{ "type": "genome", "identifier": "GCF_003076635.1", "organism": "Sphingobacterium corticibacter", "title": "Sphingobacterium corticibacter", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Research Institute of Forest Ecology Environment and Protection", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003076635.1", "bioproject": "PRJNA224116", "biosample": "SAMN08961938", "wgs_master": "QDKG00000000.1", "refseq_category": "reference genome", "taxid": "2171749", "species_taxid": "2171749", "organism_name": "Sphingobacterium corticibacter", "infraspecific_name": "strain=2c-3", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/05/01", "asm_name": "ASM307663v1", "asm_submitter": "Research Institute of Forest Ecology Environment and Protection", "gbrs_paired_asm": "GCA_003076635.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/076/635/GCF_003076635.1_ASM307663v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3907883", "genome_size_ungapped": "3907883", "gc_percent": "42.000000", "replicon_count": "0", "scaffold_count": "13", "contig_count": "13", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003076635.1-RS_2024_10_23", "annotation_date": "2024-10-23", "total_gene_count": "3413", "protein_coding_gene_count": "3354", "non_coding_gene_count": "52", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-05-01", "dateModified": "2018-05-01", "datePublished": "2018-05-01", "_annotation": { "sample_count": 1, "sample_organism": [ "Sphingobacterium corticibacter" ], "sample_taxid": [ "2171749" ], "sample_host_organism": [ "poplar" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China:Puyang City, Henan Province" ], "sample_host_location_id": [], "data_size": "1.113 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)": "3907883", "Number of Sequences": "13", "Longest Sequences (bp)": "1390400", "N50 (bp)": "620076", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "42.0", "Number of CDSs": "3357", "Average Protein Length": "347.3", "Coding Ratio (%)": "89.5", "Number of rRNAs": "3", "Number of tRNAs": "46", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Sphingobacterium corticibacter", "strain": "strain=2c-3", "accession": "GCA_003076635.1", "taxid": 2171749, "species_taxid": 2171749, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1295, "total_fragments": 1295, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Sphingobacterium chungjuense", "strain": "strain=IMCC25678", "accession": "GCA_011316935.1", "taxid": 2675553, "species_taxid": 2675553, "relation_to_type": "type", "validated": true, "ani": 90.3136, "matched_fragments": 1020, "total_fragments": 1295, "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": 79.3096, "matched_fragments": 121, "total_fragments": 1295, "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": 79.2208, "matched_fragments": 141, "total_fragments": 1295, "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": 78.8886, "matched_fragments": 133, "total_fragments": 1295, "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": 78.862, "matched_fragments": 129, "total_fragments": 1295, "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": 78.1266, "matched_fragments": 99, "total_fragments": 1295, "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": 78.1257, "matched_fragments": 108, "total_fragments": 1295, "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": 78.1061, "matched_fragments": 132, "total_fragments": 1295, "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": 77.9839, "matched_fragments": 106, "total_fragments": 1295, "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": 77.966, "matched_fragments": 108, "total_fragments": 1295, "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": 77.6493, "matched_fragments": 94, "total_fragments": 1295, "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": 77.4059, "matched_fragments": 90, "total_fragments": 1295, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobacterium hungaricum", "strain": "strain=KB22", "accession": "GCA_015210005.1", "taxid": 2082723, "species_taxid": 2082723, "relation_to_type": "type", "validated": true, "ani": 77.3559, "matched_fragments": 128, "total_fragments": 1295, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter fastidiosus", "strain": "strain=CCM 8938", "accession": "GCA_014306625.1", "taxid": 2765361, "species_taxid": 2765361, "relation_to_type": "type", "validated": true, "ani": 76.4548, "matched_fragments": 57, "total_fragments": 1295, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003076635.1", "gtdb_species": "s__Sphingobacterium sp003076635", "ani": 100.0, "matched_fragments": 1295, "total_fragments": 1295, "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_011316935.1", "gtdb_species": "s__Sphingobacterium sp011316935", "ani": 90.3136, "matched_fragments": 1020, "total_fragments": 1295, "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_001586775.1", "gtdb_species": "s__Sphingobacterium sp001586775", "ani": 83.115, "matched_fragments": 716, "total_fragments": 1295, "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_009768885.1", "gtdb_species": "s__Sphingobacterium humi", "ani": 79.215, "matched_fragments": 140, "total_fragments": 1295, "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_900116225.1", "gtdb_species": "s__Sphingobacterium wenxiniae", "ani": 78.9386, "matched_fragments": 132, "total_fragments": 1295, "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": 78.8419, "matched_fragments": 102, "total_fragments": 1295, "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_016724845.1", "gtdb_species": "s__Sphingobacterium spiritivorum_A", "ani": 78.8372, "matched_fragments": 124, "total_fragments": 1295, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.88", "min_intra_species_ani": "95.78", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.88", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_016725325.1", "gtdb_species": "s__Sphingobacterium sp002418355", "ani": 78.6467, "matched_fragments": 109, "total_fragments": 1295, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.65", "min_intra_species_ani": "97.65", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_004526235.1", "gtdb_species": "s__Sphingobacterium sp002734245", "ani": 78.4812, "matched_fragments": 120, "total_fragments": 1295, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.34", "min_intra_species_ani": "97.34", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_009829085.1", "gtdb_species": "s__Sphingobacterium bovisgrunnientis", "ani": 78.1222, "matched_fragments": 108, "total_fragments": 1295, "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_006476045.1", "gtdb_species": "s__Sphingobacterium lumbrici", "ani": 78.1028, "matched_fragments": 101, "total_fragments": 1295, "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": 77.787, "matched_fragments": 116, "total_fragments": 1295, "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": 77.4985, "matched_fragments": 95, "total_fragments": 1295, "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_015210005.1", "gtdb_species": "s__Sphingobacterium sp015210005", "ani": 77.3687, "matched_fragments": 126, "total_fragments": 1295, "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_011043525.1", "gtdb_species": "s__Sphingobacterium sp011043525", "ani": 76.8613, "matched_fragments": 85, "total_fragments": 1295, "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": "-" } ] }, "_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", "corticibacter" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }