{ "type": "genome", "identifier": "GCF_004363305.1", "organism": "Marinomonas communis", "title": "Marinomonas communis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004363305.1", "bioproject": "PRJNA224116", "biosample": "SAMN08776293", "wgs_master": "SNZA00000000.1", "refseq_category": "reference genome", "taxid": "28254", "species_taxid": "28254", "organism_name": "Marinomonas communis", "infraspecific_name": "strain=DSM 5604", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/03/22", "asm_name": "ASM436330v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_004363305.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/363/305/GCF_004363305.1_ASM436330v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3854463", "genome_size_ungapped": "3854081", "gc_percent": "46.000000", "replicon_count": "0", "scaffold_count": "11", "contig_count": "11", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004363305.1-RS_2024_04_27", "annotation_date": "2024-04-27", "total_gene_count": "3613", "protein_coding_gene_count": "3520", "non_coding_gene_count": "84", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-03-22", "dateModified": "2019-03-22", "datePublished": "2019-03-22", "_annotation": { "sample_count": 1, "sample_organism": [ "Marinomonas communis" ], "sample_taxid": [ "28254" ], "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": "1.102 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)": "3854463", "Number of Sequences": "11", "Longest Sequences (bp)": "1371506", "N50 (bp)": "575095", "Gap Ratio (%)": "0.009911", "GCcontent (%)": "45.8", "Number of CDSs": "3529", "Average Protein Length": "328.5", "Coding Ratio (%)": "90.2", "Number of rRNAs": "2", "Number of tRNAs": "69", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Marinomonas communis", "strain": "strain=DSM 5604", "accession": "GCA_004363305.1", "taxid": 28254, "species_taxid": 28254, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1279, "total_fragments": 1280, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Marinomonas aquimarina", "strain": "strain=CECT 5080", "accession": "GCA_900089755.1", "taxid": 295068, "species_taxid": 295068, "relation_to_type": "type", "validated": true, "ani": 81.9411, "matched_fragments": 545, "total_fragments": 1280, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marinomonas fungiae", "strain": "strain=JCM 18476", "accession": "GCA_001517305.1", "taxid": 1137284, "species_taxid": 1137284, "relation_to_type": "type", "validated": true, "ani": 81.9198, "matched_fragments": 591, "total_fragments": 1280, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marinomonas fungiae", "strain": "strain=JCM 18476", "accession": "GCA_001418205.1", "taxid": 1137284, "species_taxid": 1137284, "relation_to_type": "type", "validated": true, "ani": 81.9181, "matched_fragments": 591, "total_fragments": 1280, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marinomonas aquimarina", "strain": "strain=11SM4", "accession": "GCA_001639695.1", "taxid": 295068, "species_taxid": 295068, "relation_to_type": "type", "validated": true, "ani": 81.8967, "matched_fragments": 545, "total_fragments": 1280, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marinomonas ostreistagni", "strain": "strain=UST010306-043", "accession": "GCA_016888445.1", "taxid": 359209, "species_taxid": 359209, "relation_to_type": "type", "validated": true, "ani": 80.7681, "matched_fragments": 419, "total_fragments": 1280, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marinomonas gallaica", "strain": "strain=Cmf 17.2", "accession": "GCA_001639745.1", "taxid": 1806667, "species_taxid": 1806667, "relation_to_type": "type", "validated": true, "ani": 80.2311, "matched_fragments": 508, "total_fragments": 1280, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marinomonas pollencensis", "strain": "strain=CECT 7375", "accession": "GCA_003387375.1", "taxid": 491954, "species_taxid": 491954, "relation_to_type": "type", "validated": true, "ani": 78.8093, "matched_fragments": 178, "total_fragments": 1280, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marinomonas profundimaris", "strain": "strain=D104", "accession": "GCA_000508165.1", "taxid": 1208321, "species_taxid": 1208321, "relation_to_type": "type", "validated": true, "ani": 77.9831, "matched_fragments": 171, "total_fragments": 1280, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004363305.1", "gtdb_species": "s__Marinomonas communis", "ani": 100.0, "matched_fragments": 1279, "total_fragments": 1280, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.16", "min_intra_species_ani": "97.04", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.87", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_016461785.1", "gtdb_species": "s__Marinomonas ostreistagni_A", "ani": 89.3393, "matched_fragments": 936, "total_fragments": 1280, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas", "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_001418205.1", "gtdb_species": "s__Marinomonas fungiae", "ani": 81.9285, "matched_fragments": 591, "total_fragments": 1280, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900089755.1", "gtdb_species": "s__Marinomonas aquimarina", "ani": 81.9236, "matched_fragments": 547, "total_fragments": 1280, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_016888445.1", "gtdb_species": "s__Marinomonas ostreistagni", "ani": 80.7671, "matched_fragments": 419, "total_fragments": 1280, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas", "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_001639745.1", "gtdb_species": "s__Marinomonas gallaica", "ani": 80.2311, "matched_fragments": 508, "total_fragments": 1280, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.95", "min_intra_species_ani": "96.94", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_003387375.1", "gtdb_species": "s__Marinomonas pollencensis", "ani": 78.7933, "matched_fragments": 176, "total_fragments": 1280, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas", "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_000214215.1", "gtdb_species": "s__Marinomonas posidonica", "ani": 78.4066, "matched_fragments": 177, "total_fragments": 1280, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas", "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_003259225.1", "gtdb_species": "s__Marinomonas arctica", "ani": 78.3017, "matched_fragments": 162, "total_fragments": 1280, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000508165.1", "gtdb_species": "s__Marinomonas profundimaris", "ani": 77.9831, "matched_fragments": 171, "total_fragments": 1280, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas", "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": -0.302, "cell_length": 0.0, "doubling_h": null, "growth_tmp": 26.5, "optimum_tmp": 30.0, "optimum_ph": 7.0, "genome_size": 3854463.0, "gc_content": 42.6, "coding_genes": 4110.0, "rRNA16S_genes": 7.0, "tRNA_genes": 80.0, "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": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "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": [ "Marinomonas", "communis" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }