{ "type": "genome", "identifier": "GCF_900116225.1", "organism": "Sphingobacterium wenxiniae", "title": "Sphingobacterium wenxiniae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900116225.1", "bioproject": "PRJNA224116", "biosample": "SAMN05660206", "wgs_master": "FOZZ00000000.1", "refseq_category": "reference genome", "taxid": "683125", "species_taxid": "683125", "organism_name": "Sphingobacterium wenxiniae", "infraspecific_name": "strain=DSM 22789", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/11/02", "asm_name": "IMG-taxon 2634166295 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900116225.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/116/225/GCF_900116225.1_IMG-taxon_2634166295_annotated_assembly", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3844399", "genome_size_ungapped": "3842774", "gc_percent": "41.000000", "replicon_count": "0", "scaffold_count": "21", "contig_count": "21", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900116225.1-RS_2024_11_06", "annotation_date": "2024-11-06", "total_gene_count": "3396", "protein_coding_gene_count": "3322", "non_coding_gene_count": "53", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-11-02", "dateModified": "2016-11-02", "datePublished": "2016-11-02", "_annotation": { "sample_count": 1, "sample_organism": [ "Sphingobacterium wenxiniae" ], "sample_taxid": [ "683125" ], "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": "1.096 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)": "3844399", "Number of Sequences": "21", "Longest Sequences (bp)": "545704", "N50 (bp)": "284716", "Gap Ratio (%)": "0.042269", "GCcontent (%)": "40.9", "Number of CDSs": "3279", "Average Protein Length": "342.6", "Coding Ratio (%)": "87.7", "Number of rRNAs": "1", "Number of tRNAs": "48", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Sphingobacterium wenxiniae", "strain": "strain=DSM 22789", "accession": "GCA_900116225.1", "taxid": 683125, "species_taxid": 683125, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1268, "total_fragments": 1270, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Sphingobacterium thalpophilum", "strain": "strain=NCTC11429", "accession": "GCA_901482695.1", "taxid": 259, "species_taxid": 259, "relation_to_type": "type", "validated": true, "ani": 79.5844, "matched_fragments": 161, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobacterium humi", "strain": "strain=JCM 31225", "accession": "GCA_009768885.1", "taxid": 1796905, "species_taxid": 1796905, "relation_to_type": "type", "validated": true, "ani": 79.4405, "matched_fragments": 173, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobacterium phlebotomi", "strain": "strain=SSI9", "accession": "GCA_008180195.1", "taxid": 2605433, "species_taxid": 2605433, "relation_to_type": "type", "validated": true, "ani": 78.9529, "matched_fragments": 256, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobacterium psychroaquaticum", "strain": "strain=DSM 22418", "accession": "GCA_900177625.1", "taxid": 561061, "species_taxid": 561061, "relation_to_type": "type", "validated": true, "ani": 78.8328, "matched_fragments": 220, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobacterium corticibacterium", "strain": "strain=30C10-4-7", "accession": "GCA_004208525.1", "taxid": 2484746, "species_taxid": 2484746, "relation_to_type": "type", "validated": true, "ani": 78.6508, "matched_fragments": 246, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobacterium chuzhouense", "strain": "strain=KCTC 42746", "accession": "GCA_014692525.1", "taxid": 1742264, "species_taxid": 1742264, "relation_to_type": "type", "validated": true, "ani": 78.638, "matched_fragments": 246, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobacterium soli", "strain": "strain=DSM 101679", "accession": "GCA_014138555.1", "taxid": 1914757, "species_taxid": 1914757, "relation_to_type": "type", "validated": true, "ani": 78.5364, "matched_fragments": 150, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobacterium soli", "strain": "strain=CGMCC 1.15966", "accession": "GCA_014644335.1", "taxid": 1914757, "species_taxid": 1914757, "relation_to_type": "type", "validated": true, "ani": 78.4593, "matched_fragments": 143, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobacterium endophyticum", "strain": "strain=NYYP31", "accession": "GCA_009733535.1", "taxid": 2546448, "species_taxid": 2546448, "relation_to_type": "type", "validated": true, "ani": 78.3415, "matched_fragments": 158, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobacterium puteale", "strain": "strain=M05W1-28", "accession": "GCA_003627955.1", "taxid": 2420510, "species_taxid": 2420510, "relation_to_type": "type", "validated": true, "ani": 78.1567, "matched_fragments": 129, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobacterium mizutaii", "strain": "strain=NCTC12149", "accession": "GCA_900187125.1", "taxid": 1010, "species_taxid": 1010, "relation_to_type": "type", "validated": true, "ani": 77.9997, "matched_fragments": 146, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobacterium mizutaii", "strain": "strain=NBRC 14946", "accession": "GCA_007990895.1", "taxid": 1010, "species_taxid": 1010, "relation_to_type": "type", "validated": true, "ani": 77.9887, "matched_fragments": 146, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobacterium mizutaii", "strain": "strain=DSM 11724", "accession": "GCA_900102835.1", "taxid": 1010, "species_taxid": 1010, "relation_to_type": "type", "validated": true, "ani": 77.8362, "matched_fragments": 140, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobacterium gobiense", "strain": "strain=ACCC 05757", "accession": "GCA_002980575.1", "taxid": 1382456, "species_taxid": 1382456, "relation_to_type": "type", "validated": true, "ani": 77.8314, "matched_fragments": 219, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobacterium haloxyli", "strain": "strain=5JN-11", "accession": "GCA_002980525.1", "taxid": 2100533, "species_taxid": 2100533, "relation_to_type": "type", "validated": true, "ani": 77.7928, "matched_fragments": 211, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobacterium composti Ten et al. 2007 non Yoo et al. 2007", "strain": "strain=KCTC 12578", "accession": "GCA_009829075.1", "taxid": 363260, "species_taxid": 363260, "relation_to_type": "type", "validated": true, "ani": 77.7521, "matched_fragments": 180, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobacterium lumbrici", "strain": "strain=1.3611", "accession": "GCA_006476045.1", "taxid": 2559600, "species_taxid": 2559600, "relation_to_type": "type", "validated": true, "ani": 77.7451, "matched_fragments": 148, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobacterium olei", "strain": "strain=HAL-9", "accession": "GCA_005048855.1", "taxid": 2571155, "species_taxid": 2571155, "relation_to_type": "type", "validated": true, "ani": 77.6437, "matched_fragments": 175, "total_fragments": 1270, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900116225.1", "gtdb_species": "s__Sphingobacterium wenxiniae", "ani": 100.0, "matched_fragments": 1268, "total_fragments": 1270, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium", "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_008180195.1", "gtdb_species": "s__Sphingobacterium phlebotomi", "ani": 78.9686, "matched_fragments": 254, "total_fragments": 1270, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium", "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_900177625.1", "gtdb_species": "s__Sphingobacterium psychroaquaticum", "ani": 78.8119, "matched_fragments": 221, "total_fragments": 1270, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.08", "min_intra_species_ani": "99.08", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_004208525.1", "gtdb_species": "s__Sphingobacterium sp004208525", "ani": 78.6789, "matched_fragments": 244, "total_fragments": 1270, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium", "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_014692525.1", "gtdb_species": "s__Sphingobacterium chuzhouense", "ani": 78.6548, "matched_fragments": 245, "total_fragments": 1270, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium", "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_002933815.1", "gtdb_species": "s__Sphingobacterium sp002933815", "ani": 78.6204, "matched_fragments": 145, "total_fragments": 1270, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium", "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_008274825.1", "gtdb_species": "s__Sphingobacterium hotanense", "ani": 78.527, "matched_fragments": 136, "total_fragments": 1270, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.82", "min_intra_species_ani": "97.82", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_011043555.1", "gtdb_species": "s__Sphingobacterium sp011043555", "ani": 78.5023, "matched_fragments": 206, "total_fragments": 1270, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium", "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_009557615.1", "gtdb_species": "s__Sphingobacterium sp009557615", "ani": 78.4602, "matched_fragments": 132, "total_fragments": 1270, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium", "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_014692515.1", "gtdb_species": "s__Sphingobacterium sp014692515", "ani": 78.3884, "matched_fragments": 216, "total_fragments": 1270, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium", "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_009733535.1", "gtdb_species": "s__Sphingobacterium endophyticum", "ani": 78.3236, "matched_fragments": 158, "total_fragments": 1270, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium", "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_014219015.1", "gtdb_species": "s__Sphingobacterium sp002476975", "ani": 78.3215, "matched_fragments": 159, "total_fragments": 1270, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.27", "min_intra_species_ani": "97.88", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.89", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_008124885.1", "gtdb_species": "s__Sphingobacterium composti_A", "ani": 78.2842, "matched_fragments": 174, "total_fragments": 1270, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium", "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_003627955.1", "gtdb_species": "s__Sphingobacterium puteale", "ani": 78.1567, "matched_fragments": 129, "total_fragments": 1270, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium", "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_900187125.1", "gtdb_species": "s__Sphingobacterium mizutaii", "ani": 77.9811, "matched_fragments": 146, "total_fragments": 1270, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.36", "min_intra_species_ani": "98.08", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.87", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_002420705.1", "gtdb_species": "s__Sphingobacterium sp002420705", "ani": 77.9586, "matched_fragments": 129, "total_fragments": 1270, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium", "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_002980575.1", "gtdb_species": "s__Sphingobacterium gobiense", "ani": 77.8427, "matched_fragments": 219, "total_fragments": 1270, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium", "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_006476045.1", "gtdb_species": "s__Sphingobacterium lumbrici", "ani": 77.7892, "matched_fragments": 144, "total_fragments": 1270, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium", "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": 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