biostudies-literatureImprialou MWellcome TrustBiotechnology and Biological Sciences Research CouncilNIGMS NIH HHS1425-1441https://www.ebi.ac.uk/biostudies/studies/S-EPMC5378104biostudies-literatureUnknown205(4)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</GeneticsGenomic Rearrangements in &lt;i&gt;Arabidopsis&lt;/i&gt; Considered as Quantitative Traits.PMC5378104BBS/E/J/000PR9795BBS/E/J/000PR9797BB/M003809/1T32 GM007464BB/F022697/1090532/Z/09/ZBhomra AStegle OMott RSteffen JGGreenhalgh RRobert-Seilaniantz AKover PKahles AClark RMRatsch GImprialou MVisscher ATsiantis MNordborg MBelfield EGoram RHein JLempe JJones JHarberd NPGan XOsborne EJfalseGenomic Rearrangements in &lt;i&gt;Arabidopsis&lt;/i&gt; Considered as Quantitative Traits.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</2017-01-01T00:00:00Z2017 Apr2026-05-30T12:06:39.759Z2019-03-27T02:40:11ZS-EPMC53781042817936710.1534/genetics.116.192823