{ "type": "genome", "identifier": "GCF_012272835.1", "organism": "Spongiibacter thalassae", "title": "Spongiibacter thalassae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Keimyung University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_012272835.1", "bioproject": "PRJNA224116", "biosample": "SAMN14466327", "wgs_master": "JAAWWK000000000.1", "refseq_category": "reference genome", "taxid": "2721624", "species_taxid": "2721624", "organism_name": "Spongiibacter thalassae", "infraspecific_name": "strain=KMU-166", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/04/11", "asm_name": "ASM1227283v1", "asm_submitter": "Keimyung University", "gbrs_paired_asm": "GCA_012272835.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/012/272/835/GCF_012272835.1_ASM1227283v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4404448", "genome_size_ungapped": "4404062", "gc_percent": "55.500000", "replicon_count": "0", "scaffold_count": "13", "contig_count": "13", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_012272835.1-RS_2024_05_14", "annotation_date": "2024-05-14", "total_gene_count": "3939", "protein_coding_gene_count": "3870", "non_coding_gene_count": "47", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-04-11", "dateModified": "2020-04-11", "datePublished": "2020-04-11", "_annotation": { "sample_count": 1, "sample_organism": [ "Spongiibacter thalassae" ], "sample_taxid": [ "2721624" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea: Pusan" ], "sample_host_location_id": [], "data_size": "1.251 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)": "4404448", "Number of Sequences": "13", "Longest Sequences (bp)": "993779", "N50 (bp)": "554672", "Gap Ratio (%)": "0.008764", "GCcontent (%)": "55.7", "Number of CDSs": "3932", "Average Protein Length": "335.1", "Coding Ratio (%)": "89.8", "Number of rRNAs": "3", "Number of tRNAs": "38", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Spongiibacter thalassae", "strain": "strain=KMU-166", "accession": "GCA_012272835.1", "taxid": 2721624, "species_taxid": 2721624, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1460, "total_fragments": 1461, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Spongiibacter tropicus", "strain": "strain=DSM 19543", "accession": "GCA_000420325.1", "taxid": 454602, "species_taxid": 454602, "relation_to_type": "type", "validated": true, "ani": 78.8093, "matched_fragments": 318, "total_fragments": 1461, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Spongiibacter taiwanensis", "strain": "strain=SPT1", "accession": "GCA_023702635.1", "taxid": 1748242, "species_taxid": 1748242, "relation_to_type": "type", "validated": true, "ani": 78.0396, "matched_fragments": 243, "total_fragments": 1461, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Spongiibacter nanhainus", "strain": "strain=csc3.9", "accession": "GCA_016132545.1", "taxid": 2794344, "species_taxid": 2794344, "relation_to_type": "type", "validated": true, "ani": 77.999, "matched_fragments": 239, "total_fragments": 1461, "ani_threshold": 95, "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": 77.5729, "matched_fragments": 196, "total_fragments": 1461, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Zhongshania antarctica", "strain": "strain=ZS5-23", "accession": "GCA_014898265.1", "taxid": 641702, "species_taxid": 641702, "relation_to_type": "type", "validated": true, "ani": 77.4149, "matched_fragments": 186, "total_fragments": 1461, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Zhongshania antarctica", "strain": "strain=DSM 25701", "accession": "GCA_014202945.1", "taxid": 641702, "species_taxid": 641702, "relation_to_type": "type", "validated": true, "ani": 77.4065, "matched_fragments": 187, "total_fragments": 1461, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halioglobus maricola", "strain": "strain=IMCC14385", "accession": "GCA_009388985.1", "taxid": 2601894, "species_taxid": 2601894, "relation_to_type": "type", "validated": true, "ani": 77.3256, "matched_fragments": 65, "total_fragments": 1461, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marinobacter goseongensis", "strain": "strain=KCTC 12515", "accession": "GCA_023156235.1", "taxid": 453838, "species_taxid": 453838, "relation_to_type": "type", "validated": true, "ani": 76.6909, "matched_fragments": 53, "total_fragments": 1461, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marinobacter bryozoorum", "strain": "strain=DSM 15401", "accession": "GCA_023156245.1", "taxid": 256324, "species_taxid": 256324, "relation_to_type": "type", "validated": true, "ani": 76.6514, "matched_fragments": 54, "total_fragments": 1461, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Oceanimonas marisflavi", "strain": "strain=102-Na3", "accession": "GCA_003049725.1", "taxid": 2059724, "species_taxid": 2059724, "relation_to_type": "type", "validated": true, "ani": 76.0674, "matched_fragments": 52, "total_fragments": 1461, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kineobactrum sediminis", "strain": "strain=F02", "accession": "GCA_002868715.1", "taxid": 1905677, "species_taxid": 1905677, "relation_to_type": "type", "validated": true, "ani": 76.0479, "matched_fragments": 61, "total_fragments": 1461, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas otitidis", "strain": "strain=DSM 17224", "accession": "GCA_900111835.1", "taxid": 319939, "species_taxid": 319939, "relation_to_type": "suspected-type", "validated": true, "ani": 76.0315, "matched_fragments": 68, "total_fragments": 1461, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Azotobacter chroococcum subsp. isscasi", "strain": "strain=P205", "accession": "GCA_004327895.1", "taxid": 2528971, "species_taxid": 353, "relation_to_type": "type", "validated": true, "ani": 75.9322, "matched_fragments": 69, "total_fragments": 1461, "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": 75.8775, "matched_fragments": 52, "total_fragments": 1461, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_012272835.1", "gtdb_species": "s__Spongiibacter sp012272835", "ani": 100.0, "matched_fragments": 1460, "total_fragments": 1461, "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": "conclusive" }, { "accession": "GCF_000420325.1", "gtdb_species": "s__Spongiibacter tropicus", "ani": 78.8093, "matched_fragments": 318, "total_fragments": 1461, "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_000422345.1", "gtdb_species": "s__Spongiibacter marinus_A", "ani": 78.3259, "matched_fragments": 251, "total_fragments": 1461, "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_016906995.1", "gtdb_species": "s__Spongiibacter marinus", "ani": 78.2861, "matched_fragments": 275, "total_fragments": 1461, "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": "-" }, { "accession": "GCF_016132545.1", "gtdb_species": "s__CSC3-9 sp016132545", "ani": 78.0137, "matched_fragments": 240, "total_fragments": 1461, "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": 77.5538, "matched_fragments": 198, "total_fragments": 1461, "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": "GCF_902705855.1", "gtdb_species": "s__Marortus aliphaticivorans_B", "ani": 77.4545, "matched_fragments": 161, "total_fragments": 1461, "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": "GCF_001010805.1", "gtdb_species": "s__IMCC21906 sp001010805", "ani": 77.3738, "matched_fragments": 175, "total_fragments": 1461, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__IMCC21906", "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_002710725.1", "gtdb_species": "s__Litorivivens sp002710725", "ani": 77.2228, "matched_fragments": 129, "total_fragments": 1461, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Litorivivens", "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_018066965.1", "gtdb_species": "s__Marortus sp018066965", "ani": 76.9973, "matched_fragments": 130, "total_fragments": 1461, "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": "GCF_017255185.1", "gtdb_species": "s__Parahaliea mediterranea_A", "ani": 76.4903, "matched_fragments": 102, "total_fragments": 1461, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea", "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_016132445.1", "gtdb_species": "s__UBA2009 sp016132445", "ani": 76.2787, "matched_fragments": 55, "total_fragments": 1461, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.98", "min_intra_species_ani": "97.98", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900107725.1", "gtdb_species": "s__Microbulbifer marinus", "ani": 76.2493, "matched_fragments": 79, "total_fragments": 1461, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer", "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_017309075.1", "gtdb_species": "s__Motiliproteus sp017309075", "ani": 76.0131, "matched_fragments": 54, "total_fragments": 1461, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Motiliproteus", "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_008370495.1", "gtdb_species": "s__Halioglobus sp008370495", "ani": 75.7948, "matched_fragments": 63, "total_fragments": 1461, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus", "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": -0.31, "cell_length": 0.083, "doubling_h": 0.868, "growth_tmp": 28.0, "optimum_tmp": 30.416, "optimum_ph": 7.75, "genome_size": 3691442.0, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.5, "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", "thalassae" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }