{ "type": "genome", "identifier": "GCF_003990645.1", "organism": "Shimia sediminis", "title": "Shimia sediminis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Zhejiang University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003990645.1", "bioproject": "PRJNA224116", "biosample": "SAMN10617556", "wgs_master": "RYZK00000000.1", "refseq_category": "reference genome", "taxid": "2497945", "species_taxid": "2497945", "organism_name": "Shimia sediminis", "infraspecific_name": "strain=ZQ172", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/01/02", "asm_name": "ASM399064v1", "asm_submitter": "Zhejiang University", "gbrs_paired_asm": "GCA_003990645.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/990/645/GCF_003990645.1_ASM399064v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4367258", "genome_size_ungapped": "4367258", "gc_percent": "59.000000", "replicon_count": "0", "scaffold_count": "127", "contig_count": "127", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003990645.1-RS_2024_08_01", "annotation_date": "2024-08-01", "total_gene_count": "4308", "protein_coding_gene_count": "4218", "non_coding_gene_count": "51", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-01-02", "dateModified": "2019-01-02", "datePublished": "2019-01-02", "_annotation": { "sample_count": 1, "sample_organism": [ "Shimia sediminis" ], "sample_taxid": [ "2497945" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: East China Sea" ], "sample_host_location_id": [], "data_size": "1.235 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 2.46, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4367258", "Number of Sequences": "127", "Longest Sequences (bp)": "906594", "N50 (bp)": "412229", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "58.9", "Number of CDSs": "4299", "Average Protein Length": "301.0", "Coding Ratio (%)": "88.9", "Number of rRNAs": "4", "Number of tRNAs": "44", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Shimia sediminis", "strain": "strain=ZQ172", "accession": "GCA_003990645.1", "taxid": 2497945, "species_taxid": 2497945, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1414, "total_fragments": 1417, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Shimia gijangensis", "strain": "strain=DSM 100564", "accession": "GCA_900142085.1", "taxid": 1470563, "species_taxid": 1470563, "relation_to_type": "type", "validated": true, "ani": 79.2216, "matched_fragments": 559, "total_fragments": 1417, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shimia haliotis", "strain": "strain=DSM 28453", "accession": "GCA_900114415.1", "taxid": 1280847, "species_taxid": 1280847, "relation_to_type": "type", "validated": true, "ani": 78.4198, "matched_fragments": 384, "total_fragments": 1417, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Falsiruegeria litorea", "strain": "strain=CECT 7639", "accession": "GCA_900172225.1", "taxid": 1280831, "species_taxid": 1280831, "relation_to_type": "type", "validated": true, "ani": 78.3664, "matched_fragments": 405, "total_fragments": 1417, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ruegeria pomeroyi", "strain": "strain=DSS-3", "accession": "GCA_000011965.2", "taxid": 89184, "species_taxid": 89184, "relation_to_type": "suspected-type", "validated": true, "ani": 78.2981, "matched_fragments": 450, "total_fragments": 1417, "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": 78.1506, "matched_fragments": 396, "total_fragments": 1417, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leisingera methylohalidivorans", "strain": "strain=DSM 14336; MB2", "accession": "GCA_000511355.1", "taxid": 133924, "species_taxid": 133924, "relation_to_type": "type", "validated": true, "ani": 78.0736, "matched_fragments": 383, "total_fragments": 1417, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseovarius nubinhibens", "strain": "strain=ISM", "accession": "GCA_000152625.1", "taxid": 314263, "species_taxid": 314263, "relation_to_type": "type", "validated": true, "ani": 78.01, "matched_fragments": 346, "total_fragments": 1417, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shimia marina", "strain": "strain=CECT 7688", "accession": "GCA_001458175.1", "taxid": 321267, "species_taxid": 321267, "relation_to_type": "type", "validated": true, "ani": 77.9624, "matched_fragments": 319, "total_fragments": 1417, "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": 77.9613, "matched_fragments": 352, "total_fragments": 1417, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shimia marina", "strain": "strain=DSM 26895", "accession": "GCA_900112745.1", "taxid": 321267, "species_taxid": 321267, "relation_to_type": "type", "validated": true, "ani": 77.9524, "matched_fragments": 320, "total_fragments": 1417, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thalassobius aquimarinus", "strain": "strain=KMM 8518", "accession": "GCA_018219815.1", "taxid": 2785917, "species_taxid": 2785917, "relation_to_type": "type", "validated": true, "ani": 77.9044, "matched_fragments": 371, "total_fragments": 1417, "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": 77.8757, "matched_fragments": 355, "total_fragments": 1417, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aestuariivita boseongensis", "strain": "strain=BS-B2", "accession": "GCA_001262635.1", "taxid": 1470562, "species_taxid": 1470562, "relation_to_type": "type", "validated": true, "ani": 77.8749, "matched_fragments": 335, "total_fragments": 1417, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudophaeobacter arcticus", "strain": "strain=DSM 23566", "accession": "GCA_000473205.1", "taxid": 385492, "species_taxid": 385492, "relation_to_type": "type", "validated": true, "ani": 77.8569, "matched_fragments": 317, "total_fragments": 1417, "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": 77.6595, "matched_fragments": 249, "total_fragments": 1417, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudophaeobacter leonis", "strain": "strain=306", "accession": "GCA_002087335.1", "taxid": 1144477, "species_taxid": 1144477, "relation_to_type": "type", "validated": true, "ani": 77.5861, "matched_fragments": 301, "total_fragments": 1417, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sulfitobacter mediterraneus", "strain": "strain=DSM 12244", "accession": "GCA_003054325.1", "taxid": 83219, "species_taxid": 83219, "relation_to_type": "type", "validated": true, "ani": 77.5833, "matched_fragments": 276, "total_fragments": 1417, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseibacterium elongatum", "strain": "strain=DFL-43", "accession": "GCA_000590925.1", "taxid": 159346, "species_taxid": 159346, "relation_to_type": "type", "validated": true, "ani": 77.5201, "matched_fragments": 242, "total_fragments": 1417, "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": 77.5137, "matched_fragments": 307, "total_fragments": 1417, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Celeribacter litoreus", "strain": "strain=ASW11-22", "accession": "GCA_020165855.1", "taxid": 2876714, "species_taxid": 2876714, "relation_to_type": "type", "validated": true, "ani": 77.1471, "matched_fragments": 152, "total_fragments": 1417, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Alexandriicola marinus", "strain": "strain=LZ-14", "accession": "GCA_004000435.1", "taxid": 2081710, "species_taxid": 2081710, "relation_to_type": "type", "validated": true, "ani": 76.964, "matched_fragments": 215, "total_fragments": 1417, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tabrizicola sediminis", "strain": "strain=DRYC-M-16", "accession": "GCA_004745575.1", "taxid": 2486418, "species_taxid": 2486418, "relation_to_type": "type", "validated": true, "ani": 76.8114, "matched_fragments": 210, "total_fragments": 1417, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cereibacter azotoformans", "strain": "strain=KA25", "accession": "GCA_003050905.1", "taxid": 43057, "species_taxid": 43057, "relation_to_type": "type", "validated": true, "ani": 76.6634, "matched_fragments": 196, "total_fragments": 1417, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 2.46, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003990645.1", "gtdb_species": "s__Shimia sediminis", "ani": 100.0, "matched_fragments": 1414, "total_fragments": 1417, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia", "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_900114635.1", "gtdb_species": "s__Shimia aestuarii", "ani": 79.5274, 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