Uncultivated genome recovered from an assembly of the SRX834666 metagenome.

quality_assessment_method_version

1.0.6

collection_date

not applicable

mapping_method

BWA (BWA-MEM)

INSDC secondary accession

SRS2035448

metagenome_source

gut metagenome

organism

bacterium UBP9_UBA4705

environmental_sample

true

mapping_method_version

0.7.12-r1039

isolation-source

feces

quality_assessment_method

CheckM

subsrc_note

Genome binned from sequencing reads available in SRX834666 metagenome

metagenomic

true

assembly_method_version

4.4.1

assembly_method

CLC de novo assembler

sample_type

metagenomic assembly

contamination_estimated

0.00%

isolate

UBA4705

NCBI submission package

Microbe.1.0

genome_coverage

15.08

geo_loc_name

Kenya

value

This BioSample is a metagenomic assembly obtained from the gut metagenome reads: SRR1747065.

completeness_estimated

85.65%

BioSampleModel

Microbe, viral or environmental

ENA-FIRST-PUBLIC

2017-02-27

ENA-LAST-UPDATE

2017-08-15

Keywords: GSC:MIxS;MIMS:5.0

collection_date

2012-07-24

env_feature

mammalia-associated habitat

INSDC secondary accession

SRS812675

organism

gut metagenome

host_body_product

feces

host_age

6.97

NCBI submission package

MIMS.me.host-associated.5.0

env_material

feces

host_sex

female

host

Papio cynocephalus

geo_loc_name

Kenya

env_biome

mammalia-associated habitat

lat_lon

2.717 S 37.1 E

BioSampleModel

MIGS/MIMS/MIMARKS.host-associated

ENA-FIRST-PUBLIC

2015-03-02

ENA-LAST-UPDATE

2021-02-28

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX2625491" alias="SRX834666.b84.bam" center_name="University of Queensland" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX2625491</PRIMARY_ID>
    <SUBMITTER_ID namespace="University of Queensland">SRX834666.b84.bam</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>bacterium UBP9_UBA4705</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 bacterium UBP9_UBA4705 using version 0.7.12-r1039 and assembled with CLC de novo assembler 4.4.1 with a genome coverage of 15.08</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS2035448">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS2035448</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN06456592</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>SRX834666.b84.bam</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <PAIRED/>
      </LIBRARY_LAYOUT>
    </LIBRARY_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <ILLUMINA>
      <INSTRUMENT_MODEL>Illumina HiSeq 2500</INSTRUMENT_MODEL>
    </ILLUMINA>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>SRS2035448</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA543416</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=SRX2625491&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=SRX2625491&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="SRX834666" alias="F31" center_name="Duke University" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX834666</PRIMARY_ID>
    <SUBMITTER_ID namespace="Duke University">F31</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>shotgun metagenomic sequencing of fecal sample from an adult baboon: Sample F31</TITLE>
  <STUDY_REF accession="SRP051834">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP051834</PRIMARY_ID>
      <EXTERNAL_ID namespace="BioProject">PRJNA271618</EXTERNAL_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>Kapa Biosystems Library Prep Kit</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS812675">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS812675</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN03275618</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>F31</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <PAIRED/>
      </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 2500</INSTRUMENT_MODEL>
    </ILLUMINA>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>SRS812675</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA221688</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=SRX834666&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=SRX834666&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
</EXPERIMENT>
</EXPERIMENT_SET>