PMC:7519301 / 40733-42102 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7519301","sourcedb":"PMC","sourceid":"7519301","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7519301","text":"Alignments subsampled at 10% 100 times were used to estimate population differentiation. The genetic differentiation of subpopulations within sampled sequences was calculated on each gene separately using Nei’s (30) GST. Because comparisons between subpopulations of different sizes can bias genetic differentiation estimates (60), genetic differentiation was also calculated using Jost’s (31) D, which accounts for differences in genetic heterogeneity between subpopulations and is intended to correct for biases in the size of the subpopulations. Both statistics were computed with the mmod package (32) in R (v3.6.1). For each gene, statistics were calculated over 100 bootstrapped samples for each subsampled alignment. Subpopulations were defined in two ways. First, sequences originating from the initial outbreak in the Hubei province (30 sequences) were compared to all other sequences within a subsampled alignment. Second, a 1-wk sliding window was designed to compare all sequences sampled prior to a collection date (subpopulation 1) to all sequences sampled after the same collection date (subpopulation 2). The first collection date for subpopulation 1 was February 14, 2020, the week after the last sequence from the Hubei province was sampled (February 8, 2020), The window was designed to terminate when \u003c30 sequences were available in subpopulation 2.","tracks":[{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T119","span":{"begin":183,"end":187},"obj":"Body_part"},{"id":"T120","span":{"begin":630,"end":634},"obj":"Body_part"}],"attributes":[{"id":"A119","pred":"fma_id","subj":"T119","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A120","pred":"fma_id","subj":"T120","obj":"http://purl.org/sig/ont/fma/fma74402"},{"subj":"T119","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T120","pred":"source","obj":"LitCovid-PD-FMA-UBERON"}]},{"project":"LitCovid-PD-CLO","denotations":[{"id":"T297","span":{"begin":183,"end":187},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T298","span":{"begin":630,"end":634},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T299","span":{"begin":901,"end":902},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T300","span":{"begin":933,"end":934},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T301","span":{"begin":1010,"end":1011},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"attributes":[{"subj":"T297","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T298","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T299","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T300","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T301","pred":"source","obj":"LitCovid-PD-CLO"}]},{"project":"LitCovid-PubTator","denotations":[{"id":"504","span":{"begin":216,"end":219},"obj":"Gene"},{"id":"505","span":{"begin":878,"end":893},"obj":"Species"}],"attributes":[{"id":"A505","pred":"tao:has_database_id","subj":"505","obj":"Tax:28384"},{"subj":"504","pred":"source","obj":"LitCovid-PubTator"},{"subj":"505","pred":"source","obj":"LitCovid-PubTator"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}]},{"project":"LitCovid-sentences","denotations":[{"id":"T251","span":{"begin":0,"end":88},"obj":"Sentence"},{"id":"T252","span":{"begin":89,"end":220},"obj":"Sentence"},{"id":"T253","span":{"begin":221,"end":548},"obj":"Sentence"},{"id":"T254","span":{"begin":549,"end":620},"obj":"Sentence"},{"id":"T255","span":{"begin":621,"end":723},"obj":"Sentence"},{"id":"T256","span":{"begin":724,"end":764},"obj":"Sentence"},{"id":"T257","span":{"begin":765,"end":924},"obj":"Sentence"},{"id":"T258","span":{"begin":925,"end":1120},"obj":"Sentence"},{"id":"T259","span":{"begin":1121,"end":1369},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"attributes":[{"subj":"T251","pred":"source","obj":"LitCovid-sentences"},{"subj":"T252","pred":"source","obj":"LitCovid-sentences"},{"subj":"T253","pred":"source","obj":"LitCovid-sentences"},{"subj":"T254","pred":"source","obj":"LitCovid-sentences"},{"subj":"T255","pred":"source","obj":"LitCovid-sentences"},{"subj":"T256","pred":"source","obj":"LitCovid-sentences"},{"subj":"T257","pred":"source","obj":"LitCovid-sentences"},{"subj":"T258","pred":"source","obj":"LitCovid-sentences"},{"subj":"T259","pred":"source","obj":"LitCovid-sentences"}]},{"project":"2_test","denotations":[{"id":"32868447-4519626-132542427","span":{"begin":212,"end":214},"obj":"4519626"},{"id":"32868447-21375616-132542428","span":{"begin":327,"end":329},"obj":"21375616"},{"id":"32868447-19238703-132542429","span":{"begin":390,"end":392},"obj":"19238703"},{"id":"32868447-22883857-132542430","span":{"begin":602,"end":604},"obj":"22883857"}],"attributes":[{"subj":"32868447-4519626-132542427","pred":"source","obj":"2_test"},{"subj":"32868447-21375616-132542428","pred":"source","obj":"2_test"},{"subj":"32868447-19238703-132542429","pred":"source","obj":"2_test"},{"subj":"32868447-22883857-132542430","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"LitCovid-PD-FMA-UBERON","color":"#ec9593","default":true},{"id":"LitCovid-PD-CLO","color":"#93aaec"},{"id":"LitCovid-PubTator","color":"#c4ec93"},{"id":"LitCovid-sentences","color":"#ec93de"},{"id":"2_test","color":"#93ece0"}]}]}}