mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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 | 3,859,354 | 0 | T | C | 51.0% | 41.2 / inf | 344 | N255D (AAC→GAC) | yidK | putative transporter |
| * | NC_000913 | 2,462,880 | 1 | . | C | 41.3% | 24.2 / 99.1 | 46 | intergenic (+234/‑132) | fadL/yfdF | long‑chain fatty acid outer membrane transporter/uncharacterized protein |
| * | NC_000913 | 1,164,564 | 0 | G | T | 33.3% | 137.7 / 10.5 | 83 | G157V (GGA→GTA) | nagZ | beta N‑acetyl‑glucosaminidase |
| * | NC_000913 | 2,462,880 | 2 | . | C | 32.6% | 69.4 / 76.1 | 46 | intergenic (+234/‑132) | fadL/yfdF | long‑chain fatty acid outer membrane transporter/uncharacterized protein |
| * | NC_000913 | 3,908,514 | 0 | A | T | 29.2% | 216.6 / 32.0 | 131 | intergenic (‑148/+35) | pstB/pstA | phosphate ABC transporter ATPase/phosphate ABC transporter permease |
| * | NC_000913 | 4,412,779 | 0 | T | G | 27.4% | 87.0 / 13.4 | 62 | V131V (GTT→GTG) | yjfM | DUF1190 family protein |
| * | NC_000913 | 1,164,525 | 0 | C | A | 25.4% | 144.9 / 12.5 | 71 | A144E (GCA→GAA) | nagZ | beta N‑acetyl‑glucosaminidase |
| * | NC_000913 | 915,190 | 0 | C | G | 24.1% | 117.3 / 23.6 | 54 | intergenic (‑333/+162) | ybjE/aqpZ | putative transporter/aquaporin Z |
| * | NC_000913 | 4,296,060 | 0 | C | T | 23.6% | 248.6 / 76.1 | 125 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913 | 2,470,472 | 0 | G | T | 21.4% | 233.0 / 17.7 | 84 | intergenic (+10/‑343) | gtrS/tfaS | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage/pseudogene, CPS‑53 (KpLE1) prophage; tail fiber assembly protein fragment;Phage or Prophage Related |
| * | NC_000913 | 566,277 | 0 | C | T | 20.4% | 204.6 / 47.0 | 88 | pseudogene (100/279 nt) | exoD | pseudogene, DLP12 prophage; phage‑type exonuclease family;Phage or Prophage Related |
| * | NC_000913 | 3,624,845 | 0 | A | T | 20.4% | 78.1 / 23.5 | 44 | P156P (CCA→CCT) | yhhI | putative transposase |
| * | NC_000913 | 767,956 | 0 | C | A | 20.3% | 452.8 / 17.0 | 241 | P658Q (CCA→CAA) | mngA | fused 2‑O‑a‑mannosyl‑D‑glycerate specific PTS enzymes: IIA component/IIB component/IIC component |
| * | NC_000913 | 566,245 | 0 | G | A | 20.2% | 187.9 / 39.8 | 79 | pseudogene (132/279 nt) | exoD | pseudogene, DLP12 prophage; phage‑type exonuclease family;Phage or Prophage Related |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 4373296 = | 115 (1.220) | 97 (1.040) | 9/256 | 4.0 | 46.0% | 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 | 566098 = | 100 (0.990) | 25 (0.280) +GAGAGGAGGATTACAAA |
7/242 | 4.5 | 22.0% | pseudogene (279/279 nt) | exoD | pseudogene, DLP12 prophage; phage‑type exonuclease family;Phage or Prophage Related |
| ? | NC_000913 | 4397412 = | 102 (1.010) | coding (1/1848 nt) | mutL | methyl‑directed mismatch repair protein | |||||
| * | ? | NC_000913 | 375124 = | 118 (1.170) | 11 (0.160) | 3/192 | 5.3 | 10.8% | 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 = | 99 (1.420) | intergenic (+219/+5) | yaiL/frmB | DUF2058 family protein/S‑formylglutathione hydrolase | |||||
| * | ? | NC_000913 | 4373286 = | 98 (1.190) | 53 (0.640) | 4/226 | 5.5 | 35.1% | 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 | 374922 = | NA (NA) | 14 (0.150) | 5/260 | 5.6 | 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 | = 2070275 | NA (NA) | 5 (0.050) | 4/270 | 6.2 | NA | intergenic (‑95/‑2) | insC1/yoeA | IS2 repressor TnpA/CP4‑44 prophage; putative disrupted hemin or colicin receptor;Phage or Prophage Related; interrupted by IS2 and C‑terminal deletion |
| ? | NC_000913 | 2996364 = | NA (NA) | noncoding (1328/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 374963 | 90 (0.890) | 11 (0.110) | 4/268 | 6.2 | 8.4% | noncoding (34/436 nt) | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences |
| ? | NC_000913 | = 377387 | 152 (1.560) | noncoding (53/187 nt) | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences | |||||
| * | ? | NC_000913 | 525435 = | 195 (1.940) | 3 (0.030) | 3/270 | 6.8 | 2.0% | coding (2175/4281 nt) | rhsD | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| ? | NC_000913 | 1527949 = | 106 (1.080) | pseudogene (48/2037 nt) | rhsE | pseudogene, Rhs family | |||||
| * | ? | NC_000913 | 339756 = | NA (NA) | 6 (0.060) | 3/274 | 6.8 | NA | intergenic (+13/‑409) | yahG/yahI | DUF1116 family protein/carbamate kinase‑like protein |
| ? | NC_000913 | 377322 = | NA (NA) | intergenic (+11/+213) | yaiL/frmB | DUF2058 family protein/S‑formylglutathione hydrolase | |||||
| * | ? | NC_000913 | 2934059 = | 55 (0.550) | 6 (0.060) | 3/276 | 6.9 | 9.8% | intergenic (‑371/‑176) | fucA/fucP | L‑fuculose‑1‑phosphate aldolase/L‑fucose transporter |
| ? | NC_000913 | 3130146 = | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||