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	526,792	0	A	C	32.4%	97.1 / 48.4	77	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	31.1%	112.0 / 62.9	74	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	27.4%	131.4 / 41.9	74	E1180E (GAA→GAG)	rhsD	Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
*	NC_000913_3_pae_pgi	681,694	0	A	G	27.3%	23.2 / 11.7	22	intergenic (+31/+29)	djlC/hscC	J domain‑containing HscC co‑chaperone; Hsc56/Hsp70 family chaperone Hsc62; RpoD‑binding transcription inhibitor
*	NC_000913_3_pae_pgi	4,295,320	0	C	T	26.8%	72.2 / 32.6	57	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein

Marginal new junction evidence (lowest skew 10 of 34 shown)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_pgi	1207790 =	44 (0.990)	8 (0.200)	8/246	3.9	18.0%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913_3_pae_pgi	1209619 =	34 (0.860)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913_3_pae_pgi	= 1097463	18 (0.400)	9 (0.210)	8/262	4.2	35.3%	intergenic (+634/+102)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
	?	NC_000913_3_pae_pgi	= 1097467	16 (0.380)					intergenic (+638/+98)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
*	?	NC_000913_3_pae_pgi	= 1097294	12 (0.270)	8 (0.190)	8/262	4.2	36.1%	intergenic (+465/+271)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
	?	NC_000913_3_pae_pgi	= 1097455	17 (0.400)					intergenic (+626/+110)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
*	?	NC_000913_3_pae_pgi	= 1097113	39 (0.880)	8 (0.190)	8/262	4.2	22.9%	intergenic (+284/+452)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
	?	NC_000913_3_pae_pgi	= 1097455	17 (0.400)					intergenic (+626/+110)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
*	?	NC_000913_3_pae_pgi	= 1097101	30 (0.670)	9 (0.210)	8/262	4.2	28.9%	intergenic (+272/+464)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
	?	NC_000913_3_pae_pgi	= 1097467	16 (0.380)					intergenic (+638/+98)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
*	?	NC_000913_3_pae_pgi	= 1097101	30 (0.670)	9 (0.210)	8/262	4.2	33.2%	intergenic (+272/+464)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
	?	NC_000913_3_pae_pgi	= 1097286	8 (0.190)					intergenic (+457/+279)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
*	?	NC_000913_3_pae_pgi	= 1097101	30 (0.670)	9 (0.210)	8/262	4.2	22.7%	intergenic (+272/+464)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
	?	NC_000913_3_pae_pgi	= 1097105	33 (0.790)					intergenic (+276/+460)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
*	?	NC_000913_3_pae_pgi	= 4040683	50 (1.120)	13 (0.300)	7/274	4.7	21.6%	intergenic (+47/+223)	rrfA/mobB	5S ribosomal RNA of rrnA operon/molybdopterin‑guanine dinucleotide biosynthesis protein B
	?	NC_000913_3_pae_pgi	= 4213162	45 (1.030)					intergenic (+3/‑72)	rrfE/yjaA	5S ribosomal RNA of rrnE operon/stress‑induced protein
*	?	NC_000913_3_pae_pgi	= 1097282	10 (0.220)	6 (0.140)	6/262	4.9	32.1%	intergenic (+453/+283)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
	?	NC_000913_3_pae_pgi	= 1097467	16 (0.380)					intergenic (+638/+98)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
*	?	NC_000913_3_pae_pgi	= 1097282	10 (0.220)	6 (0.140)	6/262	4.9	40.8%	intergenic (+453/+283)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
	?	NC_000913_3_pae_pgi	= 1097286	8 (0.190)					intergenic (+457/+279)	ycdU/serX	putative inner membrane protein/tRNA‑Ser