{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Imprialou M"],"funding":["Wellcome Trust","Biotechnology and Biological Sciences Research Council","NIGMS NIH HHS"],"pagination":["1425-1441"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC5378104"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["205(4)"],"pubmed_abstract":["To understand the population genetics of structural variants and their effects on phenotypes, we developed an approach to mapping structural variants that segregate in a population sequenced at low coverage. We avoid calling structural variants directly. Instead, the evidence for a potential structural variant at a locus is indicated by variation in the counts of short-reads that map anomalously to that locus. These structural variant traits are treated as quantitative traits and mapped genetically, analogously to a gene expression study. Association between a structural variant trait at one locus, and genotypes at a distant locus indicate the origin and target of a transposition. Using ultra-low-coverage (0.3×) population sequence data from 488 recombinant inbred <i>Arabidopsis thaliana</"],"journal":["Genetics"],"pubmed_title":["Genomic Rearrangements in &lt;i&gt;Arabidopsis&lt;/i&gt; Considered as Quantitative Traits."],"pmcid":["PMC5378104"],"funding_grant_id":["BBS/E/J/000PR9795","BBS/E/J/000PR9797","BB/M003809/1","T32 GM007464","BB/F022697/1","090532/Z/09/Z"],"pubmed_authors":["Bhomra A","Stegle O","Mott R","Steffen JG","Greenhalgh R","Robert-Seilaniantz A","Kover P","Kahles A","Clark RM","Ratsch G","Imprialou M","Visscher A","Tsiantis M","Nordborg M","Belfield E","Goram R","Hein J","Lempe J","Jones J","Harberd NP","Gan X","Osborne EJ"],"additional_accession":[]},"is_claimable":false,"name":"Genomic Rearrangements in &lt;i&gt;Arabidopsis&lt;/i&gt; Considered as Quantitative Traits.","description":"To understand the population genetics of structural variants and their effects on phenotypes, we developed an approach to mapping structural variants that segregate in a population sequenced at low coverage. We avoid calling structural variants directly. Instead, the evidence for a potential structural variant at a locus is indicated by variation in the counts of short-reads that map anomalously to that locus. These structural variant traits are treated as quantitative traits and mapped genetically, analogously to a gene expression study. Association between a structural variant trait at one locus, and genotypes at a distant locus indicate the origin and target of a transposition. Using ultra-low-coverage (0.3×) population sequence data from 488 recombinant inbred <i>Arabidopsis thaliana</","dates":{"release":"2017-01-01T00:00:00Z","publication":"2017 Apr","modification":"2026-05-30T12:06:39.759Z","creation":"2019-03-27T02:40:11Z"},"accession":"S-EPMC5378104","cross_references":{"pubmed":["28179367"],"doi":["10.1534/genetics.116.192823"]}}