{ "type": "genome", "identifier": "GCF_003316635.1", "organism": "Roseovarius dicentrarchi", "title": "Roseovarius dicentrarchi", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Shandong University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003316635.1", "bioproject": "PRJNA224116", "biosample": "SAMN09507747", "wgs_master": "QNQP00000000.1", "refseq_category": "reference genome", "taxid": "2250573", "species_taxid": "2250573", "organism_name": "Roseovarius dicentrarchi", "infraspecific_name": "strain=YLY04", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/07/13", "asm_name": "ASM331663v1", "asm_submitter": "Shandong University", "gbrs_paired_asm": "GCA_003316635.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/316/635/GCF_003316635.1_ASM331663v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3515059", "genome_size_ungapped": "3515059", "gc_percent": "62.500000", "replicon_count": "0", "scaffold_count": "92", "contig_count": "92", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003316635.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "3428", "protein_coding_gene_count": "3307", "non_coding_gene_count": "48", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-07-13", "dateModified": "2018-07-13", "datePublished": "2018-07-13", "_annotation": { "sample_count": 1, "sample_organism": [ "Roseovarius dicentrarchi" ], "sample_taxid": [ "2250573" ], "sample_host_organism": [ "Dicentrarchus labrax" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Weihai" ], "sample_host_location_id": [], "data_size": "0.978 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)": "3515059", "Number of Sequences": "92", "Longest Sequences (bp)": "303646", "N50 (bp)": "121228", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "62.7", "Number of CDSs": "3335", "Average Protein Length": "313.1", "Coding Ratio (%)": "89.1", "Number of rRNAs": "3", "Number of tRNAs": "43", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pelagivirga dicentrarchi", "strain": "strain=YLY04", "accession": "GCA_003316635.1", "taxid": 2250573, "species_taxid": 2250573, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1128, "total_fragments": 1132, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pelagivirga sediminicola", "strain": "strain=BH-SD19", "accession": "GCA_003072125.1", "taxid": 2170575, "species_taxid": 2170575, "relation_to_type": "type", "validated": true, "ani": 84.9201, "matched_fragments": 828, "total_fragments": 1132, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseovarius pacificus", "strain": "strain=DSM 29589", "accession": "GCA_900142665.1", "taxid": 337701, "species_taxid": 337701, "relation_to_type": "type", "validated": true, "ani": 79.0806, "matched_fragments": 468, "total_fragments": 1132, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseovarius pacificus", "strain": "strain=CGMCC 1.7083", "accession": "GCA_014645335.1", "taxid": 337701, "species_taxid": 337701, "relation_to_type": "type", "validated": true, "ani": 79.0056, "matched_fragments": 472, "total_fragments": 1132, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseovarius indicus", "strain": "strain=DSM 26383", "accession": "GCA_008728195.1", "taxid": 540747, "species_taxid": 540747, "relation_to_type": "type", "validated": true, "ani": 78.9549, "matched_fragments": 433, "total_fragments": 1132, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseovarius indicus", "strain": "strain=B108", "accession": "GCA_001441635.1", "taxid": 540747, "species_taxid": 540747, "relation_to_type": "type", "validated": true, "ani": 78.7773, "matched_fragments": 433, "total_fragments": 1132, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudosulfitobacter pseudonitzschiae", "strain": "strain=H3", "accession": "GCA_000712315.1", "taxid": 1402135, "species_taxid": 1402135, "relation_to_type": "type", "validated": true, "ani": 78.3688, "matched_fragments": 403, "total_fragments": 1132, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cribrihabitans marinus", "strain": "strain=CGMCC 1.13219", "accession": "GCA_014640375.1", "taxid": 1227549, "species_taxid": 1227549, "relation_to_type": "type", "validated": true, "ani": 78.2926, "matched_fragments": 398, "total_fragments": 1132, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseovarius confluentis", "strain": "strain=SAG6", "accession": "GCA_002917925.1", "taxid": 1852027, "species_taxid": 1852027, "relation_to_type": "type", "validated": true, "ani": 78.2912, "matched_fragments": 433, "total_fragments": 1132, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudosulfitobacter pseudonitzschiae", "strain": "strain=DSM 26824", "accession": "GCA_900129395.1", "taxid": 1402135, "species_taxid": 1402135, "relation_to_type": "type", "validated": true, "ani": 78.2611, "matched_fragments": 407, "total_fragments": 1132, "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": 78.2179, "matched_fragments": 279, "total_fragments": 1132, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseovarius nitratireducens", "strain": "strain=TFZ", "accession": "GCA_002925845.1", "taxid": 2044597, "species_taxid": 2044597, "relation_to_type": "type", "validated": true, "ani": 78.1786, "matched_fragments": 399, "total_fragments": 1132, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sulfitobacter sabulilitoris", "strain": "strain=HSMS-29", "accession": "GCA_005887615.1", "taxid": 2562655, "species_taxid": 2562655, "relation_to_type": "type", "validated": true, "ani": 77.9404, "matched_fragments": 387, "total_fragments": 1132, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Palleronia sediminis", "strain": "strain=SS33", "accession": "GCA_004358695.1", "taxid": 2547833, "species_taxid": 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true, "ani": 77.7398, "matched_fragments": 296, "total_fragments": 1132, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ruegeria marina", "strain": "strain=CGMCC 1.9108", "accession": "GCA_900101475.1", "taxid": 639004, "species_taxid": 639004, "relation_to_type": "type", "validated": true, "ani": 77.6581, "matched_fragments": 350, "total_fragments": 1132, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudooceanicola nitratireducens", "strain": "strain=CGMCC 1.7292", "accession": "GCA_900109195.1", "taxid": 517719, "species_taxid": 517719, "relation_to_type": "type", "validated": true, "ani": 77.5726, "matched_fragments": 321, "total_fragments": 1132, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudooceanicola onchidii", "strain": "strain=XY-99", "accession": "GCA_004959925.1", "taxid": 2562279, "species_taxid": 2562279, "relation_to_type": "type", "validated": true, "ani": 77.5342, "matched_fragments": 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"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": 76.8792, "matched_fragments": 245, "total_fragments": 1132, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003316635.1", "gtdb_species": "s__Roseovarius dicentrarchi", "ani": 100.0, "matched_fragments": 1128, "total_fragments": 1132, "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": "conclusive" }, { "accession": 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"filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.142, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Roseovarius", "dicentrarchi" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }