{ "type": "genome", "identifier": "GCA_903898235.1", "organism": "uncultured Methylococcaceae bacterium", "title": "uncultured Methylococcaceae bacterium", "description": "derived from environmental source; derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "BILS", "publication": [ {} ], "properties": { "assembly_accession": "GCA_903898235.1", "bioproject": "PRJEB38681", "biosample": "SAMEA6947551", "wgs_master": "CAIUES000000000.1", "refseq_category": "na", "taxid": "181674", "species_taxid": "181674", "organism_name": "uncultured Methylococcaceae bacterium", "infraspecific_name": "", "isolate": "AM-lipid-02-D10_bin-0600", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/07/20", "asm_name": "freshwater MAG --- AM-lipid-02-D10_bin-0600", "submitter": "BILS", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/903/898/235/GCA_903898235.1_freshwater_MAG_---_AM-lipid-02-D10_bin-0600", "excluded_from_refseq": "derived from environmental source; derived from metagenome", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-07-20", "dateModified": "2020-07-20", "datePublished": "2020-07-20", "_annotation": { "sample_count": 1, "sample_organism": [ "uncultured Methylococcaceae bacterium" ], "sample_taxid": [ "181674" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Finland" ], "sample_host_location_id": [], "data_size": "1.828 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": 46.0, "max": 46.0 }, "completeness": 79.17, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "6369884", "Number of Sequences": "820", "Longest Sequences (bp)": "65231", "N50 (bp)": "11760", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "51.3", "Number of CDSs": "5505", "Average Protein Length": "290.4", "Coding Ratio (%)": "75.3", "Number of rRNAs": "2", "Number of tRNAs": "48", "Number of CRISPRs": "8" }, "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": 76.3125, "matched_fragments": 59, "total_fragments": 1703, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 79.17, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_003242955.1", "gtdb_species": "s__Methyloumidiphilus alinensis", "ani": 99.4748, "matched_fragments": 1469, "total_fragments": 1703, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methyloumidiphilus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.27", "min_intra_species_ani": "95.17", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.73", "num_clustered_genomes": 31, "status": "conclusive" }, { "accession": "GCA_903934875.1", "gtdb_species": "s__Methyloumidiphilus sp903934875", "ani": 81.1341, "matched_fragments": 806, "total_fragments": 1703, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methyloumidiphilus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.88", "min_intra_species_ani": "99.86", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.91", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCA_903857165.1", "gtdb_species": "s__Methyloumidiphilus sp903857165", "ani": 79.7522, 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"matched_fragments": 403, "total_fragments": 1703, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methyloumidiphilus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.43", "min_intra_species_ani": "99.36", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.86", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_903859815.1", "gtdb_species": "s__Methyloumidiphilus sp903859815", "ani": 78.613, "matched_fragments": 423, "total_fragments": 1703, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methyloumidiphilus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.87", "min_intra_species_ani": "99.84", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.89", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_012769535.1", "gtdb_species": "s__Methylococcus sp012769535", "ani": 76.2799, 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"optimum_tmp": 29.642, "optimum_ph": 7.321, "genome_size": 4860515.519, "gc_content": 53.393, "coding_genes": 4340.777, "rRNA16S_genes": 2.4, "tRNA_genes": 49.75, "gram_stain": 0.0, "sporulation": 0.066, "motility": 0.625, "range_salinity": 0.0, "facultative_respiration": 0.142, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.857, "mesophilic_range_tmp": 0.75, "thermophilic_range_tmp": 0.25, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.687, "coccus_cell_shape": 0.25, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.062, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_gtdb_taxon": [ "d__Bacteria", "p__Pseudomonadota", "c__Gammaproteobacteria", "o__Methylococcales", "f__Methylococcaceae", "g__Methylumidiphilus", "s__Methylumidiphilus alinenensis" ], "_genome_taxon": [ "uncultured", "Methylococcaceae", "bacterium", "d__Bacteria", "p__Pseudomonadota", "c__Gammaproteobacteria", "o__Methylococcales", "f__Methylococcaceae", "g__Methylumidiphilus", "s__Methylumidiphilus alinenensis", "Bacteria", "Pseudomonadota", "Gammaproteobacteria", "Methylococcales", "Methylococcaceae", "Methylumidiphilus", "Methylumidiphilus", "alinenensis" ], "_meo": [ { "id": "MEO_0000038", "label": "freshwater" }, { "id": "MEO_0000024", "label": "lake" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }