{ "type": "genome", "identifier": "GCF_001050235.1", "organism": "Longilinea arvoryzae", "title": "Longilinea arvoryzae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "National Institute of Advanced Industrial Science and Technology (AIST)", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001050235.1", "bioproject": "PRJNA224116", "biosample": "SAMD00034889", "wgs_master": "BBXY00000000.1", "refseq_category": "reference genome", "taxid": "360412", "species_taxid": "360412", "organism_name": "Longilinea arvoryzae", "infraspecific_name": "strain=KOME-1", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2015/07/24", "asm_name": "ASM105023v2", "asm_submitter": "National Institute of Advanced Industrial Science and Technology (AIST)", "gbrs_paired_asm": "GCA_001050235.2", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/050/235/GCF_001050235.1_ASM105023v2", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4438311", "genome_size_ungapped": "4431449", "gc_percent": "57.000000", "replicon_count": "0", "scaffold_count": "2", "contig_count": "25", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001050235.1-RS_2024_12_11", "annotation_date": "2024-12-11", "total_gene_count": "3952", "protein_coding_gene_count": "3873", "non_coding_gene_count": "55", "pubmed_id": "26383658" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2015-07-24", "dateModified": "2015-07-24", "datePublished": "2015-07-24", "_annotation": { "sample_count": 1, "sample_organism": [ "Longilinea arvoryzae" ], "sample_taxid": [ "360412" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Japan:Niigata, Nagaoka" ], "sample_host_location_id": [], "data_size": "1.248 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)": "4438311", "Number of Sequences": "2", "Longest Sequences (bp)": "4145241", "N50 (bp)": "4145241", "Gap Ratio (%)": "0.154608", "GCcontent (%)": "56.9", "Number of CDSs": "3936", "Average Protein Length": "335.2", "Coding Ratio (%)": "89.2", "Number of rRNAs": "6", "Number of tRNAs": "46", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Longilinea arvoryzae", "strain": "strain=KOME-1", "accession": "GCA_001050235.2", "taxid": 360412, "species_taxid": 360412, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1476, "total_fragments": 1478, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Levilinea saccharolytica", "strain": "strain=KIBI-1", "accession": "GCA_001050255.2", "taxid": 229921, "species_taxid": 229921, "relation_to_type": "type", "validated": true, "ani": 77.1803, "matched_fragments": 142, "total_fragments": 1478, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Levilinea saccharolytica", "strain": "strain=KIBI-1", "accession": "GCA_001306035.1", "taxid": 229921, "species_taxid": 229921, "relation_to_type": "type", "validated": true, "ani": 76.9933, "matched_fragments": 140, "total_fragments": 1478, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Anaerolinea thermophila", "strain": "strain=UNI-1", "accession": "GCA_000199675.1", "taxid": 167964, "species_taxid": 167964, "relation_to_type": "type", "validated": true, "ani": 76.5042, "matched_fragments": 64, "total_fragments": 1478, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aggregatilinea lenta", "strain": "strain=MO-CFX2", "accession": "GCA_003569045.1", "taxid": 913108, "species_taxid": 913108, "relation_to_type": "type", "validated": true, "ani": 75.6657, "matched_fragments": 54, "total_fragments": 1478, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001050235.1", "gtdb_species": "s__Longilinea arvoryzae", "ani": 100.0, "matched_fragments": 1477, "total_fragments": 1478, "gtdb_taxonomy": "d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Longilinea", "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_004347695.1", "gtdb_species": "s__Bellilinea sp004347695", "ani": 77.3093, "matched_fragments": 99, "total_fragments": 1478, "gtdb_taxonomy": "d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Bellilinea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.75", "min_intra_species_ani": "98.75", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001306035.1", "gtdb_species": "s__Levilinea saccharolytica", "ani": 77.0098, "matched_fragments": 139, "total_fragments": 1478, "gtdb_taxonomy": "d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Levilinea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.90", "min_intra_species_ani": "99.90", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_009772985.1", "gtdb_species": "s__UBA877 sp009772985", "ani": 76.754, "matched_fragments": 86, "total_fragments": 1478, "gtdb_taxonomy": "d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA877", "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_002385985.1", "gtdb_species": "s__UBA3924 sp002385985", "ani": 76.5647, "matched_fragments": 112, "total_fragments": 1478, "gtdb_taxonomy": "d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__UBA3924", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.86", "min_intra_species_ani": "99.86", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000199675.1", "gtdb_species": "s__Anaerolinea thermophila", "ani": 76.5106, "matched_fragments": 65, "total_fragments": 1478, "gtdb_taxonomy": "d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Anaerolinea", "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_012798515.1", "gtdb_species": "s__JAAZNB01 sp012798515", "ani": 76.505, "matched_fragments": 97, "total_fragments": 1478, "gtdb_taxonomy": "d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__JAAZNB01", "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_002298885.1", "gtdb_species": "s__UBA700 sp002298885", "ani": 76.4872, "matched_fragments": 120, "total_fragments": 1478, "gtdb_taxonomy": "d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__UBA700", "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_012797695.1", "gtdb_species": "s__UBA6107 sp012797695", "ani": 76.4122, "matched_fragments": 76, "total_fragments": 1478, "gtdb_taxonomy": "d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__UBA6107", "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_004297445.1", "gtdb_species": "s__SCUK01 sp004297445", "ani": 76.1407, "matched_fragments": 65, "total_fragments": 1478, "gtdb_taxonomy": "d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA11579;g__SCUK01", "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_002428565.1", "gtdb_species": "s__UBA6092 sp002428565", "ani": 76.1248, "matched_fragments": 113, "total_fragments": 1478, "gtdb_taxonomy": "d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA4823;g__UBA6092", "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_903875215.1", "gtdb_species": "s__UBA5195 sp903875215", "ani": 75.9942, "matched_fragments": 76, "total_fragments": 1478, "gtdb_taxonomy": "d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA5195", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.95", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.97", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCA_016927865.1", "gtdb_species": "s__Anaerolinea sp016927865", "ani": 75.9939, "matched_fragments": 92, "total_fragments": 1478, "gtdb_taxonomy": "d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Anaerolinea", "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_012516075.1", "gtdb_species": "s__JAAYXE01 sp012516075", "ani": 75.3727, "matched_fragments": 74, "total_fragments": 1478, "gtdb_taxonomy": "d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA4823;g__JAAYXE01", "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": -0.302, "cell_length": null, "doubling_h": 1.963, "growth_tmp": 37.0, "optimum_tmp": 37.0, "optimum_ph": 7.0, "genome_size": 4438311.0, "gc_content": 56.924, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "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": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 1.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Longilinea", "arvoryzae" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }