{ "type": "genome", "identifier": "GCF_003002825.1", "organism": "Spirosoma oryzae", "title": "Spirosoma oryzae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003002825.1", "bioproject": "PRJNA224116", "biosample": "SAMN07621040", "wgs_master": "PVTE00000000.1", "refseq_category": "reference genome", "taxid": "1469603", "species_taxid": "1469603", "organism_name": "Spirosoma oryzae", "infraspecific_name": "strain=DSM 28354", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/03/15", "asm_name": "ASM300282v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_003002825.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/002/825/GCF_003002825.1_ASM300282v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6569981", "genome_size_ungapped": "6569981", "gc_percent": "54.000000", "replicon_count": "0", "scaffold_count": "75", "contig_count": "75", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003002825.1-RS_2024_05_03", "annotation_date": "2024-05-03", "total_gene_count": "5581", "protein_coding_gene_count": "5502", "non_coding_gene_count": "48", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-03-15", "dateModified": "2018-03-15", "datePublished": "2018-03-15", "_annotation": { "sample_count": 1, "sample_organism": [ "Spirosoma oryzae" ], "sample_taxid": [ "1469603" ], "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": "1.869 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)": "6569981", "Number of Sequences": "75", "Longest Sequences (bp)": "478030", "N50 (bp)": "224105", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "54.1", "Number of CDSs": "5552", "Average Protein Length": "339.5", "Coding Ratio (%)": "86.1", "Number of rRNAs": "0", "Number of tRNAs": "43", "Number of CRISPRs": "5" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Spirosoma oryzae", "strain": "strain=DSM 28354", "accession": "GCA_003002825.1", "taxid": 1469603, "species_taxid": 1469603, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2149, "total_fragments": 2152, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Spirosoma agri", "strain": "strain=KCTC 52727", "accession": "GCA_010747415.1", "taxid": 1987381, "species_taxid": 1987381, "relation_to_type": "type", "validated": true, "ani": 77.6094, "matched_fragments": 393, "total_fragments": 2152, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Spirosoma lacussanchae", "strain": "strain=CPCC 100624", "accession": "GCA_005870035.1", "taxid": 1884249, "species_taxid": 1884249, "relation_to_type": "type", "validated": true, "ani": 77.3056, "matched_fragments": 418, "total_fragments": 2152, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Spirosoma rigui", "strain": "strain=KCTC 12531", "accession": "GCA_002067135.1", "taxid": 564064, "species_taxid": 564064, "relation_to_type": "type", "validated": true, "ani": 77.2729, "matched_fragments": 411, "total_fragments": 2152, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Spirosoma sordidisoli", "strain": "strain=TY50", "accession": "GCA_004138325.1", "taxid": 2502893, "species_taxid": 2502893, "relation_to_type": "type", "validated": true, "ani": 77.2423, "matched_fragments": 455, "total_fragments": 2152, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Spirosoma taeanense", "strain": "strain=TS118", "accession": "GCA_013127955.1", "taxid": 2735870, "species_taxid": 2735870, "relation_to_type": "type", "validated": true, "ani": 77.1883, "matched_fragments": 445, "total_fragments": 2152, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Spirosoma montaniterrae", "strain": "strain=DY10", "accession": "GCA_001988955.1", "taxid": 1178516, "species_taxid": 1178516, "relation_to_type": "type", "validated": true, "ani": 77.1276, "matched_fragments": 388, "total_fragments": 2152, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Spirosoma fluviale", "strain": "strain=DSM 29961", "accession": "GCA_900230225.1", "taxid": 1597977, "species_taxid": 1597977, "relation_to_type": "type", "validated": true, "ani": 77.092, "matched_fragments": 402, "total_fragments": 2152, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Spirosoma aerolatum", "strain": "strain=KACC 17939", "accession": "GCA_002056795.1", "taxid": 1211326, "species_taxid": 1211326, "relation_to_type": "type", "validated": true, "ani": 77.0241, "matched_fragments": 290, "total_fragments": 2152, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Spirosoma radiotolerans", "strain": "strain=DG5A", "accession": "GCA_000974425.1", "taxid": 1379870, "species_taxid": 1379870, "relation_to_type": "type", "validated": true, "ani": 77.0153, "matched_fragments": 302, "total_fragments": 2152, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Spirosoma panaciterrae", "strain": "strain=DSM 21099", "accession": "GCA_000374025.1", "taxid": 496058, "species_taxid": 496058, "relation_to_type": "type", "validated": true, "ani": 76.8774, "matched_fragments": 322, "total_fragments": 2152, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Spirosoma utsteinense", "strain": "strain=LMG 31447", "accession": "GCA_014282275.1", "taxid": 2585773, "species_taxid": 2585773, "relation_to_type": "type", "validated": true, "ani": 76.7531, "matched_fragments": 384, "total_fragments": 2152, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hymenobacter telluris", "strain": "strain=BT186", "accession": "GCA_017313265.1", "taxid": 2816474, "species_taxid": 2816474, "relation_to_type": "type", "validated": true, "ani": 75.7825, "matched_fragments": 53, "total_fragments": 2152, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hymenobacter metallicola", "strain": "strain=9PBR-1", "accession": "GCA_004745645.1", "taxid": 2563114, "species_taxid": 2563114, "relation_to_type": "type", "validated": true, 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}, { "accession": "GCF_012849055.1", "gtdb_species": "s__Spirosoma sp012849055", "ani": 81.9917, "matched_fragments": 1353, "total_fragments": 2152, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma", "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_013375035.1", "gtdb_species": "s__Spirosoma sp013375035", "ani": 78.0679, "matched_fragments": 477, "total_fragments": 2152, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma", "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_010747415.1", "gtdb_species": "s__Spirosoma agri", 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"spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Spirosoma", "oryzae" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }