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_tpiA	4,295,976	0	C	T	23.8%	404.8 / 129.5	214	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
*	NC_000913_3_pae_tpiA	3,439,588	0	G	C	23.7%	399.3 / 138.1	173	intergenic (‑79/+28)	yhdN/rplQ	DUF1992 family protein/50S ribosomal subunit protein L17
*	NC_000913_3_pae_tpiA	3,439,589	0	G	C	23.1%	396.1 / 136.0	173	intergenic (‑80/+27)	yhdN/rplQ	DUF1992 family protein/50S ribosomal subunit protein L17

Marginal new junction evidence (lowest skew 10 of 293 shown)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	3368204 =	162 (1.080)	38 (0.290)	31/224	8.2	20.4%	coding (378/1128 nt)	yhcG	DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily
	?	NC_000913_3_pae_tpiA	3368237 =	153 (1.160)					coding (411/1128 nt)	yhcG	DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily
*	?	NC_000913_3_pae_tpiA	2700550 =	152 (1.020)	30 (0.240)	28/216	8.7	19.2%	noncoding (31/77 nt)	ohsC	sRNA antisense regulator of shoB toxin
	?	NC_000913_3_pae_tpiA	2700601 =	124 (0.980)					intergenic (+5/+17)	ohsC/acpS	sRNA antisense regulator of shoB toxin/holo‑[acyl‑carrier‑protein] synthase 1
*	?	NC_000913_3_pae_tpiA	1096961 =	187 (1.250)	18 (0.190) +47 bp	15/160	10.0	13.3%	intergenic (+132/+604)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
	?	NC_000913_3_pae_tpiA	1097243 =	NA (NA)					intergenic (+414/+322)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
*	?	NC_000913_3_pae_tpiA	1096961 =	187 (1.250)	18 (0.190) +47 bp	15/160	10.0	15.5%	intergenic (+132/+604)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
	?	NC_000913_3_pae_tpiA	1097062 =	125 (0.840)					intergenic (+233/+503)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
*	?	NC_000913_3_pae_tpiA	= 59296	139 (0.930)	23 (0.180)	22/220	11.0	15.9%	intergenic (+17/+391)	yabP/rluA	pseudogene, pentapeptide repeats‑containing/dual specificity 23S rRNA pseudouridine(746), tRNA pseudouridine(32) synthase, SAM‑dependent
	?	NC_000913_3_pae_tpiA	= 59302	123 (0.950)					intergenic (+23/+385)	yabP/rluA	pseudogene, pentapeptide repeats‑containing/dual specificity 23S rRNA pseudouridine(746), tRNA pseudouridine(32) synthase, SAM‑dependent
*	?	NC_000913_3_pae_tpiA	2068389 =	162 (1.080)	26 (0.200)	19/218	12.1	18.0%	pseudogene (31/159 nt)	yoeH	pseudogene, CP4‑44 putative prophage remnant;Phage or Prophage Related
	?	NC_000913_3_pae_tpiA	2068430 =	98 (0.760)					intergenic (‑11/‑205)	yoeH/yoeA	pseudogene, CP4‑44 putative prophage remnant;Phage or Prophage Related/CP4‑44 prophage; putative disrupted hemin or colicin receptor;Phage or Prophage Related; interrupted by IS2 and C‑terminal deletion
*	?	NC_000913_3_pae_tpiA	= 4297108	143 (0.960)	27 (0.190)	21/236	12.3	16.8%	intergenic (‑67/+27)	yjcO/fdhF	Sel1 family TPR‑like repeat protein/formate dehydrogenase‑H, selenopolypeptide subunit
	?	NC_000913_3_pae_tpiA	= 4297112	135 (0.970)					intergenic (‑71/+23)	yjcO/fdhF	Sel1 family TPR‑like repeat protein/formate dehydrogenase‑H, selenopolypeptide subunit
*	?	NC_000913_3_pae_tpiA	= 3944978	NA (NA)	27 (0.190)	22/242	12.3	30.4%	noncoding (1275/2904 nt)	rrlC	23S ribosomal RNA of rrnC operon
	?	NC_000913_3_pae_tpiA	= 4038811	65 (0.430)					noncoding (1293/2905 nt)	rrlA	23S ribosomal RNA of rrnA operon
*	?	NC_000913_3_pae_tpiA	= 4168257	99 (0.660)	23 (0.170)	20/234	12.6	23.8%	intergenic (+141/‑31)	rrsB/gltT	16S ribosomal RNA of rrnB operon/tRNA‑Glu
	?	NC_000913_3_pae_tpiA	= 4168279	56 (0.410)					intergenic (+163/‑9)	rrsB/gltT	16S ribosomal RNA of rrnB operon/tRNA‑Glu
*	?	NC_000913_3_pae_tpiA	2729443 =	79 (0.530)	23 (0.170)	20/234	12.6	22.4%	noncoding (2/76 nt)	gltW	tRNA‑Glu
	?	NC_000913_3_pae_tpiA	= 4168247	87 (0.630)					intergenic (+131/‑41)	rrsB/gltT	16S ribosomal RNA of rrnB operon/tRNA‑Glu