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 289 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,343,821	0	C	A	53.3%	33.5 / 66.0	46	A117S (GCT→TCT)	yfaL	adhesin
*	NC_000913	357,880	0	T	C	52.9%	27.2 / 51.7	34	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	4,331,790	0	T	G	52.2%	58.4 / 76.9	46	V430G (GTT→GGT)	proP	proline/glycine betaine transporter
*	NC_000913	2,343,810	0	G	T	50.0%	50.5 / 38.7	48	N120K (AAC→AAA)	yfaL	adhesin
*	NC_000913	2,421,443	0	A	C	49.3%	99.9 / 26.2	69	Y40S (TAC→TCC)	folX	D‑erythro‑7,8‑dihydroneopterin triphosphate 2'‑epimerase and dihydroneopterin aldolase
*	NC_000913	599,576	0	T	G	49.2%	88.0 / 25.1	63	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	328,791	0	A	G	48.9%	44.6 / 23.5	47	S182P (TCC→CCC)	betI	choline‑inducible betIBA‑betT divergent operon transcriptional repressor
*	NC_000913	4,137,615	0	T	G	48.2%	83.1 / 13.2	56	T15P (ACC→CCC)	yijF	DUF1287 family protein
*	NC_000913	328,803	0	T	G	47.7%	48.0 / 28.8	44	T178P (ACC→CCC)	betI	choline‑inducible betIBA‑betT divergent operon transcriptional repressor
*	NC_000913	884,346	0	C	G	47.3%	87.0 / 17.4	56	A225G (GCG→GGG)	mdfA	multidrug efflux system protein
*	NC_000913	3,412,898	0	C	T	47.3%	36.1 / 43.0	56	A190T (GCC→ACC)	acrS	acrAB operon transcriptional repressor
*	NC_000913	4,238,049	0	A	G	46.9%	62.6 / 16.4	49	E139G (GAA→GGA)	yjbH	DUF940 family extracellular polysaccharide protein
*	NC_000913	1,097,581	0	A	G	46.7%	77.3 / 23.9	60	noncoding (72/88 nt)	serX	tRNA‑Ser
*	NC_000913	1,649,295	0	T	G	46.5%	55.8 / 10.8	43	intergenic (+254/‑314)	ydfC/dicB	uncharacterized protein, Qin prophage/Qin prophage; cell division inhibition protein
*	NC_000913	328,807	0	A	T	45.6%	52.4 / 29.7	46	D176E (GAT→GAA)	betI	choline‑inducible betIBA‑betT divergent operon transcriptional repressor
*	NC_000913	941,713	0	T	G	45.5%	78.1 / 12.4	55	V252G (GTG→GGG)	dmsA	dimethyl sulfoxide reductase, anaerobic, subunit A
*	NC_000913	2,265,639	0	A	C	45.5%	58.1 / 11.1	44	T64P (ACC→CCC)	yeiP	elongation factor P‑like protein
*	NC_000913	2,001,918	0	A	C	45.1%	81.0 / 11.6	51	intergenic (‑129/+192)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin)
*	NC_000913	4,536,197	0	A	T	44.0%	48.4 / 42.9	50	intergenic (+166/+417)	yjhR/nanS	pseudogene, helicase family; putative frameshift suppressor/9‑O‑acetyl N‑acetylneuraminic acid esterase
*	NC_000913	2,678,039	0	T	G	43.9%	97.2 / 10.7	57	N108T (AAC→ACC)	yphE	putative sugar ABC transporter ATPase

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 =	51 (0.870)	11 (0.210)	11/266	6.1	18.0%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	55 (1.050)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1207805	49 (0.830)	8 (0.150)	8/266	7.5	14.1%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	54 (1.030)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 4542690	59 (1.000)	4 (0.070)	4/280	10.3	6.3%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	63 (1.140)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	4542682 =	64 (1.090)	3 (0.050)	3/280	11.1	4.6%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	63 (1.140)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)