{ "type": "genome", "identifier": "GCF_000757725.1", "organism": "Sphingobacterium deserti", "title": "Sphingobacterium deserti", "description": "na", "data type": "Genome sequencing and assembly", "organization": "BIOTECHNOLOGY RESEARCH INSTITUTE, CAAS", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000757725.1", "bioproject": "PRJNA224116", "biosample": "SAMN02722725", "wgs_master": "JJMU00000000.1", "refseq_category": "reference genome", "taxid": "1229276", "species_taxid": "1229276", "organism_name": "Sphingobacterium deserti", "infraspecific_name": "strain=ACCC 05744", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2014/09/24", "asm_name": "ASM75772v1", "asm_submitter": "BIOTECHNOLOGY RESEARCH INSTITUTE, CAAS", "gbrs_paired_asm": "GCA_000757725.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/757/725/GCF_000757725.1_ASM75772v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4595883", "genome_size_ungapped": "4595883", "gc_percent": "42.500000", "replicon_count": "0", "scaffold_count": "75", "contig_count": "75", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000757725.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "3876", "protein_coding_gene_count": "3814", "non_coding_gene_count": "55", "pubmed_id": "25830331" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2014-09-24", "dateModified": "2014-09-24", "datePublished": "2014-09-24", "_annotation": { "sample_count": 1, "sample_organism": [ "Sphingobacterium deserti" ], "sample_taxid": [ "1229276" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Western China" ], "sample_host_location_id": [], "data_size": "1.318 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)": "4595883", "Number of Sequences": "75", "Longest Sequences (bp)": "318693", "N50 (bp)": "133866", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "42.6", "Number of CDSs": "3769", "Average Protein Length": "352.1", "Coding Ratio (%)": "86.6", "Number of rRNAs": "2", "Number of tRNAs": "48", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Sphingobacterium deserti", "strain": "strain=ACCC 05744", "accession": "GCA_000757725.1", "taxid": 1229276, "species_taxid": 1229276, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1497, "total_fragments": 1498, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Sphingobacterium paludis", "strain": "strain=CGMCC 1.12801", "accession": "GCA_004364125.1", "taxid": 1476465, "species_taxid": 1476465, "relation_to_type": "type", "validated": true, "ani": 82.398, "matched_fragments": 1031, "total_fragments": 1498, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobacterium griseoflavum", "strain": "strain=CGMCC 1.12966", "accession": "GCA_014653155.1", "taxid": 1474952, "species_taxid": 1474952, "relation_to_type": "type", "validated": true, "ani": 78.9035, "matched_fragments": 375, "total_fragments": 1498, "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": 78.6132, "matched_fragments": 179, "total_fragments": 1498, "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": 78.2862, "matched_fragments": 184, "total_fragments": 1498, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobacterium bovisgrunnientis", "strain": "strain=KCTC 52685", "accession": "GCA_009829085.1", "taxid": 1874697, "species_taxid": 1874697, "relation_to_type": "type", "validated": true, "ani": 78.2092, "matched_fragments": 103, "total_fragments": 1498, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobacterium siyangense", "strain": "strain=CGMCC 1.6855", "accession": "GCA_007830445.1", "taxid": 459529, "species_taxid": 459529, "relation_to_type": "type", "validated": true, "ani": 78.1786, "matched_fragments": 99, "total_fragments": 1498, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobacterium wenxiniae", "strain": "strain=DSM 22789", "accession": "GCA_900116225.1", "taxid": 683125, "species_taxid": 683125, "relation_to_type": "type", "validated": true, "ani": 78.1312, "matched_fragments": 175, "total_fragments": 1498, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobacterium cavernae", "strain": "strain=5.0403-2", "accession": "GCA_008520265.1", "taxid": 2592657, "species_taxid": 2592657, "relation_to_type": "type", "validated": true, "ani": 78.1212, "matched_fragments": 102, "total_fragments": 1498, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobacterium micropteri", "strain": "strain=DN00404", "accession": "GCA_014692515.1", "taxid": 2763501, "species_taxid": 2763501, "relation_to_type": "type", "validated": true, "ani": 77.9865, "matched_fragments": 188, "total_fragments": 1498, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobacterium chungjuense", "strain": "strain=IMCC25678", "accession": "GCA_011316935.1", "taxid": 2675553, "species_taxid": 2675553, "relation_to_type": "type", "validated": true, "ani": 77.8223, "matched_fragments": 105, "total_fragments": 1498, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobacterium alkalisoli", "strain": "strain=CGMCC 1.15782", "accession": "GCA_014643675.1", "taxid": 1874115, "species_taxid": 1874115, "relation_to_type": "type", "validated": true, "ani": 77.3985, "matched_fragments": 117, "total_fragments": 1498, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000757725.1", "gtdb_species": "s__Sphingobacterium deserti", "ani": 100.0, "matched_fragments": 1497, "total_fragments": 1498, "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_004364125.1", "gtdb_species": "s__Sphingobacterium paludis", "ani": 82.395, "matched_fragments": 1032, "total_fragments": 1498, "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_014653155.1", "gtdb_species": "s__Sphingobacterium griseoflavum", "ani": 78.8948, "matched_fragments": 376, "total_fragments": 1498, "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": 78.6125, "matched_fragments": 178, "total_fragments": 1498, "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": 78.2854, "matched_fragments": 183, "total_fragments": 1498, "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_008520265.1", "gtdb_species": "s__Sphingobacterium cavernae", "ani": 78.1574, "matched_fragments": 101, "total_fragments": 1498, "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_900116225.1", "gtdb_species": "s__Sphingobacterium wenxiniae", "ani": 78.1379, "matched_fragments": 174, "total_fragments": 1498, "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_002000245.1", "gtdb_species": "s__Sphingobacterium sp002000245", "ani": 78.0677, "matched_fragments": 108, "total_fragments": 1498, "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_011043555.1", "gtdb_species": "s__Sphingobacterium sp011043555", "ani": 78.0634, "matched_fragments": 176, "total_fragments": 1498, "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": "GCA_002354335.1", "gtdb_species": "s__Sphingobacterium sp002354335", "ani": 78.0083, "matched_fragments": 114, "total_fragments": 1498, "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_014692515.1", "gtdb_species": "s__Sphingobacterium sp014692515", "ani": 77.9754, "matched_fragments": 187, "total_fragments": 1498, "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_011316935.1", "gtdb_species": "s__Sphingobacterium sp011316935", "ani": 77.8546, "matched_fragments": 104, "total_fragments": 1498, "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": "GCA_002472835.1", "gtdb_species": "s__Sphingobacterium sp002472835", "ani": 77.8202, "matched_fragments": 103, "total_fragments": 1498, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.27", "min_intra_species_ani": "95.27", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.83", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_012030425.1", "gtdb_species": "s__Sphingobacterium kitahiroshimense", "ani": 77.7585, "matched_fragments": 113, "total_fragments": 1498, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.48", "min_intra_species_ani": "96.84", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.82", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCA_002500745.1", "gtdb_species": "s__Sphingobacterium sp002500745", "ani": 77.6456, "matched_fragments": 104, "total_fragments": 1498, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.61", "min_intra_species_ani": "98.61", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.219, "cell_length": 0.103, "doubling_h": null, "growth_tmp": 28.833, "optimum_tmp": 31.687, "optimum_ph": 7.192, "genome_size": 5015607.692, "gc_content": 38.627, "coding_genes": 3922.0, "rRNA16S_genes": 4.0, "tRNA_genes": 55.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.045, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Sphingobacterium", "deserti" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }