docs: correct a coverage overstatement in the D34 footnote, and repair the D34 row

README.md

@@ -43,19 +43,25 @@ SESTRAV carries the OpenSSF Best Practices **Passing** badge (project 13191), wh
 | OpenSSF Passing badge | ✓ | ✗ | ✗ | ✗ | ✗ |
 | Antigen processing as training features | `feature_mode=33` | ✓ | ✗ - binding + physicochemical + length only (PRIME2.0's 28-node input layer carries no proteasomal-cleavage or TAP feature) | ✗ | ✗ - NetChop/NetMHCstabPan run as optional post-hoc annotation on already-ranked output, not as input to a trained scorer |
 | Graph Neural Network scorer | ✓ (v2.3 GINEConv+ESM-2; research/ensemble component) | ✗ | ✗ | ✗ | ✗ |
-| Pan-allele training | ✗ - ten fixed HLA-A/-B binding columns; allele identity is not a model feature, so the production model is allele-blind. A `feature_mode=166` allele-aware track exists but was not adopted (`ROADMAP.md`), and its pocket features are under review - see claims register D30 | ✓ - pan-HLA-I predictions (allele identity is not a direct model input; abstracted through upstream MHCflurry2/NOAH) | Partial - trained/validated on an expanding but still finite HLA-I allele list; its MixMHCpred binding feature is itself pan-allele | ✓ | ✓ |
+| Pan-allele training | ✗ - ten fixed HLA-A/-B binding columns; allele identity is not a model feature, so the production model is allele-blind. A `feature_mode=166` allele-aware track exists but was not adopted (`ROADMAP.md`), and its pocket features are under review - see claims register D30 | ✓ - pan-HLA-I predictions (allele identity is not a direct model input; abstracted through upstream MHCflurry2/NOAH) | Partial - trained/validated on an expanding but still finite HLA-I allele list; its MixMHCpred binding feature is itself pan-allele | ✓ | ✓ (see note below - this cell is unverified) |
 | Multi-virus support | 9 viruses (v5 active), each a separately-validated within-virus panel - not cross-virus transfer, see LOO below: CMV, EBV, HBV, HCV, HPV, HIV-1, IAV, DENV, SARS-CoV-2 | Limited - only SARS-CoV-2 explicitly named/validated | Limited - trained mainly on tumor neoepitopes; validated prospectively on SARS-CoV-2 only | Pan-pathogen (see note below - this cell is flagged unresolved) | Tumor |
 | Wet-lab candidate protocol included | ✓ | ✗ | ✗ | ✗ | Partial |
 | AUC-PR on labeled benchmark (Tier A) | **0.828 (OOF, 30-feature, unweighted, 2026-05; not `mode_31` - see note below)** | capabilities only (see note) | capabilities only (see note) | N/A | N/A |
 
-*Every PredIG/PRIME/NetMHCpan/pVACtools cell above (B4/L-1) is bound to a primary source read in
-full - the tool's own paper and, where one exists, its GitHub README/docs - per
-`docs/claims_register.md` **D34**, which lists every source and every cell's citation. **One cell
-is deliberately left unresolved rather than published on an inferred claim:** NetMHCpan's
-"Multi-virus support" (currently "Pan-pathogen") could not be traced to primary-source language
-about pathogen/antigen-source breadth - the closest passage in its own paper only supports MHC
-allele/species breadth, a different claim - so the label is retained pending a maintainer ruling
-rather than being silently rewritten to a synthesized replacement (`docs/claims_register.md` D34).*
+*Of the 36 PredIG/PRIME/NetMHCpan/pVACtools cells above (B4/L-1), **34 are bound to a primary
+source read in full** - the tool's own paper and, where one exists, its GitHub README/docs - per
+`docs/claims_register.md` **D34**, which lists every source consulted. **Two cells are not, and
+both are flagged inline above rather than counted as verified.** (1) NetMHCpan's "Multi-virus
+support" (currently "Pan-pathogen") is **unresolved**: it could not be traced to primary-source
+language about pathogen/antigen-source breadth - the closest passage in its own paper only
+supports MHC allele/species breadth, a different claim - so the label is retained pending a
+maintainer ruling rather than being silently rewritten to a synthesized replacement. (2)
+pVACtools's "Pan-allele training" cell is **unverified**: one research pass transcribed SESTRAV's
+own column text into that row, so the row was excluded from the verification pass entirely rather
+than corrected from a guess, and the cell stands as originally written with nothing behind it.
+**An earlier version of this footnote said "every" cell was source-bound and named only the first
+exception**, which overstated the pass's coverage by one cell in the flattering direction; it is
+corrected here (`docs/claims_register.md` D34).*
 
 *Tier A 704-peptide labeled benchmark. SESTRAV RF is evaluated out-of-fold; external tools are fully scored on the same peptides. **That asymmetry does not favour the external tools as previously claimed here.** This Tier A arm's 720-peptide corpus has zero duplicate peptides (D16), so the exact-peptide leakage affecting the v5 figures below (D15) is a structural no-op here and does not apply. A different, unquantified risk does apply: 32.1% of the 704-peptide scored pool has a substring-level near-duplicate elsewhere in the pool, never filtered for this benchmark; whether it affected the score is not established (`docs/claims_register.md` D22). Every v5 cross-validation figure below is peptide-grouped as of 2026-08-10; this Tier A figure deliberately is not, and peptide-grouping would not address the substring-homology risk in any case (D16, D22). The certified head-to-head field is in External Benchmark Results below - BigMHC (0.822), MHCflurry binding-only (0.800), MixMHCpred 2.2 (0.795), and DeepImmuno (0.698), all bound to `results/table3_tier_a_metrics.csv`; the closest external tool is BigMHC (0.822). PredIG and PRIME are compared on capabilities only: their metric head-to-head is not reproducible from a certified results file and is not reported. pVACtools targets a different problem domain (patient-specific tumor neoantigens from somatic variant calls) rather than published viral epitopes from proteome sequence, so the "(neoantigens)"/"Tumor"/"N/A" cells in its column above are not a head-to-head with the viral-epitope rows. Separately, on the harder v5 generalization set (35,597 active rows, 9 viruses), canonical `mode_31` reports pooled **peptide-grouped** cross-validation AUC-PR **0.6058** (re-baselined 2026-08-10, closing D15; the prior ungrouped figure 0.8312 was leakage-inflated and is retracted) and same-pathogen (within-virus) discrimination per-virus (mean within-CV AUC-ROC **0.658**; prior ungrouped 0.751 retracted; the pooled AUC-ROC 0.9368 reported before that was separately decoy-inflated and is also retracted - see Paradigm 2 below). **0.828 is NOT a `full_31`/`mode_31` result** - it is a 30-feature, unweighted, 200-tree measurement from 2026-05, predating `feature_mode=31`'s introduction by 26 days (`docs/claims_register.md` D16); the extended `full_33` antigen-processing configuration is reported separately under Release Tracks and is not part of this certified field. Certified per-tool metrics and their scope boundaries: `results/table3_tier_a_metrics.csv` and `docs/claims_register.md`. (`results/external_benchmark_comparison.md` is a 2026-05-22 SESTRAV-vs-binding-only-only report carrying the same pre-D16 mislabel and an unresolved provenance gap - historical reference only, not a citable source for the 5-tool field above.)*