{"id":"https://openalex.org/W2921879097","doi":"https://doi.org/10.1186/s12859-019-2620-0","title":"Similarities and differences between variants called with human reference genome HG19 or HG38","display_name":"Similarities and differences between variants called with human reference genome HG19 or HG38","publication_year":2019,"publication_date":"2019-03-01","ids":{"openalex":"https://openalex.org/W2921879097","doi":"https://doi.org/10.1186/s12859-019-2620-0","mag":"2921879097","pmid":"https://pubmed.ncbi.nlm.nih.gov/30871461"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-019-2620-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2620-0","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2620-0","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2620-0","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5058605068","display_name":"Bohu Pan","orcid":"https://orcid.org/0000-0003-2812-3718"},"institutions":[{"id":"https://openalex.org/I1304557061","display_name":"National Center for Toxicological Research","ror":"https://ror.org/05jmhh281","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1304557061","https://openalex.org/I1320320070"]},{"id":"https://openalex.org/I1320320070","display_name":"United States Food and Drug Administration","ror":"https://ror.org/034xvzb47","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1320320070"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bohu Pan","raw_affiliation_strings":["Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA","institution_ids":["https://openalex.org/I1304557061","https://openalex.org/I1320320070"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000179485","display_name":"Rebecca Kusko","orcid":"https://orcid.org/0000-0001-6730-5990"},"institutions":[{"id":"https://openalex.org/I4391767868","display_name":"Immuneering (United States)","ror":"https://ror.org/00awq8a10","country_code":null,"type":"company","lineage":["https://openalex.org/I4391767868"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rebecca Kusko","raw_affiliation_strings":["Immuneering Corporation, Cambridge, MA, 02142, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Immuneering Corporation, Cambridge, MA, 02142, USA","institution_ids":["https://openalex.org/I4391767868"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079978766","display_name":"Wenming Xiao","orcid":"https://orcid.org/0000-0003-4096-9724"},"institutions":[{"id":"https://openalex.org/I1304557061","display_name":"National Center for Toxicological Research","ror":"https://ror.org/05jmhh281","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1304557061","https://openalex.org/I1320320070"]},{"id":"https://openalex.org/I1320320070","display_name":"United States Food and Drug Administration","ror":"https://ror.org/034xvzb47","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1320320070"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wenming Xiao","raw_affiliation_strings":["Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA","institution_ids":["https://openalex.org/I1304557061","https://openalex.org/I1320320070"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014881178","display_name":"Yuanting Zheng","orcid":"https://orcid.org/0000-0003-4480-8303"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuanting Zheng","raw_affiliation_strings":["Center for Pharmacogenomics, Fudan University, Shanghai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Pharmacogenomics, Fudan University, Shanghai, China","institution_ids":["https://openalex.org/I24943067"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100459811","display_name":"Zhichao Liu","orcid":"https://orcid.org/0000-0003-3542-0905"},"institutions":[{"id":"https://openalex.org/I1304557061","display_name":"National Center for Toxicological Research","ror":"https://ror.org/05jmhh281","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1304557061","https://openalex.org/I1320320070"]},{"id":"https://openalex.org/I1320320070","display_name":"United States Food and Drug Administration","ror":"https://ror.org/034xvzb47","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1320320070"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhichao Liu","raw_affiliation_strings":["Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA","institution_ids":["https://openalex.org/I1304557061","https://openalex.org/I1320320070"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075843393","display_name":"Chunlin Xiao","orcid":"https://orcid.org/0000-0001-8702-4889"},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chunlin Xiao","raw_affiliation_strings":["National Center for Biotechnological Information, National Institutes of Health, Bethesda, MD, 20894, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Center for Biotechnological Information, National Institutes of Health, Bethesda, MD, 20894, USA","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001061892","display_name":"Sugunadevi Sakkiah","orcid":"https://orcid.org/0000-0002-8337-9348"},"institutions":[{"id":"https://openalex.org/I1304557061","display_name":"National Center for Toxicological Research","ror":"https://ror.org/05jmhh281","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1304557061","https://openalex.org/I1320320070"]},{"id":"https://openalex.org/I1320320070","display_name":"United States Food and Drug Administration","ror":"https://ror.org/034xvzb47","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1320320070"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sugunadevi Sakkiah","raw_affiliation_strings":["Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA","institution_ids":["https://openalex.org/I1304557061","https://openalex.org/I1320320070"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026066382","display_name":"Wenjing Guo","orcid":"https://orcid.org/0000-0002-0814-6982"},"institutions":[{"id":"https://openalex.org/I1304557061","display_name":"National Center for Toxicological Research","ror":"https://ror.org/05jmhh281","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1304557061","https://openalex.org/I1320320070"]},{"id":"https://openalex.org/I1320320070","display_name":"United States Food and Drug Administration","ror":"https://ror.org/034xvzb47","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1320320070"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wenjing Guo","raw_affiliation_strings":["Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA","institution_ids":["https://openalex.org/I1304557061","https://openalex.org/I1320320070"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021166773","display_name":"Ping Gong","orcid":"https://orcid.org/0000-0002-4782-1741"},"institutions":[{"id":"https://openalex.org/I87303767","display_name":"U.S. Army Engineer Research and Development Center","ror":"https://ror.org/027mhn368","country_code":"US","type":"facility","lineage":["https://openalex.org/I1304082316","https://openalex.org/I1306490931","https://openalex.org/I1330347796","https://openalex.org/I87303767"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ping Gong","raw_affiliation_strings":["Environmental Laboratory, US Army Engineer Research and Development Center, Vicksburg, MS, 39180, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Environmental Laboratory, US Army Engineer Research and Development Center, Vicksburg, MS, 39180, USA","institution_ids":["https://openalex.org/I87303767"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100603445","display_name":"Chaoyang Zhang","orcid":"https://orcid.org/0000-0002-1221-0406"},"institutions":[{"id":"https://openalex.org/I44854399","display_name":"University of Southern Mississippi","ror":"https://ror.org/0270vfa57","country_code":"US","type":"education","lineage":["https://openalex.org/I4210141039","https://openalex.org/I44854399"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chaoyang Zhang","raw_affiliation_strings":["School of Computing, The University of Southern Mississippi, Hattiesburg, MS, 39406, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing, The University of Southern Mississippi, Hattiesburg, MS, 39406, USA","institution_ids":["https://openalex.org/I44854399"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109700398","display_name":"Weigong Ge","orcid":null},"institutions":[{"id":"https://openalex.org/I1304557061","display_name":"National Center for Toxicological Research","ror":"https://ror.org/05jmhh281","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1304557061","https://openalex.org/I1320320070"]},{"id":"https://openalex.org/I1320320070","display_name":"United States Food and Drug Administration","ror":"https://ror.org/034xvzb47","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1320320070"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Weigong Ge","raw_affiliation_strings":["Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA","institution_ids":["https://openalex.org/I1304557061","https://openalex.org/I1320320070"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102979537","display_name":"Leming Shi","orcid":"https://orcid.org/0000-0002-7143-2033"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Leming Shi","raw_affiliation_strings":["Center for Pharmacogenomics, Fudan University, Shanghai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Pharmacogenomics, Fudan University, Shanghai, China","institution_ids":["https://openalex.org/I24943067"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068886380","display_name":"Weida Tong","orcid":"https://orcid.org/0000-0003-3488-6148"},"institutions":[{"id":"https://openalex.org/I1304557061","display_name":"National Center for Toxicological Research","ror":"https://ror.org/05jmhh281","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1304557061","https://openalex.org/I1320320070"]},{"id":"https://openalex.org/I1320320070","display_name":"United States Food and Drug Administration","ror":"https://ror.org/034xvzb47","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1320320070"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Weida Tong","raw_affiliation_strings":["Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA","institution_ids":["https://openalex.org/I1304557061","https://openalex.org/I1320320070"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100742819","display_name":"Huixiao Hong","orcid":"https://orcid.org/0000-0001-8087-3968"},"institutions":[{"id":"https://openalex.org/I1304557061","display_name":"National Center for Toxicological Research","ror":"https://ror.org/05jmhh281","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1304557061","https://openalex.org/I1320320070"]},{"id":"https://openalex.org/I1320320070","display_name":"United States Food and Drug Administration","ror":"https://ror.org/034xvzb47","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1320320070"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Huixiao Hong","raw_affiliation_strings":["Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA. huixiao.hong@fda.hhs.gov","Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA. huixiao.hong@fda.hhs.gov","institution_ids":["https://openalex.org/I1304557061"]},{"raw_affiliation_string":"Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA","institution_ids":["https://openalex.org/I1304557061","https://openalex.org/I1320320070"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":14,"corresponding_author_ids":["https://openalex.org/A5100742819"],"corresponding_institution_ids":["https://openalex.org/I1304557061","https://openalex.org/I1320320070"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":11.8792,"has_fulltext":true,"cited_by_count":82,"citation_normalized_percentile":{"value":0.9890676,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"20","issue":"S2","first_page":"101","last_page":"101"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.4343000054359436,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.4343000054359436,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.3393999934196472,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10751","display_name":"Forensic and Genetic Research","score":0.05920000001788139,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/reference-genome","display_name":"Reference genome","score":0.5978250503540039},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5294796228408813},{"id":"https://openalex.org/keywords/human-genome","display_name":"Human genome","score":0.4558897614479065},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.44368186593055725},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.42991408705711365},{"id":"https://openalex.org/keywords/1000-genomes-project","display_name":"1000 Genomes Project","score":0.4220660924911499},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.29544469714164734},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.22525346279144287},{"id":"https://openalex.org/keywords/single-nucleotide-polymorphism","display_name":"Single-nucleotide polymorphism","score":0.06662756204605103}],"concepts":[{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.5978250503540039},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5294796228408813},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.4558897614479065},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.44368186593055725},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.42991408705711365},{"id":"https://openalex.org/C97425143","wikidata":"https://www.wikidata.org/wiki/Q164786","display_name":"1000 Genomes Project","level":5,"score":0.4220660924911499},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.29544469714164734},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.22525346279144287},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.06662756204605103},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1186/s12859-019-2620-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2620-0","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2620-0","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30871461","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30871461","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:osti.gov:1626774","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1626774","pdf_url":"https://www.osti.gov/servlets/purl/1626774","source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:aquila.usm.edu:fac_pubs-17297","is_oa":false,"landing_page_url":"https://aquila.usm.edu/fac_pubs/15986","pdf_url":null,"source":{"id":"https://openalex.org/S4306402529","display_name":"Aquila Digital Community (University of Southern Mississippi)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I44854399","host_organization_name":"University of Southern Mississippi","host_organization_lineage":["https://openalex.org/I44854399"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Faculty Publications","raw_type":"text"},{"id":"pmh:oai:doaj.org/article:49310cbfb8a84d8296ccb15718252750","is_oa":false,"landing_page_url":"https://doaj.org/article/49310cbfb8a84d8296ccb15718252750","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 20, Iss S2, Pp 17-29 (2019)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5415867","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC6419332","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:6419332","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6419332","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-019-2620-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2620-0","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2620-0","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332163","display_name":"U.S. Food and Drug Administration","ror":"https://ror.org/034xvzb47"},{"id":"https://openalex.org/F4320332178","display_name":"National Institute of Standards and Technology","ror":"https://ror.org/05xpvk416"},{"id":"https://openalex.org/F4320332382","display_name":"Oak Ridge Institute for Science and Education","ror":"https://ror.org/0526p1y61"},{"id":"https://openalex.org/F4320337538","display_name":"U.S. Army Corps of Engineers","ror":"https://ror.org/05w4e8v21"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2921879097.pdf","grobid_xml":"https://content.openalex.org/works/W2921879097.grobid-xml"},"referenced_works_count":44,"referenced_works":["https://openalex.org/W223909586","https://openalex.org/W1580163505","https://openalex.org/W1596062789","https://openalex.org/W1622500880","https://openalex.org/W1919257374","https://openalex.org/W1958673254","https://openalex.org/W1993755972","https://openalex.org/W1996181407","https://openalex.org/W1997422030","https://openalex.org/W2001815897","https://openalex.org/W2034551256","https://openalex.org/W2044539313","https://openalex.org/W2082447166","https://openalex.org/W2085315239","https://openalex.org/W2092569525","https://openalex.org/W2095680943","https://openalex.org/W2101071606","https://openalex.org/W2104595023","https://openalex.org/W2108234281","https://openalex.org/W2108274478","https://openalex.org/W2124465358","https://openalex.org/W2127230663","https://openalex.org/W2147234914","https://openalex.org/W2147733682","https://openalex.org/W2147841875","https://openalex.org/W2149992227","https://openalex.org/W2150131459","https://openalex.org/W2165460636","https://openalex.org/W2168133698","https://openalex.org/W2168397218","https://openalex.org/W2168909179","https://openalex.org/W2170551349","https://openalex.org/W2176372762","https://openalex.org/W2177379918","https://openalex.org/W2310259903","https://openalex.org/W2527456406","https://openalex.org/W2586862787","https://openalex.org/W2603734366","https://openalex.org/W2770095154","https://openalex.org/W2787788280","https://openalex.org/W2952870794","https://openalex.org/W2953263404","https://openalex.org/W3098304617","https://openalex.org/W3147425560"],"related_works":["https://openalex.org/W3137911940","https://openalex.org/W1969895229","https://openalex.org/W3217304749","https://openalex.org/W2894932706","https://openalex.org/W2066142713","https://openalex.org/W2108497208","https://openalex.org/W2767606877","https://openalex.org/W2133994800","https://openalex.org/W2289136766","https://openalex.org/W2279684808"],"abstract_inverted_index":{"BACKGROUND:":[0],"Reference":[1],"genome":[2,27,37,62],"selection":[3],"is":[4],"a":[5],"prerequisite":[6],"for":[7,239],"successful":[8],"analysis":[9,50],"of":[10,20,36,185,216,230,256],"next":[11],"generation":[12],"sequencing":[13,63],"(NGS)":[14],"data.":[15],"Current":[16],"practice":[17],"employs":[18],"one":[19],"the":[21,34,52,67,92,116,132,147,178,186,257],"two":[22,86],"most":[23],"recent":[24],"human":[25,258],"reference":[26,259],"versions:":[28],"HG19":[29,57,82,96,111,126,136,158,166,223],"or":[30,83,112,159],"HG38.":[31,84,98,160,225],"To":[32,243],"date,":[33],"impact":[35],"version":[38],"on":[39,56,227],"SNV":[40,241],"identification":[41],"has":[42],"not":[43,219],"been":[44],"rigorously":[45],"assessed.":[46],"METHODS:":[47],"We":[48],"conducted":[49],"comparing":[51],"SNVs":[53,72,94,108,153,169,176,188,196,217,252],"identified":[54,251],"based":[55],"vs":[58],"HG38,":[59,113],"leveraging":[60],"whole":[61],"(WGS)":[64],"data":[65],"from":[66,123,135,163],"genome-in-a-bottle":[68],"(GIAB)":[69],"project.":[70],"First,":[71],"were":[73,88,129,154,193,202],"called":[74,93,109],"using":[75],"26":[76],"different":[77,254],"bioinformatics":[78],"pipelines":[79],"with":[80,110],"either":[81],"Next,":[85],"tools":[87],"used":[89],"to":[90,125,137,165,182],"convert":[91],"between":[95,107,157,222,253],"and":[97,114,173,224],"Lastly":[99],"we":[100,233],"calculated":[101],"conversion":[102,121,133,142,172,180],"rates,":[103],"analyzed":[104],"discordant":[105,117,175,187],"rates":[106,122,134,143],"characterized":[115],"SNVs.":[118],"RESULTS:":[119],"The":[120,141,161],"HG38":[124,138,164,235],"(average":[127,139],"95%)":[128],"lower":[130],"than":[131,177],"99%).":[140],"varied":[144],"slightly":[145],"among":[146],"various":[148],"calling":[149],"pipelines.":[150],"Around":[151],"1.5%":[152],"discordantly":[155],"converted":[156,221],"conversions":[162],"had":[167,189],"more":[168,174],"which":[170],"failed":[171],"opposite":[179],"(HG19":[181],"HG38).":[183],"Most":[184],"low":[190,194],"read":[191],"depth,":[192],"confidence":[195],"as":[197],"defined":[198],"by":[199,204],"GIAB,":[200],"and/or":[201],"predominated":[203],"G/C":[205],"alleles":[206],"(52%":[207],"observed":[208],"versus":[209],"42%":[210],"expected).":[211],"CONCLUSION:":[212],"A":[213],"significant":[214],"number":[215],"could":[218],"be":[220],"Based":[226],"careful":[228],"review":[229],"our":[231,245],"comparisons,":[232],"recommend":[234],"(the":[236],"newer":[237],"version)":[238],"NGS":[240],"analysis.":[242],"summarize,":[244],"findings":[246],"suggest":[247],"caution":[248],"when":[249],"translating":[250],"versions":[255],"genome.":[260]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":12},{"year":2024,"cited_by_count":19},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":15},{"year":2021,"cited_by_count":13},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":3}],"updated_date":"2026-06-23T13:55:30.953635","created_date":"2025-10-10T00:00:00"}
