# README # ========================== # GENERAL INFO # ========================== URL:******* Study title:Effect of host genetics on the gut microbiome in 7,738 participants of the Dutch Microbiome Project Created by: Esteban Lopera, Serena Sanna Created on: 01/2021 # ================ DATA DESCRIPTION # ================ These are the association analyses produced from the imputed genotype data for 7738 from the Lifelines cohort who comply with this: -Have genetic data from the Global Screening Array genotyping. -Classified as European by genotype. -Have metagenomic of microbiome data and pass quality control filters for this. We evaluated only 205 pathways and 207 microbial taxa. We applied log transformation for each feature after removing the zero values, and then used a linear mixed model in SAIGE framework (which also applies inverse rank normalization), the model included age and sex as covariates and we filtered out variants with MAF<0.05 and information score <0.4. Columns: id: DBsnp rs identifier chr_pos_ref_alt: secondary position based identifier pos: position in the chromosome ref: reference allele alt: alternative alelle AF_Allele2: Allele frequency of alternative allele in the evaluated model num: Total number of individuals included in the model beta: coefficient of the genetic variant in the model (effect size) SE: standard deviation of the effect size pval: p-value imputationInfo: Information score form the imputation with HRC panel chisq: Chi-square statistic feature: microbial feature Files: : summary statistics for microbiome taxonomies. : summary statistics for bacterial pathways. # ========================= # CHANGELOG # ========================= ## 28-01-2020 ## creation of this file