A bovine long read cohort to identify SVs and quantify their impact on gene expression

This dataset contains small and structural variants identified from HiFi sequencing of 117 bulls of predominant Braunvieh ancestry. This repository contains the following data VCF used for association mapping final.117.vcf.gz TPM matrices (unfiltered and filtered/normalized) TPM_gene_testis_UNFILTERED.tsv TPM_gene_testis_FILTERED_NORM.tsv PSI/splicing matrices (unfiltered counts and filtered/normalized PSI) hifi_testis_perind_numers.counts.gz all.leafcutter.bed eQTL and sQTL results (conditional = summary stats after conditional testing for significant variant-phenotype pairs) eQTL: eQTL_conditional.txt.gz sQTL: sQTL_conditional.txt.gz covariates (covariates used for eQTL and sQTL mapping) covariates_TPM.txt covariates_PSI.txt A cross-table (HiFi_cohort_accession_numbers_zenodo.xlsx)to assign individual IDs to ENA accession IDs. source_data.zip: Numerical source data underlying graphs in the scientific manuscript The bovine ARS-UCD2.0 assembly and the Refseq annotation (release 106) were used