{ "type": "genome", "identifier": "GCA_945870545.1", "organism": "Akkermansia muciniphila", "title": "Akkermansia muciniphila", "description": "derived from metagenome; genome length too small", "data type": "Genome sequencing and assembly", "organization": "BIOLOGY CENTRE ASCR, V.V.I., INSTITUTE OF HYDROBIO", "publication": [ {} ], "properties": { "assembly_accession": "GCA_945870545.1", "bioproject": "PRJEB35640", "biosample": "SAMEA110379314", "wgs_master": "CAMBTF000000000.1", "refseq_category": "na", "taxid": "239935", "species_taxid": "239935", "organism_name": "Akkermansia muciniphila", "infraspecific_name": "", "isolate": "AH-24oct19-148", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/09/09", "asm_name": "AH-24oct19-148", "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/945/870/545/GCA_945870545.1_AH-24oct19-148", "excluded_from_refseq": "derived from metagenome; genome length too small", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-09-09", "dateModified": "2022-09-09", "datePublished": "2022-09-09", "_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": [ "Austria" ], "sample_host_location_id": [], "data_size": "0.558 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 70.83, "contamination": 0.38, "strain_heterogeneity": 100.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "1967853", "Number of Sequences": "317", "Longest Sequences (bp)": "31031", "N50 (bp)": "6751", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "59.7", "Number of CDSs": "1541", "Average Protein Length": "302.5", "Coding Ratio (%)": "71.1", "Number of rRNAs": "0", "Number of tRNAs": "31", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Luteolibacter yonseiensis", "strain": "strain=JCM 18052", "accession": "GCA_016595465.1", "taxid": 1144680, "species_taxid": 1144680, "relation_to_type": "type", "validated": true, "ani": 77.709, "matched_fragments": 156, "total_fragments": 522, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Luteolibacter ambystomatis", "strain": "strain=32A", "accession": "GCA_018137965.1", "taxid": 2824561, "species_taxid": 2824561, "relation_to_type": "type", "validated": true, "ani": 77.5576, "matched_fragments": 137, "total_fragments": 522, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Luteolibacter luteus", "strain": "strain=G-1-1-1", "accession": "GCA_012913485.1", "taxid": 2728835, "species_taxid": 2728835, "relation_to_type": "type", "validated": true, "ani": 77.2227, "matched_fragments": 90, "total_fragments": 522, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Luteolibacter pohnpeiensis", "strain": "strain=KCTC 22041", "accession": "GCA_016595435.1", "taxid": 454153, "species_taxid": 454153, "relation_to_type": "type", "validated": true, "ani": 77.0933, "matched_fragments": 59, "total_fragments": 522, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Haloferula rosea", "strain": "strain=KCTC 22201", "accession": "GCA_016595525.1", "taxid": 490093, "species_taxid": 490093, "relation_to_type": "type", "validated": true, "ani": 76.9432, "matched_fragments": 77, "total_fragments": 522, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 70.83, "contamination": 0.38, "strain_heterogeneity": 100.0 }, "gtdb_result": [ { "accession": "GCA_018402445.1", "gtdb_species": "s__Luteolibacter sp018402445", "ani": 85.8662, "matched_fragments": 380, "total_fragments": 522, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter", "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_017798145.1", "gtdb_species": "s__Luteolibacter sp017798145", "ani": 80.773, "matched_fragments": 316, "total_fragments": 522, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter", "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_905478925.1", "gtdb_species": "s__Luteolibacter sp905478925", "ani": 79.3495, "matched_fragments": 257, "total_fragments": 522, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.95", "min_intra_species_ani": "97.95", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_905182475.1", "gtdb_species": "s__Luteolibacter sp905182475", "ani": 78.4338, "matched_fragments": 204, "total_fragments": 522, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.83", "min_intra_species_ani": "99.83", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_003820635.1", "gtdb_species": "s__Luteolibacter sp003820635", "ani": 78.2343, "matched_fragments": 161, "total_fragments": 522, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter", "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_014904755.1", "gtdb_species": "s__Haloferula sp014904755", "ani": 77.8014, "matched_fragments": 137, "total_fragments": 522, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula", "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_016595465.1", "gtdb_species": "s__Luteolibacter yonseiensis", "ani": 77.709, "matched_fragments": 156, "total_fragments": 522, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter", "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_903919975.1", "gtdb_species": "s__Luteolibacter sp903919975", "ani": 77.5873, "matched_fragments": 109, "total_fragments": 522, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.90", "min_intra_species_ani": "99.84", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_016871685.1", "gtdb_species": "s__Luteolibacter sp016871685", "ani": 77.3576, "matched_fragments": 75, "total_fragments": 522, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter", "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_903908495.1", "gtdb_species": "s__Luteolibacter sp903908495", "ani": 77.2385, "matched_fragments": 95, "total_fragments": 522, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter", "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_903906515.1", "gtdb_species": "s__Luteolibacter sp903906515", "ani": 77.2134, "matched_fragments": 112, "total_fragments": 522, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.85", "min_intra_species_ani": "99.81", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_017301995.1", "gtdb_species": "s__Luteolibacter sp017301995", "ani": 77.1825, "matched_fragments": 115, "total_fragments": 522, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter", "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__Verrucomicrobiales", "f__Akkermansiaceae", "g__Luteolibacter", "s__Luteolibacter muciniphilus_A" ], "_genome_taxon": [ "Akkermansia", "muciniphila", "d__Bacteria", "p__Verrucomicrobiota", "c__Verrucomicrobiae", "o__Verrucomicrobiales", "f__Akkermansiaceae", "g__Luteolibacter", "s__Luteolibacter muciniphilus_A", "Bacteria", "Verrucomicrobiota", "Verrucomicrobiae", "Verrucomicrobiales", "Akkermansiaceae", "Luteolibacter", "Luteolibacter", "muciniphilus", "A" ], "_meo": [ { "id": "MEO_0000038", "label": "freshwater" }, { "id": "MEO_0000024", "label": "lake" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }