Uncultivated genome recovered from an assembly of the SRX461727 metagenome.

BioSample Accession(s)

SAMN06454052, SRS2033895

quality_assessment_method_version

1.0.6

mapping_method

BWA (BWA-MEM)

INSDC secondary accession

SRS2033895

organism

Candidatus Acidiferrum typicum

mapping_method_version

0.7.12-r1039

isolation-source

soil

quality_assessment_method

CheckM

subsrc_note

Genome binned from sequencing reads available in SRX461727 metagenome

geo loc name

USA: Marcell Experimental Forest

metagenomic

true

assembly_method_version

4.4.1

environmental sample

true

metagenome source

soil metagenome

contamination_estimated

1.71%

isolate

UBA7541

NCBI submission package

Microbe.1.0

assembly method

CLC de novo assembler

genome coverage

67.87

sample type

metagenomic assembly

value

This BioSample is a metagenomic assembly obtained from the soil metagenome reads: SRR1157609.

completeness_estimated

90.55%

BioSampleModel

Microbe, viral or environmental

ENA-FIRST-PUBLIC

2017-02-27

ENA-LAST-UPDATE

2024-05-23

5

BioSample Accession(s)

SAMN02364458, SRS551057

collection_date

2012-02-10

INSDC secondary accession

SRS551057

organism

soil metagenome

project_name

SPRUCE carbon cycle

NCBI submission package

MIMS.me.soil.5.0

depth

25-50

feature

bog

material

soil

biome

Forest

elev

125

geo_loc_name

USA: MN, Marcell Experimental Forest

investigation_type

metagenome

env_package

MIGS/MIMS/MIMARKS.soil

lat_lon

47.5062 N 93.45426667 W

BioSampleModel

MIGS/MIMS/MIMARKS.soil

ENA-FIRST-PUBLIC

2013-09-30

ENA-LAST-UPDATE

2021-02-28

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX461727" alias="SP0212_25cm" center_name="Georgia Institute of Technology" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX461727</PRIMARY_ID>
    <SUBMITTER_ID namespace="Georgia Institute of Technology">SP0212_25cm</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Metagenome 25cm</TITLE>
  <STUDY_REF accession="SRP030479">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP030479</PRIMARY_ID>
      <EXTERNAL_ID namespace="BioProject">PRJNA221719</EXTERNAL_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION/>
    <SAMPLE_DESCRIPTOR accession="SRS551057">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS551057</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN02364458</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>SP0212_25cm</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>size fractionation</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <PAIRED NOMINAL_SDEV="0.0E0"/>
      </LIBRARY_LAYOUT>
    </LIBRARY_DESCRIPTOR>
    <SPOT_DESCRIPTOR>
      <SPOT_DECODE_SPEC>
        <SPOT_LENGTH>200</SPOT_LENGTH>
        <READ_SPEC>
          <READ_INDEX>0</READ_INDEX>
          <READ_CLASS>Application Read</READ_CLASS>
          <READ_TYPE>Forward</READ_TYPE>
          <BASE_COORD>1</BASE_COORD>
        </READ_SPEC>
        <READ_SPEC>
          <READ_INDEX>1</READ_INDEX>
          <READ_CLASS>Application Read</READ_CLASS>
          <READ_TYPE>Reverse</READ_TYPE>
          <BASE_COORD>101</BASE_COORD>
        </READ_SPEC>
      </SPOT_DECODE_SPEC>
    </SPOT_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <ILLUMINA>
      <INSTRUMENT_MODEL>Illumina HiSeq 2000</INSTRUMENT_MODEL>
    </ILLUMINA>
  </PLATFORM>
  <PROCESSING/>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>SRS551057</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA134408</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=SRX461727&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=SRX461727&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
</EXPERIMENT>
</EXPERIMENT_SET>

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX2623940" alias="SRX461727.b4.bam" center_name="University of Queensland" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX2623940</PRIMARY_ID>
    <SUBMITTER_ID namespace="University of Queensland">SRX461727.b4.bam</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Acidobacteria bacterium UBA7541</TITLE>
  <STUDY_REF accession="SRP093542">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP093542</PRIMARY_ID>
      <EXTERNAL_ID namespace="BioProject">PRJNA348753</EXTERNAL_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>BWA (BWA-MEM) mapping of Acidobacteria bacterium UBA7541 using version 0.7.12-r1039 and assembled with CLC de novo assembler 4.4.1 with a genome coverage of 67.87</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS2033895">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS2033895</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN06454052</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>SRX461727.b4.bam</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>size fractionation</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <PAIRED/>
      </LIBRARY_LAYOUT>
    </LIBRARY_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <ILLUMINA>
      <INSTRUMENT_MODEL>Illumina HiSeq 2000</INSTRUMENT_MODEL>
    </ILLUMINA>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>SRS2033895</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA543414</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=SRX2623940&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=SRX2623940&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>