This dataset contains whole-genome nucleotide diversity estimates for 269 primate species.

DATA
The data/ folder is organized by species. Each species folder follows the structure below:

|
+-- Species_name/
|   |
|   +-- bcf/
|   |
|   +-- bed/
|   |
|   +-- cram/
|   |
|   +-- gVCF/
|   |
|   +-- gVCF_vo/


where the bcf/ subfolder contains BCF files containing only high quality variant positions, the bed/ subfolder contains BED files with the positive callability mask, the cram/ subfolder contains individual-specific CRAM files containing aligned sequencing reads, the gVCF/ subfolder contains Genomic VCF (gVCF) files at base-pair resolution and the gVCF_vo/ subfolder contains gVCF files with variant-only positions. BCF, BED and gVCF files are organised by batch and male/female ploidy (see metadata on references).

REFERENCE ALIGNMENT
The reference_alignment/ folder contains the Cactus output (primates_49_species.hal) of the whole genome alignment between 49 assemblies (47 non-human primate references used for mapping short reads, the T2T H. sapiens reference and the T. belangeri reference used as the outgroup), the filtered maf file of the alignment (primates_49_species.Homo_sapiens.maf.gz), the guide tree used in running the Cactus aligner (phylogeny_49_species.nwk) and the chains/ folder contains chain files for liftover from and to human reference genome coordinates and each of the other 48 references in the alignment.

METADATA
The metadata/ folder contains two subfolders with individual-specfic (individuals/ subfolder) and reference specific metadata (references/ subfolder). 

The files within the individuals/ subfolder are organized by genus. Each {GENUS}_individuals.txt file contains ID, mapping referece, sex and basic coverage info for individuals within the particular genus, while each {GENUS}_short_read_accession.txt file contains info on short read data for each individual within the genus.

The files within the references/ subfolder are organized by reference assembly used in read-mapping and reference alignment. The _REFERENCE_LIST.txt files contains basic info on each reference assembly. Each {REFERENCE_SPECIES}_contigs.txt file contains info on sex-linkage, male/female ploidy and batch for all contigs that belong to the specfic reference.