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 81 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,097,109	0	A	T	65.6%	4.6 / 10.1	32	intergenic (+280/+456)	ycdU/serX	uncharacterized protein YcdU/tRNA‑Ser
*	NC_000913	2,177,245	0	G	T	50.0%	‑0.3 / 15.5	43	intergenic (‑41/+267)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	2,177,221	0	T	G	48.8%	19.0 / 23.3	43	intergenic (‑17/+291)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	1,879,846	0	T	G	48.5%	0.8 / 27.1	33	T35P (ACG→CCG)	yeaR	DUF1971 domain‑containing protein YeaR
*	NC_000913	1,636,442	0	C	G	47.4%	24.3 / 18.0	39	intergenic (‑75/‑314)	nohA/ynfO	Qin prophage; putative prophage DNA‑packaging protein NohA/Qin prophage; protein YnfO
*	NC_000913	2,470,411	0	A	T	46.0%	22.1 / 26.7	37	L427F (TTA→TTT)	yfdI	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase
*	NC_000913	2,177,234	0	C	A	45.2%	5.5 / 11.8	45	intergenic (‑30/+278)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	580,761	0	A	C	44.7%	41.2 / 18.9	38	intergenic (‑316/‑73)	ylcI/nohD	DLP12 prophage; DUF3950 domain‑containing protein YlcI/DLP12 prophage; putative DNA‑packaging protein NohD
*	NC_000913	2,177,255	0	G	T	44.7%	11.7 / 31.7	47	intergenic (‑51/+257)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	1,636,440	0	T	G	43.6%	35.7 / 16.1	39	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	43.4%	42.5 / 26.0	54	Q281K (CAA→AAA)	ygeV	putative sigma(54)‑dependent transcriptional regulator YgeV
*	NC_000913	3,879,427	0	C	G	43.3%	15.5 / 14.9	38	K231N (AAG→AAC)	gyrB	DNA gyrase subunit B
*	NC_000913	1,879,848	0	C	G	42.9%	46.5 / 13.8	35	G34A (GGA→GCA)	yeaR	DUF1971 domain‑containing protein YeaR
*	NC_000913	2,177,228	0	C	G	42.4%	28.6 / 19.0	47	intergenic (‑24/+284)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	707,981	0	C	G	40.7%	34.1 / 12.7	40	intergenic (+224/‑353)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	1,636,447	0	C	G	40.6%	29.5 / 11.4	38	intergenic (‑80/‑309)	nohA/ynfO	Qin prophage; putative prophage DNA‑packaging protein NohA/Qin prophage; protein YnfO
*	NC_000913	2,470,405	0	T	G	40.5%	48.5 / 11.9	37	V425V (GTT→GTG)	yfdI	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase
*	NC_000913	3,455,677	0	A	T	40.0%	40.5 / 21.1	50	N34Y (AAT→TAT)	gspC	Type II secretion system protein GspC
*	NC_000913	3,455,680	0	G	T	40.0%	37.8 / 20.4	45	V35L (GTG→TTG)	gspC	Type II secretion system protein GspC
*	NC_000913	984,064	0	T	G	39.5%	44.0 / 18.0	43	F139V (TTT→GTT)	gloC	hydroxyacylglutathione hydrolase GloC

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	2068944 =	NA (NA)	13 (0.180)	8/252	4.8	NA	noncoding (1328/1331 nt)	IS2	repeat region
	?	NC_000913	= 2070275	NA (NA)					intergenic (‑95/‑2)	insC‑3/yoeA	CP4‑44 prophage; IS2 insertion element repressor InsA/CP4‑44 prophage; TonB‑dependent receptor plug domain‑containing protein YoeA
*	?	NC_000913	= 4542690	46 (0.640)	3 (0.040)	3/240	6.9	4.7%	intergenic (+57/‑425)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	= 4542986	78 (1.170)					intergenic (+353/‑129)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
*	?	NC_000913	1082038 =	55 (0.760)	3 (0.040)	3/258	7.2	4.1%	pseudogene (683/830 nt)	efeU	inactive ferrous iron permease EfeU, N‑terminal fragment
	?	NC_000913	= 2072743	85 (1.180)					coding (1205/3120 nt)	flu	CP4‑44 prophage; self recognizing antigen 43 (Ag43) autotransporter