diff --git a/docs/source/dataset.md b/docs/source/dataset.md
index 880436be..47503881 100644
--- a/docs/source/dataset.md
+++ b/docs/source/dataset.md
@@ -168,5 +168,18 @@ win = ds.with_seqs("variant-windows", gvl.VarWindowOpt(...)).with_output_format(
 win.fields["AF"]  # same field, alongside win.fields["start"]/["ilen"]
 ```
 
+Allele fields index per variant, aligned with the scalar fields on the same shared offsets:
+
+```python
+rv = ds.with_seqs("variants")[0, 0]
+
+for pos, alt in zip(rv.start[0][0], rv.alt[0][0]):
+    print(pos, alt)  # 10 b'A'  /  20 b'GG'
+```
+
+This requires **seqpro >= 0.22**. On earlier versions `rv.alt[0][0]` returned the
+haplotype's alleles concatenated into one `bytes`, which misaligns against
+`rv.start` as soon as a window contains an indel.
+
 See the `genvarloader` skill's `.svar2` `var_fields` section for the field-provenance and
 dummy-fill details.
diff --git a/docs/superpowers/plans/2026-07-27-seqpro-0.22-bump.md b/docs/superpowers/plans/2026-07-27-seqpro-0.22-bump.md
new file mode 100644
index 00000000..17157f54
--- /dev/null
+++ b/docs/superpowers/plans/2026-07-27-seqpro-0.22-bump.md
@@ -0,0 +1,509 @@
+# seqpro 0.22.0 Bump Implementation Plan
+
+> **For agentic workers:** REQUIRED SUB-SKILL: Use superpowers:subagent-driven-development (recommended) or superpowers:executing-plans to implement this plan task-by-task. Steps use checkbox (`- [ ]`) syntax for tracking.
+
+**Goal:** Bump seqpro 0.21.1 → 0.22.0 so `RaggedVariants.alt[i]` / `ref[i]` return per-variant alleles instead of one concatenated `bytes` per haplotype, closing [#330](https://github.com/mcvickerlab/GenVarLoader/issues/330).
+
+**Architecture:** Pure dependency bump. The defect and its fix are entirely upstream in `seqpro.rag.Ragged.__getitem__` ([ML4GLand/SeqPro#71](https://github.com/ML4GLand/SeqPro/issues/71)). gvl changes two version pins, regenerates the lock, adds the regression test whose absence let the bug ship, and documents the new access pattern. No gvl source change is expected — Task 2 exists to prove that rather than assume it.
+
+**Tech Stack:** Python 3.10, pixi (envs/deps), maturin (Rust+Python build), pytest, commitizen (versioning), seqpro 0.22.0.
+
+**Spec:** `docs/superpowers/specs/2026-07-27-seqpro-0.22-bump-design.md`
+
+## Global Constraints
+
+- **Branch:** `worktree-deps+seqpro-0.22`, already created off `origin/main`. PR targets `main`, **not** `streaming`.
+- **seqpro floor:** `seqpro>=0.22` in `pyproject.toml`; `seqpro = "==0.22.0"` in `pixi.toml`.
+- **`Cargo.toml` is not touched.** `seqpro-core = "0.1"` stays. The 0.22.0 release diff (`0.21.2...0.22.0`) changed only `python/seqpro/rag/_core.py` plus tests, docs, `pyproject.toml`, and `CHANGELOG.md` — no Rust.
+- **Breaking-change framing:** the pin-bump commit is `fix!:` with a `BREAKING CHANGE:` footer. `pyproject.toml` sets `major_version_zero = true`, so commitizen cuts **0.40.2 → 0.41.0** (not 1.0.0). Do not run `cz bump` — CI/release does that.
+- **Do not run `pixi run -e dev test` from the repo root of the main checkout.** All commands run from the worktree directory `/carter/users/dlaub/projects/GenVarLoader/.claude/worktrees/deps+seqpro-0.22`.
+- **Subagent file-edit note:** implementer subagents cannot use the Write/Edit tools inside this worktree (isolation guard). Make edits via Bash (`python - <<'EOF'`, `cat >`, etc.) and commit with plain `git`.
+- **Never** `git stash` / `git stash pop` bare — the stash stack is shared across worktrees. Use a WIP commit instead.
+
+## Environment (already set up — verify, don't rebuild)
+
+The worktree carries a working `dev` env: `.pixi/envs/dev` with **seqpro 0.21.1**, an editable `genvarloader.pth` pointing at this worktree's `python/`, and a compiled `python/genvarloader/genvarloader.abi3.so`.
+
+This matters for Task 1: the "red" step needs the env **still at 0.21.1**. Do not run `pixi install` before Task 1 Step 2.
+
+Verify before starting:
+
+```bash
+cd /carter/users/dlaub/projects/GenVarLoader/.claude/worktrees/deps+seqpro-0.22
+ls .pixi/envs/dev/lib/python3.10/site-packages/seqpro-*.dist-info   # expect seqpro-0.21.1.dist-info
+ls python/genvarloader/genvarloader.abi3.so                          # expect the file to exist
+```
+
+If the `.so` is missing, rebuild it cheaply by sharing the main checkout's cargo target dir:
+
+```bash
+CARGO_TARGET_DIR=/carter/users/dlaub/projects/GenVarLoader/target \
+  pixi run -e dev maturin develop --release
+```
+
+## File Structure
+
+| File | Change | Responsibility |
+|---|---|---|
+| `tests/unit/dataset/test_ragged_variants_indexing.py` | **create** | Regression test: allele fields index per-variant, aligned with `start`/`ilen`. The gate for #330. |
+| `pyproject.toml` | modify line 13 | Dependency floor for downstream users. |
+| `pixi.toml` | modify line 104 | Exact pin for the `py310` feature (backs `dev`, `default`, `py310`, `no-torch`, `notebook`, `splice`). |
+| `pixi.lock` | regenerate | Resolved versions for every environment. |
+| `skills/genvarloader/SKILL.md` | modify (~line 373 block, + Common gotchas) | Agent-facing reference for `RaggedVariants` access. |
+| `docs/source/dataset.md` | modify (`## Variant fields (var_fields)` section, ~line 145-172) | User-facing prose for reading variants. |
+
+`docs/source/api.md` is **not** touched — no symbol enters or leaves `__all__`.
+
+## Task Dependencies
+
+```
+Task 1 (test + bump)  ──┬──> Task 2 (whole-tree verification)  ──> Task 4 (PR)
+                        └──> Task 3 (docs)                     ──┘
+```
+
+**Tasks 2 and 3 are independent and may run in parallel** (Task 2 touches source + reports; Task 3 touches only docs). Use superpowers:dispatching-parallel-agents for them. If Task 2 uncovers fallout that changes user-visible behavior, re-open Task 3 to match.
+
+---
+
+### Task 1: Regression test + dependency bump
+
+The red/green cycle is the whole point: the test must be **seen failing on 0.21.1** before the bump, which is what proves it actually gates the fix (spec success criterion 3). The existing suite never caught #330 because `tests/unit/dataset/test_flat_variants_type.py` asserts via `.to_ak().to_list()`, which is structure-preserving and therefore blind to the `__getitem__` bug.
+
+**Files:**
+- Create: `tests/unit/dataset/test_ragged_variants_indexing.py`
+- Modify: `pyproject.toml:13`
+- Modify: `pixi.toml:104`
+- Regenerate: `pixi.lock`
+
+**Interfaces:**
+- Consumes: `genvarloader.RaggedVariants`; `seqpro.rag.Ragged.from_offsets(data, shape, offsets, str_offsets=...)` and `.to_strings()`.
+- Produces: nothing later tasks import. Task 3 documents the behavior this task locks in.
+
+- [ ] **Step 1: Write the failing test**
+
+Create `tests/unit/dataset/test_ragged_variants_indexing.py`:
+
+```python
+"""Integer indexing into RaggedVariants allele fields is per-variant.
+
+Regression test for #330 / ML4GLand/SeqPro#71: on seqpro <= 0.21.2, indexing a
+string-under-axis Ragged concatenated the whole group into one bytes object,
+discarding the per-variant boundaries that str_offsets already held. Numeric
+fields on the same shared offsets stayed per-variant, so alt/ref silently
+disagreed in length with start/ilen.
+
+The multi-byte allele below is load-bearing. With SNPs only every allele is one
+byte, the counts coincide, and this test passes on the buggy seqpro too --
+gating nothing.
+"""
+
+from __future__ import annotations
+
+import numpy as np
+from seqpro.rag import Ragged
+
+from genvarloader import RaggedVariants
+
+
+def _build_rv() -> RaggedVariants:
+    """(1, 2, ~v): hap 0 holds 2 variants (alt 'A', 'GG'), hap 1 holds 1 ('TC')."""
+    alt_chars = np.frombuffer(b"AGGTC", dtype="S1")
+    var_off = np.array([0, 2, 3], dtype=np.int64)  # hap -> variant index
+    str_off = np.array([0, 1, 3, 5], dtype=np.int64)  # variant -> byte index
+
+    alt = Ragged.from_offsets(
+        alt_chars, (1, 2, None), var_off, str_offsets=str_off
+    ).to_strings()
+    start = Ragged.from_offsets(
+        np.array([10, 20, 30], dtype=np.int32), (1, 2, None), var_off
+    )
+    ilen = Ragged.from_offsets(
+        np.array([0, 1, 1], dtype=np.int32), (1, 2, None), var_off
+    )
+    return RaggedVariants(alt=alt, start=start, ilen=ilen)
+
+
+def test_alt_indexes_per_variant_not_concatenated():
+    """alt[0][hap] yields one entry per variant, not one concatenated blob."""
+    rv = _build_rv()
+
+    assert list(rv.alt[0][0]) == [b"A", b"GG"]
+    assert list(rv.alt[0][1]) == [b"TC"]
+
+
+def test_alt_count_matches_scalar_fields():
+    """alt, start and ilen share one offsets object, so their per-hap counts agree."""
+    rv = _build_rv()
+
+    for hap, expected_n in ((0, 2), (1, 1)):
+        assert len(rv.alt[0][hap]) == expected_n
+        assert len(np.asarray(rv.start[0][hap])) == expected_n
+        assert len(np.asarray(rv.ilen[0][hap])) == expected_n
+
+
+def test_alt_aligns_elementwise_with_start():
+    """The obvious consumer pattern -- zip(start, alt) -- is correct."""
+    rv = _build_rv()
+
+    pairs = list(zip(np.asarray(rv.start[0][0]).tolist(), rv.alt[0][0]))
+
+    assert pairs == [(10, b"A"), (20, b"GG")]
+```
+
+**Why this idiom.** seqpro 0.22.0's own regression tests for #71
+(`tests/test_ragged_core.py::test_string_under_axis_index_preserves_boundaries` and
+`::test_string_under_axis_index_multidim`) establish that peeling a group returns a
+`Ragged` on which `len()` works and iteration yields `bytes` — `list(s[1]) == [b"TC"]`,
+`len(s[i]) == int(s.lengths[i])`. The multidim test uses exactly this `(b, p, ~v)` →
+`rag[0]` → `row[hap]` chain. Do not add a `bytes(...)` conversion around the iterated
+elements; they are already `bytes`.
+
+- [ ] **Step 2: Run the test and verify it FAILS on seqpro 0.21.1**
+
+```bash
+pixi run -e dev pytest tests/unit/dataset/test_ragged_variants_indexing.py -v
+```
+
+Expected: **all three tests FAIL.** On 0.21.1, `rv.alt[0][0]` returns the concatenated
+`b"AGG"` instead of a `Ragged` of two alleles, so:
+
+- `list(rv.alt[0][0])` is `[65, 71, 71]` — iterating a `bytes` object yields **ints**, not
+  `bytes` — against the expected `[b"A", b"GG"]`
+- `len(rv.alt[0][0])` is `3` (bytes) against the expected `2` (variants)
+
+**This failure is the evidence for spec success criterion 3. Record the actual failure output in the task report** — a plan step that says "expect it to fail" is not evidence; the pasted output is.
+
+If the tests *pass* here, stop and report. It means the env is not on 0.21.1, and the test is not gating anything.
+
+- [ ] **Step 3: Bump the two pins**
+
+`pyproject.toml` line 13, inside the `dependencies` list:
+
+```diff
+-    "seqpro>=0.20",
++    "seqpro>=0.22",
+```
+
+`pixi.toml` line 104, inside `[feature.py310.pypi-dependencies]`:
+
+```diff
+-seqpro = "==0.21.1"
++seqpro = "==0.22.0"
+```
+
+Leave `Cargo.toml` alone.
+
+- [ ] **Step 4: Regenerate the lock and install**
+
+```bash
+pixi install -e dev
+```
+
+This re-solves and rewrites `pixi.lock`. Confirm the new version actually landed:
+
+```bash
+grep -o "seqpro-[0-9.]*" pixi.lock | sort -u
+ls .pixi/envs/dev/lib/python3.10/site-packages/seqpro-*.dist-info
+```
+
+Expected: `seqpro-0.22.0` and no `0.21.1` remaining.
+
+- [ ] **Step 5: Run the test and verify it PASSES**
+
+```bash
+pixi run -e dev pytest tests/unit/dataset/test_ragged_variants_indexing.py -v
+```
+
+Expected: **3 passed.**
+
+- [ ] **Step 6: Lint the new test file**
+
+```bash
+pixi run -e dev ruff check tests/unit/dataset/test_ragged_variants_indexing.py
+pixi run -e dev ruff format tests/unit/dataset/test_ragged_variants_indexing.py
+```
+
+- [ ] **Step 7: Commit**
+
+```bash
+git add tests/unit/dataset/test_ragged_variants_indexing.py pyproject.toml pixi.toml pixi.lock
+git commit -F - <<'EOF'
+fix!: seqpro>=0.22 for per-variant allele indexing (#330)
+
+RaggedVariants.alt[i]/ref[i] returned one concatenated bytes per
+haplotype while start/ilen returned per-variant values, because
+seqpro's Ragged.__getitem__ mapped a string-under-axis group straight
+to a byte range and dropped the interior str_offsets. zip(start, alt)
+was silently wrong -- and invisible for SNP-only data, since 1-byte
+alleles make the counts coincide.
+
+Fixed upstream in seqpro 0.22.0 (ML4GLand/SeqPro#71): integer indexing
+on a string-under-axis Ragged now returns a Ragged of strings.
+
+Bumps the pyproject floor to >=0.22 and the pixi py310 pin to ==0.22.0.
+Cargo.toml is untouched -- the 0.22.0 diff changed no Rust. Raising the
+floor also removes a latent skew: py311-313 declare no seqpro pin and
+inherit the floor, so a lock refresh under >=0.20 would have floated
+them to 0.22 while py310 stayed at 0.21.
+
+Adds the regression test whose absence let this ship: the existing
+suite asserts via to_ak().to_list(), which is structure-preserving and
+blind to the bug. The new test uses a multi-byte allele, without which
+it would pass on the buggy version too.
+
+BREAKING CHANGE: indexing a RaggedVariants allele field by integer
+(rv.alt[b][h], rv.ref[b][h]) now yields per-variant alleles instead of
+one concatenated bytes object. Callers relying on the concatenated
+value can recover it with b"".join(...). Requires seqpro>=0.22.
+
+Closes #330
+
+Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
+EOF
+```
+
+---
+
+### Task 2: Whole-tree verification and fallout audit
+
+Proves the bump is safe. The spec predicts no gvl source change is needed, but predictions are not evidence.
+
+**Files:**
+- Read: `python/genvarloader/_shm_layout.py`, `python/genvarloader/_dataset/_query.py`, `python/genvarloader/_dataset/_tracks.py`, `python/genvarloader/_dataset/_svar2_haps.py`, `python/genvarloader/_dataset/_flat_variants.py`, `python/genvarloader/_dataset/_rag_variants.py`
+- Modify: only if the suite surfaces a real break.
+
+**Interfaces:**
+- Consumes: the bumped env from Task 1.
+- Produces: a verification report. No new symbols.
+
+- [ ] **Step 1: Generate test data if absent**
+
+```bash
+pixi run -e dev gen
+```
+
+Skip if `tests/data` is already populated from a previous run.
+
+- [ ] **Step 2: Run the whole tree**
+
+Per CLAUDE.md, run the **entire** tree — not `tests/dataset` alone. A scoped run skips `tests/unit/`, which is exactly where the new test lives.
+
+```bash
+pixi run -e dev pytest tests -q 2>&1 | tail -40
+```
+
+Expected: all pass. This takes a while; run it to completion rather than backgrounding it and moving on.
+
+- [ ] **Step 3: Run the Rust tests**
+
+```bash
+LD_LIBRARY_PATH=$PWD/.pixi/envs/dev/lib:$LD_LIBRARY_PATH cargo test --release 2>&1 | tail -20
+```
+
+The `LD_LIBRARY_PATH` prefix is required — without it the test binary cannot load `libpython`.
+
+Expected: all pass. Nothing in this change touches Rust, so a failure here means something unrelated is broken; report it, do not "fix" it into this branch.
+
+- [ ] **Step 4: Audit the six string-Ragged consumers**
+
+Read each site and confirm it only **constructs** string Raggeds (`Ragged.from_offsets(..., str_offsets=...)` → `.to_strings()`) or accesses fields **by name** (`rv[fname]`, `f._rl.str_offsets`). Neither path changed in 0.22.0. Integer indexing of a string field is the only changed behavior.
+
+```bash
+grep -n "to_chars\|str_offsets\|to_strings" \
+  python/genvarloader/_shm_layout.py \
+  python/genvarloader/_dataset/_query.py \
+  python/genvarloader/_dataset/_tracks.py \
+  python/genvarloader/_dataset/_svar2_haps.py \
+  python/genvarloader/_dataset/_flat_variants.py \
+  python/genvarloader/_dataset/_rag_variants.py
+```
+
+Pay particular attention to `_shm_layout.py` (lines ~174, 192-193, 695, 746): it decomposes allele fields into `outer_offsets` / `inner_offsets` / `leaf_data` for the `double_buffered` loader's shared-memory transport and rebuilds them with `to_strings()`. It is the most intricate consumer and the likeliest place for a representation change to bite.
+
+- [ ] **Step 5: Typecheck and lint**
+
+```bash
+pixi run -e dev typecheck
+pixi run -e dev ruff check python/ tests/
+```
+
+Cover `python/` **and** `tests/` — `python/` alone misses test-only issues.
+
+- [ ] **Step 6: Commit only if something needed fixing**
+
+If Steps 2-5 were clean, there is nothing to commit; record that in the task report and move on. Do **not** manufacture a commit.
+
+If a real break surfaced:
+
+```bash
+git add <the files you actually changed>
+git commit -m "fix: <specific description of what broke under seqpro 0.22 and why this fixes it>"
+```
+
+---
+
+### Task 3: Documentation
+
+A user-visible behavior change, so CLAUDE.md's docs-audit gate applies. Nothing currently in the docs is *false* — no prose demonstrates integer allele indexing — so this work is additive.
+
+**Files:**
+- Modify: `skills/genvarloader/SKILL.md`
+- Modify: `docs/source/dataset.md`
+
+**Interfaces:**
+- Consumes: the behavior Task 1 locked in.
+- Produces: nothing importable.
+
+- [ ] **Step 1: Update SKILL.md's `RaggedVariants` reference block**
+
+Find the bullet beginning ``- `gvl.Ragged`, `gvl.RaggedAnnotatedHaps`, `gvl.RaggedVariants`, `gvl.RaggedIntervals``` (around line 373). It already documents structural behavior, including "An int index collapses the leading axis (numpy-consistent); slice/array indexing preserves it."
+
+Immediately after that sentence, add:
+
+```markdown
+Indexing an **allele** field (`rv.alt[b][h]`, `rv.ref[b][h]`) yields the alleles of that haplotype **per variant**, aligned one-for-one with `rv.start[b][h]` / `rv.ilen[b][h]`, so `zip(rv.start[b][h], rv.alt[b][h])` pairs each position with its own allele. This requires **seqpro >= 0.22**; on older seqpro the same expression returned every allele of the group concatenated into a single `bytes`, which silently misaligned against the scalar fields for any group containing a multi-byte (indel) allele.
+```
+
+- [ ] **Step 2: Add a Common gotchas entry to SKILL.md**
+
+In the "Common gotchas" list (near the existing entries about `dosage` and flank tokens, around lines 447-453), add:
+
+```markdown
+- **Allele fields index per-variant, and need `seqpro>=0.22`.** `rv.alt[b][h]` gives one allele per variant, matching `rv.start[b][h]`. On seqpro `<0.22` it returned the group's alleles concatenated as one `bytes` — a mismatch that is invisible for SNP-only data (every allele is 1 byte, so the counts coincide) and only appears once an indel is in the window. gvl requires `seqpro>=0.22`; if you see a concatenated blob, check the installed seqpro version first.
+```
+
+- [ ] **Step 3: Add the reading example to `docs/source/dataset.md`**
+
+In the `## Variant fields (var_fields)` section, after the existing fenced example that ends with `win.fields["AF"]  # same field, alongside win.fields["start"]/["ilen"]`, add:
+
+````markdown
+Allele fields index per variant, aligned with the scalar fields on the same shared offsets:
+
+```python
+rv = ds.with_seqs("variants")[0, 0]
+
+for pos, alt in zip(rv.start[0][0], rv.alt[0][0]):
+    print(pos, alt)  # 10 b'A'  /  20 b'GG'
+```
+
+This requires **seqpro >= 0.22**. On earlier versions `rv.alt[0][0]` returned the
+haplotype's alleles concatenated into one `bytes`, which misaligns against
+`rv.start` as soon as a window contains an indel.
+````
+
+- [ ] **Step 4: Verify the docs build**
+
+```bash
+pixi run -e docs doc 2>&1 | tail -20
+```
+
+Expected: builds without new warnings. If the `docs` env is not built and building it is slow, it is acceptable to skip this step and note the skip in the task report — the edits are prose-only, in files Sphinx already renders.
+
+- [ ] **Step 5: Confirm `api.md` needs no change**
+
+```bash
+pixi run -e dev python -c "import re,genvarloader as g; api=open('docs/source/api.md').read(); print('MISSING:', [n for n in g.__all__ if n not in api] or 'none')"
+```
+
+Expected: `MISSING: none`. This change adds no public symbol; the check guards against drift.
+
+- [ ] **Step 6: Commit**
+
+```bash
+git add skills/genvarloader/SKILL.md docs/source/dataset.md
+git commit -F - <<'EOF'
+docs: per-variant allele indexing on RaggedVariants (#330)
+
+Documents that rv.alt[b][h] / rv.ref[b][h] yield one allele per
+variant, aligned with rv.start / rv.ilen, and that this requires
+seqpro >= 0.22. Adds a Common gotchas entry noting the old
+concatenating behavior was invisible for SNP-only data.
+
+Additive only -- no existing prose demonstrated integer allele
+indexing, so nothing was false before this.
+
+Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
+EOF
+```
+
+---
+
+### Task 4: Push and open the PR
+
+**Files:** none — git/GitHub operations only.
+
+**Interfaces:**
+- Consumes: commits from Tasks 1-3.
+- Produces: the PR that closes #330.
+
+- [ ] **Step 1: Confirm the branch is clean and complete**
+
+```bash
+git status --short          # expect empty
+git log --oneline origin/main..HEAD
+```
+
+Expected: the spec commit (`fcbc08fa`), Task 1's `fix!:` commit, Task 3's `docs:` commit, and Task 2's fix commit only if something genuinely broke.
+
+- [ ] **Step 2: Verify the breaking-change footer is machine-readable**
+
+```bash
+pixi run -e dev cz check --rev-range origin/main..HEAD
+```
+
+Expected: passes. commitizen must see the `BREAKING CHANGE:` footer for the 0.41.0 minor bump; a malformed footer silently degrades it to a patch.
+
+- [ ] **Step 3: Push**
+
+```bash
+git push -u origin worktree-deps+seqpro-0.22
+```
+
+- [ ] **Step 4: Open the draft PR**
+
+```bash
+gh pr create --draft --base main \
+  --title 'fix!: bump seqpro to 0.22.0 for per-variant allele indexing (#330)' \
+  --body "$(cat <<'EOF'
+Closes #330. Upstream fix: ML4GLand/SeqPro#71, released in seqpro 0.22.0.
+
+## What was wrong
+
+`RaggedVariants.alt[i]` / `ref[i]` returned one concatenated `bytes` per haplotype while `start` / `ilen` returned per-variant values, even though all four fields share one offsets object. `zip(rv.start[0][h], rv.alt[0][h])` was silently wrong — and invisible for SNP-only data, because 1-byte alleles make the counts coincide. It only misbehaved once an indel entered the window.
+
+Root cause was upstream: seqpro's `Ragged.__getitem__` mapped a string-under-axis group straight to a byte range and discarded the interior `str_offsets`.
+
+## Changes
+
+- `pyproject.toml`: `seqpro>=0.20` → `seqpro>=0.22`
+- `pixi.toml`: py310 pin `==0.21.1` → `==0.22.0`
+- `pixi.lock` regenerated
+- New regression test using a **multi-byte allele** — the existing suite asserts via `to_ak().to_list()`, which is structure-preserving and was blind to this
+- SKILL.md + `docs/source/dataset.md` document per-variant allele access and the `seqpro>=0.22` requirement
+
+`Cargo.toml` is untouched: the 0.22.0 diff changed no Rust, so `seqpro-core` needs no bump.
+
+Raising the floor also closes a latent skew — `py311`/`312`/`313` declare no seqpro pin and inherit the floor, so a lock refresh under `>=0.20` would have floated them to 0.22 while py310 stayed pinned at 0.21.
+
+## Breaking
+
+Indexing an allele field by integer now yields per-variant alleles instead of one concatenated `bytes`. Callers wanting the old value can use `b"".join(...)`. `major_version_zero = true`, so this cuts 0.40.2 → **0.41.0**.
+
+## Not included
+
+Targets `main`, not `streaming` — the defect is in the shared `RaggedVariants` read path the written `Dataset` returns too. `streaming` inherits the fix on its next routine `main` merge.
+
+🤖 Generated with [Claude Code](https://claude.com/claude-code)
+EOF
+)"
+```
+
+- [ ] **Step 5: Report the PR URL**
+
+---
+
+## Notes for the implementer
+
+- **The multi-byte allele in the regression test is not decoration.** Replacing `b"GG"` with a SNP makes every assertion pass on the broken seqpro too. If you refactor the fixture, keep at least one allele longer than one byte.
+- **Do not "fix" the old behavior in gvl.** The fix is upstream and already released. If something in gvl looks like it is compensating for the old concatenation, report it rather than removing it — it may be load-bearing for a different reason.
+- **Task 2 finding nothing is a successful outcome**, not an empty task. Report the evidence (test counts, the six audited sites) rather than inventing a change to justify the task.
diff --git a/docs/superpowers/specs/2026-07-27-seqpro-0.22-bump-design.md b/docs/superpowers/specs/2026-07-27-seqpro-0.22-bump-design.md
new file mode 100644
index 00000000..cf938449
--- /dev/null
+++ b/docs/superpowers/specs/2026-07-27-seqpro-0.22-bump-design.md
@@ -0,0 +1,160 @@
+# Design: bump seqpro to 0.22.0 (per-variant allele indexing)
+
+**Status:** ✅ approved — 2026-07-27
+**Issue:** [#330](https://github.com/mcvickerlab/GenVarLoader/issues/330)
+**Upstream:** [ML4GLand/SeqPro#71](https://github.com/ML4GLand/SeqPro/issues/71) (closed 2026-07-27, released in seqpro 0.22.0)
+**Branch:** off `main`, PR into `main`
+
+## Problem
+
+On seqpro ≤ 0.21.2, integer-indexing a **string-under-axis** `Ragged` collapsed a whole
+group into one concatenated `bytes`, discarding the per-string boundaries that
+`str_offsets` already held. Numeric fields sharing the same offsets returned one element
+per item, so the two were not shape-consistent:
+
+```python
+rv.start[0][h]  # -> array([10, 20], dtype=int32)   2 elements, per-variant
+rv.ilen[0][h]   # -> array([0, 1], dtype=int32)     2 elements, per-variant
+rv.alt[0][h]    # -> b'AGG'                          ONE bytes: 'A'+'GG' or 'AG'+'G'?
+```
+
+This surfaces through gvl's public API on `RaggedVariants`, where `alt`, `ref`, `start`,
+and `ilen` are all built on one shared offsets object (`_share_offsets`,
+`_dataset/_rag_variants.py`). The obvious consumer pattern
+`zip(rv.start[0][h], rv.alt[0][h])` was silently wrong — and **invisible for SNP-only
+data**, because 1-byte alleles make the lengths coincide. It only misbehaves once an indel
+appears.
+
+seqpro 0.22.0 fixes it upstream: integer indexing on a string-under-axis `Ragged` now
+returns a `Ragged` of strings, and peeling a record row returns opaque-string fields as a
+`Ragged` of strings rather than a concatenated `S1` array.
+
+## Scope
+
+Bump the dependency, confirm no fallout, lock the fixed behavior with a gvl-level
+regression test, and document the requirement.
+
+**Off `main`, not `streaming`.** The defect is in `RaggedVariants`, which the *written*
+`Dataset` read path returns too — `with_seqs("variants")` is not streaming-only. The
+`streaming` branch inherits the fix on its next routine `main` merge; no separate
+streaming work.
+
+## Changes
+
+### 1. Pins
+
+| File | Line | From | To |
+|---|---|---|---|
+| `pyproject.toml` | 13 | `"seqpro>=0.20"` | `"seqpro>=0.22"` |
+| `pixi.toml` | 104 (`[feature.py310.pypi-dependencies]`) | `seqpro = "==0.21.1"` | `seqpro = "==0.22.0"` |
+| `Cargo.toml` | 21 | `seqpro-core = "0.1"` | **unchanged** |
+
+Then regenerate `pixi.lock`.
+
+**`Cargo.toml` stays put.** The 0.22.0 release diff (`0.21.2...0.22.0`) touches only
+`python/seqpro/rag/_core.py` plus tests, docs, `pyproject.toml`, and `CHANGELOG.md`. No
+Rust changed, so the `seqpro-core` crate needs no bump.
+
+**The floor must move to `>=0.22`.** gvl's public allele-access behavior — and the
+regression test below — only hold on ≥ 0.22. A user whose resolver picked 0.21 would
+silently get the concatenating behavior back with no error.
+
+Raising the floor also closes a latent inconsistency. The `py310` feature backs the `dev`,
+`default`, `py310`, `no-torch`, `notebook`, and `splice` environments and hard-pins seqpro;
+`py311`, `py312`, and `py313` declare no seqpro pin at all and inherit the `pyproject.toml`
+floor. `pixi.lock` currently holds every environment at 0.21.1, but a lock refresh under
+the old `>=0.20` floor would float py311-313 to 0.22 while py310 stayed at 0.21 — two
+different allele semantics in one CI matrix.
+
+Compatibility is already satisfied: seqpro 0.22.0 requires `python>=3.10`,
+`numpy>=1.26.0`, and `numba>=0.58.1`, against the existing py310 pins of `python 3.10.*`,
+`numpy 1.26.*`, and `numba ==0.59.1`.
+
+### 2. Verification
+
+Run the **whole** tree — `pixi run -e dev test` (full pytest tree + `cargo test`), per
+CLAUDE.md, not a scoped `tests/dataset` run. This is the real blast-radius measurement.
+
+Alongside it, read the six modules that touch string-`Ragged` internals:
+
+- `_shm_layout.py` (lines 174, 192-193, 695, 746)
+- `_dataset/_query.py` (380-386)
+- `_dataset/_tracks.py` (133)
+- `_dataset/_svar2_haps.py` (992, 1031)
+- `_dataset/_flat_variants.py` (101, 119)
+- `_dataset/_rag_variants.py`
+
+Static inspection says all six only **construct** string Raggeds
+(`Ragged.from_offsets(..., str_offsets=...)` → `.to_strings()`) or access fields **by
+name** (`rv[fname]`, `f._rl.str_offsets`). Neither path changed in 0.22.0, so this is
+expected to come back clean — but it must be confirmed, not assumed. `_shm_layout.py` is
+the one to watch: it round-trips allele fields through shared memory for the
+`double_buffered` loader, decomposing them into `outer_offsets` / `inner_offsets` /
+`leaf_data` and rebuilding via `to_strings()`.
+
+If the suite does surface fallout, fix it in this branch; the fix is in scope.
+
+### 3. Regression test
+
+The suite currently contains **no** test that integer-indexes an allele field. That gap is
+exactly why #330 went unnoticed, so closing it is part of the fix rather than a nicety.
+
+Add a test in `tests/unit/dataset/` (beside `test_flat_variants_type.py`) that builds a
+`RaggedVariants` whose group holds a **multi-byte allele** — e.g. alts `b"A"` and `b"GG"`
+against starts `[10, 20]` — and asserts per-variant alignment:
+
+- indexing the allele field for a haplotype yields **two** alleles, matching the two
+  entries `start`/`ilen` yield for that same haplotype
+- those alleles equal `b"A"` and `b"GG"` respectively
+
+The exact accessor and comparison form are settled during implementation against the real
+0.22.0 return type (a `Ragged` of strings, whose element access this spec deliberately does
+not guess at). What the test must pin down is the *alignment property*, not a particular
+call.
+
+The multi-byte allele is the entire point. With SNPs only, every allele is 1 byte, the
+counts coincide, and the test passes on both 0.21 and 0.22 — gating nothing.
+
+### 4. Docs
+
+A user-visible behavior change, so CLAUDE.md's docs-audit gate applies.
+
+Nothing in the current docs is *false*: no prose demonstrates integer allele indexing, and
+`docs/source/dataset.md:164-165` shows only field access (`rv["AF"]`). The work is
+therefore additive — a short "reading variants per-variant" note in
+`skills/genvarloader/SKILL.md` and in `docs/source/dataset.md` beside that existing
+example, showing per-variant allele access and stating the `seqpro>=0.22` requirement.
+
+`docs/source/api.md` is unchanged — no symbol is added to or removed from `__all__`.
+
+### 5. Versioning and close-out
+
+Land as a conventional commit `fix!:` with a `BREAKING CHANGE:` footer, so commitizen cuts
+**0.40.2 → 0.41.0**.
+
+`RaggedVariants.alt[i]` / `ref[i]` change observable return type for gvl users, which is
+breaking regardless of arriving via a dependency. The counter-argument — that it is "just a
+dep bump" of behavior nobody could sensibly rely on — was considered and rejected: silent
+type changes in a public return value are exactly what a major/minor signal exists for.
+
+The PR closes #330 and references SeqPro#71.
+
+## Out of scope
+
+- **#328** (`var_fields` ride-alongs for `variant-windows`) and **#329** (SVAR1 per-call
+  FORMAT copy) — the other two Wave B follow-ups. Streaming-board work, unrelated to this
+  bump.
+- Any change to `Cargo.toml` / `seqpro-core`.
+- Adding seqpro pins to the `py311`/`py312`/`py313` features. Raising the shared floor is
+  sufficient; per-feature pins would duplicate the constraint in four places.
+
+## Success criteria
+
+1. `pixi.lock` resolves seqpro 0.22.0 in every environment.
+2. Full `pixi run -e dev test` green (pytest tree + cargo).
+3. The new regression test passes on 0.22.0, and is confirmed **once** during
+   implementation to fail on 0.21.1 — otherwise it does not actually gate the fix. (It is
+   not kept runnable against 0.21.1 after the floor moves.)
+4. SKILL.md and `docs/source/dataset.md` document per-variant allele access and the
+   `seqpro>=0.22` requirement.
+5. PR into `main` closes #330.
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   - loguru
   - natsort
@@ -12459,25 +12459,6 @@ packages:
   requires_dist:
   - numpy>=1.21.3
   requires_python: '>=3.10'
-- pypi: https://files.pythonhosted.org/packages/1e/51/f2d40a7ba9477f97cab5e1d06338c7f5f97f76479d1443ff4c6b5048e2bc/seqpro-0.21.1-cp39-abi3-macosx_11_0_arm64.whl
-  name: seqpro
-  version: 0.21.1
-  sha256: e40d7b20697685694a0e4ab7864f7cc93d784950d19b7160402c304e15ce725f
-  requires_dist:
-  - numba>=0.58.1
-  - numpy>=1.26.0
-  - polars>=1.21.0,<2
-  - pyranges>=0.1.3,<0.2
-  - pandera>=0.31.1
-  - pandas
-  - pyarrow
-  - natsort
-  - narwhals>=2.20.0
-  - setuptools>=70
-  - awkward>=2.5.0
-  - polars-config-meta[polars]>=0.3.2
-  - attrs
-  requires_python: '>=3.10'
 - pypi: https://files.pythonhosted.org/packages/1e/5e/d4e9f1a599fb8e573b7b87160658329fbf28d19eac2718f51fc3def3aa5a/idna-3.18-py3-none-any.whl
   name: idna
   version: '3.18'
@@ -12974,40 +12955,6 @@ packages:
   - isort ; extra == 'dev'
   - pip-tools ; extra == 'dev'
   - pytest ; extra == 'dev'
-- pypi: https://files.pythonhosted.org/packages/36/7b/889bdba263e9b600add681c88549094b3252767097393c138465b43f2abe/genoray-3.0.0-cp310-abi3-macosx_11_0_arm64.whl
-  name: genoray
-  version: 3.0.0
-  sha256: f84f6ab4372ed3056e302b35aa729bf19f9be84d70102cdb0ed9e53c053c1f6d
-  requires_dist:
-  - seqpro>=0.21.1,<0.22
-  - numpy>=1.26
-  - pandas>=2.2.3
-  - hirola>=0.3.0
-  - pgenlib>=0.91.0
-  - cyvcf2>=0.31.1
-  - pysam>=0.22
-  - polars>=1.37.1
-  - polars-bio>=0.20.1,<0.34
-  - pyranges>=0.1.3
-  - typing-extensions>=4.14
-  - pyarrow>=21
-  - tqdm>=4.65
-  - phantom-types>=3
-  - more-itertools>=10
-  - loguru>=0.7.0
-  - attrs
-  - awkward
-  - numba
-  - cyclopts
-  - zstandard
-  - pydantic
-  - oxbow>=0.5.1,<0.6
-  - joblib>=1.4.2,<2
-  - joblib-progress>=1.0.6,<2
-  - filelock>3,<4
-  - scipy>=1.10
-  - pooch>=1.7
-  requires_python: '>=3.10,<3.14'
 - pypi: https://files.pythonhosted.org/packages/38/3d/2d244233ac4f76e38533cfcb2991c9eb4c7bf688ae0a036d30725b8faafe/importlib_metadata-9.0.0-py3-none-any.whl
   name: importlib-metadata
   version: 9.0.0
@@ -13060,6 +13007,25 @@ packages:
   - pytest-enabler>=3.4 ; extra == 'enabler'
   - pytest-mypy>=1.0.1 ; platform_python_implementation != 'PyPy' and extra == 'type'
   requires_python: '>=3.10'
+- pypi: https://files.pythonhosted.org/packages/3b/92/73ab995881de743ddfebe51e6ed35aa6bd709ae7f09eea2cc8e9716bfa36/seqpro-0.22.0-cp39-abi3-macosx_11_0_arm64.whl
+  name: seqpro
+  version: 0.22.0
+  sha256: a8d40f9e5b7269a13ec2078c0e7f48e4f8f68e861bddcef9e66aff14e5be99c9
+  requires_dist:
+  - numba>=0.58.1
+  - numpy>=1.26.0
+  - polars>=1.21.0,<2
+  - pyranges>=0.1.3,<0.2
+  - pandera>=0.31.1
+  - pandas
+  - pyarrow
+  - natsort
+  - narwhals>=2.20.0
+  - setuptools>=70
+  - awkward>=2.5.0
+  - polars-config-meta[polars]>=0.3.2
+  - attrs
+  requires_python: '>=3.10'
 - pypi: https://files.pythonhosted.org/packages/3b/cd/154ca20c38269e05eff77c1464e6c1da89f50a6390b565e9d82e06bc11e1/nvidia_cublas-13.1.1.3-py3-none-manylinux_2_27_x86_64.whl
   name: nvidia-cublas
   version: 13.1.1.3
@@ -13204,6 +13170,25 @@ packages:
   - xlsxwriter>=3.0.5 ; extra == 'all'
   - zstandard>=0.19.0 ; extra == 'all'
   requires_python: '>=3.9'
+- pypi: https://files.pythonhosted.org/packages/40/cd/43eb335bf04c3bbc0a28078ad4675f61f6ccceb4d55dcdb1a0c915ae5613/seqpro-0.22.0-cp39-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
+  name: seqpro
+  version: 0.22.0
+  sha256: 53c2ec20c294e93b892d9a3bced63c229be6cbcc5b9f86175f82e6acebe030df
+  requires_dist:
+  - numba>=0.58.1
+  - numpy>=1.26.0
+  - polars>=1.21.0,<2
+  - pyranges>=0.1.3,<0.2
+  - pandera>=0.31.1
+  - pandas
+  - pyarrow
+  - natsort
+  - narwhals>=2.20.0
+  - setuptools>=70
+  - awkward>=2.5.0
+  - polars-config-meta[polars]>=0.3.2
+  - attrs
+  requires_python: '>=3.10'
 - pypi: https://files.pythonhosted.org/packages/41/09/5b161152e2d90f7b87f781c2e1267494aef9c32498df793f73ad0a0a494a/matplotlib_inline-0.2.2-py3-none-any.whl
   name: matplotlib-inline
   version: 0.2.2
@@ -14279,40 +14264,6 @@ packages:
   - packaging>=23.0
   - colorama>=0.4.6 ; sys_platform == 'win32'
   requires_python: '>=3.12'
-- pypi: https://files.pythonhosted.org/packages/74/7e/4574ad120eaddb9ff6d4bbf03136915cd058d7d272d05f89d0b3adc2e70b/genoray-3.0.0-cp310-abi3-manylinux_2_28_x86_64.whl
-  name: genoray
-  version: 3.0.0
-  sha256: 0f771686aaf99cae805c65d0b984c698c3b6fae8abb134fa7b0fef5f82a4c871
-  requires_dist:
-  - seqpro>=0.21.1,<0.22
-  - numpy>=1.26
-  - pandas>=2.2.3
-  - hirola>=0.3.0
-  - pgenlib>=0.91.0
-  - cyvcf2>=0.31.1
-  - pysam>=0.22
-  - polars>=1.37.1
-  - polars-bio>=0.20.1,<0.34
-  - pyranges>=0.1.3
-  - typing-extensions>=4.14
-  - pyarrow>=21
-  - tqdm>=4.65
-  - phantom-types>=3
-  - more-itertools>=10
-  - loguru>=0.7.0
-  - attrs
-  - awkward
-  - numba
-  - cyclopts
-  - zstandard
-  - pydantic
-  - oxbow>=0.5.1,<0.6
-  - joblib>=1.4.2,<2
-  - joblib-progress>=1.0.6,<2
-  - filelock>3,<4
-  - scipy>=1.10
-  - pooch>=1.7
-  requires_python: '>=3.10,<3.14'
 - pypi: https://files.pythonhosted.org/packages/74/dc/035d54638fc5d2971cbf1e987ccd45f1091c83bcf747281cf6cc25e72c88/pyarrow-21.0.0-cp311-cp311-manylinux_2_28_x86_64.whl
   name: pyarrow
   version: 21.0.0
@@ -14747,6 +14698,41 @@ packages:
   - testpath ; extra == 'test'
   - xmltodict ; extra == 'test'
   requires_python: '>=3.10.0'
+- pypi: https://files.pythonhosted.org/packages/84/02/a6253af89cf532e8029c7508423848704e8362d9e3080bdc5e27f34b7b12/genoray-3.3.1-cp310-abi3-manylinux_2_28_x86_64.whl
+  name: genoray
+  version: 3.3.1
+  sha256: fb7c314e013835db6bef9ab6a940219908c24888a4dd574239f1987381022ed1
+  requires_dist:
+  - seqpro>=0.21.1,<0.23
+  - numpy>=1.26
+  - pandas>=2.2.3
+  - hirola>=0.3.0
+  - pgenlib>=0.91.0
+  - cyvcf2>=0.31.1
+  - pysam>=0.22
+  - polars>=1.37.1
+  - polars-bio>=0.20.1,<0.34
+  - pyranges>=0.1.3
+  - rich>=13
+  - typing-extensions>=4.14
+  - pyarrow>=21
+  - tqdm>=4.65
+  - phantom-types>=3
+  - more-itertools>=10
+  - loguru>=0.7.0
+  - attrs
+  - awkward
+  - numba
+  - cyclopts
+  - zstandard
+  - pydantic
+  - oxbow>=0.5.1,<0.6
+  - joblib>=1.4.2,<2
+  - joblib-progress>=1.0.6,<2
+  - filelock>3,<4
+  - scipy>=1.10
+  - pooch>=1.7
+  requires_python: '>=3.10,<3.15'
 - pypi: https://files.pythonhosted.org/packages/85/dc/bf8a9b7e289dd9b0b550b9964786231fe48264583eecd733f7ab77b374b7/ncls-0.0.70-cp310-cp310-macosx_11_0_arm64.whl
   name: ncls
   version: 0.0.70
@@ -14896,25 +14882,6 @@ packages:
   - hypothesis ; extra == 'tests'
   - pytest ; extra == 'tests'
   requires_python: '>=3.9'
-- pypi: https://files.pythonhosted.org/packages/8d/78/831596c30d1520a89b367fde4857d2e51aade8fad072616a076e6c441900/seqpro-0.21.1-cp39-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
-  name: seqpro
-  version: 0.21.1
-  sha256: 6b6720c75abff0f9e5826c4e6c09000d988b0b738a81172fdf226f6763b01170
-  requires_dist:
-  - numba>=0.58.1
-  - numpy>=1.26.0
-  - polars>=1.21.0,<2
-  - pyranges>=0.1.3,<0.2
-  - pandera>=0.31.1
-  - pandas
-  - pyarrow
-  - natsort
-  - narwhals>=2.20.0
-  - setuptools>=70
-  - awkward>=2.5.0
-  - polars-config-meta[polars]>=0.3.2
-  - attrs
-  requires_python: '>=3.10'
 - pypi: https://files.pythonhosted.org/packages/8e/37/efad0257dc6e593a18957422533ff0f87ede7c9c6ea010a2177d738fb82f/pure_eval-0.2.3-py3-none-any.whl
   name: pure-eval
   version: 0.2.3
@@ -15039,6 +15006,41 @@ packages:
   requires_dist:
   - cffi ; implementation_name == 'pypy'
   requires_python: '>=3.8'
+- pypi: https://files.pythonhosted.org/packages/94/07/0884ea45f06ace0f1ee423d9184f40d598303ba746ff85a6a9a35b56cb94/genoray-3.3.1-cp310-abi3-macosx_11_0_arm64.whl
+  name: genoray
+  version: 3.3.1
+  sha256: 95c013e328b3deee12a7a5cd2aeb340469ca0f12f668cbcbe1740aca94229473
+  requires_dist:
+  - seqpro>=0.21.1,<0.23
+  - numpy>=1.26
+  - pandas>=2.2.3
+  - hirola>=0.3.0
+  - pgenlib>=0.91.0
+  - cyvcf2>=0.31.1
+  - pysam>=0.22
+  - polars>=1.37.1
+  - polars-bio>=0.20.1,<0.34
+  - pyranges>=0.1.3
+  - rich>=13
+  - typing-extensions>=4.14
+  - pyarrow>=21
+  - tqdm>=4.65
+  - phantom-types>=3
+  - more-itertools>=10
+  - loguru>=0.7.0
+  - attrs
+  - awkward
+  - numba
+  - cyclopts
+  - zstandard
+  - pydantic
+  - oxbow>=0.5.1,<0.6
+  - joblib>=1.4.2,<2
+  - joblib-progress>=1.0.6,<2
+  - filelock>3,<4
+  - scipy>=1.10
+  - pooch>=1.7
+  requires_python: '>=3.10,<3.15'
 - pypi: https://files.pythonhosted.org/packages/94/dc/80564a3071a57c20b7c32575e4a0120e8a330ef487c319b122942d665960/pyarrow-21.0.0-cp311-cp311-macosx_12_0_arm64.whl
   name: pyarrow
   version: 21.0.0
diff --git a/pixi.toml b/pixi.toml
index c0519c88..872476e8 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -101,10 +101,12 @@ numba = "==0.59.1"
 [feature.py310.pypi-dependencies]
 pyarrow = ">=21"
 hirola = "==0.3"
-seqpro = "==0.21.1"
-# genoray >=3.0.0 (first release with the INFO/FORMAT field-read API) as the prebuilt
-# abi3 wheel from PyPI — one cp310-abi3 wheel covers py310-313 on both platforms.
-genoray = ">=3.0.0,<4"
+seqpro = "==0.22.0"
+# genoray >=3.3.1 as the prebuilt abi3 wheel from PyPI — one cp310-abi3 wheel covers
+# py310-313 on both platforms. 3.0.0 was the first release with the INFO/FORMAT field-read
+# API; 3.3.1 is the first whose seqpro cap (<0.23) admits seqpro>=0.22. Mirrors the
+# pyproject floor.
+genoray = ">=3.3.1,<4"
 polars = "==1.37.1"
 loguru = "*"
 natsort = "*"
diff --git a/pyproject.toml b/pyproject.toml
index 0f9c3181..164040f8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -10,9 +10,12 @@ readme = "README.md"
 license = { file = "LICENSE.txt" }
 requires-python = ">=3.10,<3.14" # >= 3.14 blocked by pyarrow/genoray
 dependencies = [
-    "seqpro>=0.20",
-    # >=3.0.0 is the first release carrying the INFO/FORMAT field-read API gvl relies on.
-    "genoray>=3.0.0,<4",
+    "seqpro>=0.22",
+    # >=3.0.0 carried the INFO/FORMAT field-read API gvl relies on; >=3.3.1 is the first
+    # release whose seqpro cap (<0.23) admits the seqpro>=0.22 above. Earlier 3.x pin
+    # seqpro<0.22, so they are unsatisfiable here — state that instead of making the
+    # resolver discover it.
+    "genoray>=3.3.1,<4",
     "numpy",
     "loguru",
     "natsort",
diff --git a/skills/genvarloader/SKILL.md b/skills/genvarloader/SKILL.md
index b1542bb5..0b6e58e5 100644
--- a/skills/genvarloader/SKILL.md
+++ b/skills/genvarloader/SKILL.md
@@ -370,7 +370,7 @@ Footprint is computed exactly via `Dataset._output_bytes_per_instance(...)` (use
 
 - `gvl.Reference.from_path(fasta, contigs=None, in_memory=True)` — wrap a FASTA (path to a `.fa`/`.fa.bgz`, or a `.gvlfa` cache dir). Builds/reuses a sibling `.gvlfa` cache directory (self-describing, fingerprint-validated; legacy `.fa.gvl` caches auto-migrate). The cache is built atomically (temp + `os.replace`) under a best-effort lock, so concurrent builders sharing one reference are safe; the cache **auto-rebuilds** from its source when stale or missing. `in_memory=False` reads on-demand from a memory map (lower RAM) but **keeps FASTA contig order**, so `contigs` must be `None` or exactly the full FASTA order — reordering or subsetting `contigs` requires `in_memory=True` (otherwise raises `ValueError`).
 - `gvl.read_bedlike(path)` / `gvl.with_length(bed, L)` — BED helpers (re-exported from `seqpro`).
-- `gvl.Ragged`, `gvl.RaggedAnnotatedHaps`, `gvl.RaggedVariants`, `gvl.RaggedIntervals` — ragged return containers. All are backed by `seqpro.rag.Ragged` (`_core.Ragged` Rust backend); **not** `awkward`. `RaggedVariants` is a **subclass** of `seqpro.rag.Ragged` (`class RaggedVariants(seqpro.rag.Ragged)`), so `isinstance(rv, Ragged) is True`. Structural methods — indexing, `reshape`, `squeeze`, `to_packed` — are inherited from the base and **preserve the `RaggedVariants` type** (positional/structural operations return `RaggedVariants`). A **string key** (`rv["start"]`) returns a bare `Ragged` field, not a `RaggedVariants`. `reshape` takes the new shape either as unpacked ints — e.g. `rv.reshape(1, 2, None)` — or as a single tuple `rv.reshape((1, 2, None))`; the base `Ragged` signature accepts both. `squeeze(axis=None)` is a real axis-squeeze (base semantics) — it squeezes any size-1 axis, **not** a fixed "drop axis 0". An int index collapses the leading axis (numpy-consistent); slice/array indexing preserves it. Named properties (`.alt`, `.ref`, `.start`, `.ilen`, `.end`) are the primary access point; extra fields (e.g. `AF`, custom FORMAT fields) are also accessible via `rv["field"]` or `rv.field` (via `__getattr__`). `RaggedVariants` itself does not define `__eq__` (wrapper-level `==` is Python object-identity, not element-wise); to compare contents, compare individual fields — e.g. `rv["alt"] == other_alt` or `rv.start == other_start` — which use `seqpro.rag.Ragged`'s ufunc-based (element-wise) comparison. Domain methods retained on `RaggedVariants`: `.rc_()`, `.pad()`, `.to_nested_tensor_batch()`; derived read-only properties: `.ilen`, `.end`; fields: `.alt`, `.ref`, `.start`, `.dosage`.
+- `gvl.Ragged`, `gvl.RaggedAnnotatedHaps`, `gvl.RaggedVariants`, `gvl.RaggedIntervals` — ragged return containers. All are backed by `seqpro.rag.Ragged` (`_core.Ragged` Rust backend); **not** `awkward`. `RaggedVariants` is a **subclass** of `seqpro.rag.Ragged` (`class RaggedVariants(seqpro.rag.Ragged)`), so `isinstance(rv, Ragged) is True`. Structural methods — indexing, `reshape`, `squeeze`, `to_packed` — are inherited from the base and **preserve the `RaggedVariants` type** (positional/structural operations return `RaggedVariants`). A **string key** (`rv["start"]`) returns a bare `Ragged` field, not a `RaggedVariants`. `reshape` takes the new shape either as unpacked ints — e.g. `rv.reshape(1, 2, None)` — or as a single tuple `rv.reshape((1, 2, None))`; the base `Ragged` signature accepts both. `squeeze(axis=None)` is a real axis-squeeze (base semantics) — it squeezes any size-1 axis, **not** a fixed "drop axis 0". An int index collapses the leading axis (numpy-consistent); slice/array indexing preserves it. Indexing an **allele** field (`rv.alt[b][h]`, `rv.ref[b][h]`) yields the alleles of that haplotype **per variant**, aligned one-for-one with `rv.start[b][h]` / `rv.ilen[b][h]`, so `zip(rv.start[b][h], rv.alt[b][h])` pairs each position with its own allele. This requires **seqpro >= 0.22**; on older seqpro the same expression returned every allele of the group concatenated into a single `bytes`, which silently misaligned against the scalar fields for any group containing a multi-byte (indel) allele. Named properties (`.alt`, `.ref`, `.start`, `.ilen`, `.end`) are the primary access point; extra fields (e.g. `AF`, custom FORMAT fields) are also accessible via `rv["field"]` or `rv.field` (via `__getattr__`). `RaggedVariants` itself does not define `__eq__` (wrapper-level `==` is Python object-identity, not element-wise); to compare contents, compare individual fields — e.g. `rv["alt"] == other_alt` or `rv.start == other_start` — which use `seqpro.rag.Ragged`'s ufunc-based (element-wise) comparison. Domain methods retained on `RaggedVariants`: `.rc_()`, `.pad()`, `.to_nested_tensor_batch()`; derived read-only properties: `.ilen`, `.end`; fields: `.alt`, `.ref`, `.start`, `.dosage`.
 - `gvl.FlatRagged` — flat analog of `Ragged`: `.data` (flat numpy array), `.offsets` (int64), `.shape`. Methods: `.to_ragged()`, `.to_fixed(length)`, `.to_padded(pad_value)`, `.reshape(shape)`, `.squeeze(axis)`. Source: `python/genvarloader/_flat.py`.
 - `gvl.FlatIntervals` — flat-buffer interval container returned by `with_tracks(kind="intervals")` + `with_output_format("flat")`. Fields `.starts`/`.ends`/`.values` are `FlatRagged`; `.to_ragged()` → `RaggedIntervals`; `.reshape(...)`, `.squeeze(...)`, `.shape`. Source: `python/genvarloader/_ragged.py`.
 - `gvl.FlatAnnotatedHaps` — flat analog of `RaggedAnnotatedHaps`: fields `.haps`, `.var_idxs`, `.ref_coords` (each a `FlatRagged`). Methods: `.to_ragged()`, `.to_fixed(length)`, `.to_padded()`, `.reshape(shape)`, `.squeeze(axis)`. Source: `python/genvarloader/_flat.py`.
@@ -445,6 +445,7 @@ See `docs/source/format.md` for the full schema, versioning, and SVAR-link detai
 - Splicing is a read-time setting on a *flat* BED of exons — do not pre-concatenate exons before `gvl.write`.
 - `extend_to_length=False` at write time will produce haplotypes shorter than the BED region when deletions are present; downstream code must tolerate `<` region length. Not an option for a `.svar2` variant source — `gvl.write(..., variants=<.svar2>, extend_to_length=False)` raises `NotImplementedError`.
 - Missing a `dosage` field on a `RaggedVariants` output you expected? Check `var_fields` — `dosage` must be requested explicitly even if `dosages.npy` exists on disk.
+- **Allele fields index per-variant, and need `seqpro>=0.22`.** `rv.alt[b][h]` gives one allele per variant, matching `rv.start[b][h]`. On seqpro `<0.22` it returned the group's alleles concatenated as one `bytes` — a mismatch that is invisible for SNP-only data (every allele is 1 byte, so the counts coincide) and only appears once an indel is in the window. gvl requires `seqpro>=0.22`; if you see a concatenated blob, check the installed seqpro version first.
 - `FlatRagged` / `FlatVariants` offsets are **int64**. PyTorch nested tensors require int32 offsets — cast with `.astype(np.int32)` or `tensor.to(torch.int32)` before passing to `torch.nested.narrow`.
 - `kind="intervals"` cannot be re-aligned: combining it with a variant-aware seq mode (`haplotypes`/`annotated`/`variants`/`variant-windows`) raises unless `with_settings(realign_tracks=False)`. (Breaking change: `haplotypes`+`intervals` previously returned un-realigned intervals silently under the default.)
 - `with_insertion_fill` raises when `realign_tracks=False`.
diff --git a/tests/unit/dataset/test_ragged_variants_indexing.py b/tests/unit/dataset/test_ragged_variants_indexing.py
new file mode 100644
index 00000000..c748b485
--- /dev/null
+++ b/tests/unit/dataset/test_ragged_variants_indexing.py
@@ -0,0 +1,64 @@
+"""Integer indexing into RaggedVariants allele fields is per-variant.
+
+Regression test for #330 / ML4GLand/SeqPro#71: on seqpro <= 0.21.2, indexing a
+string-under-axis Ragged concatenated the whole group into one bytes object,
+discarding the per-variant boundaries that str_offsets already held. Numeric
+fields on the same shared offsets stayed per-variant, so alt/ref silently
+disagreed in length with start/ilen.
+
+The multi-byte allele below is load-bearing. With SNPs only every allele is one
+byte, the counts coincide, and this test passes on the buggy seqpro too --
+gating nothing.
+"""
+
+from __future__ import annotations
+
+import numpy as np
+from seqpro.rag import Ragged
+
+from genvarloader import RaggedVariants
+
+
+def _build_rv() -> RaggedVariants:
+    """(1, 2, ~v): hap 0 holds 2 variants (alt 'A', 'GG'), hap 1 holds 1 ('TC')."""
+    alt_chars = np.frombuffer(b"AGGTC", dtype="S1")
+    var_off = np.array([0, 2, 3], dtype=np.int64)  # hap -> variant index
+    str_off = np.array([0, 1, 3, 5], dtype=np.int64)  # variant -> byte index
+
+    alt = Ragged.from_offsets(
+        alt_chars, (1, 2, None), var_off, str_offsets=str_off
+    ).to_strings()
+    start = Ragged.from_offsets(
+        np.array([10, 20, 30], dtype=np.int32), (1, 2, None), var_off
+    )
+    ilen = Ragged.from_offsets(
+        np.array([0, 1, 1], dtype=np.int32), (1, 2, None), var_off
+    )
+    return RaggedVariants(alt=alt, start=start, ilen=ilen)
+
+
+def test_alt_indexes_per_variant_not_concatenated():
+    """alt[0][hap] yields one entry per variant, not one concatenated blob."""
+    rv = _build_rv()
+
+    assert list(rv.alt[0][0]) == [b"A", b"GG"]
+    assert list(rv.alt[0][1]) == [b"TC"]
+
+
+def test_alt_count_matches_scalar_fields():
+    """alt, start and ilen share one offsets object, so their per-hap counts agree."""
+    rv = _build_rv()
+
+    for hap, expected_n in ((0, 2), (1, 1)):
+        assert len(rv.alt[0][hap]) == expected_n
+        assert len(np.asarray(rv.start[0][hap])) == expected_n
+        assert len(np.asarray(rv.ilen[0][hap])) == expected_n
+
+
+def test_alt_aligns_elementwise_with_start():
+    """The obvious consumer pattern -- zip(start, alt) -- is correct."""
+    rv = _build_rv()
+
+    pairs = list(zip(np.asarray(rv.start[0][0]).tolist(), rv.alt[0][0]))
+
+    assert pairs == [(10, b"A"), (20, b"GG")]