breseq  version 0.35.4  revision f352f80f4bc9 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence (highest frequency 20 of 47 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	631,122	0	C	G	52.3%	50.6 / inf	235	A410G (GCT→GGT)	cstA	carbon starvation protein A
*	NC_000913	1,127,420	0	T	C	52.3%	49.7 / inf	235	G205G (GGT→GGC)	yceM	putative oxidoreductase YceM
*	NC_000913	1,094,151	0	G	A	51.8%	33.0 / inf	251	D426N (GAT→AAT)	dgcT	putative diguanylate cyclase DgcT
*	NC_000913	371,652	0	C	T	51.7%	5.2 / inf	201	G138G (GGC→GGT)	mhpC	2‑hydroxy‑6‑ketonona‑2,4‑dienedioate hydrolase
*	NC_000913	184,764	0	A	G	51.0%	13.3 / inf	243	S102S (AGT→AGC)	yaeI	phosphodiesterase YaeI
*	NC_000913	3,387,103	0	T	C	50.6%	18.0 / inf	269	T362T (ACA→ACG)	aaeB	aromatic carboxylic acid efflux pump subunit AaeB
*	NC_000913	1,444,420	0	A	G	49.8%	‑3.0 / inf	265	E457G (GAG→GGG)	ydbH	PF11739 family protein YdbH
*	NC_000913	2,938,203	0	G	A	49.1%	33.5 / inf	225	A246T (GCC→ACC)	fucK	L‑fuculokinase
*	NC_000913	3,238,555	1	.	T	49.1%	inf / inf	265	intergenic (+258/‑25)	ygjR/alx	putative oxidoreductase YgjR/putative membrane‑bound redox modulator Alx
*	NC_000913	226,952	0	A	G	48.7%	17.5 / inf	197	noncoding (1194/2904 nt)	rrlH	23S ribosomal RNA
*	NC_000913	4,128,439	0	A	G	48.1%	30.2 / inf	239	intergenic (‑44/‑233)	metJ/metB	DNA‑binding transcriptional repressor MetJ/O‑succinylhomoserine(thiol)‑lyase/O‑ succinylhomoserine lyase
*	NC_000913	2,475,462	0	C	T	46.8%	58.8 / inf	269	A160V (GCC→GTC)	yfdR	CPS‑53 (KpLE1) prophage; 5'‑deoxynucleotidase
*	NC_000913	4,606,322	1	.	G	46.5%	19.7 / inf	187	noncoding (80/87 nt)	leuQ	tRNA‑Leu
*	NC_000913	2,014,036	0	G	A	46.3%	65.4 / inf	242	A270T (GCC→ACC)	fliF	flagellar basal‑body MS‑ring and collar protein
*	NC_000913	2,092,492	0	T	C	46.2%	74.7 / inf	264	V32A (GTC→GCC)	hisC	histidinol‑phosphate aminotransferase
*	NC_000913	2,665,754	0	C	.	46.0%	inf / inf	249	coding (320/1281 nt)	csiE	stationary phase inducible protein CsiE
*	NC_000913	4,537,525	0	A	G	45.6%	95.7 / inf	305	Y24H (TAT→CAT)	nanS	N‑acetyl‑9‑O‑acetylneuraminate esterase
*	NC_000913	2,473,227	0	A	G	42.5%	140.0 / 305.6	221	L7P (CTC→CCC)	yfdO	CPS‑53 (KpLE1) prophage; putative defective phage replication protein O
*	NC_000913	3,830,694	0	G	A	31.5%	358.7 / 238.6	241	A80T (GCC→ACC)	yicH	AsmA famly protein YicH
*	NC_000913	2,250,882	0	G	A	30.3%	399.4 / 246.5	251	A15T (GCA→ACA)	nfo	endonuclease IV

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 =	151 (0.580)	107 (0.500)	73/162	5.0	44.0%	coding (290/630 nt)	ycfK	e14 prophage; protein StfP
	?	NC_000913	1209619 =	146 (0.680)					pseudogene (37/537 nt)	stfE	e14 prophage; putative side tail fiber protein fragment
*	?	NC_000913	= 1207805	159 (0.620)	81 (0.380)	61/162	7.6	37.5%	coding (305/630 nt)	ycfK	e14 prophage; protein StfP
	?	NC_000913	= 1209602	137 (0.640)					pseudogene (54/537 nt)	stfE	e14 prophage; putative side tail fiber protein fragment
*	?	NC_000913	= 71350	278 (1.080)	89 (0.360)	49/188	13.8	39.8%	intergenic (+85/‑1)	araC/yabI	DNA‑binding transcriptional dual regulator AraC/DedA family protein YabI
	?	NC_000913	= 2857042	0 (0.000)					intergenic (‑236/‑51)	ygbA/mutS	protein YgbA/DNA mismatch repair protein MutS
*	?	NC_000913	= 1209618	177 (0.690)	21 (0.100)	15/164	26.0	10.6%	pseudogene (38/537 nt)	stfE	e14 prophage; putative side tail fiber protein fragment
	?	NC_000913	2471897 =	206 (0.940)					pseudogene (166/519 nt)	yfdL	CPS‑53 (KpLE1) prophage; putative uncharacterized protein YfdL
*	?	NC_000913	4542682 =	319 (1.240)	5 (0.020)	5/176	35.2	1.7%	intergenic (+49/‑433)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	4542996 =	284 (1.210)					intergenic (+363/‑119)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit