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_tpiA4,295,9760CT26.7% 94.0 / 45.4 76intergenic (+266/+376)gltP/yjcOglutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein

Marginal new junction evidence (lowest skew 10 of 162 shown)
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913_3_pae_tpiA = 120780549 (0.930)14 (0.300) 14/250 3.1 21.6% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913_3_pae_tpiA = 1209602 58 (1.240)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913_3_pae_tpiA 1207790 =54 (1.030)12 (0.260) 12/250 3.6 18.5% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913_3_pae_tpiA 1209619 = 58 (1.240)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913_3_pae_tpiA 2024598 =54 (1.030)8 (0.160) 8/260 5.2 14.1% intergenic (+7/+37) rcsA/dsrB transcriptional regulator of colanic acid capsular biosynthesis/uncharacterized protein
?NC_000913_3_pae_tpiA 2024624 = 48 (0.990)intergenic (+33/+11) rcsA/dsrB transcriptional regulator of colanic acid capsular biosynthesis/uncharacterized protein
* ? NC_000913_3_pae_tpiA 3587430 =59 (1.120)7 (0.140) 7/262 5.7 11.0% coding (684/744 nt) ugpQ glycerophosphodiester phosphodiesterase, cytosolic
?NC_000913_3_pae_tpiA 3587464 = 59 (1.210)coding (650/744 nt) ugpQ glycerophosphodiester phosphodiesterase, cytosolic
* ? NC_000913_3_pae_tpiA = 272946435 (0.670)8 (0.160) 7/266 5.7 21.3% intergenic (‑20/+152) gltW/rrsG tRNA‑Glu/16S ribosomal RNA of rrnG operon
?NC_000913_3_pae_tpiA 4168265 = 26 (0.520)intergenic (+149/‑23) rrsB/gltT 16S ribosomal RNA of rrnB operon/tRNA‑Glu
* ? NC_000913_3_pae_tpiA = 230490226 (0.490)8 (0.200)
+33 bp		 4/216 6.1 28.7% noncoding (486/655 nt) REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences
?NC_000913_3_pae_tpiA = 2305065 NA (NA)noncoding (649/655 nt) REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences
* ? NC_000913_3_pae_tpiA = 230467634 (0.650)8 (0.200)
+33 bp		 4/216 6.1 23.5% noncoding (260/655 nt) REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences
?NC_000913_3_pae_tpiA = 2305065 NA (NA)noncoding (649/655 nt) REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences
* ? NC_000913_3_pae_tpiA = 452338767 (1.270)7 (0.140) 6/264 6.2 9.8% coding (624/1968 nt) yjhG putative dehydratase
?NC_000913_3_pae_tpiA = 4523394 66 (1.340)coding (617/1968 nt) yjhG putative dehydratase
* ? NC_000913_3_pae_tpiA = 342685325 (0.480)6 (0.120) 6/268 6.2 20.2% intergenic (‑70/+105) rrlD/alaU 23S ribosomal RNA of rrnD operon/tRNA‑Ala
?NC_000913_3_pae_tpiA 3943643 = NA (NA)intergenic (+133/‑61) gltU/rrlC tRNA‑Glu/23S ribosomal RNA of rrnC operon
* ? NC_000913_3_pae_tpiA 3173468 =54 (1.030)6 (0.120) 6/266 6.2 10.3% intergenic (+12/+36) ygiN/parE quinol monooxygenase/DNA topoisomerase IV, subunit B
?NC_000913_3_pae_tpiA 3173493 = 54 (1.090)intergenic (+37/+11) ygiN/parE quinol monooxygenase/DNA topoisomerase IV, subunit B