{ "type": "genome", "identifier": "GCF_000685295.1", "organism": "Hyphomonas oceanitis SCH89", "title": "Hyphomonas oceanitis SCH89", "description": "na", "data type": "Genome sequencing and assembly", "organization": "The Third Institute of State Oceanic Administration (SOA)", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000685295.1", "bioproject": "PRJNA224116", "biosample": "SAMN02746695", "wgs_master": "ARYL00000000.1", "refseq_category": "na", "taxid": "1280953", "species_taxid": "81033", "organism_name": "Hyphomonas oceanitis SCH89", "infraspecific_name": "strain=SCH89", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2014/05/06", "asm_name": "SOAPdenovo v1.05", "asm_submitter": "The Third Institute of State Oceanic Administration (SOA)", "gbrs_paired_asm": "GCA_000685295.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/685/295/GCF_000685295.1_SOAPdenovo_v1.05", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4280175", "genome_size_ungapped": "4280175", "gc_percent": "60.000000", "replicon_count": "0", "scaffold_count": "188", "contig_count": "188", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000685295.1-RS_2024_04_04", "annotation_date": "2024-04-04", "total_gene_count": "4209", "protein_coding_gene_count": "4110", "non_coding_gene_count": "49", "pubmed_id": "25070064" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2014-05-06", "dateModified": "2014-05-06", "datePublished": "2014-05-06", "_annotation": { "sample_count": 1, "sample_organism": [ "Hyphomonas oceanitis SCH89" ], "sample_taxid": [ "1280953" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "1.210 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)": "4280175", "Number of Sequences": "188", "Longest Sequences (bp)": "312161", "N50 (bp)": "98871", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "60.2", "Number of CDSs": "4048", "Average Protein Length": "308.9", "Coding Ratio (%)": "87.6", "Number of rRNAs": "3", "Number of tRNAs": "43", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Hyphomonas oceanitis", "strain": "strain=SCH89", "accession": "GCA_000685295.1", "taxid": 81033, "species_taxid": 81033, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1345, "total_fragments": 1349, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Hyphomonas chukchiensis", "strain": "strain=BH-BN04-4", "accession": "GCA_000682695.1", "taxid": 1280947, "species_taxid": 1280947, "relation_to_type": "type", "validated": true, "ani": 90.5143, "matched_fragments": 1015, "total_fragments": 1349, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hyphomonas johnsonii", "strain": "strain=MHS-2", "accession": "GCA_000685275.1", "taxid": 81031, "species_taxid": 81031, "relation_to_type": "type", "validated": true, "ani": 81.4973, "matched_fragments": 691, "total_fragments": 1349, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hyphomonas jannaschiana", "strain": "strain=VP2", "accession": "GCA_000685215.1", "taxid": 86, "species_taxid": 86, "relation_to_type": "type", "validated": true, "ani": 78.8557, "matched_fragments": 485, "total_fragments": 1349, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hyphomonas adhaerens", "strain": "strain=MHS-3", "accession": "GCA_000685235.1", "taxid": 81029, "species_taxid": 81029, "relation_to_type": "type", "validated": true, "ani": 78.6704, "matched_fragments": 462, "total_fragments": 1349, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hyphomonas beringensis", "strain": "strain=25B14_1", "accession": "GCA_000682755.1", "taxid": 1280946, "species_taxid": 1280946, "relation_to_type": "type", "validated": true, "ani": 78.5788, "matched_fragments": 426, "total_fragments": 1349, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hyphomonas atlantica", "strain": "strain=22II1-22F38", "accession": "GCA_000682715.1", "taxid": 1280948, "species_taxid": 1280948, "relation_to_type": "type", "validated": true, "ani": 78.2804, "matched_fragments": 368, "total_fragments": 1349, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hyphomonas pacifica", "strain": "strain=T16B2", "accession": "GCA_000682675.1", "taxid": 1280941, "species_taxid": 1280941, "relation_to_type": "type", "validated": true, "ani": 78.0774, "matched_fragments": 410, "total_fragments": 1349, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hyphomonas sediminis", "strain": "strain=WL0036", "accession": "GCA_019679475.1", "taxid": 2866160, "species_taxid": 2866160, "relation_to_type": "type", "validated": true, "ani": 78.072, "matched_fragments": 375, "total_fragments": 1349, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Henriciella aquimarina", "strain": "strain=LMG 24711", "accession": "GCA_002088975.1", "taxid": 545261, "species_taxid": 545261, "relation_to_type": "type", "validated": true, "ani": 77.759, "matched_fragments": 316, "total_fragments": 1349, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ciceribacter ferrooxidans", "strain": "strain=F8825", "accession": "GCA_004137355.1", "taxid": 2509717, "species_taxid": 2509717, "relation_to_type": "type", "validated": true, "ani": 76.3509, "matched_fragments": 57, "total_fragments": 1349, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium croatiense", "strain": "strain=13T", "accession": "GCA_019793465.1", "taxid": 2867516, "species_taxid": 2867516, "relation_to_type": "type", "validated": true, "ani": 75.9499, "matched_fragments": 76, "total_fragments": 1349, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amaricoccus solimangrovi", "strain": "strain=HB172011", "accession": "GCA_006385685.1", "taxid": 2589815, "species_taxid": 2589815, "relation_to_type": "type", "validated": true, "ani": 75.9321, "matched_fragments": 69, "total_fragments": 1349, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mangrovicoccus algicola", "strain": "strain=HB182678", "accession": "GCA_014903745.1", "taxid": 2771008, "species_taxid": 2771008, "relation_to_type": "type", "validated": true, "ani": 75.7486, "matched_fragments": 75, "total_fragments": 1349, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000685295.1", "gtdb_species": "s__Hyphomonas oceanitis", "ani": 100.0, "matched_fragments": 1345, "total_fragments": 1349, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas", "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_000682695.1", "gtdb_species": "s__Hyphomonas chukchiensis", "ani": 90.4987, "matched_fragments": 1016, "total_fragments": 1349, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas", "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_018827375.1", "gtdb_species": "s__Hyphomonas sp018827375", "ani": 87.2189, "matched_fragments": 943, "total_fragments": 1349, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.92", "min_intra_species_ani": "99.88", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.97", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_000961795.1", "gtdb_species": "s__Hyphomonas sp000961795", "ani": 83.3296, "matched_fragments": 777, "total_fragments": 1349, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas", "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_018830285.1", "gtdb_species": "s__Hyphomonas sp018830285", "ani": 82.3251, "matched_fragments": 741, "total_fragments": 1349, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas", "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_000685275.1", "gtdb_species": "s__Hyphomonas johnsonii", "ani": 81.5015, "matched_fragments": 690, "total_fragments": 1349, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas", "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_018819265.1", "gtdb_species": "s__Filomicrobium sp018819265", "ani": 75.7794, "matched_fragments": 59, "total_fragments": 1349, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Filomicrobium", "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": -0.046, "cell_length": 0.0, "doubling_h": null, "growth_tmp": 30.0, "optimum_tmp": 37.0, "optimum_ph": null, "genome_size": 4280175.0, "gc_content": 61.9, "coding_genes": 3467.333, "rRNA16S_genes": 1.0, "tRNA_genes": 43.0, "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": 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": [ "Hyphomonas", "oceanitis", "SCH89" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }