{ "type": "genome", "identifier": "GCF_004135675.1", "organism": "Marinitoga lauensis", "title": "Marinitoga lauensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Portland State University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004135675.1", "bioproject": "PRJNA224116", "biosample": "SAMN09208112", "wgs_master": "QHLX00000000.1", "refseq_category": "reference genome", "taxid": "2201189", "species_taxid": "2201189", "organism_name": "Marinitoga lauensis", "infraspecific_name": "strain=LG1", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/02/04", "asm_name": "ASM413567v1", "asm_submitter": "Portland State University", "gbrs_paired_asm": "GCA_004135675.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/135/675/GCF_004135675.1_ASM413567v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2595202", "genome_size_ungapped": "2595202", "gc_percent": "28.000000", "replicon_count": "0", "scaffold_count": "18", "contig_count": "18", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004135675.1-RS_2024_07_29", "annotation_date": "2024-07-29", "total_gene_count": "3196", "protein_coding_gene_count": "2774", "non_coding_gene_count": "63", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-02-04", "dateModified": "2019-02-04", "datePublished": "2019-02-04", "_annotation": { "sample_count": 1, "sample_organism": [ "Marinitoga lauensis" ], "sample_taxid": [ "2201189" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Pacific Ocean: Mariner vent field, Lau Basin" ], "sample_host_location_id": [], "data_size": "0.693 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 99.54, "contamination": 0.46, "strain_heterogeneity": 100.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "2595202", "Number of Sequences": "18", "Longest Sequences (bp)": "543795", "N50 (bp)": "388096", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "27.9", "Number of CDSs": "3319", "Average Protein Length": "224.8", "Coding Ratio (%)": "86.3", "Number of rRNAs": "7", "Number of tRNAs": "52", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Marinitoga lauensis", "strain": "strain=LG1", "accession": "GCA_004135675.1", "taxid": 2201189, "species_taxid": 2201189, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 856, "total_fragments": 856, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Marinitoga hydrogenitolerans", "strain": "strain=DSM 16785", "accession": "GCA_900129175.1", "taxid": 287990, "species_taxid": 287990, "relation_to_type": "type", "validated": true, "ani": 80.9489, "matched_fragments": 503, "total_fragments": 856, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marinitoga litoralis", "strain": "strain=DSM 21709", "accession": "GCA_016908145.1", "taxid": 570855, "species_taxid": 570855, "relation_to_type": "type", "validated": true, "ani": 80.7281, "matched_fragments": 454, "total_fragments": 856, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marinitoga piezophila", "strain": "strain=KA3", "accession": "GCA_000255135.1", "taxid": 149715, "species_taxid": 149715, "relation_to_type": "type", "validated": true, "ani": 79.5614, "matched_fragments": 356, "total_fragments": 856, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thermosipho affectus", "strain": "strain=ik275mar", "accession": "GCA_001990485.1", "taxid": 660294, "species_taxid": 660294, "relation_to_type": "type", "validated": true, "ani": 75.4401, "matched_fragments": 52, "total_fragments": 856, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tepidibacter formicigenes", "strain": "strain=DSM 15518", "accession": "GCA_900142235.1", "taxid": 227138, "species_taxid": 227138, "relation_to_type": "type", "validated": true, "ani": 74.6958, "matched_fragments": 51, "total_fragments": 856, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptotrichia trevisanii", "strain": "strain=DSM 22070", "accession": "GCA_000482505.1", "taxid": 109328, "species_taxid": 109328, "relation_to_type": "type", "validated": true, "ani": 74.6695, "matched_fragments": 54, "total_fragments": 856, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium moniliforme", "strain": "strain=DSM 3984", "accession": "GCA_017873235.1", "taxid": 39489, "species_taxid": 39489, "relation_to_type": "type", "validated": true, "ani": 74.5337, "matched_fragments": 57, "total_fragments": 856, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 99.54, "contamination": 0.46, "strain_heterogeneity": 100.0 }, "gtdb_result": [ { "accession": "GCF_004135675.1", "gtdb_species": "s__Marinitoga lauensis", "ani": 100.0, "matched_fragments": 856, "total_fragments": 856, "gtdb_taxonomy": "d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Petrotogaceae;g__Marinitoga", "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_900129175.1", "gtdb_species": "s__Marinitoga hydrogenitolerans", "ani": 80.9972, "matched_fragments": 497, "total_fragments": 856, "gtdb_taxonomy": "d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Petrotogaceae;g__Marinitoga", "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_016908145.1", "gtdb_species": "s__Marinitoga litoralis", "ani": 80.7132, "matched_fragments": 454, "total_fragments": 856, "gtdb_taxonomy": "d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Petrotogaceae;g__Marinitoga", "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_011057715.1", "gtdb_species": "s__Marinitoga sp011057715", "ani": 80.4612, "matched_fragments": 453, "total_fragments": 856, "gtdb_taxonomy": "d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Petrotogaceae;g__Marinitoga", "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_001021165.1", "gtdb_species": "s__Marinitoga sp001021165", "ani": 80.3992, "matched_fragments": 492, "total_fragments": 856, "gtdb_taxonomy": "d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Petrotogaceae;g__Marinitoga", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.86", "min_intra_species_ani": "96.83", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000255135.1", "gtdb_species": "s__Marinitoga piezophila", "ani": 79.5065, "matched_fragments": 356, "total_fragments": 856, "gtdb_taxonomy": "d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Petrotogaceae;g__Marinitoga", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.22", "min_intra_species_ani": "99.16", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.94", "num_clustered_genomes": 4, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.16, "cell_length": 0.088, "doubling_h": -0.008, "growth_tmp": 59.0, "optimum_tmp": 59.5, "optimum_ph": 5.91, "genome_size": 2278579.625, "gc_content": 29.184, "coding_genes": 2034.667, "rRNA16S_genes": 3.0, "tRNA_genes": 51.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "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 }, "_genome_taxon": [ "Marinitoga", "lauensis" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }