Global (Annotation-Level) Metrics

The global family lives under the top-level "global" key of a GFF-benchmark result (results[method]["global"]) and is the direct counterpart to gffcompare’s summary. Unlike the per-transcript metric families — which score matched (GT, prediction) pairs in isolation — the global family aggregates over all transcripts, including unmatched ones, so false-positive predictions and missed reference transcripts both move the numbers. Each group reports counts plus derived precision / recall / F1.

Note

This "global" → "nucleotide" key is not the same as the Nucleotide Classification family’s "nucleotide" output. The global one is a union-based, genome-level base rate (each genomic base counted once across all isoforms, gffcompare-style). The per-transcript NUCLEOTIDE_CLASSIFICATION one is computed per matched transcript and averaged. Same word, different scope — read the enclosing key to tell them apart.

The eight groups

Key	Question it answers
`nucleotide`	Base-level exon-coverage accuracy (union over isoforms; gffcompare nucleotide Sn/Sp).
`exon`	How many exons are reconstructed exactly. Each unique `(seqid, strand, start, end)` interval is counted once across all transcripts (this diverges from gffcompare’s per-isoform counting).
`exon_lenient`	Same as `exon` but terminal-exon outer boundaries need not match (only internal splice sites must be exact) — gffcompare’s default `=` leniency.
`intron_chain`	How many multi-exon intron chains match exactly (gffcompare intron-chain Sn/Sp), by coordinate-exact matching over the full reference.
`transcript_exact`	How many transcripts match exactly, coordinate-exact (gffcompare transcript Sn/Sp), over the full reference.
`transcript`	Transcript recovery from the assignment step: Sn = matched ref / total ref, Sp = matched pred / total pred (mode-dependent; retained for backward compatibility).
`gene`	How many gene loci are detected. Transcripts are clustered into loci by overlap; a locus counts as matched if any of its transcripts got a counterpart.
`locus_isoform`	How completely multi-isoform loci are recovered — the fraction of each GT locus’s isoforms that received a match. Most meaningful with `FULL_DISCOVERY`.

Scoped vs unscoped

The families that depend on which label roles count as “exon” (nucleotide, exon, exon_lenient, intron_chain, transcript_exact) nest their results under a "scopes" key, so a UTR_CDS_INTRON run reports both a transcript_exon and a cds view in one pass:

results[method]["global"]["nucleotide"]["scopes"]
# {"transcript_exon": {...}, "cds": {...}}

The remaining families (transcript, gene, locus_isoform) are unscoped.

intron_chain and transcript_exact reproduce gffcompare’s numbers by coordinate-exact structure matching over the whole reference, independent of the --locus-matching mode. See the GFF benchmark guide for how -R / -Q (incomplete-annotation corrections) interact with these.