This sample represents a metagenomic bin from the metagenomic sample(s) ERS4542325

BioSample Accession(s)

SAMEA110134537, ERS12233357

assembly software

SPAdes 3.15.3

environment (material)

caecal content

collection date

2016

sample derived from

ERS4542325

geographic location (longitude)

2.2923

binning parameters

MetaBAT default parameters

contamination score

1.12

ENA-FIRST-PUBLIC

2022-06-17

ENA-LAST-UPDATE

2022-06-17

completeness software

checkm v1.1.3

environment (biome)

host-associated habitat

environment (feature)

host-associated habitat

geographic location (country and/or sea)

France

ENA-CHECKLIST

ERC000050

binning software

MetaBAT v2.12.1

organism

uncultured Elusimicrobiales bacterium

assembly quality

Many fragments with little to no review of assembly other than reporting of standard assembly statistics

taxonomic identity marker

multi-marker approach

completeness score

96.63

geographic location (latitude)

48.8583

scientific_name

uncultured Elusimicrobiales bacterium

common name

geographic location (region and locality)

Jouy-en-Josas

investigation type

metagenome-assembled genome

metagenomic source

chicken gut metagenome

project name

MetaChick

sequencing method

Illumina HiSeq 4000

isolation_source

chicken caecal content

BioSample Accession(s)

SAMEA6814683, ERS4542325

ENA-CHECKLIST

ERC000011

Cage

TRUE

organism

chicken gut metagenome

Production Type

broiler

Production Category

br-gpar

sex

2

scientific_name

chicken gut metagenome

Antibiotic Intake

FALSE

ENA-FIRST-PUBLIC

2022-05-05

ENA-LAST-UPDATE

2022-05-05

Farm

E09

Tag

E9P04

Age

55

Go Outdoors

FALSE

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="ERX4091702" alias="exp_BRZ_GGOSW_4_H3TFLBBXX.IND27" center_name="Genoscope">
  <IDENTIFIERS>
    <PRIMARY_ID>ERX4091702</PRIMARY_ID>
    <SUBMITTER_ID namespace="Genoscope">exp_BRZ_GGOSW_4_H3TFLBBXX.IND27</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>unidentified_Illumina_W</TITLE>
  <STUDY_REF accession="ERP121563">
    <IDENTIFIERS>
      <PRIMARY_ID>ERP121563</PRIMARY_ID>
      <SECONDARY_ID>PRJEB38174</SECONDARY_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION/>
    <SAMPLE_DESCRIPTOR accession="ERS4542325">
      <IDENTIFIERS>
        <PRIMARY_ID>ERS4542325</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMEA6814683</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>BRZ_GG_W</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <PAIRED NOMINAL_LENGTH="391"/>
      </LIBRARY_LAYOUT>
      <LIBRARY_CONSTRUCTION_PROTOCOL>none provided</LIBRARY_CONSTRUCTION_PROTOCOL>
    </LIBRARY_DESCRIPTOR>
    <SPOT_DESCRIPTOR>
      <SPOT_DECODE_SPEC>
        <SPOT_LENGTH>308</SPOT_LENGTH>
        <READ_SPEC>
          <READ_INDEX>0</READ_INDEX>
          <READ_LABEL>F</READ_LABEL>
          <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_LABEL>R</READ_LABEL>
          <READ_CLASS>Application Read</READ_CLASS>
          <READ_TYPE>Reverse</READ_TYPE>
          <BASE_COORD>152</BASE_COORD>
        </READ_SPEC>
      </SPOT_DECODE_SPEC>
    </SPOT_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <ILLUMINA>
      <INSTRUMENT_MODEL>Illumina HiSeq 4000</INSTRUMENT_MODEL>
    </ILLUMINA>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>ERS4542325</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>ERA2547916</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=ERX4091702&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=ERX4091702&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="ERX4091703" alias="exp_BRZ_GGOSW_6_HC2GWBBXX.IND27" center_name="Genoscope">
  <IDENTIFIERS>
    <PRIMARY_ID>ERX4091703</PRIMARY_ID>
    <SUBMITTER_ID namespace="Genoscope">exp_BRZ_GGOSW_6_HC2GWBBXX.IND27</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>unidentified_Illumina_W</TITLE>
  <STUDY_REF accession="ERP121563">
    <IDENTIFIERS>
      <PRIMARY_ID>ERP121563</PRIMARY_ID>
      <SECONDARY_ID>PRJEB38174</SECONDARY_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION/>
    <SAMPLE_DESCRIPTOR accession="ERS4542325">
      <IDENTIFIERS>
        <PRIMARY_ID>ERS4542325</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMEA6814683</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>BRZ_GG_W</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <PAIRED NOMINAL_LENGTH="391"/>
      </LIBRARY_LAYOUT>
      <LIBRARY_CONSTRUCTION_PROTOCOL>none provided</LIBRARY_CONSTRUCTION_PROTOCOL>
    </LIBRARY_DESCRIPTOR>
    <SPOT_DESCRIPTOR>
      <SPOT_DECODE_SPEC>
        <SPOT_LENGTH>308</SPOT_LENGTH>
        <READ_SPEC>
          <READ_INDEX>0</READ_INDEX>
          <READ_LABEL>F</READ_LABEL>
          <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_LABEL>R</READ_LABEL>
          <READ_CLASS>Application Read</READ_CLASS>
          <READ_TYPE>Reverse</READ_TYPE>
          <BASE_COORD>152</BASE_COORD>
        </READ_SPEC>
      </SPOT_DECODE_SPEC>
    </SPOT_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <ILLUMINA>
      <INSTRUMENT_MODEL>Illumina HiSeq 4000</INSTRUMENT_MODEL>
    </ILLUMINA>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>ERS4542325</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>ERA2547916</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=ERX4091703&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=ERX4091703&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
</EXPERIMENT>
</EXPERIMENT_SET>