Uncultivated genome recovered from an assembly of the SRX823305 metagenome.

quality_assessment_method_version

1.0.6

collection_date

not applicable

mapping_method

BWA (BWA-MEM)

type-material

reference material of Pantoea rara

INSDC secondary accession

SRS2034797

metagenome_source

terrestrial metagenome

organism

Candidatus Pantoea rara

environmental_sample

true

mapping_method_version

0.7.12-r1039

isolation-source

metal

quality_assessment_method

CheckM

subsrc_note

Genome binned from sequencing reads available in SRX823305 metagenome

metagenomic

true

assembly_method_version

4.4.1

assembly_method

CLC de novo assembler

sample_type

metagenomic assembly

contamination_estimated

0.36%

isolate

UBA5707

NCBI submission package

Microbe.1.0

genome_coverage

40.92

geo_loc_name

USA:New York City

value

This BioSample is a metagenomic assembly obtained from the terrestrial metagenome reads: SRR1749922.

completeness_estimated

97.87%

BioSampleModel

Microbe, viral or environmental

ENA-FIRST-PUBLIC

2017-02-27

ENA-LAST-UPDATE

2024-06-23

collection_date

2013-08-07

isolate

P01365

env_feature

subway

INSDC secondary accession

SRS802994

NCBI submission package

Metagenome.environmental.1.0

env_material

metal

organism

terrestrial metagenome

host

not applicable

geo_loc_name

USA:New York City

env_biome

city

lat_lon

40.67 N 73.98 W

BioSampleModel

Metagenome or environmental

ENA-FIRST-PUBLIC

2014-12-22

ENA-LAST-UPDATE

2021-02-28

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX2624840" alias="SRX823305.b2.bam" center_name="University of Queensland" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX2624840</PRIMARY_ID>
    <SUBMITTER_ID namespace="University of Queensland">SRX823305.b2.bam</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Pantoea sp. UBA5707</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 Pantoea sp. UBA5707 using version 0.7.12-r1039 and assembled with CLC de novo assembler 4.4.1 with a genome coverage of 40.92</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS2034797">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS2034797</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN06452238</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>SRX823305.b2.bam</LIBRARY_NAME>
      <LIBRARY_STRATEGY>OTHER</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>SRS2034797</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=SRX2624840&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=SRX2624840&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="SRX823305" alias="P01365" center_name="Weill Cornell Medical College" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX823305</PRIMARY_ID>
    <SUBMITTER_ID namespace="Weill Cornell Medical College">P01365</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Shotgun sequencing of environmental sample: Sample P01365</TITLE>
  <STUDY_REF accession="SRP051511">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP051511</PRIMARY_ID>
      <EXTERNAL_ID namespace="BioProject">PRJNA271013</EXTERNAL_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>Shotgun sequencing</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS802994">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS802994</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN03271299</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>P01365</LIBRARY_NAME>
      <LIBRARY_STRATEGY>OTHER</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>250</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>126</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>SRS802994</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA228306</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=SRX823305&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=SRX823305&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
</EXPERIMENT>
</EXPERIMENT_SET>