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 1890 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	417,533	0	T	G	44.7%	210.4 / 64.8	199	V131G (GTG→GGG)	phoB	response regulator in two‑component regulatory system with PhoR
*	NC_000913	2,228,275	0	T	C	44.1%	319.6 / 59.8	237	pseudogene (335/1287 nt)	mdtQ	pseudogene; putative channel/filament proteins
*	NC_000913	743,657	0	T	G	41.2%	260.6 / 25.9	215	V22G (GTG→GGG)	ybgJ	putative allophanate hydrolase, subunit 1
*	NC_000913	433,649	0	T	G	41.2%	266.5 / 82.8	323	G65G (GGT→GGG)	ribD	fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase
*	NC_000913	283,940	0	A	G	39.6%	155.5 / 14.2	111	E247G (GAG→GGG)	yagF	CP4‑6 prophage; dehydratase family protein
*	NC_000913	4,622,250	0	A	G	38.6%	501.9 / 127.4	277	E161G (GAG→GGG)	yjjJ	putative protein kinase
*	NC_000913	4,604,344	0	C	T	38.4%	616.8 / 241.1	400	S62F (TCT→TTT)	bglJ	bgl operon transcriptional activator
*	NC_000913	811,721	0	T	G	38.3%	618.8 / 33.9	327	V67G (GTG→GGG)	bioC	malonyl‑ACP O‑methyltransferase, SAM‑dependent
*	NC_000913	3,206,446	0	C	A	38.3%	594.7 / 168.5	362	intergenic (‑190/‑17)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	2,228,272	0	A	C	38.1%	433.6 / 48.1	246	pseudogene (338/1287 nt)	mdtQ	pseudogene; putative channel/filament proteins
*	NC_000913	288,382	0	A	C	37.8%	278.7 / 39.6	173	T532P (ACC→CCC)	yagH	CP4‑6 prophage; putative xylosidase/arabinosidase
*	NC_000913	4,457,105	0	A	G	37.5%	608.1 / 139.3	342	I441V (ATC→GTC)	mpl	UDP‑N‑acetylmuramate:L‑alanyl‑gamma‑D‑glutamyl‑ meso‑diaminopimelate ligase
*	NC_000913	4,101,507	0	T	G	37.5%	981.6 / 65.7	465	intergenic (+77/‑183)	sodA/kdgT	superoxide dismutase, Mn/2‑keto‑3‑deoxy‑D‑gluconate transporter
*	NC_000913	3,401,459	0	T	C	37.5%	586.5 / 109.0	315	D625G (GAT→GGT)	csrD	targeting factor for csrBC sRNA degradation
*	NC_000913	2,151,689	0	G	T	37.4%	180.8 / 80.3	212	intergenic (+43/+22)	yegJ/yegK	uncharacterized protein/ser/thr phosphatase‑related protein
*	NC_000913	3,133,302	0	T	G	37.3%	757.8 / 111.5	376	H219P (CAC→CCC)	yghS	putative ATP‑binding protein
*	NC_000913	2,326,450	0	T	G	37.1%	680.6 / 127.3	345	G114G (GGT→GGG)	atoB	acetyl‑CoA acetyltransferase
*	NC_000913	273,676	0	T	G	37.0%	987.8 / 77.1	450	pseudogene (830/1108 nt)	ykfC	CP4‑6 prophage; conserved protein;Phage or Prophage Related
*	NC_000913	2,151,686	0	G	T	37.0%	196.1 / 88.6	212	intergenic (+40/+25)	yegJ/yegK	uncharacterized protein/ser/thr phosphatase‑related protein
*	NC_000913	2,074,044	0	T	C	36.9%	239.5 / 18.7	123	S836P (TCC→CCC)	flu	CP4‑44 prophage; antigen 43 (Ag43) phase‑variable biofilm formation autotransporter

Marginal new junction evidence (lowest skew 10 of 56 shown)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	4542682 =	500 (1.210)	29 (0.070)	25/308	9.8	6.0%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	440 (1.130)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	= 382590	NA (NA)	31 (0.080)	24/326	10.7	5.9%	noncoding (1331/1331 nt)	IS2	repeat region
	?	NC_000913	564107 =	491 (1.190)					coding (374/633 nt)	sfmZ	response regulator family protein
*	?	NC_000913	381260 =	NA (NA)	27 (0.070)	18/324	12.6	5.1%	noncoding (1/1331 nt)	IS2	repeat region
	?	NC_000913	= 564111	502 (1.220)					coding (370/633 nt)	sfmZ	response regulator family protein
*	?	NC_000913	3652036 =	NA (NA)	100 (0.240)	18/326	12.7	16.3%	noncoding (1195/1195 nt)	IS5	repeat region
	?	NC_000913	= 3890078	513 (1.240)					coding (1349/1416 nt)	tnaA	tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent
*	?	NC_000913	= 2290113	NA (NA)	17 (0.040)	16/326	13.4	3.2%	noncoding (1/1195 nt)	IS5	repeat region
	?	NC_000913	3890075 =	510 (1.230)					coding (1346/1416 nt)	tnaA	tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent
*	?	NC_000913	1097039 =	225 (0.540)	39 (0.100) +C	15/324	13.8	16.0%	intergenic (+210/+526)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
	?	NC_000913	= 1097580	187 (0.450)					noncoding (73/88 nt)	serX	tRNA‑Ser
*	?	NC_000913	= 4542690	541 (1.310)	13 (0.030)	11/308	15.1	2.7%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	440 (1.130)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	1097029 =	232 (0.560)	34 (0.080) +C	12/324	15.1	14.3%	intergenic (+200/+536)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
	?	NC_000913	= 1097570	179 (0.430)					noncoding (83/88 nt)	serX	tRNA‑Ser
*	?	NC_000913	= 3815858	424 (1.030)	10 (0.030)	9/306	16.1	2.8%	pseudogene (24/48 nt)	rph	ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH
	?	NC_000913	3815941 =	290 (0.750)					pseudogene (609/669 nt)	rph	ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH
*	?	NC_000913	= 2067353	NA (NA)	14 (0.030)	8/326	17.3	2.7%	noncoding (1/1195 nt)	IS5	repeat region
	?	NC_000913	3890075 =	510 (1.230)					coding (1346/1416 nt)	tnaA	tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent