{ "type": "genome", "identifier": "GCF_030295325.1", "organism": "Haliovirga abyssi", "title": "Haliovirga abyssi", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Kyoto University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_030295325.1", "bioproject": "PRJNA224116", "biosample": "SAMD00562171", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "2996794", "species_taxid": "2996794", "organism_name": "Haliovirga abyssi", "infraspecific_name": "strain=IC12", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2023/05/11", "asm_name": "ASM3029532v1", "asm_submitter": "Kyoto University", "gbrs_paired_asm": "GCA_030295325.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/030/295/325/GCF_030295325.1_ASM3029532v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2725473", "genome_size_ungapped": "2725473", "gc_percent": "26.500000", "replicon_count": "2", "scaffold_count": "2", "contig_count": "2", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_030295325.1-RS_2024_08_28", "annotation_date": "2024-08-28", "total_gene_count": "2330", "protein_coding_gene_count": "2260", "non_coding_gene_count": "57", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2023-05-11", "dateModified": "2023-05-11", "datePublished": "2023-05-11", "_annotation": { "sample_count": 1, "sample_organism": [ "Haliovirga abyssi" ], "sample_taxid": [ "2996794" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Japan:Mid Okinawa Trough" ], "sample_host_location_id": [], "data_size": "0.711 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)": "2725473", "Number of Sequences": "2", "Longest Sequences (bp)": "2427922", "N50 (bp)": "2427922", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "26.4", "Number of CDSs": "2290", "Average Protein Length": "354.6", "Coding Ratio (%)": "89.4", "Number of rRNAs": "13", "Number of tRNAs": "41", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Oceanivirga miroungae", "strain": "strain=ES3154-GLU", "accession": "GCA_902505095.1", "taxid": 1130046, "species_taxid": 1130046, "relation_to_type": "type", "validated": true, "ani": 75.779, "matched_fragments": 65, "total_fragments": 908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Fusobacterium hwasookii", "strain": "strain=KCOM 1249", "accession": "GCA_014217355.1", "taxid": 1583098, "species_taxid": 1583098, "relation_to_type": "type", "validated": true, "ani": 75.7482, "matched_fragments": 123, "total_fragments": 908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Fusobacterium canifelinum", "strain": "strain=FDAARGOS_1126", "accession": "GCA_016724785.1", "taxid": 285729, "species_taxid": 285729, "relation_to_type": "type", "validated": true, "ani": 75.6977, "matched_fragments": 104, "total_fragments": 908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptotrichia wadei", "strain": "strain=JCM16777", "accession": "GCA_007990545.2", "taxid": 157687, "species_taxid": 157687, "relation_to_type": "type", "validated": true, "ani": 75.6888, "matched_fragments": 103, "total_fragments": 908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Fusobacterium ulcerans", "strain": "strain=ATCC 49185", "accession": "GCA_003019675.1", "taxid": 861, "species_taxid": 861, "relation_to_type": "type", "validated": true, "ani": 75.6873, "matched_fragments": 100, "total_fragments": 908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Fusobacterium massiliense", "strain": "strain=Marseille-P2749", "accession": "GCA_900095705.1", "taxid": 1852365, "species_taxid": 1852365, "relation_to_type": "type", "validated": true, "ani": 75.5532, "matched_fragments": 104, "total_fragments": 908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Crassaminicella thermophila", "strain": "strain=SY095", "accession": "GCA_008152325.1", "taxid": 2599308, "species_taxid": 2599308, "relation_to_type": "type", "validated": true, "ani": 75.4917, "matched_fragments": 75, "total_fragments": 908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Caviibacter abscessus", "strain": "strain=CCUG 39713", "accession": "GCA_001517835.1", "taxid": 1766719, "species_taxid": 1766719, "relation_to_type": "type", "validated": true, "ani": 75.3496, "matched_fragments": 68, "total_fragments": 908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sneathia sanguinegens", "strain": "strain=CCUG41628", "accession": "GCA_001517935.1", "taxid": 40543, "species_taxid": 40543, "relation_to_type": "type", "validated": true, "ani": 75.3108, "matched_fragments": 56, "total_fragments": 908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Fusobacterium hwasookii", "strain": "strain=ChDC F128", "accession": "GCA_000292935.1", "taxid": 1583098, "species_taxid": 1583098, "relation_to_type": "type", "validated": true, "ani": 75.2712, "matched_fragments": 115, "total_fragments": 908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Fusobacterium perfoetens", "strain": "strain=ATCC 29250", "accession": "GCA_000622245.1", "taxid": 852, "species_taxid": 852, "relation_to_type": "type", "validated": true, "ani": 75.2339, "matched_fragments": 144, "total_fragments": 908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cetobacterium somerae", "strain": "strain=ATCC BAA-474", "accession": "GCA_000479045.1", "taxid": 188913, "species_taxid": 188913, "relation_to_type": "type", "validated": true, "ani": 75.0451, "matched_fragments": 105, "total_fragments": 908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptotrichia wadei", "strain": "strain=DSM 19758", "accession": "GCA_000373345.1", "taxid": 157687, "species_taxid": 157687, "relation_to_type": "type", "validated": true, "ani": 75.0042, "matched_fragments": 95, "total_fragments": 908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hydrogenothermus marinus", "strain": "strain=VM1", "accession": "GCA_003688665.1", "taxid": 133270, "species_taxid": 133270, "relation_to_type": "type", "validated": true, "ani": 74.8478, "matched_fragments": 69, "total_fragments": 908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Terrisporobacter mayombei", "strain": "strain=DSM 6539", "accession": "GCA_020748465.1", "taxid": 1541, "species_taxid": 1541, "relation_to_type": "type", "validated": true, "ani": 74.7969, "matched_fragments": 95, "total_fragments": 908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium puniceum", "strain": "strain=DSM 2619", "accession": "GCA_002006345.1", "taxid": 29367, "species_taxid": 29367, "relation_to_type": "type", "validated": true, "ani": 74.7878, "matched_fragments": 115, "total_fragments": 908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium prolinivorans", "strain": "strain=PYR-10", "accession": "GCA_004011155.1", "taxid": 2769420, "species_taxid": 2769420, "relation_to_type": "type", "validated": true, "ani": 74.7874, "matched_fragments": 93, "total_fragments": 908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tepidibacter formicigenes", "strain": "strain=DSM 15518", "accession": "GCA_900142235.1", "taxid": 227138, "species_taxid": 227138, "relation_to_type": "type", "validated": true, "ani": 74.7605, "matched_fragments": 93, "total_fragments": 908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Terrisporobacter glycolicus", "strain": "strain=DSM 1288", "accession": "GCA_000439105.1", "taxid": 36841, "species_taxid": 36841, "relation_to_type": "suspected-type", "validated": true, "ani": 74.739, "matched_fragments": 99, "total_fragments": 908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marinitoga hydrogenitolerans", "strain": "strain=DSM 16785", "accession": "GCA_900129175.1", "taxid": 287990, "species_taxid": 287990, "relation_to_type": "type", "validated": true, "ani": 74.6925, "matched_fragments": 84, "total_fragments": 908, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004365575.1", "gtdb_species": "s__Hypnocyclicus thermotrophus", "ani": 75.9621, "matched_fragments": 215, "total_fragments": 908, "gtdb_taxonomy": "d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Hypnocyclicus", "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_014337255.1", "gtdb_species": "s__Fusobacterium_A sp900015295", "ani": 75.9577, "matched_fragments": 104, "total_fragments": 908, "gtdb_taxonomy": "d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.50", "min_intra_species_ani": "99.45", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.92", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_001559795.1", "gtdb_species": "s__Streptobacillus hongkongensis", "ani": 75.5886, "matched_fragments": 69, "total_fragments": 908, "gtdb_taxonomy": "d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Streptobacillus", "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_016938425.1", "gtdb_species": "s__JAFGUR01 sp016938425", "ani": 75.559, "matched_fragments": 83, "total_fragments": 908, "gtdb_taxonomy": "d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__JAFGUR01", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.62", "min_intra_species_ani": "99.62", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_012519615.1", "gtdb_species": "s__JAAYPW01 sp012519615", "ani": 75.5482, "matched_fragments": 131, "total_fragments": 908, "gtdb_taxonomy": "d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__JAAYPW01;g__JAAYPW01", "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_000007325.1", "gtdb_species": "s__Fusobacterium nucleatum", "ani": 75.5344, "matched_fragments": 119, "total_fragments": 908, "gtdb_taxonomy": "d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.30", "min_intra_species_ani": "95.23", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.85", "num_clustered_genomes": 13, "status": "-" }, { "accession": "GCF_900095705.1", "gtdb_species": "s__Fusobacterium massiliense", "ani": 75.5302, "matched_fragments": 107, "total_fragments": 908, "gtdb_taxonomy": "d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium", "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_000158275.2", "gtdb_species": "s__Fusobacterium animalis", "ani": 75.5091, "matched_fragments": 125, "total_fragments": 908, "gtdb_taxonomy": "d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.57", "min_intra_species_ani": "95.72", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.80", "num_clustered_genomes": 29, "status": "-" }, { "accession": "GCA_905193685.1", "gtdb_species": "s__Fusobacterium_A sp900555485", "ani": 75.4165, "matched_fragments": 105, "total_fragments": 908, "gtdb_taxonomy": "d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_018058425.1", "gtdb_species": "s__Sebaldella sp018058425", "ani": 75.343, "matched_fragments": 106, "total_fragments": 908, "gtdb_taxonomy": "d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Sebaldella", "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_010367435.1", "gtdb_species": "s__Fusobacterium_B sp010367435", "ani": 75.3103, "matched_fragments": 88, "total_fragments": 908, "gtdb_taxonomy": "d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_B", "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_002342785.1", "gtdb_species": "s__Psychrilyobacter sp002342785", "ani": 75.2268, "matched_fragments": 114, "total_fragments": 908, "gtdb_taxonomy": "d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Psychrilyobacter", "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_905216205.1", "gtdb_species": "s__Cetobacterium_A sp905216205", "ani": 75.2189, "matched_fragments": 100, "total_fragments": 908, "gtdb_taxonomy": "d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Cetobacterium_A", "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_900545035.1", "gtdb_species": "s__Fusobacterium_B sp900545035", "ani": 75.1286, "matched_fragments": 52, "total_fragments": 908, "gtdb_taxonomy": "d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_B", "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_000479045.1", "gtdb_species": "s__Cetobacterium_A somerae", "ani": 75.0247, "matched_fragments": 109, "total_fragments": 908, "gtdb_taxonomy": "d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Cetobacterium_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.23", "min_intra_species_ani": "98.47", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.85", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_003391055.1", "gtdb_species": "s__Psychrilyobacter sp003391055", "ani": 74.9059, "matched_fragments": 55, "total_fragments": 908, "gtdb_taxonomy": "d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Psychrilyobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_003688665.1", "gtdb_species": "s__Hydrogenothermus marinus", "ani": 74.8478, "matched_fragments": 69, "total_fragments": 908, "gtdb_taxonomy": "d__Bacteria;p__Aquificota;c__Aquificae;o__Hydrogenothermales;f__Hydrogenothermaceae;g__Hydrogenothermus", "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_002006345.1", "gtdb_species": "s__Clostridium puniceum", "ani": 74.7834, "matched_fragments": 117, "total_fragments": 908, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium", "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": null, "cell_length": null, "doubling_h": null, "growth_tmp": null, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_genome_taxon": [ "Haliovirga", "abyssi" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }