Inference of elevated mutation rates and variant effects using 700k exomes

Contains Supplementary Tables for the preprint "Inference of elevated mutation rates and variant effects using 700k exomes". Supplementary Table 1 - Contains estimated recent demography information for ancestry labels - AFR, AMR, EAS, FIN, SAS - in gnomAD v4 dataset. Supplementary Table 2 - Contains mutation rate mean and uncertainty estimates for each Roulette bin Supplementary Table 3 - Estimates of gene specific s_het against heterozygous loss-of-function (LoF) mutants Supplementary Table 4 - Probability that a LoF variant is misannotatedThe Supplementary Table 4.txt.gz table contains LoF variants in gnomAD v4.1 (Guez, Goodrich et al., 2026, medRxiv). First line contains the column names, the columns being-#CHROM - chromosome in which variant is foundPOS - position at which variant is foundREF - hg38 reference alleleALT - alternate alleleMR - Roulette valueQUAL - quality of Roulette value (high/TFBS are filtered)gene_id - Ensembl gene IDgene_name - gene symbol transcipt_id - transcript AC_NFE - allele count in the Non-Finnish European ancestry of gnomAD v4AN_NFE - allele number (sample size) of the Non-Finnish European ancestry of gnomAD v4misannotation_probability - probability that the LoF variant is misannotated Supplementary Table 5 - Posterior probability of kappa>1. Variants leading to clonal expansion in germline have kappa>1. Supplementary Table 6 - Estimates of variant specific s_het against heterozygous missense mutantsThe Supplementary_Table_6.txt.gz table contains selection estimates against the missense variants. The values are between 10^-6 to 100. Note that this is unscaled s_het, so the reported value = Actual selection s_het* Scaling. Scaling in this case is greater than 1. s_AlphaMissense_norm performs the best in our benchmarks (Figure 5D-5F in main text). First line contains the column names, the columns being - #CHROM, POS, REF, ALT, MR, QUAL, gene_id, gene_name - The columns have the same meaning as in Supplementary Table 4.txt.gzallele_count - allele count summed across six ancestries (AFR, AMR, EAS, FIN, NFE, SAS) of gnomAD v4 allele_number - allele number (sample size) across six ancestries (AFR, AMR, EAS, FIN, NFE, SAS) of gnomAD v4 Selection estimate columnss_prior_AlphaMissense_norm - Selection estimates from prior distribution based on AlphaMissense scores_AlphaMissense_norm - Selection estimates from posterior distribution based on AlphaMissense scores_prior_popEVE_neg - Selection estimates from prior distribution based on popEVE scores_popEVE_neg - Selection estimates from posterior distribution based on popEVE scores_prior_esm_score_neg - Selection estimates from prior distribution based on ESM-1b scores_esm_score_neg - Selection estimates from posterior distribution based on ESM-1b score