mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 264,098 | G→T | L50L (CTC→CTA) | ykfH ← | uncharacterized protein |
| RA | 1,197,502 | C→T | G11R (GGA→AGA) | ymfD ← | e14 prophage; putative SAM‑dependent methyltransferase |
| MC JC | 1,299,499 | Δ1,199 bp | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| 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 | 2,679,525 | G→T | A1074D (GCT→GAT) | yphG ← | DUF4380 domain‑containing TPR repeat protein |
| RA | 2,811,215 | Δ1 bp | coding (446/531 nt) | mprA → | transcriptional repressor of microcin B17 synthesis and multidrug efflux |
| RA | 3,413,571 | T→C | intergenic (‑106/‑293) | acrS ← / → acrE | acrAB operon transcriptional repressor/cytoplasmic membrane lipoprotein |
| 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 |
| MC JC | 3,579,269 | Δ4,159 bp | IS1‑mediated | [yhhW]–yrhA | [yhhW], yhhX, ryhB, yhhY, yhhZ, yrhA |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 285199 | 285279 | 81 | 6 [4] | [4] 6 | yagF/yagG | CP4‑6 prophage; dehydratase family protein/CP4‑6 prophage; putative sugar transporter |
| * | * | ÷ | NC_000913 | 583487 | 583574 | 88 | 6 [4] | [2] 6 | tfaX/appY | pseudogene, DLP12 prophage;Phage or Prophage Related/global transcriptional activator; DLP12 prophage |
| * | * | ÷ | NC_000913 | 584451 | 584473 | 23 | 10 [5] | [2] 7 | appY/ompT | global transcriptional activator; DLP12 prophage/DLP12 prophage; outer membrane protease VII; outer membrane protein 3b |
| * | * | ÷ | NC_000913 | 1212099 | 1212163 | 65 | 6 [5] | [3] 7 | iraM/ycgX | RpoS stabilzer during Mg starvation, anti‑RssB factor/DUF1398 family protein |
| * | * | ÷ | NC_000913 | 1530046 | 1530118 | 73 | 6 [4] | [5] 8 | ydcD | putative immunity protein for RhsE |
| * | * | ÷ | NC_000913 | 1754713 | 1754833 | 121 | 6 [5] | [4] 6 | ydhY/ydhZ | putative 4Fe‑4S ferridoxin‑type protein; FNR, Nar, NarP‑regulated protein; putative subunit of YdhYVWXUT oxidoreductase complex/uncharacterized protein |
| * | * | ÷ | NC_000913 | 2057582 | 2057693 | 112 | 6 [5] | [5] 6 | yeeN/asnW | UPF0082 family protein/tRNA‑Asn |
| * | * | ÷ | NC_000913 | 2774967 | 2775054 | 88 | 7 [5] | [5] 6 | [yfjW] | [yfjW] |
| * | * | ÷ | NC_000913 | 2995169 | 2995285 | 117 | 6 [5] | [4] 6 | ygeK/ygeN | pseudogene, response regulator family, part of T3SS PAI ETT2 remnant; putative 2‑component transcriptional regulator/pseudogene, orgB family, part of T3SS PAI ETT2 remnant |
| * | * | ÷ | NC_000913 | 3423720–3424234 | 3424589–3424238 | 5–870 | 7 [5] | [2] 7 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3455440 | 3455478 | 39 | 6 [5] | [5] 7 | gspA/gspC | general secretory pathway component, cryptic/general secretory pathway component, cryptic |
| * | * | ÷ | NC_000913 | 3799171 | 3799329 | 159 | 8 [5] | [5] 6 | [waaU] | [waaU] |
| * | * | ÷ | NC_000913 | 3804359 | 3804514 | 156 | 8 [2] | [5] 6 | waaS | lipopolysaccharide rhamnose:KdoIII transferase; lipopolysaccharide core biosynthesis protein |
| * | * | ÷ | NC_000913 | 3805042 | 3805128 | 87 | 6 [5] | [4] 6 | [waaS] | [waaS] |
| * | * | ÷ | NC_000913 | 4304528 | 4304579 | 52 | 8 [0] | [5] 6 | ytcA/yjcS | putative inner membrane efflux pump‑associated DUF1656 family protein/metallo‑beta‑lactamase superfamily protein |
| * | * | ÷ | NC_000913 | 4326975 | 4327062 | 88 | 6 [5] | [5] 6 | yjdM/crfC | zinc‑ribbon family protein/clamp‑binding sister replication fork colocalization protein, dynamin‑related |
| * | * | ÷ | NC_000913 | 4340599 | 4340676 | 78 | 6 [5] | [4] 6 | adiA/melR | arginine decarboxylase/melibiose operon transcriptional regulator; autoregulator |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 5565 = | NA (NA) | 3 (0.090) +ATTG |
3/122 | 2.8 | NA | noncoding (1/105 nt) | RIP1 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP1 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913 | = 4008432 | NA (NA) | intergenic (+55/+7) | rhtC/rhtB | threonine efflux pump/homoserine, homoserine lactone and S‑methyl‑methionine efflux pump | |||||
| * | ? | NC_000913 | = 1207805 | 43 (1.210) | 12 (0.450) | 9/98 | 0.9 | 33.1% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 16 (0.600) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 4054137 | 14 (0.390) | 4 (0.130) | 4/112 | 2.3 | 22.2% | coding (1142/1410 nt) | glnG | fused DNA‑binding response regulator in two‑component regulatory system with GlnL: response regulator/sigma54 interaction protein |
| ? | NC_000913 | = 4054157 | 16 (0.520) | coding (1122/1410 nt) | glnG | fused DNA‑binding response regulator in two‑component regulatory system with GlnL: response regulator/sigma54 interaction protein | |||||