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 955 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,097,299	0	A	G	50.0%	17.5 / 45.3	42	intergenic (+470/+266)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
*	NC_000913	354,288	0	T	G	46.5%	190.0 / 48.4	127	V528G (GTG→GGG)	prpE	propionate‑‑CoA ligase
*	NC_000913	357,890	0	C	A	45.6%	45.1 / 41.1	69	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	357,880	0	T	C	45.3%	74.2 / 22.1	64	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	2,984,441	0	A	C	42.6%	212.1 / 50.2	122	G384G (GGT→GGG)	yqeF	short chain acyltransferase
*	NC_000913	3,508,657	0	A	G	42.6%	155.1 / 28.4	108	F386S (TTC→TCC)	yhfW	phosphopentomutase‑related metalloenzyme superfamily protein
*	NC_000913	298,953	0	A	C	42.3%	192.8 / 28.5	111	V661G (GTG→GGG)	paoC	PaoABC aldehyde oxidoreductase, Moco‑containing subunit
*	NC_000913	3,350,853	0	A	C	41.8%	163.4 / 11.8	91	S725A (TCA→GCA)	arcB	aerobic respiration control sensor histidine protein kinase, cognate to two‑component response regulators ArcA and RssB
*	NC_000913	1,097,392	1	.	G	41.5%	42.0 / 137.2	65	intergenic (+563/+173)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
*	NC_000913	354,318	0	T	G	41.2%	233.6 / 11.3	114	V538G (GTG→GGG)	prpE	propionate‑‑CoA ligase
*	NC_000913	3,508,662	0	T	A	41.1%	170.9 / 44.6	112	E384D (GAA→GAT)	yhfW	phosphopentomutase‑related metalloenzyme superfamily protein
*	NC_000913	298,960	0	A	C	40.9%	183.5 / 51.3	115	Y659D (TAT→GAT)	paoC	PaoABC aldehyde oxidoreductase, Moco‑containing subunit
*	NC_000913	3,001,164	0	A	C	40.4%	174.3 / 26.0	94	T274P (ACC→CCC)	xdhA	xanthine dehydrogenase, molybdenum binding subunit
*	NC_000913	987,494	0	T	G	40.0%	209.0 / 26.4	115	intergenic (‑512/+91)	ompF/asnS	outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
*	NC_000913	3,423,297	0	G	C	39.9%	263.9 / 72.5	143	intergenic (+103/+126)	yhdZ/rrfF	putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon
*	NC_000913	3,350,844	0	A	C	39.8%	174.0 / 12.5	93	L728V (TTA→GTA)	arcB	aerobic respiration control sensor histidine protein kinase, cognate to two‑component response regulators ArcA and RssB
*	NC_000913	15,410	0	T	G	39.8%	168.7 / 23.1	89	intergenic (+112/‑35)	dnaJ/insL1	chaperone Hsp40, DnaK co‑chaperone/IS186 transposase
*	NC_000913	1,261,842	0	T	G	39.6%	273.0 / 31.3	141	T12P (ACC→CCC)	prs	phosphoribosylpyrophosphate synthase
*	NC_000913	3,206,435	0	C	T	39.6%	145.5 / 93.5	135	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	1,397,830	0	T	C	39.4%	188.2 / 39.1	133	I265V (ATT→GTT)	uspE	stress‑induced protein

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	111 (0.790)	31 (0.250)	27/266	10.5	23.8%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	100 (0.800)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	1207790 =	109 (0.770)	22 (0.180)	20/266	13.4	17.7%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	107 (0.850)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1209618	116 (0.820)	26 (0.210)	6/268	22.0	18.6%	pseudogene (2/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
	?	NC_000913	2471897 =	123 (0.970)					pseudogene (226/579 nt)	yfdL	pseudogene, CPS‑53 (KpLE1) prophage;Phage or Prophage Related
*	?	NC_000913	= 4542690	180 (1.280)	3 (0.020)	3/280	25.6	1.7%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	174 (1.320)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)