{ "type": "genome", "identifier": "GCA_018436685.1", "organism": "Mesotoga sp.", "title": "Mesotoga sp.", "description": "derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "University of California, Berkeley", "publication": [ {} ], "properties": { "assembly_accession": "GCA_018436685.1", "bioproject": "PRJNA655520", "biosample": "SAMN16056005", "wgs_master": "JAHDKZ000000000.1", "refseq_category": "na", "taxid": "2053577", "species_taxid": "2053577", "organism_name": "Mesotoga sp.", "infraspecific_name": "", "isolate": "LM3-B3.2", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/05/21", "asm_name": "LM3", "submitter": "University of California, Berkeley", "gbrs_paired_asm": "GCF_018436685.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/018/436/685/GCA_018436685.1_LM3", "excluded_from_refseq": "derived from metagenome", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-05-21", "dateModified": "2021-05-21", "datePublished": "2021-05-21", "_annotation": { "sample_count": 1, "sample_organism": [ "Mesotoga sp." ], "sample_taxid": [ "2053577" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: Livermore, CA" ], "sample_host_location_id": [], "data_size": "0.738 MB", "sample_ph_range": { "min": 7.0, "max": 7.0 }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 99.54, "contamination": 0.98, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "2573950", "Number of Sequences": "112", "Longest Sequences (bp)": "145598", "N50 (bp)": "46035", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "50.6", "Number of CDSs": "2274", "Average Protein Length": "328.1", "Coding Ratio (%)": "87.0", "Number of rRNAs": "0", "Number of tRNAs": "40", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Mesotoga prima", "strain": "strain=MesG1.Ag.4.2", "accession": "GCA_000147715.3", "taxid": 1184387, "species_taxid": 1184387, "relation_to_type": "type", "validated": true, "ani": 78.3778, "matched_fragments": 99, "total_fragments": 804, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 99.54, "contamination": 0.98, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_002305955.1", "gtdb_species": "s__Mesotoga sp002305955", "ani": 99.535, "matched_fragments": 685, "total_fragments": 804, "gtdb_taxonomy": "d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Kosmotogaceae;g__Mesotoga", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.56", "min_intra_species_ani": "99.32", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.77", "num_clustered_genomes": 7, "status": "conclusive" }, { "accession": "GCF_900157305.1", "gtdb_species": "s__Mesotoga infera_B", "ani": 89.2816, "matched_fragments": 709, "total_fragments": 804, "gtdb_taxonomy": "d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Kosmotogaceae;g__Mesotoga", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.81", "min_intra_species_ani": "98.51", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.74", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_000147715.2", "gtdb_species": "s__Mesotoga prima", "ani": 78.3648, "matched_fragments": 100, "total_fragments": 804, "gtdb_taxonomy": "d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Kosmotogaceae;g__Mesotoga", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.16", "min_intra_species_ani": "96.75", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.85", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_003664995.1", "gtdb_species": "s__Mesotoga sp003664995", "ani": 78.3105, "matched_fragments": 119, "total_fragments": 804, "gtdb_taxonomy": "d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Kosmotogaceae;g__Mesotoga", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.98", "min_intra_species_ani": "98.98", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_011045915.1", "gtdb_species": "s__Mesotoga infera_D", "ani": 77.9012, "matched_fragments": 90, "total_fragments": 804, "gtdb_taxonomy": "d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Kosmotogaceae;g__Mesotoga", "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_002752635.1", "gtdb_species": "s__Mesotoga sp002752635", "ani": 77.793, "matched_fragments": 105, "total_fragments": 804, "gtdb_taxonomy": "d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Kosmotogaceae;g__Mesotoga", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.07", "min_intra_species_ani": "97.29", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.81", "num_clustered_genomes": 15, "status": "-" }, { "accession": "GCA_016933635.1", "gtdb_species": "s__Mesotoga sp016933635", "ani": 77.2005, "matched_fragments": 65, "total_fragments": 804, "gtdb_taxonomy": "d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Kosmotogaceae;g__Mesotoga", "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": 0.067, "cell_length": 0.367, "doubling_h": null, "growth_tmp": 45.0, "optimum_tmp": 43.333, "optimum_ph": 7.4, "genome_size": 3058345.0, "gc_content": 48.3, "coding_genes": 2809.0, "rRNA16S_genes": null, "tRNA_genes": 46.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 1.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "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 }, "_gtdb_taxon": [ "d__Bacteria", "p__Thermotogota", "c__Thermotogae", "o__Petrotogales", "f__Kosmotogaceae", "g__Mesotoga", "s__Mesotoga sp002305955" ], "_genome_taxon": [ "Mesotoga", "sp.", "d__Bacteria", "p__Thermotogota", "c__Thermotogae", "o__Petrotogales", "f__Kosmotogaceae", "g__Mesotoga", "s__Mesotoga sp002305955", "Bacteria", "Thermotogota", "Thermotogae", "Petrotogales", "Kosmotogaceae", "Mesotoga", "Mesotoga", "sp002305955" ], "_meo": [ { "id": "MEO_0000035", "label": "waste water" }, { "id": "MEO_0000014", "label": "activated sludge" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }