{ "type": "genome", "identifier": "GCF_012184415.1", "organism": "Ramlibacter lithotrophicus", "title": "Ramlibacter lithotrophicus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "California Institute of Technology", "publication": [ {} ], "properties": { "assembly_accession": "GCF_012184415.1", "bioproject": "PRJNA224116", "biosample": "SAMN12638106", "wgs_master": "VTOX00000000.1", "refseq_category": "reference genome", "taxid": "2606681", "species_taxid": "2606681", "organism_name": "Ramlibacter lithotrophicus", "infraspecific_name": "strain=RBP-1", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/04/08", "asm_name": "ASM1218441v1", "asm_submitter": "California Institute of Technology", "gbrs_paired_asm": "GCA_012184415.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/012/184/415/GCF_012184415.1_ASM1218441v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5263905", "genome_size_ungapped": "5263905", "gc_percent": "69.000000", "replicon_count": "0", "scaffold_count": "24", "contig_count": "24", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_012184415.1-RS_2024_03_22", "annotation_date": "2024-03-22", "total_gene_count": "5113", "protein_coding_gene_count": "5011", "non_coding_gene_count": "54", "pubmed_id": "32669693" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-04-08", "dateModified": "2020-04-08", "datePublished": "2020-04-08", "_annotation": { "sample_count": 1, "sample_organism": [ "Ramlibacter lithotrophicus" ], "sample_taxid": [ "2606681" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: North Mudd Laboratories, California Institute of Technology (Caltech)" ], "sample_host_location_id": [], "data_size": "1.422 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)": "5263905", "Number of Sequences": "24", "Longest Sequences (bp)": "1277738", "N50 (bp)": "428289", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "69.0", "Number of CDSs": "5099", "Average Protein Length": "318.5", "Coding Ratio (%)": "92.5", "Number of rRNAs": "6", "Number of tRNAs": "50", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Ramlibacter lithotrophicus", "strain": "strain=RBP-1", "accession": "GCA_012184415.1", "taxid": 2606681, "species_taxid": 2606681, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1741, "total_fragments": 1744, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Ramlibacter tataouinensis", "strain": "strain=TTB310", "accession": "GCA_000215705.1", "taxid": 94132, "species_taxid": 94132, "relation_to_type": "type", "validated": true, "ani": 82.0923, "matched_fragments": 832, "total_fragments": 1744, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ramlibacter henchirensis", "strain": "strain=DSM 14656", "accession": "GCA_004682015.1", "taxid": 204072, "species_taxid": 204072, "relation_to_type": "type", "validated": true, "ani": 81.9764, "matched_fragments": 794, "total_fragments": 1744, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ramlibacter humi", "strain": "strain=18x22-1", "accession": "GCA_004681975.1", "taxid": 2530451, "species_taxid": 2530451, "relation_to_type": "type", "validated": true, "ani": 81.9033, "matched_fragments": 793, "total_fragments": 1744, "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": 81.8994, "matched_fragments": 813, "total_fragments": 1744, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ramlibacter aquaticus", "strain": "strain=LMG 30558", "accession": "GCA_015159745.1", "taxid": 2780094, "species_taxid": 2780094, "relation_to_type": "type", "validated": true, "ani": 81.8624, "matched_fragments": 715, "total_fragments": 1744, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ramlibacter alkalitolerans", "strain": "strain=KACC 19305", "accession": "GCA_016722765.1", "taxid": 2039631, "species_taxid": 2039631, "relation_to_type": "type", "validated": true, "ani": 81.7391, "matched_fragments": 931, "total_fragments": 1744, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ramlibacter monticola", "strain": "strain=KACC 19175", "accession": "GCA_016722785.1", "taxid": 1926872, "species_taxid": 1926872, "relation_to_type": "type", "validated": true, "ani": 81.6854, "matched_fragments": 932, "total_fragments": 1744, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ramlibacter pinisoli", "strain": "strain=MAH-25", "accession": "GCA_009758015.1", "taxid": 2682844, "species_taxid": 2682844, "relation_to_type": "type", "validated": true, "ani": 81.6808, "matched_fragments": 877, "total_fragments": 1744, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ramlibacter agri", "strain": "strain=G-1-2-2", "accession": "GCA_012927085.1", "taxid": 2728837, "species_taxid": 2728837, "relation_to_type": "type", "validated": true, "ani": 81.0844, "matched_fragments": 925, "total_fragments": 1744, "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": 80.7353, "matched_fragments": 749, "total_fragments": 1744, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hydrogenophaga crocea", "strain": "strain=BA0156", "accession": "GCA_011388215.1", "taxid": 2716225, "species_taxid": 2716225, "relation_to_type": "type", "validated": true, "ani": 80.0602, "matched_fragments": 627, "total_fragments": 1744, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xylophilus ampelinus", "strain": "strain=CFBP 1192", "accession": "GCA_024832295.1", "taxid": 54067, "species_taxid": 54067, "relation_to_type": "type", "validated": true, "ani": 79.9644, "matched_fragments": 559, "total_fragments": 1744, "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": 79.3841, "matched_fragments": 630, "total_fragments": 1744, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudorhodoferax soli", "strain": "strain=DSM 21634", "accession": "GCA_003337555.1", "taxid": 545864, "species_taxid": 545864, "relation_to_type": "type", "validated": true, "ani": 79.3839, "matched_fragments": 765, "total_fragments": 1744, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_012184415.1", "gtdb_species": "s__Ramlibacter lithotrophicus", "ani": 100.0, "matched_fragments": 1741, "total_fragments": 1744, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter", "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_014874145.1", "gtdb_species": "s__Ramlibacter sp014874145", "ani": 82.2578, "matched_fragments": 838, "total_fragments": 1744, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter", "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_000215705.1", "gtdb_species": "s__Ramlibacter tataouinensis", "ani": 82.1077, "matched_fragments": 830, "total_fragments": 1744, "gtdb_taxonomy": 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