The callability classification answers one question — can standard sequencing technically resolve this gene? It says nothing about what a variant in that gene would mean. Every class, criteria code and difficulty track used on this site is defined below.
Every class, code and percentage on this site is measured against one haploid reference assembly at a time and one GIAB benchmark sample, HG002. A gene scored clean here is clean in that sample, against that assembly — which is not the same as clean in a given patient.
Three consequences, stated plainly. A benchmark that can adjudicate a call is not a pipeline that can make one — v5.0q knows the truth inside a segmental duplication precisely because it was assembled rather than read short, so a gene can be 100% benchmark-validatable and still unreadable by short reads. Difficulty is a property of the reference, so a figure measured on GRCh38 is not a claim about the same gene on T2T-CHM13; the card carries both and they disagree more often than is comfortable. And one sample cannot show you a variant it does not carry: population-specific and private variation is outside what anything here measures.
Five tiers, assigned from coding-sequence coverage against the GIAB HG002 v5.0q confident regions on each reference, plus GIAB difficult-region overlap. The rule is applied in a fixed order — Refractory, then Reference-sensitive, then Reliable, then Technology-sensitive, with Caution for everything left — and the first class a gene qualifies for is the one it gets. The classification is orthogonal to ACMG pathogenicity — it describes the assay, not the variant.
On the panel, classes 1 and 4 sit well apart: class 1 tops out at 24.9% difficult-region overlap of coding sequence and class 4 begins at 26.0%. Across all genes they do not — the lowest class-4 gene sits at 13.5%, because class 4 is also decided by segmental duplication, not by overall overlap alone. Against an independent catalog of short-read failures (Mandelker et al. 2016, high-stringency list) the five classes score an AUC of 0.924 over all 19,250 genes and 0.921 on the panel — see the validation page.
Every class carries the codes that produced it, so a rating is never a bare verdict. A gene may carry several. The date the counts were measured is given below the table.
| Code | Meaning | Genes (panel) |
|---|---|---|
| Reference / benchmark coverage | ||
| RG0 | 0% of coding sequence benchmark-validatable on GRCh38 | 682 (92) |
| RGp | Part of the coding sequence is not benchmark-validatable on GRCh38 | 546 (190) |
| RRESCUE | T2T-CHM13 validates ≥25 points more coding sequence than GRCh38 (T2T-preferred) | 279 (43) |
| RG38 | GRCh38 validates ≥25 points more coding sequence than T2T-CHM13 (GRCh38-preferred). Also carried by six pseudoautosomal genes that have no T2T-CHM13 figure | 95 (23) |
| RMAP | Short reads cannot be placed on GRCh38 but can on T2T-CHM13: low-mappability coding sequence 25 points or more higher on GRCh38, and under 10% on T2T-CHM13. Added in v1.20 (2026-10-14); measured that day | 21 (9) |
| RT2TNONE | No T2T-CHM13 comparison is available, and GRCh38 validates none of the coding sequence | 57 (4) |
| Difficult-region overlap | ||
| DADR | 50% or more of the coding sequence lies in a GIAB difficult region | 4,752 (1,100) |
| DADRp | 25% up to 50% of the coding sequence lies in a GIAB difficult region | 3,030 (901) |
| DSEG | 10% or more of the coding sequence lies in a segmental duplication | 2,034 (403) |
| DMAP | 10% or more of the coding sequence lies in a low-mappability region | 1,993 (373) |
| Technology and annotation | ||
| TPAR | Near-identical paralog — unresolvable by short reads on any reference. Fires on a Refractory (class 5) gene with half or more of its coding sequence in a segmental duplication | 349 (33) |
| TASM | Long-read assembly resolves sequence that short reads cannot. Fires when a quarter or more of the coding sequence is segmentally duplicated yet the assembly-based benchmark (v5.0q) still validates 90% or more of it, or when v5.0q validates at least 10 points more coding sequence than the short-read benchmark (v4.2.1). That second clause on its own says the newer benchmark reaches sequence the older one did not, not that short reads fail there, so on a Reliable, Caution or Reference-sensitive gene it does not turn the Sequencing tech chip red. | 1,710 (407) |
| TBOC | v4.2.1 validated ≥25 points more coding sequence than v5.0q — the 2021-era benchmark over-stated confidence and the assembly-era benchmark withdrew it | 349 (69) |
A p suffix marks a partial criterion — the limitation is present but affects a minority of the coding sequence. Partial codes were introduced on 2026-08-29; before that, 777 class-2 genes carried a class with no stated reason. DADRp is now the only partial code: DSEGp and DMAPp were retired on 2026-09-18.
Counts measured on 2026-10-01 over all 19,250 genes with a RefSeq Select transcript, with the 5,694-gene medically relevant panel in parentheses. They are recorded here, not queried, so treat the date as part of the number.
The five GIAB stratification categories drawn beneath the exon view, plus Alu elements. Colors are from the Okabe–Ito colorblind-safe palette, and every track is always labeled — color is never the only carrier of meaning.
Segmental duplications and low-mappability intervals are drawn at their full extent, even where they run far beyond the gene; the other tracks are clipped to the gene body ±2 kb. A gene showing no track is not necessarily clean — it may sit in an assembly gap, where bases belong to no track at all; those genes carry an explicit unsequenced-percentage caveat on the gene card.
Search a demo gene to see its class, the codes behind it, and the evidence for each.
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