Data and code for: Phylogenomic characterisation of L4.13, a sub-lineage of Mycobacterium tuberculosis lineage 4: SNP markers, spoligotype signature and sub-clade structure

Derived data, intermediate results and analysis scripts supporting the article «Phylogenomic characterisation of L4.13, a sub-lineage of Mycobacterium tuberculosis lineage 4: SNP markers, spoligotype signature and sub-clade structure». The record provides, for the first time in redistributable form, the per-strain variant profiles (SPDI notation against the H37Rv reference NC_000962.3) of the 258 L4.13 strains and of the 10 outgroup strains used to root the tree (232,493 strain-variant rows, 11,298 distinct variants), with the checksum of each source file. It also contains Supplementary Tables S1 to S11, the derived tables read by the analyses, the Python scripts, the text outputs of the analyses, and the ENA verification of the 268 run accessions (all resolve and are public on 2026-11-02). Two phylogenies are included. phylogeny/ holds the tree of the article: RAxML-NG under GTR+FU+G4m with ascertainment-bias correction on a 9,816-position nucleotide alignment of 268 taxa, the model having been selected among 32 candidates by ModelFinder; the alignment, the invariant-site counts and the model-selection log are in résultats/AA12_arbre_acgt/. phylogeny_binary_exploration/ holds the earlier exploratory tree inferred under BIN+G on a binary matrix, kept for comparison (Supplementary Table S11). Sequencing reads are not included: they are public runs of the INSDC, listed by run accession in Supplementary Table S1. A README describes the contents, the provenance of the profiles (TBannotator workflow, genome repository revision r46) and the limits of reproducibility of the scripts. Data and tables: CC BY 4.0. Scripts: MIT. Version 2 replaces the tree of the article: version 1 served the binary-matrix tree as phylogeny/, which the article no longer retains. Supplementary Table S11 and the model-selection outputs are new in this version.