Four annotation sets and proteomes for the llama (Lama glama) chromosome-level genome assembly GCA_028534125.1

This dataset contains four independently generated structural annotations of theLama glama genome assembly GCA_028534125.1 (DNA Zoo, chromosome level), the fourprotein sets derived from them, and the quality-control output used to evaluatethem. Three annotations project the Vicugna pacos reference annotation GCF_048564905.1,by DNA-to-DNA lift-over (Liftoff), protein-to-genome alignment (miniprot) andhybrid reconciliation (LiftOn). The fourth is reference-independent ab initioprediction (Helixer). Completeness was assessed with BUSCO 6.1.0 in protein modeagainst lineage artiodactyla_odb12 (n = 12,594), alongside the Vicugna pacosreference proteome as a ceiling and a previous unpublished in-house annotation asa baseline. At the time of deposition no public structural annotation of Lama glama wasavailable: the species is absent from Ensembl, neither INSDC assembly carries anannotation, and UniProt holds no proteome for it. IMPORTANT: the four annotation sets were not produced under equivalent conditionsand are not directly comparable without qualification. The three homologybranches did not consume the same reference annotation, although both referencescontain the same 37,446 gene models and differ only in isoform depth. Helixer wasrun on scaffolds of at least 10 kb (81.46 % of the assembled sequence) andwithout subsequence overlap, so its completeness figure is a lower bound ratherthan a representative measure of that tool. All four caveats are set out inREADME.md. File integrity can be checked against CHECKSUMS.sha256. Quality-control output isin qc.tar.gz.