BioSample Accession(s)

SAMN06452415, SRS2032261

assembly method

CLC de novo assembler

assembly_method_version

4.4.1

completeness_estimated

95.68%

contamination_estimated

0.32%

environmental sample

true

genome coverage

112.66

isolate

UBA3134

isolation-source

tap water

mapping_method

BWA (BWA-MEM)

mapping_method_version

0.7.12-r1039

metagenome source

freshwater metagenome

metagenomic

true

quality_assessment_method

CheckM

quality_assessment_method_version

1.0.6

sample type

metagenomic assembly

subsrc_note

Genome binned from sequencing reads available in SRX130437 metagenome

type-material

reference material of Candidatus Raskinella chloraquaticus

value

This BioSample is a metagenomic assembly obtained from the freshwater metagenome reads: SRR446630.

We sampled tap water from Lab which has been transported by pipelines in 2 h

BioSample Accession(s)

SAMN00829210

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX2622304" alias="SRX130437.b1.bam" center_name="University of Queensland" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX2622304</PRIMARY_ID>
    <SUBMITTER_ID namespace="University of Queensland">SRX130437.b1.bam</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Rhizobiales bacterium UBA3134</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 Rhizobiales bacterium UBA3134 using version 0.7.12-r1039 and assembled with CLC de novo assembler 4.4.1 with a genome coverage of 112.66</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS2032261">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS2032261</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN06452415</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>SRX130437.b1.bam</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>unspecified</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>SRS2032261</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA543412</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=SRX2622304&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=SRX2622304&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="SRX130437" alias="TW" center_name="Nanjing University" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX130437</PRIMARY_ID>
    <SUBMITTER_ID namespace="Nanjing University">TW</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Tap water</TITLE>
  <STUDY_REF accession="SRP011572">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP011572</PRIMARY_ID>
      <SUBMITTER_ID namespace="Nanjing University">Drinking water metagenome</SUBMITTER_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>the sequencing strategy of Index 101 PE, Paired End sequencing, 101-bp reads and 8-bp index sequence</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS301860">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS301860</PRIMARY_ID>
        <SUBMITTER_ID namespace="Nanjing University">TW</SUBMITTER_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>TW</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>unspecified</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <PAIRED NOMINAL_LENGTH="140"/>
      </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>SRS301860</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA050945</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=SRX130437&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=SRX130437&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
</EXPERIMENT>
</EXPERIMENT_SET>