{ "type": "genome", "identifier": "GCF_002869505.1", "organism": "Halioglobus japonicus", "title": "Halioglobus japonicus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Shandong University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002869505.1", "bioproject": "PRJNA224116", "biosample": "SAMN08279521", "wgs_master": "PKUR00000000.1", "refseq_category": "reference genome", "taxid": "930805", "species_taxid": "930805", "organism_name": "Halioglobus japonicus", "infraspecific_name": "strain=S1-36", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/01/09", "asm_name": "ASM286950v1", "asm_submitter": "Shandong University", "gbrs_paired_asm": "GCA_002869505.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/869/505/GCF_002869505.1_ASM286950v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4064193", "genome_size_ungapped": "4064193", "gc_percent": "57.500000", "replicon_count": "0", "scaffold_count": "23", "contig_count": "23", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002869505.1-RS_2024_04_27", "annotation_date": "2024-04-27", "total_gene_count": "3795", "protein_coding_gene_count": "3727", "non_coding_gene_count": "47", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-01-09", "dateModified": "2018-01-09", "datePublished": "2018-01-09", "_annotation": { "sample_count": 1, "sample_organism": [ "Halioglobus japonicus" ], "sample_taxid": [ "930805" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Pacific Ocean" ], "sample_host_location_id": [], "data_size": "1.156 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)": "4064193", "Number of Sequences": "23", "Longest Sequences (bp)": "1296195", "N50 (bp)": "1146205", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "57.7", "Number of CDSs": "3840", "Average Protein Length": "321.4", "Coding Ratio (%)": "91.1", "Number of rRNAs": "2", "Number of tRNAs": "41", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Halioglobus japonicus", "strain": "strain=S1-36", "accession": "GCA_002869505.1", "taxid": 930805, "species_taxid": 930805, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1345, "total_fragments": 1345, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Halioglobus japonicus", "strain": "strain=KCTC 23429", "accession": "GCA_014652255.1", "taxid": 930805, "species_taxid": 930805, "relation_to_type": "type", "validated": true, "ani": 99.9948, "matched_fragments": 1342, "total_fragments": 1345, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Halioglobus japonicus", "strain": "strain=NBRC 107739", "accession": "GCA_001983995.1", "taxid": 930805, "species_taxid": 930805, "relation_to_type": "type", "validated": true, "ani": 99.9894, "matched_fragments": 1345, "total_fragments": 1345, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Halioglobus maricola", "strain": "strain=IMCC14385", "accession": "GCA_009388985.1", "taxid": 2601894, "species_taxid": 2601894, "relation_to_type": "type", "validated": true, "ani": 79.4067, "matched_fragments": 548, "total_fragments": 1345, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Seongchinamella sediminis", "strain": "strain=U0301", "accession": "GCA_003457605.1", "taxid": 2283635, "species_taxid": 2283635, "relation_to_type": "type", "validated": true, "ani": 78.5526, "matched_fragments": 382, "total_fragments": 1345, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Seongchinamella unica", "strain": "strain=GH4-78", "accession": "GCA_004354085.1", "taxid": 2547392, "species_taxid": 2547392, "relation_to_type": "type", "validated": true, "ani": 78.3941, "matched_fragments": 350, "total_fragments": 1345, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Parahaliea mediterranea", "strain": "strain=DSM 21924", "accession": "GCA_003402235.1", "taxid": 651086, "species_taxid": 651086, "relation_to_type": "type", "validated": true, "ani": 77.9201, "matched_fragments": 287, "total_fragments": 1345, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Parahaliea aestuarii", "strain": "strain=S2-26", "accession": "GCA_008064635.1", "taxid": 1852021, "species_taxid": 1852021, "relation_to_type": "type", "validated": true, "ani": 77.565, "matched_fragments": 269, "total_fragments": 1345, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas lalucatii", "strain": "strain=R1b54", "accession": "GCA_018398425.1", "taxid": 1424203, "species_taxid": 1424203, "relation_to_type": "type", "validated": true, "ani": 76.6212, "matched_fragments": 90, "total_fragments": 1345, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbulbifer celer", "strain": "strain=KCTC 12973", "accession": "GCA_020991125.1", "taxid": 435905, "species_taxid": 435905, "relation_to_type": "type", "validated": true, "ani": 76.5013, "matched_fragments": 82, "total_fragments": 1345, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marinobacter xestospongiae", "strain": "strain=JCM 17469", "accession": "GCA_023156385.1", "taxid": 994319, "species_taxid": 994319, "relation_to_type": "type", "validated": true, "ani": 76.4842, "matched_fragments": 71, "total_fragments": 1345, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001983995.1", "gtdb_species": "s__Halioglobus japonicus", "ani": 99.9894, "matched_fragments": 1345, "total_fragments": 1345, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.41", "min_intra_species_ani": "98.25", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.92", "num_clustered_genomes": 4, "status": "conclusive" }, { "accession": "GCF_009388985.1", "gtdb_species": "s__Halioglobus maricola", "ani": 79.4067, "matched_fragments": 548, "total_fragments": 1345, "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": "-" }, { "accession": "GCF_003457605.1", "gtdb_species": "s__Halioglobus sediminis", "ani": 78.5526, "matched_fragments": 382, "total_fragments": 1345, "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": "-" }, { "accession": "GCA_004354085.1", "gtdb_species": "s__Halioglobus sp004354085", "ani": 78.3941, "matched_fragments": 350, "total_fragments": 1345, "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": "-" }, { "accession": "GCF_004745945.1", "gtdb_species": "s__Halioglobus sp004745945", "ani": 77.9993, "matched_fragments": 307, "total_fragments": 1345, "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": "-" }, { "accession": "GCF_003402235.1", "gtdb_species": "s__Parahaliea mediterranea", "ani": 77.9124, "matched_fragments": 287, "total_fragments": 1345, "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": "GCF_017255185.1", "gtdb_species": "s__Parahaliea mediterranea_A", "ani": 77.7778, "matched_fragments": 278, "total_fragments": 1345, "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": "GCF_008370495.1", "gtdb_species": "s__Halioglobus sp008370495", "ani": 77.7692, "matched_fragments": 302, "total_fragments": 1345, "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": "-" }, { "accession": "GCF_008064665.1", "gtdb_species": "s__Parahaliea maris", "ani": 77.7534, "matched_fragments": 276, "total_fragments": 1345, "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": "GCF_008064635.1", "gtdb_species": "s__Parahaliea aestuarii", "ani": 77.565, "matched_fragments": 269, "total_fragments": 1345, "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": "GCF_002866825.1", "gtdb_species": "s__Halioglobus lutimaris", "ani": 77.54, "matched_fragments": 245, "total_fragments": 1345, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.98", "min_intra_species_ani": "98.98", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_002699145.1", "gtdb_species": "s__Halioglobus sp002699145", "ani": 77.2164, "matched_fragments": 254, "total_fragments": 1345, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.96", "min_intra_species_ani": "99.96", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_002416125.1", "gtdb_species": "s__Haliea sp002416125", "ani": 76.9685, "matched_fragments": 164, "total_fragments": 1345, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.96", "min_intra_species_ani": "99.96", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.398, "cell_length": -0.398, "doubling_h": null, "growth_tmp": 25.0, "optimum_tmp": 22.5, "optimum_ph": 7.5, "genome_size": 4116358.5, "gc_content": 57.7, "coding_genes": 3595.0, "rRNA16S_genes": 2.0, "tRNA_genes": 42.0, "gram_stain": null, "sporulation": null, "motility": 0.0, "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": 0.0, "coccus_cell_shape": 1.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Halioglobus", "japonicus" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }