{ "type": "genome", "identifier": "GCF_001458295.1", "organism": "Ruegeria denitrificans", "title": "Ruegeria denitrificans", "description": "na", "data type": "Genome sequencing and assembly", "organization": "UVEG", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001458295.1", "bioproject": "PRJNA224116", "biosample": "SAMEA3542132", "wgs_master": "CYUD00000000.1", "refseq_category": "reference genome", "taxid": "1715692", "species_taxid": "1715692", "organism_name": "Ruegeria denitrificans", "infraspecific_name": "strain=CECT 5091", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2015/11/09", "asm_name": "Ruegeria_sp._CECT5091_Spades_Prokka", "asm_submitter": "UVEG", "gbrs_paired_asm": "GCA_001458295.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/458/295/GCF_001458295.1_Ruegeria_sp._CECT5091_Spades_Prokka", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4620120", "genome_size_ungapped": "4620120", "gc_percent": "56.500000", "replicon_count": "0", "scaffold_count": "42", "contig_count": "42", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001458295.1-RS_2024_08_20", "annotation_date": "2024-08-20", "total_gene_count": "4535", "protein_coding_gene_count": "4435", "non_coding_gene_count": "51", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2015-11-09", "dateModified": "2015-11-09", "datePublished": "2015-11-09", "_annotation": { "sample_count": 1, "sample_organism": [ "Ruegeria denitrificans" ], "sample_taxid": [ "1715692" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Mediterranean Sea" ], "sample_host_location_id": [], "data_size": "1.313 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)": "4620120", "Number of Sequences": "42", "Longest Sequences (bp)": "582879", "N50 (bp)": "290832", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "56.7", "Number of CDSs": "4561", "Average Protein Length": "300.0", "Coding Ratio (%)": "88.8", "Number of rRNAs": "3", "Number of tRNAs": "46", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Ruegeria denitrificans", "strain": "strain=CECT 5091", "accession": "GCA_001458295.1", "taxid": 1715692, "species_taxid": 1715692, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1513, "total_fragments": 1517, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Ruegeria atlantica", "strain": "strain=CECT 4292", "accession": "GCA_001458195.1", "taxid": 81569, "species_taxid": 81569, "relation_to_type": "suspected-type", "validated": true, "ani": 82.1843, "matched_fragments": 890, "total_fragments": 1517, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ruegeria meonggei", "strain": "strain=CECT 8411", "accession": "GCA_900172215.1", "taxid": 1446476, "species_taxid": 1446476, "relation_to_type": "type", "validated": true, "ani": 81.895, "matched_fragments": 907, "total_fragments": 1517, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ruegeria faecimaris", "strain": "strain=DSM 28009", "accession": "GCA_900182615.1", "taxid": 686389, "species_taxid": 686389, "relation_to_type": "type", "validated": true, "ani": 81.4123, "matched_fragments": 833, "total_fragments": 1517, "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": 81.3245, "matched_fragments": 752, "total_fragments": 1517, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ruegeria conchae", "strain": "strain=DSM 29317", "accession": "GCA_003664205.1", "taxid": 981384, "species_taxid": 981384, "relation_to_type": "suspected-type", "validated": true, "ani": 81.2573, "matched_fragments": 766, "total_fragments": 1517, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ruegeria halocynthiae", "strain": "strain=DSM 27839", "accession": "GCA_900106805.1", "taxid": 985054, "species_taxid": 985054, "relation_to_type": "type", "validated": true, "ani": 80.7934, "matched_fragments": 714, "total_fragments": 1517, "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": 80.6736, "matched_fragments": 728, "total_fragments": 1517, "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": 79.1063, "matched_fragments": 534, "total_fragments": 1517, "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": 77.8023, "matched_fragments": 369, "total_fragments": 1517, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tritonibacter aquimaris", "strain": "strain=SM1969", "accession": "GCA_009617595.1", "taxid": 2663379, "species_taxid": 2663379, "relation_to_type": "type", "validated": true, "ani": 77.7682, "matched_fragments": 249, "total_fragments": 1517, "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": 77.4734, "matched_fragments": 330, "total_fragments": 1517, "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": 77.0527, "matched_fragments": 266, "total_fragments": 1517, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Salinihabitans flavidus", "strain": "strain=DSM 27842", "accession": "GCA_900110425.1", "taxid": 569882, 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