diff --git a/respro/report/static/report.css b/respro/report/static/report.css
index 93d823e..a501e1e 100644
--- a/respro/report/static/report.css
+++ b/respro/report/static/report.css
@@ -74,12 +74,15 @@ body {
   line-height: 1.55;
   background-color: var(--paper);
   min-height: 100vh;
+  min-height: 100dvh;
+  overflow-x: hidden;
 }
 
 .report-container {
   display: flex;
   flex-direction: column;
   min-height: 100vh;
+  min-height: 100dvh;
   background: var(--surface-strong);
 }
 
@@ -802,6 +805,20 @@ body {
   }
 }
 
+@media (max-width: 400px) {
+  .report-main {
+    padding: 0.75rem;
+  }
+
+  .header-top {
+    padding: 0.6rem 0.75rem;
+  }
+
+  .summary-tile {
+    padding: 0.85rem;
+  }
+}
+
 /* ─── All Mutations table ─────────────────────────────────────────────────── */
 
 .mutation-toolbar {
diff --git a/respro/report/templates/report.html.j2 b/respro/report/templates/report.html.j2
index 7bdbd23..5767c00 100644
--- a/respro/report/templates/report.html.j2
+++ b/respro/report/templates/report.html.j2
@@ -2,7 +2,7 @@
 <html lang="en">
 <head>
   <meta charset="UTF-8">
-  <meta name="viewport" content="width=device-width, initial-scale=1.0">
+  <meta name="viewport" content="width=device-width, initial-scale=1.0, viewport-fit=cover">
   <title>{{ context.title }}</title>
   <link rel="icon" type="image/svg+xml" href="{{ context.favicon }}"/>
   <style>
diff --git a/tests/test_web_api.py b/tests/test_web_api.py
index b3e6b2b..7648e38 100644
--- a/tests/test_web_api.py
+++ b/tests/test_web_api.py
@@ -2328,6 +2328,241 @@ def capturing_enqueue(*args, **kwargs):
         assert enqueued_bam_paths == [None, None]
 
 
+class TestBatchRegenerateEndpoints:
+    """Batch regenerate-from-JSON endpoint: /api/regenerate/batch.
+
+    Mirrors the single ``/api/regenerate/json`` route but accepts a list of uploaded
+    results-JSON IDs. Each JSON resolves its own project DB via the stored
+    ``project_fingerprint`` (with a per-request fallback ``database_id``), so a batch
+    may span databases — unlike VCF/FASTA batches which share one ``db_path``.
+    """
+
+    @pytest.fixture(autouse=True)
+    def _reset_sample_quota(self):
+        _SAMPLE_QUOTA_COUNTER.clear()
+        reset_memory_stores()
+        yield
+        _SAMPLE_QUOTA_COUNTER.clear()
+        reset_memory_stores()
+
+    def _default_db(self, startup_config: StartupConfig) -> str:
+        return sorted(startup_config.project_databases_dir.glob('*.db'))[0].name
+
+    def _produce_results_json_bytes(
+        self,
+        client: TestClient,
+        web_sample_vcf: Path,
+        web_sample_ref_fasta: Path,
+        sample_name: str,
+    ) -> bytes:
+        """Run one VCF profile job and return the bytes of its results-JSON artifact."""
+        vcf_id = _upload_file(client, web_sample_vcf, 'vcf')
+        ref_id = _upload_file(client, web_sample_ref_fasta, 'fasta')
+        submit = client.post(
+            '/api/profile/vcf',
+            json={
+                'vcf_id': vcf_id,
+                'reference_id': ref_id,
+                'sample': sample_name,
+            },
+        )
+        assert submit.status_code == 200, submit.text
+        payload = _poll_job(client, submit.json()['job_id'])
+        assert payload['status'] == 'succeeded', payload
+        json_artifact_id = payload['result']['report_json_path']
+        return client.get('/api/artifact', params={'artifact_id': json_artifact_id}).content
+
+    def test_batch_regenerate_submit_success(
+        self,
+        client: TestClient,
+        startup_config: StartupConfig,
+        web_sample_vcf: Path,
+        web_sample_ref_fasta: Path,
+    ) -> None:
+        json_a = self._produce_results_json_bytes(
+            client, web_sample_vcf, web_sample_ref_fasta, 'batch-regen-a',
+        )
+        json_b = self._produce_results_json_bytes(
+            client, web_sample_vcf, web_sample_ref_fasta, 'batch-regen-b',
+        )
+        json_id_a = _upload_bytes(client, json_a, 'json', 'sample-a.results.json')
+        json_id_b = _upload_bytes(client, json_b, 'json', 'sample-b.results.json')
+
+        response = client.post(
+            '/api/regenerate/batch',
+            json={
+                'json_ids': [json_id_a, json_id_b],
+                'sample_names': ['regen-a', 'regen-b'],
+                'input_display_names': ['sample-a.results.json', 'sample-b.results.json'],
+                'database_id': self._default_db(startup_config),
+            },
+        )
+
+        assert response.status_code == 200, response.text
+        data = response.json()
+        assert data['total'] == 2
+        assert len(data['samples']) == 2
+        for entry in data['samples']:
+            assert entry['job_id']
+            assert entry['status'] == 'queued'
+
+    def test_batch_regenerate_jobs_resolve_to_regenerated_artifacts(
+        self,
+        client: TestClient,
+        startup_config: StartupConfig,
+        web_sample_vcf: Path,
+        web_sample_ref_fasta: Path,
+    ) -> None:
+        json_bytes = self._produce_results_json_bytes(
+            client, web_sample_vcf, web_sample_ref_fasta, 'batch-regen-resolve',
+        )
+        json_id = _upload_bytes(client, json_bytes, 'json', 'resolve.results.json')
+
+        response = client.post(
+            '/api/regenerate/batch',
+            json={
+                'json_ids': [json_id],
+                'sample_names': ['regen-resolve'],
+                'input_display_names': ['resolve.results.json'],
+                'database_id': self._default_db(startup_config),
+            },
+        )
+        assert response.status_code == 200, response.text
+        submitted = response.json()['samples']
+
+        for sample in submitted:
+            payload = _poll_job(client, sample['job_id'])
+            assert payload['status'] == 'succeeded', payload
+            result = payload['result']
+            assert result['mode'] == 'regenerate-json'
+            assert result['report_html_path']
+            assert result['report_json_path']
+            assert result['report_pdf_path']
+
+    def test_batch_regenerate_mismatched_lengths_returns_422(
+        self,
+        client: TestClient,
+        startup_config: StartupConfig,
+        web_sample_vcf: Path,
+        web_sample_ref_fasta: Path,
+    ) -> None:
+        json_bytes = self._produce_results_json_bytes(
+            client, web_sample_vcf, web_sample_ref_fasta, 'batch-regen-mismatch',
+        )
+        json_id = _upload_bytes(client, json_bytes, 'json', 'mismatch.results.json')
+
+        response = client.post(
+            '/api/regenerate/batch',
+            json={
+                'json_ids': [json_id, json_id],
+                'sample_names': ['only-one'],
+                'database_id': self._default_db(startup_config),
+            },
+        )
+
+        assert response.status_code == 422
+        assert 'json_ids and sample_names must have the same length.' in response.json()['detail']
+
+    def test_batch_regenerate_exceeds_max_size_returns_422(
+        self,
+        client: TestClient,
+        startup_config: StartupConfig,
+        web_sample_vcf: Path,
+        web_sample_ref_fasta: Path,
+    ) -> None:
+        json_bytes = self._produce_results_json_bytes(
+            client, web_sample_vcf, web_sample_ref_fasta, 'batch-regen-oversize',
+        )
+        json_id = _upload_bytes(client, json_bytes, 'json', 'oversize.results.json')
+
+        response = client.post(
+            '/api/regenerate/batch',
+            json={
+                'json_ids': [json_id] * 26,
+                'sample_names': [f'regen-{i}' for i in range(26)],
+                'database_id': self._default_db(startup_config),
+            },
+        )
+
+        assert response.status_code == 422
+        detail = str(response.json())
+        assert 'batch' in detail.lower() or '25' in detail
+
+    def test_batch_regenerate_missing_json_file_returns_404_without_partial_enqueue(
+        self,
+        client: TestClient,
+        sync_queue: Queue,
+        startup_config: StartupConfig,
+        web_sample_vcf: Path,
+        web_sample_ref_fasta: Path,
+        monkeypatch: pytest.MonkeyPatch,
+    ) -> None:
+        json_bytes = self._produce_results_json_bytes(
+            client, web_sample_vcf, web_sample_ref_fasta, 'batch-regen-partial',
+        )
+        json_id = _upload_bytes(client, json_bytes, 'json', 'partial.results.json')
+
+        enqueue_calls = 0
+        original_enqueue = sync_queue.enqueue
+
+        def counting_enqueue(*args, **kwargs):
+            nonlocal enqueue_calls
+            enqueue_calls += 1
+            return original_enqueue(*args, **kwargs)
+
+        monkeypatch.setattr(sync_queue, 'enqueue', counting_enqueue)
+
+        response = client.post(
+            '/api/regenerate/batch',
+            json={
+                'json_ids': [json_id, 'nonexistent-json-id'],
+                'sample_names': ['regen-a', 'regen-b'],
+                'database_id': self._default_db(startup_config),
+            },
+        )
+
+        assert response.status_code == 404
+        assert 'JSON file not found for sample' in response.json()['detail']
+        assert enqueue_calls == 0
+
+    def test_batch_regenerate_rate_limit_returns_429(
+        self,
+        client: TestClient,
+        startup_config: StartupConfig,
+        web_sample_vcf: Path,
+        web_sample_ref_fasta: Path,
+        monkeypatch: pytest.MonkeyPatch,
+    ) -> None:
+        """Exceeding the per-minute sample quota returns 429 with no jobs enqueued."""
+        json_bytes = self._produce_results_json_bytes(
+            client, web_sample_vcf, web_sample_ref_fasta, 'batch-regen-ratelimit',
+        )
+        json_id = _upload_bytes(client, json_bytes, 'json', 'ratelimit.results.json')
+
+        # Force the in-memory quota path (no Redis) and a fixed identity so we can
+        # pre-saturate the counter for the exact key the route will use.
+        monkeypatch.delenv('REDIS_URL', raising=False)
+        import web.backend.main as main_module
+
+        fixed_identity = 'ip:testclient'
+        monkeypatch.setattr(main_module, '_rate_limit_key', lambda request: fixed_identity)
+        max_per_minute = WEB_BACKEND_CONFIG.defaults.max_batch_size
+        window_minute = main_module._current_window_minute()
+        _SAMPLE_QUOTA_COUNTER.clear()
+        _SAMPLE_QUOTA_COUNTER[(fixed_identity, window_minute)] = max_per_minute
+
+        response = client.post(
+            '/api/regenerate/batch',
+            json={
+                'json_ids': [json_id],
+                'sample_names': ['regen-ratelimit'],
+                'database_id': self._default_db(startup_config),
+            },
+        )
+
+        assert response.status_code == 429
+
+
 class TestLegalRoute:
     """Legal notice / imprint route across the four configuration states.
 
diff --git a/web/backend/main.py b/web/backend/main.py
index 795a1a4..3a2a580 100644
--- a/web/backend/main.py
+++ b/web/backend/main.py
@@ -215,6 +215,8 @@ def create_app(startup_config: StartupConfig | None = None) -> FastAPI:
     app.include_router(
         build_regenerate_router(
             config=config,
+            sample_limit_per_minute=sample_limit_per_minute,
+            consume_sample_quota=_consume_sample_quota,
             user_facing_error_message=_user_facing_error_message,
             is_path_within_allowed_roots=is_path_within_allowed_roots,
             resolve_regenerate_project_db_path=resolve_regenerate_project_db_path,
diff --git a/web/backend/models.py b/web/backend/models.py
index 569294e..79c900a 100644
--- a/web/backend/models.py
+++ b/web/backend/models.py
@@ -135,6 +135,24 @@ class BatchProfileFastaPayload(BaseModel):
     threads: int = Field(default=1, ge=1, le=WEB_BACKEND_CONFIG.defaults.profile_max_threads)
 
 
+class BatchRegenerateJsonPayload(BaseModel):
+    """Payload for submitting a batch regenerate-from-JSON job.
+
+    Each uploaded results-JSON ID is resolved to its own project database via the
+    stored ``project_fingerprint`` (with ``database_id`` as a per-request fallback),
+    so a single batch may span databases — unlike VCF/FASTA batches which share one
+    ``db_path``. Inputs are referenced by opaque upload IDs.
+    """
+
+    json_ids: list[str] = Field(max_length=WEB_BACKEND_CONFIG.defaults.path_list_max_length)
+    sample_names: list[str] = Field(max_length=WEB_BACKEND_CONFIG.defaults.path_list_max_length)
+    input_display_names: list[str] | None = Field(
+        default=None,
+        max_length=WEB_BACKEND_CONFIG.defaults.path_list_max_length,
+    )
+    database_id: str | None = Field(default=None, max_length=WEB_BACKEND_CONFIG.defaults.opaque_id_max_length)
+
+
 class UploadResponse(BaseModel):
     """Response returned after a file is successfully uploaded.
 
diff --git a/web/backend/routes/regenerate.py b/web/backend/routes/regenerate.py
index 5492f61..c248932 100644
--- a/web/backend/routes/regenerate.py
+++ b/web/backend/routes/regenerate.py
@@ -5,6 +5,7 @@
 import logging
 from collections.abc import Callable
 from pathlib import Path
+from uuid import uuid4
 
 from fastapi import APIRouter, Depends, HTTPException, Request
 from rq import Queue
@@ -12,8 +13,17 @@
 
 from respro.db.results import load_run_from_json
 from web.backend.jobs import run_regenerate_json
-from web.backend.models import JobSubmitResponse, RegenerateJsonPayload
-from web.backend.queue import build_enqueue_job_options, get_queue
+from web.backend.models import (
+    BatchRegenerateJsonPayload,
+    BatchSampleEntry,
+    BatchSubmitResponse,
+    JobSubmitResponse,
+    RegenerateJsonPayload,
+)
+from web.backend.queue import build_enqueue_job_options, get_batch_queue, get_queue
+from web.backend.routes.profile import (
+    _resolve_batch_input_display_names,
+)
 from web.backend.services.session import (
     Session,
     record_job,
@@ -26,6 +36,8 @@
 def build_regenerate_router(
     *,
     config,
+    sample_limit_per_minute: int,
+    consume_sample_quota: Callable[[Request, int, int], None],
     user_facing_error_message: Callable[[str | None], str],
     is_path_within_allowed_roots: Callable[[Path, tuple[Path, ...]], bool],
     resolve_regenerate_project_db_path,
@@ -33,7 +45,7 @@ def build_regenerate_router(
     api_rate_limit: str,
     get_session: Callable[..., Session],
 ) -> APIRouter:
-    """Build regenerate-json route."""
+    """Build regenerate-json routes (single + batch)."""
     router = APIRouter()
 
     @router.post('/api/regenerate/json', response_model=JobSubmitResponse)
@@ -88,4 +100,109 @@ def regenerate_json_route(
         )
         return JobSubmitResponse(job_id=job.id)
 
+    @router.post('/api/regenerate/batch', response_model=BatchSubmitResponse)
+    @limiter.limit(api_rate_limit)
+    def regenerate_batch_json_route(
+        request: Request,
+        payload: BatchRegenerateJsonPayload,
+        queue: Queue = Depends(get_batch_queue),
+    ) -> BatchSubmitResponse:
+        """Enqueue one regenerate-from-JSON job per uploaded results JSON.
+
+        Unlike the VCF/FASTA batch routes, each JSON resolves its own project
+        database via the stored ``project_fingerprint`` (with ``database_id`` as a
+        shared fallback), so a single batch may regenerate reports against more
+        than one database. The per-minute sample quota applies to the batch size.
+        """
+        session = get_session(request)
+        if len(payload.json_ids) != len(payload.sample_names):
+            raise HTTPException(
+                status_code=422,
+                detail='json_ids and sample_names must have the same length.',
+            )
+        # Resolve and validate display names (length check) even though the regenerate
+        # job derives its output name from the uploaded JSON filename — this keeps the
+        # input_display_names contract consistent with the VCF/FASTA batch routes.
+        _resolve_batch_input_display_names(
+            input_paths=payload.json_ids,
+            input_display_names=payload.input_display_names,
+            path_label='json_ids',
+        )
+        max_batch = sample_limit_per_minute
+        if len(payload.json_ids) > max_batch:
+            raise HTTPException(
+                status_code=422,
+                detail=f'Batch size {len(payload.json_ids)} exceeds the maximum of {max_batch} samples per batch.',
+            )
+        consume_sample_quota(
+            request,
+            sample_count=len(payload.json_ids),
+            sample_limit_per_minute=sample_limit_per_minute,
+        )
+
+        # Resolve every uploaded JSON path and its project DB up front so a missing
+        # file or unresolvable fingerprint fails the whole batch with a clear error
+        # before any job is enqueued (no partial enqueue, mirroring VCF/FASTA batches).
+        resolved_entries: list[tuple[Path, Path]] = []
+        for index, json_id in enumerate(payload.json_ids):
+            sample_name = payload.sample_names[index]
+            try:
+                json_path = resolve_owned_path(
+                    prefix='upload',
+                    record_id=json_id,
+                    session_hash=session.session_hash,
+                    allowed_roots=config.allowed_roots,
+                )
+            except LookupError as exc:
+                raise HTTPException(
+                    status_code=404,
+                    detail=f'JSON file not found for sample {sample_name!r}.',
+                ) from exc
+            except ValueError as exc:
+                raise HTTPException(status_code=400, detail=str(exc)) from exc
+            if not json_path.is_file():
+                raise HTTPException(
+                    status_code=404,
+                    detail=f'JSON file not found for sample {sample_name!r}.',
+                )
+            try:
+                run_dict, _, _, _, _ = load_run_from_json(json_path)
+                project_db_uuid_index = request.app.state.project_db_uuid_index
+                project_db = resolve_regenerate_project_db_path(
+                    config.project_databases_dir,
+                    project_db_uuid_index,
+                    project_fingerprint=str(run_dict.get('project_fingerprint', '') or ''),
+                    fallback_database_id=payload.database_id,
+                )
+            except ValueError as exc:
+                raise HTTPException(
+                    status_code=400,
+                    detail=user_facing_error_message(str(exc)),
+                ) from exc
+            resolved_entries.append((json_path, project_db))
+
+        enqueue_options = build_enqueue_job_options()
+        samples: list[BatchSampleEntry] = []
+        for index, (json_path, project_db) in enumerate(resolved_entries):
+            job_id = str(uuid4())
+            queue.enqueue(
+                run_regenerate_json,
+                project_db=str(project_db),
+                output_dir=str(config.results_dir),
+                json_path=str(json_path),
+                job_id=job_id,
+                **enqueue_options,
+            )
+            record_job(
+                session_hash=session.session_hash,
+                upload_ids=[payload.json_ids[index]],
+                job_id=job_id,
+            )
+            samples.append(BatchSampleEntry(job_id=job_id, sample_name=payload.sample_names[index]))
+        logger.info(
+            'Batch regenerate-json jobs enqueued: count=%d',
+            len(samples),
+        )
+        return BatchSubmitResponse(samples=samples, total=len(samples))
+
     return router
diff --git a/web/frontend/package.json b/web/frontend/package.json
index 756e3d5..402a2c9 100644
--- a/web/frontend/package.json
+++ b/web/frontend/package.json
@@ -1,6 +1,6 @@
 {
   "name": "respro-web-frontend",
-  "version": "0.1.0",
+  "version": "0.1.1",
   "private": true,
   "type": "module",
   "engines": {
diff --git a/web/frontend/src/assets/file.svg b/web/frontend/src/assets/file.svg
new file mode 100644
index 0000000..378739e
--- /dev/null
+++ b/web/frontend/src/assets/file.svg
@@ -0,0 +1,24 @@
+<?xml version="1.0" encoding="utf-8"?>
+
+<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.0//EN" "http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd">
+<!-- Uploaded to: SVG Repo, www.svgrepo.com, Generator: SVG Repo Mixer Tools -->
+<svg version="1.0" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" 
+	 width="800px" height="800px" viewBox="0 0 64 64" enable-background="new 0 0 64 64" xml:space="preserve">
+<g>
+	<g>
+		<polygon fill="#9ae7d0" points="46,3.414 46,14 56.586,14 		"/>
+		<path fill="#9ae7d0" d="M45,16c-0.553,0-1-0.447-1-1V2H8C6.896,2,6,2.896,6,4v56c0,1.104,0.896,2,2,2h48c1.104,0,2-0.896,2-2V16
+			H45z"/>
+	</g>
+	<path fill="#272928" d="M14,26c0,0.553,0.447,1,1,1h34c0.553,0,1-0.447,1-1s-0.447-1-1-1H15C14.447,25,14,25.447,14,26z"/>
+	<path fill="#272928" d="M49,37H15c-0.553,0-1,0.447-1,1s0.447,1,1,1h34c0.553,0,1-0.447,1-1S49.553,37,49,37z"/>
+	<path fill="#272928" d="M49,43H15c-0.553,0-1,0.447-1,1s0.447,1,1,1h34c0.553,0,1-0.447,1-1S49.553,43,49,43z"/>
+	<path fill="#272928" d="M49,49H15c-0.553,0-1,0.447-1,1s0.447,1,1,1h34c0.553,0,1-0.447,1-1S49.553,49,49,49z"/>
+	<path fill="#272928" d="M49,31H15c-0.553,0-1,0.447-1,1s0.447,1,1,1h34c0.553,0,1-0.447,1-1S49.553,31,49,31z"/>
+	<path fill="#272928" d="M15,20h16c0.553,0,1-0.447,1-1s-0.447-1-1-1H15c-0.553,0-1,0.447-1,1S14.447,20,15,20z"/>
+	<path fill="#272928" d="M59.706,14.292L45.708,0.294C45.527,0.112,45.277,0,45,0H8C5.789,0,4,1.789,4,4v56c0,2.211,1.789,4,4,4h48
+		c2.211,0,4-1.789,4-4V15C60,14.723,59.888,14.473,59.706,14.292z M46,3.414L56.586,14H46V3.414z M58,60c0,1.104-0.896,2-2,2H8
+		c-1.104,0-2-0.896-2-2V4c0-1.104,0.896-2,2-2h36v13c0,0.553,0.447,1,1,1h13V60z"/>
+	<polygon opacity="0.15" fill="#231F20" points="46,3.414 56.586,14 46,14 	"/>
+</g>
+</svg>
\ No newline at end of file
diff --git a/web/frontend/src/assets/logo.svg b/web/frontend/src/assets/logo.svg
index 189a846..dd9418c 100644
--- a/web/frontend/src/assets/logo.svg
+++ b/web/frontend/src/assets/logo.svg
@@ -1,20 +1,35 @@
-<svg width="480" height="110" viewBox="0 0 480 110" xmlns="http://www.w3.org/2000/svg">
-  <style>
-    .t { font-family: Arial, Helvetica, sans-serif; font-size: 34px; }
-  </style>
-
-  <!-- Alignment blocks -->
-  <g transform="translate(20,55)">
-    <rect x="0"  y="-18" width="40" height="8" fill="#45577e" stroke="white" stroke-width="1"/>
-    <rect x="10" y="-6"  width="40" height="8" fill="#0f766e" stroke="white" stroke-width="1"/>
-    <rect x="5"  y="6"   width="40" height="8" fill="#45577e" stroke="white" stroke-width="1"/>
-    <rect x="15" y="18"  width="40" height="8" fill="#45577e" stroke="white" stroke-width="1"/>
-  </g>
-
-  <!-- Shifted box -->
-  <rect x="90" y="30" width="185" height="52" fill="#0f766e" rx="6"/>
-
-  <!-- Text -->
-  <text x="100" y="67" class="t" fill="white">Resistance</text>
-  <text x="280" y="67" class="t" fill="#45577e" stroke="white" stroke-width="2" paint-order="stroke fill">Profiler</text>
-</svg>
\ No newline at end of file
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
+<svg width="100%" height="100%" viewBox="0 0 2363 709" version="1.1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" xml:space="preserve" xmlns:serif="http://www.serif.com/" style="fill-rule:evenodd;clip-rule:evenodd;">
+    <g transform="matrix(1,0,0,1,17.8436,-13.4356)">
+        <path d="M2319.39,258.109L2319.39,511.186C2319.39,581.025 2262.69,637.725 2192.85,637.725L805.196,637.725C735.357,637.725 678.657,581.025 678.657,511.186L678.657,258.109C678.657,188.271 735.357,131.571 805.196,131.571L2192.85,131.571C2262.69,131.571 2319.39,188.271 2319.39,258.109Z" style="fill:rgb(15,118,110);"/>
+    </g>
+    <g transform="matrix(0.458406,0,0,1,385.4,-13.4356)">
+        <path d="M2319.39,258.109L2319.39,511.186C2319.39,581.025 2195.7,637.725 2043.35,637.725L954.698,637.725C802.347,637.725 678.657,581.025 678.657,511.186L678.657,258.109C678.657,188.271 802.347,131.571 954.698,131.571L2043.35,131.571C2195.7,131.571 2319.39,188.271 2319.39,258.109Z" style="fill:rgb(69,87,126);"/>
+    </g>
+    <g transform="matrix(0.222016,0,0,1,948.239,-13.4356)">
+        <rect x="678.657" y="131.571" width="1640.74" height="506.154" style="fill:rgb(69,87,126);"/>
+    </g>
+    <g transform="matrix(9.53928,0,0,9.53928,807.467,476.542)">
+        <text x="0px" y="0px" style="font-family:'ArialMT', 'Arial';font-size:34.07px;fill:white;">Res</text>
+    </g>
+    <g transform="matrix(1.21774,0,0,1.21774,-590.021,160.216)">
+        <g transform="matrix(266.887,0,0,266.887,2316.95,265.882)">
+        </g>
+        <text x="1738.61px" y="265.882px" style="font-family:'ArialMT', 'Arial';font-size:266.887px;fill:white;">PRO</text>
+    </g>
+    <g transform="matrix(10.8559,0,0,10.8559,-890.773,312.728)">
+        <g transform="matrix(1,0,0,1,83.2234,2.2188)">
+            <rect x="0" y="-18" width="40" height="8" style="fill:rgb(69,87,126);stroke:white;stroke-width:1px;"/>
+        </g>
+        <g transform="matrix(1,0,0,1,83.2234,2.2188)">
+            <rect x="10" y="-6" width="40" height="8" style="fill:rgb(15,118,110);stroke:white;stroke-width:1px;"/>
+        </g>
+        <g transform="matrix(1,0,0,1,83.2234,2.2188)">
+            <rect x="5" y="6" width="40" height="8" style="fill:rgb(69,87,126);stroke:white;stroke-width:1px;"/>
+        </g>
+        <g transform="matrix(1,0,0,1,83.2234,2.2188)">
+            <rect x="15" y="18" width="40" height="8" style="fill:rgb(69,87,126);stroke:white;stroke-width:1px;"/>
+        </g>
+    </g>
+</svg>
diff --git a/web/frontend/src/components/AppFooter.jsx b/web/frontend/src/components/AppFooter.jsx
index 8d767b6..4643e48 100644
--- a/web/frontend/src/components/AppFooter.jsx
+++ b/web/frontend/src/components/AppFooter.jsx
@@ -24,13 +24,13 @@ export function AppFooter({ legalLink, contactEmail, cliVersion, webVersion }) {
       {(cliVersion || webVersion) && (
         <div className="app-footer-group">
           {cliVersion && (
-            <span className="app-footer-version">ResistanceProfiler Core v{cliVersion}</span>
+            <span className="app-footer-version">respro CLI v{cliVersion}</span>
           )}
           {cliVersion && webVersion && (
             <span className="app-footer-sep" aria-hidden="true">·</span>
           )}
           {webVersion && (
-            <span className="app-footer-version">ResistanceProfiler WebApp v{webVersion}</span>
+            <span className="app-footer-version">respro WebApp v{webVersion}</span>
           )}
         </div>
       )}
diff --git a/web/frontend/src/components/AppFooter.test.jsx b/web/frontend/src/components/AppFooter.test.jsx
index 5b910dc..9eb8fec 100644
--- a/web/frontend/src/components/AppFooter.test.jsx
+++ b/web/frontend/src/components/AppFooter.test.jsx
@@ -12,8 +12,8 @@ describe('AppFooter', () => {
     render(<AppFooter />);
     expect(screen.queryByText('Legal notice')).not.toBeInTheDocument();
     expect(screen.queryByRole('link', { name: /contact/i })).not.toBeInTheDocument();
-    expect(screen.queryByText(/ResistanceProfiler Core/)).not.toBeInTheDocument();
-    expect(screen.queryByText(/ResistanceProfiler WebApp/)).not.toBeInTheDocument();
+    expect(screen.queryByText(/respro CLI/)).not.toBeInTheDocument();
+    expect(screen.queryByText(/respro WebApp/)).not.toBeInTheDocument();
   });
 
   it('renders a mailto contact link only when contactEmail is set', () => {
diff --git a/web/frontend/src/components/DashboardView.jsx b/web/frontend/src/components/DashboardView.jsx
index c98c16e..77c9150 100644
--- a/web/frontend/src/components/DashboardView.jsx
+++ b/web/frontend/src/components/DashboardView.jsx
@@ -98,6 +98,7 @@ export function DashboardView({
   setBatchMode,
   batchVcfFiles,
   batchFastaFiles,
+  batchJsonFiles,
   batchReferenceFasta,
   batchSamples,
   batchSubmitting,
@@ -113,6 +114,7 @@ export function DashboardView({
   setBatchVcfCutoffs,
   addBatchVcfFiles,
   addBatchFastaFiles,
+  addBatchJsonFiles,
   addBatchBamFiles,
   attachBatchBam,
   removeBatchFile,
@@ -176,21 +178,6 @@ export function DashboardView({
 
   return (
     <main className="dashboard-shell">
-      {/* Hamburger toggle for the off-canvas sidebar. Hidden on desktop via
-          CSS (.mobile-menu-btn is display:none above --mobile-breakpoint). */}
-      <button
-        type="button"
-        className={`mobile-menu-btn ${mobileNavOpen ? 'open' : ''}`}
-        aria-label="Toggle navigation"
-        aria-expanded={mobileNavOpen}
-        aria-controls="sidebar-rail"
-        onClick={() => setMobileNavOpen((v) => !v)}
-      >
-        <span className="mobile-menu-bar" aria-hidden="true" />
-        <span className="mobile-menu-bar" aria-hidden="true" />
-        <span className="mobile-menu-bar" aria-hidden="true" />
-      </button>
-      {/* Left rail only switches visible mode; all data lives in shared hook state. */}
       <aside
         id="sidebar-rail"
         className={`sidebar-rail ${mobileNavOpen ? 'open' : ''}`}
@@ -223,6 +210,18 @@ export function DashboardView({
 
       <div className="dashboard-main">
         <div className="top-bar">
+          <button
+            type="button"
+            className={`mobile-menu-btn ${mobileNavOpen ? 'open' : ''}`}
+            aria-label="Toggle navigation"
+            aria-expanded={mobileNavOpen}
+            aria-controls="sidebar-rail"
+            onClick={() => setMobileNavOpen((v) => !v)}
+          >
+            <span className="mobile-menu-bar" aria-hidden="true" />
+            <span className="mobile-menu-bar" aria-hidden="true" />
+            <span className="mobile-menu-bar" aria-hidden="true" />
+          </button>
           <div className="top-bar-brand-block">
             <div className="brand-logo-wrap" aria-label="ResistanceProfiler dashboard">
               <img className="brand-logo" src={logoSrc} alt="ResistanceProfiler logo" />
@@ -283,6 +282,7 @@ export function DashboardView({
               setBatchMode={setBatchMode}
               batchVcfFiles={batchVcfFiles}
               batchFastaFiles={batchFastaFiles}
+              batchJsonFiles={batchJsonFiles}
               batchReferenceFasta={batchReferenceFasta}
               batchSamples={batchSamples}
               batchSubmitting={batchSubmitting}
@@ -297,6 +297,7 @@ export function DashboardView({
               setBatchVcfCutoffs={setBatchVcfCutoffs}
               addBatchVcfFiles={addBatchVcfFiles}
               addBatchFastaFiles={addBatchFastaFiles}
+              addBatchJsonFiles={addBatchJsonFiles}
               addBatchBamFiles={addBatchBamFiles}
               attachBatchBam={attachBatchBam}
               removeBatchFile={removeBatchFile}
diff --git a/web/frontend/src/components/tabs/AnalyzeTab.jsx b/web/frontend/src/components/tabs/AnalyzeTab.jsx
index d4cecce..a274944 100644
--- a/web/frontend/src/components/tabs/AnalyzeTab.jsx
+++ b/web/frontend/src/components/tabs/AnalyzeTab.jsx
@@ -3,14 +3,10 @@ import { useEffect, useRef, useState } from 'react';
 import analyzeIconSrc from '../../assets/icon-analyze.svg';
 import batchIconSrc from '../../assets/batch.svg';
 import exampleIconSrc from '../../assets/example.svg';
+import fileIconSrc from '../../assets/file.svg';
 import infoIconSrc from '../../assets/info.svg';
 import { Spinner } from '../Spinner';
 
-const ANALYZE_SUBMODES = [
-  { id: 'single', label: 'One Sample', iconSrc: analyzeIconSrc },
-  { id: 'batch', label: 'Multiple Samples', iconSrc: batchIconSrc },
-];
-
 export function AnalyzeTab({
   selectedDatabase,
   vcfInput,
@@ -46,6 +42,7 @@ export function AnalyzeTab({
   setBatchMode,
   batchVcfFiles,
   batchFastaFiles,
+  batchJsonFiles,
   batchReferenceFasta,
   batchSamples,
   batchSubmitting,
@@ -60,6 +57,7 @@ export function AnalyzeTab({
   setBatchVcfCutoffs,
   addBatchVcfFiles,
   addBatchFastaFiles,
+  addBatchJsonFiles,
   addBatchBamFiles,
   attachBatchBam,
   removeBatchFile,
@@ -202,13 +200,6 @@ export function AnalyzeTab({
         <div className="analyze-shell-header section-header">
           <div>
             <h2>{analyzeSubMode === 'batch' ? 'Analyze multiple samples' : 'Analyze'}</h2>
-            <p>
-              {analyzeSubMode === 'batch'
-                ? 'Submit multiple sequence file at once (max 25 per batch and minute).'
-                : 'Profile vcf files or consensus fasta sequence or regenerate a previous report. Bam files are optional and can be used for coverage analysis.'}
-            </p>
-          </div>
-          <div className="analyze-submode-row" role="group" aria-label="Analysis workflow" ref={analyzeSubmodeRowRef}>
             {selectedDatabase?.has_example ? (
               <button
                 type="button"
@@ -225,53 +216,13 @@ export function AnalyzeTab({
                 Example
               </button>
             ) : null}
-            {ANALYZE_SUBMODES.map((subMode) => (
-              <button
-                key={subMode.id}
-                type="button"
-                className={`analyze-submode-btn ${analyzeSubMode === subMode.id ? 'active' : ''}`}
-                onClick={() => {
-                  if (subMode.id === 'single') {
-                    setActiveProfileMode('vcf');
-                    setAnalyzeSubMode('single');
-                    return;
-                  }
-
-                  if (subMode.id === 'batch') {
-                    setBatchMode('vcf');
-                    resetBatch();
-                    setAnalyzeSubMode('batch');
-                    return;
-                  }
-                }}
-                disabled={isAnalyzeScopeLocked}
-              >
-                <span className="sidebar-icon-mask analyze-submode-icon" style={{ '--icon-src': `url(${subMode.iconSrc})` }} aria-hidden="true" />
-                {subMode.label}
-              </button>
-            ))}
+            <p>
+              Profile VCF files, consensus FASTA sequences, or regenerate a previous report from JSON.
+              BAM files are optional and can be used for coverage analysis.
+            </p>
           </div>
-        </div>
-
-        {/* SINGLE SAMPLE submode */}
-        {analyzeSubMode === 'single' ? (
-          <div className="profile-input-subtile section-subtile">
-            <div className="profile-mode-row">
-              <div className="profile-settings-row" role="group" aria-label="Profiling mode">
-                <div className="database-phenotype-switch">
-                  {PROFILE_MODES.map((mode) => (
-                    <button
-                      key={mode.id}
-                      type="button"
-                      className={activeProfileMode === mode.id ? 'active' : ''}
-                      onClick={() => setActiveProfileMode(mode.id)}
-                      disabled={activeProfileMode === 'regenerate' ? isRegenerateBusy : isProfileBusy}
-                    >
-                      {mode.label}
-                    </button>
-                  ))}
-                </div>
-              </div>
+          {analyzeSubMode === 'single' || !batchSubmitted ? (
+            <div className="analyze-submode-progress">
               <div className="upload-progress" aria-label="Upload progress">
                 <div className="upload-progress-head">
                   <span>Upload progress</span>
@@ -282,6 +233,97 @@ export function AnalyzeTab({
                 </div>
               </div>
             </div>
+          ) : null}
+          <div className="analyze-submode-row" role="group" aria-label="Analysis workflow" ref={analyzeSubmodeRowRef}>
+            <div className="analyze-submode-controls">
+              <div
+                className="analyze-submode-switch"
+                role="switch"
+                aria-label="One or multiple samples"
+                aria-checked={analyzeSubMode === 'batch'}
+                data-state={analyzeSubMode}
+              >
+                <button
+                  type="button"
+                  className={`analyze-submode-switch-option ${analyzeSubMode === 'single' ? 'active' : ''}`}
+                  onClick={() => {
+                    setActiveProfileMode('vcf');
+                    setAnalyzeSubMode('single');
+                  }}
+                  disabled={isAnalyzeScopeLocked}
+                >
+                  <span className="sidebar-icon-mask analyze-submode-icon" style={{ '--icon-src': `url(${analyzeIconSrc})` }} aria-hidden="true" />
+                  One Sample
+                </button>
+                <button
+                  type="button"
+                  className={`analyze-submode-switch-option ${analyzeSubMode === 'batch' ? 'active' : ''}`}
+                  onClick={() => {
+                    setBatchMode('vcf');
+                    resetBatch();
+                    setAnalyzeSubMode('batch');
+                  }}
+                  disabled={isAnalyzeScopeLocked}
+                >
+                  <span className="sidebar-icon-mask analyze-submode-icon" style={{ '--icon-src': `url(${batchIconSrc})` }} aria-hidden="true" />
+                  Multiple Samples
+                </button>
+                <span className="analyze-submode-switch-knob" aria-hidden="true" />
+              </div>
+              {analyzeSubMode === 'single' ? (
+                <div className="profile-settings-row" role="group" aria-label="Profiling mode">
+                  <div className="database-phenotype-switch" data-active-mode={activeProfileMode}>
+                    {PROFILE_MODES.map((mode) => (
+                      <button
+                        key={mode.id}
+                        type="button"
+                        className={activeProfileMode === mode.id ? 'active' : ''}
+                        onClick={() => setActiveProfileMode(mode.id)}
+                        disabled={activeProfileMode === 'regenerate' ? isRegenerateBusy : isProfileBusy}
+                      >
+                        {mode.label}
+                      </button>
+                    ))}
+                  </div>
+                </div>
+              ) : null}
+              {analyzeSubMode === 'batch' && !batchSubmitted ? (
+                <div className="profile-settings-row" role="group" aria-label="Batch mode">
+                  <div className="database-phenotype-switch" data-active-mode={batchMode}>
+                    <button
+                      type="button"
+                      className={batchMode === 'vcf' ? 'active' : ''}
+                      onClick={() => setBatchMode('vcf')}
+                      disabled={batchSubmitting}
+                    >
+                      VCF
+                    </button>
+                    <button
+                      type="button"
+                      className={batchMode === 'fasta' ? 'active' : ''}
+                      onClick={() => setBatchMode('fasta')}
+                      disabled={batchSubmitting}
+                    >
+                      FASTA
+                    </button>
+                    <button
+                      type="button"
+                      className={batchMode === 'json' ? 'active' : ''}
+                      onClick={() => setBatchMode('json')}
+                      disabled={batchSubmitting}
+                    >
+                      JSON
+                    </button>
+                  </div>
+                </div>
+              ) : null}
+            </div>
+          </div>
+        </div>
+
+        {/* SINGLE SAMPLE submode */}
+        {analyzeSubMode === 'single' ? (
+          <div className="profile-input-subtile section-subtile">
 
             {activeProfileMode === 'vcf' ? (
               <div className="profile-upload-row profile-upload-row-vcf">
@@ -524,6 +566,15 @@ export function AnalyzeTab({
                 Download TSV
               </button>
             </div>
+
+            {!inlineReportPath ? (
+              <div className="report-placeholder">
+                <div className="report-placeholder-icon-wrap">
+                  <img src={fileIconSrc} alt="" className="report-placeholder-icon" aria-hidden="true" />
+                </div>
+                <p className="report-placeholder-text">Your analysis report will open here</p>
+              </div>
+            ) : null}
           </div>
         ) : null}
 
@@ -532,39 +583,6 @@ export function AnalyzeTab({
           <div className="profile-input-subtile section-subtile">
           {!batchSubmitted ? (
             <>
-              {/* Mode sub-selector */}
-              <div className="profile-mode-row">
-                <div className="profile-settings-row" role="group" aria-label="Batch mode">
-                  <div className="database-phenotype-switch">
-                    <button
-                      type="button"
-                      className={batchMode === 'vcf' ? 'active' : ''}
-                      onClick={() => setBatchMode('vcf')}
-                      disabled={batchSubmitting}
-                    >
-                      VCF batch
-                    </button>
-                    <button
-                      type="button"
-                      className={batchMode === 'fasta' ? 'active' : ''}
-                      onClick={() => setBatchMode('fasta')}
-                      disabled={batchSubmitting}
-                    >
-                      FASTA batch
-                    </button>
-                  </div>
-                </div>
-                <div className="upload-progress" aria-label="Batch upload progress">
-                  <div className="upload-progress-head">
-                    <span>Upload progress</span>
-                    <span>{uploadProgress.percent}%</span>
-                  </div>
-                  <div className="upload-progress-track" aria-hidden="true">
-                    <div className="upload-progress-fill" style={{ width: `${uploadProgress.percent}%` }} />
-                  </div>
-                </div>
-              </div>
-
               {/* File upload area */}
               {batchMode === 'vcf' ? (
                 <div className="profile-upload-row profile-upload-row-batch-vcf">
@@ -649,7 +667,7 @@ export function AnalyzeTab({
                     />
                   </label>
                 </div>
-              ) : (
+              ) : batchMode === 'fasta' ? (
                 <div className="profile-upload-row">
                   <label>
                     <span className="input-label-row">FASTA files <button type="button" className="input-info-btn" aria-label="Batch FASTA help" title="Upload one or more consensus FASTA files."><img className="input-info-icon" src={infoIconSrc} alt="" aria-hidden="true" /></button></span>
@@ -668,14 +686,36 @@ export function AnalyzeTab({
                     />
                   </label>
                 </div>
+              ) : (
+                <div className="profile-upload-row profile-upload-row-batch-json">
+                  <label>
+                    <span className="input-label-row">Results JSON files <button type="button" className="input-info-btn" aria-label="Batch JSON help" title="Upload one or more prior results JSON files exported by ResistanceProfiler. Each JSON is matched to its database by a unique project fingerprint."><img className="input-info-icon" src={infoIconSrc} alt="" aria-hidden="true" /></button></span>
+                    <input
+                      type="file"
+                      multiple
+                      accept=".json"
+                      disabled={batchSubmitting}
+                      onChange={(event) => {
+                        if (!event.target.files) {
+                          return;
+                        }
+                        addBatchJsonFiles(event.target.files);
+                        event.target.value = '';
+                      }}
+                    />
+                  </label>
+                </div>
               )}
 
               {/* Uploaded file list */}
-              {(batchMode === 'vcf' ? batchVcfFiles : batchFastaFiles).length > 0 ? (
+              {(() => {
+                const batchFiles = batchMode === 'vcf' ? batchVcfFiles : batchMode === 'fasta' ? batchFastaFiles : batchJsonFiles;
+                const fileColumnLabel = batchMode === 'vcf' ? 'VCF file' : batchMode === 'fasta' ? 'FASTA file' : 'JSON file';
+                return batchFiles.length > 0 ? (
                 <div className="profile-upload-row profile-upload-row-batch-files">
                   <p className="field-optional">
-                    {(batchMode === 'vcf' ? batchVcfFiles : batchFastaFiles).length} / {batchMaxSamples} files
-                    {(batchMode === 'vcf' ? batchVcfFiles : batchFastaFiles).length >= batchMaxSamples ? (
+                    {batchFiles.length} / {batchMaxSamples} files
+                    {batchFiles.length >= batchMaxSamples ? (
                       <span style={{ color: 'var(--color-error, #c2410c)', marginLeft: '0.4em' }}>Limit reached</span>
                     ) : null}
                   </p>
@@ -683,7 +723,7 @@ export function AnalyzeTab({
                     <table className="batch-uploaded-table">
                       <thead>
                         <tr>
-                          <th>{batchMode === 'vcf' ? 'VCF file' : 'FASTA file'}</th>
+                          <th>{fileColumnLabel}</th>
                           <th>Size</th>
                           {batchMode === 'vcf' ? <th>BAM file</th> : null}
                           {batchMode === 'vcf' ? <th>BAM size</th> : null}
@@ -692,7 +732,7 @@ export function AnalyzeTab({
                         </tr>
                       </thead>
                       <tbody>
-                        {(batchMode === 'vcf' ? batchVcfFiles : batchFastaFiles).map((file, index) => (
+                        {batchFiles.map((file, index) => (
                           <tr key={file.uploadId}>
                             <td className="batch-uploaded-cell-name" title={file.name}>{file.name}</td>
                             <td className="batch-uploaded-cell-size field-optional">{Math.round(file.size / 1024)} KB</td>
@@ -741,7 +781,8 @@ export function AnalyzeTab({
                     </table>
                   </div>
                 </div>
-              ) : null}
+              ) : null;
+              })()}
 
               {/* Shared reference FASTA selection status (VCF mode) */}
               {batchMode === 'vcf' && batchReferenceFasta ? (
@@ -757,7 +798,7 @@ export function AnalyzeTab({
                   disabled={
                     batchSubmitting
                     || batchRateLimitCooldown > 0
-                    || (batchMode === 'vcf' ? batchVcfFiles : batchFastaFiles).length === 0
+                    || (batchMode === 'vcf' ? batchVcfFiles : batchMode === 'fasta' ? batchFastaFiles : batchJsonFiles).length === 0
                     || (batchMode === 'vcf' && !batchReferenceFasta)
                   }
                 >
diff --git a/web/frontend/src/components/tabs/ResultsTab.jsx b/web/frontend/src/components/tabs/ResultsTab.jsx
index 128f8e8..22d0df1 100644
--- a/web/frontend/src/components/tabs/ResultsTab.jsx
+++ b/web/frontend/src/components/tabs/ResultsTab.jsx
@@ -30,6 +30,15 @@ export function ResultsTab({
   fetchComparisonData,
   clearComparison,
 }) {
+  const selectedResults = [...selectedResultIndices]
+    .map((i) => sessionResults[i])
+    .filter(Boolean);
+  const selectedDbIds = new Set(selectedResults.map((r) => r.database_id || ''));
+  const selectedRefNames = new Set(selectedResults.map((r) => r.reference_name || ''));
+  const isSelectionComparable = selectedResults.length >= 2
+    && selectedDbIds.size === 1
+    && selectedRefNames.size === 1;
+
   return (
     <article className="card full-width-tile tab-primary-tile">
       <div className="workspace-output-header section-header">
@@ -37,6 +46,20 @@ export function ResultsTab({
           <h2>Session results</h2>
           <p>All analysis outputs from this session. Results are cleared on page reload.</p>
         </div>
+        {sessionResults.length > 0 ? (
+          <button
+            type="button"
+            className="analyze-primary results-download-btn"
+            onClick={() => downloadSelectedArtifacts()}
+            disabled={selectedResultIndices.size === 0 || isSessionDownloadBusy}
+          >
+            {isSessionDownloadBusy ? (
+              <><Spinner /> Preparing...</>
+            ) : (
+              'Download'
+            )}
+          </button>
+        ) : null}
       </div>
       {sessionResults.length === 0 ? (
         <p className="status">No results yet. Run an analysis to see results here.</p>
@@ -46,7 +69,20 @@ export function ResultsTab({
           <table>
             <thead>
               <tr>
-                <th className="checkbox-col"></th>
+                <th className="checkbox-col">
+                  <input
+                    type="checkbox"
+                    aria-label="Select all results"
+                    checked={sessionResults.length > 0 && selectedResultIndices.size === sessionResults.length}
+                    onChange={(e) => {
+                      if (e.target.checked) {
+                        setSelectedResultIndices(new Set(sessionResults.map((_, i) => i)));
+                      } else {
+                        setSelectedResultIndices(new Set());
+                      }
+                    }}
+                  />
+                </th>
                 <th>Mode</th>
                 <th>Sample</th>
                 <th>Reference</th>
@@ -104,32 +140,10 @@ export function ResultsTab({
             </tbody>
           </table>
         </div>
-        <div className="profile-analyze-row">
-          <button
-            type="button"
-            className="analyze-primary"
-            onClick={() => downloadAllSessionArtifacts()}
-            disabled={isSessionDownloadBusy}
-          >
-            {isSessionDownloadBusy ? (
-              <><Spinner /> Preparing...</>
-            ) : (
-              'Download all'
-            )}
-          </button>
-          <button
-            type="button"
-            className="analyze-primary"
-            onClick={() => downloadSelectedArtifacts()}
-            disabled={selectedResultIndices.size === 0 || isSessionDownloadBusy}
-          >
-            Download selected
-          </button>
-        </div>
         <div className="profile-analyze-row comparison-actions">
           <button
             type="button"
-            className="analyze-primary"
+            className="analyze-primary comparison-secondary"
             onClick={() => selectAllComparable()}
             disabled={selectedResultIndices.size === 0}
           >
@@ -139,19 +153,21 @@ export function ResultsTab({
             type="button"
             className="analyze-primary"
             onClick={() => fetchComparisonData()}
-            disabled={selectedResultIndices.size < 2 || isComparisonBusy}
+            disabled={selectedResultIndices.size < 2 || isComparisonBusy || !isSelectionComparable}
           >
             {isComparisonBusy ? <><Spinner /> Comparing...</> : 'Compare selected'}
           </button>
           <button
             type="button"
-            className="comparison-clear-btn"
+            className="analyze-primary"
             onClick={() => clearComparison()}
             disabled={!comparisonData}
           >
             Clear comparison
           </button>
         </div>
+        {comparisonData && (
+          <>
         <div className="comparison-filters">
           <label className="comparison-switch" title="Show only non-synonymous mutations">
             <input
@@ -180,8 +196,7 @@ export function ResultsTab({
             <span>DB hits only</span>
           </label>
         </div>
-        {comparisonData && (
-          <section className="comparison-section">
+        <section className="comparison-section">
             <div className="workspace-output-header section-header">
               <div>
                 <h3>Comparison heatmap
@@ -204,6 +219,7 @@ export function ResultsTab({
             </div>
             <ComparisonHeatmap data={comparisonData} isBusy={isComparisonBusy} />
           </section>
+          </>
         )}
         </>
       )}
diff --git a/web/frontend/src/constants.js b/web/frontend/src/constants.js
index 4213638..ba52e44 100644
--- a/web/frontend/src/constants.js
+++ b/web/frontend/src/constants.js
@@ -1,5 +1,5 @@
 export const PROFILE_MODES = [
-  { id: 'vcf', label: 'VCF mode' },
-  { id: 'fasta', label: 'FASTA mode' },
-  { id: 'regenerate', label: 'Regenerate mode' },
+  { id: 'vcf', label: 'VCF' },
+  { id: 'fasta', label: 'FASTA' },
+  { id: 'regenerate', label: 'JSON' },
 ];
diff --git a/web/frontend/src/hooks/useBatchManager.js b/web/frontend/src/hooks/useBatchManager.js
index e77da7a..47290b0 100644
--- a/web/frontend/src/hooks/useBatchManager.js
+++ b/web/frontend/src/hooks/useBatchManager.js
@@ -14,6 +14,7 @@ export function useBatchManager({
   const [batchMode, setBatchMode] = useState('vcf');
   const [batchVcfFiles, setBatchVcfFiles] = useState([]);
   const [batchFastaFiles, setBatchFastaFiles] = useState([]);
+  const [batchJsonFiles, setBatchJsonFiles] = useState([]);
   const [batchReferenceFasta, setBatchReferenceFastaState] = useState(null);
   const [batchSamples, setBatchSamples] = useState([]);
   const [batchSubmitting, setBatchSubmitting] = useState(false);
@@ -188,11 +189,36 @@ export function useBatchManager({
     }
   };
 
+  const addBatchJsonFiles = async (files) => {
+    const toUpload = Array.from(files).slice(0, batchMaxSamples - batchJsonFiles.length);
+    for (const file of toUpload) {
+      try {
+        setUploadProgress({
+          percent: 0,
+          fileName: `BATCH JSON - ${file.name}`,
+        });
+        const response = await apiUpload('/api/upload/json', file, (percent) => {
+          setUploadProgress((prev) => ({
+            ...prev,
+            percent,
+          }));
+        });
+        setUploadProgress((prev) => ({ ...prev, percent: 100 }));
+        setBatchJsonFiles((prev) => [...prev, { uploadId: response.upload_id, name: file.name, size: file.size }]);
+        addUploadedPath(response.upload_id);
+      } catch (error) {
+        setBatchError(formatUserError(error.message));
+      }
+    }
+  };
+
   const removeBatchFile = (index) => {
     if (batchMode === 'vcf') {
       setBatchVcfFiles((prev) => prev.filter((_, i) => i !== index));
-    } else {
+    } else if (batchMode === 'fasta') {
       setBatchFastaFiles((prev) => prev.filter((_, i) => i !== index));
+    } else {
+      setBatchJsonFiles((prev) => prev.filter((_, i) => i !== index));
     }
   };
 
@@ -278,7 +304,7 @@ export function useBatchManager({
   const submitBatch = async () => {
     setBatchError(null);
     setBatchSubmitting(true);
-    const files = batchMode === 'vcf' ? batchVcfFiles : batchFastaFiles;
+    const files = batchMode === 'vcf' ? batchVcfFiles : batchMode === 'fasta' ? batchFastaFiles : batchJsonFiles;
     if (files.length === 0) {
       setBatchError('No files uploaded.');
       setBatchSubmitting(false);
@@ -316,7 +342,7 @@ export function useBatchManager({
           throw new Error(formatUserError(payload.detail || `Request failed: ${response.status}`));
         }
         responseData = await response.json();
-      } else {
+      } else if (batchMode === 'fasta') {
         const sampleNames = batchFastaFiles.map((file) => formatPathStem(file.name));
         const body = {
           fasta_ids: batchFastaFiles.map((f) => f.uploadId),
@@ -335,6 +361,27 @@ export function useBatchManager({
           throw new Error(formatUserError(payload.detail || `Request failed: ${response.status}`));
         }
         responseData = await response.json();
+      } else {
+        // JSON regenerate batch: each results-JSON resolves its own project DB via the
+        // stored fingerprint on the backend, so no shared db_path is sent.
+        const sampleNames = batchJsonFiles.map((file) => formatPathStem(file.name));
+        const body = {
+          json_ids: batchJsonFiles.map((f) => f.uploadId),
+          sample_names: sampleNames,
+          input_display_names: batchJsonFiles.map((f) => f.name),
+          database_id: selectedDatabaseId,
+        };
+        const response = await apiPostRaw('/api/regenerate/batch', body);
+        if (response.status === 429) {
+          setBatchRateLimitCooldown(60);
+          setBatchError(`Rate limit reached. At most ${sampleLimitPerMinute} samples can be analyzed per minute.`);
+          return;
+        }
+        if (!response.ok) {
+          const payload = await response.json().catch(() => ({}));
+          throw new Error(formatUserError(payload.detail || `Request failed: ${response.status}`));
+        }
+        responseData = await response.json();
       }
       const initialSamples = responseData.samples.map((s) => ({
         ...s,
@@ -357,6 +404,7 @@ export function useBatchManager({
   const resetBatch = () => {
     setBatchVcfFiles([]);
     setBatchFastaFiles([]);
+    setBatchJsonFiles([]);
     setBatchReferenceFastaState(null);
     setBatchSamples([]);
     setBatchSubmitting(false);
@@ -389,6 +437,7 @@ export function useBatchManager({
     setBatchMode,
     batchVcfFiles,
     batchFastaFiles,
+    batchJsonFiles,
     batchReferenceFasta,
     batchSamples,
     batchSubmitting,
@@ -405,6 +454,7 @@ export function useBatchManager({
     setBatchVcfCutoffs,
     addBatchVcfFiles,
     addBatchFastaFiles,
+    addBatchJsonFiles,
     addBatchBamFiles,
     attachBatchBam,
     removeBatchBam,
diff --git a/web/frontend/src/hooks/useBatchManager.test.js b/web/frontend/src/hooks/useBatchManager.test.js
index af82c61..dc508f9 100644
--- a/web/frontend/src/hooks/useBatchManager.test.js
+++ b/web/frontend/src/hooks/useBatchManager.test.js
@@ -330,3 +330,138 @@ describe('useBatchManager — batch BAM auto-pairing and per-row override', () =
     });
   });
 });
+
+describe('useBatchManager — JSON regenerate batch', () => {
+  beforeEach(() => {
+    vi.clearAllMocks();
+    global.fetch.mockReset();
+    mockXHRInstances.length = 0;
+  });
+
+  afterEach(() => {
+    vi.restoreAllMocks();
+  });
+
+  // Upload a results-JSON file into the hook via addBatchJsonFiles.
+  async function uploadJson(result, fileName, uploadId) {
+    const file = new File(['{"run":{}}'], fileName, { type: 'application/json' });
+    let promise;
+    await act(async () => {
+      promise = result.current.addBatchJsonFiles([file]);
+      mockXHRInstance.triggerSuccess({ upload_id: uploadId, file_type: 'json', size_bytes: 12 });
+      await promise;
+    });
+  }
+
+  it('addBatchJsonFiles uploads via /api/upload/json and records the file', async () => {
+    const stubs = makeStubs();
+    const { result } = renderHook(() => useBatchManager(stubs));
+
+    await uploadJson(result, 'sample1.results.json', 'up-json-1');
+
+    expect(result.current.batchJsonFiles).toHaveLength(1);
+    expect(result.current.batchJsonFiles[0].uploadId).toBe('up-json-1');
+    expect(result.current.batchJsonFiles[0].name).toBe('sample1.results.json');
+    expect(stubs.addUploadedPath).toHaveBeenCalledWith('up-json-1');
+  });
+
+  it('removeBatchFile drops a JSON row in json mode', async () => {
+    const stubs = makeStubs();
+    const { result } = renderHook(() => useBatchManager(stubs));
+
+    await uploadJson(result, 'sample1.results.json', 'up-json-1');
+    await uploadJson(result, 'sample2.results.json', 'up-json-2');
+    act(() => {
+      result.current.setBatchMode('json');
+    });
+
+    act(() => {
+      result.current.removeBatchFile(0);
+    });
+
+    expect(result.current.batchJsonFiles).toHaveLength(1);
+    expect(result.current.batchJsonFiles[0].name).toBe('sample2.results.json');
+  });
+
+  it('submitBatch JSON branch POSTs /api/regenerate/batch with json_ids and database_id', async () => {
+    const stubs = makeStubs();
+    const { result } = renderHook(() => useBatchManager(stubs));
+
+    await uploadJson(result, 'sample1.results.json', 'up-json-1');
+    await uploadJson(result, 'sample2.results.json', 'up-json-2');
+    act(() => {
+      result.current.setBatchMode('json');
+    });
+
+    let submittedBody;
+    global.fetch.mockImplementation(async (url, options) => {
+      if (options && options.body) {
+        submittedBody = JSON.parse(options.body);
+      }
+      return {
+        ok: true,
+        status: 200,
+        json: async () => ({
+          samples: [
+            { job_id: 'j1', sample_name: 'sample1', status: 'succeeded' },
+            { job_id: 'j2', sample_name: 'sample2', status: 'succeeded' },
+          ],
+          total: 2,
+        }),
+      };
+    });
+
+    await act(async () => {
+      await result.current.submitBatch();
+    });
+
+    await waitFor(() => {
+      expect(global.fetch).toHaveBeenCalled();
+    });
+    expect(submittedBody.json_ids).toEqual(['up-json-1', 'up-json-2']);
+    expect(submittedBody.sample_names).toEqual(['sample1.results', 'sample2.results']);
+    expect(submittedBody.input_display_names).toEqual(['sample1.results.json', 'sample2.results.json']);
+    expect(submittedBody.database_id).toBe('db1');
+    // JSON regenerate has no shared reference or cutoffs.
+    expect(submittedBody.reference_id).toBeUndefined();
+    expect(submittedBody.db_path).toBeUndefined();
+    expect(submittedBody.min_af).toBeUndefined();
+  });
+
+  it('submitBatch JSON branch surfaces a 429 rate limit via batchError', async () => {
+    const stubs = makeStubs();
+    const { result } = renderHook(() => useBatchManager(stubs));
+
+    await uploadJson(result, 'sample1.results.json', 'up-json-1');
+    act(() => {
+      result.current.setBatchMode('json');
+    });
+
+    global.fetch.mockImplementation(async () => ({
+      ok: false,
+      status: 429,
+      json: async () => ({ detail: 'rate limited' }),
+    }));
+
+    await act(async () => {
+      await result.current.submitBatch();
+    });
+
+    await waitFor(() => {
+      expect(result.current.batchError).toMatch(/Rate limit/);
+      expect(result.current.batchRateLimitCooldown).toBe(60);
+    });
+  });
+
+  it('resetBatch clears JSON files', async () => {
+    const stubs = makeStubs();
+    const { result } = renderHook(() => useBatchManager(stubs));
+
+    await uploadJson(result, 'sample1.results.json', 'up-json-1');
+    act(() => {
+      result.current.resetBatch();
+    });
+
+    expect(result.current.batchJsonFiles).toHaveLength(0);
+  });
+});
diff --git a/web/frontend/src/styles.css b/web/frontend/src/styles.css
index dc15ae4..1abc707 100644
--- a/web/frontend/src/styles.css
+++ b/web/frontend/src/styles.css
@@ -31,6 +31,8 @@
   --font-size-caption: var(--font-size-xs);
   --font-size-table: var(--font-size-sm);
   --font-size-button: var(--font-size-sm);
+  --analysis-slider-width: 21.5rem;
+  --analysis-progress-width: 28rem;
   --radius-sm: 6px;
   --radius-md: 10px;
   --radius-lg: 14px;
@@ -56,7 +58,7 @@
   --neutral-border: #d3dde6;
   /* Webapp-only structural tokens (not used by the report) */
   --topbar-logo-width: 380px;
-  --topbar-logo-height: 68px;
+  --topbar-logo-height: 55px;
   --topbar-link-icon-size: 32px;
   --sidebar-width: 118px;
   --sidebar-logo-gap: 5px;
@@ -123,6 +125,7 @@ small {
 
 #root {
   min-height: 100vh;
+  min-height: 100dvh;
   background: transparent;
 }
 
@@ -885,6 +888,7 @@ th {
   margin-left: var(--sidebar-width);
   width: auto;
   min-height: 100vh;
+  min-height: 100dvh;
   padding: 0;
   display: flex;
   flex-direction: column;
@@ -1400,6 +1404,7 @@ th {
 
 .mutation-browser-tile {
   height: calc(100vh - 74px - 0.8rem - 1rem);
+  height: calc(100dvh - 74px - 0.8rem - 1rem);
   grid-template-rows: auto auto 1fr auto;
   overflow: hidden;
 }
@@ -1508,10 +1513,21 @@ th {
   min-width: 0;
 }
 
-.comparison-actions .analyze-primary,
-.comparison-actions .comparison-clear-btn {
-  flex: 0 0 auto;
-  white-space: nowrap;
+.comparison-actions .analyze-primary {
+  flex: 1 1 0;
+  min-width: 0;
+  white-space: normal;
+  text-align: center;
+}
+
+.comparison-actions .comparison-secondary {
+  background-color: var(--neutral-text);
+  border-color: var(--neutral-text);
+}
+
+.comparison-actions .comparison-secondary:hover {
+  background-color: var(--muted-strong);
+  border-color: var(--muted-strong);
 }
 
 .comparison-filters {
@@ -1558,27 +1574,177 @@ th {
 
   .analyze-shell-header h2 {
     grid-column: 1;
+    grid-row: 1;
+  }
+
+  .analyze-shell-header .example-btn {
+    grid-column: 2;
+    grid-row: 1;
+    align-self: center;
+    justify-self: end;
   }
 
   .analyze-shell-header p {
-    grid-column: 1 / -1;
+    grid-column: 1;
+    grid-row: 2;
+  }
+
+  .analyze-submode-progress {
+    grid-column: 2;
+    grid-row: 2;
   }
 
   .analyze-submode-row {
+    grid-column: 1 / -1;
+    grid-row: 3;
+  }
+}
+
+@media (max-width: 820px) {
+  .analyze-shell-header > div:first-child {
+    display: grid;
+    grid-template-columns: minmax(0, 1fr) auto;
+    align-items: center;
+    column-gap: 0.75rem;
+    row-gap: 0.35rem;
+  }
+
+  .analyze-shell-header h2 {
+    grid-column: 1;
+    grid-row: 1;
+  }
+
+  .analyze-shell-header .example-btn {
     grid-column: 2;
     grid-row: 1;
+    align-self: center;
+    height: 2rem;
+  }
+
+  .analyze-shell-header p {
+    grid-column: 1 / -1;
+    grid-row: 2;
   }
 }
 
 .analyze-submode-row {
+  display: flex;
+  align-items: center;
+  gap: 0.75rem;
+  width: 100%;
+}
+
+.analyze-submode-progress {
+  width: var(--analysis-progress-width);
+}
+
+.analyze-submode-progress .upload-progress {
+  width: 100%;
+  min-width: 0;
+  max-width: none;
+  margin: 0;
+}
+
+.analyze-submode-controls {
+  order: 1;
   display: inline-flex;
-  gap: 0.35rem;
   align-items: center;
-  justify-self: end;
-  flex-shrink: 0;
+  gap: 0.75rem;
   flex-wrap: wrap;
 }
 
+/* One/multiple-sample toggle — an animated sliding switch (track + knob). */
+.analyze-submode-switch {
+  position: relative;
+  display: grid;
+  grid-template-columns: repeat(2, minmax(0, 1fr));
+  align-items: center;
+  width: var(--analysis-slider-width);
+  min-width: 0;
+  border: 1px solid var(--accent);
+  border-radius: 999px;
+  background: var(--accent);
+  height: 2rem;
+  padding: 0.14rem;
+  gap: 0;
+  isolation: isolate;
+  box-shadow: inset 0 1px 2px rgb(0 0 0 / 16%);
+}
+
+.analyze-submode-switch-option {
+  position: relative;
+  z-index: 2;
+  display: inline-flex;
+  align-items: center;
+  gap: 0.35rem;
+  border: none;
+  background: transparent;
+  color: var(--on-accent);
+  height: 100%;
+  padding: 0 0.65rem;
+  font-size: var(--font-size-button);
+  font-weight: 700;
+  cursor: pointer;
+  white-space: nowrap;
+  border-radius: 999px;
+  transition: color 0.22s ease, opacity 0.22s ease;
+}
+
+.analyze-submode-switch-option.active {
+  color: var(--accent);
+}
+
+.analyze-submode-switch-option:hover:not(:disabled) {
+  background: transparent;
+}
+
+.analyze-submode-switch-option.active:hover:not(:disabled) {
+  color: var(--accent);
+}
+
+.analyze-submode-switch-option:not(.active):hover:not(:disabled) {
+  color: var(--on-accent);
+  opacity: 0.82;
+}
+
+.analyze-submode-switch-option:focus-visible {
+  outline: 2px solid var(--accent);
+  outline-offset: 2px;
+}
+
+.analyze-submode-switch-option .analyze-submode-icon {
+  opacity: 0.82;
+  transition: opacity 0.22s ease;
+}
+
+.analyze-submode-switch-option.active .analyze-submode-icon {
+  opacity: 1;
+}
+
+.analyze-submode-switch-option:disabled {
+  cursor: not-allowed;
+  opacity: 0.48;
+}
+
+/* The sliding knob sits behind the options and translates to the active side. */
+.analyze-submode-switch-knob {
+  position: absolute;
+  z-index: 1;
+  top: 0.14rem;
+  left: 0.14rem;
+  bottom: 0.14rem;
+  width: calc(50% - 0.14rem);
+  border-radius: 999px;
+  background: var(--surface-strong);
+  box-shadow: 0 2px 5px rgb(0 0 0 / 18%), inset 0 1px rgb(255 255 255 / 72%);
+  transition: transform 0.32s cubic-bezier(0.22, 1, 0.36, 1);
+}
+
+/* When the switch is in the "batch" state, slide the knob to the right half. */
+.analyze-submode-switch[data-state='batch'] .analyze-submode-switch-knob {
+  transform: translateX(100%);
+}
+
 .analyze-regenerate-progress-row {
   display: flex;
   justify-content: flex-end;
@@ -1619,6 +1785,77 @@ th {
   cursor: not-allowed;
 }
 
+.example-btn {
+  display: inline-flex;
+  width: fit-content;
+  height: 2rem;
+  padding: 0 0.72rem;
+}
+
+/* Profile input modes use the same filled-slider language as the workflow switch. */
+.profile-settings-row .database-phenotype-switch {
+  --profile-mode-accent: #7e7f80;
+  position: relative;
+  display: grid;
+  grid-template-columns: repeat(3, minmax(0, 1fr));
+  width: var(--analysis-slider-width);
+  min-width: 0;
+  height: 2rem;
+  gap: 0;
+  padding: 0.14rem;
+  border: 1px solid var(--profile-mode-accent);
+  border-radius: 999px;
+  background: var(--profile-mode-accent);
+  isolation: isolate;
+  box-shadow: inset 0 1px 2px rgb(0 0 0 / 16%);
+}
+
+.profile-settings-row .database-phenotype-switch::before {
+  position: absolute;
+  z-index: 1;
+  top: 0.14rem;
+  bottom: 0.14rem;
+  left: 0.14rem;
+  width: calc((100% - 0.28rem) / 3);
+  border-radius: 999px;
+  background: var(--surface-strong);
+  box-shadow: 0 2px 5px rgb(0 0 0 / 18%), inset 0 1px rgb(255 255 255 / 72%);
+  content: '';
+  transition: transform 0.32s cubic-bezier(0.22, 1, 0.36, 1);
+}
+
+.profile-settings-row .database-phenotype-switch[data-active-mode='fasta']::before {
+  transform: translateX(100%);
+}
+
+.profile-settings-row .database-phenotype-switch[data-active-mode='regenerate']::before,
+.profile-settings-row .database-phenotype-switch[data-active-mode='json']::before {
+  transform: translateX(200%);
+}
+
+.profile-settings-row .database-phenotype-switch button {
+  position: relative;
+  z-index: 2;
+  height: 100%;
+  border: none;
+  border-radius: 999px;
+  background: transparent;
+  color: var(--on-accent);
+  padding: 0 0.55rem;
+}
+
+.profile-settings-row .database-phenotype-switch button.active,
+.profile-settings-row .database-phenotype-switch button.active:hover:not(:disabled) {
+  border-color: transparent;
+  background: transparent;
+  color: var(--profile-mode-accent);
+}
+
+.profile-settings-row .database-phenotype-switch button:hover:not(:disabled) {
+  background: transparent;
+  color: var(--on-accent);
+}
+
 .analyze-submode-icon {
   width: 14px;
   height: 14px;
@@ -1649,17 +1886,43 @@ th {
   .analyze-submode-row {
     width: 100%;
     justify-self: stretch;
+    flex-wrap: wrap;
+  }
+
+  .analyze-submode-progress {
+    width: 100%;
+    margin-left: 0;
+  }
+
+  .analyze-submode-controls {
+    width: 100%;
+    flex-wrap: wrap;
   }
 
   /* Let submode pills shrink and wrap their label instead of overflowing
      past the card edge when "Multiple Sample(s)" doesn't fit on one line. */
-  .analyze-submode-btn {
+  .analyze-submode-btn,
+  .analyze-submode-switch-option {
     flex: 1 1 auto;
     min-width: 0;
     white-space: normal;
     text-align: center;
     justify-content: center;
   }
+
+  .analyze-submode-switch {
+    width: 100%;
+  }
+
+  .profile-settings-row .database-phenotype-switch {
+    min-width: 0;
+    width: 100%;
+  }
+
+  .analyze-submode-switch-option {
+    flex: 1 1 auto;
+    justify-content: center;
+  }
 }
 
 .analyze-status-inline {
@@ -1779,6 +2042,66 @@ th {
   min-width: 0;
 }
 
+/* ── Custom file input styling ─────────────────────────────────────────
+   Replace the browser-default "Choose File" control with a styled
+   drop-zone that matches the app's design tokens. */
+.profile-upload-row input[type="file"],
+.profile-upload-row-batch-files input[type="file"] {
+  display: block;
+  width: 100%;
+  min-height: 2.75rem;
+  padding: 0.3rem 0.5rem;
+  border: 1.5px solid var(--line-strong);
+  border-radius: var(--radius-md);
+  background: var(--paper-soft);
+  color: var(--muted);
+  font-size: var(--font-size-sm);
+  cursor: pointer;
+  transition: border-color 0.15s ease, background 0.15s ease;
+}
+
+.profile-upload-row input[type="file"]:hover,
+.profile-upload-row-batch-files input[type="file"]:hover {
+  border-color: var(--accent);
+  background: var(--accent-tint);
+}
+
+.profile-upload-row input[type="file"]:disabled,
+.profile-upload-row-batch-files input[type="file"]:disabled {
+  opacity: 0.55;
+  cursor: not-allowed;
+  border-style: solid;
+}
+
+.profile-upload-row input[type="file"]::file-selector-button,
+.profile-upload-row-batch-files input[type="file"]::file-selector-button {
+  display: inline-flex;
+  align-items: center;
+  gap: 0.35rem;
+  border: 1px solid var(--accent);
+  border-radius: var(--radius-sm);
+  background: var(--accent);
+  color: var(--on-accent);
+  font-size: var(--font-size-button);
+  font-weight: 700;
+  padding: 0.3rem 0.7rem;
+  margin-right: 0.5rem;
+  cursor: pointer;
+  transition: background 0.15s ease, border-color 0.15s ease;
+}
+
+.profile-upload-row input[type="file"]:hover::file-selector-button,
+.profile-upload-row-batch-files input[type="file"]:hover::file-selector-button {
+  background: var(--accent-hover);
+  border-color: var(--accent-hover);
+}
+
+.profile-upload-row input[type="file"]:disabled::file-selector-button,
+.profile-upload-row-batch-files input[type="file"]:disabled::file-selector-button {
+  cursor: not-allowed;
+  opacity: 1;
+}
+
 .profile-upload-row-batch-files {
   grid-template-columns: minmax(0, 1fr);
 }
@@ -1806,6 +2129,10 @@ th {
   grid-column: 1 / -1;
 }
 
+.database-algorithm-table th {
+  white-space: nowrap;
+}
+
 .database-algorithm-table td {
   vertical-align: top;
 }
@@ -1940,8 +2267,8 @@ th {
   top: 0;
   left: 0;
   width: var(--sidebar-width);
+  height: 100vh;
   height: 100dvh;
-  min-height: 100vh;
   background: linear-gradient(180deg, #142236, #0f1a28);
   border-right: 1px solid #28384e;
   z-index: 30;
@@ -2166,7 +2493,7 @@ th {
   border: none;
   border-radius: 0;
   border-bottom: 1px solid var(--line);
-  padding: 0.15rem 0.7rem;
+  padding: 0.5rem 0.7rem;
   margin-bottom: 0.8rem;
   display: flex;
   align-items: center;
@@ -2187,6 +2514,42 @@ th {
   box-shadow: var(--shadow-sm);
 }
 
+/* Placeholder shown before a report is generated */
+.report-placeholder {
+  display: flex;
+  flex-direction: column;
+  align-items: center;
+  justify-content: center;
+  gap: 1rem;
+  padding: 3rem 1.5rem;
+  margin-block: auto;
+  min-height: 14rem;
+}
+
+.report-placeholder-icon-wrap {
+  display: flex;
+  align-items: center;
+  justify-content: center;
+  width: 96px;
+  height: 96px;
+  border-radius: 50%;
+  background: var(--accent-tint);
+  border: 2px solid var(--accent-soft);
+}
+
+.report-placeholder-icon {
+  width: 44px;
+  height: 44px;
+  opacity: 0.75;
+}
+
+.report-placeholder-text {
+  margin: 0;
+  color: var(--muted);
+  font-size: var(--font-size-md);
+  font-weight: 600;
+}
+
 .workspace-output-header {
   display: flex;
   flex-wrap: wrap;
@@ -2268,25 +2631,21 @@ th.sortable-col {
 }
 
 /* ── Mobile hamburger toggle ──────────────────────────────────────────────
-   Hidden on desktop; revealed inside the ≤768px media block below. The
-   button is fixed top-left so it stays reachable above the top bar. */
+   Hidden on desktop; revealed inside the ≤820px media block below.
+   Sits inside the top bar as a centered, borderless button. */
 .mobile-menu-btn {
   display: none;
-  position: fixed;
-  top: 0.5rem;
-  left: 0.5rem;
-  z-index: 40;
   width: var(--mobile-tap-target);
   height: var(--mobile-tap-target);
-  padding: 0.55rem;
-  border: 1px solid var(--line-strong);
+  padding: 0.7rem;
+  border: none;
   border-radius: var(--radius-md);
-  background: var(--surface-strong);
+  background: transparent;
   color: var(--ink);
   flex-direction: column;
   justify-content: center;
   gap: 5px;
-  box-shadow: var(--shadow-sm);
+  cursor: pointer;
 }
 
 .mobile-menu-bar {
@@ -2308,6 +2667,7 @@ th.sortable-col {
   .sidebar-rail {
     width: var(--sidebar-width);
     height: 100vh;
+    height: 100dvh;
     border-right: 1px solid #28384e;
     border-bottom: none;
   }
@@ -2412,6 +2772,7 @@ th.sortable-col {
 
   .sidebar-rail {
     width: var(--sidebar-width);
+    height: 100vh;
     height: 100dvh;
     transform: translateX(-100%);
     transition: transform 0.22s ease;
@@ -2446,17 +2807,26 @@ th.sortable-col {
     width: 100%;
   }
 
-  /* Add top padding so content clears the fixed hamburger button. */
+  /* Add top padding so content clears the top bar. */
   .top-bar {
     display: grid;
-    grid-template-columns: minmax(0, 1fr) auto;
-    padding-left: calc(var(--mobile-tap-target) + 0.85rem);
+    grid-template-columns: var(--mobile-tap-target) minmax(0, 1fr) auto;
+    align-items: center;
+    padding-left: 0.45rem;
+    padding-right: 0.45rem;
     padding-top: 0.15rem;
     padding-bottom: 0.5rem;
     row-gap: 0.35rem;
     margin-bottom: 0.3rem;
   }
 
+  .mobile-menu-btn {
+    grid-column: 1;
+    grid-row: 1 / span 2;
+    justify-self: start;
+    align-self: center;
+  }
+
   /* ── T3: top bar / brand block fluid on mobile ────────────────────────
      Let the logo scale down rather than clip, and allow the brand block to
      wrap the DB selector / page links onto their own rows. */
@@ -2480,14 +2850,14 @@ th.sortable-col {
   }
 
   .brand-logo-wrap {
-    grid-column: 1;
+    grid-column: 2;
     grid-row: 1;
     margin-left: 0;
     order: initial;
   }
 
   .page-links {
-    grid-column: 2;
+    grid-column: 3;
     grid-row: 1;
     margin-left: auto;
     flex-shrink: 0;
@@ -2495,7 +2865,7 @@ th.sortable-col {
   }
 
   .topbar-db-bar {
-    grid-column: 1 / -1;
+    grid-column: 2 / -1;
     grid-row: 2;
     width: 100%;
     min-width: 0;
@@ -2536,7 +2906,17 @@ th.sortable-col {
     flex-wrap: wrap;
   }
 
-  .analyze-submode-btn {
+  .analyze-submode-progress,
+  .analyze-submode-controls {
+    width: 100%;
+  }
+
+  .analyze-submode-progress {
+    margin-left: 0;
+  }
+
+  .analyze-submode-btn,
+  .analyze-submode-switch-option {
     flex: 1 1 8rem;
     min-width: 0;
     max-width: 100%;
@@ -2545,6 +2925,20 @@ th.sortable-col {
     justify-content: center;
   }
 
+  .analyze-submode-switch {
+    width: 100%;
+    min-width: 0;
+  }
+
+  .profile-settings-row {
+    width: 100%;
+  }
+
+  .profile-settings-row .database-phenotype-switch {
+    width: 100%;
+    min-width: 0;
+  }
+
   .profile-upload-row,
   .profile-upload-row-fasta,
   .profile-upload-row-vcf,
@@ -2705,7 +3099,7 @@ th.sortable-col {
     justify-content: space-between;
     align-items: center;
     flex-wrap: wrap;
-    padding: 0.35rem 0.6rem 0.35rem calc(var(--mobile-tap-target) + 0.85rem);
+    padding: 0.35rem 0.6rem 0.35rem 0.45rem;
   }
 
   .page-links {
@@ -2785,7 +3179,7 @@ th.sortable-col {
 
   /* Ensure tappable controls meet the ≥44px target size on touch devices. */
   .sidebar-rail-link,
-  .analyze-submode-btn,
+  .analyze-submode-btn:not(.example-btn),
   .mutation-download-button,
   .mutation-reset-button,
   .mobile-menu-btn {
@@ -2811,11 +3205,18 @@ th.sortable-col {
   }
 
   .top-bar {
-    padding: 0.15rem 0.45rem 0.15rem calc(var(--mobile-tap-target) + 0.45rem);
+    padding-top: 0.3rem;
+    padding-bottom: 0.3rem;
+    padding-left: 0.65rem;
+    padding-right: 0.65rem;
   }
 
   .panel-stack {
-    padding: 0 0.5rem 0.5rem;
+    padding: 0 0.65rem 0.65rem;
+  }
+
+  .topbar-db-bar .header-db-select {
+    min-width: 90px;
   }
 }
 
@@ -2975,6 +3376,17 @@ th.sortable-col {
   text-align: center;
 }
 
+.results-download-btn {
+  align-self: flex-start;
+  white-space: nowrap;
+  flex-shrink: 0;
+  margin-left: auto;
+}
+
+.full-width-tile > .workspace-output-header:first-child {
+  flex-wrap: nowrap;
+}
+
 .app-footer {
   display: flex;
   justify-content: center;
diff --git a/web/frontend/src/useDashboardLogic.js b/web/frontend/src/useDashboardLogic.js
index 92cfacf..f9eef86 100644
--- a/web/frontend/src/useDashboardLogic.js
+++ b/web/frontend/src/useDashboardLogic.js
@@ -246,6 +246,7 @@ export function useDashboardLogic() {
     setBatchMode: batch.setBatchMode,
     batchVcfFiles: batch.batchVcfFiles,
     batchFastaFiles: batch.batchFastaFiles,
+    batchJsonFiles: batch.batchJsonFiles,
     batchReferenceFasta: batch.batchReferenceFasta,
     batchSamples: batch.batchSamples,
     batchSubmitting: batch.batchSubmitting,
@@ -260,6 +261,7 @@ export function useDashboardLogic() {
     setBatchVcfCutoffs: batch.setBatchVcfCutoffs,
     addBatchVcfFiles: batch.addBatchVcfFiles,
     addBatchFastaFiles: batch.addBatchFastaFiles,
+    addBatchJsonFiles: batch.addBatchJsonFiles,
     addBatchBamFiles: batch.addBatchBamFiles,
     attachBatchBam: batch.attachBatchBam,
     removeBatchFile: batch.removeBatchFile,
