Relate-estimated coalescence rates, allele ages, and selection p-values for the 1000 Genomes Project
DOI10.5281/zenodo.3234689Zenodo3234689MaRDI QIDQ6703801FDOQ6703801
Dataset published at Zenodo repository.
Marie Forest, Simon Myers, Sinan Shi, Leo Speidel
Publication date: 29 May 2019
Copyright license: Creative Commons Attribution 4.0 International
Overview Coalescence rates, allele ages, and p-values for evidence of positive selection calculated for 2478samples of the1000 Genomes Projectusing Relate. We estimated the joint genealogy of all 1000 GP populations and then extracted the embedded genealogy for each population. For the genealogy of each population, we jointly estimated the population size history and branch lengths. Variants segregating in more than onepopulationtherefore havecorrelated but different allele ages in each population. Please refer toSpeidel et al.Nature Genetics (2019)for more details or email leo.speidel@outlook.com for any queries. Coalescence rates The zipped directorycoalescence_rates.zipcontains coalescence rates for 26 populations in the 1000 Genomes Project data set. The .coal files show the haploid coalescence rates, please refer to theRelate documentationfor the file format. The popsize.RData file is an R data frame storing the diploid population sizes (0.5/coalescence rate) calculated using the .coal files. The columns of this data frame, named pop_size,are gens_ago: Time in generations at which epoch starts. (To get years from generations, we multiply by 28.) population_size: Diploid population size in this epoch. population: Name of population region: Name of region (AFR, AMR, EAS, EUR, SAS) Allele ages and selection p-values The zipped directoriesallele_ages_*.zipcontainRdata frames for each 1000GP population storing allele ages and selection p-values. Please note that only mutations that segregate in the population and map to a unique branch in the Relate-estimated marginal trees are included. Selection p-values are only provided for mutations of DAF 2 that pass quality filters (see Speidel et al., 2019). To get an age estimate for a neutral mutation, use0.5*(lower_age + upper_age). To get years from generations, we multiply by 28. The columns of thesedata frames, named allele_ages,are CHR: chromosome index BP: base-pair position (GRCh37) ID: id of SNP lower_age: Age in generations of coalescence event at the lower end of the branch onto which the mutation maps upper_age: Age in generations of coalescence event at the upper end of the branch onto which the mutation maps ancestral/derived: Ancestral/derived allele upstream: Upstream (5) allele downstream: Downstream (3) allele DAF: Derived-allele frequency pvalue: log10 p-value for selection evidence
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