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

BioSample Accession(s)

SAMEA114830235, ERS17255102

ENA-CHECKLIST

ERC000011

binning software

MetaBAT2, GraphMB, SemiBin2, DAS Tool, mmlong2

organism

uncultured Alphaproteobacteria bacterium

broad-scale environmental context

Dunes

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

2021-09-30

sample derived from

ERS14381666

geographic location (longitude)

15.0805

taxonomic identity marker

multi-marker approach

binning parameters

Ensemble iterative binning using coverage and kmer

completeness score

97.86

contamination score

1.51

environmental medium

not collected

geographic location (latitude)

54.9907

scientific_name

uncultured Alphaproteobacteria bacterium

local environmental context

Sea dunes

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

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

BioSample Accession(s)

SAMEA112270811, ERS14381666

ENA-CHECKLIST

ERC000011

organism

soil metagenome

collection date

not provided

scientific_name

soil metagenome

geographic location (country and/or sea)

not provided

Metadata as EBI XML

<EXPERIMENT_SET>
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    <SUBMITTER_ID namespace="Center for Microbial Communities">ena-EXPERIMENT-TAB-06-06-2023-17:33:05:754-55829</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="ERS14381666">
      <IDENTIFIERS>
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        <EXTERNAL_ID namespace="BioSample">SAMEA112270811</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>LIB-MS-R1041-MFD09495</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>
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    <EXPERIMENT_LINK>
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Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="ERX10683776" alias="ena-EXPERIMENT-TAB-29-04-2023-08:11:00:571-47994" center_name="Center for Microbial Communities">
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  </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/>
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      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>LIB-MS-R1041-MFD09495</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>
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  <EXPERIMENT_LINKS>
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    <EXPERIMENT_LINK>
      <XREF_LINK>
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    <EXPERIMENT_LINK>
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  <EXPERIMENT_ATTRIBUTES>
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Metadata as EBI XML

<EXPERIMENT_SET>
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  </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="ERS14381666">
      <IDENTIFIERS>
        <PRIMARY_ID>ERS14381666</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMEA112270811</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>LIB-MS-R1041-MFD09495</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>
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    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
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      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-FASTQ-FILES</DB>
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  <EXPERIMENT_ATTRIBUTES>
    <EXPERIMENT_ATTRIBUTE>
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      <VALUE>4</VALUE>
    </EXPERIMENT_ATTRIBUTE>
  </EXPERIMENT_ATTRIBUTES>
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</EXPERIMENT_SET>

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="ERX10683778" alias="ena-EXPERIMENT-TAB-29-04-2023-08:11:00:571-47998" center_name="Center for Microbial Communities">
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  </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="ERS14381666">
      <IDENTIFIERS>
        <PRIMARY_ID>ERS14381666</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMEA112270811</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>LIB-MS-R1041-MFD09495</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>
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      <XREF_LINK>
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        <DB>ENA-FASTQ-FILES</DB>
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      <XREF_LINK>
        <DB>ENA-SUBMITTED-FILES</DB>
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      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
  <EXPERIMENT_ATTRIBUTES>
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