{
    "type": "genome",
    "identifier": "GCF_900114415.1",
    "organism": "Shimia haliotis",
    "title": "Shimia haliotis",
    "description": "na",
    "data type": "Genome sequencing and assembly",
    "organization": "DOE - JOINT GENOME INSTITUTE",
    "publication": [
        {}
    ],
    "properties": {
        "assembly_accession": "GCF_900114415.1",
        "bioproject": "PRJNA224116",
        "biosample": "SAMN04488036",
        "wgs_master": "FOSZ00000000.1",
        "refseq_category": "reference genome",
        "taxid": "1280847",
        "species_taxid": "1280847",
        "organism_name": "Shimia haliotis",
        "infraspecific_name": "strain=DSM 28453",
        "isolate": "na",
        "version_status": "latest",
        "assembly_level": "Contig",
        "release_type": "Major",
        "genome_rep": "Full",
        "seq_rel_date": "2016/11/02",
        "asm_name": "IMG-taxon 2619619046 annotated assembly",
        "asm_submitter": "DOE - JOINT GENOME INSTITUTE",
        "gbrs_paired_asm": "GCA_900114415.1",
        "paired_asm_comp": "identical",
        "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/114/415/GCF_900114415.1_IMG-taxon_2619619046_annotated_assembly",
        "excluded_from_refseq": "na",
        "relation_to_type_material": "assembly from type material",
        "asm_not_live_date": "na        ",
        "assembly_type": "haploid",
        "group": "bacteria",
        "genome_size": "3995969",
        "genome_size_ungapped": "3995969",
        "gc_percent": "58.000000",
        "replicon_count": "0",
        "scaffold_count": "22",
        "contig_count": "22",
        "annotation_provider": "NCBI RefSeq",
        "annotation_name": "GCF_900114415.1-RS_2024_04_24",
        "annotation_date": "2024-04-24",
        "total_gene_count": "3930",
        "protein_coding_gene_count": "3861",
        "non_coding_gene_count": "52",
        "pubmed_id": "na"
    },
    "dbXrefs": [],
    "distribution": null,
    "Download": null,
    "status": "public",
    "visibility": null,
    "dateCreated": "2016-11-02",
    "dateModified": "2016-11-02",
    "datePublished": "2016-11-02",
    "_annotation": {
        "sample_count": 1,
        "sample_organism": [
            "Shimia haliotis"
        ],
        "sample_taxid": [
            "1280847"
        ],
        "sample_host_organism": [],
        "sample_host_organism_id": [],
        "sample_host_disease": [],
        "sample_host_disease_id": [],
        "sample_host_location": [
            "missing"
        ],
        "sample_host_location_id": [],
        "data_size": "1.128 MB",
        "sample_ph_range": {
            "min": null,
            "max": null
        },
        "sample_temperature_range": {
            "min": null,
            "max": null
        },
        "completeness": 100.0,
        "contamination": 0.0,
        "strain_heterogeneity": 0.0,
        "genome_count": 1
    },
    "data_type": "G",
    "data_source": "RefSeq",
    "_dfast": {
        "Total Sequence Length (bp)": "3995969",
        "Number of Sequences": "22",
        "Longest Sequences (bp)": "1084472",
        "N50 (bp)": "499081",
        "Gap Ratio (%)": "0.000000",
        "GCcontent (%)": "58.0",
        "Number of CDSs": "3896",
        "Average Protein Length": "308.8",
        "Coding Ratio (%)": "90.3",
        "Number of rRNAs": "4",
        "Number of tRNAs": "44",
        "Number of CRISPRs": "0"
    },
    "has_analysis": true,
    "_dfastqc": {
        "tc_result": [
            {
                "organism_name": "Shimia haliotis",
                "strain": "strain=DSM 28453",
                "accession": "GCA_900114415.1",
                "taxid": 1280847,
                "species_taxid": 1280847,
                "relation_to_type": "type",
                "validated": true,
                "ani": 100.0,
                "matched_fragments": 1322,
                "total_fragments": 1322,
                "ani_threshold": 95,
                "status": "conclusive"
            },
            {
                "organism_name": "Shimia isoporae",
                "strain": "strain=DSM 26433",
                "accession": "GCA_004346865.1",
                "taxid": 647720,
                "species_taxid": 647720,
                "relation_to_type": "type",
                "validated": true,
                "ani": 80.8807,
                "matched_fragments": 757,
                "total_fragments": 1322,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Shimia marina",
                "strain": "strain=DSM 26895",
                "accession": "GCA_900112745.1",
                "taxid": 321267,
                "species_taxid": 321267,
                "relation_to_type": "type",
                "validated": true,
                "ani": 79.5236,
                "matched_fragments": 479,
                "total_fragments": 1322,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Shimia marina",
                "strain": "strain=CECT 7688",
                "accession": "GCA_001458175.1",
                "taxid": 321267,
                "species_taxid": 321267,
                "relation_to_type": "type",
                "validated": true,
                "ani": 79.5125,
                "matched_fragments": 482,
                "total_fragments": 1322,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Shimia sediminis",
                "strain": "strain=ZQ172",
                "accession": "GCA_003990645.1",
                "taxid": 2497945,
                "species_taxid": 2497945,
                "relation_to_type": "type",
                "validated": true,
                "ani": 78.4318,
                "matched_fragments": 388,
                "total_fragments": 1322,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Shimia abyssi",
                "strain": "strain=DSM 100673",
                "accession": "GCA_003014475.1",
                "taxid": 1662395,
                "species_taxid": 1662395,
                "relation_to_type": "type",
                "validated": true,
                "ani": 78.0932,
                "matched_fragments": 386,
                "total_fragments": 1322,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Shimia thalassica",
                "strain": "strain=CECT 7735",
                "accession": "GCA_001458215.1",
                "taxid": 1715693,
                "species_taxid": 1715693,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.9115,
                "matched_fragments": 330,
                "total_fragments": 1322,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Falsiruegeria litorea",
                "strain": "strain=CECT 7639",
                "accession": "GCA_900172225.1",
                "taxid": 1280831,
                "species_taxid": 1280831,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.9086,
                "matched_fragments": 330,
                "total_fragments": 1322,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Leisingera methylohalidivorans",
                "strain": "strain=DSM 14336; MB2",
                "accession": "GCA_000511355.1",
                "taxid": 133924,
                "species_taxid": 133924,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.8571,
                "matched_fragments": 301,
                "total_fragments": 1322,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Leisingera caerulea",
                "strain": "strain=DSM 24564",
                "accession": "GCA_000473325.1",
                "taxid": 506591,
                "species_taxid": 506591,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.7921,
                "matched_fragments": 341,
                "total_fragments": 1322,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Salipiger pallidus",
                "strain": "strain=CGMCC 1.15762",
                "accession": "GCA_014643635.1",
                "taxid": 1775170,
                "species_taxid": 1775170,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.0502,
                "matched_fragments": 202,
                "total_fragments": 1322,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Pseudooceanicola antarcticus",
                "strain": "strain=CGMCC 1.12662",
                "accession": "GCA_900215355.1",
                "taxid": 1247613,
                "species_taxid": 1247613,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.0219,
                "matched_fragments": 212,
                "total_fragments": 1322,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Pseudooceanicola antarcticus",
                "strain": "strain=Ar-45",
                "accession": "GCA_002786285.1",
                "taxid": 1247613,
                "species_taxid": 1247613,
                "relation_to_type": "type",
                "validated": true,
                "ani": 76.9896,
                "matched_fragments": 216,
                "total_fragments": 1322,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Antarcticimicrobium luteum",
                "strain": "strain=318-1",
                "accession": "GCA_004358185.1",
                "taxid": 2547397,
                "species_taxid": 2547397,
                "relation_to_type": "type",
                "validated": true,
                "ani": 76.9794,
                "matched_fragments": 271,
                "total_fragments": 1322,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Rhodobacter amnigenus",
                "strain": "strain=HSP-20",
                "accession": "GCA_009908265.2",
                "taxid": 2852097,
                "species_taxid": 2852097,
                "relation_to_type": "type",
                "validated": true,
                "ani": 76.8011,
                "matched_fragments": 175,
                "total_fragments": 1322,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Rhodobacter amnigenus",
                "strain": "strain=HSP-20",
                "accession": "GCA_019130055.1",
                "taxid": 2852097,
                "species_taxid": 2852097,
                "relation_to_type": "type",
                "validated": true,
                "ani": 76.8011,
                "matched_fragments": 175,
                "total_fragments": 1322,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Pseudooceanicola aestuarii",
                "strain": "strain=E2-1",
                "accession": "GCA_010614805.1",
                "taxid": 2697319,
                "species_taxid": 2697319,
                "relation_to_type": "type",
                "validated": true,
                "ani": 76.794,
                "matched_fragments": 171,
                "total_fragments": 1322,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Rhodobacter ruber",
                "strain": "strain=CCP-1",
                "accession": "GCA_009908315.1",
                "taxid": 1985673,
                "species_taxid": 1985673,
                "relation_to_type": "type",
                "validated": true,
                "ani": 76.3657,
                "matched_fragments": 160,
                "total_fragments": 1322,
                "ani_threshold": 95,
                "status": "below_threshold"
            }
        ],
        "cc_result": {
            "completeness": 100.0,
            "contamination": 0.0,
            "strain_heterogeneity": 0.0
        },
        "gtdb_result": [
            {
                "accession": "GCF_900114415.1",
                "gtdb_species": "s__Shimia haliotis",
                "ani": 100.0,
                "matched_fragments": 1322,
                "total_fragments": 1322,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia",
                "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": "conclusive"
            },
            {
                "accession": "GCF_004346865.1",
                "gtdb_species": "s__Shimia isoporae",
                "ani": 80.8817,
                "matched_fragments": 756,
                "total_fragments": 1322,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia",
                "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": "GCF_001292625.1",
                "gtdb_species": "s__Shimia sp001292625",
                "ani": 80.8754,
                "matched_fragments": 788,
                "total_fragments": 1322,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia",
                "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": "GCF_001458175.1",
                "gtdb_species": "s__Shimia marina",
                "ani": 79.5181,
                "matched_fragments": 481,
                "total_fragments": 1322,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.13",
                "min_intra_species_ani": "96.28",
                "mean_intra_species_af": "0.94",
                "min_intra_species_af": "0.89",
                "num_clustered_genomes": 3,
                "status": "-"
            },
            {
                "accession": "GCA_014872815.1",
                "gtdb_species": "s__Shimia sp014872815",
                "ani": 79.4727,
                "matched_fragments": 561,
                "total_fragments": 1322,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "97.10",
                "min_intra_species_ani": "97.10",
                "mean_intra_species_af": "0.91",
                "min_intra_species_af": "0.91",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCF_017743735.1",
                "gtdb_species": "s__Shimia sp017743735",
                "ani": 79.4653,
                "matched_fragments": 574,
                "total_fragments": 1322,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "95.87",
                "min_intra_species_ani": "95.63",
                "mean_intra_species_af": "0.93",
                "min_intra_species_af": "0.93",
                "num_clustered_genomes": 3,
                "status": "-"
            },
            {
                "accession": "GCF_017744095.1",
                "gtdb_species": "s__Shimia sp017744095",
                "ani": 79.3747,
                "matched_fragments": 509,
                "total_fragments": 1322,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia",
                "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": "GCF_900114635.1",
                "gtdb_species": "s__Shimia aestuarii",
                "ani": 78.6859,
                "matched_fragments": 488,
                "total_fragments": 1322,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia",
                "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": "GCF_016019955.1",
                "gtdb_species": "s__Shimia sp016019955",
                "ani": 78.1656,
                "matched_fragments": 441,
                "total_fragments": 1322,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.56",
                "min_intra_species_ani": "99.56",
                "mean_intra_species_af": "0.93",
                "min_intra_species_af": "0.93",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCA_900143615.1",
                "gtdb_species": "s__Shimia sp900143615",
                "ani": 78.1192,
                "matched_fragments": 441,
                "total_fragments": 1322,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia",
                "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": "GCF_003014475.1",
                "gtdb_species": "s__Shimia abyssi",
                "ani": 78.0883,
                "matched_fragments": 386,
                "total_fragments": 1322,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia",
                "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": "GCF_016888515.1",
                "gtdb_species": "s__Shimia_A biformata",
                "ani": 77.9655,
                "matched_fragments": 381,
                "total_fragments": 1322,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia_A",
                "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": "GCF_000511355.1",
                "gtdb_species": "s__Leisingera methylohalidivorans",
                "ani": 77.8578,
                "matched_fragments": 299,
                "total_fragments": 1322,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera",
                "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": "-"
            }
        ]
    },
    "_bac2feature": {
        "phenotypes": null,
        "cell_diameter": -0.097,
        "cell_length": 0.301,
        "doubling_h": null,
        "growth_tmp": 30.0,
        "optimum_tmp": 30.0,
        "optimum_ph": 7.0,
        "genome_size": 3995969.0,
        "gc_content": null,
        "coding_genes": null,
        "rRNA16S_genes": null,
        "tRNA_genes": null,
        "gram_stain": 0.0,
        "sporulation": 0.0,
        "motility": 1.0,
        "range_salinity": null,
        "facultative_respiration": 0.0,
        "anaerobic_respiration": 0.0,
        "aerobic_respiration": 1.0,
        "mesophilic_range_tmp": null,
        "thermophilic_range_tmp": null,
        "psychrophilic_range_tmp": null,
        "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
    },
    "_genome_taxon": [
        "Shimia",
        "haliotis"
    ],
    "quality": 5,
    "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f"
}