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 |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 275,065 | G→A | T18I (ACC→ATC) | insH1 ← | IS5 transposase and trans‑activator |
| RA | 1,197,502 | C→T | G11R (GGA→AGA) | ymfD ← | e14 prophage; putative SAM‑dependent methyltransferase |
| RA | 1,544,022 | C→A | L13F (TTG→TTT) | narU ← | nitrate/nitrite transporter |
| RA | 1,774,576 | G→A | G263E (GGG→GAG) | ydiB → | quinate/shikimate 5‑dehydrogenase, NAD(P)‑binding |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 2,106,741 | A→T | S162S (TCT→TCA) | wbbH ← | O‑antigen polymerase |
| 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 | 2,795,396 | C→A | Q382K (CAG→AAG) | gabP → | gamma‑aminobutyrate transporter |
| 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 | 4,111,662 | G→A | L179L (CTG→TTG) | yiiQ ← | DUF1454 family putative periplasmic protein |
| RA | 4,296,363 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,604,698 | C→A | A186E (GCA→GAA) | bglJ → | bgl operon transcriptional activator |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913_3_hsa_tpiA | 3423743–3424234 | 3424553–3424239 | 6–811 | 21 [20] | [18] 21 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_hsa_tpiA | 1207790 = | 30 (0.570) | 17 (0.360) | 17/264 | 2.8 | 38.3% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_hsa_tpiA | 1209619 = | 28 (0.590) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_hsa_tpiA | = 1207805 | 30 (0.570) | 19 (0.400) | 17/264 | 2.8 | 41.0% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_hsa_tpiA | = 1209602 | 28 (0.590) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_hsa_tpiA | = 1299498 | 0 (0.000) | 34 (0.660) | 29/288 | 1.2 | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913_3_hsa_tpiA | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913_3_hsa_tpiA | 4218462 = | NA (NA) | 68 (1.460) | 42/260 | 0.2 | NA | noncoding (45/132 nt) | REP311 (repetitive extragenic palindromic) element; contains 3 REP sequences | REP311 (repetitive extragenic palindromic) element; contains 3 REP sequences |
| ? | NC_000913_3_hsa_tpiA | = 4235439 | NA (NA) | noncoding (37/77 nt) | REP313 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP313 (repetitive extragenic palindromic) element; contains 2 REP sequences | |||||