88 (0.700)	25 (0.220)	24/266	10.2	23.5%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	84 (0.750)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	1411899 =	136 (1.090)	8 (0.080)	8/246	17.3	6.8%	coding (50/936 nt)	ttcA	tRNA s(2)C32 thioltransferase, iron sulfur cluster protein
	?	NC_000913	= 1434958	106 (1.030)					pseudogene (51/51 nt)	ttcC	pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related
*	?	NC_000913	= 1209618	100 (0.800)	36 (0.320)	3/268	23.0	24.8%	pseudogene (2/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
	?	NC_000913	2471897 =	129 (1.150)					pseudogene (226/579 nt)	yfdL	pseudogene, CPS‑53 (KpLE1) prophage;Phage or Prophage Related
*	?	NC_000913	1722616 =	104 (0.830)	3 (0.030)	3/276	23.5	3.1%	coding (496/2013 nt)	ydhK	putative efflux protein (PET) component of YdhJK efflux pump
	?	NC_000913	= 1722612	91 (0.790)					coding (492/2013 nt)	ydhK	putative efflux protein (PET) component of YdhJK efflux pump
*	?	NC_000913	= 4542690	120 (0.960)	3 (0.030)	3/280	23.7	2.6%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	113 (0.960)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)