{ "type": "genome", "identifier": "GCF_003001895.1", "organism": "Salegentibacter salegens", "title": "Salegentibacter salegens", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003001895.1", "bioproject": "PRJNA224116", "biosample": "SAMN05661042", "wgs_master": "PVNF00000000.1", "refseq_category": "na", "taxid": "143223", "species_taxid": "143223", "organism_name": "Salegentibacter salegens", "infraspecific_name": "strain=DSM 5424", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/03/15", "asm_name": "ASM300189v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_003001895.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/001/895/GCF_003001895.1_ASM300189v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3872766", "genome_size_ungapped": "3869045", "gc_percent": "37.000000", "replicon_count": "0", "scaffold_count": "99", "contig_count": "99", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003001895.1-RS_2024_12_23", "annotation_date": "2024-12-23", "total_gene_count": "3536", "protein_coding_gene_count": "3412", "non_coding_gene_count": "50", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-03-15", "dateModified": "2018-03-15", "datePublished": "2018-03-15", "_annotation": { "sample_count": 1, "sample_organism": [ "Salegentibacter salegens" ], "sample_taxid": [ "143223" ], "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": "1.093 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)": "3872766", "Number of Sequences": "99", "Longest Sequences (bp)": "259918", "N50 (bp)": "94597", "Gap Ratio (%)": "0.096081", "GCcontent (%)": "37.1", "Number of CDSs": "3341", "Average Protein Length": "337.5", "Coding Ratio (%)": "87.3", "Number of rRNAs": "4", "Number of tRNAs": "39", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Salegentibacter salegens", "strain": "strain=DSM 5424", "accession": "GCA_003001895.1", "taxid": 143223, "species_taxid": 143223, "relation_to_type": "type", "validated": true, "ani": 99.9982, "matched_fragments": 1233, "total_fragments": 1239, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Salegentibacter salegens", "strain": "strain=ACAM 48", "accession": "GCA_900142975.1", "taxid": 143223, "species_taxid": 143223, "relation_to_type": "type", "validated": true, "ani": 99.9897, "matched_fragments": 1238, "total_fragments": 1239, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Salegentibacter agarivorans", "strain": "strain=DSM 23515", "accession": "GCA_900113135.1", "taxid": 345907, "species_taxid": 345907, "relation_to_type": "type", "validated": true, "ani": 88.0144, "matched_fragments": 1015, "total_fragments": 1239, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Salegentibacter salinarum", "strain": "strain=KCTC 12975", "accession": "GCA_002833365.1", "taxid": 447422, "species_taxid": 447422, "relation_to_type": "type", "validated": true, "ani": 86.9451, "matched_fragments": 974, "total_fragments": 1239, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Salegentibacter lacus", "strain": "strain=LM13S", "accession": "GCA_020164555.1", "taxid": 2873599, "species_taxid": 2873599, "relation_to_type": "type", "validated": true, "ani": 86.1, "matched_fragments": 912, "total_fragments": 1239, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Salegentibacter mishustinae", "strain": "strain=KCTC 12263", "accession": "GCA_014651335.1", "taxid": 270918, "species_taxid": 270918, "relation_to_type": "type", "validated": true, "ani": 85.1503, "matched_fragments": 875, "total_fragments": 1239, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Salegentibacter mishustinae", "strain": "strain=DSM 23404", "accession": "GCA_002900095.1", "taxid": 270918, "species_taxid": 270918, "relation_to_type": "type", "validated": true, "ani": 85.1483, "matched_fragments": 883, "total_fragments": 1239, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Salegentibacter tibetensis", "strain": "strain=JZCK2", "accession": "GCA_020164485.1", "taxid": 2873600, "species_taxid": 2873600, "relation_to_type": "type", "validated": true, "ani": 84.7873, "matched_fragments": 853, "total_fragments": 1239, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Salegentibacter holothuriorum", "strain": "strain=DSM 23405", "accession": "GCA_900168045.1", "taxid": 241145, "species_taxid": 241145, "relation_to_type": "type", "validated": true, "ani": 84.3433, "matched_fragments": 841, "total_fragments": 1239, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gramella crocea", "strain": "strain=YB25", "accession": "GCA_022410465.1", "taxid": 2904124, "species_taxid": 2904124, "relation_to_type": "type", "validated": true, "ani": 77.4586, "matched_fragments": 196, "total_fragments": 1239, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hanstruepera marina", "strain": "strain=NBU2968", "accession": "GCA_019880635.1", "taxid": 2873265, "species_taxid": 2873265, "relation_to_type": "type", "validated": true, "ani": 76.5109, "matched_fragments": 71, "total_fragments": 1239, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Joostella atrarenae", "strain": "strain=M1-2", "accession": "GCA_021764745.1", "taxid": 679257, "species_taxid": 679257, "relation_to_type": "type", "validated": true, "ani": 76.4016, "matched_fragments": 97, "total_fragments": 1239, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900142975.1", "gtdb_species": "s__Salegentibacter salegens", "ani": 99.9897, "matched_fragments": 1238, "total_fragments": 1239, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": 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"mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900168265.1", "gtdb_species": "s__Salegentibacter salarius", "ani": 85.5213, "matched_fragments": 850, "total_fragments": 1239, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "0.99", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_002900095.1", "gtdb_species": "s__Salegentibacter mishustinae", "ani": 85.1512, "matched_fragments": 883, "total_fragments": 1239, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_000745315.1", "gtdb_species": "s__Salegentibacter sp000745315", "ani": 84.8425, "matched_fragments": 895, "total_fragments": 1239, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter", "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_900168045.1", "gtdb_species": "s__Salegentibacter holothuriorum", "ani": 84.3397, "matched_fragments": 842, "total_fragments": 1239, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter", "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": -0.263, "cell_length": 0.436, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": 27.142, "optimum_ph": 7.787, "genome_size": 3941382.5, "gc_content": 36.939, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.2, "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": [ "Salegentibacter", "salegens" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }