Pairwise Distances of EGP Results

Data from the following EGP results on Publicly Available Genomes:

Public Dataset
Zenodo DOI

Simons Genome Diversity Project
https://doi.org/10.5281/zenodo.13835663

Human Genome Diversity Project
https://doi.org/10.5281/zenodo.13835739

Gambian Genome Variation Project
https://doi.org/10.5281/zenodo.13839400

1000G 698
https://doi.org/10.5281/zenodo.13839442

1000G 2504
https://doi.org/10.5281/zenodo.13839949

GIAB Trio
https://doi.org/10.5281/zenodo.13839913

was downloaded locally. Analyses steps:

All the files with the suffix of .mega were concatenated together to make one file containing the 4,706 mitochondrial genomes generated by EGP across all the datasets.

The sequences then underwent multi-sequence alignment using Clustal in MEGA version 11 (software available at https://www.megasoftware.net/).

Pairwise distances were calculated using MEGA version 11.

The table was exported from MEGA, and a custom python script was used to convert the MEGA format to a pairwise table.

The pairwise table is available here as a .csv file. Please note the file is quite large with 11,070,866 lines. This is because there is a header line, and we are expecting (4706 individuals * 4706 individuals)-4706 = 11,070,865 pairwise values due to the absence of a comparison of self-self.

The md5 for the data is:

MD5 (pairwise_alignments_EGP_09282024.tar.bz2) = 520d7510a076219082d7821b2ecbbb38