WGS

<!DOCTYPE html> <html lang="en"> <head> <meta charset="UTF-8" /> <meta property="og:title" content="WGS" /> <meta property="og:url" content="https://www.ddbj.nig.ac.jp/ddbj/wgs-e.html" /> <meta property="og:description" content="The whole genome shotgun approach (the whole genome is once blasted into million..." /> <meta property6="og:image" content="/images/thumbnail/logo_ddbj_fb.png" /> <meta name="viewport" content="width=device-width, initial-scale=1.0" /> <title>WGS</title> <script async src="https://www.google-analytics.com/analytics.js"></script> <script src="https://code.jquery.com/jquery-3.5.0.js" integrity="sha256-r/AaFHrszJtwpe+tHyNi/XCfMxYpbsRg2Uqn0x3s2zc=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery.hoverintent/1.10.1/jquery.hoverIntent.min.js" integrity="sha512-gx3WTM6qxahpOC/hBNUvkdZARQ2ObXSp/m+jmsEN8ZNJPymj8/Jamf8+/3kJQY1RZA2DR+KQfT+b3JEB0r9YRg==" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/spin.js/4.1.0/spin.min.js" integrity="sha512-CbohqWjAgarTqRHcX1MbwkF2pujwbsCee1PABpnBWC+VqSldvlNEEI5+4OSsR/HbFQOFFpwY2YvZZNjBMxNnXg==" crossorigin="anonymous"></script> <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/jquery.colorbox/1.6.4/jquery.colorbox-min.js"></script> <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/jquery-deparam/0.5.3/jquery-deparam.min.js"></script> <script type="text/javascript" src="https://www.ddbj.nig.ac.jp/assets/js/jquery.trace.js"></script> <script type="text/javascript" src="https://www.ddbj.nig.ac.jp/assets/js/jquery.json_search.js"></script> <link rel="icon" href="https://www.ddbj.nig.ac.jp/assets/images/favicon_ddbj.ico"> <link rel="stylesheet" href="https://www.ddbj.nig.ac.jp/assets/css/colorbox.css" /> <link rel="stylesheet" href="https://www.ddbj.nig.ac.jp/assets/css/main.css" /> <link rel="alternate" type="application/rss+xml" title="My Site RSS" href="/feed.xml" /> <script src="https://www.ddbj.nig.ac.jp/assets/js/main.js"></script> </head> <body data-category="ddbj"> <script src="https://www.ddbj.nig.ac.jp/assets/js/ddbj_common_framework.js" id="DDBJ_common_framework" style="display: block; 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If you wish to publicize raw read sequences, we recommend you to contact <a href="/dra/index-e.html">DDBJ Sequence Read Archive (DRA)</a>. </dd> <dd> <ul> <li>The WGS entries are contigs (overlapping reads) and/or the scaffolds (assembled contigs separated by gaps).</li> <li>The WGS entries can contain consecutive "n" s to represent sequencing gaps.</li> </ul> </dd> <h2 id="unacceptable-wgs-data">Unacceptable WGS data</h2> <ul> <li>Assembled genome sequences from multiple organisms that are not metagenomes.</li> <li>The following cases without chromosome assembly (contigs and scaffolds) <ul> <li>Organelle genome contigs alone.</li> <li>Plasmids contigs alone.</li> </ul> </li> </ul> <h2 id="submission-of-wgs-entry">Submission of WGS entry</h2> <p>The Submitters visit the <a href="https://mss.ddbj.nig.ac.jp/home">MSS form</a> site and make an application.</p> <ul> <li>Prior to assembly sequence data submission, it is required to submit to BioProject and BioSample databases.</li> <li>If you wish to annotate all protein-coding genes and non-protein-coding RNA genes on the assembly sequences, please register a locus_tag prefix when submitting each BioSample.</li> <li>Sample annotation: <a href="https://docs.google.com/spreadsheets/d/15gLGL5FMV8gRt46ezc2Gmb-R1NbYsIGMssB0MyHkcwE/edit?pli=1&gid=1134992157#gid=1134992157">(WGS sample annotation)</a>.</li> </ul> <h2 id="flat-file">Sample flat file</h2> <p>Aspects of WGS</p> <ul> <li>Basically, each WGS sequence submitted to DDBJ is assigned an accession number that consists of 6 alphabet characters and 9 digits (since January 2024) or 4 alphabet characters and 8 digits.</li> <li>“WGS” and either of controlled terms （STANDARD_DRAFT, HIGH_QUALITY_DRAFT, IMPROVED_HIGH_QUALITY_DRAFT, ANNOTATION_GRADE, NON_CONTIGUOUS_FINISHED) indicating the degree of completion as genome sequence are indicated in <a href="#KeywordsA">KEYWORDS</a> line. The definitions of each KEYWORD can be found on the following website<a href="https://www.insdc.org/submitting-standards/methodological-keywords/">(INSDC agreed methodological keywords)</a>.</li> <li>A summary of the assembly is displayed in the COMMENT.</li> </ul> <table> <tr> <td> Tag name </td> <td>Value （information） </td> </tr> <tr> <td>Assembly Method </td> <td>Name of the assembly algorithm(s) with version number it was run. </td> </tr> <tr> <td>Assembly Name </td> <td>A brief name suitable for display that does not include the organism name. This is mandatory for eukaryotes. </td> </tr> <tr> <td>Genome Coverage </td> <td>The estimated base coverage across the genome. </td> </tr> <tr> <td>Sequencing Technology </td> <td>Sequencing platform(s) used. </td> </tr> </table> <p><br /></p>  <pre><code><a id="LocusA" href="/ddbj/flat-file-e#LocusB">LOCUS</a> <a id="LocusNameA" href="/ddbj/flat-file-e#LocusNameB">ZZZZZZ010000001</a> <a id="SequenceLengthA" href="/ddbj/flat-file-e#SequenceLengthB">123456 bp</a> <a id="MoleculeTypeA" href="/ddbj/flat-file-e#MoleculeTypeB">DNA</a> <a id="MoleculeFormA" href="/ddbj/flat-file-e#MoleculeFormB">linear</a> <a id="DivisionA" href="/ddbj/flat-file-e#DivisionB">ROD</a> <a id="ModificationDateA" href="/ddbj/flat-file-e#ModificationDateB">07-AUG-2024</a> <a id="DefinitionA" href="/ddbj/flat-file-e#DefinitionB">DEFINITION</a> Mus musculus C57BL6 DNA, EN0001. <a id="AccessionA" href="/ddbj/flat-file-e#AccessionB">ACCESSION</a> ZZZZZZ010000001 ZZZZZZ010000000 <a id="VersionA" href="/ddbj/flat-file-e#VersionB">VERSION</a> ZZZZZZ010000001.1 <a id="DblinkA" href="/ddbj/flat-file-e#DblinkB">DBLINK</a> BioProject:PRJDB99999 Sequence Read Archive:DRR999998, DRR999999 BioSample:SAMD99999999 <a id="KeywordsA" href="/ddbj/flat-file-e#KeywordsB">KEYWORDS</a> WGS; STANDARD_DRAFT. <a id="SourceA" href="/ddbj/flat-file-e#SourceB">SOURCE</a> Mus musculus <a id="OrganismA" href="/ddbj/flat-file-e#OrganismB">ORGANISM</a> Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;Murinae; Mus; Mus. <a id="Reference1A" href="/ddbj/flat-file-e#Reference1B">REFERENCE 1</a> (bases 1 to 123456) <a id="AuthorsA" href="/ddbj/flat-file-e#AuthorsB">AUTHORS</a> Mishima,H. and Shizuoka,T. <a id="TitleA" href="/ddbj/flat-file-e#TitleB">TITLE</a> Direct Submission <a id="JournalA" href="/ddbj/flat-file-e#JournalB">JOURNAL</a> Submitted (01-MAY-2024) to the DDBJ/EMBL/GenBank databases. Contact:Hanako Mishima National Institute of Genetics, DNA Data Bank of Japan; Yata 1111, Mishima, Shizuoka 411-8540, Japan <a id="Reference2A" href="/ddbj/flat-file-e#Reference2B">REFERENCE 2</a> AUTHORS Mishima,H., Shizuoka,T. and Fuji,I. TITLE Mouse whole genome shotgun sequence JOURNAL Unpublished (2024) <a id="CommentA" href="/ddbj/flat-file-e#CommentB">COMMENT</a> Whole genome shotgun sequencing project. #Genome-Assembly-Data-START## Assembly Method :: HGAP v. 1.0; Celera Assembler v. 7.0; Quiver v. 1.4.0; Sequencher v. 5.1 Assembly Name :: MusC56 v1 Genome Coverage :: 238x Sequencing Technology :: PacBio RS, Illumina GAIIx ##Genome-Assembly-Data-END## <a id="FeaturesA" href="/ddbj/flat-file-e#FeaturesB">FEATURES</a> Location/Qualifiers <a id="FeaturesSourceA" href="/ddbj/flat-file-e#FeaturesSourceB">source</a> <a href="/ddbj/location.html">1..123456</a> /<a href="/ddbj/qualifiers.html-e#mol_type">collection_date</a>="missing: lab stock" /<a href="/ddbj/qualifiers.html-e#db_xref">db_xref</a>="taxon:10090" /<a href="/ddbj/qualifiers.html-e#geo_loc_name">geo_loc_name</a>="Japan" /<a href="/ddbj/qualifiers.html-e#mol_type">mol_type</a>="genomic DNA" /<a href="/ddbj/qualifiers.html-e#organism">organism</a>="Mus musculus" /<a href="/ddbj/qualifiers.html-e#strain">strain</a>="C57BL6" /<a href="/ddbj/qualifiers.html-e#submitter_seqid">submitter_seqid</a>="EN0001" <a id="FeaturesCDSA" href="/ddbj/flat-file-e#FeaturesCDSB">CDS</a> <a href="/ddbj/location.html">complement(join(147..1241,1364..1816))</a> /<a href="/ddbj/qualifiers.html-e#codn_start">codon_start</a>=1 /<a href="/ddbj/qualifiers.html-e#locus_tag">locus_tag</a>="DDBJGEN_0001G0001" /<a href="/ddbj/qualifiers.html-e#product">product</a>="hypothetical protein" /<a href="/ddbj/qualifiers.html-e#protein_id">protein_id</a>="xxxxxxxxxx.1" /<a href="/ddbj/qualifiers.html-e#transl_table">transl_table</a>=1 /<a href="/ddbj/qualifiers.html-e#translation">translation</a>="MTEHIFEKISLNLSNIINKCVYKQTTLNDAQNE IKETMNVIINQYNHYITKDVMDEILILTSKLLYSQNIESLIIYLNKL (snipped) GFFRMYQIWNVS" <a id="Featuresassembly_gapA" href="/ddbj/flat-file-e#Featuresassembly_gapB">assembly_gap</a> <a href="/ddbj/location.html">2982..3269</a> /<a href="/ddbj/qualifiers.html-e#estimated_length">estimated_length</a>=288 /<a href="/ddbj/qualifiers.html-e#gap_type">gap_type</a>="within scaffold" /<a href="/ddbj/qualifiers.html-e#linkage_evidence">linkage_evidence</a>="paired_ends" <a id="FeaturestRNA" href="/ddbj/flat-file-e#FeaturestRNAB">tRNA</a> <a href="/ddbj/location.html">3569..3643</a> /<a href="/ddbj/qualifiers.html-e#locus_tag">locus_tag</a>="DDBJGEN_t0001G0001" /<a href="/ddbj/qualifiers.html-e#product">product</a>="tRNA-Ser" -- The rest is snipped -- <a id="EndA" href="/ddbj/flat-file-e#EndB">//</a></code></pre> </main> <aside class="related-pages"> <h2 class="caption">Related pages</h2> <div class="navigation"> <nav> <ul> <li> <a href="/ddbj/genome-e.html">Data Submission from Genome Project</a> </li> <li> <a href="/ddbj/con-e.html">CON</a> </li> <li> <a href="/ddbj/gss-e.html">GSS</a> </li> <li> <a href="/ddbj/htg-e.html">HTG</a> </li> <li> <a href="/ddbj/environmental-e.html">Submission of environmental sequences</a> </li> <li> <a href="/ddbj/env-e.html">ENV</a> </li> <li> <a href="/ddbj/tls-e.html">TLS</a> </li> <li> <a href="/ddbj/transcriptome-e.html">Data Submission from Transcriptome Project</a> </li> <li> <a href="/ddbj/tsa-e.html">TSA</a> </li> <li> <a href="/ddbj/est-a.html">EST</a> </li> <li> <a href="/ddbj/htc-e.html">HTC</a> </li> <li> <a href="/ddbj/tpa-e.html">Third Party Data (TPA)</a> </li> </ul> </nav> </div> </aside> </section> </div> </section> </div> <footer></footer> <div id="back-top"></div> </body> </html>

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WGS