{
    "type": "genome",
    "identifier": "GCF_025152405.1",
    "organism": "[Ruminococcus] lactaris ATCC 29176",
    "title": "[Ruminococcus] lactaris ATCC 29176",
    "description": "na",
    "data type": "Genome sequencing and assembly",
    "organization": "Stanford University",
    "publication": [
        {}
    ],
    "properties": {
        "assembly_accession": "GCF_025152405.1",
        "bioproject": "PRJNA224116",
        "biosample": "SAMN20222711",
        "wgs_master": "na",
        "refseq_category": "reference genome",
        "taxid": "471875",
        "species_taxid": "46228",
        "organism_name": "[Ruminococcus] lactaris ATCC 29176",
        "infraspecific_name": "strain=ATCC 29176",
        "isolate": "na",
        "version_status": "latest",
        "assembly_level": "Complete Genome",
        "release_type": "Major",
        "genome_rep": "Full",
        "seq_rel_date": "2022/09/12",
        "asm_name": "ASM2515240v1",
        "asm_submitter": "Stanford University",
        "gbrs_paired_asm": "GCA_025152405.1",
        "paired_asm_comp": "identical",
        "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/025/152/405/GCF_025152405.1_ASM2515240v1",
        "excluded_from_refseq": "na",
        "relation_to_type_material": "assembly from type material",
        "asm_not_live_date": "na        ",
        "assembly_type": "haploid",
        "group": "bacteria",
        "genome_size": "2733858",
        "genome_size_ungapped": "2733858",
        "gc_percent": "42.500000",
        "replicon_count": "1",
        "scaffold_count": "1",
        "contig_count": "1",
        "annotation_provider": "NCBI RefSeq",
        "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)",
        "annotation_date": "2024-02-29",
        "total_gene_count": "2576",
        "protein_coding_gene_count": "2431",
        "non_coding_gene_count": "73",
        "pubmed_id": "36070752"
    },
    "dbXrefs": [],
    "distribution": null,
    "Download": null,
    "status": "public",
    "visibility": null,
    "dateCreated": "2022-09-12",
    "dateModified": "2022-09-12",
    "datePublished": "2022-09-12",
    "_annotation": {
        "sample_count": 1,
        "sample_organism": [
            "[Ruminococcus] lactaris ATCC 29176"
        ],
        "sample_taxid": [
            "471875"
        ],
        "sample_host_organism": [
            "Homo sapiens"
        ],
        "sample_host_organism_id": [],
        "sample_host_disease": [],
        "sample_host_disease_id": [],
        "sample_host_location": [
            "not applicable"
        ],
        "sample_host_location_id": [],
        "data_size": "0.762 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)": "2733858",
        "Number of Sequences": "1",
        "Longest Sequences (bp)": "2733858",
        "N50 (bp)": "2733858",
        "Gap Ratio (%)": "0.000000",
        "GCcontent (%)": "42.7",
        "Number of CDSs": "2523",
        "Average Protein Length": "314.4",
        "Coding Ratio (%)": "87.1",
        "Number of rRNAs": "15",
        "Number of tRNAs": "54",
        "Number of CRISPRs": "2"
    },
    "has_analysis": true,
    "_dfastqc": {
        "tc_result": [
            {
                "organism_name": "[Ruminococcus] lactaris",
                "strain": "strain=ATCC 29176",
                "accession": "GCA_025152405.1",
                "taxid": 46228,
                "species_taxid": 46228,
                "relation_to_type": "type",
                "validated": true,
                "ani": 100.0,
                "matched_fragments": 910,
                "total_fragments": 911,
                "ani_threshold": 95,
                "status": "conclusive"
            },
            {
                "organism_name": "[Ruminococcus] lactaris",
                "strain": "strain=ATCC 29176",
                "accession": "GCA_000155205.1",
                "taxid": 46228,
                "species_taxid": 46228,
                "relation_to_type": "type",
                "validated": true,
                "ani": 99.9289,
                "matched_fragments": 877,
                "total_fragments": 911,
                "ani_threshold": 95,
                "status": "conclusive"
            },
            {
                "organism_name": "Mediterraneibacter butyricigenes",
                "strain": "strain=KCTC 15684",
                "accession": "GCA_003574295.1",
                "taxid": 2316025,
                "species_taxid": 2316025,
                "relation_to_type": "type",
                "validated": true,
                "ani": 80.162,
                "matched_fragments": 203,
                "total_fragments": 911,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "[Ruminococcus] gnavus",
                "strain": "strain=JCM6515",
                "accession": "GCA_008121495.1",
                "taxid": 33038,
                "species_taxid": 33038,
                "relation_to_type": "suspected-type",
                "validated": true,
                "ani": 79.6021,
                "matched_fragments": 230,
                "total_fragments": 911,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "[Ruminococcus] gnavus",
                "strain": "strain=ATCC 29149",
                "accession": "GCA_002959615.1",
                "taxid": 33038,
                "species_taxid": 33038,
                "relation_to_type": "suspected-type",
                "validated": true,
                "ani": 79.5844,
                "matched_fragments": 223,
                "total_fragments": 911,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "[Ruminococcus] gnavus",
                "strain": "strain=ATCC 29149",
                "accession": "GCA_000169475.1",
                "taxid": 33038,
                "species_taxid": 33038,
                "relation_to_type": "suspected-type",
                "validated": true,
                "ani": 79.3005,
                "matched_fragments": 221,
                "total_fragments": 911,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Jingyaoa shaoxingensis",
                "strain": "strain=NSJ-46",
                "accession": "GCA_014385005.1",
                "taxid": 2763671,
                "species_taxid": 2763671,
                "relation_to_type": "type",
                "validated": true,
                "ani": 78.9621,
                "matched_fragments": 115,
                "total_fragments": 911,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Roseburia faecis",
                "strain": "strain=M72",
                "accession": "GCA_001406815.1",
                "taxid": 301302,
                "species_taxid": 301302,
                "relation_to_type": "type",
                "validated": true,
                "ani": 78.8521,
                "matched_fragments": 101,
                "total_fragments": 911,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Mediterraneibacter massiliensis",
                "strain": "strain=Marseille-P2086",
                "accession": "GCA_001487105.1",
                "taxid": 1720300,
                "species_taxid": 1720300,
                "relation_to_type": "type",
                "validated": true,
                "ani": 78.7739,
                "matched_fragments": 151,
                "total_fragments": 911,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "[Ruminococcus] torques",
                "strain": "strain=ATCC 27756",
                "accession": "GCA_000153925.1",
                "taxid": 33039,
                "species_taxid": 33039,
                "relation_to_type": "type",
                "validated": true,
                "ani": 78.7445,
                "matched_fragments": 184,
                "total_fragments": 911,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Mediterraneibacter catenae",
                "strain": "strain=SW178",
                "accession": "GCA_008691045.1",
                "taxid": 2594882,
                "species_taxid": 2594882,
                "relation_to_type": "type",
                "validated": true,
                "ani": 78.3929,
                "matched_fragments": 178,
                "total_fragments": 911,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Faecalicatena faecalis",
                "strain": "strain=AGMB00832",
                "accession": "GCA_012524165.2",
                "taxid": 2726362,
                "species_taxid": 2726362,
                "relation_to_type": "type",
                "validated": true,
                "ani": 78.3866,
                "matched_fragments": 162,
                "total_fragments": 911,
                "ani_threshold": 95,
                "status": "below_threshold"
            }
        ],
        "cc_result": {
            "completeness": 100.0,
            "contamination": 0.0,
            "strain_heterogeneity": 0.0
        },
        "gtdb_result": [
            {
                "accession": "GCF_000155205.1",
                "gtdb_species": "s__Mediterraneibacter lactaris",
                "ani": 99.9289,
                "matched_fragments": 877,
                "total_fragments": 911,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.88",
                "min_intra_species_ani": "98.36",
                "mean_intra_species_af": "0.88",
                "min_intra_species_af": "0.80",
                "num_clustered_genomes": 12,
                "status": "conclusive"
            },
            {
                "accession": "GCA_001312505.1",
                "gtdb_species": "s__Mediterraneibacter faecis",
                "ani": 80.81,
                "matched_fragments": 330,
                "total_fragments": 911,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "96.72",
                "min_intra_species_ani": "95.03",
                "mean_intra_species_af": "0.76",
                "min_intra_species_af": "0.67",
                "num_clustered_genomes": 61,
                "status": "-"
            },
            {
                "accession": "GCF_003574295.1",
                "gtdb_species": "s__Mediterraneibacter_A butyricigenes",
                "ani": 80.2627,
                "matched_fragments": 203,
                "total_fragments": 911,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter_A",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.15",
                "min_intra_species_ani": "98.07",
                "mean_intra_species_af": "0.82",
                "min_intra_species_af": "0.80",
                "num_clustered_genomes": 5,
                "status": "-"
            },
            {
                "accession": "GCF_001404875.1",
                "gtdb_species": "s__Dorea_A longicatena_B",
                "ani": 80.0688,
                "matched_fragments": 184,
                "total_fragments": 911,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "97.75",
                "min_intra_species_ani": "96.72",
                "mean_intra_species_af": "0.80",
                "min_intra_species_af": "0.69",
                "num_clustered_genomes": 20,
                "status": "-"
            },
            {
                "accession": "GCA_003480425.1",
                "gtdb_species": "s__Schaedlerella sp900066545",
                "ani": 79.7184,
                "matched_fragments": 204,
                "total_fragments": 911,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "97.16",
                "min_intra_species_ani": "96.52",
                "mean_intra_species_af": "0.81",
                "min_intra_species_af": "0.77",
                "num_clustered_genomes": 11,
                "status": "-"
            },
            {
                "accession": "GCF_008121495.1",
                "gtdb_species": "s__Ruminococcus_B gnavus",
                "ani": 79.6436,
                "matched_fragments": 227,
                "total_fragments": 911,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ruminococcus_B",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.58",
                "min_intra_species_ani": "96.13",
                "mean_intra_species_af": "0.80",
                "min_intra_species_af": "0.66",
                "num_clustered_genomes": 102,
                "status": "-"
            },
            {
                "accession": "GCF_003435815.1",
                "gtdb_species": "s__CAG-317 sp000433215",
                "ani": 79.1885,
                "matched_fragments": 195,
                "total_fragments": 911,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-317",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.71",
                "min_intra_species_ani": "98.41",
                "mean_intra_species_af": "0.89",
                "min_intra_species_af": "0.86",
                "num_clustered_genomes": 9,
                "status": "-"
            },
            {
                "accession": "GCA_004556565.1",
                "gtdb_species": "s__Schaedlerella sp004556565",
                "ani": 78.5125,
                "matched_fragments": 140,
                "total_fragments": 911,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella",
                "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_002159505.1",
                "gtdb_species": "s__Mediterraneibacter ornithocaccae",
                "ani": 78.4754,
                "matched_fragments": 182,
                "total_fragments": 911,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "97.93",
                "min_intra_species_ani": "97.52",
                "mean_intra_species_af": "0.83",
                "min_intra_species_af": "0.82",
                "num_clustered_genomes": 3,
                "status": "-"
            },
            {
                "accession": "GCF_002160525.1",
                "gtdb_species": "s__Mediterraneibacter cottocaccae",
                "ani": 78.2991,
                "matched_fragments": 188,
                "total_fragments": 911,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.81",
                "min_intra_species_ani": "98.78",
                "mean_intra_species_af": "0.88",
                "min_intra_species_af": "0.86",
                "num_clustered_genomes": 3,
                "status": "-"
            },
            {
                "accession": "GCF_900120155.1",
                "gtdb_species": "s__Mediterraneibacter sp900120155",
                "ani": 78.2612,
                "matched_fragments": 166,
                "total_fragments": 911,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter",
                "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_900544395.1",
                "gtdb_species": "s__Ruminococcus_B sp900544395",
                "ani": 78.1227,
                "matched_fragments": 171,
                "total_fragments": 911,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ruminococcus_B",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.21",
                "min_intra_species_ani": "99.21",
                "mean_intra_species_af": "0.88",
                "min_intra_species_af": "0.88",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCA_904377845.1",
                "gtdb_species": "s__Mediterraneibacter sp904377845",
                "ani": 77.7529,
                "matched_fragments": 181,
                "total_fragments": 911,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter",
                "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_019119745.1",
                "gtdb_species": "s__Mediterraneibacter gallistercoris",
                "ani": 77.7214,
                "matched_fragments": 140,
                "total_fragments": 911,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter",
                "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_900550865.1",
                "gtdb_species": "s__Dorea_A sp900550865",
                "ani": 77.6905,
                "matched_fragments": 157,
                "total_fragments": 911,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_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": "GCA_019119265.1",
                "gtdb_species": "s__Mediterraneibacter intestinigallinarum",
                "ani": 77.688,
                "matched_fragments": 159,
                "total_fragments": 911,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter",
                "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_019119995.1",
                "gtdb_species": "s__Mediterraneibacter faecavium",
                "ani": 77.6816,
                "matched_fragments": 168,
                "total_fragments": 911,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.90",
                "min_intra_species_ani": "99.90",
                "mean_intra_species_af": "0.92",
                "min_intra_species_af": "0.92",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCA_019115385.1",
                "gtdb_species": "s__Mediterraneibacter avicola",
                "ani": 77.509,
                "matched_fragments": 144,
                "total_fragments": 911,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.73",
                "min_intra_species_ani": "98.73",
                "mean_intra_species_af": "0.86",
                "min_intra_species_af": "0.86",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCA_905209865.1",
                "gtdb_species": "s__Mediterraneibacter sp900752395",
                "ani": 77.4508,
                "matched_fragments": 154,
                "total_fragments": 911,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.94",
                "min_intra_species_ani": "99.94",
                "mean_intra_species_af": "0.94",
                "min_intra_species_af": "0.94",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCA_019120275.1",
                "gtdb_species": "s__Mediterraneibacter excrementavium",
                "ani": 77.3763,
                "matched_fragments": 144,
                "total_fragments": 911,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter",
                "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_019119675.1",
                "gtdb_species": "s__Mediterraneibacter faecipullorum",
                "ani": 77.1892,
                "matched_fragments": 194,
                "total_fragments": 911,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter",
                "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": null,
        "cell_length": null,
        "doubling_h": null,
        "growth_tmp": null,
        "optimum_tmp": null,
        "optimum_ph": null,
        "genome_size": null,
        "gc_content": null,
        "coding_genes": null,
        "rRNA16S_genes": null,
        "tRNA_genes": null,
        "gram_stain": null,
        "sporulation": null,
        "motility": null,
        "range_salinity": null,
        "facultative_respiration": null,
        "anaerobic_respiration": null,
        "aerobic_respiration": null,
        "mesophilic_range_tmp": null,
        "thermophilic_range_tmp": null,
        "psychrophilic_range_tmp": null,
        "bacillus_cell_shape": null,
        "coccus_cell_shape": null,
        "filament_cell_shape": null,
        "coccobacillus_cell_shape": null,
        "vibrio_cell_shape": null,
        "spiral_cell_shape": null
    },
    "_genome_taxon": [
        "[Ruminococcus]",
        "lactaris",
        "ATCC",
        "29176"
    ],
    "quality": 5,
    "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f"
}