gnomAD polymorphism and de novo mutation data for analysis of mutation rates in highly mutable gene classes

Research datakeyboard_double_arrow_right Dataset 20 Feb 2023Publisher:ZenodoFunded by:NIH | Integrated pathogenicity ..., NIH | HARVARD-MIT-NEMC RESEARCH..., NIH | Functional and population... +2 projects

Authors: Koch, Evan;

doi: 10.5281/zenodo.7659046 , 10.5281/zenodo.7659045

gnomAD polymorphism and de novo mutation data for analysis of mutation rates in highly mutable gene classes

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Abstract

We analyze the human mutation rate in three gene classes (IGK, RNU, and tRNA) which deviate from the expectations of a mutation rate model. We examine the distribution of allele frequencies for SNVs within these genes and we analyze the counts of de novo mutations stratified by whether the SNV was observed or not. {CHR}_IGK_SFS_v2_denovo.gz: allele frequencies, mutation rate estimates, and whether the de novo mutation was observed for IGK, RNU, and tRNA genes. Based on gnomAD v3. {CHR}_indiv_mu.csv: quality information for variants in these gene classes from the 1kg subset of gnomAD. "CHR", "POS", "REF", "ALT", "FILTER", "AC", "AN", "MQRankSum", "pab_max", "VQSLOD", "AB", "PN", "MR", "AR", "MG", "MC", "QUAL" all_variants_chr21_mu_h.csv.gz: all variants from chromosome 21 to use for comparing allele frequencies to those in our gene classes. 21_indiv_mu_all.csv.gz: quality information from all variants on chromosome 21 from the 1kg subset of gnomAD to use for comparison with gene classes. "CHR", "POS", "REF", "ALT", "FILTER", "AC", "AN", "MQRankSum", "pab_max", "VQSLOD", "AB", "PN", "MR", "AR", "MG", "MC", "QUAL"

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