{ "type": "genome", "identifier": "GCF_013179735.1", "organism": "Permianibacter fluminis", "title": "Permianibacter fluminis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Inha University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_013179735.1", "bioproject": "PRJNA224116", "biosample": "SAMN14986807", "wgs_master": "JABMEG000000000.1", "refseq_category": "reference genome", "taxid": "2738515", "species_taxid": "2738515", "organism_name": "Permianibacter fluminis", "infraspecific_name": "strain=IMCC34836", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/05/27", "asm_name": "ASM1317973v1", "asm_submitter": "Inha University", "gbrs_paired_asm": "GCA_013179735.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/013/179/735/GCF_013179735.1_ASM1317973v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4359061", "genome_size_ungapped": "4359061", "gc_percent": "59.000000", "replicon_count": "0", "scaffold_count": "5", "contig_count": "5", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_013179735.1-RS_2024_12_11", "annotation_date": "2024-12-11", "total_gene_count": "3818", "protein_coding_gene_count": "3742", "non_coding_gene_count": "55", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-05-27", "dateModified": "2020-05-27", "datePublished": "2020-05-27", "_annotation": { "sample_count": 1, "sample_organism": [ "Permianibacter fluminis" ], "sample_taxid": [ "2738515" ], "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": 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)": "4359061", "Number of Sequences": "5", "Longest Sequences (bp)": "3483234", "N50 (bp)": "3483234", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "59.1", "Number of CDSs": "3845", "Average Protein Length": "330.5", "Coding Ratio (%)": "87.5", "Number of rRNAs": "3", "Number of tRNAs": "48", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Permianibacter fluminis", "strain": "strain=IMCC34836", "accession": "GCA_013179735.1", "taxid": 2738515, "species_taxid": 2738515, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1450, "total_fragments": 1451, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Permianibacter aggregans", "strain": "strain=DSM 103792", "accession": "GCA_004363125.1", "taxid": 1510150, "species_taxid": 1510150, "relation_to_type": "type", "validated": true, "ani": 77.6196, "matched_fragments": 334, "total_fragments": 1451, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Permianibacter aggregans", "strain": "strain=HW001", "accession": "GCA_009756665.1", "taxid": 1510150, "species_taxid": 1510150, "relation_to_type": "type", "validated": true, "ani": 77.5593, "matched_fragments": 347, "total_fragments": 1451, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas carbonaria", "strain": "strain=CIP 111764", "accession": "GCA_904061905.1", "taxid": 2762745, "species_taxid": 2762745, "relation_to_type": "type", "validated": true, "ani": 76.3419, "matched_fragments": 101, "total_fragments": 1451, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas oryzae", "strain": "strain=KCTC 32247", "accession": "GCA_900104805.1", "taxid": 1392877, "species_taxid": 1392877, "relation_to_type": "type", "validated": true, "ani": 76.2026, "matched_fragments": 114, "total_fragments": 1451, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas alcaliphila", "strain": "strain=NBRC 102411", "accession": "GCA_002091495.1", "taxid": 101564, "species_taxid": 101564, "relation_to_type": "type", "validated": true, "ani": 76.1247, "matched_fragments": 103, "total_fragments": 1451, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas sagittaria", "strain": "strain=JCM 18195", "accession": "GCA_900115715.1", "taxid": 1135990, "species_taxid": 1135990, "relation_to_type": "type", "validated": true, "ani": 76.1137, "matched_fragments": 123, "total_fragments": 1451, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas alcaliphila", "strain": "strain=JCM 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291995, "species_taxid": 291995, "relation_to_type": "type", "validated": true, "ani": 76.0504, "matched_fragments": 101, "total_fragments": 1451, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Luteimonas gilva", "strain": "strain=H23", "accession": "GCA_005239095.1", "taxid": 2572684, "species_taxid": 2572684, "relation_to_type": "type", "validated": true, "ani": 76.0078, "matched_fragments": 80, "total_fragments": 1451, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dyella amyloliquefaciens", "strain": "strain=DHC06", "accession": "GCA_004296575.1", "taxid": 1770545, "species_taxid": 1770545, "relation_to_type": "type", "validated": true, "ani": 76.0034, "matched_fragments": 92, "total_fragments": 1451, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas nicosulfuronedens", "strain": "strain=LAM1902", "accession": "GCA_005877905.1", "taxid": 2571105, "species_taxid": 2571105, "relation_to_type": "type", "validated": true, "ani": 75.9791, "matched_fragments": 108, "total_fragments": 1451, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dyella kyungheensis", "strain": "strain=THG-B117", "accession": "GCA_016905005.1", "taxid": 1242174, "species_taxid": 1242174, "relation_to_type": "type", "validated": true, "ani": 75.9544, "matched_fragments": 80, "total_fragments": 1451, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas parafulva", "strain": "strain=DSM 17004", "accession": "GCA_000425765.1", "taxid": 157782, "species_taxid": 157782, "relation_to_type": "suspected-type", "validated": true, "ani": 75.9489, "matched_fragments": 68, "total_fragments": 1451, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas fakonensis", "strain": "strain=COW40", "accession": "GCA_019139895.1", "taxid": 2842355, "species_taxid": 2842355, "relation_to_type": "type", "validated": true, "ani": 75.9469, "matched_fragments": 120, "total_fragments": 1451, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas aeruginosa", "strain": "strain=DSM 50071", "accession": "GCA_012987025.1", "taxid": 287, "species_taxid": 287, "relation_to_type": "type", "validated": true, "ani": 75.9273, "matched_fragments": 109, "total_fragments": 1451, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Luteimonas lumbrici", "strain": "strain=1.1416", "accession": "GCA_006476065.1", "taxid": 2559601, "species_taxid": 2559601, "relation_to_type": "type", "validated": true, "ani": 75.8376, "matched_fragments": 70, "total_fragments": 1451, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Luteimonas aquatica", "strain": "strain=RIB1-20", "accession": "GCA_022662575.1", "taxid": 450364, "species_taxid": 450364, "relation_to_type": "type", "validated": true, "ani": 75.8202, "matched_fragments": 90, "total_fragments": 1451, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas aeruginosa", "strain": "strain=DSM 50071", "accession": "GCA_900167195.1", "taxid": 287, "species_taxid": 287, "relation_to_type": "type", "validated": true, "ani": 75.8113, "matched_fragments": 111, "total_fragments": 1451, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas psychrotolerans", "strain": "strain=DSM 15758", "accession": "GCA_900102665.1", "taxid": 237610, "species_taxid": 237610, "relation_to_type": "suspected-type", "validated": true, "ani": 75.6432, "matched_fragments": 102, "total_fragments": 1451, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Frateuria terrea", "strain": "strain=DSM 26515", "accession": "GCA_900109025.1", "taxid": 529704, "species_taxid": 529704, "relation_to_type": "type", "validated": true, "ani": 75.4851, "matched_fragments": 69, "total_fragments": 1451, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Frateuria terrea", "strain": "strain=CGMCC 1.7053", "accession": "GCA_900115705.1", "taxid": 529704, "species_taxid": 529704, "relation_to_type": "type", "validated": true, "ani": 75.2851, "matched_fragments": 68, "total_fragments": 1451, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_013179735.1", "gtdb_species": "s__Permianibacter fluminis", "ani": 100.0, "matched_fragments": 1450, "total_fragments": 1451, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__DSM-103792;g__Permianibacter", "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_009756665.1", "gtdb_species": "s__Permianibacter aggregans", "ani": 77.5593, 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