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_tpiA4,295,9760CT25.0% 138.8 / 43.1 89intergenic (+266/+376)gltP/yjcOglutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
*NC_000913_3_pae_tpiA1,544,0221.A20.0% 115.4 / 36.9 45coding (39/1389 nt)narUnitrate/nitrite transporter

Marginal new junction evidence (lowest skew 10 of 216 shown)
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913_3_pae_tpiA = 120780539 (0.740)13 (0.280) 13/252 3.4 25.6% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913_3_pae_tpiA = 1209602 41 (0.870)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913_3_pae_tpiA = 349969NA (NA)6 (0.190)
+59 bp
4/166 4.8 NA noncoding (365/365 nt) REP25 (repetitive extragenic palindromic) element; contains 8 REP sequences REP25 (repetitive extragenic palindromic) element; contains 8 REP sequences
?NC_000913_3_pae_tpiA = 349972 NA (NA)intergenic (+400/‑40) prpB/prpC 2‑methylisocitrate lyase/2‑methylcitrate synthase
* ? NC_000913_3_pae_tpiA = 34987659 (1.110)6 (0.190)
+59 bp
4/166 4.8 14.8% noncoding (272/365 nt) REP25 (repetitive extragenic palindromic) element; contains 8 REP sequences REP25 (repetitive extragenic palindromic) element; contains 8 REP sequences
?NC_000913_3_pae_tpiA = 349972 NA (NA)intergenic (+400/‑40) prpB/prpC 2‑methylisocitrate lyase/2‑methylcitrate synthase
* ? NC_000913_3_pae_tpiA = 34978354 (1.020)6 (0.190)
+59 bp
4/166 4.8 16.0% noncoding (179/365 nt) REP25 (repetitive extragenic palindromic) element; contains 8 REP sequences REP25 (repetitive extragenic palindromic) element; contains 8 REP sequences
?NC_000913_3_pae_tpiA = 349972 NA (NA)intergenic (+400/‑40) prpB/prpC 2‑methylisocitrate lyase/2‑methylcitrate synthase
* ? NC_000913_3_pae_tpiA 632111 =NA (NA)4 (0.120)
+52 bp
4/180 5.2 NA intergenic (+112/‑71) cstA/ybdD carbon starvation protein involved in peptide utilization; APC peptide transporter family protein/DUF466 family protein
?NC_000913_3_pae_tpiA 3676139 = NA (NA)noncoding (19/161 nt) RIP264 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site RIP264 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site
* ? NC_000913_3_pae_tpiA = 303783449 (0.920)8 (0.160) 8/268 5.4 14.3% coding (273/1734 nt) recJ ssDNA exonuclease, 5' ‑‑> 3'‑specific
?NC_000913_3_pae_tpiA = 3037842 50 (1.000)coding (265/1734 nt) recJ ssDNA exonuclease, 5' ‑‑> 3'‑specific
* ? NC_000913_3_pae_tpiA 3676121 =NA (NA)7 (0.140) 7/270 5.9 NA noncoding (1/161 nt) RIP264 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site RIP264 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site
?NC_000913_3_pae_tpiA 3676146 = NA (NA)noncoding (26/161 nt) RIP264 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site RIP264 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site
* ? NC_000913_3_pae_tpiA 3297032 =NA (NA)7 (0.140) 7/270 5.9 NA noncoding (34/84 nt) REP240 (repetitive extragenic palindromic) element; contains 2 REP sequences REP240 (repetitive extragenic palindromic) element; contains 2 REP sequences
?NC_000913_3_pae_tpiA 4295751 = NA (NA)noncoding (1/600 nt) RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites
* ? NC_000913_3_pae_tpiA 3297025 =NA (NA)7 (0.140) 7/270 5.9 11.1% noncoding (27/84 nt) REP240 (repetitive extragenic palindromic) element; contains 2 REP sequences REP240 (repetitive extragenic palindromic) element; contains 2 REP sequences
?NC_000913_3_pae_tpiA 4296321 = 56 (1.110)noncoding (571/600 nt) RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites
* ? NC_000913_3_pae_tpiA 3296999 =NA (NA)7 (0.140) 7/270 5.9 NA noncoding (1/84 nt) REP240 (repetitive extragenic palindromic) element; contains 2 REP sequences REP240 (repetitive extragenic palindromic) element; contains 2 REP sequences
?NC_000913_3_pae_tpiA 3297032 = NA (NA)noncoding (34/84 nt) REP240 (repetitive extragenic palindromic) element; contains 2 REP sequences REP240 (repetitive extragenic palindromic) element; contains 2 REP sequences