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 47 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,859,705	0	G	C	54.2%	12.1 / 35.3	28	L138V (CTC→GTC)	yidK	putative transporter YidK
*	NC_000913	3,877,611	0	C	A	52.9%	3.1 / 16.3	17	intergenic (‑146/+94)	yidB/gyrB	conserved protein YidB/DNA gyrase subunit B
*	NC_000913	2,177,245	0	G	T	50.0%	5.2 / 19.1	43	intergenic (‑41/+267)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	2,177,234	0	C	A	46.4%	11.6 / 11.4	41	intergenic (‑30/+278)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	2,177,228	0	C	G	46.2%	9.6 / 18.5	40	intergenic (‑24/+284)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	4,604,344	0	C	G	44.8%	34.1 / 10.3	32	S62C (TCT→TGT)	bglJ	DNA‑binding transcriptional regulator BglJ
*	NC_000913	2,177,255	0	G	T	44.4%	14.4 / 24.9	45	intergenic (‑51/+257)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	2,177,221	0	T	G	43.6%	20.5 / 15.9	39	intergenic (‑17/+291)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	2,470,472	0	G	T	40.0%	14.3 / 10.2	25	intergenic (+10/+605)	yfdI/yfdK	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase/CPS‑53 (KpLE1) prophage; putative tail fiber assembly protein YfdK
*	NC_000913	4,220,007	0	T	G	40.0%	7.2 / 11.6	25	V471G (GTG→GGG)	aceK	isocitrate dehydrogenase kinase/phosphatase
*	NC_000913	4,050,007	0	A	T	36.7%	31.7 / 12.7	30	noncoding (109/109 nt)	spf	small regulatory RNA Spot 42
*	NC_000913	2,139,581	0	T	G	35.6%	23.9 / 10.3	45	intergenic (+96/+178)	yegH/asmA	inner membrane protein YegH/putative assembly protein AsmA
*	NC_000913	2,560,485	0	G	C	34.2%	74.0 / 10.9	43	E77Q (GAA→CAA)	yffL	CPZ‑55 prophage; uncharacterized protein YffL
*	NC_000913	931,029	0	G	C	34.0%	76.4 / 22.3	47	intergenic (‑67/+56)	cydD/trxB	glutathione/L‑cysteine ABC exporter subunit CydD/thioredoxin reductase
*	NC_000913	1,759,036	0	G	C	33.3%	46.8 / 15.0	27	V85V (GTC→GTG)	sufE	sulfur acceptor for SufS cysteine desulfurase
*	NC_000913	2,139,578	0	T	G	33.3%	39.1 / 10.9	45	intergenic (+93/+181)	yegH/asmA	inner membrane protein YegH/putative assembly protein AsmA
*	NC_000913	4,283,221	0	T	C	33.3%	38.7 / 10.6	32	intergenic (‑146/+32)	yjcF/actP	pentapeptide repeat‑containing protein YjcF/acetate/glycolate:cation symporter
*	NC_000913	1,879,846	0	T	G	32.4%	51.5 / 11.3	39	T35P (ACG→CCG)	yeaR	DUF1971 domain‑containing protein YeaR
*	NC_000913	4,296,060	0	C	T	31.5%	129.3 / 82.7	94	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
*	NC_000913	1,425,560	0	A	T	31.0%	199.4 / 35.6	118	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	1411899 =	111 (1.920)	12 (0.260)	11/204	2.3	14.4%	coding (50/936 nt)	ttcA	tRNA cytosine(32) 2‑sulfurtransferase TtcA
	?	NC_000913	= 1434958	54 (1.170)					pseudogene (51/51 nt)	ttcC	putative tRNA 2‑thiocytidine (s(2)C32) synthase
*	?	NC_000913	= 1207805	45 (0.780)	9 (0.180)	9/224	3.1	18.5%	coding (305/630 nt)	ycfK	e14 prophage; protein StfP
	?	NC_000913	= 1209602	40 (0.790)					pseudogene (54/537 nt)	stfE	e14 prophage; putative side tail fiber protein fragment
*	?	NC_000913	1207790 =	44 (0.760)	10 (0.200)	9/224	3.1	20.1%	coding (290/630 nt)	ycfK	e14 prophage; protein StfP
	?	NC_000913	1209619 =	41 (0.810)					pseudogene (37/537 nt)	stfE	e14 prophage; putative side tail fiber protein fragment
*	?	NC_000913	4542682 =	53 (0.920)	6 (0.110)	6/238	4.2	10.5%	intergenic (+49/‑433)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	4542996 =	53 (0.990)					intergenic (+363/‑119)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit