The impact of ancestral, genetic, and environmental influences on germline de novo mutation rates and spectra

Supplementary Data 11. Summary statistics for sex-combined DNM rate GWAS. DNM counts per individual (i.e., phased DNMs) were residualised according to Model 3. Residualised DNM counts were used as phenotypes for GWAS across 15,885 individuals genetically identified as European descendants (Methods). Column key: “chrom”: chromosome, “pos”: GRCh38 assembly position. “marker.id”: Construct of “chrom:pos_other.allele_effect.allele”. “other.allele”: allele NOT used for regression estimate. “effect.allele”: Allele used as reference for beta effect; “af_effect.allele”: Sample subset specific allele frequency of the effect allele. “Beta”: Regression beta effect (SAIGE); “se”: Standard error for beta effect; “p.value” P value for beta effect.

Supplementary Data 12. Summary statistics for paternal DNM rate GWAS. Paternally phased DNM counts were residualised according to Model 4 (Methods). Residualised DNM counts were used as phenotypes for GWAS across 7,982 individuals (trio fathers genetically identified as European descendants, Methods). Column contents match those of Supplementary Data 10. Column contents match those of Supplementary Data 10.

Supplementary Data 13. Summary statistics for maternal DNM rate GWAS. Maternally phased DNM counts were residualised according to Model 5 (Methods). Residualised DNM counts were used as phenotypes for GWAS across 7,993 individuals (trio mothers genetically identified as European descendants, Methods). Column contents match those of Supplementary Data 10. Column contents match those of Supplementary Data 10.