{ "type": "genome", "identifier": "GCF_003865405.1", "organism": "Paenimyroides tangerinum", "title": "Paenimyroides tangerinum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Yunnan Institute of Microbiology", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003865405.1", "bioproject": "PRJNA224116", "biosample": "SAMN10426406", "wgs_master": "RQVQ00000000.1", "refseq_category": "reference genome", "taxid": "2488728", "species_taxid": "2488728", "organism_name": "Paenimyroides tangerinum", "infraspecific_name": "strain=YIM 102701-2", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/12/05", "asm_name": "ASM386540v1", "asm_submitter": "Yunnan Institute of Microbiology", "gbrs_paired_asm": "GCA_003865405.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/865/405/GCF_003865405.1_ASM386540v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3453487", "genome_size_ungapped": "3453259", "gc_percent": "31.000000", "replicon_count": "0", "scaffold_count": "114", "contig_count": "114", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003865405.1-RS_2024_11_06", "annotation_date": "2024-11-06", "total_gene_count": "3338", "protein_coding_gene_count": "3227", "non_coding_gene_count": "72", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-12-05", "dateModified": "2018-12-05", "datePublished": "2018-12-05", "_annotation": { "sample_count": 1, "sample_organism": [ "Paenimyroides tangerinum" ], "sample_taxid": [ "2488728" ], "sample_host_organism": [ "Hoolock hoolock" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China" ], "sample_host_location_id": [], "data_size": "0.952 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 8.33, "strain_heterogeneity": 100.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "3453487", "Number of Sequences": "114", "Longest Sequences (bp)": "197016", "N50 (bp)": "79891", "Gap Ratio (%)": "0.006602", "GCcontent (%)": "30.9", "Number of CDSs": "3214", "Average Protein Length": "312.5", "Coding Ratio (%)": "87.2", "Number of rRNAs": "4", "Number of tRNAs": "60", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Flavobacterium tangerinum", "strain": "strain=YIM 102701-2", "accession": "GCA_003865405.1", "taxid": 2488728, "species_taxid": 2488728, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1081, "total_fragments": 1094, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Flavobacterium viscosum", "strain": "strain=YIM 102796", "accession": "GCA_003858535.1", "taxid": 2488729, "species_taxid": 2488729, "relation_to_type": "type", "validated": true, "ani": 79.4034, "matched_fragments": 324, "total_fragments": 1094, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium ummariense", "strain": "strain=DS-12", "accession": "GCA_900115115.1", "taxid": 913024, "species_taxid": 913024, "relation_to_type": "type", "validated": true, "ani": 78.5856, "matched_fragments": 280, "total_fragments": 1094, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium baculatum", "strain": "strain=SNL9", "accession": "GCA_008629655.1", "taxid": 2608000, "species_taxid": 2608000, "relation_to_type": "type", "validated": true, "ani": 78.2019, "matched_fragments": 276, "total_fragments": 1094, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Myroides marinus", "strain": "strain=DSM 23048", "accession": "GCA_900109075.1", "taxid": 703342, "species_taxid": 703342, "relation_to_type": "type", "validated": true, "ani": 78.1118, "matched_fragments": 152, "total_fragments": 1094, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium channae", "strain": "strain=KSM-R2A30", "accession": "GCA_021172165.1", "taxid": 2897181, "species_taxid": 2897181, "relation_to_type": "type", "validated": true, "ani": 77.9407, "matched_fragments": 208, "total_fragments": 1094, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Myroides profundi", "strain": "strain=D25", "accession": "GCA_000833025.1", "taxid": 480520, "species_taxid": 480520, "relation_to_type": "type", "validated": true, "ani": 77.9392, "matched_fragments": 124, "total_fragments": 1094, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Myroides odoratimimus", "strain": "strain=NCTC11180", "accession": "GCA_900453765.1", "taxid": 76832, "species_taxid": 76832, "relation_to_type": "type", "validated": true, "ani": 77.7691, "matched_fragments": 134, "total_fragments": 1094, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Myroides odoratimimus", "strain": "strain=CCUG39352", "accession": "GCA_001485415.1", "taxid": 76832, "species_taxid": 76832, "relation_to_type": "type", "validated": true, "ani": 77.7266, "matched_fragments": 134, "total_fragments": 1094, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium aquaticum", "strain": "strain=CGMCC 1.12398", "accession": "GCA_003259835.1", "taxid": 1236486, "species_taxid": 1236486, "relation_to_type": "type", "validated": true, "ani": 77.7084, "matched_fragments": 222, "total_fragments": 1094, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium proteolyticum", "strain": "strain=1Y8A", "accession": "GCA_015223105.1", "taxid": 2911683, "species_taxid": 2911683, "relation_to_type": "type", "validated": true, "ani": 77.7044, "matched_fragments": 194, "total_fragments": 1094, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Myroides phaeus", "strain": "strain=DSM 23313", "accession": "GCA_900099675.1", "taxid": 702745, "species_taxid": 702745, "relation_to_type": "type", "validated": true, "ani": 77.6416, "matched_fragments": 200, "total_fragments": 1094, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium terrae", "strain": "strain=DSM 18829", "accession": "GCA_900142035.1", "taxid": 415425, "species_taxid": 415425, "relation_to_type": "type", "validated": true, "ani": 77.6337, "matched_fragments": 174, "total_fragments": 1094, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium urocaniciphilum", "strain": "strain=DSM 27078", "accession": "GCA_900110615.1", "taxid": 1299341, "species_taxid": 1299341, "relation_to_type": "type", "validated": true, "ani": 77.6249, "matched_fragments": 221, "total_fragments": 1094, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Myroides injenensis", "strain": "strain=M09-0166", "accession": "GCA_000246945.2", "taxid": 1183151, "species_taxid": 1183151, "relation_to_type": "type", "validated": true, "ani": 77.5247, "matched_fragments": 152, "total_fragments": 1094, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium oreochromis", "strain": "strain=Costa Rica 04-02-TN", "accession": "GCA_019565455.1", "taxid": 2906078, "species_taxid": 2906078, "relation_to_type": "type", "validated": true, "ani": 77.2663, "matched_fragments": 138, "total_fragments": 1094, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium aquariorum", "strain": "strain=IMCC34762", "accession": "GCA_003254745.1", "taxid": 2217670, "species_taxid": 2217670, "relation_to_type": "type", "validated": true, "ani": 77.2592, "matched_fragments": 133, "total_fragments": 1094, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium gelidilacus", "strain": "strain=DSM 15343", "accession": "GCA_000422685.1", "taxid": 206041, "species_taxid": 206041, "relation_to_type": "type", "validated": true, "ani": 77.2511, "matched_fragments": 225, "total_fragments": 1094, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium hiemivividum", "strain": "strain=TSA-D2", "accession": "GCA_004349145.1", "taxid": 2541734, "species_taxid": 2541734, "relation_to_type": "type", "validated": true, "ani": 77.2251, "matched_fragments": 136, "total_fragments": 1094, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium filum", "strain": "strain=DSM 17961", "accession": "GCA_000425465.1", "taxid": 370974, "species_taxid": 370974, "relation_to_type": "type", "validated": true, "ani": 77.2244, "matched_fragments": 136, "total_fragments": 1094, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium pokkalii", "strain": "strain=L1I52", "accession": "GCA_014596575.1", "taxid": 1940408, "species_taxid": 1940408, "relation_to_type": "type", "validated": true, "ani": 77.2241, "matched_fragments": 127, "total_fragments": 1094, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium alkalisoli", "strain": "strain=XS-5", "accession": "GCA_008000935.1", "taxid": 2602769, "species_taxid": 2602769, "relation_to_type": "type", "validated": true, "ani": 77.0654, "matched_fragments": 73, "total_fragments": 1094, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Psychroserpens luteolus", "strain": "strain=XSD401", "accession": "GCA_021032705.1", "taxid": 2855840, "species_taxid": 2855840, "relation_to_type": "type", "validated": true, "ani": 76.471, "matched_fragments": 78, "total_fragments": 1094, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Algibacter pacificus", "strain": "strain=H164", "accession": "GCA_008033385.1", "taxid": 2599389, "species_taxid": 2599389, "relation_to_type": "type", "validated": true, "ani": 76.4544, "matched_fragments": 99, "total_fragments": 1094, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hanstruepera marina", "strain": "strain=NBU2968", "accession": "GCA_019880635.1", "taxid": 2873265, "species_taxid": 2873265, "relation_to_type": "type", "validated": true, "ani": 76.3918, "matched_fragments": 70, "total_fragments": 1094, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 8.33, "strain_heterogeneity": 100.0 }, "gtdb_result": [ { "accession": "GCF_003865405.1", "gtdb_species": "s__Flavobacterium tangerinum", "ani": 100.0, "matched_fragments": 1083, "total_fragments": 1094, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium", "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_013389595.1", "gtdb_species": "s__Flavobacterium sp013389595", "ani": 85.5166, "matched_fragments": 800, "total_fragments": 1094, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium", "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": "-" }, { "accession": "GCF_013874595.1", "gtdb_species": "s__Flavobacterium sp013874595", "ani": 78.7964, "matched_fragments": 295, "total_fragments": 1094, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_900115115.1", "gtdb_species": "s__Flavobacterium ummariense", "ani": 78.5701, "matched_fragments": 280, "total_fragments": 1094, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium", "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": "-" }, { "accession": "GCA_002360925.1", "gtdb_species": "s__Flavobacterium sp002360925", "ani": 78.3239, "matched_fragments": 328, "total_fragments": 1094, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium", "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": "-" }, { "accession": "GCF_004151275.1", "gtdb_species": "s__Flavobacterium sp004151275", "ani": 78.2347, "matched_fragments": 285, "total_fragments": 1094, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium", "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": "-" }, { "accession": "GCF_900108395.1", "gtdb_species": "s__Flavobacterium marinum", "ani": 78.2274, "matched_fragments": 254, "total_fragments": 1094, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium", "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": "-" }, { "accession": "GCF_008629655.1", "gtdb_species": "s__Flavobacterium baculatum", "ani": 78.1998, "matched_fragments": 275, "total_fragments": 1094, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium", "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": "-" }, { "accession": "GCF_900109075.1", "gtdb_species": "s__Flavobacterium marinum_A", "ani": 78.1318, "matched_fragments": 150, "total_fragments": 1094, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.64", "min_intra_species_ani": "97.56", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_001485415.1", "gtdb_species": "s__Flavobacterium odoratimimum", "ani": 77.7607, "matched_fragments": 134, "total_fragments": 1094, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.35", "min_intra_species_ani": "97.00", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.88", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCF_015223105.1", "gtdb_species": "s__Flavobacterium aquaticum_A", "ani": 77.7288, "matched_fragments": 194, "total_fragments": 1094, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium", "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": "-" }, { "accession": "GCF_900099675.1", "gtdb_species": "s__Flavobacterium phaeum", "ani": 77.6547, "matched_fragments": 202, "total_fragments": 1094, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium", "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": "-" }, { "accession": "GCA_002483315.1", "gtdb_species": "s__Flavobacterium sp002483315", "ani": 77.5832, "matched_fragments": 198, "total_fragments": 1094, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium", "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": "-" }, { "accession": "GCF_000246945.1", "gtdb_species": "s__Flavobacterium injenense", "ani": 77.5322, "matched_fragments": 154, "total_fragments": 1094, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium", "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": "-" }, { "accession": "GCA_001708385.1", "gtdb_species": "s__Flavobacterium psychrophilum_A", "ani": 77.1524, "matched_fragments": 78, "total_fragments": 1094, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_013294005.1", "gtdb_species": "s__Flavobacterium sp013294005", "ani": 76.81, "matched_fragments": 154, "total_fragments": 1094, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.41", "min_intra_species_ani": "97.36", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.85", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_015277675.1", "gtdb_species": "s__Flavobacterium soyangense", "ani": 76.4447, "matched_fragments": 116, "total_fragments": 1094, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium", "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": "-" }, { "accession": "GCF_003143755.1", "gtdb_species": "s__Algibacter_B sp003143755", "ani": 76.2156, "matched_fragments": 93, "total_fragments": 1094, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B", "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": null, "growth_tmp": null, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_genome_taxon": [ "Paenimyroides", "tangerinum" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }