{ "type": "genome", "identifier": "GCF_900116725.1", "organism": "Aliiroseovarius crassostreae", "title": "Aliiroseovarius crassostreae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900116725.1", "bioproject": "PRJNA224116", "biosample": "SAMN04488527", "wgs_master": "FPBS00000000.1", "refseq_category": "na", "taxid": "154981", "species_taxid": "154981", "organism_name": "Aliiroseovarius crassostreae", "infraspecific_name": "strain=DSM 16950", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/11/02", "asm_name": "IMG-taxon 2619619030 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900116725.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/116/725/GCF_900116725.1_IMG-taxon_2619619030_annotated_assembly", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3662395", "genome_size_ungapped": "3661210", "gc_percent": "58.500000", "replicon_count": "0", "scaffold_count": "90", "contig_count": "90", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900116725.1-RS_2024_12_23", "annotation_date": "2024-12-23", "total_gene_count": "3718", "protein_coding_gene_count": "3540", "non_coding_gene_count": "54", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-11-02", "dateModified": "2016-11-02", "datePublished": "2016-11-02", "_annotation": { "sample_count": 1, "sample_organism": [ "Aliiroseovarius crassostreae" ], "sample_taxid": [ "154981" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.035 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)": "3662395", "Number of Sequences": "90", "Longest Sequences (bp)": "582305", "N50 (bp)": "105626", "Gap Ratio (%)": "0.032356", "GCcontent (%)": "58.5", "Number of CDSs": "3626", "Average Protein Length": "290.3", "Coding Ratio (%)": "86.2", "Number of rRNAs": "5", "Number of tRNAs": "48", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Aliiroseovarius crassostreae", "strain": "strain=DSM 16950", "accession": "GCA_900116725.1", "taxid": 154981, "species_taxid": 154981, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1165, "total_fragments": 1174, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Aliiroseovarius crassostreae", "strain": "strain=CV919-312", "accession": "GCA_001307765.1", "taxid": 154981, "species_taxid": 154981, "relation_to_type": "type", "validated": true, "ani": 99.9962, "matched_fragments": 1171, "total_fragments": 1174, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Aliiroseovarius marinus", "strain": "strain=A6024", "accession": "GCA_004360145.1", "taxid": 2500159, "species_taxid": 2500159, "relation_to_type": "type", "validated": true, "ani": 79.7239, "matched_fragments": 444, "total_fragments": 1174, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aliiroseovarius zhejiangensis", "strain": "strain=KCTC 42443", "accession": "GCA_014656375.1", "taxid": 1632025, "species_taxid": 1632025, "relation_to_type": "type", "validated": true, "ani": 79.4875, "matched_fragments": 457, "total_fragments": 1174, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aliiroseovarius pelagivivens", "strain": "strain=CECT 8811", "accession": "GCA_900302485.1", "taxid": 1639690, "species_taxid": 1639690, "relation_to_type": "type", "validated": true, "ani": 79.4015, "matched_fragments": 405, "total_fragments": 1174, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aliiroseovarius halocynthiae", "strain": "strain=MA1-10", "accession": "GCA_007004645.1", "taxid": 985055, "species_taxid": 985055, "relation_to_type": "type", "validated": true, "ani": 78.9398, "matched_fragments": 401, "total_fragments": 1174, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thalassobius mangrovi", "strain": "strain=GS-10", "accession": "GCA_009857745.1", "taxid": 2692236, "species_taxid": 2692236, "relation_to_type": "type", "validated": true, "ani": 78.107, "matched_fragments": 302, "total_fragments": 1174, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phaeobacter gallaeciensis", "strain": "strain=DSM 26640", "accession": "GCA_000511385.1", "taxid": 60890, "species_taxid": 60890, "relation_to_type": "type", "validated": true, "ani": 78.091, "matched_fragments": 268, "total_fragments": 1174, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phaeobacter gallaeciensis", "strain": "strain=DSM 26640", "accession": "GCA_000819625.1", "taxid": 60890, "species_taxid": 60890, "relation_to_type": "type", "validated": true, "ani": 78.0413, "matched_fragments": 265, "total_fragments": 1174, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phaeobacter piscinae", "strain": "strain=P14", "accession": "GCA_002407245.1", "taxid": 1580596, "species_taxid": 1580596, "relation_to_type": "type", "validated": true, "ani": 77.9744, "matched_fragments": 290, "total_fragments": 1174, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tritonibacter mobilis", "strain": "strain=DSM 23403", "accession": "GCA_900106635.1", "taxid": 379347, "species_taxid": 379347, "relation_to_type": "type", "validated": true, "ani": 77.9045, "matched_fragments": 241, "total_fragments": 1174, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tritonibacter mobilis", "strain": "strain=NBRC101030", "accession": "GCA_001681715.1", "taxid": 379347, "species_taxid": 379347, "relation_to_type": "type", "validated": true, "ani": 77.8203, "matched_fragments": 245, "total_fragments": 1174, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudophaeobacter flagellatus", "strain": "strain=MA21411-1", "accession": "GCA_021228235.1", "taxid": 2899119, "species_taxid": 2899119, "relation_to_type": "type", "validated": true, "ani": 77.377, "matched_fragments": 255, "total_fragments": 1174, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseovarius aestuarii", "strain": "strain=KCTC 22174", "accession": "GCA_019966515.1", "taxid": 475083, "species_taxid": 475083, "relation_to_type": "type", "validated": true, "ani": 77.3185, "matched_fragments": 205, "total_fragments": 1174, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudooceanicola aestuarii", "strain": "strain=E2-1", "accession": "GCA_010614805.1", "taxid": 2697319, "species_taxid": 2697319, "relation_to_type": "type", "validated": true, "ani": 77.2548, "matched_fragments": 194, "total_fragments": 1174, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodovulum sulfidophilum", "strain": "strain=DSM 1374", "accession": "GCA_000520135.2", "taxid": 35806, "species_taxid": 35806, "relation_to_type": "type", "validated": true, "ani": 77.2537, "matched_fragments": 211, "total_fragments": 1174, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Salipiger pallidus", "strain": "strain=CGMCC 1.15762", "accession": "GCA_014643635.1", "taxid": 1775170, "species_taxid": 1775170, "relation_to_type": "type", "validated": true, "ani": 77.24, "matched_fragments": 188, "total_fragments": 1174, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Salipiger marinus", "strain": "strain=DSM 26424", "accession": "GCA_900100085.1", "taxid": 555512, "species_taxid": 555512, "relation_to_type": "type", "validated": true, "ani": 77.2159, "matched_fragments": 266, "total_fragments": 1174, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodovulum sulfidophilum", "strain": "strain=DSM 1374", "accession": "GCA_001633165.1", "taxid": 35806, "species_taxid": 35806, "relation_to_type": "type", "validated": true, "ani": 77.1888, "matched_fragments": 212, "total_fragments": 1174, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Zongyanglinia huanghaiensis", "strain": "strain=CY05", "accession": "GCA_009753675.1", "taxid": 2682100, "species_taxid": 2682100, "relation_to_type": "type", "validated": true, "ani": 77.1098, "matched_fragments": 169, "total_fragments": 1174, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phaeovulum veldkampii", "strain": "strain=DSM 11550", "accession": "GCA_003034995.1", "taxid": 33049, "species_taxid": 33049, "relation_to_type": "type", "validated": true, "ani": 77.0735, "matched_fragments": 190, "total_fragments": 1174, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phaeovulum veldkampii", "strain": "strain=DSM 11550", "accession": "GCA_016653435.1", "taxid": 33049, "species_taxid": 33049, "relation_to_type": "type", "validated": true, "ani": 77.0349, "matched_fragments": 189, "total_fragments": 1174, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phaeovulum veldkampii", "strain": "strain=DSM 11550", "accession": "GCA_004363195.1", "taxid": 33049, "species_taxid": 33049, "relation_to_type": "type", "validated": true, "ani": 77.0319, "matched_fragments": 192, "total_fragments": 1174, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001307765.1", "gtdb_species": "s__Aliiroseovarius crassostreae", "ani": 99.9962, "matched_fragments": 1171, "total_fragments": 1174, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.06", "min_intra_species_ani": "95.64", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.84", "num_clustered_genomes": 18, "status": "conclusive" }, { "accession": "GCF_004360145.1", "gtdb_species": "s__Aliiroseovarius marinus", "ani": 79.7239, "matched_fragments": 444, "total_fragments": 1174, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius", "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_010500215.1", "gtdb_species": "s__Aliiroseovarius sp010500215", "ani": 79.6737, "matched_fragments": 448, "total_fragments": 1174, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius", "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_014656375.1", "gtdb_species": "s__Aliiroseovarius zhejiangensis", "ani": 79.4765, "matched_fragments": 458, "total_fragments": 1174, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius", "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_900302485.1", "gtdb_species": "s__Aliiroseovarius pelagivivens", "ani": 79.4015, "matched_fragments": 405, "total_fragments": 1174, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius", "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_002340515.1", "gtdb_species": "s__Aliiroseovarius sp002340515", "ani": 79.034, "matched_fragments": 455, "total_fragments": 1174, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius", "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_007004645.1", "gtdb_species": "s__Aliiroseovarius halocynthiae", "ani": 78.9511, "matched_fragments": 400, "total_fragments": 1174, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius", "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_018599245.1", "gtdb_species": "s__Aliiroseovarius lamellibrachiae", "ani": 78.9256, "matched_fragments": 482, "total_fragments": 1174, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius", "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_009857745.1", "gtdb_species": "s__Thalassobius mangrovi", "ani": 78.107, "matched_fragments": 302, "total_fragments": 1174, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius", "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_000511385.1", "gtdb_species": "s__Phaeobacter gallaeciensis", "ani": 78.091, "matched_fragments": 268, "total_fragments": 1174, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.42", "min_intra_species_ani": "98.01", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.96", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_000473325.1", "gtdb_species": "s__Leisingera caerulea", "ani": 78.0438, "matched_fragments": 327, "total_fragments": 1174, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera", "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_002407245.1", "gtdb_species": "s__Phaeobacter piscinae", "ani": 77.9743, "matched_fragments": 290, "total_fragments": 1174, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.42", "min_intra_species_ani": "96.04", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.90", "num_clustered_genomes": 10, "status": "-" }, { "accession": "GCF_001681715.1", "gtdb_species": "s__Epibacterium mobile", "ani": 77.8073, "matched_fragments": 246, "total_fragments": 1174, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.01", "min_intra_species_ani": "96.41", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.87", "num_clustered_genomes": 56, "status": "-" }, { "accession": "GCA_002367285.1", "gtdb_species": "s__Aliiroseovarius sp002367285", "ani": 77.7649, "matched_fragments": 299, "total_fragments": 1174, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius", "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_900109145.1", "gtdb_species": "s__Marinovum algicola", "ani": 77.4901, "matched_fragments": 293, "total_fragments": 1174, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.11", "min_intra_species_ani": "98.22", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.88", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_900172285.1", "gtdb_species": "s__Roseovarius aestuarii", "ani": 77.3373, "matched_fragments": 202, "total_fragments": 1174, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius", "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_003034995.1", "gtdb_species": "s__Phaeovulum veldkampii", "ani": 77.086, "matched_fragments": 189, "total_fragments": 1174, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeovulum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.97", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.94", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_017854585.1", "gtdb_species": "s__JAFMHK01 sp017854585", "ani": 76.6439, "matched_fragments": 129, "total_fragments": 1174, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAFMHK01", "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": 0.447, "doubling_h": null, "growth_tmp": 27.5, "optimum_tmp": 34.0, "optimum_ph": 7.25, "genome_size": 3692925.0, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": null, "motility": 1.0, "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": 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": [ "Aliiroseovarius", "crassostreae" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }