{
    "type": "genome",
    "identifier": "GCF_000260985.4",
    "organism": "Methylophaga nitratireducenticrescens",
    "title": "Methylophaga nitratireducenticrescens",
    "description": "na",
    "data type": "Genome sequencing and assembly",
    "organization": "INRS-Institut Armand-Frappier",
    "publication": [
        {}
    ],
    "properties": {
        "assembly_accession": "GCF_000260985.4",
        "bioproject": "PRJNA224116",
        "biosample": "SAMN02603342",
        "wgs_master": "na",
        "refseq_category": "reference genome",
        "taxid": "754476",
        "species_taxid": "754476",
        "organism_name": "Methylophaga nitratireducenticrescens",
        "infraspecific_name": "strain=JAM1",
        "isolate": "na",
        "version_status": "latest",
        "assembly_level": "Complete Genome",
        "release_type": "Major",
        "genome_rep": "Full",
        "seq_rel_date": "2017/06/27",
        "asm_name": "ASM26098v3",
        "asm_submitter": "INRS-Institut Armand-Frappier",
        "gbrs_paired_asm": "GCA_000260985.3",
        "paired_asm_comp": "identical",
        "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/260/985/GCF_000260985.4_ASM26098v3",
        "excluded_from_refseq": "na",
        "relation_to_type_material": "assembly from type material",
        "asm_not_live_date": "na        ",
        "assembly_type": "haploid",
        "group": "bacteria",
        "genome_size": "3137100",
        "genome_size_ungapped": "3137100",
        "gc_percent": "44.500000",
        "replicon_count": "1",
        "scaffold_count": "1",
        "contig_count": "1",
        "annotation_provider": "NCBI RefSeq",
        "annotation_name": "GCF_000260985.4-RS_2024_12_11",
        "annotation_date": "2024-12-11",
        "total_gene_count": "3006",
        "protein_coding_gene_count": "2921",
        "non_coding_gene_count": "57",
        "pubmed_id": "23148104;22815445"
    },
    "dbXrefs": [],
    "distribution": null,
    "Download": null,
    "status": "public",
    "visibility": null,
    "dateCreated": "2017-06-27",
    "dateModified": "2017-06-27",
    "datePublished": "2017-06-27",
    "_annotation": {
        "sample_count": 1,
        "sample_organism": [
            "Methylophaga nitratireducenticrescens"
        ],
        "sample_taxid": [
            "754476"
        ],
        "sample_host_organism": [],
        "sample_host_organism_id": [],
        "sample_host_disease": [],
        "sample_host_disease_id": [],
        "sample_host_location": [],
        "sample_host_location_id": [],
        "data_size": "0.891 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)": "3137100",
        "Number of Sequences": "1",
        "Longest Sequences (bp)": "3137100",
        "N50 (bp)": "3137100",
        "Gap Ratio (%)": "0.000000",
        "GCcontent (%)": "44.7",
        "Number of CDSs": "2971",
        "Average Protein Length": "315.8",
        "Coding Ratio (%)": "89.7",
        "Number of rRNAs": "9",
        "Number of tRNAs": "44",
        "Number of CRISPRs": "1"
    },
    "has_analysis": true,
    "_dfastqc": {
        "tc_result": [
            {
                "organism_name": "Methylophaga nitratireducenticrescens",
                "strain": "strain=JAM1",
                "accession": "GCA_000260985.3",
                "taxid": 754476,
                "species_taxid": 754476,
                "relation_to_type": "type",
                "validated": true,
                "ani": 100.0,
                "matched_fragments": 1045,
                "total_fragments": 1045,
                "ani_threshold": 95,
                "status": "conclusive"
            },
            {
                "organism_name": "Methylophaga pinxianii",
                "strain": "strain=TMB456",
                "accession": "GCA_020447225.1",
                "taxid": 2881052,
                "species_taxid": 2881052,
                "relation_to_type": "type",
                "validated": true,
                "ani": 82.5632,
                "matched_fragments": 617,
                "total_fragments": 1045,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Methylophaga aminisulfidivorans",
                "strain": "strain=MP",
                "accession": "GCA_000214595.2",
                "taxid": 230105,
                "species_taxid": 230105,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.8254,
                "matched_fragments": 158,
                "total_fragments": 1045,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Methylophaga thiooxydans",
                "strain": "strain=DMS010",
                "accession": "GCA_000156355.1",
                "taxid": 392484,
                "species_taxid": 392484,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.729,
                "matched_fragments": 139,
                "total_fragments": 1045,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Methylophaga lonarensis",
                "strain": "strain=MPL",
                "accession": "GCA_000349205.1",
                "taxid": 999151,
                "species_taxid": 999151,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.2776,
                "matched_fragments": 162,
                "total_fragments": 1045,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Methylophaga sulfidovorans",
                "strain": "strain=DSM 11578",
                "accession": "GCA_900114205.1",
                "taxid": 45496,
                "species_taxid": 45496,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.1985,
                "matched_fragments": 142,
                "total_fragments": 1045,
                "ani_threshold": 95,
                "status": "below_threshold"
            }
        ],
        "cc_result": {
            "completeness": 100.0,
            "contamination": 0.0,
            "strain_heterogeneity": 0.0
        },
        "gtdb_result": [
            {
                "accession": "GCF_000260985.4",
                "gtdb_species": "s__Methylophaga nitratireducenticrescens",
                "ani": 100.0,
                "matched_fragments": 1045,
                "total_fragments": 1045,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.21",
                "min_intra_species_ani": "99.21",
                "mean_intra_species_af": "0.92",
                "min_intra_species_af": "0.92",
                "num_clustered_genomes": 2,
                "status": "conclusive"
            },
            {
                "accession": "GCA_002354555.1",
                "gtdb_species": "s__Methylophaga sp002354555",
                "ani": 90.5599,
                "matched_fragments": 707,
                "total_fragments": 1045,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.87",
                "min_intra_species_ani": "98.17",
                "mean_intra_species_af": "0.91",
                "min_intra_species_af": "0.88",
                "num_clustered_genomes": 3,
                "status": "-"
            },
            {
                "accession": "GCA_002696735.1",
                "gtdb_species": "s__Methylophaga sp002696735",
                "ani": 89.8568,
                "matched_fragments": 811,
                "total_fragments": 1045,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.51",
                "min_intra_species_ani": "97.89",
                "mean_intra_species_af": "0.93",
                "min_intra_species_af": "0.90",
                "num_clustered_genomes": 20,
                "status": "-"
            },
            {
                "accession": "GCA_002363955.1",
                "gtdb_species": "s__Methylophaga sp002363955",
                "ani": 82.8446,
                "matched_fragments": 649,
                "total_fragments": 1045,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.95",
                "min_intra_species_ani": "98.64",
                "mean_intra_species_af": "0.94",
                "min_intra_species_af": "0.91",
                "num_clustered_genomes": 14,
                "status": "-"
            },
            {
                "accession": "GCF_001720165.1",
                "gtdb_species": "s__Methylophaga muralis",
                "ani": 82.6856,
                "matched_fragments": 611,
                "total_fragments": 1045,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "97.83",
                "min_intra_species_ani": "97.83",
                "mean_intra_species_af": "0.96",
                "min_intra_species_af": "0.96",
                "num_clustered_genomes": 2,
                "status": "-"
            }
        ]
    },
    "_bac2feature": {
        "phenotypes": null,
        "cell_diameter": -0.222,
        "cell_length": 0.176,
        "doubling_h": null,
        "growth_tmp": 29.0,
        "optimum_tmp": 30.0,
        "optimum_ph": 8.0,
        "genome_size": 3137173.2,
        "gc_content": 44.7,
        "coding_genes": 2946.0,
        "rRNA16S_genes": 3.0,
        "tRNA_genes": 44.0,
        "gram_stain": 0.0,
        "sporulation": 0.0,
        "motility": 1.0,
        "range_salinity": 1.0,
        "facultative_respiration": 1.0,
        "anaerobic_respiration": 0.0,
        "aerobic_respiration": 0.0,
        "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
    },
    "_genome_taxon": [
        "Methylophaga",
        "nitratireducenticrescens"
    ],
    "quality": 5,
    "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f"
}