{ "type": "genome", "identifier": "GCF_017873415.1", "organism": "Methanolobus bombayensis", "title": "Methanolobus bombayensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_017873415.1", "bioproject": "PRJNA224116", "biosample": "SAMN18247048", "wgs_master": "JAGGKD000000000.1", "refseq_category": "reference genome", "taxid": "38023", "species_taxid": "38023", "organism_name": "Methanolobus bombayensis", "infraspecific_name": "strain=DSM 7082", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/04/08", "asm_name": "ASM1787341v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_017873415.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/017/873/415/GCF_017873415.1_ASM1787341v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "archaea", "genome_size": "3122090", "genome_size_ungapped": "3122090", "gc_percent": "39.500000", "replicon_count": "0", "scaffold_count": "35", "contig_count": "35", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_017873415.1-RS_2024_04_29", "annotation_date": "2024-04-29", "total_gene_count": "2932", "protein_coding_gene_count": "2857", "non_coding_gene_count": "54", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-04-08", "dateModified": "2021-04-08", "datePublished": "2021-04-08", "_annotation": { "sample_count": 1, "sample_organism": [ "Methanolobus bombayensis" ], "sample_taxid": [ "38023" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "0.883 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "3122090", "Number of Sequences": "35", "Longest Sequences (bp)": "475351", "N50 (bp)": "270112", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "39.7", "Number of CDSs": "2873", "Average Protein Length": "313.9", "Coding Ratio (%)": "86.6", "Number of rRNAs": "2", "Number of tRNAs": "43", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Methanolobus bombayensis", "strain": "strain=DSM 7082", "accession": "GCA_017873415.1", "taxid": 38023, "species_taxid": 38023, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1019, "total_fragments": 1023, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Methanolobus tindarius", "strain": "strain=DSM 2278", "accession": "GCA_000504205.1", "taxid": 2221, "species_taxid": 2221, "relation_to_type": "type", "validated": true, "ani": 83.9359, "matched_fragments": 688, "total_fragments": 1023, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methanolobus vulcani", "strain": "strain=PL 12/M", "accession": "GCA_900100715.1", "taxid": 38026, "species_taxid": 38026, "relation_to_type": "type", "validated": true, "ani": 83.8829, "matched_fragments": 707, "total_fragments": 1023, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methanolobus profundi", "strain": "strain=Mob M", "accession": "GCA_900114835.1", "taxid": 487685, "species_taxid": 487685, "relation_to_type": "type", "validated": true, "ani": 80.4803, "matched_fragments": 491, "total_fragments": 1023, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methanolobus psychrotolerans", "strain": "strain=YSF-03", "accession": "GCA_002243045.1", "taxid": 1874706, "species_taxid": 1874706, "relation_to_type": "type", "validated": true, "ani": 79.3062, "matched_fragments": 447, "total_fragments": 1023, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methanococcoides vulcani", "strain": "", "accession": "GCA_900773955.1", "taxid": 1353158, "species_taxid": 1353158, "relation_to_type": "type", "validated": true, "ani": 76.9289, "matched_fragments": 84, "total_fragments": 1023, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_017873415.1", "gtdb_species": "s__Methanolobus bombayensis", "ani": 100.0, "matched_fragments": 1019, "total_fragments": 1023, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanolobus", "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": "conclusive" }, { "accession": "GCF_000504205.1", "gtdb_species": "s__Methanolobus tindarius", "ani": 83.9354, "matched_fragments": 687, "total_fragments": 1023, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanolobus", "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_900100715.1", "gtdb_species": "s__Methanolobus vulcani", "ani": 83.8854, "matched_fragments": 705, "total_fragments": 1023, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanolobus", "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_006546655.1", "gtdb_species": "s__Methanolobus vulcani_A", "ani": 83.651, "matched_fragments": 664, "total_fragments": 1023, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanolobus", "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_900114835.1", "gtdb_species": "s__Methanolobus profundi", "ani": 80.4677, "matched_fragments": 491, "total_fragments": 1023, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanolobus", "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_002507205.1", "gtdb_species": "s__Methanolobus sp002507205", "ani": 79.6205, "matched_fragments": 395, "total_fragments": 1023, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanolobus", "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": 0.0, "cell_length": 0.176, "doubling_h": 0.666, "growth_tmp": 35.9, "optimum_tmp": 37.0, "optimum_ph": 7.2, "genome_size": 3027553.5, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": null, "motility": 0.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 1.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": 0.0, "coccus_cell_shape": 1.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Methanolobus", "bombayensis" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }