Closest-reference screening
Preliminary screening result
Analysis ID: —
Waiting for analysis.
Results will appear after the analysis engine returns a response.
What this step shows
This step summarizes the query quality control and closest-reference screening result: sequence length, ORF5 coverage, ambiguous bases, best reference match, nucleotide identity, orientation, support level, and the closest references returned by the engine.
Screening process
Closest PRRSV-2 ORF5 references
This table summarizes the closest references returned by the Python engine. Closest references are reported for context. A reliable lineage signal is reported only when the configured support thresholds are met.
| Rank | Reference | Lineage | Identity | Mismatches | Orientation | Metadata |
|---|---|---|---|---|---|---|
| Run the analysis to display closest references. | ||||||
Master tree context
Phylogenetic context from the PRRSV-2 ORF5 master tree
Tree context will appear when the closest reference is represented in the PRRSV-2 ORF5 master tree.
What this step shows
This step selects a visual reference context from all near-best references within the configured margin. Sublineages are collapsed to their major lineage, and the tree is centered on the best reference within the dominant major lineage. This rule controls visualization only and is not a phylogenetic lineage assignment.
Local phylogenetic context
Reduced local tree view around the selected context anchor.
Displayed reference window
Small capped reference window around the selected context anchor. The table distinguishes the closest individual reference from the context anchor. This view is not a phylogenetic placement of the query.
| Tree ID | Accession | Country | Lineage | Sublineage | Context role |
|---|---|---|---|---|---|
| Tree neighborhood will appear after analysis. | |||||
ORF5 amino acid comparison
Translated GP5 comparison
Amino acid comparison will appear after the sequence is translated in the inferred ORF5 coding frame.
What this step shows
This step translates the submitted ORF5 sequence into amino acids using the orientation and reference-frame context inferred by the nucleotide screening. It compares the derived GP5 sequence against all exact nucleotide co-best references when a true tie is present, plus a fixed vaccine reference panel. This allows the nucleotide tie to be examined at GP5 level without changing the lineage-screening result.
Protein interpretation note
No protein-level warnings were returned.
Jalview-style protein view
ORF5 amino acid alignment viewer
Rows include fixed vaccine references, all nucleotide co-best references compatible with the shared visual frame, and the submitted sequence translated into the ORF5 frame. Scroll horizontally to inspect positions 1–200.
Same as submitted sequence
Different amino acid
Submitted sequence differs from the primary comparison reference
Not covered / gap
Ambiguous amino acid
Stop codon
Nucleotide co-best amino acid comparison
| Reference | Lineage | NT identity | AA identity | AA differences | Role |
|---|---|---|---|---|---|
| Co-best amino acid comparison will appear after analysis. | |||||
| Vaccine reference | Lineage | AA identity | AA differences | Comparable AA |
|---|---|---|---|---|
| Vaccine amino acid comparison will appear after analysis. | ||||
Report and traceability
Public analysis report
Download a single-file HTML report or open a print-optimized PDF-ready report after the analysis is completed.
Reports are generated as a single-file HTML report and a print-optimized PDF-ready view.
Both exclude the submitted nucleotide sequence, the reference FASTA, the curated metadata table,
alignments, and the master tree file.
Storage status
Storage status will appear after analysis.
Advanced technical output: raw JSON response
Technical review only.
This section is intended for validation, debugging, and traceability during testing. It does not include the submitted nucleotide sequence, the complete reference FASTA, the master Newick tree, the alignment, or the curated metadata table. It may include the derived translated amino acid sequence used for the on-screen protein comparison. Submitted form metadata may still appear because it is part of the analysis request.
No API response yet.