{ "type": "genome", "identifier": "GCF_004342685.1", "organism": "Sphingobacterium alimentarium", "title": "Sphingobacterium alimentarium", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004342685.1", "bioproject": "PRJNA224116", "biosample": "SAMN10363321", "wgs_master": "SMBZ00000000.1", "refseq_category": "reference genome", "taxid": "797292", "species_taxid": "797292", "organism_name": "Sphingobacterium alimentarium", "infraspecific_name": "strain=DSM 22362", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/03/11", "asm_name": "ASM434268v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_004342685.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/342/685/GCF_004342685.1_ASM434268v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3576798", "genome_size_ungapped": "3576798", "gc_percent": "38.500000", "replicon_count": "0", "scaffold_count": "107", "contig_count": "107", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004342685.1-RS_2024_10_23", "annotation_date": "2024-10-23", "total_gene_count": "3396", "protein_coding_gene_count": "3275", "non_coding_gene_count": "68", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-03-11", "dateModified": "2019-03-11", "datePublished": "2019-03-11", "_annotation": { "sample_count": 1, "sample_organism": [ "Sphingobacterium alimentarium" ], "sample_taxid": [ "797292" ], "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": "1.024 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)": "3576798", "Number of Sequences": "107", "Longest Sequences (bp)": "200171", "N50 (bp)": "65045", "Gap Ratio (%)": "0.000112", "GCcontent (%)": "38.6", "Number of CDSs": "3245", "Average Protein Length": "320.7", "Coding Ratio (%)": "87.3", "Number of rRNAs": "2", "Number of tRNAs": "63", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Sphingobacterium alimentarium", "strain": "strain=DSM 22362", "accession": "GCA_004342685.1", "taxid": 797292, "species_taxid": 797292, "relation_to_type": "type", "validated": true, "ani": 99.9999, "matched_fragments": 1139, "total_fragments": 1144, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Sphingobacterium litopenaei", "strain": "strain=DN04309", "accession": "GCA_014692495.1", "taxid": 2763500, "species_taxid": 2763500, "relation_to_type": "type", "validated": true, "ani": 81.0962, "matched_fragments": 489, "total_fragments": 1144, "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": 81.0828, "matched_fragments": 465, "total_fragments": 1144, "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": 80.889, "matched_fragments": 488, "total_fragments": 1144, "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": 80.7785, "matched_fragments": 459, "total_fragments": 1144, "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": 79.0137, "matched_fragments": 247, "total_fragments": 1144, "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": 78.7801, "matched_fragments": 179, 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"status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004342685.1", "gtdb_species": "s__Sphingobacterium alimentarium", "ani": 99.9999, "matched_fragments": 1139, "total_fragments": 1144, "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_009829085.1", "gtdb_species": "s__Sphingobacterium bovisgrunnientis", "ani": 81.0865, "matched_fragments": 466, "total_fragments": 1144, "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", 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