{ "type": "genome", "identifier": "GCF_000620925.1", "organism": "Conchiformibius steedae DSM 2580", "title": "Conchiformibius steedae DSM 2580", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000620925.1", "bioproject": "PRJNA224116", "biosample": "SAMN02743966", "wgs_master": "JHZP00000000.1", "refseq_category": "na", "taxid": "1121352", "species_taxid": "153493", "organism_name": "Conchiformibius steedae DSM 2580", "infraspecific_name": "strain=DSM 2580", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2014/04/08", "asm_name": "ASM62092v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_000620925.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/620/925/GCF_000620925.1_ASM62092v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2146492", "genome_size_ungapped": "2146037", "gc_percent": "51.000000", "replicon_count": "0", "scaffold_count": "23", "contig_count": "26", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000620925.1-RS_2024_05_08", "annotation_date": "2024-05-08", "total_gene_count": "2146", "protein_coding_gene_count": "2051", "non_coding_gene_count": "67", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2014-04-08", "dateModified": "2014-04-08", "datePublished": "2014-04-08", "_annotation": { "sample_count": 1, "sample_organism": [ "Conchiformibius steedae DSM 2580" ], "sample_taxid": [ "1121352" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "0.594 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)": "2146492", "Number of Sequences": "23", "Longest Sequences (bp)": "1188031", "N50 (bp)": "1188031", "Gap Ratio (%)": "0.021197", "GCcontent (%)": "50.8", "Number of CDSs": "2039", "Average Protein Length": "311.9", "Coding Ratio (%)": "88.9", "Number of rRNAs": "0", "Number of tRNAs": "50", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Conchiformibius steedae", "strain": "strain=DSM 2580", "accession": "GCA_000620925.1", "taxid": 153493, "species_taxid": 153493, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 702, "total_fragments": 703, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Conchiformibius steedae", "strain": "strain=DSM 2580", "accession": "GCA_023547005.1", "taxid": 153493, "species_taxid": 153493, "relation_to_type": "type", "validated": true, "ani": 99.9976, "matched_fragments": 680, "total_fragments": 703, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Conchiformibius steedae", "strain": "strain=DSM 2580", "accession": "GCA_014054725.1", "taxid": 153493, "species_taxid": 153493, "relation_to_type": "type", "validated": true, "ani": 99.9914, "matched_fragments": 702, "total_fragments": 703, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Conchiformibius kuhniae", "strain": "strain=DSM 17694", "accession": "GCA_000428785.1", "taxid": 211502, "species_taxid": 211502, "relation_to_type": "type", "validated": true, "ani": 82.0215, "matched_fragments": 474, "total_fragments": 703, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Conchiformibius kuhniae", "strain": "strain=17694", "accession": "GCA_022871025.1", "taxid": 211502, "species_taxid": 211502, "relation_to_type": "type", "validated": true, "ani": 81.9444, "matched_fragments": 485, "total_fragments": 703, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Alysiella crassa", "strain": "strain=S6", "accession": "GCA_022871045.1", "taxid": 153491, "species_taxid": 153491, "relation_to_type": "type", "validated": true, "ani": 78.306, "matched_fragments": 263, "total_fragments": 703, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Alysiella crassa", "strain": "strain=DSM 2578", "accession": "GCA_000745955.1", "taxid": 153491, "species_taxid": 153491, "relation_to_type": "type", "validated": true, "ani": 78.302, "matched_fragments": 261, "total_fragments": 703, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Alysiella crassa", "strain": "strain=NCTC10283", "accession": "GCA_900445245.1", "taxid": 153491, "species_taxid": 153491, "relation_to_type": "type", "validated": true, "ani": 78.2679, "matched_fragments": 262, "total_fragments": 703, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kingella bonacorsii", "strain": "strain=Marseille-Q4569", "accession": "GCA_016623605.1", "taxid": 2796361, "species_taxid": 2796361, "relation_to_type": "type", "validated": true, "ani": 77.7929, "matched_fragments": 226, "total_fragments": 703, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Neisseria meningitidis", "strain": "strain=PartJ-Nmeningitidis-RM8376", "accession": "GCA_022869645.1", "taxid": 487, "species_taxid": 487, "relation_to_type": "type", "validated": true, "ani": 77.4005, "matched_fragments": 163, "total_fragments": 703, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kingella kingae", "strain": "strain=4177/66", "accession": "GCA_022871005.1", "taxid": 504, "species_taxid": 504, "relation_to_type": "type", "validated": true, "ani": 77.3799, "matched_fragments": 215, "total_fragments": 703, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Uruburuella testudinis", "strain": "strain=CCUG 63373m", "accession": "GCA_022870865.1", "taxid": 1282863, "species_taxid": 1282863, "relation_to_type": "type", "validated": true, "ani": 77.2886, "matched_fragments": 194, "total_fragments": 703, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Neisseria arctica", "strain": "strain=KH1503", "accession": "GCA_022870905.1", "taxid": 1470200, "species_taxid": 1470200, "relation_to_type": "type", "validated": true, "ani": 77.0272, "matched_fragments": 104, "total_fragments": 703, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_014054725.1", "gtdb_species": "s__Conchiformibius steedae", "ani": 99.9914, "matched_fragments": 702, "total_fragments": 703, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Conchiformibius", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.09", "min_intra_species_ani": "96.18", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.87", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_000428785.1", "gtdb_species": "s__Conchiformibius kuhniae", "ani": 81.9851, "matched_fragments": 476, "total_fragments": 703, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Conchiformibius", "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_000745955.1", "gtdb_species": "s__Alysiella crassa", "ani": 78.3573, "matched_fragments": 259, "total_fragments": 703, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Alysiella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.94", "min_intra_species_ani": "99.94", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014054525.1", "gtdb_species": "s__Alysiella filiformis", "ani": 78.0283, "matched_fragments": 283, "total_fragments": 703, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Alysiella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000190695.1", "gtdb_species": "s__Kingella_A denitrificans", "ani": 77.8661, "matched_fragments": 201, "total_fragments": 703, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Kingella_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.63", "min_intra_species_ani": "96.04", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.93", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_014054985.1", "gtdb_species": "s__Kingella_B oralis", "ani": 77.7242, "matched_fragments": 220, "total_fragments": 703, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Kingella_B", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.22", "min_intra_species_ani": "96.45", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.91", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_014055005.1", "gtdb_species": "s__Neisseria dentiae", "ani": 77.6588, "matched_fragments": 189, "total_fragments": 703, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.98", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_900636765.1", "gtdb_species": "s__Neisseria canis", "ani": 77.4805, "matched_fragments": 172, "total_fragments": 703, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900187305.1", "gtdb_species": "s__Neisseria zoodegmatis", "ani": 77.4377, "matched_fragments": 199, "total_fragments": 703, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.30", "min_intra_species_ani": "96.60", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.90", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_001618085.1", "gtdb_species": "s__Neisseria flavescens_C", "ani": 77.3256, "matched_fragments": 142, "total_fragments": 703, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria", "ani_circumscription_radius": 95.4709, "mean_intra_species_ani": "96.21", "min_intra_species_ani": "96.21", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900113545.1", "gtdb_species": "s__Neisseria elongata", "ani": 77.3124, "matched_fragments": 157, "total_fragments": 703, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.68", "min_intra_species_ani": "96.06", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.86", "num_clustered_genomes": 20, "status": "-" }, { "accession": "GCF_900638685.1", "gtdb_species": "s__Neisseria weaveri", "ani": 77.3048, "matched_fragments": 147, "total_fragments": 703, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.19", "min_intra_species_ani": "98.86", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.97", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_003351665.1", "gtdb_species": "s__Neisseria perflava", "ani": 77.2726, "matched_fragments": 149, "total_fragments": 703, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria", "ani_circumscription_radius": 95.6726, "mean_intra_species_ani": "97.77", "min_intra_species_ani": "96.48", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.95", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_014297595.1", "gtdb_species": "s__Neisseria musculi", "ani": 77.2725, "matched_fragments": 173, "total_fragments": 703, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.59", "min_intra_species_ani": "98.59", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_003044645.1", "gtdb_species": "s__Neisseria subflava_B", "ani": 77.2479, "matched_fragments": 145, "total_fragments": 703, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria", "ani_circumscription_radius": 95.654, "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_013267835.1", "gtdb_species": "s__Neisseria sp000186165", "ani": 77.2218, "matched_fragments": 153, "total_fragments": 703, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria", "ani_circumscription_radius": 95.0019, "mean_intra_species_ani": "96.64", "min_intra_species_ani": "96.07", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.88", "num_clustered_genomes": 22, "status": "-" }, { "accession": "GCA_905372165.1", "gtdb_species": "s__CAJPNX01 sp905372165", "ani": 77.1732, "matched_fragments": 168, "total_fragments": 703, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__CAJPNX01", "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_001648355.1", "gtdb_species": "s__Eikenella longinqua", "ani": 76.8738, "matched_fragments": 150, "total_fragments": 703, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella", "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": 0.397, "cell_length": null, "doubling_h": null, "growth_tmp": 37.0, "optimum_tmp": 8.0, "optimum_ph": null, "genome_size": 2148680.0, "gc_content": 56.2, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": null, "motility": 1.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": 0.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 1.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Conchiformibius", "steedae", "DSM", "2580" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }