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td-sidebar-link__section tree-root" id=m-datasetsdocsv1><span>Documentation</span></a><ul class=ul-1><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child" id=m-datasetsdocsv1getting_started-li><a href=/datasets/docs/v1/getting_started/ class="align-left ps-0 td-sidebar-link
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td-sidebar-link__page" id=m-datasetsdocsv1getting_started><span>Getting started</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child" id=m-datasetsdocsv1download-and-install-li><a href=/datasets/docs/v1/download-and-install/ class="align-left ps-0 td-sidebar-link
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td-sidebar-link__page" id=m-datasetsdocsv1download-and-install><span>Download and install</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child" id=m-datasetsdocsv1how-tos-li><a href=/datasets/docs/v1/how-tos/ class="align-left ps-0 td-sidebar-link
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td-sidebar-link__section" id=m-datasetsdocsv1how-tos><span>How-to guides</span></a><ul class="ul-2 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv1how-tosgenes-li><a href=/datasets/docs/v1/how-tos/genes/ class="align-left ps-0 td-sidebar-link
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td-sidebar-link__section" id=m-datasetsdocsv1how-tosgenes><span>Genes</span></a><ul class="ul-3 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1how-tosgenesget-gene-metadata-li><a href=/datasets/docs/v1/how-tos/genes/get-gene-metadata/ class="align-left ps-0 td-sidebar-link
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td-sidebar-link__page" id=m-datasetsdocsv1how-tosgenesget-gene-metadata><span>Get gene metadata</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1how-tosgenesdownload-gene-data-package-li><a href=/datasets/docs/v1/how-tos/genes/download-gene-data-package/ title="Download a gene data package" class="align-left ps-0 td-sidebar-link
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td-sidebar-link__page" id=m-datasetsdocsv1how-tosgenesdownload-gene-data-package><span>Download genes</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1how-tosgenesdownload-ortholog-dataset-li><a href=/datasets/docs/v1/how-tos/genes/download-ortholog-dataset/ title="Download a gene ortholog data package" class="align-left ps-0 td-sidebar-link
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td-sidebar-link__page" id=m-datasetsdocsv1how-tosgenesdownload-ortholog-dataset><span>Download gene orthologs</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1how-tosgenesortholog-get-one-isoform-li><a href=/datasets/docs/v1/how-tos/genes/ortholog-get-one-isoform/ title="Get representative protein sequences from Ortholog sets" class="align-left ps-0 td-sidebar-link
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td-sidebar-link__page" id=m-datasetsdocsv1how-tosgenesortholog-get-one-isoform><span>Get the longest isoform</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv1how-tosgenomes-li><a href=/datasets/docs/v1/how-tos/genomes/ class="align-left ps-0 td-sidebar-link
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td-sidebar-link__section" id=m-datasetsdocsv1how-tosgenomes><span>Genomes</span></a><ul class="ul-3 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1how-tosgenomesget-genome-metadata-li><a href=/datasets/docs/v1/how-tos/genomes/get-genome-metadata/ class="align-left ps-0 td-sidebar-link
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td-sidebar-link__page" id=m-datasetsdocsv1how-tosgenomesget-genome-metadata><span>Get genome metadata</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1how-tosgenomesdownload-genome-li><a href=/datasets/docs/v1/how-tos/genomes/download-genome/ title="Download a genome data package" class="align-left ps-0 td-sidebar-link
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td-sidebar-link__page" id=m-datasetsdocsv1how-tosgenomesdownload-genome><span>Download genome data</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1how-tosgenomeslarge-download-li><a href=/datasets/docs/v1/how-tos/genomes/large-download/ title="Download large genome data packages" class="align-left ps-0 td-sidebar-link
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td-sidebar-link__page" id=m-datasetsdocsv1how-tosgenomeslarge-download><span>Large genome downloads</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv1how-tosvirus-li><a href=/datasets/docs/v1/how-tos/virus/ class="align-left ps-0 td-sidebar-link
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td-sidebar-link__section" id=m-datasetsdocsv1how-tosvirus><span>Virus</span></a><ul class="ul-3 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1how-tosvirusget-sars2-genomes-li><a href=/datasets/docs/v1/how-tos/virus/get-sars2-genomes/ title="Download SARS-CoV-2 genomes" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1how-tosvirusget-sars2-genomes><span>SARS-CoV-2 genomes</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1how-tosvirusget-sars2-proteins-li><a href=/datasets/docs/v1/how-tos/virus/get-sars2-proteins/ title="Download SARS-CoV-2 protein sequences" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1how-tosvirusget-sars2-proteins><span>SARS-CoV-2 proteins</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv1how-tosdata-reports-li><a href=/datasets/docs/v1/how-tos/data-reports/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv1how-tosdata-reports><span>Working with JSON</span></a><ul class="ul-3 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1how-tosdata-reportsworking-with-jsonl-data-reports-li><a href=/datasets/docs/v1/how-tos/data-reports/working-with-jsonl-data-reports/ title="Working with JSON Lines data reports" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1how-tosdata-reportsworking-with-jsonl-data-reports><span>Working with data reports</span></a></li></ul></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child" id=m-datasetsdocsv1languages-li><a href=/datasets/docs/v1/languages/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv1languages><span>Supported programming languages</span></a><ul class="ul-2 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv1languagespython-li><a href=/datasets/docs/v1/languages/python/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv1languagespython><span>Python</span></a><ul class="ul-3 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv1languagespythonapi-li><a href=/datasets/docs/v1/languages/python/api/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv1languagespythonapi><span>Python API</span></a><ul class="ul-4 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasets-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/ title="Package: ncbi.datasets" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv1languagespythonapincbidatasets><span>ncbi.datasets</span></a><ul class="ul-5 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsmetadata-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/metadata/ title="Package: ncbi.datasets.metadata" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv1languagespythonapincbidatasetsmetadata><span>metadata</span></a><ul class="ul-6 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsmetadatagene-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/metadata/gene/ title="Module: ncbi.datasets.metadata.gene" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsmetadatagene><span>gene</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsmetadatagenome-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/metadata/genome/ title="Module: ncbi.datasets.metadata.genome" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsmetadatagenome><span>genome</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapi-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/ title="Package: ncbi.datasets.openapi" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapi><span>openapi</span></a><ul class="ul-6 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapiapi-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/api/ title="Package: ncbi.datasets.openapi.api" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapiapi><span>api</span></a><ul class="ul-7 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapiapigene_api-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/api/gene_api/ title="Module: ncbi.datasets.openapi.api.gene_api" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapiapigene_api><span>gene_api</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapiapigenome_api-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/api/genome_api/ title="Module: ncbi.datasets.openapi.api.genome_api" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapiapigenome_api><span>genome_api</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapiapiprokaryote_api-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/api/prokaryote_api/ title="Module: ncbi.datasets.openapi.api.prokaryote_api" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapiapiprokaryote_api><span>prokaryote_api</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapiapitaxonomy_api-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/api/taxonomy_api/ title="Module: ncbi.datasets.openapi.api.taxonomy_api" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapiapitaxonomy_api><span>taxonomy_api</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapiapiversion_api-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/api/version_api/ title="Module: ncbi.datasets.openapi.api.version_api" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapiapiversion_api><span>version_api</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapiapivirus_api-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/api/virus_api/ title="Module: ncbi.datasets.openapi.api.virus_api" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapiapivirus_api><span>virus_api</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapiapi_client-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/api_client/ title="Module: ncbi.datasets.openapi.api_client" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapiapi_client><span>api_client</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapiapis-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/apis/ title="Module: ncbi.datasets.openapi.apis" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapiapis><span>apis</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapiconfiguration-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/configuration/ title="Module: ncbi.datasets.openapi.configuration" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapiconfiguration><span>configuration</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapiexceptions-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/exceptions/ title="Module: ncbi.datasets.openapi.exceptions" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapiexceptions><span>exceptions</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodel_utils-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model_utils/ title="Module: ncbi.datasets.openapi.model_utils" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodel_utils><span>model_utils</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodel-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/ title="Module: OpenAPI Models" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodel><span>models</span></a><ul class="ul-7 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelprotobuf_any-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/protobuf_any/ title="Module: ncbi.datasets.openapi.model.protobuf_any" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelprotobuf_any><span>protobuf_any</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelrpc_status-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/rpc_status/ title="Module: ncbi.datasets.openapi.model.rpc_status" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelrpc_status><span>rpc_status</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_accessions-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_accessions/ title="Module: ncbi.datasets.openapi.model.v1_accessions" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_accessions><span>v1_accessions</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_annotated_assemblies-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_annotated_assemblies/ title="Module: ncbi.datasets.openapi.model.v1_annotated_assemblies" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_annotated_assemblies><span>v1_annotated_assemblies</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_annotation-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_annotation/ title="Module: ncbi.datasets.openapi.model.v1_annotation" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_annotation><span>v1_annotation</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_annotation_for_assembly-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_annotation_for_assembly/ title="Module: ncbi.datasets.openapi.model.v1_annotation_for_assembly" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_annotation_for_assembly><span>v1_annotation_for_assembly</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_annotation_for_assembly_file-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_annotation_for_assembly_file/ title="Module: ncbi.datasets.openapi.model.v1_annotation_for_assembly_file" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_annotation_for_assembly_file><span>v1_annotation_for_assembly_file</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_annotation_for_assembly_type-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_annotation_for_assembly_type/ title="Module: ncbi.datasets.openapi.model.v1_annotation_for_assembly_type" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_annotation_for_assembly_type><span>v1_annotation_for_assembly_type</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_annotation_for_virus_type-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_annotation_for_virus_type/ title="Module: ncbi.datasets.openapi.model.v1_annotation_for_virus_type" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_annotation_for_virus_type><span>v1_annotation_for_virus_type</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_assembly_dataset_availability-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_assembly_dataset_availability/ title="Module: ncbi.datasets.openapi.model.v1_assembly_dataset_availability" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_assembly_dataset_availability><span>v1_assembly_dataset_availability</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_assembly_dataset_descriptor-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_assembly_dataset_descriptor/ title="Module: ncbi.datasets.openapi.model.v1_assembly_dataset_descriptor" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_assembly_dataset_descriptor><span>v1_assembly_dataset_descriptor</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_assembly_dataset_descriptor_chromosome-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_assembly_dataset_descriptor_chromosome/ title="Module: ncbi.datasets.openapi.model.v1_assembly_dataset_descriptor_chromosome" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_assembly_dataset_descriptor_chromosome><span>v1_assembly_dataset_descriptor_chromosome</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_assembly_dataset_descriptors_filter-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_assembly_dataset_descriptors_filter/ title="Module: ncbi.datasets.openapi.model.v1_assembly_dataset_descriptors_filter" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_assembly_dataset_descriptors_filter><span>v1_assembly_dataset_descriptors_filter</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_assembly_dataset_descriptors_filter_assembly_level-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_assembly_dataset_descriptors_filter_assembly_level/ title="Module: ncbi.datasets.openapi.model.v1_assembly_dataset_descriptors_filter_assembly_level" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_assembly_dataset_descriptors_filter_assembly_level><span>v1_assembly_dataset_descriptors_filter_assembly_level</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_assembly_dataset_descriptors_filter_assembly_source-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_assembly_dataset_descriptors_filter_assembly_source/ title="Module: ncbi.datasets.openapi.model.v1_assembly_dataset_descriptors_filter_assembly_source" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_assembly_dataset_descriptors_filter_assembly_source><span>v1_assembly_dataset_descriptors_filter_assembly_source</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_assembly_dataset_descriptors_filter_assembly_version-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_assembly_dataset_descriptors_filter_assembly_version/ title="Module: ncbi.datasets.openapi.model.v1_assembly_dataset_descriptors_filter_assembly_version" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_assembly_dataset_descriptors_filter_assembly_version><span>v1_assembly_dataset_descriptors_filter_assembly_version</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_assembly_dataset_descriptors_request_content_type-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_assembly_dataset_descriptors_request_content_type/ title="Module: ncbi.datasets.openapi.model.v1_assembly_dataset_descriptors_request_content_type" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_assembly_dataset_descriptors_request_content_type><span>v1_assembly_dataset_descriptors_request_content_type</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_assembly_dataset_request-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_assembly_dataset_request/ title="Module: ncbi.datasets.openapi.model.v1_assembly_dataset_request" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_assembly_dataset_request><span>v1_assembly_dataset_request</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_assembly_dataset_request_resolution-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_assembly_dataset_request_resolution/ title="Module: ncbi.datasets.openapi.model.v1_assembly_dataset_request_resolution" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_assembly_dataset_request_resolution><span>v1_assembly_dataset_request_resolution</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_assembly_match-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_assembly_match/ title="Module: ncbi.datasets.openapi.model.v1_assembly_match" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_assembly_match><span>v1_assembly_match</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_assembly_metadata-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_assembly_metadata/ title="Module: ncbi.datasets.openapi.model.v1_assembly_metadata" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_assembly_metadata><span>v1_assembly_metadata</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_assembly_metadata_request-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_assembly_metadata_request/ title="Module: ncbi.datasets.openapi.model.v1_assembly_metadata_request" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_assembly_metadata_request><span>v1_assembly_metadata_request</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_assembly_metadata_request_bioprojects-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_assembly_metadata_request_bioprojects/ title="Module: ncbi.datasets.openapi.model.v1_assembly_metadata_request_bioprojects" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_assembly_metadata_request_bioprojects><span>v1_assembly_metadata_request_bioprojects</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_assembly_metadata_request_content_type-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_assembly_metadata_request_content_type/ title="Module: ncbi.datasets.openapi.model.v1_assembly_metadata_request_content_type" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_assembly_metadata_request_content_type><span>v1_assembly_metadata_request_content_type</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_bio_project-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_bio_project/ title="Module: ncbi.datasets.openapi.model.v1_bio_project" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_bio_project><span>v1_bio_project</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_bio_project_lineage-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_bio_project_lineage/ title="Module: ncbi.datasets.openapi.model.v1_bio_project_lineage" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_bio_project_lineage><span>v1_bio_project_lineage</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_busco_stat-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_busco_stat/ title="Module: ncbi.datasets.openapi.model.v1_busco_stat" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_busco_stat><span>v1_busco_stat</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_count_type-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_count_type/ title="Module: ncbi.datasets.openapi.model.v1_count_type" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_count_type><span>v1_count_type</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_dataset_request-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_dataset_request/ title="Module: ncbi.datasets.openapi.model.v1_dataset_request" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_dataset_request><span>v1_dataset_request</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_download_summary-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_download_summary/ title="Module: ncbi.datasets.openapi.model.v1_download_summary" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_download_summary><span>v1_download_summary</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_download_summary_available_files-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_download_summary_available_files/ title="Module: ncbi.datasets.openapi.model.v1_download_summary_available_files" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_download_summary_available_files><span>v1_download_summary_available_files</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_download_summary_dehydrated-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_download_summary_dehydrated/ title="Module: ncbi.datasets.openapi.model.v1_download_summary_dehydrated" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_download_summary_dehydrated><span>v1_download_summary_dehydrated</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_download_summary_file_summary-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_download_summary_file_summary/ title="Module: ncbi.datasets.openapi.model.v1_download_summary_file_summary" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_download_summary_file_summary><span>v1_download_summary_file_summary</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_download_summary_hydrated-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_download_summary_hydrated/ title="Module: ncbi.datasets.openapi.model.v1_download_summary_hydrated" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_download_summary_hydrated><span>v1_download_summary_hydrated</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_element_flank_config-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_element_flank_config/ title="Module: ncbi.datasets.openapi.model.v1_element_flank_config" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_element_flank_config><span>v1_element_flank_config</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_error-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_error/ title="Module: ncbi.datasets.openapi.model.v1_error" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_error><span>v1_error</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_error_assembly_error_code-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_error_assembly_error_code/ title="Module: ncbi.datasets.openapi.model.v1_error_assembly_error_code" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_error_assembly_error_code><span>v1_error_assembly_error_code</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_error_gene_error_code-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_error_gene_error_code/ title="Module: ncbi.datasets.openapi.model.v1_error_gene_error_code" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_error_gene_error_code><span>v1_error_gene_error_code</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_error_virus_error_code-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_error_virus_error_code/ title="Module: ncbi.datasets.openapi.model.v1_error_virus_error_code" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_error_virus_error_code><span>v1_error_virus_error_code</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_fasta-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_fasta/ title="Module: ncbi.datasets.openapi.model.v1_fasta" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_fasta><span>v1_fasta</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_feature_counts-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_feature_counts/ title="Module: ncbi.datasets.openapi.model.v1_feature_counts" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_feature_counts><span>v1_feature_counts</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_gene_counts-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_gene_counts/ title="Module: ncbi.datasets.openapi.model.v1_gene_counts" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_gene_counts><span>v1_gene_counts</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_gene_dataset_request-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_gene_dataset_request/ title="Module: ncbi.datasets.openapi.model.v1_gene_dataset_request" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_gene_dataset_request><span>v1_gene_dataset_request</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_gene_dataset_request_content_type-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_gene_dataset_request_content_type/ title="Module: ncbi.datasets.openapi.model.v1_gene_dataset_request_content_type" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_gene_dataset_request_content_type><span>v1_gene_dataset_request_content_type</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_gene_dataset_request_sort-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_gene_dataset_request_sort/ title="Module: ncbi.datasets.openapi.model.v1_gene_dataset_request_sort" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_gene_dataset_request_sort><span>v1_gene_dataset_request_sort</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_gene_dataset_request_sort_field-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_gene_dataset_request_sort_field/ title="Module: ncbi.datasets.openapi.model.v1_gene_dataset_request_sort_field" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_gene_dataset_request_sort_field><span>v1_gene_dataset_request_sort_field</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_gene_dataset_request_symbols_for_taxon-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_gene_dataset_request_symbols_for_taxon/ title="Module: ncbi.datasets.openapi.model.v1_gene_dataset_request_symbols_for_taxon" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_gene_dataset_request_symbols_for_taxon><span>v1_gene_dataset_request_symbols_for_taxon</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_gene_descriptor-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_gene_descriptor/ title="Module: ncbi.datasets.openapi.model.v1_gene_descriptor" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_gene_descriptor><span>v1_gene_descriptor</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_gene_descriptor_gene_type-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_gene_descriptor_gene_type/ title="Module: ncbi.datasets.openapi.model.v1_gene_descriptor_gene_type" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_gene_descriptor_gene_type><span>v1_gene_descriptor_gene_type</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_gene_descriptor_rna_type-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/model/v1_gene_descriptor_rna_type/ title="Module: ncbi.datasets.openapi.model.v1_gene_descriptor_rna_type" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodelv1_gene_descriptor_rna_type><span>v1_gene_descriptor_rna_type</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodels-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/models/ title="Module: OpenAPI Models" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapimodels><span>models</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapirest-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/openapi/rest/ title="Module: ncbi.datasets.openapi.rest" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetsopenapirest><span>rest</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetspackage-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/package/ title="Package: ncbi.datasets.package" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv1languagespythonapincbidatasetspackage><span>package</span></a><ul class="ul-6 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagespythonapincbidatasetspackagedataset-li><a href=/datasets/docs/v1/languages/python/api/ncbi.datasets/package/dataset/ title="Module: ncbi.datasets.package.dataset" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1languagespythonapincbidatasetspackagedataset><span>dataset</span></a></li></ul></li></ul></li></ul></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1languagesr-li><a href=/datasets/docs/v1/languages/r/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv1languagesr><span>R</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child active-path" id=m-datasetsdocsv1reference-docs-li><a href=/datasets/docs/v1/reference-docs/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv1reference-docs><span>Reference</span></a><ul class="ul-2 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child" id=m-datasetsdocsv1reference-docscommand-line-li><a href=/datasets/docs/v1/reference-docs/command-line/ title="Command line tool reference" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv1reference-docscommand-line><span>Command line</span></a><ul class="ul-3 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv1reference-docscommand-linedataformat-li><a href=/datasets/docs/v1/reference-docs/command-line/dataformat/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv1reference-docscommand-linedataformat><span>dataformat</span></a><ul class="ul-4 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv1reference-docscommand-linedataformattsv-li><a href=/datasets/docs/v1/reference-docs/command-line/dataformat/tsv/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv1reference-docscommand-linedataformattsv><span>tsv</span></a><ul class="ul-5 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedataformattsvdataformat_tsv_genome-li><a href=/datasets/docs/v1/reference-docs/command-line/dataformat/tsv/dataformat_tsv_genome/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedataformattsvdataformat_tsv_genome><span>genome</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedataformattsvdataformat_tsv_genome-seq-li><a href=/datasets/docs/v1/reference-docs/command-line/dataformat/tsv/dataformat_tsv_genome-seq/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedataformattsvdataformat_tsv_genome-seq><span>genome-seq</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedataformattsvdataformat_tsv_gene-li><a href=/datasets/docs/v1/reference-docs/command-line/dataformat/tsv/dataformat_tsv_gene/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedataformattsvdataformat_tsv_gene><span>gene</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedataformattsvdataformat_tsv_virus-genome-li><a href=/datasets/docs/v1/reference-docs/command-line/dataformat/tsv/dataformat_tsv_virus-genome/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedataformattsvdataformat_tsv_virus-genome><span>virus-genome</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedataformattsvdataformat_tsv_microbigge-li><a href=/datasets/docs/v1/reference-docs/command-line/dataformat/tsv/dataformat_tsv_microbigge/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedataformattsvdataformat_tsv_microbigge><span>microbigge</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedataformattsvdataformat_tsv_prok-gene-li><a href=/datasets/docs/v1/reference-docs/command-line/dataformat/tsv/dataformat_tsv_prok-gene/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedataformattsvdataformat_tsv_prok-gene><span>prok-gene</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedataformattsvdataformat_tsv_prok-gene-location-li><a href=/datasets/docs/v1/reference-docs/command-line/dataformat/tsv/dataformat_tsv_prok-gene-location/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedataformattsvdataformat_tsv_prok-gene-location><span>prok-gene-location</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv1reference-docscommand-linedataformatexcel-li><a href=/datasets/docs/v1/reference-docs/command-line/dataformat/excel/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv1reference-docscommand-linedataformatexcel><span>excel</span></a><ul class="ul-5 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedataformatexceldataformat_excel_genome-li><a href=/datasets/docs/v1/reference-docs/command-line/dataformat/excel/dataformat_excel_genome/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedataformatexceldataformat_excel_genome><span>genome</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedataformatexceldataformat_excel_genome-seq-li><a href=/datasets/docs/v1/reference-docs/command-line/dataformat/excel/dataformat_excel_genome-seq/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedataformatexceldataformat_excel_genome-seq><span>genome-seq</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedataformatexceldataformat_excel_gene-li><a href=/datasets/docs/v1/reference-docs/command-line/dataformat/excel/dataformat_excel_gene/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedataformatexceldataformat_excel_gene><span>gene</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedataformatexceldataformat_excel_virus-genome-li><a href=/datasets/docs/v1/reference-docs/command-line/dataformat/excel/dataformat_excel_virus-genome/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedataformatexceldataformat_excel_virus-genome><span>virus-genome</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedataformatexceldataformat_excel_microbigge-li><a href=/datasets/docs/v1/reference-docs/command-line/dataformat/excel/dataformat_excel_microbigge/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedataformatexceldataformat_excel_microbigge><span>microbigge</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedataformatexceldataformat_excel_prok-gene-li><a href=/datasets/docs/v1/reference-docs/command-line/dataformat/excel/dataformat_excel_prok-gene/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedataformatexceldataformat_excel_prok-gene><span>prok-gene</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedataformatexceldataformat_excel_prok-gene-location-li><a href=/datasets/docs/v1/reference-docs/command-line/dataformat/excel/dataformat_excel_prok-gene-location/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedataformatexceldataformat_excel_prok-gene-location><span>prok-gene-location</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedataformatdataformat_catalog-li><a href=/datasets/docs/v1/reference-docs/command-line/dataformat/dataformat_catalog/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedataformatdataformat_catalog><span>catalog</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv1reference-docscommand-linedataformatcompletion-li><a href=/datasets/docs/v1/reference-docs/command-line/dataformat/completion/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv1reference-docscommand-linedataformatcompletion><span>completion</span></a><ul class="ul-5 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedataformatcompletiondataformat_completion_bash-li><a href=/datasets/docs/v1/reference-docs/command-line/dataformat/completion/dataformat_completion_bash/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedataformatcompletiondataformat_completion_bash><span>bash</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedataformatcompletiondataformat_completion_zsh-li><a href=/datasets/docs/v1/reference-docs/command-line/dataformat/completion/dataformat_completion_zsh/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedataformatcompletiondataformat_completion_zsh><span>zsh</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedataformatcompletiondataformat_completion_fish-li><a href=/datasets/docs/v1/reference-docs/command-line/dataformat/completion/dataformat_completion_fish/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedataformatcompletiondataformat_completion_fish><span>fish</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedataformatcompletiondataformat_completion_powershell-li><a href=/datasets/docs/v1/reference-docs/command-line/dataformat/completion/dataformat_completion_powershell/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedataformatcompletiondataformat_completion_powershell><span>powershell</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedataformatdataformat_version-li><a href=/datasets/docs/v1/reference-docs/command-line/dataformat/dataformat_version/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedataformatdataformat_version><span>version</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv1reference-docscommand-linedatasets-li><a href=/datasets/docs/v1/reference-docs/command-line/datasets/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv1reference-docscommand-linedatasets><span>datasets</span></a><ul class="ul-4 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv1reference-docscommand-linedatasetssummary-li><a href=/datasets/docs/v1/reference-docs/command-line/datasets/summary/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv1reference-docscommand-linedatasetssummary><span>summary</span></a><ul class="ul-5 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv1reference-docscommand-linedatasetssummaryvirus-li><a href=/datasets/docs/v1/reference-docs/command-line/datasets/summary/virus/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv1reference-docscommand-linedatasetssummaryvirus><span>virus</span></a><ul class="ul-6 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv1reference-docscommand-linedatasetssummaryvirusgenome-li><a href=/datasets/docs/v1/reference-docs/command-line/datasets/summary/virus/genome/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv1reference-docscommand-linedatasetssummaryvirusgenome><span>genome</span></a><ul class="ul-7 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedatasetssummaryvirusgenomedatasets_summary_virus_genome_taxon-li><a href=/datasets/docs/v1/reference-docs/command-line/datasets/summary/virus/genome/datasets_summary_virus_genome_taxon/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedatasetssummaryvirusgenomedatasets_summary_virus_genome_taxon><span>taxon</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedatasetssummaryvirusgenomedatasets_summary_virus_genome_accession-li><a href=/datasets/docs/v1/reference-docs/command-line/datasets/summary/virus/genome/datasets_summary_virus_genome_accession/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedatasetssummaryvirusgenomedatasets_summary_virus_genome_accession><span>accession</span></a></li></ul></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv1reference-docscommand-linedatasetssummarygene-li><a href=/datasets/docs/v1/reference-docs/command-line/datasets/summary/gene/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv1reference-docscommand-linedatasetssummarygene><span>gene</span></a><ul class="ul-6 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedatasetssummarygenedatasets_summary_gene_gene-id-li><a href=/datasets/docs/v1/reference-docs/command-line/datasets/summary/gene/datasets_summary_gene_gene-id/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedatasetssummarygenedatasets_summary_gene_gene-id><span>gene-id</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedatasetssummarygenedatasets_summary_gene_symbol-li><a href=/datasets/docs/v1/reference-docs/command-line/datasets/summary/gene/datasets_summary_gene_symbol/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedatasetssummarygenedatasets_summary_gene_symbol><span>symbol</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedatasetssummarygenedatasets_summary_gene_accession-li><a href=/datasets/docs/v1/reference-docs/command-line/datasets/summary/gene/datasets_summary_gene_accession/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedatasetssummarygenedatasets_summary_gene_accession><span>accession</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedatasetssummarygenedatasets_summary_gene_taxon-li><a href=/datasets/docs/v1/reference-docs/command-line/datasets/summary/gene/datasets_summary_gene_taxon/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedatasetssummarygenedatasets_summary_gene_taxon><span>taxon</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv1reference-docscommand-linedatasetssummarygenome-li><a href=/datasets/docs/v1/reference-docs/command-line/datasets/summary/genome/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv1reference-docscommand-linedatasetssummarygenome><span>genome</span></a><ul class="ul-6 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedatasetssummarygenomedatasets_summary_genome_accession-li><a href=/datasets/docs/v1/reference-docs/command-line/datasets/summary/genome/datasets_summary_genome_accession/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedatasetssummarygenomedatasets_summary_genome_accession><span>accession</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedatasetssummarygenomedatasets_summary_genome_taxon-li><a href=/datasets/docs/v1/reference-docs/command-line/datasets/summary/genome/datasets_summary_genome_taxon/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedatasetssummarygenomedatasets_summary_genome_taxon><span>taxon</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv1reference-docscommand-linedatasetssummaryortholog-li><a href=/datasets/docs/v1/reference-docs/command-line/datasets/summary/ortholog/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv1reference-docscommand-linedatasetssummaryortholog><span>ortholog</span></a><ul class="ul-6 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedatasetssummaryorthologdatasets_summary_ortholog_gene-id-li><a href=/datasets/docs/v1/reference-docs/command-line/datasets/summary/ortholog/datasets_summary_ortholog_gene-id/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedatasetssummaryorthologdatasets_summary_ortholog_gene-id><span>gene-id</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedatasetssummaryorthologdatasets_summary_ortholog_symbol-li><a href=/datasets/docs/v1/reference-docs/command-line/datasets/summary/ortholog/datasets_summary_ortholog_symbol/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedatasetssummaryorthologdatasets_summary_ortholog_symbol><span>symbol</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedatasetssummaryorthologdatasets_summary_ortholog_accession-li><a href=/datasets/docs/v1/reference-docs/command-line/datasets/summary/ortholog/datasets_summary_ortholog_accession/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedatasetssummaryorthologdatasets_summary_ortholog_accession><span>accession</span></a></li></ul></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv1reference-docscommand-linedatasetsdownload-li><a href=/datasets/docs/v1/reference-docs/command-line/datasets/download/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv1reference-docscommand-linedatasetsdownload><span>download</span></a><ul class="ul-5 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv1reference-docscommand-linedatasetsdownloadgene-li><a href=/datasets/docs/v1/reference-docs/command-line/datasets/download/gene/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv1reference-docscommand-linedatasetsdownloadgene><span>gene</span></a><ul class="ul-6 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedatasetsdownloadgenedatasets_download_gene_gene-id-li><a href=/datasets/docs/v1/reference-docs/command-line/datasets/download/gene/datasets_download_gene_gene-id/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedatasetsdownloadgenedatasets_download_gene_gene-id><span>gene-id</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedatasetsdownloadgenedatasets_download_gene_symbol-li><a href=/datasets/docs/v1/reference-docs/command-line/datasets/download/gene/datasets_download_gene_symbol/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedatasetsdownloadgenedatasets_download_gene_symbol><span>symbol</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedatasetsdownloadgenedatasets_download_gene_accession-li><a href=/datasets/docs/v1/reference-docs/command-line/datasets/download/gene/datasets_download_gene_accession/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedatasetsdownloadgenedatasets_download_gene_accession><span>accession</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedatasetsdownloadgenedatasets_download_gene_taxon-li><a href=/datasets/docs/v1/reference-docs/command-line/datasets/download/gene/datasets_download_gene_taxon/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedatasetsdownloadgenedatasets_download_gene_taxon><span>taxon</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv1reference-docscommand-linedatasetsdownloadgenome-li><a href=/datasets/docs/v1/reference-docs/command-line/datasets/download/genome/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv1reference-docscommand-linedatasetsdownloadgenome><span>genome</span></a><ul class="ul-6 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedatasetsdownloadgenomedatasets_download_genome_accession-li><a href=/datasets/docs/v1/reference-docs/command-line/datasets/download/genome/datasets_download_genome_accession/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedatasetsdownloadgenomedatasets_download_genome_accession><span>accession</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedatasetsdownloadgenomedatasets_download_genome_taxon-li><a href=/datasets/docs/v1/reference-docs/command-line/datasets/download/genome/datasets_download_genome_taxon/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedatasetsdownloadgenomedatasets_download_genome_taxon><span>taxon</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv1reference-docscommand-linedatasetsdownloadvirus-li><a href=/datasets/docs/v1/reference-docs/command-line/datasets/download/virus/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv1reference-docscommand-linedatasetsdownloadvirus><span>virus</span></a><ul class="ul-6 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv1reference-docscommand-linedatasetsdownloadvirusgenome-li><a href=/datasets/docs/v1/reference-docs/command-line/datasets/download/virus/genome/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv1reference-docscommand-linedatasetsdownloadvirusgenome><span>genome</span></a><ul class="ul-7 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedatasetsdownloadvirusgenomedatasets_download_virus_genome_accession-li><a href=/datasets/docs/v1/reference-docs/command-line/datasets/download/virus/genome/datasets_download_virus_genome_accession/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedatasetsdownloadvirusgenomedatasets_download_virus_genome_accession><span>accession</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedatasetsdownloadvirusgenomedatasets_download_virus_genome_taxon-li><a href=/datasets/docs/v1/reference-docs/command-line/datasets/download/virus/genome/datasets_download_virus_genome_taxon/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedatasetsdownloadvirusgenomedatasets_download_virus_genome_taxon><span>taxon</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedatasetsdownloadvirusdatasets_download_virus_protein-li><a href=/datasets/docs/v1/reference-docs/command-line/datasets/download/virus/datasets_download_virus_protein/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedatasetsdownloadvirusdatasets_download_virus_protein><span>protein</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv1reference-docscommand-linedatasetsdownloadortholog-li><a href=/datasets/docs/v1/reference-docs/command-line/datasets/download/ortholog/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv1reference-docscommand-linedatasetsdownloadortholog><span>ortholog</span></a><ul class="ul-6 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedatasetsdownloadorthologdatasets_download_ortholog_gene-id-li><a href=/datasets/docs/v1/reference-docs/command-line/datasets/download/ortholog/datasets_download_ortholog_gene-id/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedatasetsdownloadorthologdatasets_download_ortholog_gene-id><span>gene-id</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedatasetsdownloadorthologdatasets_download_ortholog_symbol-li><a href=/datasets/docs/v1/reference-docs/command-line/datasets/download/ortholog/datasets_download_ortholog_symbol/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedatasetsdownloadorthologdatasets_download_ortholog_symbol><span>symbol</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedatasetsdownloadorthologdatasets_download_ortholog_accession-li><a href=/datasets/docs/v1/reference-docs/command-line/datasets/download/ortholog/datasets_download_ortholog_accession/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedatasetsdownloadorthologdatasets_download_ortholog_accession><span>accession</span></a></li></ul></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedatasetsdatasets_rehydrate-li><a href=/datasets/docs/v1/reference-docs/command-line/datasets/datasets_rehydrate/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedatasetsdatasets_rehydrate><span>rehydrate</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv1reference-docscommand-linedatasetscompletion-li><a href=/datasets/docs/v1/reference-docs/command-line/datasets/completion/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv1reference-docscommand-linedatasetscompletion><span>completion</span></a><ul class="ul-5 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedatasetscompletiondatasets_completion_bash-li><a href=/datasets/docs/v1/reference-docs/command-line/datasets/completion/datasets_completion_bash/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedatasetscompletiondatasets_completion_bash><span>bash</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedatasetscompletiondatasets_completion_zsh-li><a href=/datasets/docs/v1/reference-docs/command-line/datasets/completion/datasets_completion_zsh/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedatasetscompletiondatasets_completion_zsh><span>zsh</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedatasetscompletiondatasets_completion_fish-li><a href=/datasets/docs/v1/reference-docs/command-line/datasets/completion/datasets_completion_fish/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedatasetscompletiondatasets_completion_fish><span>fish</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedatasetscompletiondatasets_completion_powershell-li><a href=/datasets/docs/v1/reference-docs/command-line/datasets/completion/datasets_completion_powershell/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedatasetscompletiondatasets_completion_powershell><span>powershell</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docscommand-linedatasetsdatasets_version-li><a href=/datasets/docs/v1/reference-docs/command-line/datasets/datasets_version/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docscommand-linedatasetsdatasets_version><span>version</span></a></li></ul></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child active-path" id=m-datasetsdocsv1reference-docsfile-formats-li><a href=/datasets/docs/v1/reference-docs/file-formats/ title="Annotation file formats" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv1reference-docsfile-formats><span>File formats</span></a><ul class="ul-3 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child" id=m-datasetsdocsv1reference-docsfile-formatsabout-ncbi-gbff-li><a href=/datasets/docs/v1/reference-docs/file-formats/about-ncbi-gbff/ title="GBFF format" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docsfile-formatsabout-ncbi-gbff><span>GBFF</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child active-path" id=m-datasetsdocsv1reference-docsfile-formatsabout-ncbi-gff3-li><a href=/datasets/docs/v1/reference-docs/file-formats/about-ncbi-gff3/ title="GFF3 format" class="align-left ps-0 active td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docsfile-formatsabout-ncbi-gff3><span class=td-sidebar-nav-active-item>GFF3</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child" id=m-datasetsdocsv1reference-docsdata-reports-li><a href=/datasets/docs/v1/reference-docs/data-reports/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv1reference-docsdata-reports><span>Report schemas</span></a><ul class="ul-3 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docsdata-reportsgene-li><a href=/datasets/docs/v1/reference-docs/data-reports/gene/ title="Gene report" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docsdata-reportsgene><span>Gene</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docsdata-reportsgenome-assembly-li><a href=/datasets/docs/v1/reference-docs/data-reports/genome-assembly/ title="Genome assembly report" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docsdata-reportsgenome-assembly><span>Genome assembly</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docsdata-reportsgenome-sequence-li><a href=/datasets/docs/v1/reference-docs/data-reports/genome-sequence/ title="Genome sequence report" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docsdata-reportsgenome-sequence><span>Genome sequence</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docsdata-reportsmicrobigge-li><a href=/datasets/docs/v1/reference-docs/data-reports/microbigge/ title="MicroBIGG-E report" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docsdata-reportsmicrobigge><span>MicroBIGG-E</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docsdata-reportsprokaryote-gene-li><a href=/datasets/docs/v1/reference-docs/data-reports/prokaryote-gene/ title="Prokaryote gene report" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docsdata-reportsprokaryote-gene><span>Prok. gene</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docsdata-reportsprokaryote-gene-location-li><a href=/datasets/docs/v1/reference-docs/data-reports/prokaryote-gene-location/ title="Prokaryote gene location report" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docsdata-reportsprokaryote-gene-location><span>Prok. gene location</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docsdata-reportsvirus-li><a href=/datasets/docs/v1/reference-docs/data-reports/virus/ title="Virus report" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docsdata-reportsvirus><span>Virus</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child" id=m-datasetsdocsv1reference-docsdata-packages-li><a href=/datasets/docs/v1/reference-docs/data-packages/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv1reference-docsdata-packages><span>Data packages</span></a><ul class="ul-3 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docsdata-packagesgene-package-li><a href=/datasets/docs/v1/reference-docs/data-packages/gene-package/ title="NCBI Datasets Gene Package" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docsdata-packagesgene-package><span>Gene package</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docsdata-packagesgenome-li><a href=/datasets/docs/v1/reference-docs/data-packages/genome/ title="NCBI Datasets Genome Package" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docsdata-packagesgenome><span>Genome package</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docsdata-packagessars-cov-2-genome-li><a href=/datasets/docs/v1/reference-docs/data-packages/sars-cov-2-genome/ title="NCBI Datasets SARS-CoV-2 Data Package" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docsdata-packagessars-cov-2-genome><span>SARS-CoV-2 data package</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child" id=m-datasetsdocsv1reference-docsgca-and-gcf-explained-li><a href=/datasets/docs/v1/reference-docs/gca-and-gcf-explained/ title="GenBank (GCA) and RefSeq (GCF) genome assemblies" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docsgca-and-gcf-explained><span>GCA and GCF genomes</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child" id=m-datasetsdocsv1reference-docsjq-cheatsheet-li><a href=/datasets/docs/v1/reference-docs/jq-cheatsheet/ title="jq cheatsheet for genome metadata" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docsjq-cheatsheet><span>jq cheatsheet</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child" id=m-datasetsdocsv1reference-docsrest-api-li><a href=/datasets/docs/v1/reference-docs/rest-api/ title="NCBI Datasets v1 REST API" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv1reference-docsrest-api><span>REST API</span></a><ul class="ul-3 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docsrest-apiauthentication-li><a href=/datasets/docs/v1/reference-docs/rest-api/authentication/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docsrest-apiauthentication><span>Authentication</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1reference-docsrest-apideprecated_apis-li><a href=/datasets/docs/v1/reference-docs/rest-api/deprecated_apis/ title="Retired API Endpoints" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1reference-docsrest-apideprecated_apis><span>Retired Endpoints</span></a></li></ul></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child" id=m-datasetsdocsv1troubleshooting-li><a href=/datasets/docs/v1/troubleshooting/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv1troubleshooting><span>FAQs and troubleshooting</span></a><ul class="ul-2 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1troubleshootingfaq-li><a href=/datasets/docs/v1/troubleshooting/faq/ title=FAQs class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1troubleshootingfaq><span>Frequently asked Questions</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv1troubleshootingmac-zip-bug-li><a href=/datasets/docs/v1/troubleshooting/mac-zip-bug/ title="Mac Safari zip archive bug" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv1troubleshootingmac-zip-bug><span>Mac zip bug</span></a></li></ul></li></ul></li></ul></nav><script src=/datasets/docs/v1/js/sidebar-tree.js></script><div id=doc-version-selector-container><div>Documentation version</div><select><option value=v1>CLI v13.x (API v1)</option><option value=v2>CLI v16+ (API v2)</option></select>
|
||
<a href=/datasets/docs/v2/troubleshooting/faq/#which-version-of-the-documentation-should-i-use>Learn more</a></div></div></div><div class="d-none d-xl-block col-xl-2 td-sidebar-toc d-print-none"><div class=td-toc><nav id=TableOfContents><ul><li><a href=#directives>Directives</a><ul><li><a href=#official-directives>Official directives</a></li><li><a href=#unofficial-directives>Unofficial directives</a></li></ul></li><li><a href=#column-specifications>Column Specifications</a></li><li><a href=#attribute-specifications>Attribute Specifications</a><ul><li><a href=#official-gff3-attributes>Official GFF3 attributes</a></li><li><a href=#unofficial-attributes>Unofficial attributes</a></li></ul></li><li><a href=#annotation-data-model>Annotation Data Model</a></li><li><a href=#additional-details>Additional Details</a><ul><li><a href=#the-source-region-feature>The source ‘region’ feature</a></li><li><a href=#utrs>UTRs</a></li><li><a href=#start-and-stop-codons>Start and stop codons</a></li><li><a href=#origin-spanning-features>Origin-spanning features</a></li><li><a href=#annotation-accommodations-for-putative-assembly-errors>Annotation accommodations for putative assembly errors</a></li><li><a href=#ribosomal-slippage>Ribosomal slippage</a></li></ul></li><li><a href=#alignments>Alignments</a><ul><li><a href=#official-gff3-attributes-1>Official GFF3 attributes</a></li><li><a href=#unofficial-attributes-1>Unofficial attributes</a></li></ul></li></ul></nav></div></div><main class="col-12 col-md-9 col-xl-8 pl-md-5" role=main><div id=possible-banner></div><div class=watermarked data-watermark=" Retired "></div><nav aria-label=breadcrumb class=d-print-none><ol class="breadcrumb spb-1"><li class=breadcrumb-item><a href=/datasets/docs/v1/>Documentation</a></li><li class=breadcrumb-item><a href=/datasets/docs/v1/reference-docs/>Reference</a></li><li class=breadcrumb-item><a href=/datasets/docs/v1/reference-docs/file-formats/>File formats</a></li><li class="breadcrumb-item active" aria-current=page><a href=/datasets/docs/v1/reference-docs/file-formats/about-ncbi-gff3/>GFF3</a></li></ol></nav><h1 class="mb-4 font-weight-bold">GFF3 format</h1><p class="lead pb-2">Supports all annotated assemblies</p><div class="d-xl-none td-toc td-toc--inline d-print-none"><a id=td-content__toc-link href=#td-content__toc data-toggle=collapse aria-controls=td-docs-toc aria-expanded=false aria-label="Toggle toc navigation"><span class=lead>Contents<i class="fas fa-chevron-right ml-2"></i></span></a><div id=td-content__toc class=collapse><nav id=TableOfContents><ul><li><a href=#directives>Directives</a><ul><li><a href=#official-directives>Official directives</a></li><li><a href=#unofficial-directives>Unofficial directives</a></li></ul></li><li><a href=#column-specifications>Column Specifications</a></li><li><a href=#attribute-specifications>Attribute Specifications</a><ul><li><a href=#official-gff3-attributes>Official GFF3 attributes</a></li><li><a href=#unofficial-attributes>Unofficial attributes</a></li></ul></li><li><a href=#annotation-data-model>Annotation Data Model</a></li><li><a href=#additional-details>Additional Details</a><ul><li><a href=#the-source-region-feature>The source ‘region’ feature</a></li><li><a href=#utrs>UTRs</a></li><li><a href=#start-and-stop-codons>Start and stop codons</a></li><li><a href=#origin-spanning-features>Origin-spanning features</a></li><li><a href=#annotation-accommodations-for-putative-assembly-errors>Annotation accommodations for putative assembly errors</a></li><li><a href=#ribosomal-slippage>Ribosomal slippage</a></li></ul></li><li><a href=#alignments>Alignments</a><ul><li><a href=#official-gff3-attributes-1>Official GFF3 attributes</a></li><li><a href=#unofficial-attributes-1>Unofficial attributes</a></li></ul></li></ul></nav></div><button id=td-content__toc-link-expanded href=#td-content__toc class="btn btn-small ml-1 my-2 py-0 px-3" data-toggle=collapse aria-controls=td-docs-toc aria-expanded=true aria-label="Toggle toc navigation"></button></div><style>.td-content table{border:1px solid #ccc}@media screen and (min-width:600px){.td-content table{display:table}}@media screen and (max-width:400px){.td-content table td{white-space:nowrap!important}}.td-content table th{white-space:nowrap}summary>h3{display:inline-block}</style><div class=td-content><h1>GFF3 format</h1><div class=lead>Supports all annotated assemblies</div><header class=article-meta></header><p>Genome annotation files are provided in GFF3 format for all annotated assemblies included in NCBI’s Genomes FTP resource.
|
||
GFF3 files are formatted according to the <a href=https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md target=_blank>specifications</a>
|
||
published by the Sequence Ontology.</p><p>NCBI’s GFF3 files differ from the official GFF3 specifications for certain attributes and formatting details.</p><h2 id=directives>Directives</h2><h3 id=official-directives>Official directives</h3><p>The following directives or pragmas are provided according to the GFF3
|
||
specifications:</p><p><strong>##gff-version</strong></p><p><strong>##sequence-region</strong></p><p><strong>##species</strong></p><h3 id=unofficial-directives>Unofficial directives</h3><p>The following directives are not part of the official GFF3 specifications and
|
||
have been proposed or are provided as additional information to aid in
|
||
parsing the files. They are indicated by a leading ‘#!’.</p><p><strong>#!gff-spec-version</strong>
|
||
specific version of the GFF3 specification that the files conform to</p><p><strong>#!processor</strong>
|
||
NCBI application used to generate the files</p><p><strong>#!genome-build</strong>
|
||
Assembly name, if the set of seqids included in the file correspond to a
|
||
specific genome assembly</p><p><strong>#!genome-build-accession</strong>
|
||
Assembly accession.version as defined in NCBI’s Assembly resource. This is
|
||
a stable, unique identifier for the set of sequence records included in an
|
||
assembly as found in INSDC or RefSeq, and it is highly recommended to use
|
||
the assembly accession.version in addition to or instead of the assembly
|
||
name to ensure consistency in datasets.</p><p><strong>#!annotation-date</strong>
|
||
Date the annotation was produced, if available</p><p><strong>#!annotation-source</strong>
|
||
Source and name to use for the annotation, if available</p><h2 id=column-specifications>Column Specifications</h2><p><strong>Column 1: “seqid”</strong>
|
||
Accession.version of the annotated genomic sequence.
|
||
NCBI files universally use accession.version because it provides an
|
||
unambiguous identifier for the annotated sequence, and does not require
|
||
additional knowledge of the species, assembly and version, and data source.
|
||
We strongly recommend using accession.version instead of ambiguous seqids
|
||
such as ‘chr1’ to avoid errors due to mis-associating features with the
|
||
wrong genomic location.</p><p><strong>Column 2: “source”</strong>
|
||
For annotations produced by one of NCBI’s pipelines, the method used to
|
||
generate the annotation is provided in column 2. The method is found in the
|
||
ModelEvidence object in ASN.1 format, and appears in the flatfile format as
|
||
a structured note. For example:
|
||
“Derived by automated computational analysis using gene prediction method:
|
||
BestRefSeq”</p><p>The reported methods for RefSeq eukaryotic annotations include:</p><p><em>BestRefSeq:</em> feature projected from the alignment of a “known” RefSeq transcript to the genome</p><p><em>Curated Genomic:</em> feature projected from the alignment of a curated RefSeq genomic sequence to the genome</p><p><em>Gnomon:</em> feature predicted by Gnomon, using transcript and protein evidence and/or ab initio</p><p><em>BestRefSeq,Gnomon:</em> gene with children features predicted by BestRefSeq and Gnomon</p><p><em>Curated Genomic,Gnomon:</em> gene with children features predicted Curated Genomic or Gnomon</p><p><em>tRNAscan-SE:</em> feature predicted by tRNAscan-SE</p><p>The reported methods for RefSeq prokaryotic annotations include:</p><p><em>GeneMarkS+:</em> feature predicted by GeneMarkS+</p><p><em>Protein Homology:</em> feature predicted by protein alignment</p><p><em>cmsearch:</em> feature predicted by cmsearch</p><p><em>tRNAscan-SE:</em> feature predicted by tRNAscan-SE</p><p>If the annotation method is not available, the source column is based on the
|
||
source database for the record (RefSeq, GenBank, EMBL, DDBJ).</p><p><strong>Column 3: “type”</strong>
|
||
The SOFA feature type most equivalent to the feature found in the source
|
||
annotation. The original GenBank feature type is also provided by the “gbkey”
|
||
attribute in column 9.</p><p><strong>Columns 4 & 5: “start” and “end”</strong>
|
||
Start and end coordinates of the feature in 1-based coordinates. Note two
|
||
exon or CDS rows of the same feature may overlap or be separated by an
|
||
artificial “micro-intron” in order to represent cases of ribosomal slippage
|
||
or putative assembly errors. See Additional Details below for more
|
||
information.</p><p><strong>Column 6: “score”</strong>
|
||
Currently only provided for alignments, if they contain a score named
|
||
“score”. The definition of this score may vary depending on the type of
|
||
alignment.</p><p><strong>Column 7: “strand”</strong>
|
||
The strand of the feature</p><p><strong>Column 8: “phase”</strong>
|
||
The phase of the CDS feature, which is related to /codon_start in the
|
||
flatfile specification. The phase is computed based on the known phase at
|
||
the start of the CDS and computed for subsequent CDS rows. It may not be
|
||
accurate if the CDS contains internal frameshifts, which can occur in
|
||
pseudogenes and in genomes with indels, assembly gaps, and other errors.
|
||
See Additional Details below for more information.</p><p><strong>Column 9: “attributes”</strong>
|
||
A semicolon delimited list of official and additional attributes describing
|
||
the feature.</p><h2 id=attribute-specifications>Attribute Specifications</h2><p>Attributes in column 9 conform to the GFF3 specification, which uses a starting
|
||
Capital letter for official attributes and starting lower-case letter for other
|
||
attributes.</p><h3 id=official-gff3-attributes>Official GFF3 attributes</h3><p><strong>ID</strong>
|
||
A unique identifier for the feature. Most IDs are generated on-the-fly
|
||
during file generation. They are not intended to be used as stable feature
|
||
identifiers, and they are likely to change between annotation versions.
|
||
Multiple rows with the same ID designate a single feature that is
|
||
composed of multiple parts, most common for CDSes and multi-exon alignments
|
||
but possible for other feature types as well. Note other attributes such as
|
||
gene symbols, GeneIDs, and transcript or protein accessions may occur on
|
||
multiple features, whereas the ID is globally unique for an individual file.</p><p><strong>Parent</strong>
|
||
ID of the parent of the feature</p><p><strong>Dbxref</strong>
|
||
A set of comma-separated tag:ID pairs corresponding to the /db_xref
|
||
qualifiers provided in the source annotation. Note that database IDs can contain
|
||
colons, so a format such as “HGNC:HGNC:1100” is expected and should be
|
||
parsed on the first colon. See NCBI’s <a href=https://www.ncbi.nlm.nih.gov/genbank/collab/db_xref target=_blank>documentation on the db_xref qualifier</a>
|
||
for more details, including URLs corresponding to specific database tags.</p><p>Most Dbxref tags known to NCBI are also available in the <a href=http://amigo.geneontology.org/xrefs target=_blank>list</a>
|
||
provided by
|
||
the <a href=http://geneontology.org/ target=_blank>Gene Ontology Consortium</a>
|
||
.</p><p><strong>Name</strong>
|
||
A suggested display name for the feature, currently populated for specific
|
||
features:
|
||
region “landmark” feature – chromosome or linkage group, if available
|
||
gene – gene symbol or locus_tag
|
||
RNA (multiple types) and CDS – product accession.version (if exists)</p><p><strong>Note</strong>
|
||
feature comment. This appears as a /note qualifier in the GenBank format.
|
||
Additional text may appear in the flatfile /note that internally is not part
|
||
of a comment, and is not included in the GFF3 Note attribute.</p><p><strong>Is_circular</strong>
|
||
provided on the landmark “region” feature as ‘Is_circular=true’ if the record
|
||
is annotated to be a circular chromosome.</p><h3 id=unofficial-attributes>Unofficial attributes</h3><p>This section describes the unofficial attributes that are the most informative for interpreting NCBI’s GFF3 files. Many of the unofficial attributes correspond to qualifiers that are described for the [GenBank flatfile format](<a href=http://www.insdc.org/files/feature_table.html#7.2%5D(http://www.insdc.org/files/feature_table.html#7.2)>http://www.insdc.org/files/feature_table.html#7.2](http://www.insdc.org/files/feature_table.html#7.2)</a></p><p><strong>anticodon</strong>
|
||
Position of the anticodon on the seq-id for a tRNA feature</p><p><strong>description</strong>
|
||
The gene full name, corresponding to /gene_desc in the flatfile format.</p><p><strong>exception</strong>
|
||
indicates that the transcription or translation product of the feature as
|
||
derived from the annotated sequence does not match the sequence of the
|
||
product. There are several common usages in annotations from the RefSeq
|
||
eukaryotic genome annotation pipeline (e.g. RefSeq annotation for human):</p><ol><li>features corresponding to known RefSeq transcripts (NM_) or proteins (NP_)
|
||
that have mismatches, indels, or additional sequence compared to the
|
||
genome. These use the “exception=annotated by transcript or
|
||
proteomic data”.</li><li>features corresponding to model RefSeq transcripts (XM_) or proteins (XP_)
|
||
that have additional sequence compared to the genome. These use
|
||
“exception=annotated by transcript or proteomic data”.</li><li>features corresponding to model RefSeq transcripts (XM_) or proteins (XP_)
|
||
annotated as having indels compared to the genome. These use
|
||
“exception=unclassified transcription discrepancy” or
|
||
“exception=unclassified translation discrepancy”.</li><li>features that undergo programmed genomic rearrangements in order to
|
||
generate a functional transcript and protein product. These use
|
||
“exception=rearrangement required for product”.</li><li>CDS features that undergo +1 or -1 translation frameshifts (aka ribosomal
|
||
slippage) use “exception=ribosomal slippage”. See Additional Details for
|
||
more information.</li></ol><p>These and other exceptions may also appear in INSDC annotations, with
|
||
similar meanings.</p><p><strong>exon_number</strong>
|
||
The GFF3 specification does not include explicit numbering of exons, as is
|
||
sometimes found in GTF files. Occasionally an exon_number attribute is
|
||
present on exon features that are annotated separately from an RNA feature.
|
||
Exon features that are children of mRNA or other transcript features do not
|
||
include an explicit exon_number attribute, and their relative order should be
|
||
inferred from the order on the genome.</p><p><strong>gbkey</strong>
|
||
The original GenBank feature type, before conversion into the SOFA type
|
||
indicated in column 3. INSDC describes <a href=http://www.insdc.org/files/feature_table.html#7.2 target=_blank>feature keys</a>
|
||
in the DDBJ/ENA/GenBank Feature Table Definition.</p><p><strong>gene</strong>
|
||
The primary gene symbol.</p><p><strong>gene_biotype</strong>
|
||
Attribute computed on gene features based on the set of child features to
|
||
indicate the overall biotype for the gene annotation at this location.
|
||
This attribute was introduced in June 2015, and is not present in older
|
||
files. Values are:</p><p><em>protein_coding:</em> gene has at least one CDS feature, and is not a Ig/TCR segment or pseudogene</p><p><em>V_region, V_segment, D_segment, J_segment, C_region, tRNA, rRNA, snRNA, snoRNA, tmRNA, miscRNA:</em> gene has one or more of the child features, and no other type, and is not a pseudogene</p><p><em>V_region_pseudogene, etc:</em> same as above, but the gene is marked as a pseudogene</p><p><em>transcribed_pseudogene:</em> only has miscRNA child feature(s) marked as pseudogene</p><p><em>lncRNA, and additional ncRNA classes:</em> gene has one or more child ncRNA features of a single ncRNA_class. If ncRNA_class=“other”, then the gene_biotype=ncRNA. INSDC provides a <a href=http://www.insdc.org/rna_vocab.html target=_blank>controlled vocabulary for ncRNA classes</a>
|
||
.</p><p><em>miRNA:</em> a gene with only miRNA child features, or both miRNA and precursor_RNA</p><p><em>segment:</em> gene has a CDS with a “rearrangment required for product” exception, no specific region or segment feature, and is not a pseudogene</p><p><em>segment_pseudogene:</em> same as segment, but is a pseudogene</p><p><em>pseudogene:</em> marked as a pseudogene, but does not meet any of the more specific criteria above.</p><p><em>other:</em> rare cases where gene does not meet any of the above criteria. For
|
||
example, a partial gene with only mRNA and no CDS child feature(s) is
|
||
sometimes annotated by RefSeq to represent a location that contains
|
||
only 5' or 3' UTR, or a gene feature that is not marked as a pseudogene
|
||
but has no child features.</p><p>Note: There may be multiple gene features on a single assembly annotated
|
||
with the same GeneID dbxref because they are considered to be different
|
||
parts or alleles of the same gene. In these cases, it’s possible for the
|
||
gene features to be annotated with different gene_biotype values, such as
|
||
protein_coding and transcribed_pseudogene or protein_coding and other.</p><p><strong>gene_synonym</strong>
|
||
One or more additional synonyms for gene symbol.</p><p><strong>locus_tag</strong>
|
||
locus_tag is intended to be a unique value on each gene feature, and is
|
||
also propagated to child features. In some cases it may not be unique because
|
||
of errors in data files. Annotations from the RefSeq eukaryotic annotation
|
||
pipeline do not use locus_tag.</p><p><strong>ncrna_class</strong>
|
||
An additional qualifier provided on ncRNA features to indicate a specific
|
||
feature subtype, such as miRNA or lncRNA. INSDC provides a <a href=http://www.insdc.org/rna_vocab.html target=_blank>controlled vocabulary for ncRNA classes</a>
|
||
.</p><p><strong>part</strong>
|
||
A proposed attribute for the official GFF3 specification that has not yet
|
||
been finalized. Indicates the order in which multiple rows for the same ID
|
||
should be joined, using the format “part=X/Y”, where X is the row order and
|
||
Y is the total number of rows. Only found on some types of features such as
|
||
genes that are rarely represented as more than one range.</p><p><strong>partial</strong>
|
||
Indicates that the feature is considered to be partial, either internally or
|
||
at one or both ends. The start_range and end_range attributes indicate which
|
||
end of an interval is partial. The partial attribute always appears with the
|
||
value ‘true’ (i.e. partial=true).</p><p><strong>product</strong>
|
||
Name of the transcript or protein product, corresponding to /product in the
|
||
GenBank flatfile format.</p><p><strong>protein_id</strong>
|
||
Accession.version of the product record for the protein feature, if one
|
||
exists.</p><p><strong>pseudo</strong>
|
||
The feature, or its parent, is annotated as a non-functional version. If
|
||
present, it is always provided with the value ‘true’ (i.e. pseudo=true).</p><p><strong>pseudogene</strong>
|
||
A more specific attribute indicating the feature is considered to be a
|
||
pseudogene. INSDC provides a <a href=http://www.insdc.org/documents/pseudogene-qualifier-vocabulary target=_blank>controlled vocabulary for the pseudogene qualifier</a>
|
||
.</p><p><strong>start_range</strong></p><p><strong>end_range</strong></p><p>Attributes adapted from GVF to indicate partial feature boundaries. The value
|
||
is two integers (or a ‘.’ for an unknown value) separated by a comma, where
|
||
the two values indicate the range of ambiguity for that boundary. The
|
||
start_range attribute applies to column 4, and end_range applies to column 5.
|
||
If a ‘.’ is used for the outer range value, as is always the case in NCBI’s
|
||
current files, then presence of a start_range attribute can simply be
|
||
interpreted as column 4 is partial, and an end_range attribute as column 5
|
||
is partial, regardless of strand, without further analysis of the tag value.
|
||
Further details about the attributes are available in the <a href=https://github.com/The-Sequence-Ontology/Specifications/blob/master/gvf.md target=_blank>GVF specifications</a>
|
||
provided by the Sequence Ontology.</p><p><strong>transcript_id</strong>
|
||
Accession.version of the product record for the transcript feature, if one
|
||
exists.</p><p><strong>transl_except</strong>
|
||
One or more translation exceptions, found on CDS features. These indicate
|
||
codons on the genome (in coordinates corresponding to the column 1 seq-id)
|
||
that should be considered to be translated as a different amino acid than
|
||
expected by the codon sequence and translation table for this organism. The
|
||
format corresponds to that used in the flatfile format, with some encoded
|
||
characters. For example:
|
||
transl_except=(pos:25802093..25802095%2Caa:OTHER)
|
||
means the codon at the indicated position should be translated as “X”,
|
||
typically instead of a stop codon.</p><h2 id=annotation-data-model>Annotation Data Model</h2><p>The annotation in GFF3 format reflects the annotation in the source GenBank or
|
||
RefSeq records, adapted according to the GFF3 specifications. Thus, the data
|
||
model may vary depending on what information was provided by the annotation
|
||
submitter. Annotations in RefSeq are more standardized through the use of
|
||
NCBI’s own annotation pipelines or additional cleanup steps applied when
|
||
propagating INSDC submitted annotation into RefSeq records.</p><p>In general, annotations conform to the central dogma of gene-mRNA-CDS, or
|
||
gene-RNA for non-coding genes, with some exceptions:</p><p>Protein-coding gene annotations in prokaryotes, organelles, and some
|
||
eukaryote records lack mRNA features in INSDC and RefSeq annotations, and
|
||
therefore lack mRNA features in the GFF3 files, as allowed by the GFF3
|
||
specifications. See “NOTE 2” in the GFF3 specifications for more details.</p><p>Gene segment annotations for immunoglobulin and T-cell receptor genes that
|
||
undergo genomic rearrangements are commonly represented by gene,
|
||
C/V/D/J_gene_segment, and CDS features corresponding to individual segments
|
||
of the overall gene. The C/V/D/J_gene_segment feature with one or more child
|
||
exon features can be treated similar to a transcript feature. Currently, the
|
||
CDS features for gene segments use the Gene feature as the Parent.</p><p>Some pseudogene annotations are represented by a CDS feature with no
|
||
corresponding mRNA Parent feature.</p><p>Some RNA annotations, especially tRNAs, may not have a corresponding Gene
|
||
parent. This is more common in older annotation submissions.</p><p><a href=https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ target=_blank>RefSeq annotations</a>
|
||
from NCBI’s eukaryotic genome annotation pipeline include
|
||
additional conventions that may be relevant for processing.</p><p>Notable conventions used in RefSeq annotations from NCBI’s eukaryotic genome
|
||
annotation pipeline are:</p><p>Transcribed genes, both protein-coding and non-coding, may be annotated with
|
||
multiple transcript variants and protein isoforms. A single gene may have
|
||
both “known” (NM/NR/NP) and “model” (XM/XR/XP) RefSeq products. Known RefSeqs
|
||
are created both through curation done at NCBI, and automated processes
|
||
using annotated INSDC sequences, whereas model RefSeqs are created by
|
||
automated processes primarily based on alignment evidence supplemented with
|
||
ab initio prediction.</p><p>A protein-coding gene may have both coding and non-coding transcript child
|
||
features. Coding transcripts are represented by mRNA-exon-CDS features, and
|
||
non-coding transcripts are represented by transcript-exon features.</p><p>Non-transcribed pseudogenes are annotated with a gene feature, and may have
|
||
child exon features if sufficient evidence was available to define the pseudo
|
||
exon structure. No mRNA or CDS feature is annotated because the gene is
|
||
thought to not produce an RNA or protein.</p><p>Transcribed pseudogenes are annotated with a gene feature and one or more
|
||
transcript-exon features.</p><p>MicroRNAs are annotated as gene-primary_transcript-exon features based on
|
||
the stem-loop sequence identified by miRBase. Additional ncRNA child
|
||
features with the attribute ncrna_class=miRNA are annotated to represent the
|
||
mature miRNA products. The miRNA features currently have the Gene feature as
|
||
the parent.</p><p>Additional non-coding transcripts are annotated as ncRNA, rRNA, or tRNA
|
||
features with one or more exon child features.</p><p>Both “known” (NM/NR/NP) and “model” (XM/XR/XP) RefSeq transcript and protein
|
||
products may have differences (mismatches or indels) or additional sequence
|
||
compared to the sequence of the corresponding genome feature. These differences
|
||
are conveyed in several ways:</p><p>A Note describing the differences is provided on the affected transcript or
|
||
CDS feature.</p><p>For RefSeqs with indels or additional 5' or internal sequence, an alignment
|
||
between the transcript and genome is provided that can be used to map
|
||
between genome, transcript, and protein coordinates. These alignments are
|
||
found at the end of each seq-id. See below for details on the alignment
|
||
format specifications.</p><p>More recent GFF files under the /genomes/<genus_species> FTP path incorporate
|
||
the use of short overlaps or micro-introns to adjust the annotated feature
|
||
for insertions or deletions in the coding region compared to the RefSeq
|
||
product. See Additional Details below for more information.</p><p>For CDS features with internal stop codons compared to the RefSeq product,
|
||
a transl_except attribute is provided to indicate the location of the stop
|
||
codon, and the amino acid that is thought to be encoded at that position.
|
||
Model RefSeqs use aa:OTHER to indicate the stop codon in the genome may be
|
||
in error, but the correct sequence is unknown. Known RefSeqs may also use
|
||
aa:OTHER in older files (fixed in mid 2015). The transl_except attribute is
|
||
also used to indicate stop codons in the genome that are naturally translated
|
||
as selenocysteine (Sec).</p><p>RefSeqs with additional sequence that does not align to the genome, with the
|
||
exception of 3' polyA tails and very short unaligned 5' sequence, are
|
||
annotated with partial features. This markup includes a partial=true
|
||
attribute on all rows of the affected feature, and a start_range and/or
|
||
end_range attribute on the specific rows that are marked as partial (see
|
||
above for a description of start_range/end_range). The most common partial
|
||
markup is for the 5'-most or 3'-most end of the mRNA and CDS to be marked
|
||
as partial, but it is also possible for internal sequence to be missing, in
|
||
which case internal exon and CDS rows will be marked with start_range or
|
||
end_range.</p><h2 id=additional-details>Additional Details</h2><h3 id=the-source-region-feature>The source ‘region’ feature</h3><p>The first feature row for every seqid is a “region” feature spanning the
|
||
entire range of the sequence, and corresponds to the “source feature” that
|
||
appears in the GenBank flatfile format. It can be identified by the
|
||
“gbkey=Src” attribute, and can function as the landmark feature that is used
|
||
by some software but is not well defined in the current GFF3 specifications.
|
||
It contains many qualifiers with information about the source of the record.
|
||
These include:</p><p><strong>Name</strong>
|
||
Currently set to the source chromosome value, if known. The value chosen for
|
||
Name may be revised in the future to better address requirements for some
|
||
software.</p><p><strong>chromosome</strong>
|
||
The chromosome of the record, if one is assigned. Note some scaffolds may be
|
||
assigned to a specific chromosome even if they are not part of a single
|
||
record for that chromosome (“unlocalized scaffolds”).</p><p><strong>Is_circular</strong>
|
||
see official GFF3 attributes above</p><p><strong>genome</strong>
|
||
The genome source of the record, corresponding to “source genome <value>” in
|
||
the ASN.1 specification, and indexed as “gene in <value>[properties]” in the
|
||
Entrez nucleotide indexing system.</p><p><strong>linkage-group</strong>
|
||
The linkage group of the record, if one is assigned. Similar to chromosome.</p><p><strong>mol_type</strong>
|
||
The molecule type of the record, such as “genomic DNA” or “mRNA”</p><p><strong>transl_table</strong>
|
||
The genetic code table to use for translation of CDS features, if other than
|
||
the universal table. INSDC provides a <a href=http://www.insdc.org/files/feature_table.html#7.4.5 target=_blank>controlled vocabulary for genetic code tables</a>
|
||
.</p><h3 id=utrs>UTRs</h3><p>5' and 3' UTR features for mRNAs are not explicitly annotated, but can be
|
||
inferred from the difference between the child exon and CDS features. For
|
||
applications that require explicit five_prime_UTR and three_prime_UTR features, NCBI provides
|
||
a <a href=https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/add_utrs_to_gff/ target=_blank>Python script</a>
|
||
to add UTR features.</p><h3 id=start-and-stop-codons>Start and stop codons</h3><p>start_codon and stop_codon features are not explicitly annotated, but can be
|
||
inferred from the beginning and end of the CDS feature, if that CDS feature is
|
||
not partial on the end in question. Partialness is represented by start_range
|
||
and end_range attributes in NCBI’s GFF3 files, using a format adapted from GVF.</p><p>More specifically:</p><ol><li><p>the CDS is 5' partial and does not include a start codon if:
|
||
a) the first CDS row is on the + strand and has a start_range=.,### attribute.
|
||
b) the first CDS row is on the - strand and has an end_range=###,. attribute.</p></li><li><p>the CDS is 3' partial and does not include a stop codon if:
|
||
a) the last CDS row is on the + strand and has an end_range=###,. attribute.
|
||
b) the last CDS row is on the - strand and has a start_range=.,### attribute.</p></li></ol><p>If those conditions are not met, then you can infer the start_codon and
|
||
stop_codon position from the first or last 3 bp of the CDS feature.</p><h3 id=origin-spanning-features>Origin-spanning features</h3><p>If an interval (an individual row) spans the origin of a circular sequence, the
|
||
column 5 coordinate is extended into virtual space. This means that a parent
|
||
feature may be extended into virtual space, but its child features are not, and
|
||
some child features may not fall within the span of the parent. For example:</p><p>A simple case, with single interval gene and CDS features that both span the
|
||
origin:</p><pre><code>##sequence-region NC_005213.1 1 490885
|
||
NC_005213.1 RefSeq gene 490883 491764 . - . ID=gene1
|
||
NC_005213.1 RefSeq CDS 490883 491764 . - 0 ID=cds0;;Parent=gene1
|
||
</code></pre><p>A complex multi-exon case, where the gene and mRNA features span the origin, but
|
||
none of the individual exon or CDS rows span the origin. Note the exon and CDS
|
||
at 959..966(-) that do not fall within the span of the Parent mRNA:</p><pre><code>##sequence-region NC_004367.1 1 149696
|
||
NC_004367.1 RefSeq gene 138637 150662 . - . ID=gene0
|
||
NC_004367.1 RefSeq mRNA 138637 150662 . - . ID=rna0;Parent=gene0
|
||
NC_004367.1 RefSeq exon 959 966 . - . ID=id1;Parent=rna0
|
||
NC_004367.1 RefSeq exon 140247 140485 . - . ID=id2;Parent=rna0
|
||
NC_004367.1 RefSeq exon 140075 140167 . - . ID=id3;Parent=rna0
|
||
NC_004367.1 RefSeq exon 139744 139992 . - . ID=id4;Parent=rna0
|
||
NC_004367.1 RefSeq exon 139572 139661 . - . ID=id5;Parent=rna0
|
||
NC_004367.1 RefSeq exon 139294 139458 . - . ID=id6;Parent=rna0
|
||
NC_004367.1 RefSeq exon 139106 139219 . - . ID=id7;Parent=rna0
|
||
NC_004367.1 RefSeq exon 138904 139005 . - . ID=id8;Parent=rna0
|
||
NC_004367.1 RefSeq exon 138637 138818 . - . ID=id9;Parent=rna0
|
||
NC_004367.1 RefSeq CDS 959 966 . - 0 ID=cds0;Parent=rna0
|
||
NC_004367.1 RefSeq CDS 140247 140485 . - 1 ID=cds0;Parent=rna0
|
||
NC_004367.1 RefSeq CDS 140075 140167 . - 2 ID=cds0;Parent=rna0
|
||
NC_004367.1 RefSeq CDS 139744 139992 . - 2 ID=cds0;Parent=rna0
|
||
NC_004367.1 RefSeq CDS 139572 139661 . - 2 ID=cds0;Parent=rna0
|
||
NC_004367.1 RefSeq CDS 139294 139458 . - 2 ID=cds0;Parent=rna0
|
||
NC_004367.1 RefSeq CDS 139106 139219 . - 2 ID=cds0;Parent=rna0
|
||
NC_004367.1 RefSeq CDS 138904 139005 . - 2 ID=cds0;Parent=rna0
|
||
NC_004367.1 RefSeq CDS 138637 138818 . - 2 ID=cds0;Parent=rna0
|
||
</code></pre><h3 id=annotation-accommodations-for-putative-assembly-errors>Annotation accommodations for putative assembly errors</h3><p>The INSDC annotation specification includes several options for annotating mRNA
|
||
and CDS features affected by putative assembly errors, and these conventions can
|
||
also appear in the GFF3 format for both GenBank and RefSeq genomes.</p><p>CDSes with internal stop codons that are believed to be in error can be
|
||
annotated with a transl_except attribute on the CDS feature to indicate the
|
||
location of the internal stop codon and its replacement amino acid.</p><p>mRNA and CDS features disrupted by frameshifting insertions or deletions that
|
||
are thought to represent assembly errors may be adjusted through the use of
|
||
short overlaps or “micro-introns” between exon and CDS rows of the same mRNA
|
||
feature. These adjustments artificially appear to split a single exon into two,
|
||
but serve to restore the reading frame and allow representation of a complete
|
||
CDS in the correct frame. In the case of an overlap, the overlapping base does
|
||
not necessarily represent the correct sequence, but serves to represent an
|
||
insertion of a length that restores the proper reading frame.</p><p>The overlap/micro-intron format is a compromise designed to allow processing by
|
||
most software; however, some software may not properly accommodate overlaps, in
|
||
which case the annotation may require modification.</p><p>If the software supports internal phase shifts with a partial codon in the
|
||
middle of the CDS, then an overlap can be adjusted by trimming the
|
||
coordinate of the first row (modify column 5 if the feature is on the +
|
||
strand, and column 4 if the feature is on the - strand), without altering
|
||
the phase column:</p><p>original:
|
||
seq1 GenBank CDS 100 150 . + 0 ID=cds1
|
||
seq1 GenBank CDS 150 200 . + 0 ID=cds1</p><p>altered:
|
||
seq1 GenBank CDS 100 149 . + 0 ID=cds1
|
||
seq1 GenBank CDS 150 200 . + 0 ID=cds1</p><p>If the software does not support either overlaps or internal phase shifts,
|
||
then the alternative is to adjust the first row by a multiple of three,
|
||
creating a micro-intron that maintains the proper phase:</p><p>original:
|
||
seq1 GenBank CDS 100 150 . + 0 ID=cds1
|
||
seq1 GenBank CDS 150 200 . + 0 ID=cds1</p><p>altered:
|
||
seq1 GenBank CDS 100 147 . + 0 ID=cds1
|
||
seq1 GenBank CDS 150 200 . + 0 ID=cds1</p><h3 id=ribosomal-slippage>Ribosomal slippage</h3><p>Some proteins are expressed by a process involving +1 or -1 translation
|
||
frameshifts (aka ribosomal slippage). In this case the CDS feature for what is
|
||
a single exon is split into two intervals, with either a small gap (positive
|
||
slippage) or a slight overlap (negative slippage), similar to how some putative
|
||
assembly error cases are annotated. However, for ribosomal slippage annotations
|
||
the exons of the corresponding mRNA feature do NOT include the slippage because
|
||
only the translated protein is affected by the slippage event. These types of
|
||
CDS features can be identified by the attribute “exception=ribosomal slippage”.</p><h2 id=alignments>Alignments</h2><p>Alignments are provided according to the GFF3 specifications. They are
|
||
identified by the SO type in column 3:
|
||
cDNA_match – used for mRNA-genome alignments
|
||
EST_match – used for EST-genome alignments
|
||
protein_match – used for protein-genome alignments
|
||
match – used for all other alignments, including transcripts other than mRNA</p><p>They appear in several places:</p><p>Genomic annotation GFF3 files include alignments for genomic RefSeq (NGs),
|
||
and those transcript RefSeqs (NM/NR and XM/XR accession prefixes) where the
|
||
transcript does not map perfectly to the feature (see ANNOTATION DATA MODEL).</p><p><a href=https://ftp.ncbi.nlm.nih.gov/pub/remap/ target=_blank>Genome-genome alignment files</a>
|
||
as used by NCBI’s Remap service.</p><p><a href=https://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/latest_assembly_versions/GCF_000001405.40_GRCh38.p14/GCF_000001405.40_GRCh38.p14_assembly_structure/ALT_REF_LOCI_1/alt_scaffolds/alignments/ target=_blank>Primary-ALT_LOCI and primary-PATCH alignment files</a>
|
||
, provided as part of
|
||
the human and mouse GRC assemblies, indicating correspondence between
|
||
locations on the primary assembly and sequences of alternate loci.</p><p><a href=https://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Mus_musculus/annotation_releases/108/GCF_000001635.27_GRCm38.p6/Evidence_alignments/ target=_blank>Transcript alignment files</a>
|
||
for eukaryotes produced by NCBI’s eukaryotic
|
||
genome annotation pipeline, provided in the Evidence_alignments sub-directory.</p><p>RefSeq transcript and RefSeqGene genomic alignments for <a href=https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/alignments/ target=_blank>human</a>
|
||
and <a href=https://ftp.ncbi.nlm.nih.gov/refseq/M_musculus/annotation_releases/current/GCF_000001635.27_GRCm39/RefSeq_transcripts_alignments/ target=_blank>mouse</a>
|
||
.</p><h3 id=official-gff3-attributes-1>Official GFF3 attributes</h3><p><strong>ID</strong>
|
||
A unique identifier for the alignment. Some alignments use a long UUID string
|
||
as a stable alignment identifier. Multiple rows with the same ID indicate
|
||
parts of the same alignment. For example, transcript alignments are
|
||
represented with a separate row representing each exon of the transcript.</p><p><strong>Target</strong>
|
||
The accession.version of the sequence aligned to the reference sequence
|
||
indicated in column 1. The format is “target_id start end strand”, where
|
||
start < end.</p><p><strong>Gap</strong>
|
||
Location of Gaps (indels) in the alignment in the Exonerate CIGAR format
|
||
where ‘M’ indicates an aligned base (which may be either a match or
|
||
mismatch). The locations of mismatches must be computed by comparing the
|
||
Target and Reference sequences. The Gap attribute is omitted if there are
|
||
no indels within the alignment Target range.</p><p>The Gap attribute is relative to the Target sequence and range
|
||
for that row of the alignment. If the Target is in minus orientation, then
|
||
the Gap string is read from end to start. For example:
|
||
ID=aln1;Target=NG_033055.1 1 7866 -;Gap=M7047 D1 M819
|
||
indicates:
|
||
NG_0033055.1:7866..820 “match”
|
||
followed by a deletion of 1 bp (the extra base is present in the
|
||
reference sequence, and missing from the target)
|
||
NG_0033055.1:819..1 “match”</p><p>Note gaps can also be represented by ranges of the Target (either at the
|
||
beginning, end, or internally) that are not found in any row of the
|
||
alignment.</p><h3 id=unofficial-attributes-1>Unofficial attributes</h3><p>A wide variety of scores may be present in alignment files depending on the
|
||
process that generated them. Many aren’t of direct use to most users. Most
|
||
reported scores, including all scores listed below, apply to the alignment as
|
||
a whole (all rows with the same ID). The most useful scores are described here:</p><p><strong>gap_count</strong>
|
||
number of gap openings in the alignment. Equal to the number of D or I codes
|
||
in the Gap string.</p><p><strong>num_ident</strong>
|
||
number of identities in the alignment</p><p><strong>num_mismatch</strong>
|
||
number of mismatches in the alignment. If num_mismatch=0, then there are no
|
||
mismatches within the aligned portion of the Target and Reference (for any
|
||
match row with the same ID)</p><p><strong>pct_coverage</strong>
|
||
Gapped percent coverage of the Target sequence.</p><p><strong>pct_identity_gap</strong>
|
||
Gapped percent identity, for the aligned portion of the Target. This is the
|
||
standard BLAST percent identity score. Unaligned portions of the Target
|
||
(not included in any match row with the same ID) do not affect the reported
|
||
identity.</p><p><strong>pct_identity_gapopen_only</strong>
|
||
Percent identity, counting gaps as a mismatch regardless of length.</p><p><strong>pct_identity_ungap</strong>
|
||
Percent identity, ignoring gaps</p><p><strong>reciprocity</strong>
|
||
Used for assembly-assembly alignments. Values:
|
||
3 == alignment is best for both Reference and Target. Also referred to as
|
||
‘First-Pass Alignments’
|
||
1 or 2 == alignment is best for one sequence, but a better alignment is
|
||
reported for the other sequence. Also referred to as ‘Second-Pass
|
||
Alignments’</p><p>More details on some of the reported scores is available in the
|
||
<a href=https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/classCSeq__align.html#a0a7501fd78111aeea55afdf681847c01 target=_blank>NCBI C++ Toolkit documentation</a></p>Generated March 11, 2025</div><div class=c-global-meta-links><div class="td-page-meta ml-2 pb-1 pt-2 mb-0"></div></div></main></div></div></div><footer><section class=icon-section><div id=icon-section-header class=icon-section_header>Follow NCBI</div><div class="grid-container container"><div class=icon-section_container><a class=footer-icon id=footer_twitter href=https://twitter.com/ncbi aria-label=Twitter><svg width="40" height="40" viewBox="0 0 40 37" fill="none" xmlns="http://www.w3.org/2000/svg"><title>Twitter</title><g id="twitterx1008"><path id="path1008" d="M6.06736 7 16.8778 20.8991 6.00001 32.2H10.2l8.4-9.1 7.068 9.1H34L22.8 17.5 31.9 7H28.4l-7.7 8.4L14.401 7H6.06898 6.06736zM9.66753 8.73423H12.9327l16.8 21.73157h-3.163L9.66753 8.73423z" fill="#5b616b"/></g></svg></a><a class=footer-icon 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