breseq  version 0.35.4  revision f352f80f4bc9 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_pae_pgi	225,465	0	A	.	50.0%	3.3 / 23.1	11	intergenic (+8/‑35)	ileV/alaV	tRNA‑Ile/tRNA‑Ala
*	NC_000913_3_pae_pgi	225,467	1	.	T	41.7%	13.0 / 21.8	12	intergenic (+10/‑33)	ileV/alaV	tRNA‑Ile/tRNA‑Ala
*	NC_000913_3_pae_pgi	4,295,320	0	C	T	35.1%	91.0 / 80.5	94	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
*	NC_000913_3_pae_pgi	526,792	0	A	C	31.8%	92.0 / 87.0	88	S1178R (AGC→CGC)	rhsD	Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
*	NC_000913_3_pae_pgi	526,796	0	C	G	31.4%	125.7 / 88.7	86	A1179G (GCG→GGG)	rhsD	Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
*	NC_000913_3_pae_pgi	526,800	0	A	G	28.9%	121.0 / 59.3	83	E1180E (GAA→GAG)	rhsD	Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor

Marginal new junction evidence (lowest skew 10 of 367 shown)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_pgi	225468 =	6 (0.100)	17 (0.290)	15/258	4.6	75.2%	intergenic (+11/‑32)	ileV/alaV	tRNA‑Ile/tRNA‑Ala
	?	NC_000913_3_pae_pgi	= 3427068	NA (NA)					intergenic (‑35/+8)	alaU/ileU	tRNA‑Ala/tRNA‑Ile
*	?	NC_000913_3_pae_pgi	225456 =	4 (0.060)	16 (0.270)	13/258	5.2	81.1%	noncoding (76/77 nt)	ileV	tRNA‑Ile
	?	NC_000913_3_pae_pgi	= 3427056	NA (NA)					intergenic (‑23/+20)	alaU/ileU	tRNA‑Ala/tRNA‑Ile
*	?	NC_000913_3_pae_pgi	1096961 =	58 (0.920)	14 (0.340) +47 bp	7/182	5.4	26.9%	intergenic (+132/+604)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
	?	NC_000913_3_pae_pgi	1097243 =	NA (NA)					intergenic (+414/+322)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
*	?	NC_000913_3_pae_pgi	1096961 =	58 (0.920)	14 (0.340) +47 bp	7/182	5.4	30.3%	intergenic (+132/+604)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
	?	NC_000913_3_pae_pgi	1097062 =	40 (0.630)					intergenic (+233/+503)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
*	?	NC_000913_3_pae_pgi	= 1672798	61 (0.970)	14 (0.240)	12/256	5.5	19.5%	intergenic (+17/+22)	ydgD/mdtI	putative peptidase/multidrug efflux system transporter
	?	NC_000913_3_pae_pgi	= 1672804	59 (1.010)					intergenic (+23/+16)	ydgD/mdtI	putative peptidase/multidrug efflux system transporter
*	?	NC_000913_3_pae_pgi	= 382205	NA (NA)	16 (0.260)	13/274	5.6	NA	coding (532/906 nt)	insD1	IS2 transposase TnpB
	?	NC_000913_3_pae_pgi	= 382224	NA (NA)					coding (551/906 nt)	insD1	IS2 transposase TnpB
*	?	NC_000913_3_pae_pgi	2729955 =	NA (NA)	18 (0.300)	11/264	6.1	NA	noncoding (1203/1542 nt)	rrsG	16S ribosomal RNA of rrnG operon
	?	NC_000913_3_pae_pgi	2729972 =	NA (NA)					noncoding (1186/1542 nt)	rrsG	16S ribosomal RNA of rrnG operon
*	?	NC_000913_3_pae_pgi	= 224973	20 (0.320)	18 (0.300)	11/264	6.1	48.5%	noncoding (1203/1542 nt)	rrsH	16S ribosomal RNA of rrnH operon
	?	NC_000913_3_pae_pgi	2729972 =	NA (NA)					noncoding (1186/1542 nt)	rrsG	16S ribosomal RNA of rrnG operon
*	?	NC_000913_3_pae_pgi	3383284 =	62 (0.980)	10 (0.170)	10/252	6.2	14.8%	intergenic (+17/+46)	degS/mdh	serine endoprotease, periplasmic/malate dehydrogenase, NAD(P)‑binding
	?	NC_000913_3_pae_pgi	3383314 =	59 (1.030)					intergenic (+47/+16)	degS/mdh	serine endoprotease, periplasmic/malate dehydrogenase, NAD(P)‑binding
*	?	NC_000913_3_pae_pgi	4346627 =	54 (0.860)	9 (0.150)	9/258	6.7	14.6%	intergenic (‑41/+37)	fumB/dcuB	anaerobic class I fumarate hydratase (fumarase B)/C4‑dicarboxylate transporter, anaerobic; DcuS co‑sensor
	?	NC_000913_3_pae_pgi	4346655 =	55 (0.930)					intergenic (‑69/+9)	fumB/dcuB	anaerobic class I fumarate hydratase (fumarase B)/C4‑dicarboxylate transporter, anaerobic; DcuS co‑sensor