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 43 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	707,981	0	C	G	75.0%	7.9 / 10.8	31	intergenic (+224/‑353)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	707,989	0	C	G	64.7%	‑2.7 / 19.1	29	intergenic (+232/‑345)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	454,919	0	G	T	61.9%	5.5 / 18.5	22	intergenic (+130/‑214)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	708,004	0	C	A	57.7%	7.3 / 21.8	28	intergenic (+247/‑330)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	707,976	0	T	G	54.8%	‑4.6 / 16.5	31	intergenic (+219/‑358)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	2,177,221	0	T	G	54.5%	3.8 / 33.4	33	intergenic (‑17/+291)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	707,984	0	C	G	53.3%	‑2.4 / 21.4	31	intergenic (+227/‑350)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	2,177,228	0	C	T	47.4%	‑3.2 / 18.3	32	intergenic (‑24/+284)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	1,879,846	0	T	G	46.9%	12.8 / 12.6	32	T35P (ACG→CCG)	yeaR	DUF1971 domain‑containing protein YeaR
*	NC_000913	1,636,442	0	C	G	44.4%	28.8 / 13.2	27	intergenic (‑75/‑314)	nohA/ynfO	Qin prophage; putative prophage DNA‑packaging protein NohA/Qin prophage; protein YnfO
*	NC_000913	2,177,255	0	G	T	43.6%	7.2 / 23.2	39	intergenic (‑51/+257)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	2,570,480	0	G	C	42.4%	25.6 / 17.2	33	A424A (GCC→GCG)	eutE	putative aldehyde dehydrogenase, ethanolamine utilization protein
*	NC_000913	3,004,946	0	G	T	41.9%	27.8 / 19.3	43	Q281K (CAA→AAA)	ygeV	putative sigma(54)‑dependent transcriptional regulator YgeV
*	NC_000913	1,991,744	0	G	C	41.0%	57.4 / 14.7	39	intergenic (‑125/+71)	yecA/leuZ	UPF0149 family protein YecA/tRNA‑Leu
*	NC_000913	1,636,440	0	T	G	40.7%	26.7 / 10.5	27	intergenic (‑73/‑316)	nohA/ynfO	Qin prophage; putative prophage DNA‑packaging protein NohA/Qin prophage; protein YnfO
*	NC_000913	2,185,429	0	T	G	35.1%	40.7 / 11.0	37	intergenic (‑128/+95)	thiM/rcnR	hydroxyethylthiazole kinase/DNA‑binding transcriptional repressor RcnR
*	NC_000913	2,185,436	0	C	G	35.1%	64.3 / 12.6	37	intergenic (‑135/+88)	thiM/rcnR	hydroxyethylthiazole kinase/DNA‑binding transcriptional repressor RcnR
*	NC_000913	238,535	0	G	T	34.3%	69.5 / 12.4	71	H68N (CAT→AAT)	ykfM	uncharacterized protein YkfM
*	NC_000913	3,672,125	0	T	A	34.0%	81.0 / 23.1	53	intergenic (‑231/‑289)	yhjB/yhjC	putative DNA‑binding transcriptional regulator YhjB/putative DNA‑binding transcriptional regulator YhjC
*	NC_000913	411,586	0	C	A	33.3%	86.8 / 27.8	63	C299F (TGT→TTT)	araJ	putative transport protein AraJ

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 =	58 (1.010)	9 (0.180)	9/224	3.1	17.5%	coding (290/630 nt)	ycfK	e14 prophage; protein StfP
	?	NC_000913	1209619 =	34 (0.680)					pseudogene (37/537 nt)	stfE	e14 prophage; putative side tail fiber protein fragment
*	?	NC_000913	= 1207805	51 (0.890)	7 (0.140)	6/224	4.1	15.4%	coding (305/630 nt)	ycfK	e14 prophage; protein StfP
	?	NC_000913	= 1209602	32 (0.640)					pseudogene (54/537 nt)	stfE	e14 prophage; putative side tail fiber protein fragment
*	?	NC_000913	2093392 =	56 (0.980)	4 (0.070)	4/248	5.4	7.2%	coding (995/1071 nt)	hisC	histidinol‑phosphate aminotransferase
	?	NC_000913	= 3598263	49 (0.880)					coding (280/384 nt)	panZ	PanD maturation factor