{
  "input": "/mnt/c/dev/phage/web/data/local/uploads/2a102036-dc1d-4447-b90e-88e3d3d8c78f/demo_phage.fasta",
  "header": "DemoPhage synthetic mini sequence for Phase 0 harness testing",
  "target": "phage",
  "sequence": {
    "length_bp": 228,
    "gc_percent": 56.58,
    "ambiguous_bases": {}
  },
  "warnings": [
    "Sequence is 228 bp, which is much shorter than a typical complete phage genome.",
    "Baseline ORFs are not final gene calls.",
    "Compare against Glimmer/GeneMark/PHEONA and instructor review before accepting annotations."
  ],
  "baseline_orfs": {
    "count": 2,
    "items": [
      {
        "id": "+1.1",
        "end": 114,
        "frame": 1,
        "start": 10,
        "strand": "+",
        "length_aa": 34,
        "length_nt": 105,
        "stop_codon": "TAA",
        "start_codon": "ATG"
      },
      {
        "id": "+1.2",
        "end": 228,
        "frame": 1,
        "start": 124,
        "strand": "+",
        "length_aa": 34,
        "length_nt": 105,
        "stop_codon": "TAG",
        "start_codon": "ATG"
      }
    ],
    "method": "six-frame start/stop ORF scan",
    "minimum_amino_acids": 30
  },
  "tool_availability": {
    "blastn": {
      "path": "",
      "command": "blastn",
      "installed": false
    },
    "blastp": {
      "path": "",
      "command": "blastp",
      "installed": false
    },
    "aragorn": {
      "path": "",
      "command": "aragorn",
      "installed": false
    },
    "hmmscan": {
      "path": "",
      "command": "hmmscan",
      "installed": false
    },
    "genemark": {
      "path": "",
      "command": "gmhmmp",
      "installed": false
    },
    "glimmer3": {
      "path": "",
      "command": "glimmer3",
      "installed": false
    },
    "makeblastdb": {
      "path": "",
      "command": "makeblastdb",
      "installed": false
    },
    "trnascan_se": {
      "path": "",
      "command": "tRNAscan-SE",
      "installed": false
    }
  }
}