{ "type": "genome", "identifier": "GCF_003590775.1", "organism": "Sphingomonas cavernae", "title": "Sphingomonas cavernae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Chinese Academy of Sciences", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003590775.1", "bioproject": "PRJNA224116", "biosample": "SAMN10055688", "wgs_master": "QYUM00000000.1", "refseq_category": "reference genome", "taxid": "2320861", "species_taxid": "2320861", "organism_name": "Sphingomonas cavernae", "infraspecific_name": "strain=K2R01-6", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/09/24", "asm_name": "ASM359077v1", "asm_submitter": "Chinese Academy of Sciences", "gbrs_paired_asm": "GCA_003590775.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/590/775/GCF_003590775.1_ASM359077v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4244097", "genome_size_ungapped": "4244097", "gc_percent": "64.000000", "replicon_count": "0", "scaffold_count": "5", "contig_count": "5", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003590775.1-RS_2024_03_27", "annotation_date": "2024-03-27", "total_gene_count": "4068", "protein_coding_gene_count": "3938", "non_coding_gene_count": "68", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-09-24", "dateModified": "2018-09-24", "datePublished": "2018-09-24", "_annotation": { "sample_count": 1, "sample_organism": [ "Sphingomonas cavernae" ], "sample_taxid": [ "2320861" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Guizhou" ], "sample_host_location_id": [], "data_size": "1.170 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)": "4244097", "Number of Sequences": "5", "Longest Sequences (bp)": "1598275", "N50 (bp)": "1558539", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "63.9", "Number of CDSs": "4020", "Average Protein Length": "316.3", "Coding Ratio (%)": "89.9", "Number of rRNAs": "6", "Number of tRNAs": "57", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Sphingomonas cavernae", "strain": "strain=K2R01-6", "accession": "GCA_003590775.1", "taxid": 2320861, "species_taxid": 2320861, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1409, "total_fragments": 1412, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Sphingomonas colocasiae", "strain": "strain=JCM 31229", "accession": "GCA_019880585.1", "taxid": 1848973, "species_taxid": 1848973, "relation_to_type": "type", "validated": true, "ani": 80.3733, "matched_fragments": 656, "total_fragments": 1412, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas gilva", "strain": "strain=ZDH117", "accession": "GCA_003515075.1", "taxid": 2305907, "species_taxid": 2305907, "relation_to_type": "type", "validated": true, "ani": 79.0618, "matched_fragments": 517, "total_fragments": 1412, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas naasensis", "strain": "strain=KIS18-15", "accession": "GCA_004792695.1", "taxid": 1344951, "species_taxid": 1344951, "relation_to_type": "type", "validated": true, "ani": 79.0043, "matched_fragments": 519, "total_fragments": 1412, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": 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"strain=NBRC 104936", "accession": "GCA_000974765.1", "taxid": 529705, "species_taxid": 529705, "relation_to_type": "type", "validated": true, "ani": 78.6629, "matched_fragments": 394, "total_fragments": 1412, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas metalli", "strain": "strain=CGMCC 1.15330", "accession": "GCA_014641735.1", "taxid": 1779358, "species_taxid": 1779358, "relation_to_type": "type", "validated": true, "ani": 78.5911, "matched_fragments": 396, "total_fragments": 1412, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobium ummariense", "strain": "strain=RL-3", "accession": "GCA_000447205.1", "taxid": 420994, "species_taxid": 420994, "relation_to_type": "type", "validated": true, "ani": 78.5867, "matched_fragments": 374, "total_fragments": 1412, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas flavalba", "strain": "strain=ZLT-5", "accession": "GCA_004796535.1", 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78.2843, "matched_fragments": 366, "total_fragments": 1412, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobium baderi", "strain": "strain=LL03", "accession": "GCA_001046655.1", "taxid": 1332080, "species_taxid": 1332080, "relation_to_type": "type", "validated": true, "ani": 78.245, "matched_fragments": 344, "total_fragments": 1412, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobium chlorophenolicum", "strain": "strain=NBRC 16172", "accession": "GCA_001598515.1", "taxid": 46429, "species_taxid": 46429, "relation_to_type": "type", "validated": true, "ani": 78.0822, "matched_fragments": 330, "total_fragments": 1412, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobium chlorophenolicum", "strain": "strain=NBRC 16172", "accession": "GCA_000722875.1", "taxid": 46429, "species_taxid": 46429, "relation_to_type": "type", "validated": true, "ani": 77.9944, "matched_fragments": 353, "total_fragments": 1412, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas deserti", "strain": "strain=GL-C-18", "accession": "GCA_003012735.1", "taxid": 2116704, "species_taxid": 2116704, "relation_to_type": "type", "validated": true, "ani": 77.6737, "matched_fragments": 368, "total_fragments": 1412, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003590775.1", "gtdb_species": "s__Sphingobium_A sp003590775", "ani": 100.0, "matched_fragments": 1409, "total_fragments": 1412, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium_A", "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": 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