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Most studies of\n                    <jats:italic>P. falciparum<\/jats:italic>\n                    genetic diversity have focused on single-nucleotide polymorphisms (SNPs), assisting the identification of drug resistance-associated loci such as the chloroquine related\n                    <jats:italic>crt<\/jats:italic>\n                    and sulfadoxine-pyrimethamine related\n                    <jats:italic>dhfr<\/jats:italic>\n                    . Whilst larger structural variants are known to impact adaptation, for example,\n                    <jats:italic>mdr1<\/jats:italic>\n                    duplications with anti-malarial resistance, no large-scale, genome-wide study on clinical isolates has been undertaken using whole genome sequencing data. By applying a structural variant detection pipeline across whole genome sequence data from 2,855 clinical isolates in 21 malaria-endemic countries, we identified &gt;70,000 specific deletions and &gt;600 duplications. Most structural variants are rare (48.5% of deletions and 94.7% of duplications are found in single isolates) with 2.4% of deletions and 0.2% of duplications found in &gt;5% of global isolates. A subset of variants was present at high frequency in drug-resistance related genes including\n                    <jats:italic>mdr1<\/jats:italic>\n                    , the\n                    <jats:italic>gch1<\/jats:italic>\n                    promoter region, and a putative novel duplication of\n                    <jats:italic>crt<\/jats:italic>\n                    . Regional-specific variants were identified, and a companion visualisation tool has been developed to assist web-based investigation of these polymorphisms by the wider scientific community.\n                  <\/jats:p>","DOI":"10.1038\/s41598-019-44599-0","type":"journal-article","created":{"date-parts":[[2019,6,4]],"date-time":"2019-06-04T06:07:20Z","timestamp":1559628440000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":20,"title":["An analysis of large structural variation in global Plasmodium falciparum isolates identifies a novel duplication of the chloroquine resistance associated gene"],"prefix":"10.1038","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7818-2348","authenticated-orcid":false,"given":"Matt","family":"Ravenhall","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4313-4290","authenticated-orcid":false,"given":"Ernest Diez","family":"Benavente","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1592-6407","authenticated-orcid":false,"given":"Colin J.","family":"Sutherland","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5490-8933","authenticated-orcid":false,"given":"David A.","family":"Baker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susana","family":"Campino","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8985-9265","authenticated-orcid":false,"given":"Taane G.","family":"Clark","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2019,6,4]]},"reference":[{"key":"44599_CR1","unstructured":"World Health Organization. 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