Nanopore reads (R10.4.1 chemistry) basecalled in SUP mode, Fast5 is VBZ-compressed

BioSample Accession(s)

SAMEA112270764, ERS14381619

ENA-CHECKLIST

ERC000011

organism

soil metagenome

collection date

not provided

scientific_name

soil metagenome

geographic location (country and/or sea)

not provided

HQ MAG for uncultured Gammaproteobacteria bacterium, recovered from an environmental sample from Denmark

BioSample Accession(s)

SAMEA114808182, ERS17233049

ENA-CHECKLIST

ERC000011

binning software

MetaBAT2, GraphMB, SemiBin2, DAS Tool, mmlong2

organism

uncultured Gammaproteobacteria bacterium

broad-scale environmental context

Forests

assembly quality

Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs

collection date

2019-08-14

sample derived from

ERS14381619

geographic location (longitude)

11.4075

taxonomic identity marker

multi-marker approach

binning parameters

Ensemble iterative binning using coverage and kmer

completeness score

93.18

contamination score

0.35

environmental medium

not collected

geographic location (latitude)

55.4191

scientific_name

uncultured Gammaproteobacteria bacterium

local environmental context

Temperate forests

metagenomic source

soil metagenome

project name

Microflora Danica

completeness software

CheckM2

geographic location (country and/or sea)

Denmark

isolation_source

Soil

ENA-LAST-UPDATE

2023-12-07

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="ERX10607238" alias="ena-EXPERIMENT-TAB-29-03-2023-07:22:24:338-17" center_name="Center for Microbial Communities">
  <IDENTIFIERS>
    <PRIMARY_ID>ERX10607238</PRIMARY_ID>
    <SUBMITTER_ID namespace="Center for Microbial Communities">ena-EXPERIMENT-TAB-29-03-2023-07:22:24:338-17</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>PromethION sequencing</TITLE>
  <STUDY_REF accession="ERP143702">
    <IDENTIFIERS>
      <PRIMARY_ID>ERP143702</PRIMARY_ID>
      <SECONDARY_ID>PRJEB58634</SECONDARY_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION/>
    <SAMPLE_DESCRIPTOR accession="ERS14381619">
      <IDENTIFIERS>
        <PRIMARY_ID>ERS14381619</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMEA112270764</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>LIB-MS-R1041-MFD00031</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <SINGLE/>
      </LIBRARY_LAYOUT>
    </LIBRARY_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <OXFORD_NANOPORE>
      <INSTRUMENT_MODEL>PromethION</INSTRUMENT_MODEL>
    </OXFORD_NANOPORE>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>ERS14381619</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>ERA21254474</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-FASTQ-FILES</DB>
        <ID><![CDATA[https://www.ebi.ac.uk/ena/portal/api/filereport?accession=ERX10607238&result=read_run&fields=run_accession,fastq_ftp,fastq_md5,fastq_bytes]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMITTED-FILES</DB>
        <ID><![CDATA[https://www.ebi.ac.uk/ena/portal/api/filereport?accession=ERX10607238&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
  <EXPERIMENT_ATTRIBUTES>
    <EXPERIMENT_ATTRIBUTE>
      <TAG>ENA-STATUS-ID</TAG>
      <VALUE>4</VALUE>
    </EXPERIMENT_ATTRIBUTE>
  </EXPERIMENT_ATTRIBUTES>
</EXPERIMENT>
</EXPERIMENT_SET>

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="ERX10607239" alias="ena-EXPERIMENT-TAB-29-03-2023-07:22:24:341-19" center_name="Center for Microbial Communities">
  <IDENTIFIERS>
    <PRIMARY_ID>ERX10607239</PRIMARY_ID>
    <SUBMITTER_ID namespace="Center for Microbial Communities">ena-EXPERIMENT-TAB-29-03-2023-07:22:24:341-19</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>PromethION sequencing</TITLE>
  <STUDY_REF accession="ERP143702">
    <IDENTIFIERS>
      <PRIMARY_ID>ERP143702</PRIMARY_ID>
      <SECONDARY_ID>PRJEB58634</SECONDARY_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION/>
    <SAMPLE_DESCRIPTOR accession="ERS14381619">
      <IDENTIFIERS>
        <PRIMARY_ID>ERS14381619</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMEA112270764</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>LIB-MS-R1041-MFD00031</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <SINGLE/>
      </LIBRARY_LAYOUT>
    </LIBRARY_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <OXFORD_NANOPORE>
      <INSTRUMENT_MODEL>PromethION</INSTRUMENT_MODEL>
    </OXFORD_NANOPORE>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>ERS14381619</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>ERA21254474</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-FASTQ-FILES</DB>
        <ID><![CDATA[https://www.ebi.ac.uk/ena/portal/api/filereport?accession=ERX10607239&result=read_run&fields=run_accession,fastq_ftp,fastq_md5,fastq_bytes]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMITTED-FILES</DB>
        <ID><![CDATA[https://www.ebi.ac.uk/ena/portal/api/filereport?accession=ERX10607239&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
  <EXPERIMENT_ATTRIBUTES>
    <EXPERIMENT_ATTRIBUTE>
      <TAG>ENA-STATUS-ID</TAG>
      <VALUE>4</VALUE>
    </EXPERIMENT_ATTRIBUTE>
  </EXPERIMENT_ATTRIBUTES>
</EXPERIMENT>
</EXPERIMENT_SET>

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="ERX10607240" alias="ena-EXPERIMENT-TAB-29-03-2023-07:22:24:341-21" center_name="Center for Microbial Communities">
  <IDENTIFIERS>
    <PRIMARY_ID>ERX10607240</PRIMARY_ID>
    <SUBMITTER_ID namespace="Center for Microbial Communities">ena-EXPERIMENT-TAB-29-03-2023-07:22:24:341-21</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>PromethION sequencing</TITLE>
  <STUDY_REF accession="ERP143702">
    <IDENTIFIERS>
      <PRIMARY_ID>ERP143702</PRIMARY_ID>
      <SECONDARY_ID>PRJEB58634</SECONDARY_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION/>
    <SAMPLE_DESCRIPTOR accession="ERS14381619">
      <IDENTIFIERS>
        <PRIMARY_ID>ERS14381619</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMEA112270764</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>LIB-MS-R1041-MFD00031</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <SINGLE/>
      </LIBRARY_LAYOUT>
    </LIBRARY_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <OXFORD_NANOPORE>
      <INSTRUMENT_MODEL>PromethION</INSTRUMENT_MODEL>
    </OXFORD_NANOPORE>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>ERS14381619</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>ERA21254474</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-FASTQ-FILES</DB>
        <ID><![CDATA[https://www.ebi.ac.uk/ena/portal/api/filereport?accession=ERX10607240&result=read_run&fields=run_accession,fastq_ftp,fastq_md5,fastq_bytes]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMITTED-FILES</DB>
        <ID><![CDATA[https://www.ebi.ac.uk/ena/portal/api/filereport?accession=ERX10607240&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
  <EXPERIMENT_ATTRIBUTES>
    <EXPERIMENT_ATTRIBUTE>
      <TAG>ENA-STATUS-ID</TAG>
      <VALUE>4</VALUE>
    </EXPERIMENT_ATTRIBUTE>
  </EXPERIMENT_ATTRIBUTES>
</EXPERIMENT>
</EXPERIMENT_SET>

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="ERX10967324" alias="webin-reads-MFD00031" center_name="Center for Microbial Communities">
  <IDENTIFIERS>
    <PRIMARY_ID>ERX10967324</PRIMARY_ID>
    <SUBMITTER_ID namespace="Center for Microbial Communities">webin-reads-MFD00031</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Raw reads: MFD00031</TITLE>
  <STUDY_REF accession="ERP143702">
    <IDENTIFIERS>
      <PRIMARY_ID>ERP143702</PRIMARY_ID>
      <SECONDARY_ID>PRJEB58634</SECONDARY_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>unspecified</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="ERS14381619">
      <IDENTIFIERS>
        <PRIMARY_ID>ERS14381619</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMEA112270764</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>LIB-MS-R1041-MFD00031</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <SINGLE/>
      </LIBRARY_LAYOUT>
    </LIBRARY_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <OXFORD_NANOPORE>
      <INSTRUMENT_MODEL>PromethION</INSTRUMENT_MODEL>
    </OXFORD_NANOPORE>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>ERS14381619</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>ERA24066154</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-FASTQ-FILES</DB>
        <ID><![CDATA[https://www.ebi.ac.uk/ena/portal/api/filereport?accession=ERX10967324&result=read_run&fields=run_accession,fastq_ftp,fastq_md5,fastq_bytes]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMITTED-FILES</DB>
        <ID><![CDATA[https://www.ebi.ac.uk/ena/portal/api/filereport?accession=ERX10967324&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
  <EXPERIMENT_ATTRIBUTES>
    <EXPERIMENT_ATTRIBUTE>
      <TAG>ENA-STATUS-ID</TAG>
      <VALUE>4</VALUE>
    </EXPERIMENT_ATTRIBUTE>
  </EXPERIMENT_ATTRIBUTES>
</EXPERIMENT>
</EXPERIMENT_SET>