{ "type": "genome", "identifier": "GCF_012769535.1", "organism": "Methylococcus geothermalis", "title": "Methylococcus geothermalis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Chungkbuk National University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_012769535.1", "bioproject": "PRJNA224116", "biosample": "SAMN13402798", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "2681310", "species_taxid": "2681310", "organism_name": "Methylococcus geothermalis", "infraspecific_name": "strain=IM1", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/04/24", "asm_name": "ASM1276953v1", "asm_submitter": "Chungkbuk National University", "gbrs_paired_asm": "GCA_012769535.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/012/769/535/GCF_012769535.1_ASM1276953v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3371031", "genome_size_ungapped": "3371031", "gc_percent": "63.000000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_012769535.1-RS_2024_12_09", "annotation_date": "2024-12-09", "total_gene_count": "3176", "protein_coding_gene_count": "3054", "non_coding_gene_count": "57", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-04-24", "dateModified": "2020-04-24", "datePublished": "2020-04-24", "_annotation": { "sample_count": 1, "sample_organism": [ "Methylococcus geothermalis" ], "sample_taxid": [ "2681310" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea" ], "sample_host_location_id": [], "data_size": "0.936 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 98.96, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "3371031", "Number of Sequences": "1", "Longest Sequences (bp)": "3371031", "N50 (bp)": "3371031", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "63.2", "Number of CDSs": "3098", "Average Protein Length": "323.5", "Coding Ratio (%)": "89.2", "Number of rRNAs": "6", "Number of tRNAs": "48", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Methylococcus geothermalis", "strain": "strain=IM1", "accession": "GCA_012769535.1", "taxid": 2681310, "species_taxid": 2681310, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1122, "total_fragments": 1123, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Methylococcus capsulatus", "strain": "strain=Texas", "accession": "GCA_000297615.1", "taxid": 414, "species_taxid": 414, "relation_to_type": "type", "validated": true, "ani": 86.4156, "matched_fragments": 849, "total_fragments": 1123, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylococcus capsulatus", "strain": "strain=ATCC 19069", "accession": "GCA_000424685.1", "taxid": 414, "species_taxid": 414, "relation_to_type": "type", "validated": true, "ani": 86.3372, "matched_fragments": 891, "total_fragments": 1123, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methyloterricola oryzae", "strain": "strain=73a", "accession": "GCA_000934725.1", "taxid": 1495050, "species_taxid": 1495050, "relation_to_type": "type", "validated": true, "ani": 78.3126, "matched_fragments": 291, "total_fragments": 1123, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylogaea oryzae", "strain": "strain=E10", "accession": "GCA_019669985.1", "taxid": 1295382, "species_taxid": 1295382, "relation_to_type": "type", "validated": true, "ani": 78.0733, "matched_fragments": 258, "total_fragments": 1123, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylomagnum ishizawai", "strain": "strain=RS11D-Pr", "accession": "GCA_019670005.1", "taxid": 1760988, "species_taxid": 1760988, "relation_to_type": "type", "validated": true, "ani": 78.0435, "matched_fragments": 300, "total_fragments": 1123, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylogaea oryzae", "strain": "strain=JCM 16910", "accession": "GCA_001312345.1", "taxid": 1295382, "species_taxid": 1295382, "relation_to_type": "type", "validated": true, "ani": 77.9686, "matched_fragments": 189, "total_fragments": 1123, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thiohalobacter thiocyanaticus", "strain": "strain=Hrh1", "accession": "GCA_003932505.1", "taxid": 585455, "species_taxid": 585455, "relation_to_type": "type", "validated": true, "ani": 77.5181, "matched_fragments": 139, "total_fragments": 1123, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylocaldum marinum", "strain": "strain=S8", "accession": "GCA_003584645.1", "taxid": 1432792, "species_taxid": 1432792, "relation_to_type": "type", "validated": true, "ani": 77.4543, "matched_fragments": 208, "total_fragments": 1123, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas hydrolytica", "strain": "strain=DSWY01", "accession": "GCA_021495345.2", "taxid": 2493633, "species_taxid": 2493633, "relation_to_type": "type", "validated": true, "ani": 77.1897, "matched_fragments": 130, "total_fragments": 1123, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas aromaticivorans", "strain": "strain=MAP12", "accession": "GCA_019097855.1", "taxid": 2849492, "species_taxid": 2849492, "relation_to_type": "type", "validated": true, "ani": 77.1537, "matched_fragments": 146, "total_fragments": 1123, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas xantholysinigenes", "strain": "strain=RW9S1A", "accession": "GCA_014268885.2", "taxid": 2745490, "species_taxid": 2745490, "relation_to_type": "type", "validated": true, "ani": 76.8265, "matched_fragments": 107, "total_fragments": 1123, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Plasticicumulans lactativorans", "strain": "strain=DSM 25287", "accession": "GCA_004341245.1", "taxid": 1133106, "species_taxid": 1133106, "relation_to_type": "type", "validated": true, "ani": 76.7979, "matched_fragments": 162, "total_fragments": 1123, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas aeruginosa", "strain": "strain=DSM 50071", "accession": "GCA_024169805.1", "taxid": 287, "species_taxid": 287, "relation_to_type": "type", "validated": true, "ani": 76.7675, "matched_fragments": 155, "total_fragments": 1123, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas lalucatii", "strain": "strain=R1b54", "accession": "GCA_018398425.1", "taxid": 1424203, "species_taxid": 1424203, "relation_to_type": "type", "validated": true, "ani": 76.7578, "matched_fragments": 154, "total_fragments": 1123, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas lactosivorans", "strain": "strain=KCTC 52281", "accession": "GCA_003254665.1", "taxid": 2185141, "species_taxid": 2185141, "relation_to_type": "type", "validated": true, "ani": 76.5651, "matched_fragments": 127, "total_fragments": 1123, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas aeruginosa", "strain": "strain=JCM 5962", "accession": "GCA_022496575.1", "taxid": 287, "species_taxid": 287, "relation_to_type": "type", "validated": true, "ani": 76.5415, "matched_fragments": 160, "total_fragments": 1123, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 98.96, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_012769535.1", "gtdb_species": "s__Methylococcus sp012769535", "ani": 100.0, "matched_fragments": 1121, "total_fragments": 1123, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylococcus", "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_000424685.1", "gtdb_species": "s__Methylococcus capsulatus", "ani": 86.3287, "matched_fragments": 892, "total_fragments": 1123, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.39", "min_intra_species_ani": "98.77", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.95", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_016106025.1", "gtdb_species": "s__Methylococcus sp016106025", "ani": 85.881, "matched_fragments": 878, "total_fragments": 1123, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylococcus", "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_016925495.1", "gtdb_species": "s__EFPC2 sp016925495", "ani": 78.6618, "matched_fragments": 291, "total_fragments": 1123, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__EFPC2", "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_000934725.1", "gtdb_species": "s__Methyloterricola oryzae", "ani": 78.2987, "matched_fragments": 290, "total_fragments": 1123, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methyloterricola", "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_001312345.1", "gtdb_species": "s__Methylogaea oryzae", "ani": 77.9686, "matched_fragments": 189, "total_fragments": 1123, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylogaea", "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_900155475.1", "gtdb_species": "s__Methylomagnum ishizawai", "ani": 77.9408, "matched_fragments": 283, "total_fragments": 1123, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylomagnum", "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_002005105.1", "gtdb_species": "s__Methylocaldum sp002005105", "ani": 77.6465, "matched_fragments": 197, "total_fragments": 1123, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylocaldum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.51", "min_intra_species_ani": "98.17", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.88", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCA_902810705.1", "gtdb_species": "s__CADDYU01 sp902810705", "ani": 77.6193, "matched_fragments": 211, "total_fragments": 1123, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__CADDYU01", "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_003932505.1", "gtdb_species": "s__Thiohalobacter thiocyanaticus", "ani": 77.4962, "matched_fragments": 140, "total_fragments": 1123, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter", "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_014268885.2", "gtdb_species": "s__Pseudomonas_E sp014268885", "ani": 76.8138, "matched_fragments": 107, "total_fragments": 1123, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "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_900103845.1", "gtdb_species": "s__Pseudomonas jinjuensis", "ani": 76.7008, "matched_fragments": 151, "total_fragments": 1123, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014779595.1", "gtdb_species": "s__Halomonas_B sp014779595", "ani": 76.2259, "matched_fragments": 105, "total_fragments": 1123, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B", "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": null, "cell_length": null, "doubling_h": 1.781, "growth_tmp": 38.7, "optimum_tmp": 45.0, "optimum_ph": null, "genome_size": 3292683.143, "gc_content": 63.533, "coding_genes": 2959.0, "rRNA16S_genes": 2.0, "tRNA_genes": 46.0, "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": 0.0, "thermophilic_range_tmp": 1.0, "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": [ "Methylococcus", "geothermalis" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }