{ "type": "genome", "identifier": "GCF_015209965.1", "organism": "Sphingobacterium pedocola", "title": "Sphingobacterium pedocola", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Seqomics Ltd.", "publication": [ {} ], "properties": { "assembly_accession": "GCF_015209965.1", "bioproject": "PRJNA224116", "biosample": "SAMN08474032", "wgs_master": "PSKQ00000000.1", "refseq_category": "reference genome", "taxid": "2082722", "species_taxid": "2082722", "organism_name": "Sphingobacterium pedocola", "infraspecific_name": "strain=Ka21", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/11/02", "asm_name": "ASM1520996v1", "asm_submitter": "Seqomics Ltd.", "gbrs_paired_asm": "GCA_015209965.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/015/209/965/GCF_015209965.1_ASM1520996v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5234653", "genome_size_ungapped": "5205271", "gc_percent": "41.000000", "replicon_count": "0", "scaffold_count": "8", "contig_count": "27", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_015209965.1-RS_2024_10_11", "annotation_date": "2024-10-11", "total_gene_count": "4313", "protein_coding_gene_count": "4240", "non_coding_gene_count": "59", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-11-02", "dateModified": "2020-11-02", "datePublished": "2020-11-02", "_annotation": { "sample_count": 1, "sample_organism": [ "Sphingobacterium pedocola" ], "sample_taxid": [ "2082722" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Hungary" ], "sample_host_location_id": [], "data_size": "1.483 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)": "5234550", "Number of Sequences": "7", "Longest Sequences (bp)": "2428369", "N50 (bp)": "1447597", "Gap Ratio (%)": "0.561366", "GCcontent (%)": "41.0", "Number of CDSs": "4176", "Average Protein Length": "364.2", "Coding Ratio (%)": "87.2", "Number of rRNAs": "4", "Number of tRNAs": "52", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Sphingobacterium olei", "strain": "strain=HAL-9", "accession": "GCA_005048855.1", "taxid": 2571155, "species_taxid": 2571155, "relation_to_type": "type", "validated": true, "ani": 86.4037, "matched_fragments": 1174, "total_fragments": 1742, "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": 85.3312, "matched_fragments": 710, "total_fragments": 1742, "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": 84.2915, "matched_fragments": 1077, "total_fragments": 1742, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobacterium alkalisoli", "strain": "strain=Y3L14", "accession": "GCA_005049105.1", "taxid": 1874115, "species_taxid": 1874115, "relation_to_type": "type", "validated": true, "ani": 84.2512, "matched_fragments": 1083, "total_fragments": 1742, "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": 78.4521, "matched_fragments": 155, "total_fragments": 1742, "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": 78.2489, "matched_fragments": 164, "total_fragments": 1742, "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": 78.1757, "matched_fragments": 172, "total_fragments": 1742, "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": 78.1654, "matched_fragments": 175, "total_fragments": 1742, "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": 78.0966, "matched_fragments": 158, "total_fragments": 1742, "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": 77.9111, "matched_fragments": 149, "total_fragments": 1742, "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": 77.7904, "matched_fragments": 147, "total_fragments": 1742, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_015209965.1", "gtdb_species": "s__Sphingobacterium sp015209965", "ani": 99.995, "matched_fragments": 1733, "total_fragments": 1742, "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_005048855.1", "gtdb_species": "s__Sphingobacterium olei", "ani": 86.4017, "matched_fragments": 1174, "total_fragments": 1742, "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": 85.3553, "matched_fragments": 708, "total_fragments": 1742, "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_005049105.1", "gtdb_species": "s__Sphingobacterium alkalisoli", "ani": 84.2521, "matched_fragments": 1081, "total_fragments": 1742, "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_000416985.1", "gtdb_species": "s__Sphingobacterium paucimobilis", "ani": 78.5004, "matched_fragments": 155, "total_fragments": 1742, "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_009829075.1", "gtdb_species": "s__Sphingobacterium composti", "ani": 78.3046, "matched_fragments": 163, "total_fragments": 1742, "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_011043515.1", "gtdb_species": "s__Sphingobacterium sp011043515", "ani": 78.1069, "matched_fragments": 181, "total_fragments": 1742, "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_016746095.1", "gtdb_species": "s__Sphingobacterium sp016746095", "ani": 78.0752, "matched_fragments": 158, "total_fragments": 1742, "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_011007365.1", "gtdb_species": "s__Sphingobacterium sp011007365", "ani": 77.9875, "matched_fragments": 163, "total_fragments": 1742, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.58", "min_intra_species_ani": "99.33", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.93", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_014219015.1", "gtdb_species": "s__Sphingobacterium sp002476975", "ani": 77.9132, "matched_fragments": 132, "total_fragments": 1742, "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": "GCA_000938735.2", "gtdb_species": "s__Sphingobacterium sp000938735", "ani": 77.6576, "matched_fragments": 130, "total_fragments": 1742, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.17", "min_intra_species_ani": "98.17", "mean_intra_species_af": "0.81", "min_intra_species_af": "0.81", "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", "pedocola" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }