mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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 |
| JC JC | 486,122 | IS1 (–) +8 bp | coding (362‑369/648 nt) | acrR → | transcriptional repressor |
| 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 | 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 |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 580713 | 580733 | 21 | 3 [2] | [2] 4 | ylcI/nohD | DUF3950 family protein, DLP12 prophage/DLP12 prophage; DNA packaging protein |
| * | * | ÷ | NC_000913 | 1119132 | 1119150 | 19 | 4 [2] | [1] 3 | yceJ/yceO | putative cytochrome b561/uncharacterized protein |
| * | * | ÷ | NC_000913 | 2951917 | 2951946 | 30 | 4 [2] | [2] 3 | recD | exonuclease V (RecBCD complex), alpha chain |
| * | * | ÷ | NC_000913 | 3423703–3424234 | 3424594–3424238 | 5–892 | 3 [2] | [2] 3 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 291401 | NA (NA) | 57 (2.540) | 29/132 | 0.0 | 89.1% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 807574 | 7 (0.310) | coding (336/477 nt) | ybhB | kinase inhibitor homolog, UPF0098 family | |||||
| * | ? | NC_000913 | 580753 = | 5 (0.220) | 3 (0.180) | 3/100 | 1.6 | 47.0% | intergenic (‑308/‑81) | ylcI/nohD | DUF3950 family protein, DLP12 prophage/DLP12 prophage; DNA packaging protein |
| ? | NC_000913 | 580810 = | 3 (0.180) | intergenic (‑365/‑24) | ylcI/nohD | DUF3950 family protein, DLP12 prophage/DLP12 prophage; DNA packaging protein | |||||
| * | ? | NC_000913 | 771005 = | 15 (0.670) | 42 (1.870) | 27/132 | 0.0 | 73.7% | intergenic (+394/‑453) | mngB/cydA | alpha‑mannosidase/cytochrome d terminal oxidase, subunit I |
| ? | NC_000913 | = 1050545 | NA (NA) | noncoding (768/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | = 857615 | 34 (1.790) | 12 (0.630) | 6/112 | 1.0 | 26.1% | intergenic (+60/+181) | ybiT/ybiU | ABC‑F family putative regulatory ATPase/DUF1479 family protein |
| ? | NC_000913 | = 857713 | NA (NA) | noncoding (98/98 nt) | RIP79 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP79 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913 | 1207790 = | 1 (0.040) | 16 (0.950) | 12/100 | 0.2 | 84.8% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 5 (0.300) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 2 (0.090) | 10 (0.590) | 7/100 | 0.7 | 75.4% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 5 (0.300) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 3255241 = | NA (NA) | 4 (0.210) | 4/112 | 1.5 | 40.0% | noncoding (25/103 nt) | REP236 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP236 (repetitive extragenic palindromic) element; contains 2 REP sequences |
| ? | NC_000913 | 3255294 = | 6 (0.320) | noncoding (78/103 nt) | REP236 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP236 (repetitive extragenic palindromic) element; contains 2 REP sequences | |||||
| * | ? | NC_000913 | = 3968672 | 10 (0.450) | 3 (0.160) | 3/112 | 1.8 | 21.9% | coding (757/1104 nt) | wecA | UDP‑GlcNAc:undecaprenylphosphate GlcNAc‑1‑phosphate transferase |
| ? | NC_000913 | = 3968690 | 13 (0.680) | coding (775/1104 nt) | wecA | UDP‑GlcNAc:undecaprenylphosphate GlcNAc‑1‑phosphate transferase | |||||