{ "type": "genome", "identifier": "GCF_000156355.1", "organism": "Methylophaga thiooxydans DMS010", "title": "Methylophaga thiooxydans DMS010", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Moore Foundation", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000156355.1", "bioproject": "PRJNA224116", "biosample": "SAMN02436314", "wgs_master": "ABXT00000000.1", "refseq_category": "reference genome", "taxid": "637616", "species_taxid": "392484", "organism_name": "Methylophaga thiooxydans DMS010", "infraspecific_name": "strain=DMS010", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2009/03/02", "asm_name": "ASM15635v1", "asm_submitter": "Moore Foundation", "gbrs_paired_asm": "GCA_000156355.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/156/355/GCF_000156355.1_ASM15635v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3047652", "genome_size_ungapped": "3018159", "gc_percent": "46.000000", "replicon_count": "0", "scaffold_count": "26", "contig_count": "43", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000156355.1-RS_2024_11_26", "annotation_date": "2024-11-26", "total_gene_count": "3201", "protein_coding_gene_count": "3133", "non_coding_gene_count": "49", "pubmed_id": "21478352" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2009-03-02", "dateModified": "2009-03-02", "datePublished": "2009-03-02", "_annotation": { "sample_count": 1, "sample_organism": [ "Methylophaga thiooxydans DMS010" ], "sample_taxid": [ "637616" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "0.865 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 85.42, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "3047652", "Number of Sequences": "26", "Longest Sequences (bp)": "600827", "N50 (bp)": "198717", "Gap Ratio (%)": "0.967729", "GCcontent (%)": "46.2", "Number of CDSs": "3108", "Average Protein Length": "296.4", "Coding Ratio (%)": "90.7", "Number of rRNAs": "7", "Number of tRNAs": "38", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Methylophaga thiooxydans", "strain": "strain=DMS010", "accession": "GCA_000156355.1", "taxid": 392484, "species_taxid": 392484, "relation_to_type": "type", "validated": true, "ani": 99.9847, "matched_fragments": 927, "total_fragments": 1002, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Methylophaga sulfidovorans", "strain": "strain=DSM 11578", "accession": "GCA_900114205.1", "taxid": 45496, "species_taxid": 45496, "relation_to_type": "type", "validated": true, "ani": 78.3794, "matched_fragments": 238, "total_fragments": 1002, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylophaga aminisulfidivorans", "strain": "strain=MP", "accession": "GCA_000214595.2", "taxid": 230105, "species_taxid": 230105, "relation_to_type": "type", "validated": true, "ani": 78.3102, "matched_fragments": 242, "total_fragments": 1002, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylophaga nitratireducenticrescens", "strain": "strain=JAM1", "accession": "GCA_000260985.3", "taxid": 754476, "species_taxid": 754476, "relation_to_type": "type", "validated": true, "ani": 77.559, "matched_fragments": 137, "total_fragments": 1002, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylophaga pinxianii", "strain": "strain=TMB456", "accession": "GCA_020447225.1", "taxid": 2881052, "species_taxid": 2881052, "relation_to_type": "type", "validated": true, "ani": 77.2825, "matched_fragments": 113, "total_fragments": 1002, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 85.42, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000156355.1", "gtdb_species": "s__Methylophaga thiooxydans", "ani": 99.9848, "matched_fragments": 930, "total_fragments": 1002, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.48", "min_intra_species_ani": "96.37", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.88", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCA_011052985.1", "gtdb_species": "s__Methylophaga aminisulfidivorans_A", "ani": 79.3358, "matched_fragments": 126, "total_fragments": 1002, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga", "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_009711715.1", "gtdb_species": "s__Methylophaga sp009711715", "ani": 78.6257, "matched_fragments": 262, "total_fragments": 1002, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga", "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_900114205.1", "gtdb_species": "s__Methylophaga sulfidovorans", "ani": 78.3812, "matched_fragments": 238, "total_fragments": 1002, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga", "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_000214595.1", "gtdb_species": "s__Methylophaga aminisulfidivorans", "ani": 78.3261, "matched_fragments": 241, "total_fragments": 1002, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.12", "min_intra_species_ani": "97.07", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.92", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_002706095.1", "gtdb_species": "s__Methylophaga sp002706095", "ani": 78.225, "matched_fragments": 222, "total_fragments": 1002, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.12", "min_intra_species_ani": "97.28", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.89", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCA_014762585.1", "gtdb_species": "s__Methylophaga sp014762585", "ani": 78.0602, "matched_fragments": 199, "total_fragments": 1002, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga", "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_002696735.1", "gtdb_species": "s__Methylophaga sp002696735", "ani": 77.5798, "matched_fragments": 137, "total_fragments": 1002, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.51", "min_intra_species_ani": "97.89", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.90", "num_clustered_genomes": 20, "status": "-" }, { "accession": "GCF_000260985.4", "gtdb_species": "s__Methylophaga nitratireducenticrescens", "ani": 77.5562, "matched_fragments": 138, "total_fragments": 1002, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.21", "min_intra_species_ani": "99.21", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001720165.1", "gtdb_species": "s__Methylophaga muralis", "ani": 77.1642, "matched_fragments": 129, "total_fragments": 1002, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.83", "min_intra_species_ani": "97.83", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_002363955.1", "gtdb_species": "s__Methylophaga sp002363955", "ani": 76.8538, "matched_fragments": 117, "total_fragments": 1002, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.95", "min_intra_species_ani": "98.64", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.91", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCA_014859375.1", "gtdb_species": "s__GCA-002733105 sp014859375", "ani": 76.8499, "matched_fragments": 93, "total_fragments": 1002, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105", "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_002354555.1", "gtdb_species": "s__Methylophaga sp002354555", "ani": 76.8106, "matched_fragments": 117, "total_fragments": 1002, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.87", "min_intra_species_ani": "98.17", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.88", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_003645385.1", "gtdb_species": "s__GCA-002733105 sp003645385", "ani": 76.6895, "matched_fragments": 55, "total_fragments": 1002, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.88", "min_intra_species_ani": "98.88", "mean_intra_species_af": "0.61", "min_intra_species_af": "0.61", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_905479985.1", "gtdb_species": "s__GCA-002733105 sp905479985", "ani": 76.5333, "matched_fragments": 72, "total_fragments": 1002, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105", "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": -0.529, "cell_length": 0.085, "doubling_h": null, "growth_tmp": 29.214, "optimum_tmp": 31.625, "optimum_ph": 8.5, "genome_size": 2881741.8, "gc_content": 47.423, "coding_genes": 2776.166, "rRNA16S_genes": 3.0, "tRNA_genes": 42.5, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 1.0, "facultative_respiration": 0.166, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.833, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Methylophaga", "thiooxydans", "DMS010" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }