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td-sidebar-link__section tree-root" id=m-datasetsdocsv2><span>Documentation</span></a><ul class=ul-1><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child" id=m-datasetsdocsv2getting_started-li><a href=/datasets/docs/v2/getting_started/ class="align-left ps-0 td-sidebar-link
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td-sidebar-link__page" id=m-datasetsdocsv2getting_started><span>Getting started</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child" id=m-datasetsdocsv2command-line-tools-li><a href=/datasets/docs/v2/command-line-tools/ class="align-left ps-0 td-sidebar-link
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td-sidebar-link__section" id=m-datasetsdocsv2command-line-tools><span>Command line tools</span></a><ul class="ul-2 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2command-line-toolsdownload-and-install-li><a href=/datasets/docs/v2/command-line-tools/download-and-install/ title="Download and Install" class="align-left ps-0 td-sidebar-link
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td-sidebar-link__page" id=m-datasetsdocsv2command-line-toolsdownload-and-install><span>Download and install</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2command-line-toolsusing-dataformat-li><a href=/datasets/docs/v2/command-line-tools/using-dataformat/ class="align-left ps-0 td-sidebar-link
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td-sidebar-link__section" id=m-datasetsdocsv2command-line-toolsusing-dataformat><span>Using dataformat</span></a><ul class="ul-3 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2command-line-toolsusing-dataformatgene-data-reports-li><a href=/datasets/docs/v2/command-line-tools/using-dataformat/gene-data-reports/ title="Gene Data Reports" class="align-left ps-0 td-sidebar-link
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td-sidebar-link__page" id=m-datasetsdocsv2command-line-toolsusing-dataformatgene-data-reports><span>Gene data reports</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2command-line-toolsusing-dataformatgenome-data-reports-li><a href=/datasets/docs/v2/command-line-tools/using-dataformat/genome-data-reports/ title="Genome Data Reports" class="align-left ps-0 td-sidebar-link
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td-sidebar-link__page" id=m-datasetsdocsv2command-line-toolsusing-dataformatgenome-data-reports><span>Genome data reports</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2command-line-toolsusing-dataformatvirus-data-reports-li><a href=/datasets/docs/v2/command-line-tools/using-dataformat/virus-data-reports/ title="Virus Data Reports" class="align-left ps-0 td-sidebar-link
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td-sidebar-link__page" id=m-datasetsdocsv2command-line-toolsusing-dataformatvirus-data-reports><span>Virus data reports</span></a></li></ul></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child" id=m-datasetsdocsv2how-tos-li><a href=/datasets/docs/v2/how-tos/ class="align-left ps-0 td-sidebar-link
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td-sidebar-link__section" id=m-datasetsdocsv2how-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-datasetsdocsv2how-tosgenes-li><a href=/datasets/docs/v2/how-tos/genes/ class="align-left ps-0 td-sidebar-link
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td-sidebar-link__section" id=m-datasetsdocsv2how-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-datasetsdocsv2how-tosgenesget-gene-metadata-li><a href=/datasets/docs/v2/how-tos/genes/get-gene-metadata/ class="align-left ps-0 td-sidebar-link
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td-sidebar-link__page" id=m-datasetsdocsv2how-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-datasetsdocsv2how-tosgenesdownload-gene-data-package-li><a href=/datasets/docs/v2/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-datasetsdocsv2how-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-datasetsdocsv2how-tosgenesdownload-ortholog-data-package-li><a href=/datasets/docs/v2/how-tos/genes/download-ortholog-data-package/ title="Download an ortholog data package" class="align-left ps-0 td-sidebar-link
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td-sidebar-link__page" id=m-datasetsdocsv2how-tosgenesdownload-ortholog-data-package><span>Download orthologs</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2how-tosgenomes-li><a href=/datasets/docs/v2/how-tos/genomes/ class="align-left ps-0 td-sidebar-link
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td-sidebar-link__section" id=m-datasetsdocsv2how-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-datasetsdocsv2how-tosgenomesget-genome-metadata-li><a href=/datasets/docs/v2/how-tos/genomes/get-genome-metadata/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2how-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-datasetsdocsv2how-tosgenomesdownload-genome-li><a href=/datasets/docs/v2/how-tos/genomes/download-genome/ title="Download a genome data package" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2how-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-datasetsdocsv2how-tosgenomeslarge-download-li><a href=/datasets/docs/v2/how-tos/genomes/large-download/ title="Download large genome data packages" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2how-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-datasetsdocsv2how-tostaxonomy-li><a href=/datasets/docs/v2/how-tos/taxonomy/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2how-tostaxonomy><span>Taxonomy</span></a><ul class="ul-3 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2how-tostaxonomytaxonomy-li><a href=/datasets/docs/v2/how-tos/taxonomy/taxonomy/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2how-tostaxonomytaxonomy><span>Get taxonomy metadata</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2how-tosvirus-li><a href=/datasets/docs/v2/how-tos/virus/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2how-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-datasetsdocsv2how-tosvirusinfluenza-metadata-li><a href=/datasets/docs/v2/how-tos/virus/influenza-metadata/ title="Get Alphainfluenza virus genome metadata" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2how-tosvirusinfluenza-metadata><span>Get Alphainfluenza virus metadata</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2how-tosvirusvirus-metadata-li><a href=/datasets/docs/v2/how-tos/virus/virus-metadata/ title="Get virus genome metadata" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2how-tosvirusvirus-metadata><span>Get virus metadata</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2how-tosvirusvirus-download-li><a href=/datasets/docs/v2/how-tos/virus/virus-download/ title="Download a virus genome data package" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2how-tosvirusvirus-download><span>Download virus genomes</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2how-tosvirusget-influenza-genomes-li><a href=/datasets/docs/v2/how-tos/virus/get-influenza-genomes/ title="Download an Alphainfluenza genome data package" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2how-tosvirusget-influenza-genomes><span>Download Alphainfluenza genomes</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2how-tosvirusget-sars2-genomes-li><a href=/datasets/docs/v2/how-tos/virus/get-sars2-genomes/ title="Download a SARS-CoV-2 genome data package" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2how-tosvirusget-sars2-genomes><span>Download SARS-CoV-2 genomes</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2how-tosvirusget-sars2-proteins-li><a href=/datasets/docs/v2/how-tos/virus/get-sars2-proteins/ title="Download a SARS-CoV-2 protein data package" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2how-tosvirusget-sars2-proteins><span>Download SARS-CoV-2 proteins</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2how-tosvalidation-li><a href=/datasets/docs/v2/how-tos/validation/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2how-tosvalidation><span>File validation</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child" id=m-datasetsdocsv2tutorials-li><a href=/datasets/docs/v2/tutorials/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2tutorials><span>Tutorials</span></a><ul class="ul-2 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2tutorialsortholog-get-one-isoform-li><a href=/datasets/docs/v2/tutorials/ortholog-get-one-isoform/ title="Get one protein per gene from a set of orthologs" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2tutorialsortholog-get-one-isoform><span>Get one protein from an ortholog set</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2tutorialsrename-files-li><a href=/datasets/docs/v2/tutorials/rename-files/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2tutorialsrename-files><span>Rename downloaded files</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2tutorialsdownload-ortholog-dataset-li><a href=/datasets/docs/v2/tutorials/download-ortholog-dataset/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2tutorialsdownload-ortholog-dataset><span>Retrieve ortholog data and metadata</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2tutorialsworking-with-jsonl-data-reports-li><a href=/datasets/docs/v2/tutorials/working-with-jsonl-data-reports/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2tutorialsworking-with-jsonl-data-reports><span>Working with JSON Lines data reports</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child" id=m-datasetsdocsv2api-li><a href=/datasets/docs/v2/api/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2api><span>API</span></a><ul class="ul-2 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2apirest-api-li><a href=/datasets/docs/v2/api/rest-api/ title="NCBI Datasets v2 REST API" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2apirest-api><span>REST API</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2apiapi-keys-li><a href=/datasets/docs/v2/api/api-keys/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2apiapi-keys><span>API keys</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2apilanguages-li><a href=/datasets/docs/v2/api/languages/ title="Supported programming languages" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2apilanguages><span>Programming Languages</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2apideprecated-apis-li><a href=/datasets/docs/v2/api/deprecated-apis/ title="Retired API Endpoints" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2apideprecated-apis><span>Retired Endpoints</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child" id=m-datasetsdocsv2policies-annotation-li><a href=/datasets/docs/v2/policies-annotation/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2policies-annotation><span>NCBI Genome Data Processing</span></a><ul class="ul-2 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2policies-annotationgenome-processing-li><a href=/datasets/docs/v2/policies-annotation/genome-processing/ title="NCBI Genome Data Processing" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2policies-annotationgenome-processing><span>Genome Data Processing</span></a><ul class="ul-3 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2policies-annotationgenome-processingversion-status-li><a href=/datasets/docs/v2/policies-annotation/genome-processing/version-status/ title="Assembly Versioning and Status" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2policies-annotationgenome-processingversion-status><span>Assembly version and status</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2policies-annotationgenome-processingreference-selection-li><a href=/datasets/docs/v2/policies-annotation/genome-processing/reference-selection/ title="Selecting Reference Genomes" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2policies-annotationgenome-processingreference-selection><span>Reference Genomes</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2policies-annotationgenome-processingrefseq-selection-li><a href=/datasets/docs/v2/policies-annotation/genome-processing/refseq-selection/ title="Genomes Selected for RefSeq Annotation" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2policies-annotationgenome-processingrefseq-selection><span>RefSeq Genomes</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2policies-annotationgenome-processinggenome_notes-li><a href=/datasets/docs/v2/policies-annotation/genome-processing/genome_notes/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2policies-annotationgenome-processinggenome_notes><span>Genome Notes</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2policies-annotationgenome-processingtype-material-li><a href=/datasets/docs/v2/policies-annotation/genome-processing/type-material/ title="What is Type Material?" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2policies-annotationgenome-processingtype-material><span>Type Material</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2policies-annotationpipelines-li><a href=/datasets/docs/v2/policies-annotation/pipelines/ title="NCBI RefSeq Genome Annotation Pipelines" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2policies-annotationpipelines><span>Genome Annotation Pipelines</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2policies-annotationquality-li><a href=/datasets/docs/v2/policies-annotation/quality/ title="NCBI Genome Quality Analysis" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2policies-annotationquality><span>Genome Quality Analysis</span></a><ul class="ul-3 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2policies-annotationqualitycontamination-li><a href=/datasets/docs/v2/policies-annotation/quality/contamination/ title="NCBI Contamination Screening" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2policies-annotationqualitycontamination><span>Contamination Screening</span></a><ul class="ul-4 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2policies-annotationqualitycontaminationfcs-contamination-li><a href=/datasets/docs/v2/policies-annotation/quality/contamination/fcs-contamination/ title="Foreign Contamination Screen (FCS)" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2policies-annotationqualitycontaminationfcs-contamination><span>FCS</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2policies-annotationqualitycontaminationani-contamination-li><a href=/datasets/docs/v2/policies-annotation/quality/contamination/ani-contamination/ title="Average Nucleotide Identity (ANI)" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2policies-annotationqualitycontaminationani-contamination><span>ANI</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2policies-annotationqualityani-li><a href=/datasets/docs/v2/policies-annotation/quality/ani/ title="Average Nucleotide Identity (ANI)" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2policies-annotationqualityani><span>ANI Overview</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2policies-annotationqualitybusco-li><a href=/datasets/docs/v2/policies-annotation/quality/busco/ title="Benchmarking Universal Single-Copy Orthologs (BUSCO) Analysis" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2policies-annotationqualitybusco><span>BUSCO</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2policies-annotationqualitycheckm-li><a href=/datasets/docs/v2/policies-annotation/quality/checkm/ title="CheckM Analysis" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2policies-annotationqualitycheckm><span>CheckM</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2policies-annotationdata-model-li><a href=/datasets/docs/v2/policies-annotation/data-model/ title="The NCBI Genome Assembly Data Model" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2policies-annotationdata-model><span>Data model</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2policies-annotationgenomeftp-li><a href=/datasets/docs/v2/policies-annotation/genomeftp/ title="NCBI Genomes FTP" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2policies-annotationgenomeftp><span>Genomes FTP</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2policies-annotationortholog-calculation-li><a href=/datasets/docs/v2/policies-annotation/ortholog-calculation/ title="How Are Orthologs Calculated?" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2policies-annotationortholog-calculation><span>Ortholog Calculation</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child" id=m-datasetsdocsv2troubleshooting-li><a href=/datasets/docs/v2/troubleshooting/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2troubleshooting><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-datasetsdocsv2troubleshootingfaq-li><a href=/datasets/docs/v2/troubleshooting/faq/ title=FAQs class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2troubleshootingfaq><span>Frequently asked Questions</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2troubleshootingmac-zip-bug-li><a href=/datasets/docs/v2/troubleshooting/mac-zip-bug/ title="Mac zip archive bugs" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2troubleshootingmac-zip-bug><span>Mac zip bugs</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child active-path" id=m-datasetsdocsv2reference-docs-li><a href=/datasets/docs/v2/reference-docs/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-line-li><a href=/datasets/docs/v2/reference-docs/command-line/ title="Command line tool reference" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedataformat-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedataformattsv-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/tsv/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedataformattsvdataformat_tsv_genome-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/tsv/dataformat_tsv_genome/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedataformattsvdataformat_tsv_genome-seq-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/tsv/dataformat_tsv_genome-seq/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedataformattsvdataformat_tsv_gene-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/tsv/dataformat_tsv_gene/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedataformattsvdataformat_tsv_gene-product-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/tsv/dataformat_tsv_gene-product/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedataformattsvdataformat_tsv_gene-product><span>gene-product</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformattsvdataformat_tsv_virus-genome-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/tsv/dataformat_tsv_virus-genome/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedataformattsvdataformat_tsv_virus-annotation-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/tsv/dataformat_tsv_virus-annotation/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedataformattsvdataformat_tsv_virus-annotation><span>virus-annotation</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformattsvdataformat_tsv_microbigge-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/tsv/dataformat_tsv_microbigge/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedataformattsvdataformat_tsv_prok-gene-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/tsv/dataformat_tsv_prok-gene/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedataformattsvdataformat_tsv_prok-gene-location-li><a href=/datasets/docs/v2/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-datasetsdocsv2reference-docscommand-linedataformattsvdataformat_tsv_prok-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-datasetsdocsv2reference-docscommand-linedataformattsvdataformat_tsv_genome-annotations-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/tsv/dataformat_tsv_genome-annotations/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedataformattsvdataformat_tsv_genome-annotations><span>genome-annotations</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformattsvdataformat_tsv_taxonomy-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/tsv/dataformat_tsv_taxonomy/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedataformattsvdataformat_tsv_taxonomy><span>taxonomy</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformattsvdataformat_tsv_organelle-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/tsv/dataformat_tsv_organelle/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedataformattsvdataformat_tsv_organelle><span>organelle</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformatexcel-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/excel/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedataformatexceldataformat_excel_genome-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/excel/dataformat_excel_genome/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedataformatexceldataformat_excel_genome-seq-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/excel/dataformat_excel_genome-seq/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedataformatexceldataformat_excel_gene-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/excel/dataformat_excel_gene/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedataformatexceldataformat_excel_gene-product-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/excel/dataformat_excel_gene-product/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedataformatexceldataformat_excel_gene-product><span>gene-product</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformatexceldataformat_excel_virus-genome-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/excel/dataformat_excel_virus-genome/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedataformatexceldataformat_excel_virus-annotation-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/excel/dataformat_excel_virus-annotation/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedataformatexceldataformat_excel_virus-annotation><span>virus-annotation</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformatexceldataformat_excel_microbigge-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/excel/dataformat_excel_microbigge/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedataformatexceldataformat_excel_prok-gene-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/excel/dataformat_excel_prok-gene/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedataformatexceldataformat_excel_prok-gene-location-li><a href=/datasets/docs/v2/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-datasetsdocsv2reference-docscommand-linedataformatexceldataformat_excel_prok-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-datasetsdocsv2reference-docscommand-linedataformatexceldataformat_excel_genome-annotations-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/excel/dataformat_excel_genome-annotations/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedataformatexceldataformat_excel_genome-annotations><span>genome-annotations</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformatexceldataformat_excel_taxonomy-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/excel/dataformat_excel_taxonomy/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedataformatexceldataformat_excel_taxonomy><span>taxonomy</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformatexceldataformat_excel_organelle-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/excel/dataformat_excel_organelle/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedataformatexceldataformat_excel_organelle><span>organelle</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformatdataformat_catalog-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/dataformat_catalog/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedataformatdataformat_catalog><span>catalog</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2reference-docscommand-linedataformatcompletion-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/completion/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedataformatcompletiondataformat_completion_bash-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/completion/dataformat_completion_bash/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedataformatcompletiondataformat_completion_zsh-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/completion/dataformat_completion_zsh/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedataformatcompletiondataformat_completion_fish-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/completion/dataformat_completion_fish/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedataformatcompletiondataformat_completion_powershell-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/completion/dataformat_completion_powershell/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedataformatdataformat_version-li><a href=/datasets/docs/v2/reference-docs/command-line/dataformat/dataformat_version/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedatasets-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedatasetssummary-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/summary/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedatasetssummarygene-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/summary/gene/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedatasetssummarygenedatasets_summary_gene_gene-id-li><a href=/datasets/docs/v2/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-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedatasetssummarygenedatasets_summary_gene_symbol-li><a href=/datasets/docs/v2/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-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedatasetssummarygenedatasets_summary_gene_accession-li><a href=/datasets/docs/v2/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-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedatasetssummarygenedatasets_summary_gene_taxon-li><a href=/datasets/docs/v2/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-datasetsdocsv2reference-docscommand-linedatasetssummarygenedatasets_summary_gene_taxon><span>taxon</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetssummarygenedatasets_summary_gene_locus-tag-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/summary/gene/datasets_summary_gene_locus-tag/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedatasetssummarygenedatasets_summary_gene_locus-tag><span>locus-tag</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetssummarygenome-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/summary/genome/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedatasetssummarygenomedatasets_summary_genome_accession-li><a href=/datasets/docs/v2/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-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedatasetssummarygenomedatasets_summary_genome_taxon-li><a href=/datasets/docs/v2/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-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedatasetssummaryvirus-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/summary/virus/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedatasetssummaryvirusgenome-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/summary/virus/genome/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedatasetssummaryvirusgenomedatasets_summary_virus_genome_taxon-li><a href=/datasets/docs/v2/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-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedatasetssummaryvirusgenomedatasets_summary_virus_genome_accession-li><a href=/datasets/docs/v2/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-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedatasetssummarytaxonomy-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/summary/taxonomy/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-docscommand-linedatasetssummarytaxonomy><span>taxonomy</span></a><ul class="ul-6 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetssummarytaxonomydatasets_summary_taxonomy_taxon-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/summary/taxonomy/datasets_summary_taxonomy_taxon/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedatasetssummarytaxonomydatasets_summary_taxonomy_taxon><span>taxon</span></a></li></ul></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetsdownload-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/download/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedatasetsdownloadgene-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/download/gene/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedatasetsdownloadgenedatasets_download_gene_gene-id-li><a href=/datasets/docs/v2/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-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedatasetsdownloadgenedatasets_download_gene_symbol-li><a href=/datasets/docs/v2/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-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedatasetsdownloadgenedatasets_download_gene_accession-li><a href=/datasets/docs/v2/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-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedatasetsdownloadgenedatasets_download_gene_taxon-li><a href=/datasets/docs/v2/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-datasetsdocsv2reference-docscommand-linedatasetsdownloadgenedatasets_download_gene_taxon><span>taxon</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetsdownloadgenedatasets_download_gene_locus-tag-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/download/gene/datasets_download_gene_locus-tag/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedatasetsdownloadgenedatasets_download_gene_locus-tag><span>locus-tag</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetsdownloadgenome-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/download/genome/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedatasetsdownloadgenomedatasets_download_genome_accession-li><a href=/datasets/docs/v2/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-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedatasetsdownloadgenomedatasets_download_genome_taxon-li><a href=/datasets/docs/v2/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-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedatasetsdownloadtaxonomy-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/download/taxonomy/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-docscommand-linedatasetsdownloadtaxonomy><span>taxonomy</span></a><ul class="ul-6 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetsdownloadtaxonomydatasets_download_taxonomy_taxon-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/download/taxonomy/datasets_download_taxonomy_taxon/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedatasetsdownloadtaxonomydatasets_download_taxonomy_taxon><span>taxon</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetsdownloadvirus-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/download/virus/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedatasetsdownloadvirusgenome-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/download/virus/genome/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedatasetsdownloadvirusgenomedatasets_download_virus_genome_accession-li><a href=/datasets/docs/v2/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-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedatasetsdownloadvirusgenomedatasets_download_virus_genome_taxon-li><a href=/datasets/docs/v2/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-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedatasetsdownloadvirusdatasets_download_virus_protein-li><a href=/datasets/docs/v2/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-datasetsdocsv2reference-docscommand-linedatasetsdownloadvirusdatasets_download_virus_protein><span>protein</span></a></li></ul></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetsdatasets_rehydrate-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/datasets_rehydrate/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedatasetsdatasets_rehydrate><span>rehydrate</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2reference-docscommand-linedatasetscompletion-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/completion/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedatasetscompletiondatasets_completion_bash-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/completion/datasets_completion_bash/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedatasetscompletiondatasets_completion_zsh-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/completion/datasets_completion_zsh/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedatasetscompletiondatasets_completion_fish-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/completion/datasets_completion_fish/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-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-datasetsdocsv2reference-docscommand-linedatasetscompletiondatasets_completion_powershell-li><a href=/datasets/docs/v2/reference-docs/command-line/datasets/completion/datasets_completion_powershell/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docscommand-linedatasetscompletiondatasets_completion_powershell><span>powershell</span></a></li></ul></li></ul></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child" id=m-datasetsdocsv2reference-docsfile-formats-li><a href=/datasets/docs/v2/reference-docs/file-formats/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-docsfile-formats><span>File formats</span></a><ul class="ul-3 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2reference-docsfile-formatsannotation-files-li><a href=/datasets/docs/v2/reference-docs/file-formats/annotation-files/ title="Annotation file formats" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-docsfile-formatsannotation-files><span>Annotation files</span></a><ul class="ul-4 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docsfile-formatsannotation-filesabout-ncbi-gbff-li><a href=/datasets/docs/v2/reference-docs/file-formats/annotation-files/about-ncbi-gbff/ title="GBFF format" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docsfile-formatsannotation-filesabout-ncbi-gbff><span>GBFF</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docsfile-formatsannotation-filesabout-ncbi-gff3-li><a href=/datasets/docs/v2/reference-docs/file-formats/annotation-files/about-ncbi-gff3/ title="GFF3 format" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docsfile-formatsannotation-filesabout-ncbi-gff3><span>GFF3</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child collapse" id=m-datasetsdocsv2reference-docsfile-formatsmetadata-files-li><a href=/datasets/docs/v2/reference-docs/file-formats/metadata-files/ title="Metadata file formats" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-docsfile-formatsmetadata-files><span>Metadata files</span></a><ul class="ul-4 foldable"><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docsfile-formatsmetadata-filesabout-json-and-tabular-li><a href=/datasets/docs/v2/reference-docs/file-formats/metadata-files/about-json-and-tabular/ title="Summary of JSON, JSON Lines, and CSV/TSV tabular formats" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docsfile-formatsmetadata-filesabout-json-and-tabular><span>Summary of metadata file formats</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docsfile-formatsmetadata-fileswhy-jsonl-li><a href=/datasets/docs/v2/reference-docs/file-formats/metadata-files/why-jsonl/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docsfile-formatsmetadata-fileswhy-jsonl><span>Why JSON and JSON Lines</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docsfile-formatsmetadata-filestools-for-jsonl-li><a href=/datasets/docs/v2/reference-docs/file-formats/metadata-files/tools-for-jsonl/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docsfile-formatsmetadata-filestools-for-jsonl><span>Tools for JSON and JSON Lines</span></a></li></ul></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child" id=m-datasetsdocsv2reference-docsrelease-notes-li><a href=/datasets/docs/v2/reference-docs/release-notes/ title="NCBI Datasets release notes" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-docsrelease-notes><span>Release notes</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child active-path" id=m-datasetsdocsv2reference-docsdata-reports-li><a href=/datasets/docs/v2/reference-docs/data-reports/ title="Data report schemas" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-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" id=m-datasetsdocsv2reference-docsdata-reportsgene-li><a href=/datasets/docs/v2/reference-docs/data-reports/gene/ title="Gene report" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docsdata-reportsgene><span>Gene</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child" id=m-datasetsdocsv2reference-docsdata-reportsgene-product-li><a href=/datasets/docs/v2/reference-docs/data-reports/gene-product/ title="Gene product report" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docsdata-reportsgene-product><span>Gene product</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child active-path" id=m-datasetsdocsv2reference-docsdata-reportsgenome-assembly-li><a href=/datasets/docs/v2/reference-docs/data-reports/genome-assembly/ title="Genome assembly report" class="align-left ps-0 active td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docsdata-reportsgenome-assembly><span class=td-sidebar-nav-active-item>Genome assembly</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child" id=m-datasetsdocsv2reference-docsdata-reportsgenome-sequence-li><a href=/datasets/docs/v2/reference-docs/data-reports/genome-sequence/ title="Genome sequence report" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docsdata-reportsgenome-sequence><span>Genome sequence</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child" id=m-datasetsdocsv2reference-docsdata-reportsmicrobigge-li><a href=/datasets/docs/v2/reference-docs/data-reports/microbigge/ title="MicroBIGG-E report" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docsdata-reportsmicrobigge><span>MicroBIGG-E</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child" id=m-datasetsdocsv2reference-docsdata-reportsprokaryote-gene-li><a href=/datasets/docs/v2/reference-docs/data-reports/prokaryote-gene/ title="Prokaryote gene report" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docsdata-reportsprokaryote-gene><span>Prok. gene</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child" id=m-datasetsdocsv2reference-docsdata-reportsprokaryote-gene-location-li><a href=/datasets/docs/v2/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-datasetsdocsv2reference-docsdata-reportsprokaryote-gene-location><span>Prok. gene location</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child" id=m-datasetsdocsv2reference-docsdata-reportstaxonomy-li><a href=/datasets/docs/v2/reference-docs/data-reports/taxonomy/ title="Taxonomy report" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docsdata-reportstaxonomy><span>Taxonomy</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child" id=m-datasetsdocsv2reference-docsdata-reportstaxonomy-names-li><a href=/datasets/docs/v2/reference-docs/data-reports/taxonomy-names/ title="Taxonomy names report" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docsdata-reportstaxonomy-names><span>Taxonomy names</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child" id=m-datasetsdocsv2reference-docsdata-reportsvirus-li><a href=/datasets/docs/v2/reference-docs/data-reports/virus/ title="Virus report" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docsdata-reportsvirus><span>Virus</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child" id=m-datasetsdocsv2reference-docsdata-reportsvirus-annotation-li><a href=/datasets/docs/v2/reference-docs/data-reports/virus-annotation/ title="Virus annotation report" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docsdata-reportsvirus-annotation><span>Virus annotation</span></a></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section with-child" id=m-datasetsdocsv2reference-docsdata-packages-li><a href=/datasets/docs/v2/reference-docs/data-packages/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__section" id=m-datasetsdocsv2reference-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-datasetsdocsv2reference-docsdata-packagesgene-package-li><a href=/datasets/docs/v2/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-datasetsdocsv2reference-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-datasetsdocsv2reference-docsdata-packagesgenome-li><a href=/datasets/docs/v2/reference-docs/data-packages/genome/ title="NCBI Datasets Genome Package" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docsdata-packagesgenome><span>Genome package</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docsdata-packagestaxonomy-li><a href=/datasets/docs/v2/reference-docs/data-packages/taxonomy/ title="NCBI Datasets Taxonomy Package" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docsdata-packagestaxonomy><span>Taxonomy package</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child collapse" id=m-datasetsdocsv2reference-docsdata-packagesvirus-genome-li><a href=/datasets/docs/v2/reference-docs/data-packages/virus-genome/ title="NCBI Datasets Virus Data Package" class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2reference-docsdata-packagesvirus-genome><span>Virus data package</span></a></li></ul></li></ul></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child" id=m-datasetsdocsv2glossary-li><a href=/datasets/docs/v2/glossary/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2glossary><span>Glossary</span></a></li><li class="td-sidebar-nav__section-title td-sidebar-nav__section without-child" id=m-datasetsdocsv2citing-datasets-li><a href=/datasets/docs/v2/citing-datasets/ class="align-left ps-0 td-sidebar-link
|
||
td-sidebar-link__page" id=m-datasetsdocsv2citing-datasets><span>Cite Us</span></a></li></ul></li></ul></nav><script src=/datasets/docs/v2/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><ul><li><a href=#sample-report>Sample report</a></li><li><a href=#ncbi-datasets-v2-reports-AssemblyDataReport>AssemblyDataReport Structure</a></li><li><a href=#ncbi-datasets-v2-reports-ANIMatch>ANIMatch Structure</a></li><li><a href=#ncbi-datasets-v2-reports-AdditionalSubmitter>AdditionalSubmitter Structure</a></li><li><a href=#ncbi-datasets-v2-reports-AnnotationInfo>AnnotationInfo Structure</a></li><li><a href=#ncbi-datasets-v2-reports-AssemblyInfo>AssemblyInfo Structure</a></li><li><a href=#ncbi-datasets-v2-reports-AssemblyStats>AssemblyStats Structure</a></li><li><a href=#ncbi-datasets-v2-reports-AtypicalInfo>AtypicalInfo Structure</a></li><li><a href=#ncbi-datasets-v2-reports-AverageNucleotideIdentity>AverageNucleotideIdentity Structure</a></li><li><a href=#ncbi-datasets-v2-reports-BioProject>BioProject Structure</a></li><li><a href=#ncbi-datasets-v2-reports-BioProjectLineage>BioProjectLineage Structure</a></li><li><a href=#ncbi-datasets-v2-reports-BioSampleAttribute>BioSampleAttribute Structure</a></li><li><a href=#ncbi-datasets-v2-reports-BioSampleContact>BioSampleContact Structure</a></li><li><a href=#ncbi-datasets-v2-reports-BioSampleDescription>BioSampleDescription Structure</a></li><li><a href=#ncbi-datasets-v2-reports-BioSampleDescriptor>BioSampleDescriptor Structure</a></li><li><a href=#ncbi-datasets-v2-reports-BioSampleId>BioSampleId Structure</a></li><li><a href=#ncbi-datasets-v2-reports-BioSampleOwner>BioSampleOwner Structure</a></li><li><a href=#ncbi-datasets-v2-reports-BioSampleStatus>BioSampleStatus Structure</a></li><li><a href=#ncbi-datasets-v2-reports-BuscoStat>BuscoStat Structure</a></li><li><a href=#ncbi-datasets-v2-reports-CheckM>CheckM Structure</a></li><li><a href=#ncbi-datasets-v2-reports-FeatureCounts>FeatureCounts Structure</a></li><li><a href=#ncbi-datasets-v2-reports-GeneCounts>GeneCounts Structure</a></li><li><a href=#ncbi-datasets-v2-reports-InfraspecificNames>InfraspecificNames Structure</a></li><li><a href=#ncbi-datasets-v2-reports-LinkedAssembly>LinkedAssembly Structure</a></li><li><a href=#ncbi-datasets-v2-reports-OrganelleInfo>OrganelleInfo Structure</a></li><li><a href=#ncbi-datasets-v2-reports-PairedAssembly>PairedAssembly Structure</a></li><li><a href=#ncbi-datasets-v2-reports-TypeMaterial>TypeMaterial Structure</a></li><li><a href=#ncbi-datasets-v2-reports-WGSInfo>WGSInfo Structure</a></li><li><a href=#ncbi-datasets-v2-reports-ANITypeCategory>ANITypeCategory Enumeration</a></li><li><a href=#ncbi-datasets-v2-reports-AssemblyStatus>AssemblyStatus Enumeration</a></li><li><a href=#ncbi-datasets-v2-reports-AverageNucleotideIdentity-MatchStatus>AverageNucleotideIdentity.MatchStatus Enumeration</a></li><li><a href=#ncbi-datasets-v2-reports-AverageNucleotideIdentity-TaxonomyCheckStatus>AverageNucleotideIdentity.TaxonomyCheckStatus Enumeration</a></li><li><a href=#ncbi-datasets-v2-reports-LinkedAssemblyType>LinkedAssemblyType Enumeration</a></li><li><a href=#ncbi-datasets-v2-reports-SourceDatabase>SourceDatabase Enumeration</a></li><li><a href=#scalar-value-types>Scalar Value Types</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><nav aria-label=breadcrumb class=d-print-none><ol class="breadcrumb spb-1"><li class=breadcrumb-item><a href=/datasets/docs/v2/>Documentation</a></li><li class=breadcrumb-item><a href=/datasets/docs/v2/reference-docs/>Reference</a></li><li class=breadcrumb-item><a href=/datasets/docs/v2/reference-docs/data-reports/>Report schemas</a></li><li class="breadcrumb-item active" aria-current=page><a href=/datasets/docs/v2/reference-docs/data-reports/genome-assembly/>Genome assembly</a></li></ol></nav><h1 class="mb-4 font-weight-bold">Genome assembly report</h1><p class="lead pb-2">Genome record accession, organism, assembly statistics, and annotation info</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><ul><li><a href=#sample-report>Sample report</a></li><li><a href=#ncbi-datasets-v2-reports-AssemblyDataReport>AssemblyDataReport Structure</a></li><li><a href=#ncbi-datasets-v2-reports-ANIMatch>ANIMatch Structure</a></li><li><a href=#ncbi-datasets-v2-reports-AdditionalSubmitter>AdditionalSubmitter Structure</a></li><li><a href=#ncbi-datasets-v2-reports-AnnotationInfo>AnnotationInfo Structure</a></li><li><a href=#ncbi-datasets-v2-reports-AssemblyInfo>AssemblyInfo Structure</a></li><li><a href=#ncbi-datasets-v2-reports-AssemblyStats>AssemblyStats Structure</a></li><li><a href=#ncbi-datasets-v2-reports-AtypicalInfo>AtypicalInfo Structure</a></li><li><a href=#ncbi-datasets-v2-reports-AverageNucleotideIdentity>AverageNucleotideIdentity Structure</a></li><li><a href=#ncbi-datasets-v2-reports-BioProject>BioProject Structure</a></li><li><a href=#ncbi-datasets-v2-reports-BioProjectLineage>BioProjectLineage Structure</a></li><li><a href=#ncbi-datasets-v2-reports-BioSampleAttribute>BioSampleAttribute Structure</a></li><li><a href=#ncbi-datasets-v2-reports-BioSampleContact>BioSampleContact Structure</a></li><li><a href=#ncbi-datasets-v2-reports-BioSampleDescription>BioSampleDescription Structure</a></li><li><a href=#ncbi-datasets-v2-reports-BioSampleDescriptor>BioSampleDescriptor Structure</a></li><li><a href=#ncbi-datasets-v2-reports-BioSampleId>BioSampleId Structure</a></li><li><a href=#ncbi-datasets-v2-reports-BioSampleOwner>BioSampleOwner Structure</a></li><li><a href=#ncbi-datasets-v2-reports-BioSampleStatus>BioSampleStatus Structure</a></li><li><a href=#ncbi-datasets-v2-reports-BuscoStat>BuscoStat Structure</a></li><li><a href=#ncbi-datasets-v2-reports-CheckM>CheckM Structure</a></li><li><a href=#ncbi-datasets-v2-reports-FeatureCounts>FeatureCounts Structure</a></li><li><a href=#ncbi-datasets-v2-reports-GeneCounts>GeneCounts Structure</a></li><li><a href=#ncbi-datasets-v2-reports-InfraspecificNames>InfraspecificNames Structure</a></li><li><a href=#ncbi-datasets-v2-reports-LinkedAssembly>LinkedAssembly Structure</a></li><li><a href=#ncbi-datasets-v2-reports-OrganelleInfo>OrganelleInfo Structure</a></li><li><a href=#ncbi-datasets-v2-reports-PairedAssembly>PairedAssembly Structure</a></li><li><a href=#ncbi-datasets-v2-reports-TypeMaterial>TypeMaterial Structure</a></li><li><a href=#ncbi-datasets-v2-reports-WGSInfo>WGSInfo Structure</a></li><li><a href=#ncbi-datasets-v2-reports-ANITypeCategory>ANITypeCategory Enumeration</a></li><li><a href=#ncbi-datasets-v2-reports-AssemblyStatus>AssemblyStatus Enumeration</a></li><li><a href=#ncbi-datasets-v2-reports-AverageNucleotideIdentity-MatchStatus>AverageNucleotideIdentity.MatchStatus Enumeration</a></li><li><a href=#ncbi-datasets-v2-reports-AverageNucleotideIdentity-TaxonomyCheckStatus>AverageNucleotideIdentity.TaxonomyCheckStatus Enumeration</a></li><li><a href=#ncbi-datasets-v2-reports-LinkedAssemblyType>LinkedAssemblyType Enumeration</a></li><li><a href=#ncbi-datasets-v2-reports-SourceDatabase>SourceDatabase Enumeration</a></li><li><a href=#scalar-value-types>Scalar Value Types</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>Genome assembly report</h1><div class=lead>Genome record accession, organism, assembly statistics, and annotation info</div><header class=article-meta></header><div class=dataset-filename-content><p>The downloaded genome package contains a genome assembly
|
||
data report in <a href=https://jsonlines.readthedocs.io/>JSON Lines</a>
|
||
format in the file:<br><br><em>ncbi_dataset/data/assembly_data_report.jsonl</em><br><br>Each line of the genome assembly data report file is a hierarchical <a href=https://www.json.org/json-en.html>JSON</a>
|
||
object that represents a single genome assembly record. The schema of the genome assembly record is defined in the tables
|
||
below where each row describes a single field in the report or a sub-structure, which is a collection of fields.
|
||
The outermost structure of the report is <em>AssemblyDataReport</em>.</p><p>Table fields that include a <em>Table Field Mnemonic</em> can be used with the
|
||
<a href=/datasets/docs/v2/reference-docs/command-line/dataformat/>dataformat</a> command-line tool's <nobr><code>--fields</code></nobr> option
|
||
Refer to the <a href=/datasets/docs/v2/reference-docs/command-line/dataformat/>dataformat</a> CLI tool reference to see how you can use this
|
||
tool to transform assembly data reports from JSON Lines to tabular formats.</p></div><details class=data-report-sample><summary><h3 id=sample-report>Sample report</h3></summary><div class=highlight><pre style=background-color:#f0f3f3;-moz-tab-size:4;-o-tab-size:4;tab-size:4><code class=language-json data-lang=json>{
|
||
<span style=color:#309;font-weight:700>"accession"</span>: <span style=color:#c30>"GCF_000001405.40"</span>,
|
||
<span style=color:#309;font-weight:700>"annotationInfo"</span>: {
|
||
<span style=color:#309;font-weight:700>"busco"</span>: {
|
||
<span style=color:#309;font-weight:700>"buscoLineage"</span>: <span style=color:#c30>"primates_odb10"</span>,
|
||
<span style=color:#309;font-weight:700>"buscoVer"</span>: <span style=color:#c30>"5.7.1"</span>,
|
||
<span style=color:#309;font-weight:700>"complete"</span>: <span style=color:#f60>0.9887518</span>,
|
||
<span style=color:#309;font-weight:700>"duplicated"</span>: <span style=color:#f60>0.009433962</span>,
|
||
<span style=color:#309;font-weight:700>"fragmented"</span>: <span style=color:#f60>0.0045718434</span>,
|
||
<span style=color:#309;font-weight:700>"missing"</span>: <span style=color:#f60>0.0066763423</span>,
|
||
<span style=color:#309;font-weight:700>"singleCopy"</span>: <span style=color:#f60>0.97931784</span>,
|
||
<span style=color:#309;font-weight:700>"totalCount"</span>: <span style=color:#c30>"13780"</span>
|
||
},
|
||
<span style=color:#309;font-weight:700>"method"</span>: <span style=color:#c30>"Best-placed RefSeq; Gnomon; RefSeqFE; cmsearch; tRNAscan-SE"</span>,
|
||
<span style=color:#309;font-weight:700>"name"</span>: <span style=color:#c30>"GCF_000001405.40-RS_2024_08"</span>,
|
||
<span style=color:#309;font-weight:700>"pipeline"</span>: <span style=color:#c30>"NCBI eukaryotic genome annotation pipeline"</span>,
|
||
<span style=color:#309;font-weight:700>"provider"</span>: <span style=color:#c30>"NCBI RefSeq"</span>,
|
||
<span style=color:#309;font-weight:700>"releaseDate"</span>: <span style=color:#c30>"2024-08-23"</span>,
|
||
<span style=color:#309;font-weight:700>"reportUrl"</span>: <span style=color:#c30>"https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Homo_sapiens/GCF_000001405.40-RS_2024_08.html"</span>,
|
||
<span style=color:#309;font-weight:700>"softwareVersion"</span>: <span style=color:#c30>"10.3"</span>,
|
||
<span style=color:#309;font-weight:700>"stats"</span>: {
|
||
<span style=color:#309;font-weight:700>"geneCounts"</span>: {
|
||
<span style=color:#309;font-weight:700>"nonCoding"</span>: <span style=color:#f60>22163</span>,
|
||
<span style=color:#309;font-weight:700>"other"</span>: <span style=color:#f60>411</span>,
|
||
<span style=color:#309;font-weight:700>"proteinCoding"</span>: <span style=color:#f60>20078</span>,
|
||
<span style=color:#309;font-weight:700>"pseudogene"</span>: <span style=color:#f60>17063</span>,
|
||
<span style=color:#309;font-weight:700>"total"</span>: <span style=color:#f60>59715</span>
|
||
}
|
||
},
|
||
<span style=color:#309;font-weight:700>"status"</span>: <span style=color:#c30>"Updated annotation"</span>
|
||
},
|
||
<span style=color:#309;font-weight:700>"assemblyInfo"</span>: {
|
||
<span style=color:#309;font-weight:700>"assemblyLevel"</span>: <span style=color:#c30>"Chromosome"</span>,
|
||
<span style=color:#309;font-weight:700>"assemblyName"</span>: <span style=color:#c30>"GRCh38.p14"</span>,
|
||
<span style=color:#309;font-weight:700>"assemblyStatus"</span>: <span style=color:#c30>"current"</span>,
|
||
<span style=color:#309;font-weight:700>"assemblyType"</span>: <span style=color:#c30>"haploid-with-alt-loci"</span>,
|
||
<span style=color:#309;font-weight:700>"bioprojectAccession"</span>: <span style=color:#c30>"PRJNA31257"</span>,
|
||
<span style=color:#309;font-weight:700>"bioprojectLineage"</span>: [
|
||
{
|
||
<span style=color:#309;font-weight:700>"bioprojects"</span>: [
|
||
{
|
||
<span style=color:#309;font-weight:700>"accession"</span>: <span style=color:#c30>"PRJNA31257"</span>,
|
||
<span style=color:#309;font-weight:700>"title"</span>: <span style=color:#c30>"The Human Genome Project, currently maintained by the Genome Reference Consortium (GRC)"</span>
|
||
}
|
||
]
|
||
}
|
||
],
|
||
<span style=color:#309;font-weight:700>"blastUrl"</span>: <span style=color:#c30>"https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&PROG_DEF=blastn&BLAST_SPEC=GDH_GCF_000001405.40"</span>,
|
||
<span style=color:#309;font-weight:700>"description"</span>: <span style=color:#c30>"Genome Reference Consortium Human Build 38 patch release 14 (GRCh38.p14)"</span>,
|
||
<span style=color:#309;font-weight:700>"pairedAssembly"</span>: {
|
||
<span style=color:#309;font-weight:700>"accession"</span>: <span style=color:#c30>"GCA_000001405.29"</span>,
|
||
<span style=color:#309;font-weight:700>"onlyGenbank"</span>: <span style=color:#c30>"4 unlocalized and unplaced scaffolds."</span>,
|
||
<span style=color:#309;font-weight:700>"status"</span>: <span style=color:#c30>"current"</span>
|
||
},
|
||
<span style=color:#309;font-weight:700>"refseqCategory"</span>: <span style=color:#c30>"reference genome"</span>,
|
||
<span style=color:#309;font-weight:700>"releaseDate"</span>: <span style=color:#c30>"2022-02-03"</span>,
|
||
<span style=color:#309;font-weight:700>"submitter"</span>: <span style=color:#c30>"Genome Reference Consortium"</span>,
|
||
<span style=color:#309;font-weight:700>"synonym"</span>: <span style=color:#c30>"hg38"</span>
|
||
},
|
||
<span style=color:#309;font-weight:700>"assemblyStats"</span>: {
|
||
<span style=color:#309;font-weight:700>"contigL50"</span>: <span style=color:#f60>18</span>,
|
||
<span style=color:#309;font-weight:700>"contigN50"</span>: <span style=color:#f60>57879411</span>,
|
||
<span style=color:#309;font-weight:700>"gapsBetweenScaffoldsCount"</span>: <span style=color:#f60>349</span>,
|
||
<span style=color:#309;font-weight:700>"gcCount"</span>: <span style=color:#c30>"1374283647"</span>,
|
||
<span style=color:#309;font-weight:700>"gcPercent"</span>: <span style=color:#f60>41.0</span>,
|
||
<span style=color:#309;font-weight:700>"numberOfComponentSequences"</span>: <span style=color:#f60>35611</span>,
|
||
<span style=color:#309;font-weight:700>"numberOfContigs"</span>: <span style=color:#f60>996</span>,
|
||
<span style=color:#309;font-weight:700>"numberOfOrganelles"</span>: <span style=color:#f60>1</span>,
|
||
<span style=color:#309;font-weight:700>"numberOfScaffolds"</span>: <span style=color:#f60>470</span>,
|
||
<span style=color:#309;font-weight:700>"scaffoldL50"</span>: <span style=color:#f60>16</span>,
|
||
<span style=color:#309;font-weight:700>"scaffoldN50"</span>: <span style=color:#f60>67794873</span>,
|
||
<span style=color:#309;font-weight:700>"totalNumberOfChromosomes"</span>: <span style=color:#f60>24</span>,
|
||
<span style=color:#309;font-weight:700>"totalSequenceLength"</span>: <span style=color:#c30>"3099441038"</span>,
|
||
<span style=color:#309;font-weight:700>"totalUngappedLength"</span>: <span style=color:#c30>"2948318359"</span>
|
||
},
|
||
<span style=color:#309;font-weight:700>"currentAccession"</span>: <span style=color:#c30>"GCF_000001405.40"</span>,
|
||
<span style=color:#309;font-weight:700>"organelleInfo"</span>: [
|
||
{
|
||
<span style=color:#309;font-weight:700>"description"</span>: <span style=color:#c30>"Mitochondrion"</span>,
|
||
<span style=color:#309;font-weight:700>"submitter"</span>: <span style=color:#c30>"Genome Reference Consortium"</span>,
|
||
<span style=color:#309;font-weight:700>"totalSeqLength"</span>: <span style=color:#c30>"16569"</span>
|
||
}
|
||
],
|
||
<span style=color:#309;font-weight:700>"organism"</span>: {
|
||
<span style=color:#309;font-weight:700>"commonName"</span>: <span style=color:#c30>"human"</span>,
|
||
<span style=color:#309;font-weight:700>"organismName"</span>: <span style=color:#c30>"Homo sapiens"</span>,
|
||
<span style=color:#309;font-weight:700>"taxId"</span>: <span style=color:#f60>9606</span>
|
||
},
|
||
<span style=color:#309;font-weight:700>"pairedAccession"</span>: <span style=color:#c30>"GCA_000001405.29"</span>,
|
||
<span style=color:#309;font-weight:700>"sourceDatabase"</span>: <span style=color:#c30>"SOURCE_DATABASE_REFSEQ"</span>
|
||
}</code></pre></div></details><h3 id=ncbi-datasets-v2-reports-AssemblyDataReport>AssemblyDataReport Structure</h3><table><thead><tr><th>Field</th><th>Table Field Mnemonic</th><th>Table Column Name</th><th>Type</th><th>Description</th><th>Examples</th></tr></thead><tbody><tr><td><code>accession</code></td><td><code>accession</code></td><td>Assembly Accession</td><td><a href=#string><code>string</code></a></td><td>The GenColl assembly accession</td><td><code>GCF_000001405.40</code><br></td></tr><tr><td><code>currentAccession</code></td><td><code>current-accession</code></td><td>Current Accession</td><td><a href=#string><code>string</code></a></td><td>The latest GenColl assembly accession for this revision chain</td><td><code>GCF_000001405.40</code><br></td></tr><tr><td><code>sourceDatabase</code></td><td><code>source_database</code></td><td>Source Database</td><td><a href=#ncbi-datasets-v2-reports-SourceDatabase><code>SourceDatabase</code></a></td><td>Source of the accession. The paired accession, if it exists, is from the other database.</td><td><code>REFSEQ</code><br><code>GENBANK</code><br></td></tr><tr><td><code>organism</code></td><td><code>organism-</code></td><td>Organism</td><td><a href=#ncbi-datasets-v2-reports-Organism><code>Organism</code></a></td><td></td><td></td></tr><tr><td><code>assemblyInfo</code></td><td><code>assminfo-</code></td><td>Assembly</td><td><a href=#ncbi-datasets-v2-reports-AssemblyInfo><code>AssemblyInfo</code></a></td><td>Metadata for the genome assembly submission</td><td></td></tr><tr><td><code>assemblyStats</code></td><td><code>assmstats-</code></td><td>Assembly Stats</td><td><a href=#ncbi-datasets-v2-reports-AssemblyStats><code>AssemblyStats</code></a></td><td>Global statistics for the genome assembly</td><td></td></tr><tr><td><code>organelleInfo repeated</code></td><td><code>organelle-</code></td><td>Organelle</td><td><a href=#ncbi-datasets-v2-reports-OrganelleInfo><code>OrganelleInfo</code></a></td><td>Metadata for all associated organelle genomes</td><td></td></tr><tr><td><code>additionalSubmitters repeated</code></td><td></td><td></td><td><a href=#ncbi-datasets-v2-reports-AdditionalSubmitter><code>AdditionalSubmitter</code></a></td><td>Submitter data for all associated extra sequences</td><td></td></tr><tr><td><code>annotationInfo</code></td><td><code>annotinfo-</code></td><td>Annotation</td><td><a href=#ncbi-datasets-v2-reports-AnnotationInfo><code>AnnotationInfo</code></a></td><td>Metadata and statistics for the genome assembly annotation, when available</td><td></td></tr><tr><td><code>wgsInfo</code></td><td><code>wgs-</code></td><td>WGS</td><td><a href=#ncbi-datasets-v2-reports-WGSInfo><code>WGSInfo</code></a></td><td>Metadata pertaining to the Whole Genome Shotgun (WGS) record for the genome assembliesthat are complete genomes. Those that are clone-based do not haveWGS-master records.</td><td></td></tr><tr><td><code>typeMaterial</code></td><td><code>type_material-</code></td><td>Type Material</td><td><a href=#ncbi-datasets-v2-reports-TypeMaterial><code>TypeMaterial</code></a></td><td></td><td></td></tr><tr><td><code>checkmInfo</code></td><td><code>checkm-</code></td><td>CheckM</td><td><a href=#ncbi-datasets-v2-reports-CheckM><code>CheckM</code></a></td><td>Metadata on the completeness and contamination of this assembly</td><td></td></tr><tr><td><code>averageNucleotideIdentity</code></td><td><code>ani-</code></td><td>ANI</td><td><a href=#ncbi-datasets-v2-reports-AverageNucleotideIdentity><code>AverageNucleotideIdentity</code></a></td><td></td><td></td></tr></tbody></table><h3 id=ncbi-datasets-v2-reports-ANIMatch>ANIMatch Structure</h3><table><thead><tr><th>Field</th><th>Table Field Mnemonic</th><th>Table Column Name</th><th>Type</th><th>Description</th><th>Examples</th></tr></thead><tbody><tr><td><code>assembly</code></td><td><code>assembly</code></td><td>Assembly</td><td><a href=#string><code>string</code></a></td><td>Accession of the submitted organism best match type-strain assembly or best match type-strain assembly</td><td><code>GCA_010191885.1</code><br></td></tr><tr><td><code>organismName</code></td><td><code>organism</code></td><td>Organism</td><td><a href=#string><code>string</code></a></td><td>Taxonomic name of the submitted organism or best match type-strain organism</td><td><code>Salmonella enterica subsp. enterica serovar Typhimurium</code><br></td></tr><tr><td><code>category</code></td><td><code>category</code></td><td>Type Category</td><td><a href=#ncbi-datasets-v2-reports-ANITypeCategory><code>ANITypeCategory</code></a></td><td>Type category</td><td><code>Type material</code><br></td></tr><tr><td><code>ani</code></td><td><code>ani</code></td><td>ANI</td><td><a href=#float><code>float</code></a></td><td>Percent average nucleotide identity</td><td><code>98.5</code><br></td></tr><tr><td><code>assemblyCoverage</code></td><td><code>assembly_coverage</code></td><td>Assembly Coverage</td><td><a href=#float><code>float</code></a></td><td>Percent coverage of the query assembly by the submitted organism or best match type assembly</td><td><code>90.75</code><br></td></tr><tr><td><code>typeAssemblyCoverage</code></td><td><code>type_assembly_coverage</code></td><td>Type Assembly Coverage</td><td><a href=#float><code>float</code></a></td><td>Percent coverage of the submitted organism or best match type assembly by the query assembly</td><td><code>89.60</code><br></td></tr></tbody></table><h3 id=ncbi-datasets-v2-reports-AdditionalSubmitter>AdditionalSubmitter Structure</h3><table><thead><tr><th>Field</th><th>Table Field Mnemonic</th><th>Table Column Name</th><th>Type</th><th>Description</th><th>Examples</th></tr></thead><tbody><tr><td><code>genbankAccession</code></td><td><em>coming soon</em></td><td><em>coming soon</em></td><td><a href=#string><code>string</code></a></td><td>genbank accession of extra sequence</td><td></td></tr><tr><td><code>refseqAccession</code></td><td><em>coming soon</em></td><td><em>coming soon</em></td><td><a href=#string><code>string</code></a></td><td>genbank accession of extra sequence</td><td></td></tr><tr><td><code>chrName</code></td><td><em>coming soon</em></td><td><em>coming soon</em></td><td><a href=#string><code>string</code></a></td><td>chromosome name</td><td></td></tr><tr><td><code>moleculeType</code></td><td><em>coming soon</em></td><td><em>coming soon</em></td><td><a href=#string><code>string</code></a></td><td>molecule type</td><td></td></tr><tr><td><code>submitter</code></td><td><em>coming soon</em></td><td><em>coming soon</em></td><td><a href=#string><code>string</code></a></td><td>Name of submitter</td><td></td></tr><tr><td><code>bioprojectAccession</code></td><td><em>coming soon</em></td><td><em>coming soon</em></td><td><a href=#string><code>string</code></a></td><td>Bioproject accession</td><td></td></tr></tbody></table><h3 id=ncbi-datasets-v2-reports-AnnotationInfo>AnnotationInfo Structure</h3><table><thead><tr><th>Field</th><th>Table Field Mnemonic</th><th>Table Column Name</th><th>Type</th><th>Description</th><th>Examples</th></tr></thead><tbody><tr><td><code>name</code></td><td><code>name</code></td><td>Name</td><td><a href=#string><code>string</code></a></td><td>Annotation name</td><td></td></tr><tr><td><code>provider</code></td><td><code>provider</code></td><td>Provider</td><td><a href=#string><code>string</code></a></td><td>Source of the annotation</td><td></td></tr><tr><td><code>releaseDate</code></td><td><code>release-date</code></td><td>Release Date</td><td><a href=#string><code>string</code></a></td><td>Annotation release date</td><td></td></tr><tr><td><code>reportUrl</code></td><td><code>report-url</code></td><td>Report URL</td><td><a href=#string><code>string</code></a></td><td>Annotation report web address</td><td></td></tr><tr><td><code>stats</code></td><td><code>featcount-</code></td><td>Count</td><td><a href=#ncbi-datasets-v2-reports-FeatureCounts><code>FeatureCounts</code></a></td><td></td><td></td></tr><tr><td><code>busco</code></td><td><code>busco-</code></td><td>BUSCO</td><td><a href=#ncbi-datasets-v2-reports-BuscoStat><code>BuscoStat</code></a></td><td></td><td></td></tr><tr><td><code>method</code></td><td><code>method</code></td><td>Method</td><td><a href=#string><code>string</code></a></td><td>Software tools used to calculate annotation</td><td></td></tr><tr><td><code>pipeline</code></td><td><code>pipeline</code></td><td>Pipeline</td><td><a href=#string><code>string</code></a></td><td>NCBI annotation pipeline used to calculate annotation</td><td></td></tr><tr><td><code>softwareVersion</code></td><td><code>software-version</code></td><td>Software Version</td><td><a href=#string><code>string</code></a></td><td>NCBI annotation pipeline software version</td><td></td></tr><tr><td><code>status</code></td><td><code>status</code></td><td>Status</td><td><a href=#string><code>string</code></a></td><td>Type of annotation</td><td></td></tr></tbody></table><h3 id=ncbi-datasets-v2-reports-AssemblyInfo>AssemblyInfo Structure</h3><table><thead><tr><th>Field</th><th>Table Field Mnemonic</th><th>Table Column Name</th><th>Type</th><th>Description</th><th>Examples</th></tr></thead><tbody><tr><td><code>assemblyLevel</code></td><td><code>level</code></td><td>Level</td><td><a href=#string><code>string</code></a></td><td>The level at which a genome has been assembled</td><td><code>chromosome</code><br><code>scaffold</code><br><code>contig</code><br></td></tr><tr><td><code>assemblyStatus</code></td><td><code>status</code></td><td>Status</td><td><a href=#ncbi-datasets-v2-reports-AssemblyStatus><code>AssemblyStatus</code></a></td><td>The GenColl assembly status</td><td><code>current</code><br></td></tr><tr><td><code>pairedAssembly</code></td><td><code>paired-assm-</code></td><td>Paired Assembly</td><td><a href=#ncbi-datasets-v2-reports-PairedAssembly><code>PairedAssembly</code></a></td><td>Metadata from the GenBank or RefSeq assembly paired with this one</td><td></td></tr><tr><td><code>assemblyName</code></td><td><code>name</code></td><td>Name</td><td><a href=#string><code>string</code></a></td><td>The assembly submitter’s name for the genome assembly, when provided. Otherwise, a default name in theform ASM#####v# is assigned</td><td><code>GRCh38.p14</code><br><code>ASM985889v3</code><br></td></tr><tr><td><code>assemblyLongName</code></td><td><code>long-name</code></td><td>LongName</td><td><a href=#string><code>string</code></a></td><td></td><td><code>Genome Reference Consortium Human Build 38 patch release 14 (GRCh38.p14)</code><br></td></tr><tr><td><code>assemblyType</code></td><td><code>type</code></td><td>Type</td><td><a href=#string><code>string</code></a></td><td>Chromosome content of the submitted genome assembly</td><td><code>haploid-with-alt-loci</code><br><code>haploid</code><br></td></tr><tr><td><code>bioprojectLineage repeated</code></td><td><code>bioproject-</code></td><td>BioProject</td><td><a href=#ncbi-datasets-v2-reports-BioProjectLineage><code>BioProjectLineage</code></a></td><td>The lineage of BioProject accessions. The specific BioProject which produced the sequences in thegenome assembly is listed first, followed in order by its antecedents.</td><td></td></tr><tr><td><code>bioprojectAccession</code></td><td><code>bioproject</code></td><td>BioProject Accession</td><td><a href=#string><code>string</code></a></td><td></td><td></td></tr><tr><td><code>releaseDate</code></td><td><code>release-date</code></td><td>Release Date</td><td><a href=#string><code>string</code></a></td><td>Date the assembly was made available by NCBI. This field is not returned by versions of the datasets Command Line Interface (CLI) program < 15.</td><td></td></tr><tr><td><code>description</code></td><td><code>description</code></td><td>Description</td><td><a href=#string><code>string</code></a></td><td>Long description for this genome</td><td></td></tr><tr><td><code>submitter</code></td><td><code>submitter</code></td><td>Submitter</td><td><a href=#string><code>string</code></a></td><td>The submitting consortium or organization. Full submitter information is available in the BioProject</td><td></td></tr><tr><td><code>refseqCategory</code></td><td><code>refseq-category</code></td><td>Refseq Category</td><td><a href=#string><code>string</code></a></td><td>The RefSeq Category, if present, indicates whether the assembly is a reference genome</td><td><code>reference genome</code><br></td></tr><tr><td><code>synonym</code></td><td><code>synonym</code></td><td>Synonym</td><td><a href=#string><code>string</code></a></td><td>Genome name ascribed to this assembly by the UC Santa Cruz genome browser</td><td><code>hg38</code><br></td></tr><tr><td><code>linkedAssemblies repeated</code></td><td><code>linked-assm-</code></td><td>Linked Assembly</td><td><a href=#ncbi-datasets-v2-reports-LinkedAssembly><code>LinkedAssembly</code></a></td><td>Genome assemblies derived from the same diploid individual</td><td></td></tr><tr><td><code>atypical</code></td><td><code>atypical</code></td><td>Atypical</td><td><a href=#ncbi-datasets-v2-reports-AtypicalInfo><code>AtypicalInfo</code></a></td><td>Information on atypical genomes - genomes that have assembly issues or are otherwise atypical</td><td></td></tr><tr><td><code>genomeNotes repeated</code></td><td><code>notes</code></td><td>Notes</td><td><a href=#string><code>string</code></a></td><td>All the RefSeq messages associated with this assembly</td><td></td></tr><tr><td><code>sequencingTech</code></td><td><code>sequencing-tech</code></td><td>Sequencing Tech</td><td><a href=#string><code>string</code></a></td><td>Sequencing technology used to sequence this genome</td><td></td></tr><tr><td><code>assemblyMethod</code></td><td><code>assembly-method</code></td><td>Assembly Method</td><td><a href=#string><code>string</code></a></td><td>Genome assembly method</td><td></td></tr><tr><td><code>groupingMethod</code></td><td><code>grouping-method</code></td><td>Grouping Method</td><td><a href=#string><code>string</code></a></td><td></td><td></td></tr><tr><td><code>biosample</code></td><td><code>biosample-</code></td><td>BioSample</td><td><a href=#ncbi-datasets-v2-reports-BioSampleDescriptor><code>BioSampleDescriptor</code></a></td><td>NCBI BioSample from which the sequences in the genome assembly were obtained.</td><td></td></tr><tr><td><code>blastUrl</code></td><td><code>blast-url</code></td><td>Blast URL</td><td><a href=#string><code>string</code></a></td><td>URL to blast page for this assembly</td><td></td></tr><tr><td><code>comments</code></td><td><em>coming soon</em></td><td><em>coming soon</em></td><td><a href=#string><code>string</code></a></td><td>Freeform comments</td><td></td></tr><tr><td><code>suppressionReason</code></td><td><code>suppression-reason</code></td><td>Suppression Reason</td><td><a href=#string><code>string</code></a></td><td>The reason for the assembly is suppressed, for suppressed assemblies</td><td></td></tr><tr><td><code>diploidRole</code></td><td></td><td></td><td><a href=#ncbi-datasets-v2-reports-LinkedAssemblyType><code>LinkedAssemblyType</code></a></td><td></td><td></td></tr></tbody></table><h3 id=ncbi-datasets-v2-reports-AssemblyStats>AssemblyStats Structure</h3><table><thead><tr><th>Field</th><th>Table Field Mnemonic</th><th>Table Column Name</th><th>Type</th><th>Description</th><th>Examples</th></tr></thead><tbody><tr><td><code>totalNumberOfChromosomes</code></td><td><code>total-number-of-chromosomes</code></td><td>Total Number of Chromosomes</td><td><a href=#uint32><code>uint32</code></a></td><td>Count of nuclear chromosomes, organelles and plasmids in a submitted genome assembly</td><td></td></tr><tr><td><code>totalSequenceLength</code></td><td><code>total-sequence-len</code></td><td>Total Sequence Length</td><td><a href=#uint64><code>uint64</code></a></td><td>Total sequence length of the nuclear genome including unplaced and unlocalized sequences</td><td></td></tr><tr><td><code>totalUngappedLength</code></td><td><code>total-ungapped-len</code></td><td>Total Ungapped Length</td><td><a href=#uint64><code>uint64</code></a></td><td>Total length of all top-level sequences ignoring gaps. Any stretch of 10 or more Ns in a sequence is treated like a gap</td><td></td></tr><tr><td><code>numberOfContigs</code></td><td><code>number-of-contigs</code></td><td>Number of Contigs</td><td><a href=#uint32><code>uint32</code></a></td><td>Total number of sequence contigs in the assembly. Any stretch of 10 or more Ns in a sequence is treated as a gap between twocontigs in a scaffold when counting contigs and calculating contig N50 & L50 values</td><td></td></tr><tr><td><code>contigN50</code></td><td><code>contig-n50</code></td><td>Contig N50</td><td><a href=#uint32><code>uint32</code></a></td><td>Length such that sequence contigs of this length or longer include half the bases of the assembly</td><td></td></tr><tr><td><code>contigL50</code></td><td><code>contig-l50</code></td><td>Contig L50</td><td><a href=#uint32><code>uint32</code></a></td><td>Number of sequence contigs that are longer than, or equal to, the N50 length and therefore include half the bases of the assembly</td><td></td></tr><tr><td><code>numberOfScaffolds</code></td><td><code>number-of-scaffolds</code></td><td>Number of Scaffolds</td><td><a href=#uint32><code>uint32</code></a></td><td>Number of scaffolds including placed, unlocalized, unplaced, alternate loci and patch scaffolds</td><td></td></tr><tr><td><code>scaffoldN50</code></td><td><code>scaffold-n50</code></td><td>Scaffold N50</td><td><a href=#uint32><code>uint32</code></a></td><td>Length such that scaffolds of this length or longer include half the bases of the assembly</td><td></td></tr><tr><td><code>scaffoldL50</code></td><td><code>scaffold-l50</code></td><td>Scaffold L50</td><td><a href=#uint32><code>uint32</code></a></td><td>Number of scaffolds that are longer than, or equal to, the N50 length and therefore include half the bases of the assembly</td><td></td></tr><tr><td><code>gapsBetweenScaffoldsCount</code></td><td><code>gaps-between-scaffolds-count</code></td><td>Gaps Between Scaffolds Count</td><td><a href=#uint32><code>uint32</code></a></td><td>Number of unspanned gaps between scaffolds</td><td></td></tr><tr><td><code>numberOfComponentSequences</code></td><td><code>number-of-component-sequences</code></td><td>Number of Component Sequences</td><td><a href=#uint32><code>uint32</code></a></td><td>Total number of component WGS or clone sequences in the assembly</td><td></td></tr><tr><td><code>gcPercent</code></td><td><code>gc-percent</code></td><td>GC Percent</td><td><a href=#float><code>float</code></a></td><td>The percentage of GC base-pairs in the assembly</td><td></td></tr><tr><td><code>genomeCoverage</code></td><td><code>genome-coverage</code></td><td>Genome Coverage</td><td><a href=#string><code>string</code></a></td><td>Genome assembly coverage</td><td></td></tr><tr><td><code>numberOfOrganelles</code></td><td><code>number-of-organelles</code></td><td>Number of Organelles</td><td><a href=#uint32><code>uint32</code></a></td><td>number of organelles</td><td></td></tr></tbody></table><h3 id=ncbi-datasets-v2-reports-AtypicalInfo>AtypicalInfo Structure</h3><table><thead><tr><th>Field</th><th>Table Field Mnemonic</th><th>Table Column Name</th><th>Type</th><th>Description</th><th>Examples</th></tr></thead><tbody><tr><td><code>isAtypical</code></td><td><code>is-atypical</code></td><td>Is Atypical</td><td><a href=#bool><code>bool</code></a></td><td>If true there are assembly issues or the assembly is in some way non-standard</td><td></td></tr><tr><td><code>warnings repeated</code></td><td><code>warnings</code></td><td>Warnings</td><td><a href=#string><code>string</code></a></td><td>The reasons that the assembly is considered atypical</td><td></td></tr></tbody></table><h3 id=ncbi-datasets-v2-reports-AverageNucleotideIdentity>AverageNucleotideIdentity Structure</h3><table><thead><tr><th>Field</th><th>Table Field Mnemonic</th><th>Table Column Name</th><th>Type</th><th>Description</th><th>Examples</th></tr></thead><tbody><tr><td><code>taxonomyCheckStatus</code></td><td><code>check-status</code></td><td>Check status</td><td><a href=#ncbi-datasets-v2-reports-AverageNucleotideIdentity-TaxonomyCheckStatus><code>AverageNucleotideIdentity.TaxonomyCheckStatus</code></a></td><td>Indicates whether the ANI result is consistent with the submitted organism</td><td><code>ok</code><br><code>failed</code><br><code>inconclusive</code><br></td></tr><tr><td><code>matchStatus</code></td><td><code>best-match-status</code></td><td>Best match status</td><td><a href=#ncbi-datasets-v2-reports-AverageNucleotideIdentity-MatchStatus><code>AverageNucleotideIdentity.MatchStatus</code></a></td><td>Indicates the specific type of ANI result that supports the Taxonomy check status</td><td><code>derived-species-match</code><br></td></tr><tr><td><code>submittedOrganism</code></td><td><code>submitted-organism</code></td><td>Submitted organism</td><td><a href=#string><code>string</code></a></td><td>Taxonomic name of the query assembly</td><td><code>Salmonella enterica subsp. enterica serovar Tennessee str. CDC07-0191</code><br></td></tr><tr><td><code>submittedSpecies</code></td><td><code>submitted-species</code></td><td>Submitted species</td><td><a href=#string><code>string</code></a></td><td>Species name of the query assembly</td><td><code>Salmonella enterica</code><br></td></tr><tr><td><code>category</code></td><td><code>category</code></td><td>Category</td><td><a href=#ncbi-datasets-v2-reports-ANITypeCategory><code>ANITypeCategory</code></a></td><td>Category of type or validated assembly</td><td><code>syntype</code><br></td></tr><tr><td><code>submittedAniMatch</code></td><td><code>submitted-ani-match-</code></td><td>Declared ANI match</td><td><a href=#ncbi-datasets-v2-reports-ANIMatch><code>ANIMatch</code></a></td><td></td><td></td></tr><tr><td><code>bestAniMatch</code></td><td><code>best-ani-match-</code></td><td>Best ANI match</td><td><a href=#ncbi-datasets-v2-reports-ANIMatch><code>ANIMatch</code></a></td><td></td><td></td></tr><tr><td><code>comment</code></td><td><code>comment</code></td><td>Comment</td><td><a href=#string><code>string</code></a></td><td>Additional information about the ANI result</td><td></td></tr></tbody></table><h3 id=ncbi-datasets-v2-reports-BioProject>BioProject Structure</h3><p>A BioProject is a collection of biological data related to a
|
||
single initiative, originating from a single organization or from a
|
||
consortium. A BioProject record provides users a single place to find links
|
||
to the diverse data types generated for that project. The record can be
|
||
retrieved from <a href=https://www.ncbi.nlm.nih.gov/bioproject/>NCBI BioProject</a></p><table><thead><tr><th>Field</th><th>Table Field Mnemonic</th><th>Table Column Name</th><th>Type</th><th>Description</th><th>Examples</th></tr></thead><tbody><tr><td><code>accession</code></td><td><code>accession</code></td><td>Accession</td><td><a href=#string><code>string</code></a></td><td>BioProject accession</td><td><code>PRJEB35387</code><br></td></tr><tr><td><code>title</code></td><td><code>title</code></td><td>Title</td><td><a href=#string><code>string</code></a></td><td>Title of the BioProject provided by the submitter</td><td><code>Sciurus carolinensis (grey squirrel) genome assembly, mSciCar1</code><br></td></tr><tr><td><code>parentAccessions repeated</code></td><td><code>parent-accessions</code></td><td>Parent Accessions</td><td><a href=#string><code>string</code></a></td><td>BioProject accession containing multiple children BioProjects</td><td><code>["PRJNA489243","PRJEB33226","PRJEB40665"]</code><br></td></tr></tbody></table><h3 id=ncbi-datasets-v2-reports-BioProjectLineage>BioProjectLineage Structure</h3><table><thead><tr><th>Field</th><th>Table Field Mnemonic</th><th>Table Column Name</th><th>Type</th><th>Description</th><th>Examples</th></tr></thead><tbody><tr><td><code>bioprojects repeated</code></td><td><code>lineage-</code></td><td>Lineage</td><td><a href=#ncbi-datasets-v2-reports-BioProject><code>BioProject</code></a></td><td>A BioProject is a collection of biological data related to a single initiative, originating from a single organization or from a consortium</td><td></td></tr></tbody></table><h3 id=ncbi-datasets-v2-reports-BioSampleAttribute>BioSampleAttribute Structure</h3><table><thead><tr><th>Field</th><th>Table Field Mnemonic</th><th>Table Column Name</th><th>Type</th><th>Description</th><th>Examples</th></tr></thead><tbody><tr><td><code>name</code></td><td><code>name</code></td><td>Name</td><td><a href=#string><code>string</code></a></td><td></td><td></td></tr><tr><td><code>value</code></td><td><code>value</code></td><td>Value</td><td><a href=#string><code>string</code></a></td><td></td><td></td></tr></tbody></table><h3 id=ncbi-datasets-v2-reports-BioSampleContact>BioSampleContact Structure</h3><table><thead><tr><th>Field</th><th>Table Field Mnemonic</th><th>Table Column Name</th><th>Type</th><th>Description</th><th>Examples</th></tr></thead><tbody><tr><td><code>lab</code></td><td><code>lab</code></td><td>Lab</td><td><a href=#string><code>string</code></a></td><td>Submitter lab name.</td><td></td></tr></tbody></table><h3 id=ncbi-datasets-v2-reports-BioSampleDescription>BioSampleDescription Structure</h3><p>Description of the BioSample object</p><table><thead><tr><th>Field</th><th>Table Field Mnemonic</th><th>Table Column Name</th><th>Type</th><th>Description</th><th>Examples</th></tr></thead><tbody><tr><td><code>title</code></td><td><code>title</code></td><td>Title</td><td><a href=#string><code>string</code></a></td><td></td><td></td></tr><tr><td><code>organism</code></td><td><code>organism-</code></td><td>Organism</td><td><a href=#ncbi-datasets-v2-reports-Organism><code>Organism</code></a></td><td></td><td></td></tr><tr><td><code>comment</code></td><td><code>comment</code></td><td>Comment</td><td><a href=#string><code>string</code></a></td><td></td><td></td></tr></tbody></table><h3 id=ncbi-datasets-v2-reports-BioSampleDescriptor>BioSampleDescriptor Structure</h3><p>This describes BioSample data that is included in the genome assembly data report</p><table><thead><tr><th>Field</th><th>Table Field Mnemonic</th><th>Table Column Name</th><th>Type</th><th>Description</th><th>Examples</th></tr></thead><tbody><tr><td><code>accession</code></td><td><code>accession</code></td><td>Accession</td><td><a href=#string><code>string</code></a></td><td></td><td><code>SAMN20055006</code><br></td></tr><tr><td><code>lastUpdated</code></td><td><code>last-updated</code></td><td>Last updated</td><td><a href=#string><code>string</code></a></td><td></td><td></td></tr><tr><td><code>publicationDate</code></td><td><code>publication-date</code></td><td>Publication date</td><td><a href=#string><code>string</code></a></td><td></td><td></td></tr><tr><td><code>submissionDate</code></td><td><code>submission-date</code></td><td>Submission date</td><td><a href=#string><code>string</code></a></td><td></td><td></td></tr><tr><td><code>sampleIds repeated</code></td><td><code>ids-</code></td><td>Sample Identifiers</td><td><a href=#ncbi-datasets-v2-reports-BioSampleId><code>BioSampleId</code></a></td><td></td><td></td></tr><tr><td><code>description</code></td><td><code>description-</code></td><td>Description</td><td><a href=#ncbi-datasets-v2-reports-BioSampleDescription><code>BioSampleDescription</code></a></td><td></td><td></td></tr><tr><td><code>owner</code></td><td><code>owner-</code></td><td>Owner</td><td><a href=#ncbi-datasets-v2-reports-BioSampleOwner><code>BioSampleOwner</code></a></td><td></td><td></td></tr><tr><td><code>models repeated</code></td><td><code>models</code></td><td>Models</td><td><a href=#string><code>string</code></a></td><td></td><td></td></tr><tr><td><code>bioprojects repeated</code></td><td><code>bioproject-</code></td><td>BioProject</td><td><a href=#ncbi-datasets-v2-reports-BioProject><code>BioProject</code></a></td><td></td><td></td></tr><tr><td><code>package</code></td><td><code>package</code></td><td>Package</td><td><a href=#string><code>string</code></a></td><td></td><td><code>MIGS.ba.air.4.0</code><br></td></tr><tr><td><code>attributes repeated</code></td><td><code>attribute-</code></td><td>Attribute</td><td><a href=#ncbi-datasets-v2-reports-BioSampleAttribute><code>BioSampleAttribute</code></a></td><td></td><td></td></tr><tr><td><code>status</code></td><td><code>status-</code></td><td>Status</td><td><a href=#ncbi-datasets-v2-reports-BioSampleStatus><code>BioSampleStatus</code></a></td><td></td><td></td></tr><tr><td><code>age</code></td><td><code>age</code></td><td>Age</td><td><a href=#string><code>string</code></a></td><td>Age at the time of sampling</td><td></td></tr><tr><td><code>biomaterialProvider</code></td><td><code>biomaterial-provider</code></td><td>Biomaterial provider</td><td><a href=#string><code>string</code></a></td><td>Name and address of the lab or PI</td><td></td></tr><tr><td><code>breed</code></td><td><code>breed</code></td><td>Breed</td><td><a href=#string><code>string</code></a></td><td>Breed name</td><td></td></tr><tr><td><code>collectedBy</code></td><td><code>collected-by</code></td><td>Collected by</td><td><a href=#string><code>string</code></a></td><td>Name of persons or institute who collected the sample</td><td></td></tr><tr><td><code>collectionDate</code></td><td><code>collection-date</code></td><td>Collection date</td><td><a href=#string><code>string</code></a></td><td>Date on which the sample was collected</td><td></td></tr><tr><td><code>cultivar</code></td><td><code>cultivar</code></td><td>Cultivar</td><td><a href=#string><code>string</code></a></td><td>Cultivated variety of plant</td><td></td></tr><tr><td><code>devStage</code></td><td><code>development-stage</code></td><td>Development stage</td><td><a href=#string><code>string</code></a></td><td>Developmental stage at the time of sampling</td><td></td></tr><tr><td><code>ecotype</code></td><td><code>ecotype</code></td><td>Ecotype</td><td><a href=#string><code>string</code></a></td><td>Population within a given species adapted to a local habitat</td><td></td></tr><tr><td><code>geoLocName</code></td><td><code>geo-loc-name</code></td><td>Geographic location</td><td><a href=#string><code>string</code></a></td><td>Geographical origin of the sample</td><td></td></tr><tr><td><code>host</code></td><td><code>host</code></td><td>Host</td><td><a href=#string><code>string</code></a></td><td>The natural host to the organism</td><td></td></tr><tr><td><code>hostDisease</code></td><td><code>host-disease</code></td><td>Host disease</td><td><a href=#string><code>string</code></a></td><td>Name of relevant disease</td><td></td></tr><tr><td><code>identifiedBy</code></td><td><code>identified-by</code></td><td>Identified by</td><td><a href=#string><code>string</code></a></td><td>Name of the taxonomist who identified the specimen</td><td></td></tr><tr><td><code>ifsacCategory</code></td><td><code>ifsac-category</code></td><td>IFSAC category</td><td><a href=#string><code>string</code></a></td><td>Interagency Food Safety Analytics Collaboration (IFSAC) category</td><td></td></tr><tr><td><code>isolate</code></td><td><code>isolate</code></td><td>Isolate</td><td><a href=#string><code>string</code></a></td><td>Description of the specific individual from which the sample was derived</td><td></td></tr><tr><td><code>isolateNameAlias</code></td><td><code>isolate-name-alias</code></td><td>Isolate name alias</td><td><a href=#string><code>string</code></a></td><td>Other IDs associated with this isolate</td><td></td></tr><tr><td><code>isolationSource</code></td><td><code>isolation-source</code></td><td>Isolation source</td><td><a href=#string><code>string</code></a></td><td>Source of the sample</td><td></td></tr><tr><td><code>latLon</code></td><td><code>lat-lon</code></td><td>Latitude and Longitude</td><td><a href=#string><code>string</code></a></td><td>Geographic coordinates of the location where the sample was collected</td><td></td></tr><tr><td><code>projectName</code></td><td><code>project-name</code></td><td>Project name</td><td><a href=#string><code>string</code></a></td><td>Name of the project</td><td></td></tr><tr><td><code>sampleName</code></td><td><code>sample-name</code></td><td>Sample name</td><td><a href=#string><code>string</code></a></td><td>Sample name in source database</td><td></td></tr><tr><td><code>serovar</code></td><td><code>serovar</code></td><td>Serovar</td><td><a href=#string><code>string</code></a></td><td>Taxonomic name below subspecies. Same as serotype.</td><td></td></tr><tr><td><code>sex</code></td><td><code>sex</code></td><td>Sex</td><td><a href=#string><code>string</code></a></td><td>Physical sex of sampled organism</td><td></td></tr><tr><td><code>sourceType</code></td><td><code>source-type</code></td><td>Source type</td><td><a href=#string><code>string</code></a></td><td>Controlled vocabulary describing the isolation source</td><td></td></tr><tr><td><code>strain</code></td><td><code>strain</code></td><td>Strain</td><td><a href=#string><code>string</code></a></td><td>Strain name</td><td></td></tr><tr><td><code>subSpecies</code></td><td><code>sub-species</code></td><td>Sub-species</td><td><a href=#string><code>string</code></a></td><td>Sub-species taxonomic name</td><td></td></tr><tr><td><code>tissue</code></td><td><code>tissue</code></td><td>Tissue</td><td><a href=#string><code>string</code></a></td><td>Type of tissue from which the sample was derived</td><td></td></tr><tr><td><code>serotype</code></td><td><code>serotype</code></td><td>Serotype</td><td><a href=#string><code>string</code></a></td><td>Taxonomic name below subspecies. Same as serovar</td><td></td></tr></tbody></table><h3 id=ncbi-datasets-v2-reports-BioSampleId>BioSampleId Structure</h3><table><thead><tr><th>Field</th><th>Table Field Mnemonic</th><th>Table Column Name</th><th>Type</th><th>Description</th><th>Examples</th></tr></thead><tbody><tr><td><code>db</code></td><td><code>db</code></td><td>Database</td><td><a href=#string><code>string</code></a></td><td></td><td><code>Wellcome Sanger Institute</code><br></td></tr><tr><td><code>label</code></td><td><code>label</code></td><td>Label</td><td><a href=#string><code>string</code></a></td><td></td><td><code>Sample name</code><br></td></tr><tr><td><code>value</code></td><td><code>value</code></td><td>Value</td><td><a href=#string><code>string</code></a></td><td></td><td><code>COG-UK/ALDP-17A6A8C</code><br></td></tr></tbody></table><h3 id=ncbi-datasets-v2-reports-BioSampleOwner>BioSampleOwner Structure</h3><table><thead><tr><th>Field</th><th>Table Field Mnemonic</th><th>Table Column Name</th><th>Type</th><th>Description</th><th>Examples</th></tr></thead><tbody><tr><td><code>name</code></td><td><code>name</code></td><td>Name</td><td><a href=#string><code>string</code></a></td><td></td><td></td></tr><tr><td><code>contacts repeated</code></td><td><code>contact-</code></td><td>Contact</td><td><a href=#ncbi-datasets-v2-reports-BioSampleContact><code>BioSampleContact</code></a></td><td></td><td></td></tr></tbody></table><h3 id=ncbi-datasets-v2-reports-BioSampleStatus>BioSampleStatus Structure</h3><table><thead><tr><th>Field</th><th>Table Field Mnemonic</th><th>Table Column Name</th><th>Type</th><th>Description</th><th>Examples</th></tr></thead><tbody><tr><td><code>status</code></td><td><code>status</code></td><td>Status</td><td><a href=#string><code>string</code></a></td><td></td><td><code>live</code><br></td></tr><tr><td><code>when</code></td><td><code>when</code></td><td>When</td><td><a href=#string><code>string</code></a></td><td></td><td></td></tr></tbody></table><h3 id=ncbi-datasets-v2-reports-BuscoStat>BuscoStat Structure</h3><table><thead><tr><th>Field</th><th>Table Field Mnemonic</th><th>Table Column Name</th><th>Type</th><th>Description</th><th>Examples</th></tr></thead><tbody><tr><td><code>buscoLineage</code></td><td><code>lineage</code></td><td>Lineage</td><td><a href=#string><code>string</code></a></td><td>BUSCO Lineage</td><td></td></tr><tr><td><code>buscoVer</code></td><td><code>ver</code></td><td>Version</td><td><a href=#string><code>string</code></a></td><td>BUSCO Version</td><td></td></tr><tr><td><code>complete</code></td><td><code>complete</code></td><td>Complete</td><td><a href=#float><code>float</code></a></td><td>BUSCO score: Complete</td><td></td></tr><tr><td><code>singleCopy</code></td><td><code>singlecopy</code></td><td>Single Copy</td><td><a href=#float><code>float</code></a></td><td>BUSCO score: Single Copy</td><td></td></tr><tr><td><code>duplicated</code></td><td><code>duplicated</code></td><td>Duplicated</td><td><a href=#float><code>float</code></a></td><td>BUSCO score: Duplicated</td><td></td></tr><tr><td><code>fragmented</code></td><td><code>fragmented</code></td><td>Fragmented</td><td><a href=#float><code>float</code></a></td><td>BUSCO score: Fragmented</td><td></td></tr><tr><td><code>missing</code></td><td><code>missing</code></td><td>Missing</td><td><a href=#float><code>float</code></a></td><td>BUSCO score: Missing</td><td></td></tr><tr><td><code>totalCount</code></td><td><code>totalcount</code></td><td>Total Count</td><td><a href=#uint64><code>uint64</code></a></td><td>BUSCO score: Total Count</td><td></td></tr></tbody></table><h3 id=ncbi-datasets-v2-reports-CheckM>CheckM Structure</h3><table><thead><tr><th>Field</th><th>Table Field Mnemonic</th><th>Table Column Name</th><th>Type</th><th>Description</th><th>Examples</th></tr></thead><tbody><tr><td><code>checkmMarkerSet</code></td><td><code>marker-set</code></td><td>marker set</td><td><a href=#string><code>string</code></a></td><td>What taxonomic group is used as the basis for comparison with this assembly with regards to checkM values</td><td><code>Mycobacterium avium</code><br></td></tr><tr><td><code>checkmSpeciesTaxId</code></td><td><code>species-tax-id</code></td><td>species tax id</td><td><a href=#uint32><code>uint32</code></a></td><td>The species-level taxid for this assemblies checkM dataset</td><td><code>1764</code><br></td></tr><tr><td><code>checkmMarkerSetRank</code></td><td><code>marker-set-rank</code></td><td>marker set rank</td><td><a href=#string><code>string</code></a></td><td>CheckM taxonomic rank of checkm_marker_set</td><td><code>species</code><br><code>genus</code><br></td></tr><tr><td><code>checkmVersion</code></td><td><code>version</code></td><td>version</td><td><a href=#string><code>string</code></a></td><td>CheckM software version</td><td><code>v1.2.0</code><br></td></tr><tr><td><code>completeness</code></td><td><code>completeness</code></td><td>completeness</td><td><a href=#float><code>float</code></a></td><td>What percent complete is this assembly</td><td><code>86.83</code><br></td></tr><tr><td><code>contamination</code></td><td><code>contamination</code></td><td>contamination</td><td><a href=#float><code>float</code></a></td><td>What is the contamination percentage for this assembly</td><td><code>5.18</code><br></td></tr><tr><td><code>completenessPercentile</code></td><td><code>completeness-percentile</code></td><td>completeness percentile</td><td><a href=#float><code>float</code></a></td><td>The percent of assemblies under the taxonomic grouping ‘checkm_marker_set’ that this assembly is as-or-more complete than.</td><td><code>79</code><br></td></tr></tbody></table><h3 id=ncbi-datasets-v2-reports-FeatureCounts>FeatureCounts Structure</h3><table><thead><tr><th>Field</th><th>Table Field Mnemonic</th><th>Table Column Name</th><th>Type</th><th>Description</th><th>Examples</th></tr></thead><tbody><tr><td><code>geneCounts</code></td><td><code>gene-</code></td><td>Gene</td><td><a href=#ncbi-datasets-v2-reports-GeneCounts><code>GeneCounts</code></a></td><td>Counts of gene types</td><td></td></tr></tbody></table><h3 id=ncbi-datasets-v2-reports-GeneCounts>GeneCounts Structure</h3><table><thead><tr><th>Field</th><th>Table Field Mnemonic</th><th>Table Column Name</th><th>Type</th><th>Description</th><th>Examples</th></tr></thead><tbody><tr><td><code>total</code></td><td><code>total</code></td><td>Total</td><td><a href=#uint32><code>uint32</code></a></td><td>Total number of annotated genes</td><td></td></tr><tr><td><code>proteinCoding</code></td><td><code>protein-coding</code></td><td>Protein-coding</td><td><a href=#uint32><code>uint32</code></a></td><td>Count of annotated genes that encode a protein</td><td></td></tr><tr><td><code>nonCoding</code></td><td><code>non-coding</code></td><td>Non-coding</td><td><a href=#uint32><code>uint32</code></a></td><td>Count of transcribed non-coding genes (e.g. lncRNAs, miRNAs, rRNAs, etc…) excludes transcribed pseudogenes</td><td></td></tr><tr><td><code>pseudogene</code></td><td><code>pseudogene</code></td><td>Pseudogene</td><td><a href=#uint32><code>uint32</code></a></td><td>Count of transcribed and non-transcribed pseudogenes</td><td></td></tr><tr><td><code>other</code></td><td><code>other</code></td><td>Other</td><td><a href=#uint32><code>uint32</code></a></td><td>Count of genic region GeneIDs and non-genic regulatory GeneIDs</td><td></td></tr></tbody></table><h3 id=ncbi-datasets-v2-reports-InfraspecificNames>InfraspecificNames Structure</h3><table><thead><tr><th>Field</th><th>Table Field Mnemonic</th><th>Table Column Name</th><th>Type</th><th>Description</th><th>Examples</th></tr></thead><tbody><tr><td><code>breed</code></td><td><code>breed</code></td><td>Breed</td><td><a href=#string><code>string</code></a></td><td>A homogenous group of animals within a domesticated species</td><td><code>Hereford</code><br><code>boxer</code><br></td></tr><tr><td><code>cultivar</code></td><td><code>cultivar</code></td><td>Cultivar</td><td><a href=#string><code>string</code></a></td><td>A variety of plant within a species produced and maintained by cultivation</td><td><code>B73</code><br></td></tr><tr><td><code>ecotype</code></td><td><code>ecotype</code></td><td>Ecotype</td><td><a href=#string><code>string</code></a></td><td>A population or subspecies occupying a distinct habitat</td><td><code>Alpine</code><br></td></tr><tr><td><code>isolate</code></td><td><code>isolate</code></td><td>Isolate</td><td><a href=#string><code>string</code></a></td><td>The individual isolate from which the sequences in the genome assembly were derived</td><td><code>L1 Dominette 01449 registration number 42190680</code><br><code>Pmale09</code><br></td></tr><tr><td><code>sex</code></td><td><code>sex</code></td><td>Sex</td><td><a href=#string><code>string</code></a></td><td>Male or female</td><td><code>female</code><br></td></tr><tr><td><code>strain</code></td><td><code>strain</code></td><td>Strain</td><td><a href=#string><code>string</code></a></td><td>A genetic variant, subtype or culture within a species</td><td><code>SE11</code><br></td></tr></tbody></table><h3 id=ncbi-datasets-v2-reports-LinkedAssembly>LinkedAssembly Structure</h3><table><thead><tr><th>Field</th><th>Table Field Mnemonic</th><th>Table Column Name</th><th>Type</th><th>Description</th><th>Examples</th></tr></thead><tbody><tr><td><code>linkedAssembly</code></td><td><code>accession</code></td><td>Accession</td><td><a href=#string><code>string</code></a></td><td>The linked assembly accession</td><td><code>GCA_000212995.1</code><br></td></tr><tr><td><code>assemblyType</code></td><td><code>type</code></td><td>Type</td><td><a href=#ncbi-datasets-v2-reports-LinkedAssemblyType><code>LinkedAssemblyType</code></a></td><td>The linked assembly type</td><td></td></tr></tbody></table><h3 id=ncbi-datasets-v2-reports-OrganelleInfo>OrganelleInfo Structure</h3><table><thead><tr><th>Field</th><th>Table Field Mnemonic</th><th>Table Column Name</th><th>Type</th><th>Description</th><th>Examples</th></tr></thead><tbody><tr><td><code>infraspecificName</code></td><td><code>infraspecific-name</code></td><td>Infraspecific Name</td><td><a href=#string><code>string</code></a></td><td>The strain, breed, cultivar or ecotype of the organism from which the sequences in the assembly were derived</td><td></td></tr><tr><td><code>bioproject repeated</code></td><td><code>bioproject-accessions</code></td><td>BioProject Accessions</td><td><a href=#string><code>string</code></a></td><td>The associated BioProject accession, when available</td><td></td></tr><tr><td><code>description</code></td><td><code>description</code></td><td>Description</td><td><a href=#string><code>string</code></a></td><td>Long description of the organelle genome</td><td></td></tr><tr><td><code>totalSeqLength</code></td><td><code>total-seq-length</code></td><td>Total Seq Length</td><td><a href=#uint64><code>uint64</code></a></td><td>Sequence length of the organelle genome</td><td></td></tr><tr><td><code>submitter</code></td><td><code>submitter</code></td><td>Submitter</td><td><a href=#string><code>string</code></a></td><td>Name of submitter</td><td></td></tr></tbody></table><h3 id=ncbi-datasets-v2-reports-PairedAssembly>PairedAssembly Structure</h3><table><thead><tr><th>Field</th><th>Table Field Mnemonic</th><th>Table Column Name</th><th>Type</th><th>Description</th><th>Examples</th></tr></thead><tbody><tr><td><code>accession</code></td><td><code>accession</code></td><td>Accession</td><td><a href=#string><code>string</code></a></td><td>The GenColl assembly accession of the GenBank or RefSeq assembly paired with this one</td><td><code>GCF_000001405.40</code><br></td></tr><tr><td><code>status</code></td><td><code>status</code></td><td>Status</td><td><a href=#ncbi-datasets-v2-reports-AssemblyStatus><code>AssemblyStatus</code></a></td><td>GenColl Assembly status from paired record</td><td><code>current</code><br></td></tr><tr><td><code>annotationName</code></td><td><code>name</code></td><td>Name</td><td><a href=#string><code>string</code></a></td><td>Annotation name from paired record</td><td></td></tr><tr><td><code>onlyGenbank</code></td><td><code>only-genbank</code></td><td>Only Genbank</td><td><a href=#string><code>string</code></a></td><td>Sequences that are only included in the GenBank assembly</td><td></td></tr><tr><td><code>onlyRefseq</code></td><td><code>only-refseq</code></td><td>Only RefSeq</td><td><a href=#string><code>string</code></a></td><td>Sequences that are only included in the RefSeq assembly</td><td></td></tr><tr><td><code>changed</code></td><td><code>changed</code></td><td>Changed</td><td><a href=#string><code>string</code></a></td><td>Sequences present on both the GenBank and the RefSeq assemblies that have been changed, e.g., contaminated sequence in the GenBank assembly has been replaced with a gap</td><td></td></tr><tr><td><code>manualDiff</code></td><td><code>manual-diff</code></td><td>Manual Diff</td><td><a href=#string><code>string</code></a></td><td>Additional details about sequence differences between the GenBank and RefSeq assemblies</td><td></td></tr><tr><td><code>refseqGenbankAreDifferent</code></td><td><code>refseq-genbank-are-different</code></td><td>RefSeq GenBank Are Different</td><td><a href=#bool><code>bool</code></a></td><td>boolean indication on whether there are any differences between the GenBank and RefSeq assemblies</td><td></td></tr></tbody></table><h3 id=ncbi-datasets-v2-reports-TypeMaterial>TypeMaterial Structure</h3><table><thead><tr><th>Field</th><th>Table Field Mnemonic</th><th>Table Column Name</th><th>Type</th><th>Description</th><th>Examples</th></tr></thead><tbody><tr><td><code>typeLabel</code></td><td><code>label</code></td><td>Label</td><td><a href=#string><code>string</code></a></td><td></td><td></td></tr><tr><td><code>typeDisplayText</code></td><td><code>display_text</code></td><td>Display Text</td><td><a href=#string><code>string</code></a></td><td></td><td></td></tr></tbody></table><h3 id=ncbi-datasets-v2-reports-WGSInfo>WGSInfo Structure</h3><p>Whole Genome Shotgun (WGS) projects are genome assemblies of incomplete genomes or incomplete chromosomes of prokaryotes
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or eukaryotes that are generally being sequenced by a whole genome shotgun strategy.</p><table><thead><tr><th>Field</th><th>Table Field Mnemonic</th><th>Table Column Name</th><th>Type</th><th>Description</th><th>Examples</th></tr></thead><tbody><tr><td><code>wgsProjectAccession</code></td><td><code>project-accession</code></td><td>project accession</td><td><a href=#string><code>string</code></a></td><td>WGS project accession</td><td><code>AAEX03</code><br><code>CABHLF01</code><br></td></tr><tr><td><code>masterWgsUrl</code></td><td><code>url</code></td><td>URL</td><td><a href=#string><code>string</code></a></td><td>WGS project Nucleotide web address</td><td><code>https://www.ncbi.nlm.nih.gov/nuccore/AAEX00000000.3</code><br></td></tr><tr><td><code>wgsContigsUrl</code></td><td><code>contigs-url</code></td><td>contigs URL</td><td><a href=#string><code>string</code></a></td><td>WGS project Sequence set browser web address</td><td><code>https://www.ncbi.nlm.nih.gov/Traces/wgs/AAEX03</code><br></td></tr></tbody></table><h3 id=ncbi-datasets-v2-reports-ANITypeCategory>ANITypeCategory Enumeration</h3><table><thead><tr><th>Name</th><th>Number</th><th>Description</th></tr></thead><tbody><tr><td><code>ANI_CATEGORY_UNKNOWN</code></td><td><code>0</code></td><td></td></tr><tr><td><code>claderef</code></td><td><code>1</code></td><td></td></tr><tr><td><code>category_na</code></td><td><code>2</code></td><td></td></tr><tr><td><code>neotype</code></td><td><code>3</code></td><td></td></tr><tr><td><code>no_type</code></td><td><code>4</code></td><td></td></tr><tr><td><code>pathovar</code></td><td><code>5</code></td><td></td></tr><tr><td><code>reftype</code></td><td><code>6</code></td><td></td></tr><tr><td><code>suspected_type</code></td><td><code>7</code></td><td></td></tr><tr><td><code>syntype</code></td><td><code>8</code></td><td></td></tr><tr><td><code>type</code></td><td><code>9</code></td><td></td></tr></tbody></table><h3 id=ncbi-datasets-v2-reports-AssemblyStatus>AssemblyStatus Enumeration</h3><table><thead><tr><th>Name</th><th>Number</th><th>Description</th></tr></thead><tbody><tr><td><code>ASSEMBLY_STATUS_UNKNOWN</code></td><td><code>0</code></td><td></td></tr><tr><td><code>current</code></td><td><code>1</code></td><td></td></tr><tr><td><code>previous</code></td><td><code>2</code></td><td></td></tr><tr><td><code>suppressed</code></td><td><code>3</code></td><td></td></tr><tr><td><code>retired</code></td><td><code>4</code></td><td>This is deprecated - should no longer be seen in the data</td></tr></tbody></table><h3 id=ncbi-datasets-v2-reports-AverageNucleotideIdentity-MatchStatus>AverageNucleotideIdentity.MatchStatus Enumeration</h3><table><thead><tr><th>Name</th><th>Number</th><th>Description</th></tr></thead><tbody><tr><td><code>BEST_MATCH_STATUS_UNKNOWN</code></td><td><code>0</code></td><td></td></tr><tr><td><code>approved_mismatch</code></td><td><code>1</code></td><td></td></tr><tr><td><code>below_threshold_match</code></td><td><code>2</code></td><td></td></tr><tr><td><code>below_threshold_mismatch</code></td><td><code>3</code></td><td></td></tr><tr><td><code>best_match_status</code></td><td><code>4</code></td><td></td></tr><tr><td><code>derived_species_match</code></td><td><code>5</code></td><td></td></tr><tr><td><code>genus_match</code></td><td><code>6</code></td><td></td></tr><tr><td><code>low_coverage</code></td><td><code>7</code></td><td></td></tr><tr><td><code>mismatch</code></td><td><code>8</code></td><td></td></tr><tr><td><code>status_na</code></td><td><code>9</code></td><td></td></tr><tr><td><code>species_match</code></td><td><code>10</code></td><td></td></tr><tr><td><code>subspecies_match</code></td><td><code>11</code></td><td></td></tr><tr><td><code>synonym_match</code></td><td><code>12</code></td><td></td></tr><tr><td><code>lineage_match</code></td><td><code>13</code></td><td></td></tr><tr><td><code>below_threshold_lineage_match</code></td><td><code>14</code></td><td></td></tr></tbody></table><h3 id=ncbi-datasets-v2-reports-AverageNucleotideIdentity-TaxonomyCheckStatus>AverageNucleotideIdentity.TaxonomyCheckStatus Enumeration</h3><table><thead><tr><th>Name</th><th>Number</th><th>Description</th></tr></thead><tbody><tr><td><code>TAXONOMY_CHECK_STATUS_UNKNOWN</code></td><td><code>0</code></td><td></td></tr><tr><td><code>OK</code></td><td><code>1</code></td><td></td></tr><tr><td><code>Failed</code></td><td><code>2</code></td><td></td></tr><tr><td><code>Inconclusive</code></td><td><code>3</code></td><td></td></tr></tbody></table><h3 id=ncbi-datasets-v2-reports-LinkedAssemblyType>LinkedAssemblyType Enumeration</h3><table><thead><tr><th>Name</th><th>Number</th><th>Description</th></tr></thead><tbody><tr><td><code>LINKED_ASSEMBLY_TYPE_UNKNOWN</code></td><td><code>0</code></td><td></td></tr><tr><td><code>alternate_pseudohaplotype_of_diploid</code></td><td><code>1</code></td><td>SEQUI-5245</td></tr><tr><td><code>principal_pseudohaplotype_of_diploid</code></td><td><code>2</code></td><td></td></tr><tr><td><code>maternal_haplotype_of_diploid</code></td><td><code>3</code></td><td></td></tr><tr><td><code>paternal_haplotype_of_diploid</code></td><td><code>4</code></td><td></td></tr><tr><td><code>haplotype_1</code></td><td><code>6</code></td><td></td></tr><tr><td><code>haplotype_2</code></td><td><code>7</code></td><td></td></tr><tr><td><code>haplotype_3</code></td><td><code>8</code></td><td></td></tr><tr><td><code>haplotype_4</code></td><td><code>9</code></td><td></td></tr><tr><td><code>haploid</code></td><td><code>10</code></td><td>Catch all for any value that is not explicitly listed above</td></tr></tbody></table><h3 id=ncbi-datasets-v2-reports-SourceDatabase>SourceDatabase Enumeration</h3><table><thead><tr><th>Name</th><th>Number</th><th>Description</th></tr></thead><tbody><tr><td><code>SOURCE_DATABASE_UNSPECIFIED</code></td><td><code>0</code></td><td></td></tr><tr><td><code>SOURCE_DATABASE_GENBANK</code></td><td><code>1</code></td><td></td></tr><tr><td><code>SOURCE_DATABASE_REFSEQ</code></td><td><code>2</code></td><td></td></tr></tbody></table><h3 id=scalar-value-types>Scalar Value Types</h3><table><thead><tr><th>Protocol buffers type</th><th>Notes</th><th>C++</th><th>Python</th><th>Java</th><th>Go</th></tr></thead><tbody><tr><td><a name=double><code>double</code></td><td></td><td><code>double</code></td><td><code>float</code></td><td><code>double</code></td><td><code>float64</code></td></tr><tr><td><a name=float><code>float</code></td><td></td><td><code>float</code></td><td><code>float</code></td><td><code>float</code></td><td><code>float32</code></td></tr><tr><td><a name=int32><code>int32</code></td><td>Uses variable-length encoding. Inefficient for encoding negative numbers – if your field is likely to have negative values, use sint32 instead.</td><td><code>int32</code></td><td><code>int</code></td><td><code>int</code></td><td><code>int32</code></td></tr><tr><td><a name=int64><code>int64</code></td><td>Uses variable-length encoding. Inefficient for encoding negative numbers – if your field is likely to have negative values, use sint64 instead.</td><td><code>int64</code></td><td><code>int/long</code></td><td><code>long</code></td><td><code>int64</code></td></tr><tr><td><a name=uint32><code>uint32</code></td><td>Uses variable-length encoding.</td><td><code>uint32</code></td><td><code>int/long</code></td><td><code>int</code></td><td><code>uint32</code></td></tr><tr><td><a name=uint64><code>uint64</code></td><td>Uses variable-length encoding.</td><td><code>uint64</code></td><td><code>int/long</code></td><td><code>long</code></td><td><code>uint64</code></td></tr><tr><td><a name=sint32><code>sint32</code></td><td>Uses variable-length encoding. Signed int value. These more efficiently encode negative numbers than regular int32s.</td><td><code>int32</code></td><td><code>int</code></td><td><code>int</code></td><td><code>int32</code></td></tr><tr><td><a name=sint64><code>sint64</code></td><td>Uses variable-length encoding. Signed int value. These more efficiently encode negative numbers than regular int64s.</td><td><code>int64</code></td><td><code>int/long</code></td><td><code>long</code></td><td><code>int64</code></td></tr><tr><td><a name=fixed32><code>fixed32</code></td><td>Always four bytes. More efficient than uint32 if values are often greater than 2^28.</td><td><code>uint32</code></td><td><code>int</code></td><td><code>int</code></td><td><code>uint32</code></td></tr><tr><td><a name=fixed64><code>fixed64</code></td><td>Always eight bytes. More efficient than uint64 if values are often greater than 2^56.</td><td><code>uint64</code></td><td><code>int/long</code></td><td><code>long</code></td><td><code>uint64</code></td></tr><tr><td><a name=sfixed32><code>sfixed32</code></td><td>Always four bytes.</td><td><code>int32</code></td><td><code>int</code></td><td><code>int</code></td><td><code>int32</code></td></tr><tr><td><a name=sfixed64><code>sfixed64</code></td><td>Always eight bytes.</td><td><code>int64</code></td><td><code>int/long</code></td><td><code>long</code></td><td><code>int64</code></td></tr><tr><td><a name=bool><code>bool</code></td><td></td><td><code>bool</code></td><td><code>boolean</code></td><td><code>boolean</code></td><td><code>bool</code></td></tr><tr><td><a name=string><code>string</code></td><td>A string must always contain UTF-8 encoded or 7-bit ASCII text.</td><td><code>string</code></td><td><code>str/unicode</code></td><td><code>String</code></td><td><code>string</code></td></tr><tr><td><a 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