{ "type": "genome", "identifier": "GCF_003014615.1", "organism": "Marinobacterium halophilum", "title": "Marinobacterium halophilum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003014615.1", "bioproject": "PRJNA224116", "biosample": "SAMN07621472", "wgs_master": "PYGI00000000.1", "refseq_category": "reference genome", "taxid": "267374", "species_taxid": "267374", "organism_name": "Marinobacterium halophilum", "infraspecific_name": "strain=DSM 17586", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/03/23", "asm_name": "ASM301461v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_003014615.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/014/615/GCF_003014615.1_ASM301461v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3653655", "genome_size_ungapped": "3653180", "gc_percent": "56.000000", "replicon_count": "0", "scaffold_count": "47", "contig_count": "47", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003014615.1-RS_2024_05_03", "annotation_date": "2024-05-03", "total_gene_count": "3438", "protein_coding_gene_count": "3333", "non_coding_gene_count": "78", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-03-23", "dateModified": "2018-03-23", "datePublished": "2018-03-23", "_annotation": { "sample_count": 1, "sample_organism": [ "Marinobacterium halophilum" ], "sample_taxid": [ "267374" ], "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": "1.038 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)": "3653655", "Number of Sequences": "47", "Longest Sequences (bp)": "280933", "N50 (bp)": "130350", "Gap Ratio (%)": "0.013001", "GCcontent (%)": "56.0", "Number of CDSs": "3381", "Average Protein Length": "326.7", "Coding Ratio (%)": "90.7", "Number of rRNAs": "3", "Number of tRNAs": "73", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Marinobacterium halophilum", "strain": "strain=DSM 17586", "accession": "GCA_003014615.1", "taxid": 267374, "species_taxid": 267374, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1192, "total_fragments": 1195, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Marinobacterium stanieri", "strain": "strain=DSM 7027", "accession": "GCA_900155945.1", "taxid": 49186, "species_taxid": 49186, "relation_to_type": "type", "validated": true, "ani": 80.6036, "matched_fragments": 605, "total_fragments": 1195, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marinobacterium alkalitolerans", "strain": "strain=AK62", "accession": "GCA_017776525.1", "taxid": 1542925, "species_taxid": 1542925, "relation_to_type": "type", "validated": true, "ani": 80.4032, "matched_fragments": 534, "total_fragments": 1195, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marinobacterium georgiense", "strain": "strain=DSM 11526", "accession": "GCA_900107855.1", "taxid": 48076, "species_taxid": 48076, "relation_to_type": "type", "validated": true, "ani": 80.3324, "matched_fragments": 504, "total_fragments": 1195, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marinobacterium ramblicola", "strain": "strain=D7", "accession": "GCA_019084545.1", "taxid": 2849041, "species_taxid": 2849041, "relation_to_type": "type", "validated": true, "ani": 78.5423, "matched_fragments": 319, "total_fragments": 1195, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marinobacterium zhoushanense", "strain": "strain=CGMCC 1.15341", "accession": "GCA_014641945.1", "taxid": 1679163, "species_taxid": 1679163, "relation_to_type": "type", "validated": true, "ani": 78.4697, "matched_fragments": 306, "total_fragments": 1195, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marinobacterium litorale", "strain": "strain=DSM 23545", "accession": "GCA_000428985.1", "taxid": 404770, "species_taxid": 404770, "relation_to_type": "type", "validated": true, "ani": 78.3878, "matched_fragments": 227, "total_fragments": 1195, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marinobacterium arenosum", "strain": "strain=CAU 1594", "accession": "GCA_019795155.1", "taxid": 2862496, "species_taxid": 2862496, "relation_to_type": "type", "validated": true, "ani": 78.2982, "matched_fragments": 269, "total_fragments": 1195, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marinobacterium aestuarii", "strain": "strain=ST58-10", "accession": "GCA_001651805.1", "taxid": 1821621, "species_taxid": 1821621, "relation_to_type": "type", "validated": true, "ani": 77.8258, "matched_fragments": 239, "total_fragments": 1195, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nitrincola iocasae", "strain": "strain=KXZD1103", "accession": "GCA_008727795.1", "taxid": 2614693, "species_taxid": 2614693, "relation_to_type": "type", "validated": true, "ani": 77.8148, "matched_fragments": 117, "total_fragments": 1195, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marinobacterium rhizophilum", "strain": "strain=DSM 18822", "accession": "GCA_000378045.1", "taxid": 420402, "species_taxid": 420402, "relation_to_type": "type", "validated": true, "ani": 77.7573, "matched_fragments": 235, "total_fragments": 1195, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marinobacterium profundum", "strain": "strain=PAMC 27536", "accession": "GCA_001528745.1", "taxid": 1714300, "species_taxid": 1714300, "relation_to_type": "type", "validated": true, "ani": 77.5851, "matched_fragments": 219, "total_fragments": 1195, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nitrincola lacisaponensis", "strain": "strain=4CA", "accession": "GCA_000691225.1", "taxid": 267850, "species_taxid": 267850, "relation_to_type": "type", "validated": true, "ani": 77.5656, "matched_fragments": 144, "total_fragments": 1195, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stutzerimonas frequens", "strain": "strain=DNSP21", "accession": "GCA_002890935.1", "taxid": 2968969, "species_taxid": 2968969, "relation_to_type": "type", "validated": true, "ani": 76.6194, "matched_fragments": 116, "total_fragments": 1195, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stutzerimonas frequens", "strain": "strain=FDAARGOS_877", "accession": "GCA_016028515.1", "taxid": 2968969, "species_taxid": 2968969, "relation_to_type": "type", "validated": true, "ani": 76.5869, "matched_fragments": 116, "total_fragments": 1195, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stutzerimonas frequens", "strain": "strain=DNSP21", "accession": "GCA_024448335.1", "taxid": 2968969, "species_taxid": 2968969, "relation_to_type": "type", "validated": true, "ani": 76.4569, "matched_fragments": 114, "total_fragments": 1195, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Larsenimonas suaedae", "strain": "strain=DSM 22428", "accession": "GCA_023712105.1", "taxid": 1851019, 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"mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_013868415.1", "gtdb_species": "s__Marinobacterium sp013868415", "ani": 80.4268, "matched_fragments": 578, "total_fragments": 1195, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium", "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_017776525.1", "gtdb_species": "s__Marinobacterium alkalitolerans", "ani": 80.4066, "matched_fragments": 534, "total_fragments": 1195, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium", "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_900107855.1", "gtdb_species": "s__Marinobacterium georgiense", "ani": 80.3107, "matched_fragments": 504, "total_fragments": 1195, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.23", "min_intra_species_ani": "97.23", "mean_intra_species_af": "0.75", "min_intra_species_af": "0.75", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_019084545.1", "gtdb_species": "s__Marinobacterium sp019084545", "ani": 78.5538, "matched_fragments": 316, "total_fragments": 1195, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium", "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_014641945.1", "gtdb_species": "s__Marinobacterium zhoushanense", "ani": 78.4334, "matched_fragments": 308, "total_fragments": 1195, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium", "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_000428985.1", "gtdb_species": "s__Marinobacterium litorale", "ani": 78.3512, "matched_fragments": 228, "total_fragments": 1195, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.80", "min_intra_species_ani": "97.80", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_907163115.1", "gtdb_species": "s__Pseudomonas_A stutzeri_AL", "ani": 76.6524, "matched_fragments": 113, "total_fragments": 1195, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.05", "min_intra_species_ani": "96.55", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.91", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_003205815.1", "gtdb_species": "s__Pseudomonas_A sp003205815", "ani": 76.5892, "matched_fragments": 121, "total_fragments": 1195, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.18", "min_intra_species_ani": "96.58", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.87", "num_clustered_genomes": 27, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.302, "cell_length": 0.322, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": 30.407, "optimum_ph": 7.541, "genome_size": 3653655.0, "gc_content": 58.65, "coding_genes": 4429.0, "rRNA16S_genes": 6.0, "tRNA_genes": 83.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "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": [ "Marinobacterium", "halophilum" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }