{ "type": "genome", "identifier": "GCF_900475315.1", "organism": "Neisseria cinerea", "title": "Neisseria cinerea", "description": "na", "data type": "Genome sequencing and assembly", "organization": "SC", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900475315.1", "bioproject": "PRJNA224116", "biosample": "SAMEA3714889", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "483", "species_taxid": "483", "organism_name": "Neisseria cinerea", "infraspecific_name": "strain=NCTC10294", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/06/17", "asm_name": "43721_G02", "asm_submitter": "SC", "gbrs_paired_asm": "GCA_900475315.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/475/315/GCF_900475315.1_43721_G02", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "1832904", "genome_size_ungapped": "1832904", "gc_percent": "51.000000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900475315.1-RS_2024_09_02", "annotation_date": "2024-09-02", "total_gene_count": "1829", "protein_coding_gene_count": "1707", "non_coding_gene_count": "75", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-06-17", "dateModified": "2018-06-17", "datePublished": "2018-06-17", "_annotation": { "sample_count": 1, "sample_organism": [ "Neisseria cinerea" ], "sample_taxid": [ "483" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [ "not available: to be reported later" ], "sample_host_disease_id": [], "sample_host_location": [ "Germany" ], "sample_host_location_id": [], "data_size": "0.515 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)": "1832904", "Number of Sequences": "1", "Longest Sequences (bp)": "1832904", "N50 (bp)": "1832904", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "50.9", "Number of CDSs": "1724", "Average Protein Length": "305.7", "Coding Ratio (%)": "86.3", "Number of rRNAs": "12", "Number of tRNAs": "60", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Neisseria cinerea", "strain": "strain=NCTC10294", "accession": "GCA_900475315.1", "taxid": 483, "species_taxid": 483, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 609, "total_fragments": 610, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Neisseria cinerea", "strain": "strain=FDAARGOS_871", "accession": "GCA_016028715.1", "taxid": 483, "species_taxid": 483, "relation_to_type": "type", "validated": true, "ani": 99.9997, "matched_fragments": 610, "total_fragments": 610, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Neisseria cinerea", "strain": "strain=CCUG 2156", "accession": "GCA_021025975.1", "taxid": 483, "species_taxid": 483, "relation_to_type": "type", "validated": true, "ani": 97.0633, "matched_fragments": 563, "total_fragments": 610, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Neisseria cinerea", "strain": "strain=ATCC 14685", "accession": "GCA_000173895.1", "taxid": 483, "species_taxid": 483, "relation_to_type": "type", "validated": true, "ani": 97.0618, "matched_fragments": 560, "total_fragments": 610, "ani_threshold": 95, "status": "conclusive" }, { "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": 90.3929, "matched_fragments": 532, "total_fragments": 610, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Neisseria lactamica", "strain": "strain=NCTC10617", "accession": "GCA_901482445.1", "taxid": 486, "species_taxid": 486, "relation_to_type": "type", "validated": true, "ani": 90.3128, "matched_fragments": 543, "total_fragments": 610, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Morococcus cerebrosus", "strain": "strain=CIP 81.93", "accession": "GCA_000813705.1", "taxid": 1056807, "species_taxid": 1056807, "relation_to_type": "type", "validated": true, "ani": 86.5904, "matched_fragments": 381, "total_fragments": 610, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Morococcus cerebrosus", "strain": "strain=CIP 81.93", "accession": "GCA_022749515.1", "taxid": 1056807, "species_taxid": 1056807, "relation_to_type": "type", "validated": true, "ani": 86.5867, "matched_fragments": 421, "total_fragments": 610, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Neisseria flavescens", "strain": "strain=NCTC8263", "accession": "GCA_900453805.1", "taxid": 484, "species_taxid": 484, "relation_to_type": "type", "validated": true, "ani": 86.2503, "matched_fragments": 404, "total_fragments": 610, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Neisseria perflava", "strain": "strain=CCUG 17915", "accession": "GCA_023472875.1", "taxid": 33053, "species_taxid": 33053, "relation_to_type": "suspected-type", "validated": true, "ani": 85.206, "matched_fragments": 370, "total_fragments": 610, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900475315.1", "gtdb_species": "s__Neisseria cinerea", "ani": 100.0, "matched_fragments": 609, "total_fragments": 610, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.50", "min_intra_species_ani": "96.82", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.93", "num_clustered_genomes": 8, "status": "conclusive" }, { "accession": "GCF_000176735.1", "gtdb_species": "s__Neisseria polysaccharea", "ani": 91.4359, "matched_fragments": 514, "total_fragments": 610, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.23", "min_intra_species_ani": "95.40", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.88", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_003044455.1", "gtdb_species": "s__Neisseria bergeri", "ani": 91.1066, "matched_fragments": 537, "total_fragments": 610, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.18", "min_intra_species_ani": "96.14", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.92", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_000193795.1", "gtdb_species": "s__Neisseria lactamica_A", "ani": 90.5114, "matched_fragments": 501, "total_fragments": 610, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria", "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_901482445.1", "gtdb_species": "s__Neisseria lactamica", "ani": 90.3292, "matched_fragments": 544, "total_fragments": 610, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.73", "min_intra_species_ani": "97.33", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.89", "num_clustered_genomes": 36, "status": "-" }, { "accession": "GCF_900638555.1", "gtdb_species": "s__Neisseria meningitidis", "ani": 90.3114, "matched_fragments": 538, "total_fragments": 610, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria", "ani_circumscription_radius": 95.0389, "mean_intra_species_ani": "97.78", "min_intra_species_ani": "97.16", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.86", "num_clustered_genomes": 2138, "status": "-" }, { "accession": "GCF_003315235.1", "gtdb_species": "s__Neisseria gonorrhoeae", "ani": 89.8908, "matched_fragments": 507, "total_fragments": 610, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria", "ani_circumscription_radius": 95.0389, "mean_intra_species_ani": "99.56", "min_intra_species_ani": "98.98", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.89", "num_clustered_genomes": 796, "status": "-" }, { "accession": "GCF_005221285.1", "gtdb_species": "s__Neisseria flavescens", "ani": 86.1954, "matched_fragments": 398, "total_fragments": 610, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.29", "min_intra_species_ani": "96.65", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.93", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_001618085.1", "gtdb_species": "s__Neisseria flavescens_C", "ani": 85.7482, "matched_fragments": 369, "total_fragments": 610, "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_003045025.1", "gtdb_species": "s__Neisseria subflava_A", "ani": 85.7317, "matched_fragments": 389, "total_fragments": 610, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria", "ani_circumscription_radius": 95.3115, "mean_intra_species_ani": "96.25", "min_intra_species_ani": "95.58", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.91", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCF_013267835.1", "gtdb_species": "s__Neisseria sp000186165", "ani": 85.4849, "matched_fragments": 382, "total_fragments": 610, "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": "GCF_003351665.1", "gtdb_species": "s__Neisseria perflava", "ani": 85.4777, "matched_fragments": 384, "total_fragments": 610, "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_003044645.1", "gtdb_species": "s__Neisseria subflava_B", "ani": 85.377, "matched_fragments": 379, "total_fragments": 610, "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_001618065.1", "gtdb_species": "s__Neisseria flavescens_A", "ani": 85.3484, "matched_fragments": 368, "total_fragments": 610, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria", "ani_circumscription_radius": 95.6469, "mean_intra_species_ani": "95.75", "min_intra_species_ani": "95.69", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.91", "num_clustered_genomes": 4, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.086, "cell_length": -0.056, "doubling_h": -0.218, "growth_tmp": 34.0, "optimum_tmp": 37.0, "optimum_ph": 7.0, "genome_size": 1852836.5, "gc_content": 50.85, "coding_genes": 1733.0, "rRNA16S_genes": 4.014, "tRNA_genes": 59.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.0, "coccus_cell_shape": 1.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Neisseria", "cinerea" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }