{ "type": "genome", "identifier": "GCF_000429465.1", "organism": "Algoriphagus vanfongensis DSM 17529", "title": "Algoriphagus vanfongensis DSM 17529", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000429465.1", "bioproject": "PRJNA224116", "biosample": "SAMN02441203", "wgs_master": "AUBX00000000.1", "refseq_category": "reference genome", "taxid": "1120968", "species_taxid": "426371", "organism_name": "Algoriphagus vanfongensis DSM 17529", "infraspecific_name": "strain=DSM 17529", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/07/15", "asm_name": "ASM42946v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_000429465.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/429/465/GCF_000429465.1_ASM42946v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4712065", "genome_size_ungapped": "4711845", "gc_percent": "43.000000", "replicon_count": "0", "scaffold_count": "17", "contig_count": "18", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000429465.1-RS_2024_05_02", "annotation_date": "2024-05-02", "total_gene_count": "4019", "protein_coding_gene_count": "3964", "non_coding_gene_count": "48", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-07-15", "dateModified": "2013-07-15", "datePublished": "2013-07-15", "_annotation": { "sample_count": 1, "sample_organism": [ "Algoriphagus vanfongensis DSM 17529" ], "sample_taxid": [ "1120968" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Viet Nam" ], "sample_host_location_id": [], "data_size": "1.336 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)": "4712065", "Number of Sequences": "17", "Longest Sequences (bp)": "871606", "N50 (bp)": "482381", "Gap Ratio (%)": "0.004669", "GCcontent (%)": "42.8", "Number of CDSs": "3929", "Average Protein Length": "354.8", "Coding Ratio (%)": "88.8", "Number of rRNAs": "3", "Number of tRNAs": "39", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Algoriphagus vanfongensis", "strain": "strain=DSM 17529", "accession": "GCA_000429465.1", "taxid": 426371, "species_taxid": 426371, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1561, "total_fragments": 1561, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Algoriphagus zhangzhouensis", "strain": "strain=DSM 25035", "accession": "GCA_900148515.1", "taxid": 1073327, "species_taxid": 1073327, "relation_to_type": "type", "validated": true, "ani": 80.4776, "matched_fragments": 711, "total_fragments": 1561, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Algoriphagus zhangzhouensis", "strain": "strain=CGMCC 1.11027", "accession": "GCA_004366575.1", "taxid": 1073327, "species_taxid": 1073327, "relation_to_type": "type", "validated": true, "ani": 80.4028, "matched_fragments": 707, "total_fragments": 1561, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Algoriphagus ornithinivorans", "strain": "strain=DSM 15282", "accession": "GCA_900115305.1", "taxid": 226506, "species_taxid": 226506, "relation_to_type": "type", "validated": true, "ani": 78.44, "matched_fragments": 332, "total_fragments": 1561, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Algoriphagus algorifonticola", "strain": "strain=hg1", "accession": "GCA_007655305.1", "taxid": 2593007, "species_taxid": 2593007, "relation_to_type": "type", "validated": true, "ani": 78.2061, "matched_fragments": 355, "total_fragments": 1561, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Algoriphagus hitonicola", "strain": "strain=DSM 19315", "accession": "GCA_900113375.1", "taxid": 435880, "species_taxid": 435880, "relation_to_type": "type", "validated": true, "ani": 77.8617, "matched_fragments": 283, "total_fragments": 1561, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Algoriphagus terrigena", "strain": "strain=DSM 22685", "accession": "GCA_000429445.1", "taxid": 344884, "species_taxid": 344884, "relation_to_type": "type", "validated": true, "ani": 77.3786, "matched_fragments": 234, "total_fragments": 1561, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Algoriphagus aquaeductus", "strain": "strain=T4", "accession": "GCA_003253485.1", "taxid": 475299, "species_taxid": 475299, "relation_to_type": "type", "validated": true, "ani": 77.3697, "matched_fragments": 236, "total_fragments": 1561, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Algoriphagus aquimarinus", "strain": "strain=DSM 23399", "accession": "GCA_900112005.1", "taxid": 237018, "species_taxid": 237018, "relation_to_type": "type", "validated": true, "ani": 77.3628, "matched_fragments": 237, "total_fragments": 1561, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Algoriphagus aquimaris", "strain": "strain=F21", "accession": "GCA_004358035.1", "taxid": 2547398, "species_taxid": 2547398, "relation_to_type": "type", "validated": true, "ani": 77.3297, "matched_fragments": 253, "total_fragments": 1561, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Algoriphagus formosus", "strain": "strain=XAY3209", "accession": "GCA_002807035.1", "taxid": 2007308, "species_taxid": 2007308, "relation_to_type": "type", "validated": true, "ani": 77.3084, "matched_fragments": 262, "total_fragments": 1561, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Belliella baltica", "strain": "strain=DSM 15883", "accession": "GCA_000265405.1", "taxid": 232259, "species_taxid": 232259, "relation_to_type": "type", "validated": true, "ani": 76.9566, "matched_fragments": 111, "total_fragments": 1561, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Echinicola marina", "strain": "strain=SCS 3-6", "accession": "GCA_020463795.1", "taxid": 2859768, "species_taxid": 2859768, "relation_to_type": "type", "validated": true, "ani": 76.9423, "matched_fragments": 98, "total_fragments": 1561, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000429465.1", "gtdb_species": "s__Algoriphagus vanfongensis", "ani": 100.0, "matched_fragments": 1561, "total_fragments": 1561, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus", "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_900148515.1", "gtdb_species": "s__Algoriphagus zhangzhouensis", "ani": 80.4956, "matched_fragments": 708, "total_fragments": 1561, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus", "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_900115305.1", "gtdb_species": "s__Algoriphagus ornithinivorans", "ani": 78.4515, "matched_fragments": 331, "total_fragments": 1561, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.91", "min_intra_species_ani": "95.63", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.85", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_007655305.1", "gtdb_species": "s__Algoriphagus sp007655305", "ani": 78.2162, "matched_fragments": 354, "total_fragments": 1561, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus", "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_900113375.1", "gtdb_species": "s__Algoriphagus hitonicola", "ani": 77.8617, "matched_fragments": 283, "total_fragments": 1561, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus", "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_014838715.1", "gtdb_species": "s__Algoriphagus sp014838715", "ani": 77.6793, "matched_fragments": 233, "total_fragments": 1561, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus", "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_900101705.1", "gtdb_species": "s__Algoriphagus faecimaris", "ani": 77.6259, "matched_fragments": 288, "total_fragments": 1561, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_013373335.1", "gtdb_species": "s__Algoriphagus sp013373335", "ani": 77.5861, "matched_fragments": 167, "total_fragments": 1561, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus", "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_004571135.1", "gtdb_species": "s__Algoriphagus kandeliae", "ani": 77.5069, "matched_fragments": 267, "total_fragments": 1561, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus", "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_000429445.1", "gtdb_species": "s__Algoriphagus terrigena", "ani": 77.3823, "matched_fragments": 233, "total_fragments": 1561, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus", "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_900112005.1", "gtdb_species": "s__Algoriphagus aquimarinus", "ani": 77.3587, "matched_fragments": 236, "total_fragments": 1561, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus", "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_002807035.1", "gtdb_species": "s__Algoriphagus formosus", "ani": 77.3084, "matched_fragments": 262, "total_fragments": 1561, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.55", "min_intra_species_ani": "97.55", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_007997215.1", "gtdb_species": "s__Algoriphagus aquimarinus_A", "ani": 77.1822, "matched_fragments": 272, "total_fragments": 1561, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus", "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_009885605.1", "gtdb_species": "s__Algoriphagus sp009885605", "ani": 77.0554, "matched_fragments": 157, "total_fragments": 1561, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus", "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": -0.372, "cell_length": 0.138, "doubling_h": 0.69, "growth_tmp": 28.0, "optimum_tmp": 23.5, "optimum_ph": 7.375, "genome_size": 4711955.0, "gc_content": 42.8, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": 1.0, "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": [ "Algoriphagus", "vanfongensis", "DSM", "17529" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }