{
    "type": "genome",
    "identifier": "GCA_025994975.1",
    "organism": "Pelagibacteraceae bacterium",
    "title": "Pelagibacteraceae bacterium",
    "description": "derived from metagenome; genus undefined",
    "data type": "Genome sequencing and assembly",
    "organization": "Stanford University",
    "publication": [
        {}
    ],
    "properties": {
        "assembly_accession": "GCA_025994975.1",
        "bioproject": "PRJNA819083",
        "biosample": "SAMN30106610",
        "wgs_master": "JAPDIK000000000.1",
        "refseq_category": "na",
        "taxid": "2026775",
        "species_taxid": "2026775",
        "organism_name": "Pelagibacteraceae bacterium",
        "infraspecific_name": "",
        "isolate": "SFB_34D_5_2",
        "version_status": "latest",
        "assembly_level": "Contig",
        "release_type": "Major",
        "genome_rep": "Full",
        "seq_rel_date": "2022/11/04",
        "asm_name": "ASM2599497v1",
        "submitter": "Stanford University",
        "gbrs_paired_asm": "na",
        "paired_asm_comp": "na",
        "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/025/994/975/GCA_025994975.1_ASM2599497v1",
        "excluded_from_refseq": "derived from metagenome; genus undefined",
        "relation_to_type_material": "",
        "asm_not_live_date": "na"
    },
    "dbXrefs": [],
    "distribution": null,
    "Download": null,
    "status": "public",
    "visibility": null,
    "dateCreated": "2022-11-04",
    "dateModified": "2022-11-04",
    "datePublished": "2022-11-04",
    "_annotation": {
        "sample_count": 1,
        "sample_organism": [
            "Pelagibacteraceae bacterium"
        ],
        "sample_taxid": [
            "2026775"
        ],
        "sample_host_organism": [],
        "sample_host_organism_id": [],
        "sample_host_disease": [],
        "sample_host_disease_id": [],
        "sample_host_location": [
            "USA: California, San Francisco Bay"
        ],
        "sample_host_location_id": [],
        "data_size": "0.202 MB",
        "sample_ph_range": {
            "min": null,
            "max": null
        },
        "sample_temperature_range": {
            "min": null,
            "max": null
        },
        "completeness": 70.83,
        "contamination": 0.46,
        "strain_heterogeneity": 0.0,
        "genome_count": 1
    },
    "data_type": "MAG",
    "data_source": "INSDC",
    "_dfast": {
        "Total Sequence Length (bp)": "721976",
        "Number of Sequences": "77",
        "Longest Sequences (bp)": "62657",
        "N50 (bp)": "22189",
        "Gap Ratio (%)": "0.000000",
        "GCcontent (%)": "29.5",
        "Number of CDSs": "718",
        "Average Protein Length": "293.8",
        "Coding Ratio (%)": "87.7",
        "Number of rRNAs": "0",
        "Number of tRNAs": "24",
        "Number of CRISPRs": "0"
    },
    "has_analysis": true,
    "_dfastqc": {
        "tc_result": [
            {
                "organism_name": "Candidatus Pelagibacter ubique",
                "strain": "strain=HTCC1062",
                "accession": "GCA_000012345.1",
                "taxid": 198252,
                "species_taxid": 198252,
                "relation_to_type": "suspected-type",
                "validated": true,
                "ani": 78.7729,
                "matched_fragments": 136,
                "total_fragments": 209,
                "ani_threshold": 95,
                "status": "below_threshold"
            }
        ],
        "cc_result": {
            "completeness": 70.83,
            "contamination": 0.46,
            "strain_heterogeneity": 0.0
        },
        "gtdb_result": [
            {
                "accession": "GCA_008638165.1",
                "gtdb_species": "s__Pelagibacter sp008638165",
                "ani": 98.8078,
                "matched_fragments": 186,
                "total_fragments": 209,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.93",
                "min_intra_species_ani": "98.78",
                "mean_intra_species_af": "0.83",
                "min_intra_species_af": "0.76",
                "num_clustered_genomes": 5,
                "status": "conclusive"
            },
            {
                "accession": "GCF_900177485.1",
                "gtdb_species": "s__Pelagibacter sp900177485",
                "ani": 87.3857,
                "matched_fragments": 193,
                "total_fragments": 209,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "N/A",
                "min_intra_species_ani": "N/A",
                "mean_intra_species_af": "N/A",
                "min_intra_species_af": "N/A",
                "num_clustered_genomes": 1,
                "status": "-"
            },
            {
                "accession": "GCA_902571235.1",
                "gtdb_species": "s__Pelagibacter sp902571235",
                "ani": 81.0931,
                "matched_fragments": 119,
                "total_fragments": 209,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "N/A",
                "min_intra_species_ani": "N/A",
                "mean_intra_species_af": "N/A",
                "min_intra_species_af": "N/A",
                "num_clustered_genomes": 1,
                "status": "-"
            },
            {
                "accession": "GCA_902520685.1",
                "gtdb_species": "s__Pelagibacter sp902520685",
                "ani": 81.0319,
                "matched_fragments": 126,
                "total_fragments": 209,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "N/A",
                "min_intra_species_ani": "N/A",
                "mean_intra_species_af": "N/A",
                "min_intra_species_af": "N/A",
                "num_clustered_genomes": 1,
                "status": "-"
            },
            {
                "accession": "GCA_902622805.1",
                "gtdb_species": "s__Pelagibacter sp902622805",
                "ani": 80.8916,
                "matched_fragments": 122,
                "total_fragments": 209,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.81",
                "min_intra_species_ani": "99.81",
                "mean_intra_species_af": "0.79",
                "min_intra_species_af": "0.79",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCA_017880265.1",
                "gtdb_species": "s__Pelagibacter sp017880265",
                "ani": 79.4823,
                "matched_fragments": 104,
                "total_fragments": 209,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "97.65",
                "min_intra_species_ani": "97.65",
                "mean_intra_species_af": "0.82",
                "min_intra_species_af": "0.82",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCF_000155895.1",
                "gtdb_species": "s__Pelagibacter sp000155895",
                "ani": 79.184,
                "matched_fragments": 139,
                "total_fragments": 209,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "96.42",
                "min_intra_species_ani": "95.11",
                "mean_intra_species_af": "0.93",
                "min_intra_species_af": "0.90",
                "num_clustered_genomes": 6,
                "status": "-"
            },
            {
                "accession": "GCA_902555655.1",
                "gtdb_species": "s__Pelagibacter sp902555655",
                "ani": 79.1676,
                "matched_fragments": 108,
                "total_fragments": 209,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "N/A",
                "min_intra_species_ani": "N/A",
                "mean_intra_species_af": "N/A",
                "min_intra_species_af": "N/A",
                "num_clustered_genomes": 1,
                "status": "-"
            },
            {
                "accession": "GCA_902569055.1",
                "gtdb_species": "s__Pelagibacter sp902569055",
                "ani": 78.9566,
                "matched_fragments": 119,
                "total_fragments": 209,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.72",
                "min_intra_species_ani": "99.72",
                "mean_intra_species_af": "0.75",
                "min_intra_species_af": "0.75",
                "num_clustered_genomes": 2,
                "status": "-"
            }
        ]
    },
    "_bac2feature": {
        "phenotypes": null,
        "cell_diameter": -0.921,
        "cell_length": null,
        "doubling_h": 1.539,
        "growth_tmp": 17.5,
        "optimum_tmp": 37.0,
        "optimum_ph": 7.8,
        "genome_size": 1339460.152,
        "gc_content": 30.033,
        "coding_genes": 1406.332,
        "rRNA16S_genes": 1.0,
        "tRNA_genes": 33.0,
        "gram_stain": 0.0,
        "sporulation": 0.0,
        "motility": 0.0,
        "range_salinity": null,
        "facultative_respiration": null,
        "anaerobic_respiration": null,
        "aerobic_respiration": null,
        "mesophilic_range_tmp": 1.0,
        "thermophilic_range_tmp": 0.0,
        "psychrophilic_range_tmp": 0.0,
        "bacillus_cell_shape": 1.0,
        "coccus_cell_shape": 0.0,
        "filament_cell_shape": 0.0,
        "coccobacillus_cell_shape": 0.0,
        "vibrio_cell_shape": 0.0,
        "spiral_cell_shape": 0.0
    },
    "_gtdb_taxon": [
        "d__Bacteria",
        "p__Pseudomonadota",
        "c__Alphaproteobacteria",
        "o__Pelagibacterales",
        "f__Pelagibacteraceae",
        "g__Pelagibacter",
        "s__Pelagibacter sp008638165"
    ],
    "_genome_taxon": [
        "Pelagibacteraceae",
        "bacterium",
        "d__Bacteria",
        "p__Pseudomonadota",
        "c__Alphaproteobacteria",
        "o__Pelagibacterales",
        "f__Pelagibacteraceae",
        "g__Pelagibacter",
        "s__Pelagibacter sp008638165",
        "Bacteria",
        "Pseudomonadota",
        "Alphaproteobacteria",
        "Pelagibacterales",
        "Pelagibacteraceae",
        "Pelagibacter",
        "Pelagibacter",
        "sp008638165"
    ],
    "_meo": [
        {
            "id": "MEO_0000087",
            "label": "estuary"
        }
    ],
    "quality": 3,
    "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f"
}