{ "type": "genome", "identifier": "GCA_024490875.1", "organism": "Methanocaldococcus sp.", "title": "Methanocaldococcus sp.", "description": "derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "Portland State University", "publication": [ {} ], "properties": { "assembly_accession": "GCA_024490875.1", "bioproject": "PRJNA495050", "biosample": "SAMN15465779", "wgs_master": "JACCLX000000000.1", "refseq_category": "na", "taxid": "2152917", "species_taxid": "2152917", "organism_name": "Methanocaldococcus sp.", "infraspecific_name": "", "isolate": "T11_73", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/07/29", "asm_name": "ASM2449087v1", "submitter": "Portland State University", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/024/490/875/GCA_024490875.1_ASM2449087v1", "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": "2022-07-29", "dateModified": "2022-07-29", "datePublished": "2022-07-29", "_annotation": { "sample_count": 1, "sample_organism": [ "Methanocaldococcus sp." ], "sample_taxid": [ "2152917" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Pacific Ocean" ], "sample_host_location_id": [], "data_size": "0.400 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "1468100", "Number of Sequences": "44", "Longest Sequences (bp)": "148662", "N50 (bp)": "64370", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "28.5", "Number of CDSs": "1526", "Average Protein Length": "286.7", "Coding Ratio (%)": "89.4", "Number of rRNAs": "1", "Number of tRNAs": "33", "Number of CRISPRs": "10" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Methanocaldococcus bathoardescens", "strain": "strain=JH146", "accession": "GCA_000739065.1", "taxid": 1301915, "species_taxid": 1301915, "relation_to_type": "type", "validated": true, "ani": 81.1379, "matched_fragments": 331, "total_fragments": 467, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methanocaldococcus jannaschii", "strain": "strain=DSM 2661", "accession": "GCA_000091665.1", "taxid": 2190, "species_taxid": 2190, "relation_to_type": "type", "validated": true, "ani": 79.8958, "matched_fragments": 312, "total_fragments": 467, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methanocaldococcus fervens", "strain": "strain=AG86", "accession": "GCA_000023985.1", "taxid": 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"min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000739065.1", "gtdb_species": "s__Methanocaldococcus bathoardescens", "ani": 81.1581, "matched_fragments": 330, "total_fragments": 467, "gtdb_taxonomy": "d__Archaea;p__Methanobacteriota_A;c__Methanococci;o__Methanococcales;f__Methanocaldococcaceae;g__Methanocaldococcus", "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_000091665.1", "gtdb_species": "s__Methanocaldococcus jannaschii", "ani": 79.8471, "matched_fragments": 315, "total_fragments": 467, "gtdb_taxonomy": "d__Archaea;p__Methanobacteriota_A;c__Methanococci;o__Methanococcales;f__Methanocaldococcaceae;g__Methanocaldococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": 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"1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000092305.1", "gtdb_species": "s__Methanocaldococcus_A infernus", "ani": 76.9501, "matched_fragments": 92, "total_fragments": 467, "gtdb_taxonomy": "d__Archaea;p__Methanobacteriota_A;c__Methanococci;o__Methanococcales;f__Methanocaldococcaceae;g__Methanocaldococcus_A", "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_000179575.2", "gtdb_species": "s__Methanothermococcus_A okinawensis", "ani": 75.9335, "matched_fragments": 76, "total_fragments": 467, "gtdb_taxonomy": "d__Archaea;p__Methanobacteriota_A;c__Methanococci;o__Methanococcales;f__Methanococcaceae;g__Methanothermococcus_A", "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": 0.029, "cell_length": 0.029, "doubling_h": -0.25, "growth_tmp": 82.611, "optimum_tmp": 81.194, "optimum_ph": 6.441, "genome_size": 1528839.866, "gc_content": 31.816, "coding_genes": 1617.266, "rRNA16S_genes": 2.0, "tRNA_genes": 37.2, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.714, "range_salinity": 1.0, "facultative_respiration": 0.0, "anaerobic_respiration": 1.0, "aerobic_respiration": 0.0, "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 }, "_gtdb_taxon": [ "d__Archaea", "p__Methanobacteriota_A", "c__Methanococci", "o__Methanococcales", "f__Methanocaldococcaceae", "g__Methanocaldococcus", "s__Methanocaldococcus sp024490875" ], 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