{ "type": "genome", "identifier": "GCF_004363245.1", "organism": "Sphingobacterium yanglingense", "title": "Sphingobacterium yanglingense", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004363245.1", "bioproject": "PRJNA224116", "biosample": "SAMN07620953", "wgs_master": "SNYV00000000.1", "refseq_category": "reference genome", "taxid": "1437280", "species_taxid": "1437280", "organism_name": "Sphingobacterium yanglingense", "infraspecific_name": "strain=DSM 28353", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/03/22", "asm_name": "ASM436324v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_004363245.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/363/245/GCF_004363245.1_ASM436324v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5485389", "genome_size_ungapped": "5485331", "gc_percent": "40.500000", "replicon_count": "0", "scaffold_count": "20", "contig_count": "20", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004363245.1-RS_2024_10_23", "annotation_date": "2024-10-23", "total_gene_count": "4661", "protein_coding_gene_count": "4591", "non_coding_gene_count": "60", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-03-22", "dateModified": "2019-03-22", "datePublished": "2019-03-22", "_annotation": { "sample_count": 1, "sample_organism": [ "Sphingobacterium yanglingense" ], "sample_taxid": [ "1437280" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.562 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)": "5485389", "Number of Sequences": "20", "Longest Sequences (bp)": "1463928", "N50 (bp)": "626301", "Gap Ratio (%)": "0.001057", "GCcontent (%)": "40.5", "Number of CDSs": "4542", "Average Protein Length": "357.7", "Coding Ratio (%)": "88.8", "Number of rRNAs": "3", "Number of tRNAs": "55", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Sphingobacterium yanglingense", "strain": "strain=DSM 28353", "accession": "GCA_004363245.1", "taxid": 1437280, "species_taxid": 1437280, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1813, "total_fragments": 1816, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Sphingobacterium tabacisoli", "strain": "strain=h337", "accession": "GCA_017908035.1", "taxid": 2044855, "species_taxid": 2044855, "relation_to_type": "type", "validated": true, "ani": 87.9499, "matched_fragments": 1249, "total_fragments": 1816, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobacterium faecale", "strain": "strain=C459-1", "accession": "GCA_016746095.1", "taxid": 2803775, "species_taxid": 2803775, "relation_to_type": "type", "validated": true, "ani": 83.1304, "matched_fragments": 877, "total_fragments": 1816, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobacterium paucimobilis", "strain": "strain=HER1398", "accession": "GCA_000416985.1", "taxid": 1385985, "species_taxid": 1385985, "relation_to_type": "type", "validated": true, "ani": 82.9697, "matched_fragments": 878, "total_fragments": 1816, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobacterium nematocida", "strain": "strain=DSM 24091", "accession": "GCA_900168125.1", "taxid": 1513896, "species_taxid": 1513896, "relation_to_type": "type", "validated": true, "ani": 82.062, "matched_fragments": 735, "total_fragments": 1816, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobacterium rhinopitheci", "strain": "strain=WQ 047", "accession": "GCA_022627575.1", "taxid": 2781960, "species_taxid": 2781960, "relation_to_type": "type", "validated": true, "ani": 78.4144, "matched_fragments": 207, "total_fragments": 1816, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobacterium litopenaei", "strain": "strain=DN04309", "accession": "GCA_014692495.1", "taxid": 2763500, "species_taxid": 2763500, "relation_to_type": "type", "validated": true, "ani": 78.292, "matched_fragments": 200, "total_fragments": 1816, "ani_threshold": 95, "status": 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78.3296, "matched_fragments": 205, "total_fragments": 1816, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium", "ani_circumscription_radius": 96.1642, "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_011043515.1", "gtdb_species": "s__Sphingobacterium sp011043515", "ani": 78.2975, "matched_fragments": 192, "total_fragments": 1816, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.84", "min_intra_species_ani": "98.84", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_012030425.1", "gtdb_species": "s__Sphingobacterium kitahiroshimense", "ani": 77.2477, 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"filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Sphingobacterium", "yanglingense" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }