{ "type": "genome", "identifier": "GCF_900111945.1", "organism": "Litoreibacter janthinus", "title": "Litoreibacter janthinus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900111945.1", "bioproject": "PRJNA224116", "biosample": "SAMN04488002", "wgs_master": "FOYO00000000.1", "refseq_category": "reference genome", "taxid": "670154", "species_taxid": "670154", "organism_name": "Litoreibacter janthinus", "infraspecific_name": "strain=DSM 26921", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/11/02", "asm_name": "IMG-taxon 2617270836 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900111945.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/111/945/GCF_900111945.1_IMG-taxon_2617270836_annotated_assembly", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3754758", "genome_size_ungapped": "3754393", "gc_percent": "57.500000", "replicon_count": "0", "scaffold_count": "4", "contig_count": "4", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900111945.1-RS_2024_05_03", "annotation_date": "2024-05-03", "total_gene_count": "3751", "protein_coding_gene_count": "3684", "non_coding_gene_count": "48", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-11-02", "dateModified": "2016-11-02", "datePublished": "2016-11-02", "_annotation": { "sample_count": 1, "sample_organism": [ "Litoreibacter janthinus" ], "sample_taxid": [ "670154" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.065 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)": "3754758", "Number of Sequences": "4", "Longest Sequences (bp)": "3571921", "N50 (bp)": "3571921", "Gap Ratio (%)": "0.009721", "GCcontent (%)": "57.5", "Number of CDSs": "3716", "Average Protein Length": "307.1", "Coding Ratio (%)": "91.2", "Number of rRNAs": "3", "Number of tRNAs": "42", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Litoreibacter janthinus", "strain": "strain=DSM 26921", "accession": "GCA_900111945.1", "taxid": 670154, "species_taxid": 670154, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1250, "total_fragments": 1250, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Litoreibacter ascidiaceicola", "strain": "strain=DSM 100566", "accession": "GCA_900129235.1", "taxid": 1486859, "species_taxid": 1486859, "relation_to_type": "type", "validated": true, "ani": 82.1321, "matched_fragments": 726, "total_fragments": 1250, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Litoreibacter halocynthiae", "strain": "strain=DSM 29467", "accession": "GCA_004365635.1", "taxid": 1242689, "species_taxid": 1242689, "relation_to_type": "type", "validated": true, "ani": 81.5957, "matched_fragments": 718, "total_fragments": 1250, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Litoreibacter meonggei", "strain": "strain=DSM 29466", "accession": "GCA_003663885.1", "taxid": 1049199, "species_taxid": 1049199, "relation_to_type": "type", "validated": true, "ani": 81.233, "matched_fragments": 716, "total_fragments": 1250, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Litoreibacter arenae", "strain": "strain=DSM 19593", "accession": "GCA_000442275.2", "taxid": 491388, "species_taxid": 491388, "relation_to_type": "type", "validated": true, "ani": 80.9109, "matched_fragments": 652, "total_fragments": 1250, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Litoreibacter albidus", "strain": "strain=DSM 26922", "accession": "GCA_900107015.1", "taxid": 670155, "species_taxid": 670155, "relation_to_type": "type", "validated": true, "ani": 80.2477, "matched_fragments": 625, "total_fragments": 1250, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Litoreibacter ponti", "strain": "strain=DSM 100977", "accession": "GCA_003054285.1", "taxid": 1510457, "species_taxid": 1510457, "relation_to_type": "type", "validated": true, "ani": 78.7109, "matched_fragments": 502, "total_fragments": 1250, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudosulfitobacter pseudonitzschiae", "strain": "strain=H3", "accession": "GCA_000712315.1", "taxid": 1402135, "species_taxid": 1402135, "relation_to_type": "type", "validated": true, "ani": 77.205, "matched_fragments": 210, "total_fragments": 1250, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Celeribacter litoreus", "strain": "strain=ASW11-22", "accession": "GCA_020165855.1", "taxid": 2876714, "species_taxid": 2876714, "relation_to_type": "type", "validated": true, "ani": 76.9206, "matched_fragments": 134, "total_fragments": 1250, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmobacter fulva", "strain": "strain=con5", "accession": "GCA_018798885.1", "taxid": 2840474, "species_taxid": 2840474, "relation_to_type": "type", "validated": true, "ani": 76.7465, "matched_fragments": 144, "total_fragments": 1250, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Alexandriicola marinus", "strain": "strain=LZ-14", "accession": "GCA_004000435.1", "taxid": 2081710, "species_taxid": 2081710, "relation_to_type": "type", "validated": true, "ani": 76.6871, "matched_fragments": 154, "total_fragments": 1250, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodobacter amnigenus", "strain": "strain=HSP-20", "accession": "GCA_019130055.1", "taxid": 2852097, "species_taxid": 2852097, "relation_to_type": "type", "validated": true, "ani": 76.5226, "matched_fragments": 143, "total_fragments": 1250, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodobacter amnigenus", "strain": "strain=HSP-20", "accession": "GCA_009908265.2", "taxid": 2852097, "species_taxid": 2852097, "relation_to_type": "type", "validated": true, "ani": 76.5226, "matched_fragments": 143, "total_fragments": 1250, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900111945.1", "gtdb_species": "s__Litoreibacter janthinus", "ani": 100.0, "matched_fragments": 1250, "total_fragments": 1250, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter", "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_900129235.1", "gtdb_species": "s__Litoreibacter ascidiaceicola", "ani": 82.1321, "matched_fragments": 726, "total_fragments": 1250, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter", "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_004365635.1", "gtdb_species": "s__Litoreibacter halocynthiae", "ani": 81.5957, "matched_fragments": 718, "total_fragments": 1250, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter", "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_003663885.1", "gtdb_species": "s__Litoreibacter meonggei", "ani": 81.233, "matched_fragments": 716, "total_fragments": 1250, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter", "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_000442275.2", "gtdb_species": "s__Litoreibacter arenae", "ani": 80.9101, "matched_fragments": 652, "total_fragments": 1250, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter", "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_900107015.1", "gtdb_species": "s__Litoreibacter albidus", "ani": 80.2235, "matched_fragments": 624, "total_fragments": 1250, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter", "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_003054285.1", "gtdb_species": "s__Litoreibacter ponti", "ani": 78.7026, "matched_fragments": 503, "total_fragments": 1250, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter", "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_900129395.1", "gtdb_species": "s__Ascidiaceihabitans pseudonitzschiae", "ani": 77.1999, "matched_fragments": 208, "total_fragments": 1250, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.97", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.96", "num_clustered_genomes": 4, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.302, "cell_length": 0.278, "doubling_h": null, "growth_tmp": 25.0, "optimum_tmp": 26.5, "optimum_ph": 7.75, "genome_size": 3754758.0, "gc_content": 60.2, "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": 0.0, "aerobic_respiration": 1.0, "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": [ "Litoreibacter", "janthinus" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }