{
 "about": {
  "generatedBy": "pipeline/plasmid-map/reference.py",
  "scriptSha256": "be3394834b93e14844cfc7ebaa7addf596adc464f3cf22d5836f1f6caf75779b",
  "recordedOn": "2026-10-06",
  "oracle": "Biopython 1.88",
  "oracleLicence": "Biopython Licence Agreement or BSD-3-Clause",
  "text": "The app's sample GenBank exports read by Biopython's GenBank parser: the accession line, every /provenance value, the identifier qualifiers on each feature, whether every /note is ASCII without straight double quotes, and for each CDS Biopython's translation with cds=True in the CDS's table against the exported /translation (the CSO's test: equal where one is written, refused where none is).",
  "biopython": "1.88",
  "rebaseRelease": "404",
  "python": "3.11.15"
 },
 "cases": [
  {
   "id": "pbr322-edits",
   "fileSha256": "6aa4d34cc35eeb24101d2d915c2c7a2e27ba3a56efd4a624f825dbf175291565",
   "accession": [
    "."
   ],
   "id_read": ".",
   "comment": "Sequence from a pasted or opened file.\nWritten by Sample App 0.1.0 on 2026-10-06; not an NCBI record.\n/provenance marks features the user added or edited, or the app's\nfeature library found; each /note says which. Unmarked features are\nas received. /provenance is not an INSDC qualifier: remove it\nbefore submitting this file to a database.",
   "features": [
    {
     "key": "misc_binding",
     "location": "[23:27](+)",
     "provenance": null,
     "identifiers": [],
     "notesAscii": true
    },
    {
     "key": "regulatory",
     "location": "[26:33](-)",
     "provenance": null,
     "identifiers": [],
     "notesAscii": true
    },
    {
     "key": "misc_binding",
     "location": "[38:42](+)",
     "provenance": null,
     "identifiers": [],
     "notesAscii": true
    },
    {
     "key": "regulatory",
     "location": "[42:49](+)",
     "provenance": null,
     "identifiers": [],
     "notesAscii": true
    },
    {
     "key": "misc_binding",
     "location": "[52:56](+)",
     "provenance": null,
     "identifiers": [],
     "notesAscii": true
    },
    {
     "key": "misc_binding",
     "location": "[66:70](+)",
     "provenance": null,
     "identifiers": [],
     "notesAscii": true
    },
    {
     "key": "misc_binding",
     "location": "[79:83](+)",
     "provenance": null,
     "identifiers": [],
     "notesAscii": true
    },
    {
     "key": "CDS",
     "location": "[85:1279](+)",
     "provenance": "edited",
     "identifiers": [],
     "notesAscii": true,
     "table": 11,
     "exported": null,
     "biopython": null,
     "refused": "Final codon 'ATG' is not a stop codon",
     "agrees": true
    },
    {
     "key": "CDS",
     "location": "[85:1276](+)",
     "provenance": "library",
     "identifiers": [
      "inference"
     ],
     "notesAscii": true,
     "table": 11,
     "exported": "MKSNNALIVILGTVTLDAVGIGLVMPVLPGLLRDIVHSDSIASHYGVLLALYALMQFLCAPVLGALSDRFGRRPVLLASLLGATIDYAIMATTPVLWILYAGRIVAGITGATGAVAGAYIADITDGEDRARHFGLMSACFGVGMVAGPVAGGLLGAISLHAPFLAAAVLNGLNLLLGCFLMQESHKGERRPMPLRAFNPVSSFRWARGMTIVAALMTVFFIMQLVGQVPAALWVIFGEDRFRWSATMIGLSLAVFGILHALAQAFVTGPATKRFGEKQAIIAGMAADALGYVLLAFATRGWMAFPIMILLASGGIGMPALQAMLSRQVDDDHQGQLQGSLAALTSLTSITGPLIVTAIYAASASTWNGLAWIVGAALYLVCLPALRRGAWSRATST",
     "biopython": "MKSNNALIVILGTVTLDAVGIGLVMPVLPGLLRDIVHSDSIASHYGVLLALYALMQFLCAPVLGALSDRFGRRPVLLASLLGATIDYAIMATTPVLWILYAGRIVAGITGATGAVAGAYIADITDGEDRARHFGLMSACFGVGMVAGPVAGGLLGAISLHAPFLAAAVLNGLNLLLGCFLMQESHKGERRPMPLRAFNPVSSFRWARGMTIVAALMTVFFIMQLVGQVPAALWVIFGEDRFRWSATMIGLSLAVFGILHALAQAFVTGPATKRFGEKQAIIAGMAADALGYVLLAFATRGWMAFPIMILLASGGIGMPALQAMLSRQVDDDHQGQLQGSLAALTSLTSITGPLIVTAIYAASASTWNGLAWIVGAALYLVCLPALRRGAWSRATST",
     "refused": null,
     "agrees": true
    },
    {
     "key": "misc_feature",
     "location": "[140:142](-)",
     "provenance": null,
     "identifiers": [],
     "notesAscii": true
    },
    {
     "key": "misc_feature",
     "location": "[145:147](+)",
     "provenance": null,
     "identifiers": [],
     "notesAscii": true
    },
    {
     "key": "misc_binding",
     "location": "[410:414](+)",
     "provenance": null,
     "identifiers": [],
     "notesAscii": true
    },
    {
     "key": "misc_difference",
     "location": "[425:426](+)",
     "provenance": null,
     "identifiers": [
      "citation"
     ],
     "notesAscii": true
    },
    {
     "key": "misc_binding",
     "location": "[468:472](+)",
     "provenance": null,
     "identifiers": [],
     "notesAscii": true
    },
    {
     "key": "old_sequence",
     "location": "[525:528](+)",
     "provenance": null,
     "identifiers": [
      "citation"
     ],
     "notesAscii": true
    },
    {
     "key": "repeat_region",
     "location": "[1514:1519](-)",
     "provenance": null,
     "identifiers": [],
     "notesAscii": true
    },
    {
     "key": "misc_feature",
     "location": "[1635:1762](+)",
     "provenance": null,
     "identifiers": [],
     "notesAscii": true
    },
    {
     "key": "repeat_region",
     "location": "[1787:1792](-)",
     "provenance": null,
     "identifiers": [],
     "notesAscii": true
    },
    {
     "key": "misc_difference",
     "location": "[1890:1892](+)",
     "provenance": null,
     "identifiers": [
      "citation"
     ],
     "notesAscii": true
    },
    {
     "key": "old_sequence",
     "location": "[1891:1893](+)",
     "provenance": null,
     "identifiers": [
      "citation"
     ],
     "notesAscii": true
    },
    {
     "key": "regulatory",
     "location": "[1904:1910](+)",
     "provenance": null,
     "identifiers": [],
     "notesAscii": true
    },
    {
     "key": "regulatory",
     "location": "[1904:1909](+)",
     "provenance": null,
     "identifiers": [],
     "notesAscii": true
    },
    {
     "key": "misc_difference",
     "location": "[1912:1914](+)",
     "provenance": null,
     "identifiers": [
      "citation"
     ],
     "notesAscii": true
    },
    {
     "key": "old_sequence",
     "location": "[1913:1915](+)",
     "provenance": null,
     "identifiers": [
      "citation"
     ],
     "notesAscii": true
    },
    {
     "key": "CDS",
     "location": "[1914:2106](+)",
     "provenance": "edited",
     "identifiers": [],
     "notesAscii": true,
     "table": 11,
     "exported": "MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHADELYRSCLARFGDDGENL",
     "biopython": "MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHADELYRSCLARFGDDGENL",
     "refused": null,
     "agrees": true
    },
    {
     "key": "CDS",
     "location": "[1914:2106](+)",
     "provenance": null,
     "identifiers": [
      "protein_id"
     ],
     "notesAscii": true,
     "table": 11,
     "exported": "MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHADELYRSCLARFGDDGENL",
     "biopython": "MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHADELYRSCLARFGDDGENL",
     "refused": null,
     "agrees": true
    },
    {
     "key": "CDS",
     "location": "[1917:2106](+)",
     "provenance": "added",
     "identifiers": [],
     "notesAscii": true,
     "table": 1,
     "exported": null,
     "biopython": null,
     "refused": "First codon 'ACC' is not a start codon",
     "agrees": true
    },
    {
     "key": "misc_feature",
     "location": "[2010:2167](+)",
     "provenance": null,
     "identifiers": [
      "citation"
     ],
     "notesAscii": true
    },
    {
     "key": "repeat_region",
     "location": "[2244:2249](-)",
     "provenance": null,
     "identifiers": [],
     "notesAscii": true
    },
    {
     "key": "misc_feature",
     "location": "[2350:2414](-)",
     "provenance": null,
     "identifiers": [
      "citation"
     ],
     "notesAscii": true
    },
    {
     "key": "misc_binding",
     "location": "[2438:2447](+)",
     "provenance": null,
     "identifiers": [],
     "notesAscii": true
    },
    {
     "key": "rep_origin",
     "location": "[2534:2535](+)",
     "provenance": null,
     "identifiers": [],
     "notesAscii": true
    },
    {
     "key": "old_sequence",
     "location": "[2728:2730](+)",
     "provenance": null,
     "identifiers": [
      "citation"
     ],
     "notesAscii": true
    },
    {
     "key": "old_sequence",
     "location": "[2728:2729](+)",
     "provenance": null,
     "identifiers": [
      "citation"
     ],
     "notesAscii": true
    },
    {
     "key": "old_sequence",
     "location": "[2729:2730](+)",
     "provenance": null,
     "identifiers": [
      "citation"
     ],
     "notesAscii": true
    },
    {
     "key": "rep_origin",
     "location": "[2975:3082](+)",
     "provenance": "library",
     "identifiers": [
      "inference"
     ],
     "notesAscii": true
    },
    {
     "key": "mobile_element",
     "location": "[3147:4361](+)",
     "provenance": null,
     "identifiers": [],
     "notesAscii": true
    },
    {
     "key": "repeat_region",
     "location": "[3147:3185](+)",
     "provenance": null,
     "identifiers": [],
     "notesAscii": true
    },
    {
     "key": "CDS",
     "location": "[3292:4153](-)",
     "provenance": "library",
     "identifiers": [
      "inference"
     ],
     "notesAscii": true,
     "table": 11,
     "exported": "MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW",
     "biopython": "MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW",
     "refused": null,
     "agrees": true
    },
    {
     "key": "CDS",
     "location": "[3292:4153](-)",
     "provenance": null,
     "identifiers": [
      "protein_id"
     ],
     "notesAscii": true,
     "table": 11,
     "exported": "MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW",
     "biopython": "MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW",
     "refused": null,
     "agrees": true
    },
    {
     "key": "mat_peptide",
     "location": "[3295:4084](-)",
     "provenance": null,
     "identifiers": [],
     "notesAscii": true
    },
    {
     "key": "sig_peptide",
     "location": "[4084:4153](-)",
     "provenance": null,
     "identifiers": [],
     "notesAscii": true
    },
    {
     "key": "regulatory",
     "location": "[4160:4165](-)",
     "provenance": null,
     "identifiers": [],
     "notesAscii": true
    },
    {
     "key": "regulatory",
     "location": "[4187:4194](-)",
     "provenance": null,
     "identifiers": [],
     "notesAscii": true
    },
    {
     "key": "misc_binding",
     "location": "[4267:4271](-)",
     "provenance": null,
     "identifiers": [],
     "notesAscii": true
    },
    {
     "key": "misc_binding",
     "location": "[4279:4283](-)",
     "provenance": null,
     "identifiers": [],
     "notesAscii": true
    },
    {
     "key": "misc_binding",
     "location": "[4284:4288](-)",
     "provenance": null,
     "identifiers": [],
     "notesAscii": true
    },
    {
     "key": "misc_binding",
     "location": "[4295:4299](-)",
     "provenance": null,
     "identifiers": [],
     "notesAscii": true
    },
    {
     "key": "misc_binding",
     "location": "[4310:4314](-)",
     "provenance": null,
     "identifiers": [],
     "notesAscii": true
    },
    {
     "key": "misc_binding",
     "location": "[4316:4320](-)",
     "provenance": null,
     "identifiers": [],
     "notesAscii": true
    },
    {
     "key": "misc_binding",
     "location": "[4330:4334](-)",
     "provenance": null,
     "identifiers": [],
     "notesAscii": true
    }
   ]
  },
  {
   "id": "puc19-edits",
   "fileSha256": "385e396e1ff5b8fd90dccdab5919268f6c133505edbe54191976bf2a7add363d",
   "accession": [
    "."
   ],
   "id_read": ".",
   "comment": "Sequence from GenBank L09137.2.\nWritten by Sample App 0.1.0 on 2026-10-06; not an NCBI record.\n/provenance marks features the user added or edited, or the app's\nfeature library found; each /note says which. Unmarked features are\nas received. /provenance is not an INSDC qualifier: remove it\nbefore submitting this file to a database.",
   "features": [
    {
     "key": "misc_feature",
     "location": "[395:454](+)",
     "provenance": "added",
     "identifiers": [],
     "notesAscii": true
    },
    {
     "key": "misc_feature",
     "location": "[395:452](-)",
     "provenance": "library",
     "identifiers": [
      "inference"
     ],
     "notesAscii": true
    },
    {
     "key": "promoter",
     "location": "[469:591](-)",
     "provenance": "library",
     "identifiers": [
      "inference"
     ],
     "notesAscii": true
    },
    {
     "key": "protein_bind",
     "location": "[486:507](-)",
     "provenance": "library",
     "identifiers": [
      "inference"
     ],
     "notesAscii": true
    },
    {
     "key": "protein_bind",
     "location": "[553:591](-)",
     "provenance": "library",
     "identifiers": [
      "inference"
     ],
     "notesAscii": true
    },
    {
     "key": "rep_origin",
     "location": "[1308:1415](+)",
     "provenance": "library",
     "identifiers": [
      "inference"
     ],
     "notesAscii": true
    },
    {
     "key": "CDS",
     "location": "[1625:2486](-)",
     "provenance": "edited",
     "identifiers": [],
     "notesAscii": true,
     "table": 11,
     "exported": "MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW",
     "biopython": "MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW",
     "refused": null,
     "agrees": true
    },
    {
     "key": "CDS",
     "location": "[1625:2484](-)",
     "provenance": "added",
     "identifiers": [],
     "notesAscii": true,
     "table": 1,
     "exported": null,
     "biopython": null,
     "refused": "First codon 'GAG' is not a start codon",
     "agrees": true
    },
    {
     "key": "CDS",
     "location": "[1628:2486](-)",
     "provenance": "added",
     "identifiers": [],
     "notesAscii": true,
     "table": 1,
     "exported": null,
     "biopython": null,
     "refused": "Final codon 'TGG' is not a stop codon",
     "agrees": true
    }
   ]
  }
 ]
}