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_000913624,5960AT29.4% 108.7 / 10.8 68intergenic (‑86/‑289)fepB/entCferrienterobactin ABC transporter periplasmic binding protein/isochorismate synthase 1
*NC_0009133,624,8450AT26.0% 72.9 / 38.3 50P156P (CCA→CCTyhhIputative transposase
*NC_000913843,2020GT25.0% 134.2 / 11.5 72A291S (GCC→TCC) rlmF23S rRNA m(6)A1618 methyltransferase, SAM‑dependent
*NC_000913915,2130AT21.9% 93.9 / 12.4 65intergenic (‑356/+139)ybjE/aqpZputative transporter/aquaporin Z
*NC_000913915,2050CG21.3% 134.0 / 10.0 61intergenic (‑348/+147)ybjE/aqpZputative transporter/aquaporin Z
*NC_000913566,2450GA20.0% 199.9 / 43.6 85pseudogene (132/279 nt)exoDpseudogene, DLP12 prophage; phage‑type exonuclease family;Phage or Prophage Related

Marginal new junction evidence (lowest skew 10 of 14 shown)
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 566098 =95 (1.080)14 (0.180)
+GAGAGGAGGATTACAAA
9/242 2.7 12.9% pseudogene (279/279 nt) exoD pseudogene, DLP12 prophage; phage‑type exonuclease family;Phage or Prophage Related
?NC_000913 4397412 = 120 (1.370)coding (1/1848 nt) mutL methyl‑directed mismatch repair protein
* ? NC_000913 = 120780552 (0.590)12 (0.150) 7/244 3.2 25.0% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 26 (0.340)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 1207790 =58 (0.660)11 (0.140) 6/244 3.5 22.2% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 26 (0.340)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 375124 =117 (1.330)9 (0.150) 4/192 3.5 11.3% noncoding (195/436 nt) REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences
?NC_000913 377530 = 60 (0.990)intergenic (+219/+5) yaiL/frmB DUF2058 family protein/S‑formylglutathione hydrolase
* ? NC_000913 374922 =NA (NA)8 (0.100) 5/260 4.0 NA intergenic (+41/‑537) mhpE/mhpT 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter
?NC_000913 377329 = NA (NA)intergenic (+18/+206) yaiL/frmB DUF2058 family protein/S‑formylglutathione hydrolase
* ? NC_000913 = 37495880 (0.910)4 (0.060) 3/202 4.1 5.1% noncoding (29/436 nt) REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences
?NC_000913 = 377392 90 (1.410)noncoding (58/187 nt) REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences
* ? NC_000913 4373296 =86 (1.050)85 (1.050) 4/256 4.4 49.9% intergenic (+134/+69) yjeI/yjeJ DUF4156 family lipoprotein/uncharacterized protein
?NC_000913 4374498 = NA (NA)noncoding (1/99 nt) RIP329 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site RIP329 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site
* ? NC_000913 4373286 =74 (1.030)53 (0.740) 3/226 4.4 41.7% noncoding (90/99 nt) RIP328 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site RIP328 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site
?NC_000913 4374508 = NA (NA)noncoding (11/99 nt) RIP329 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site RIP329 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site
* ? NC_000913 = 1050545NA (NA)107 (1.220) 4/276 4.6 69.0% noncoding (768/768 nt) IS1 repeat region
?NC_000913 = 2760086 48 (0.550)coding (1102/1410 nt) yfjI CP4‑57 prophage; uncharacterized protein
* ? NC_000913 375248 =124 (1.410)8 (0.110) 3/238 4.6 7.8% noncoding (319/436 nt) REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences
?NC_000913 377507 = 83 (1.100)noncoding (173/187 nt) REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences