{ "type": "genome", "identifier": "GCF_000349205.1", "organism": "Methylophaga lonarensis MPL", "title": "Methylophaga lonarensis MPL", "description": "na", "data type": "Genome sequencing and assembly", "organization": "National Centre for Cell Science", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000349205.1", "bioproject": "PRJNA224116", "biosample": "SAMN02470674", "wgs_master": "APHR00000000.1", "refseq_category": "reference genome", "taxid": "1286106", "species_taxid": "999151", "organism_name": "Methylophaga lonarensis MPL", "infraspecific_name": "strain=MPL", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/03/26", "asm_name": "MPLversion1", "asm_submitter": "National Centre for Cell Science", "gbrs_paired_asm": "GCA_000349205.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/349/205/GCF_000349205.1_MPLversion1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2637625", "genome_size_ungapped": "2637625", "gc_percent": "49.500000", "replicon_count": "0", "scaffold_count": "116", "contig_count": "116", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000349205.1-RS_2024_12_09", "annotation_date": "2024-12-09", "total_gene_count": "2678", "protein_coding_gene_count": "2555", "non_coding_gene_count": "59", "pubmed_id": "23661481" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-03-26", "dateModified": "2013-03-26", "datePublished": "2013-03-26", "_annotation": { "sample_count": 1, "sample_organism": [ "Methylophaga lonarensis MPL" ], "sample_taxid": [ "1286106" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "India" ], "sample_host_location_id": [], "data_size": "0.754 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)": "2637625", "Number of Sequences": "116", "Longest Sequences (bp)": "97708", "N50 (bp)": "45830", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "49.7", "Number of CDSs": "2533", "Average Protein Length": "307.5", "Coding Ratio (%)": "88.6", "Number of rRNAs": "5", "Number of tRNAs": "42", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Methylophaga lonarensis", "strain": "strain=MPL", "accession": "GCA_000349205.1", "taxid": 999151, "species_taxid": 999151, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 819, "total_fragments": 823, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Methylophaga thiooxydans", "strain": "strain=DMS010", "accession": "GCA_000156355.1", "taxid": 392484, "species_taxid": 392484, "relation_to_type": "type", "validated": true, "ani": 77.3923, "matched_fragments": 104, "total_fragments": 823, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylophaga frappieri", "strain": "strain=JAM7", "accession": "GCA_000260965.1", "taxid": 754477, "species_taxid": 754477, "relation_to_type": "type", "validated": true, "ani": 77.3556, "matched_fragments": 102, "total_fragments": 823, "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": 77.2439, "matched_fragments": 150, "total_fragments": 823, "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": 77.1419, "matched_fragments": 103, "total_fragments": 823, "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": 77.0974, "matched_fragments": 144, "total_fragments": 823, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000349205.1", "gtdb_species": "s__Methylophaga lonarensis", "ani": 100.0, "matched_fragments": 819, "total_fragments": 823, "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": "conclusive" }, { "accession": "GCA_007117275.1", "gtdb_species": "s__Methylophaga sp007117275", "ani": 84.1364, "matched_fragments": 254, "total_fragments": 823, "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": 77.4577, "matched_fragments": 161, "total_fragments": 823, "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_000260965.1", "gtdb_species": "s__Methylophaga frappieri", "ani": 77.3556, "matched_fragments": 102, "total_fragments": 823, "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": 77.3533, "matched_fragments": 137, "total_fragments": 823, "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_002363955.1", "gtdb_species": "s__Methylophaga sp002363955", "ani": 77.2926, "matched_fragments": 159, "total_fragments": 823, "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": "GCF_000260985.4", "gtdb_species": "s__Methylophaga nitratireducenticrescens", "ani": 77.2439, "matched_fragments": 150, "total_fragments": 823, "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": "GCA_002354555.1", "gtdb_species": "s__Methylophaga sp002354555", "ani": 76.9449, "matched_fragments": 136, "total_fragments": 823, "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_014762585.1", "gtdb_species": "s__Methylophaga sp014762585", "ani": 76.8883, "matched_fragments": 122, "total_fragments": 823, "gtdb_taxonomy": 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2637620.0, "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": 0.0, "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": 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", "lonarensis", "MPL" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }