{ "type": "genome", "identifier": "GCF_016906995.1", "organism": "Spongiibacter marinus", "title": "Spongiibacter marinus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_016906995.1", "bioproject": "PRJNA224116", "biosample": "SAMN17620324", "wgs_master": "JAFBBD000000000.1", "refseq_category": "reference genome", "taxid": "354246", "species_taxid": "354246", "organism_name": "Spongiibacter marinus", "infraspecific_name": "strain=DSM 17750", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/02/19", "asm_name": "ASM1690699v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_016906995.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/016/906/995/GCF_016906995.1_ASM1690699v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3572376", "genome_size_ungapped": "3572186", "gc_percent": "55.500000", "replicon_count": "0", "scaffold_count": "29", "contig_count": "29", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_016906995.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "3399", "protein_coding_gene_count": "3330", "non_coding_gene_count": "47", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-02-19", "dateModified": "2021-02-19", "datePublished": "2021-02-19", "_annotation": { "sample_count": 1, "sample_organism": [ "Spongiibacter marinus" ], "sample_taxid": [ "354246" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Norway: Sula, Sula Ridge" ], "sample_host_location_id": [], "data_size": "1.018 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)": "3572376", "Number of Sequences": "29", "Longest Sequences (bp)": "531766", "N50 (bp)": "392873", "Gap Ratio (%)": "0.005319", "GCcontent (%)": "55.5", "Number of CDSs": "3365", "Average Protein Length": "321.7", "Coding Ratio (%)": "90.9", "Number of rRNAs": "3", "Number of tRNAs": "39", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Spongiibacter tropicus", "strain": "strain=DSM 19543", "accession": "GCA_000420325.1", "taxid": 454602, "species_taxid": 454602, "relation_to_type": "type", "validated": true, "ani": 79.6843, "matched_fragments": 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"status": "below_threshold" }, { "organism_name": "Spongiibacter pelagi", "strain": "strain=KMU-158", "accession": "GCA_014705705.1", "taxid": 2760804, "species_taxid": 2760804, "relation_to_type": "type", "validated": true, "ani": 78.235, "matched_fragments": 195, "total_fragments": 1177, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halioglobus japonicus", "strain": "strain=NBRC 107739", "accession": "GCA_001983995.1", "taxid": 930805, "species_taxid": 930805, "relation_to_type": "type", "validated": true, "ani": 76.7153, "matched_fragments": 71, "total_fragments": 1177, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas proteolytica", "strain": "strain=CCUG 51515T", "accession": "GCA_008692865.1", "taxid": 219574, "species_taxid": 219574, "relation_to_type": "type", "validated": true, "ani": 76.7072, "matched_fragments": 52, "total_fragments": 1177, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas proteolytica", "strain": "strain=DSM 15321", "accession": "GCA_007858275.1", "taxid": 219574, "species_taxid": 219574, "relation_to_type": "type", "validated": true, "ani": 76.6736, "matched_fragments": 52, "total_fragments": 1177, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas brassicae", "strain": "strain=MAFF 212427", "accession": "GCA_010671725.1", "taxid": 2708063, "species_taxid": 2708063, "relation_to_type": "type", "validated": true, "ani": 76.0378, "matched_fragments": 54, "total_fragments": 1177, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_016906995.1", "gtdb_species": "s__Spongiibacter marinus", "ani": 100.0, "matched_fragments": 1175, "total_fragments": 1177, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.69", "min_intra_species_ani": "97.65", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.86", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_000422345.1", "gtdb_species": "s__Spongiibacter marinus_A", "ani": 94.5988, "matched_fragments": 987, "total_fragments": 1177, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter", "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_000420325.1", "gtdb_species": "s__Spongiibacter tropicus", "ani": 79.6843, "matched_fragments": 403, "total_fragments": 1177, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.00", "min_intra_species_ani": "97.89", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.88", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_012272835.1", "gtdb_species": "s__Spongiibacter sp012272835", "ani": 78.5865, "matched_fragments": 264, "total_fragments": 1177, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter", "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_016132545.1", "gtdb_species": "s__CSC3-9 sp016132545", "ani": 78.5422, "matched_fragments": 232, "total_fragments": 1177, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__CSC3-9", "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_014705705.1", "gtdb_species": "s__KMU-158 sp014705705", "ani": 78.2274, "matched_fragments": 196, "total_fragments": 1177, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__KMU-158", "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_018067195.1", "gtdb_species": "s__Marortus sp018067195", "ani": 76.8214, "matched_fragments": 142, "total_fragments": 1177, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus", "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_002699145.1", "gtdb_species": "s__Halioglobus sp002699145", "ani": 76.7764, "matched_fragments": 62, "total_fragments": 1177, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.96", "min_intra_species_ani": "99.96", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002806685.1", "gtdb_species": "s__Pseudomonas_E qingdaonensis", "ani": 76.4008, "matched_fragments": 56, "total_fragments": 1177, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.05", "min_intra_species_ani": "98.91", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.89", "num_clustered_genomes": 13, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.222, "cell_length": 0.212, "doubling_h": 0.868, "growth_tmp": 28.0, "optimum_tmp": 28.333, "optimum_ph": 8.0, "genome_size": 3435542.0, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "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": [ "Spongiibacter", "marinus" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }