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Submit to trace archives and INSDC |
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Investigation type (i.e., report type) |
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Project name |
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Study |
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Environment |
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Geographic location (latitude and longitude (float (point, transect and region)), depth and altitude of sample (integer) |
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Time of sample collection (UTC) |
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Habitat |
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MIMS extension: select to report a set of uniform measurements for a given habitat: |
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Water body: (temperature, pH, salinity, pressure, chlorophyll, conductivity, light intensity, dissolved organic carbon (DOC), current, atmospheric data, density, alkalinity, dissolved oxygen, particulate organic carbon (POC), phosphate, nitrate, sulfates, sulfides, primary production) (integer, unit) |
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Nucleic acid sequence source |
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Subspecific genetic lineage (below lowest rank of NCBI taxonomy, which is subspecies) (e.g., serovar, biotype, ecotype) (CABRI) |
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Ploidy (e.g., allopolyploid, polyploid) (PATO) |
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Number of replicons (EU, BA: chromosomes (haploid count); VI: segments) (integer) |
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Extrachromosomal elements (integer) |
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Estimated size (before sequencing; to apply to all draft genomes) (integer; base pairs) |
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Reference for biomaterial (primary publication if isolated before genome publication; otherwise, primary genome report) (PMID or DOI) |
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BioSource material identifiers: (cultures of microorganisms: identifiers(alphanumeric) for two culture collections(OBI); specimens (e.g., organelles and Eukarya): voucher condition and location(CV))ll |
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Known pathogenicity |
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Biotic relationship (e.g., free-living, parasite, commensal, symbiont) (OBI) |
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Specific host (e.g., host taxid, unknown, environmental) (EnvO) |
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Host specificity or range(taxid) |
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Health or disease status of specific host at time of collection (e.g., alive, asymptomatic) (PATO) |
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Trophic level (e.g., autotroph, heterotroph) (PATO) |
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Propagation (phage: lytic or lysogenic; plasmid: incompatibility group) (CV) |
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Encoded traits (e.g., plasmid: antibiotic resistance; phage: converting genes) (CV; see caption) |
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Relationship to oxygen (e.g., aerobic, anaerobic) (PATO) |
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Isolation and growth conditions (PMID or DOI) |
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Biomaterial treatment (e.g., filtering of sea water) (OBI) |
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Volume of sample (integer) |
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Sampling strategy (enriched, screened, normalized) (CV) |
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Assay |
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Sequencing |
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Nucleic acid preparation (extraction method(CV); amplification(CV) |
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Library construction (library size (integer), number of reads sequenced (integer), vector(CV) |
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Sequencing method (e.g., dideoxysequencing, pyrosequencing, polony) (OBI) |
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Assembly (assembly method (CV), estimated error rate (unit) and method of calculation (CV)) |
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Finishing strategy (status—e.g., complete or draft (CV), coverage (integer), contigs (integer)) |
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Relevant Standard Operating Procedures (SOPs) |
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Relevant electronic resources |
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