{ "type": "genome", "identifier": "GCA_945873715.1", "organism": "Akkermansia muciniphila", "title": "Akkermansia muciniphila", "description": "derived from metagenome; genome length too large", "data type": "Genome sequencing and assembly", "organization": "BIOLOGY CENTRE ASCR, V.V.I., INSTITUTE OF HYDROBIO", "publication": [ {} ], "properties": { "assembly_accession": "GCA_945873715.1", "bioproject": "PRJEB35640", "biosample": "SAMEA110379822", "wgs_master": "CAMCFL000000000.1", "refseq_category": "na", "taxid": "239935", "species_taxid": "239935", "organism_name": "Akkermansia muciniphila", "infraspecific_name": "", "isolate": "MH-21oct19-97", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/09/10", "asm_name": "MH-21oct19-97", "submitter": "BIOLOGY CENTRE ASCR, V.V.I., INSTITUTE OF HYDROBIO", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/945/873/715/GCA_945873715.1_MH-21oct19-97", "excluded_from_refseq": "derived from metagenome; genome length too large", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-09-10", "dateModified": "2022-09-10", "datePublished": "2022-09-10", "_annotation": { "sample_count": 1, "sample_organism": [ "Akkermansia muciniphila" ], "sample_taxid": [ "239935" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Czech Republic" ], "sample_host_location_id": [], "data_size": "1.005 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 56.77, "contamination": 4.17, "strain_heterogeneity": 100.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "3596346", "Number of Sequences": "573", "Longest Sequences (bp)": "28901", "N50 (bp)": "6809", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "64.7", "Number of CDSs": "2343", "Average Protein Length": "335.5", "Coding Ratio (%)": "65.6", "Number of rRNAs": "0", "Number of tRNAs": "30", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [], "cc_result": { "completeness": 56.77, "contamination": 4.17, "strain_heterogeneity": 100.0 }, "gtdb_result": [ { "accession": "GCA_903842505.1", "gtdb_species": "s__UBA6176 sp903842505", "ani": 79.3508, "matched_fragments": 446, "total_fragments": 968, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__UBA6176", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.72", "min_intra_species_ani": "99.54", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.90", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_002422905.1", "gtdb_species": "s__UBA6176 sp002422905", "ani": 77.8466, "matched_fragments": 298, "total_fragments": 968, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__UBA6176", "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_903880005.1", "gtdb_species": "s__UBA6176 sp903880005", "ani": 77.3831, "matched_fragments": 196, "total_fragments": 968, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__UBA6176", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.64", "min_intra_species_ani": "99.45", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.88", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_016871615.1", "gtdb_species": "s__SXXZ01 sp016871615", "ani": 77.0563, "matched_fragments": 148, "total_fragments": 968, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__SXXZ01", "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_008933025.1", "gtdb_species": "s__UBA6176 sp008933025", "ani": 76.9776, "matched_fragments": 205, "total_fragments": 968, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__UBA6176", "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_903925515.1", "gtdb_species": "s__UBA6176 sp903925515", "ani": 76.8961, "matched_fragments": 164, "total_fragments": 968, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__UBA6176", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.40", "min_intra_species_ani": "99.34", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.83", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_903922605.1", "gtdb_species": "s__CAIVQB01 sp903922605", "ani": 76.8216, "matched_fragments": 145, "total_fragments": 968, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__CAIVQB01", "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_903907995.1", "gtdb_species": "s__CAIVQB01 sp903907995", "ani": 76.7518, "matched_fragments": 129, "total_fragments": 968, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__CAIVQB01", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.97", "min_intra_species_ani": "99.94", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.95", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCA_903910585.1", "gtdb_species": "s__CAIWAH01 sp903910585", "ani": 76.6076, "matched_fragments": 148, "total_fragments": 968, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__CAIWAH01", "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_016871805.1", "gtdb_species": "s__UBA9464 sp016871805", "ani": 76.4962, "matched_fragments": 124, "total_fragments": 968, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__UBA9464", "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_903854475.1", "gtdb_species": "s__SXXZ01 sp903854475", "ani": 76.2215, "matched_fragments": 76, "total_fragments": 968, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__SXXZ01", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.91", "min_intra_species_ani": "98.91", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_017309115.1", "gtdb_species": "s__UBA9464 sp017309115", "ani": 76.2103, "matched_fragments": 107, "total_fragments": 968, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__UBA9464", "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_017302195.1", "gtdb_species": "s__UBA9464 sp017302195", "ani": 76.2098, "matched_fragments": 123, "total_fragments": 968, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__UBA9464", "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_009773355.1", "gtdb_species": "s__SXTU01 sp009773355", "ani": 76.0279, "matched_fragments": 108, "total_fragments": 968, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__SXTU01;g__SXTU01", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.97", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_016871715.1", "gtdb_species": "s__VHCO01 sp016871715", "ani": 75.6121, "matched_fragments": 66, "total_fragments": 968, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__J093;g__VHCO01", "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": -0.222, "cell_length": null, "doubling_h": null, "growth_tmp": 37.0, "optimum_tmp": 37.0, "optimum_ph": null, "genome_size": 2687294.429, "gc_content": 55.767, "coding_genes": 2234.25, "rRNA16S_genes": 3.0, "tRNA_genes": 52.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 1.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 1.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_gtdb_taxon": [ "d__Bacteria", "p__Verrucomicrobiota", "c__Verrucomicrobiae", "o__Limisphaerales", "f__UBA9464", "g__UBA6176", "s__UBA6176 sp945873715" ], "_genome_taxon": [ "Akkermansia", "muciniphila", "d__Bacteria", "p__Verrucomicrobiota", "c__Verrucomicrobiae", "o__Limisphaerales", "f__UBA9464", "g__UBA6176", "s__UBA6176 sp945873715", "Bacteria", "Verrucomicrobiota", "Verrucomicrobiae", "Limisphaerales", "UBA9464", "UBA6176", "UBA6176", "sp945873715" ], "_meo": [ { "id": "MEO_0000038", "label": "freshwater" }, { "id": "MEO_0000024", "label": "lake" } ], "quality": 2, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f" }