{
    "type": "genome",
    "identifier": "GCF_900112745.1",
    "organism": "Shimia marina",
    "title": "Shimia marina",
    "description": "na",
    "data type": "Genome sequencing and assembly",
    "organization": "DOE - JOINT GENOME INSTITUTE",
    "publication": [
        {}
    ],
    "properties": {
        "assembly_accession": "GCF_900112745.1",
        "bioproject": "PRJNA224116",
        "biosample": "SAMN04488037",
        "wgs_master": "FOMU00000000.1",
        "refseq_category": "reference genome",
        "taxid": "321267",
        "species_taxid": "321267",
        "organism_name": "Shimia marina",
        "infraspecific_name": "strain=DSM 26895",
        "isolate": "na",
        "version_status": "latest",
        "assembly_level": "Scaffold",
        "release_type": "Major",
        "genome_rep": "Full",
        "seq_rel_date": "2019/09/11",
        "asm_name": "IMG-taxon 2619618961 annotated assembly",
        "asm_submitter": "DOE - JOINT GENOME INSTITUTE",
        "gbrs_paired_asm": "GCA_900112745.1",
        "paired_asm_comp": "identical",
        "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/112/745/GCF_900112745.1_IMG-taxon_2619618961_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": "4061252",
        "genome_size_ungapped": "4059992",
        "gc_percent": "57.500000",
        "replicon_count": "0",
        "scaffold_count": "32",
        "contig_count": "32",
        "annotation_provider": "NCBI RefSeq",
        "annotation_name": "GCF_900112745.1-RS_2024_10_27",
        "annotation_date": "2024-10-27",
        "total_gene_count": "3958",
        "protein_coding_gene_count": "3870",
        "non_coding_gene_count": "55",
        "pubmed_id": "na"
    },
    "dbXrefs": [],
    "distribution": null,
    "Download": null,
    "status": "public",
    "visibility": null,
    "dateCreated": "2019-09-11",
    "dateModified": "2019-09-11",
    "datePublished": "2019-09-11",
    "_annotation": {
        "sample_count": 1,
        "sample_organism": [
            "Shimia marina"
        ],
        "sample_taxid": [
            "321267"
        ],
        "sample_host_organism": [],
        "sample_host_organism_id": [],
        "sample_host_disease": [],
        "sample_host_disease_id": [],
        "sample_host_location": [
            "missing"
        ],
        "sample_host_location_id": [],
        "data_size": "1.148 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)": "4061252",
        "Number of Sequences": "32",
        "Longest Sequences (bp)": "768578",
        "N50 (bp)": "323790",
        "Gap Ratio (%)": "0.031025",
        "GCcontent (%)": "57.4",
        "Number of CDSs": "3946",
        "Average Protein Length": "305.5",
        "Coding Ratio (%)": "89.1",
        "Number of rRNAs": "3",
        "Number of tRNAs": "47",
        "Number of CRISPRs": "0"
    },
    "has_analysis": true,
    "_dfastqc": {
        "tc_result": [
            {
                "organism_name": "Shimia marina",
                "strain": "strain=DSM 26895",
                "accession": "GCA_900112745.1",
                "taxid": 321267,
                "species_taxid": 321267,
                "relation_to_type": "type",
                "validated": true,
                "ani": 100.0,
                "matched_fragments": 1334,
                "total_fragments": 1338,
                "ani_threshold": 95,
                "status": "conclusive"
            },
            {
                "organism_name": "Shimia marina",
                "strain": "strain=CECT 7688",
                "accession": "GCA_001458175.1",
                "taxid": 321267,
                "species_taxid": 321267,
                "relation_to_type": "type",
                "validated": true,
                "ani": 99.9825,
                "matched_fragments": 1302,
                "total_fragments": 1338,
                "ani_threshold": 95,
                "status": "conclusive"
            },
            {
                "organism_name": "Shimia haliotis",
                "strain": "strain=DSM 28453",
                "accession": "GCA_900114415.1",
                "taxid": 1280847,
                "species_taxid": 1280847,
                "relation_to_type": "type",
                "validated": true,
                "ani": 79.671,
                "matched_fragments": 475,
                "total_fragments": 1338,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Alexandriicola marinus",
                "strain": "strain=LZ-14",
                "accession": "GCA_004000435.1",
                "taxid": 2081710,
                "species_taxid": 2081710,
                "relation_to_type": "type",
                "validated": true,
                "ani": 79.6605,
                "matched_fragments": 148,
                "total_fragments": 1338,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Shimia isoporae",
                "strain": "strain=DSM 26433",
                "accession": "GCA_004346865.1",
                "taxid": 647720,
                "species_taxid": 647720,
                "relation_to_type": "type",
                "validated": true,
                "ani": 78.8107,
                "matched_fragments": 345,
                "total_fragments": 1338,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Tritonibacter mobilis",
                "strain": "strain=NBRC101030",
                "accession": "GCA_001681715.1",
                "taxid": 379347,
                "species_taxid": 379347,
                "relation_to_type": "type",
                "validated": true,
                "ani": 78.6002,
                "matched_fragments": 300,
                "total_fragments": 1338,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Actibacterium atlanticum",
                "strain": "strain=22II-S11-z10",
                "accession": "GCA_000671395.1",
                "taxid": 1461693,
                "species_taxid": 1461693,
                "relation_to_type": "type",
                "validated": true,
                "ani": 78.3665,
                "matched_fragments": 223,
                "total_fragments": 1338,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Cognatishimia activa",
                "strain": "strain=CECT 5113",
                "accession": "GCA_001458335.1",
                "taxid": 1715691,
                "species_taxid": 1715691,
                "relation_to_type": "type",
                "validated": true,
                "ani": 78.2995,
                "matched_fragments": 229,
                "total_fragments": 1338,
                "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": 78.0408,
                "matched_fragments": 285,
                "total_fragments": 1338,
                "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": 78.0178,
                "matched_fragments": 337,
                "total_fragments": 1338,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Actibacterium pelagium",
                "strain": "strain=JN33",
                "accession": "GCA_002285415.1",
                "taxid": 2029103,
                "species_taxid": 2029103,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.9191,
                "matched_fragments": 169,
                "total_fragments": 1338,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Aliiroseovarius marinus",
                "strain": "strain=A6024",
                "accession": "GCA_004360145.1",
                "taxid": 2500159,
                "species_taxid": 2500159,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.7564,
                "matched_fragments": 207,
                "total_fragments": 1338,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Zongyanglinia marina",
                "strain": "strain=DSW4-44",
                "accession": "GCA_005771405.1",
                "taxid": 2578117,
                "species_taxid": 2578117,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.6221,
                "matched_fragments": 190,
                "total_fragments": 1338,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Shimia gijangensis",
                "strain": "strain=DSM 100564",
                "accession": "GCA_900142085.1",
                "taxid": 1470563,
                "species_taxid": 1470563,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.598,
                "matched_fragments": 266,
                "total_fragments": 1338,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Pseudophaeobacter flagellatus",
                "strain": "strain=MA21411-1",
                "accession": "GCA_021228235.1",
                "taxid": 2899119,
                "species_taxid": 2899119,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.3109,
                "matched_fragments": 259,
                "total_fragments": 1338,
                "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": 76.8837,
                "matched_fragments": 126,
                "total_fragments": 1338,
                "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": 76.8811,
                "matched_fragments": 126,
                "total_fragments": 1338,
                "ani_threshold": 95,
                "status": "below_threshold"
            }
        ],
        "cc_result": {
            "completeness": 100.0,
            "contamination": 0.0,
            "strain_heterogeneity": 0.0
        },
        "gtdb_result": [
            {
                "accession": "GCF_001458175.1",
                "gtdb_species": "s__Shimia marina",
                "ani": 99.9825,
                "matched_fragments": 1302,
                "total_fragments": 1338,
                "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": "conclusive"
            },
            {
                "accession": "GCF_017743735.1",
                "gtdb_species": "s__Shimia sp017743735",
                "ani": 82.0447,
                "matched_fragments": 770,
                "total_fragments": 1338,
                "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": 81.885,
                "matched_fragments": 721,
                "total_fragments": 1338,
                "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": "GCA_014872815.1",
                "gtdb_species": "s__Shimia sp014872815",
                "ani": 80.4843,
                "matched_fragments": 701,
                "total_fragments": 1338,
                "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": "GCA_900537125.1",
                "gtdb_species": "s__Shimia sp900537125",
                "ani": 79.8681,
                "matched_fragments": 657,
                "total_fragments": 1338,
                "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_900114415.1",
                "gtdb_species": "s__Shimia haliotis",
                "ani": 79.6281,
                "matched_fragments": 479,
                "total_fragments": 1338,
                "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_004346865.1",
                "gtdb_species": "s__Shimia isoporae",
                "ani": 78.8107,
                "matched_fragments": 345,
                "total_fragments": 1338,
                "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_001458335.1",
                "gtdb_species": "s__Cognatishimia activa",
                "ani": 78.2818,
                "matched_fragments": 229,
                "total_fragments": 1338,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cognatishimia",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.97",
                "min_intra_species_ani": "99.97",
                "mean_intra_species_af": "0.99",
                "min_intra_species_af": "0.99",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCF_000169455.1",
                "gtdb_species": "s__Pseudophaeobacter sp000169455",
                "ani": 77.6675,
                "matched_fragments": 252,
                "total_fragments": 1338,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter",
                "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_013032505.1",
                "gtdb_species": "s__Ruegeria atlantica_F",
                "ani": 77.1555,
                "matched_fragments": 206,
                "total_fragments": 1338,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria",
                "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_018500075.1",
                "gtdb_species": "s__Lentibacter sp018500075",
                "ani": 76.703,
                "matched_fragments": 161,
                "total_fragments": 1338,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lentibacter",
                "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": -0.523,
        "cell_length": -0.097,
        "doubling_h": null,
        "growth_tmp": 30.0,
        "optimum_tmp": 32.5,
        "optimum_ph": 7.0,
        "genome_size": 4026636.0,
        "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",
        "marina"
    ],
    "quality": 4,
    "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f"
}