Pterobacter report
This summary is derived from the JSON report, which is authoritative. Assemblies: 2.
Assembly 1: RHBSTW-00333
Input file: GCA_013738375.1.fna
Final call
Call status: assigned
- Species: assigned — Enterobacter xiangfangensis (ECTX-SP025)
- Subspecies: assigned — Enterobacter xiangfangensis subsp. hoffmannii (ECTX-SS007)
- Genomovar: ECTX-GV-2026-10-02-v1-GV10
- Reasons: —
- Subspecies reason: diagnostic_candidate_only
- Call basis: skani
- Nearest parent (not an assignment): species ECTX-SP025, skani ANI 100.0 %
Analysis settings and execution
- ANI thresholds: standard
- Validation status: not_yet_validated
- Minimum species ANI: 96
- Minimum subspecies ANI: 98
- Minimum aligned fraction (both directions): 80
- Subspecies margin (percentage points): 1
- Conflict ANI: 96
- Trigger lower ANI: 94.5
- Whole-assembly ANI method: skani
- Boundary ANI method: ANIm using MUMmer4
- Execution: complete at stage genomovar
Initial skani result and ANIm
- Initial skani result: assigned (species ECTX-SP025; reasons —)
- Trigger: false (at_or_above_96_v1_route)
- Rescue state: not_triggered
- Competitor panel: not_required
- Challenge check: not_applicable
- ANIm pairs: 0 required, 0 attempted, 0 completed, 0 no alignment, 0 failed, 0 not run
- skani panel: 140 references, 140 returned, 0 not returned
Strongest matches
The five highest skani references are shown, plus every exact tie at fifth place. Rows in one tie group are ordered by reference ID for display only; the order does not choose a winner. Each reference is evidence, not a vote. ANI methods are not mixed in one ranking: skani orders this table and any ANIm values are shown beside it.
| Tie group | Reference | Parent | skani ANI % | AF query % | AF reference % | ANIm identity QR/RQ % |
|---|---|---|---|---|---|---|
| 0 | primary_whole:GCA_013738375.1 | species ECTX-SP025 | 100.0 | 99.99 | 99.99 | — |
| 1 | primary_whole:GCA_001729745.1 | species ECTX-SP025 | 98.97 | 82.69 | 92.17 | — |
| 1 | primary_whole:GCA_013625435.1 | species ECTX-SP025 | 98.97 | 85.66 | 90.75 | — |
| 1 | primary_whole:GCA_052922205.1 | species ECTX-SP025 | 98.97 | 85.51 | 91.21 | — |
| 2 | primary_whole:GCA_027595125.1 | species ECTX-SP025 | 98.92 | 83.07 | 90.16 | — |
Whole-panel species and lineage summary
| Parent | Panel references | Returned | Best skani ANI % | Among strongest matches | Challenging references |
|---|---|---|---|---|---|
| species ECTX-SP025 | 30 | 30 | 100.0 | yes | — |
| species ECTX-SP009 | 5 | 5 | 94.32 | no | — |
| species ECTX-SP018 | 1 | 1 | 93.76 | no | — |
| species ECTX-SP016 | 2 | 2 | 91.5 | no | — |
| species ECTX-SP003 | 8 | 8 | 89.67 | no | — |
| species ECTX-SP007 | 4 | 4 | 89.48 | no | — |
| species ECTX-SP019 | 14 | 14 | 89.29 | no | — |
| species ECTX-SP014 | 1 | 1 | 89.17 | no | — |
| species ECTX-SP013 | 8 | 8 | 89.14 | no | — |
| species ECTX-SP002 | 8 | 8 | 89.01 | no | — |
| species ECTX-SP017 | 4 | 4 | 88.7 | no | — |
| species ECTX-SP023 | 7 | 7 | 88.63 | no | — |
| species ECTX-SP015 | 1 | 1 | 88.62 | no | — |
| species ECTX-SP011 | 8 | 8 | 88.59 | no | — |
| species ECTX-SP024 | 3 | 3 | 88.56 | no | — |
| species ECTX-SP005 | 3 | 3 | 88.54 | no | — |
| species ECTX-SP010 | 1 | 1 | 88.48 | no | — |
| species ECTX-SP021 | 4 | 4 | 88.34 | no | — |
| species ECTX-SP008 | 13 | 13 | 88.33 | no | — |
| species ECTX-SP006 | 1 | 1 | 87.99 | no | — |
| species ECTX-SP001 | 1 | 1 | 87.77 | no | — |
| species ECTX-SP012 | 8 | 8 | 87.67 | no | — |
| species ECTX-SP004 | 3 | 3 | 87.55 | no | — |
| species ECTX-SP022 | 2 | 2 | 86.9 | no | — |
Challenges
Not applicable: no rescue was attempted, so no challenge test ran.
Supplementary results
- MLST: complete
- state exact_profile_match, sequence type 286 (supplementary; it never sets a taxon)
- Genomovar search: assigned
Provenance
- Query SHA-256:
603ed679732e01cb7d1a06ec73d89a53fc12b6f6b22f071df5dee866cdf982b9 - Bases: 5215023; records: 8
- Evidence SHA-256: fa30effe40ead1906508371b3e110d4a4a982991c675e2122d7703767103b9b7
Data selection, citation and retained evidence:
{
"anim_evidence_directory": "batch-alignments",
"anim_manifest_sha256": "02cd57a36119558ae62b93d8d87b1ef5563f3c8009040fa0867da13027ad195d",
"anim_trust": "embedded_catalogue",
"catalogue_sha256": "873353f91dee10efc5f41ec86daceeeb5a6e841e97e885fdd7912853dda25ff9",
"citation": {
"doi": "10.6084/m9.figshare.34640883.v1",
"record_version": 1,
"title": "Enterobacter reference database for Pterobacter, version 2026-10-15",
"url": "https://figshare.com/articles/dataset/Enterobacter_reference_database_for_Pterobacter_version_2026-10-15/34640883"
},
"database": "enterobacter-reference",
"mlst_manifest_sha256": "0f0a4bd051e7a29d97f530a38982026df10ca223805e7b0147b19796763978dd",
"mlst_requested": true,
"mlst_trust": "embedded_catalogue",
"reference_manifest_sha256": "f7c82d8e912fdb08aec93b190316f482fd462b3c514c5b374f8c694af1278e28",
"reference_trust": "embedded_catalogue",
"status": "published",
"version": "2026-10-15"
}
- Reference package 2026-10-15, manifest SHA-256 f7c82d8e912fdb08aec93b190316f482fd462b3c514c5b374f8c694af1278e28
- Software version: 0.0.0. Exact schema, method and analysis identities are retained in report.json.
What to do next
The assignment is conditional on the approved rules and the supplied sequence. It does not establish that the isolate is pure.
Assembly 2: ECC-219
Input file: GCA_043966805.1.fna
Final call
Call status: unresolved
- Species: unresolved (no assignment)
- Subspecies: unresolved (no assignment)
- Genomovar: none reported
- Reasons: ANIm_no_strict_witness
- Subspecies reason: parent_species_unresolved
- Nearest parent (not an assignment): Enterobacter nematophilus (species ECTX-SP014), skani ANI 94.83 %
Analysis settings and execution
- ANI thresholds: standard
- Validation status: not_yet_validated
- Minimum species ANI: 96
- Minimum subspecies ANI: 98
- Minimum aligned fraction (both directions): 80
- Subspecies margin (percentage points): 1
- Conflict ANI: 96
- Trigger lower ANI: 94.5
- Whole-assembly ANI method: skani
- Boundary ANI method: ANIm using MUMmer4
- Execution: complete at stage genomovar
Initial skani result and ANIm
- Initial skani result: unresolved (species —; reasons nearest_below_species_ANI)
- Trigger: true (triggered_with_witness_candidate)
- Rescue state: withheld
- Competitor panel: not_required_no_witness
- Challenge check: not_assessed
- ANIm pairs: 1 required, 1 attempted, 1 completed, 0 no alignment, 0 failed, 0 not run
- skani panel: 140 references, 140 returned, 0 not returned
Strongest matches
The five highest skani references are shown, plus every exact tie at fifth place. Rows in one tie group are ordered by reference ID for display only; the order does not choose a winner. Each reference is evidence, not a vote. ANI methods are not mixed in one ranking: skani orders this table and any ANIm values are shown beside it.
| Tie group | Reference | Parent | skani ANI % | AF query % | AF reference % | ANIm identity QR/RQ % |
|---|---|---|---|---|---|---|
| 0 | primary_whole:GCA_026344075.1 | species ECTX-SP014 | 94.83 | 82.65 | 88.26 | 95.02964941527868 / 95.0343144759382 |
| 1 | primary_whole:GCA_031218175.1 | species ECTX-SP003 | 94.31 | 80.89 | 85.57 | — |
| 2 | primary_whole:GCA_043970685.1 | species ECTX-SP003 | 94.3 | 80.33 | 86.03 | — |
| 3 | primary_whole:GCA_043967505.1 | species ECTX-SP003 | 94.18 | 81.06 | 85.68 | — |
| 4 | primary_whole:GCA_043966825.1 | species ECTX-SP003 | 94.06 | 80.54 | 84.03 | — |
Whole-panel species and lineage summary
| Parent | Panel references | Returned | Best skani ANI % | Among strongest matches | Challenging references |
|---|---|---|---|---|---|
| species ECTX-SP014 | 1 | 1 | 94.83 | yes | — |
| species ECTX-SP003 | 8 | 8 | 94.31 | yes | — |
| species ECTX-SP007 | 4 | 4 | 93.37 | no | — |
| species ECTX-SP002 | 8 | 8 | 92.48 | no | — |
| species ECTX-SP017 | 4 | 4 | 91.98 | no | — |
| species ECTX-SP023 | 7 | 7 | 91.97 | no | — |
| species ECTX-SP019 | 14 | 14 | 91.85 | no | — |
| species ECTX-SP005 | 3 | 3 | 91.63 | no | — |
| species ECTX-SP011 | 8 | 8 | 91.63 | no | — |
| species ECTX-SP006 | 1 | 1 | 91.11 | no | — |
| species ECTX-SP021 | 4 | 4 | 90.82 | no | — |
| species ECTX-SP013 | 8 | 8 | 90.68 | no | — |
| species ECTX-SP001 | 1 | 1 | 90.02 | no | — |
| species ECTX-SP024 | 3 | 3 | 89.63 | no | — |
| species ECTX-SP008 | 13 | 13 | 89.51 | no | — |
| species ECTX-SP025 | 30 | 30 | 89.45 | no | — |
| species ECTX-SP009 | 5 | 5 | 89.4 | no | — |
| species ECTX-SP010 | 1 | 1 | 89.22 | no | — |
| species ECTX-SP016 | 2 | 2 | 89.22 | no | — |
| species ECTX-SP018 | 1 | 1 | 89.21 | no | — |
| species ECTX-SP012 | 8 | 8 | 89.04 | no | — |
| species ECTX-SP015 | 1 | 1 | 88.65 | no | — |
| species ECTX-SP004 | 3 | 3 | 87.98 | no | — |
| species ECTX-SP022 | 2 | 2 | 87.15 | no | — |
Challenges
Not assessed: the run stopped before the competitor panel was measured, or the analysis did not need it. The absence of a listed challenge is not a negative result.
Supplementary results
- MLST: complete
- state exact_profile_match, sequence type 2274 (supplementary; it never sets a taxon)
- Genomovar search: withheld
Provenance
- Query SHA-256:
34f4924c5954e5c424ecdb5476386a3f5ddbfc7d09aa6be2f32c049806b177a0 - Bases: 5027913; records: 1
- Evidence SHA-256: b801c8ca941599167b057f88ffe6a8316a3d32bd0dfdc1362b4aa680e1e8c9c3
Data selection, citation and retained evidence:
{
"anim_evidence_directory": "batch-alignments",
"anim_manifest_sha256": "02cd57a36119558ae62b93d8d87b1ef5563f3c8009040fa0867da13027ad195d",
"anim_trust": "embedded_catalogue",
"catalogue_sha256": "873353f91dee10efc5f41ec86daceeeb5a6e841e97e885fdd7912853dda25ff9",
"citation": {
"doi": "10.6084/m9.figshare.34640883.v1",
"record_version": 1,
"title": "Enterobacter reference database for Pterobacter, version 2026-10-15",
"url": "https://figshare.com/articles/dataset/Enterobacter_reference_database_for_Pterobacter_version_2026-10-15/34640883"
},
"database": "enterobacter-reference",
"mlst_manifest_sha256": "0f0a4bd051e7a29d97f530a38982026df10ca223805e7b0147b19796763978dd",
"mlst_requested": true,
"mlst_trust": "embedded_catalogue",
"reference_manifest_sha256": "f7c82d8e912fdb08aec93b190316f482fd462b3c514c5b374f8c694af1278e28",
"reference_trust": "embedded_catalogue",
"status": "published",
"version": "2026-10-15"
}
- Reference package 2026-10-15, manifest SHA-256 f7c82d8e912fdb08aec93b190316f482fd462b3c514c5b374f8c694af1278e28
- Software version: 0.0.0. Exact schema, method and analysis identities are retained in report.json.
What to do next
No assignment was made. Read the reasons, compare the strongest matches and any challenges, then follow the manual-review steps in the usage guide (docs/usage.md): a tree and an ANI check against the named references. The software does not invent a label.