{ "type": "genome", "identifier": "GCF_005938215.1", "organism": "Ruegeria sediminis", "title": "Ruegeria sediminis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Chung-Ang University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_005938215.1", "bioproject": "PRJNA224116", "biosample": "SAMN11860882", "wgs_master": "VCPD00000000.1", "refseq_category": "reference genome", "taxid": "2583820", "species_taxid": "2583820", "organism_name": "Ruegeria sediminis", "infraspecific_name": "strain=CAU 1488", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/06/03", "asm_name": "ASM593821v1", "asm_submitter": "Chung-Ang University", "gbrs_paired_asm": "GCA_005938215.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/005/938/215/GCF_005938215.1_ASM593821v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4230323", "genome_size_ungapped": "4230323", "gc_percent": "63.000000", "replicon_count": "0", "scaffold_count": "18", "contig_count": "18", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_005938215.1-RS_2024_05_04", "annotation_date": "2024-05-04", "total_gene_count": "4168", "protein_coding_gene_count": "4074", "non_coding_gene_count": "54", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-06-03", "dateModified": "2019-06-03", "datePublished": "2019-06-03", "_annotation": { "sample_count": 1, "sample_organism": [ "Ruegeria sediminis" ], "sample_taxid": [ "2583820" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea" ], "sample_host_location_id": [], "data_size": "1.175 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)": "4230323", "Number of Sequences": "18", "Longest Sequences (bp)": "900989", "N50 (bp)": "623971", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "63.2", "Number of CDSs": "4104", "Average Protein Length": "308.4", "Coding Ratio (%)": "89.8", "Number of rRNAs": "3", "Number of tRNAs": "48", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Ruegeria sediminis", "strain": "strain=CAU 1488", "accession": "GCA_005938215.1", "taxid": 2583820, "species_taxid": 2583820, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1401, "total_fragments": 1401, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Ruegeria marisrubri", "strain": "strain=ZGT118", "accession": "GCA_001507595.1", "taxid": 1685379, "species_taxid": 1685379, "relation_to_type": "type", "validated": true, "ani": 84.3419, "matched_fragments": 964, "total_fragments": 1401, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ruegeria intermedia", "strain": "strain=DSM 29341", "accession": "GCA_900129345.1", "taxid": 996115, "species_taxid": 996115, "relation_to_type": "type", "validated": true, "ani": 82.5408, "matched_fragments": 786, "total_fragments": 1401, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cribrihabitans marinus", "strain": "strain=DSM 29340", "accession": "GCA_900109035.1", "taxid": 1227549, "species_taxid": 1227549, "relation_to_type": "type", "validated": true, "ani": 81.2316, "matched_fragments": 720, "total_fragments": 1401, "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": 81.1722, "matched_fragments": 714, "total_fragments": 1401, "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": 81.164, "matched_fragments": 793, "total_fragments": 1401, "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": 80.97, "matched_fragments": 792, "total_fragments": 1401, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Antarcticimicrobium luteum", "strain": "strain=318-1", "accession": "GCA_004358185.1", "taxid": 2547397, "species_taxid": 2547397, "relation_to_type": "type", "validated": true, "ani": 80.1914, "matched_fragments": 660, "total_fragments": 1401, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leisingera aquaemixtae", "strain": "strain=CECT 8399", "accession": "GCA_001458395.1", "taxid": 1396826, "species_taxid": 1396826, "relation_to_type": "type", "validated": true, "ani": 79.8909, "matched_fragments": 657, "total_fragments": 1401, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ruegeria conchae", "strain": "strain=TW15", "accession": "GCA_000192475.2", "taxid": 981384, "species_taxid": 981384, "relation_to_type": "suspected-type", "validated": true, "ani": 78.9531, "matched_fragments": 518, "total_fragments": 1401, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodovulum tesquicola", "strain": "strain=A-36s", "accession": "GCA_024128855.1", "taxid": 540254, "species_taxid": 540254, "relation_to_type": "type", "validated": true, "ani": 78.5772, "matched_fragments": 420, "total_fragments": 1401, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cereibacter sediminicola", "strain": "strain=JA983", "accession": "GCA_007668225.1", "taxid": 2584941, "species_taxid": 2584941, "relation_to_type": "type", "validated": true, "ani": 78.4834, "matched_fragments": 359, "total_fragments": 1401, "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": 78.2369, "matched_fragments": 385, "total_fragments": 1401, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Palleronia sediminis", "strain": "strain=SS33", "accession": "GCA_004358695.1", "taxid": 2547833, "species_taxid": 2547833, "relation_to_type": "type", "validated": true, "ani": 77.8659, "matched_fragments": 335, "total_fragments": 1401, "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": 77.8497, "matched_fragments": 348, "total_fragments": 1401, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_005938215.1", "gtdb_species": "s__Ruegeria sediminis", "ani": 100.0, "matched_fragments": 1401, "total_fragments": 1401, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria", "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, 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