{ "type": "genome", "identifier": "GCF_003843835.1", "organism": "Tibeticola sediminis", "title": "Tibeticola sediminis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003843835.1", "bioproject": "PRJNA224116", "biosample": "SAMN10362947", "wgs_master": "RKQL00000000.1", "refseq_category": "reference genome", "taxid": "1917811", "species_taxid": "1917811", "organism_name": "Tibeticola sediminis", "infraspecific_name": "strain=DSM 101684", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/11/23", "asm_name": "ASM384383v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_003843835.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/843/835/GCF_003843835.1_ASM384383v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2733067", "genome_size_ungapped": "2732876", "gc_percent": "66.500000", "replicon_count": "0", "scaffold_count": "10", "contig_count": "10", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003843835.1-RS_2024_05_04", "annotation_date": "2024-05-04", "total_gene_count": "2597", "protein_coding_gene_count": "2526", "non_coding_gene_count": "51", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-11-23", "dateModified": "2018-11-23", "datePublished": "2018-11-23", "_annotation": { "sample_count": 1, "sample_organism": [ "Tibeticola sediminis" ], "sample_taxid": [ "1917811" ], "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": "0.750 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)": "2733067", "Number of Sequences": "10", "Longest Sequences (bp)": "1055579", "N50 (bp)": "421623", "Gap Ratio (%)": "0.006988", "GCcontent (%)": "66.4", "Number of CDSs": "2520", "Average Protein Length": "330.0", "Coding Ratio (%)": "91.3", "Number of rRNAs": "3", "Number of tRNAs": "45", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Hydrogenophaga crocea", "strain": "strain=BA0156", "accession": "GCA_011388215.1", "taxid": 2716225, "species_taxid": 2716225, "relation_to_type": "type", "validated": true, "ani": 79.6531, "matched_fragments": 458, "total_fragments": 906, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Extensimonas perlucida", "strain": "strain=HX2-24", "accession": "GCA_007655255.1", "taxid": 2590786, "species_taxid": 2590786, "relation_to_type": "type", "validated": true, "ani": 79.1367, "matched_fragments": 364, "total_fragments": 906, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ramlibacter rhizophilus", "strain": "strain=CCTCC AB2015357", "accession": "GCA_004681965.1", "taxid": 1781167, "species_taxid": 1781167, "relation_to_type": "type", "validated": true, "ani": 79.0796, "matched_fragments": 365, "total_fragments": 906, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hydrogenophaga intermedia", "strain": "strain=S1", "accession": "GCA_000723405.1", "taxid": 65786, "species_taxid": 65786, "relation_to_type": "type", "validated": true, "ani": 79.0561, "matched_fragments": 414, "total_fragments": 906, "ani_threshold": 95, "status": "below_threshold" }, { 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"strain=CY1", "accession": "GCA_000282995.1", "taxid": 1165852, "species_taxid": 1165852, "relation_to_type": "type", "validated": true, "ani": 78.9267, "matched_fragments": 277, "total_fragments": 906, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ottowia beijingensis", "strain": "strain=GCS-AN-3", "accession": "GCA_013423955.1", "taxid": 1207057, "species_taxid": 1207057, "relation_to_type": "type", "validated": true, "ani": 78.9174, "matched_fragments": 448, "total_fragments": 906, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Extensimonas vulgaris", "strain": "strain=CGMCC 1.10977", "accession": "GCA_007830535.1", "taxid": 1031594, "species_taxid": 1031594, "relation_to_type": "type", "validated": true, "ani": 78.8746, "matched_fragments": 373, "total_fragments": 906, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Extensimonas vulgaris", "strain": "strain=S4", "accession": "GCA_007996985.1", "taxid": 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"validated": true, "ani": 78.7777, "matched_fragments": 376, "total_fragments": 906, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ramlibacter algicola", "strain": "strain=CrO1", "accession": "GCA_016641735.1", "taxid": 2795217, "species_taxid": 2795217, "relation_to_type": "type", "validated": true, "ani": 78.7639, "matched_fragments": 372, "total_fragments": 906, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Acidovorax cattleyae", "strain": "strain=DSM 17101", "accession": "GCA_900104515.1", "taxid": 80868, "species_taxid": 80868, "relation_to_type": "type", "validated": true, "ani": 78.6093, "matched_fragments": 364, "total_fragments": 906, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Melaminivora jejuensis", "strain": "strain=KCTC 32230", "accession": "GCA_017811175.1", "taxid": 1267217, "species_taxid": 1267217, "relation_to_type": "type", "validated": true, "ani": 78.6004, "matched_fragments": 377, "total_fragments": 906, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Acidovorax oryzae", "strain": "strain=ATCC 19882", "accession": "GCA_000687165.1", "taxid": 862720, "species_taxid": 862720, "relation_to_type": "type", "validated": true, "ani": 78.594, "matched_fragments": 383, "total_fragments": 906, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xylophilus ampelinus", "strain": "strain=CECT 7646", "accession": "GCA_003217575.1", "taxid": 54067, "species_taxid": 54067, "relation_to_type": "type", "validated": true, "ani": 78.4859, "matched_fragments": 317, "total_fragments": 906, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ramlibacter lithotrophicus", "strain": "strain=RBP-1", "accession": "GCA_012184415.1", "taxid": 2606681, "species_taxid": 2606681, "relation_to_type": "type", "validated": true, "ani": 78.4687, "matched_fragments": 377, "total_fragments": 906, "ani_threshold": 95, "status": 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906, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.75", "min_intra_species_ani": "98.75", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_017307855.1", "gtdb_species": "s__JAGOCV01 sp017307855", "ani": 78.7835, "matched_fragments": 369, "total_fragments": 906, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAGOCV01", "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_001724785.1", "gtdb_species": "s__Giesbergeria sp001724785", "ani": 78.743, "matched_fragments": 279, "total_fragments": 906, "gtdb_taxonomy": 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