Structural polymorphism and population-variable coding capacity of HERV-K(HML-2) in human pangenomes

Code and derived data accompanying “Structural polymorphism and population-variable coding capacity of HERV-K(HML-2) in human pangenomes.” Version 0.4.2 adds the final Table 2 calculation for 282 matched donors and 83 loci. It compares annotations derived from short-read sequencing in the phased high-coverage 1000 Genomes VCF panel against long-read calls. The new calculation separates intact and combined ORF screens and Type-II Env from theoretical N-terminally truncated Type-I Env. Translation of the latter product has not been demonstrated. Normal programmed gag/pro/pol frame transitions are permitted. The combined screen additionally retains the caller’s stop-free altered-frame candidates. The archive includes the standard-library reproduction script, per-locus counts, donor–locus observations and input provenance. All seven original aggregate totals reproduce exactly, and the frozen comparison inputs are unchanged. All earlier scientific results and public sequence inputs are retained. This release also incorporates the post-v0.4.1 documentation corrections and Figure 6C palette correction already present on GitHub. The manuscript has seven main figures and eighteen supplementary figures. FIGURE_TABLE_MAP.md and SUPPLEMENTARY_TABLE_NUMBERING.tsv connect final labels to retained source filenames. No ORF-break dating analysis, private collaborator source data or licensed BioRender artwork is added. Original code is MIT licensed and original derived data are CC BY 4.0. Third-party sources retain their existing terms and citations. Download the code archive and every derived-data part. Extract all ZIP files into the same release folder. Do not concatenate the parts. README.txt gives extraction instructions and checksums. These files contain the complete release.