mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.27.1 revision 87c22d663cc3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| JC | 1,673,557 | Δ120 bp | intergenic (‑56/‑237) | mdtJ ← / → tqsA | multidrug efflux system transporter/pheromone AI‑2 transporter |
| RA | 2,173,363 | Δ2 bp | intergenic (‑1/+1) | gatC ← / ← gatC | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 3,560,455 | +G | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 3,815,883 | +C | pseudogene (667/669 nt) | rph ← | ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1673489 | 1676609 | 3121 | 358 [355] | [354] 360 | [mdtJ]–[pntA] | [mdtJ], tqsA, pntB, [pntA] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 257907 | 42 (0.080) | 490 (1.030) | 230/284 | 0.0 | 96.1% | intergenic (+8/‑769) | crl/crl | pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator;regulator; Surface structures; transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator;regulator; Surface structures; transcriptional regulator of cryptic csgA gene for curli surface fibers |
| ? | NC_000913 | 258684 = | 0 (0.000) | pseudogene (9/331 nt) | crl | pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator;regulator; Surface structures; transcriptional regulator of cryptic csgA gene for curli surface fibers | |||||
| * | ? | NC_000913 | 273955 = | NA (NA) | 375 (0.750) | 174/300 | 2.9 | 58.3% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 565828 | 268 (0.530) | coding (151/1164 nt) | intD | DLP12 prophage; putative phage integrase | |||||
| * | ? | NC_000913 | 1207790 = | 76 (0.150) | 336 (0.750) | 183/268 | 0.5 | 83.1% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 69 (0.150) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 75 (0.150) | 395 (0.880) | 192/268 | 0.2 | 85.3% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 69 (0.150) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 537 (1.100) | 236/292 | 0.0 | 99.8% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 2 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 1978502 | 29 (0.060) | 540 (1.140) | 233/284 | 0.0 | 97.5% | intergenic (‑305/+16) | flhD/insB1 | flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B |
| ? | NC_000913 | 1979279 = | 0 (0.000) | intergenic (‑64/‑474) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | = 2558698 | 254 (0.510) | 259 (0.550) | 171/284 | 2.2 | 53.3% | intergenic (‑19/‑160) | eutB/intZ | ethanolamine ammonia‑lyase, large subunit, heavy chain/CPZ‑55 prophage; putative phage integrase |
| ? | NC_000913 | 2565489 = | 213 (0.450) | coding (1396/1404 nt) | eutA | reactivating factor for ethanolamine ammonia lyase | |||||
| * | ? | NC_000913 | = 3393157 | 287 (0.570) | 312 (0.620) | 180/300 | 2.3 | 52.1% | coding (3102/3801 nt) | yhdP | DUF3971‑AsmA2 domains protein |
| ? | NC_000913 | 3583428 = | NA (NA) | noncoding (1/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | 3583428 = | NA (NA) | 309 (0.620) | 176/298 | 2.6 | 46.7% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 4542049 | 353 (0.710) | coding (13/597 nt) | fimE | tyrosine recombinase/inversion of on/off regulator of fimA | |||||
| * | ? | NC_000913 | 4542682 = | 272 (0.540) | 318 (0.670) | 185/282 | 1.0 | 55.7% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4542996 = | 250 (0.530) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | = 4542690 | 272 (0.540) | 296 (0.630) | 179/282 | 1.4 | 53.9% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4542986 | 250 (0.530) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||