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 26 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	707,976	0	T	G	56.7%	2.4 / 21.5	30	intergenic (+219/‑358)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	2,177,221	0	T	G	55.0%	‑1.4 / 13.0	20	intergenic (‑17/+291)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	1,636,447	0	C	G	52.0%	8.9 / 29.6	26	intergenic (‑80/‑309)	nohA/ynfO	Qin prophage; putative prophage DNA‑packaging protein NohA/Qin prophage; protein YnfO
*	NC_000913	2,177,228	0	C	T	50.0%	‑6.8 / 10.7	21	intergenic (‑24/+284)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	2,177,255	0	G	T	50.0%	0.5 / 11.9	22	intergenic (‑51/+257)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	4,378,973	0	G	C	47.6%	‑5.5 / 10.1	21	intergenic (‑29/+34)	ampC/frdD	beta‑lactamase/fumarate reductase membrane protein FrdD
*	NC_000913	3,245,340	0	G	A	42.2%	17.3 / 56.2	45	E39E (GAG→GAA)	exuT	hexuronate transporter
*	NC_000913	707,981	0	C	G	40.9%	16.5 / 13.0	32	intergenic (+224/‑353)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	1,636,440	0	T	G	40.7%	19.8 / 12.9	27	intergenic (‑73/‑316)	nohA/ynfO	Qin prophage; putative prophage DNA‑packaging protein NohA/Qin prophage; protein YnfO
*	NC_000913	3,004,946	0	G	T	34.9%	46.4 / 17.9	43	Q281K (CAA→AAA)	ygeV	putative sigma(54)‑dependent transcriptional regulator YgeV
*	NC_000913	2,560,455	0	G	C	34.2%	72.5 / 10.2	41	A67P (GCA→CCA)	yffL	CPZ‑55 prophage; uncharacterized protein YffL
*	NC_000913	3,455,677	0	A	T	34.2%	43.0 / 13.9	41	N34Y (AAT→TAT)	gspC	Type II secretion system protein GspC
*	NC_000913	4,296,060	0	C	T	33.9%	75.0 / 57.1	59	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
*	NC_000913	1,297,110	0	A	G	33.3%	28.1 / 10.7	34	S338P (TCC→CCC)	adhE	aldehyde‑alcohol dehydrogenase
*	NC_000913	3,120,265	0	A	C	33.3%	45.8 / 12.9	39	F339V (TTT→GTT)	glcA	glycolate/lactate:H(+) symporter GlcA
*	NC_000913	1,530,561	0	C	A	32.6%	82.3 / 13.3	49	intergenic (‑57/‑25)	yncO/yncI	protein YncO/putative transposase YncI
*	NC_000913	411,595	0	G	C	32.0%	77.6 / 12.1	50	A296G (GCT→GGT)	araJ	putative transport protein AraJ
*	NC_000913	1,530,570	0	T	A	31.9%	73.4 / 13.1	47	intergenic (‑66/‑16)	yncO/yncI	protein YncO/putative transposase YncI
*	NC_000913	1,530,539	0	C	A	31.7%	71.9 / 15.8	41	intergenic (‑35/‑47)	yncO/yncI	protein YncO/putative transposase YncI
*	NC_000913	1,425,560	0	A	T	30.8%	74.9 / 11.9	52	M62L (ATG→TTG)	ynaK	Rac prophage; ParB‑like nuclease domain‑containing protein YnaK

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	445643 =	24 (0.520)	3 (0.070)	3/248	4.8	8.0%	coding (1024/1365 nt)	yajR	putative major facilitator superfamily transport protein YajR
	?	NC_000913	2624313 =	46 (1.030)					coding (1270/2067 nt)	ppk	polyphosphate kinase
*	?	NC_000913	4498181 =	NA (NA)	7 (0.150)	3/254	4.9	NA	noncoding (1/1331 nt)	IS2	repeat region
	?	NC_000913	= 4499512	NA (NA)					intergenic (+12/+81)	insD‑6/yjgX	KpLE2 phage‑like element; IS2 insertion element protein InsB/KpLE2 phage‑like element; putative phosphoethanolamine transferase YjgX, N‑terminal fragment
*	?	NC_000913	381258 =	NA (NA)	7 (0.150)	3/252	4.9	NA	pseudogene (3/417 nt)	yaiX	putative acyltransferase, N‑terminal fragment
	?	NC_000913	= 382589	NA (NA)					noncoding (1330/1331 nt)	IS2	repeat region