{ "type": "genome", "identifier": "GCF_000422925.1", "organism": "Paludibacterium yongneupense DSM 18731", "title": "Paludibacterium yongneupense DSM 18731", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000422925.1", "bioproject": "PRJNA224116", "biosample": "SAMN02440653", "wgs_master": "AUGZ00000000.1", "refseq_category": "na", "taxid": "1122928", "species_taxid": "400061", "organism_name": "Paludibacterium yongneupense DSM 18731", "infraspecific_name": "strain=DSM 18731", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/07/11", "asm_name": "ASM42292v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_000422925.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/422/925/GCF_000422925.1_ASM42292v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4332940", "genome_size_ungapped": "4327049", "gc_percent": "62.000000", "replicon_count": "0", "scaffold_count": "53", "contig_count": "62", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000422925.1-RS_2024_05_15", "annotation_date": "2024-05-15", "total_gene_count": "4125", "protein_coding_gene_count": "4010", "non_coding_gene_count": "74", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-07-11", "dateModified": "2013-07-11", "datePublished": "2013-07-11", "_annotation": { "sample_count": 1, "sample_organism": [ "Paludibacterium yongneupense DSM 18731" ], "sample_taxid": [ "1122928" ], "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": "1.214 MB", "sample_ph_range": { "min": 4080.0, "max": 4080.0 }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4332940", "Number of Sequences": "53", "Longest Sequences (bp)": "487467", "N50 (bp)": "193084", "Gap Ratio (%)": "0.135958", "GCcontent (%)": "62.2", "Number of CDSs": "4001", "Average Protein Length": "316.9", "Coding Ratio (%)": "87.8", "Number of rRNAs": "1", "Number of tRNAs": "62", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Paludibacterium yongneupense", "strain": "strain=DSM 18731", "accession": "GCA_000422925.1", "taxid": 400061, "species_taxid": 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315, "total_fragments": 1420, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chromobacterium sinusclupearum", "strain": "strain=MWU13-2610", "accession": "GCA_002902845.1", "taxid": 2077146, "species_taxid": 2077146, "relation_to_type": "type", "validated": true, "ani": 78.3205, "matched_fragments": 389, "total_fragments": 1420, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chromobacterium alticapitis", "strain": "strain=MWU14-2602", "accession": "GCA_002924365.1", "taxid": 2073169, "species_taxid": 2073169, "relation_to_type": "type", "validated": true, "ani": 78.2788, "matched_fragments": 379, "total_fragments": 1420, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Crenobacter intestini", "strain": "strain=GY 70310", "accession": "GCA_004919095.1", "taxid": 2563443, "species_taxid": 2563443, "relation_to_type": "type", "validated": true, "ani": 78.2427, "matched_fragments": 318, "total_fragments": 1420, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chromobacterium sphagni", "strain": "strain=IIBBL 14B-1", "accession": "GCA_001855555.1", "taxid": 1903179, "species_taxid": 1903179, "relation_to_type": "type", "validated": true, "ani": 78.239, "matched_fragments": 373, "total_fragments": 1420, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chromobacterium piscinae", "strain": "strain=DSM 23278", "accession": "GCA_021129175.1", "taxid": 686831, "species_taxid": 686831, "relation_to_type": "type", "validated": true, "ani": 78.2329, "matched_fragments": 397, "total_fragments": 1420, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chromobacterium amazonense", "strain": "strain=DSM 26508", "accession": "GCA_001855565.1", "taxid": 1382803, "species_taxid": 1382803, "relation_to_type": "type", "validated": true, "ani": 78.1773, "matched_fragments": 384, "total_fragments": 1420, "ani_threshold": 95, "status": 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suis", "strain": "strain=DSM 17474", "accession": "GCA_004341385.1", "taxid": 252130, "species_taxid": 252130, "relation_to_type": "type", "validated": true, "ani": 75.7895, "matched_fragments": 65, "total_fragments": 1420, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000422925.1", "gtdb_species": "s__Paludibacterium yongneupense", "ani": 100.0, "matched_fragments": 1416, "total_fragments": 1420, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Paludibacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_000527175.1", "gtdb_species": "s__Pseudogulbenkiania sp000527175", "ani": 78.8015, 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