{ "type": "genome", "identifier": "GCF_002115745.1", "organism": "Thalassospira alkalitolerans", "title": "Thalassospira alkalitolerans", "description": "na", "data type": "Genome sequencing and assembly", "organization": "The Third Institute of State Oceanic Administration (SOA)", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002115745.1", "bioproject": "PRJNA224116", "biosample": "SAMN02671741", "wgs_master": "JFKB00000000.1", "refseq_category": "reference genome", "taxid": "1293890", "species_taxid": "1293890", "organism_name": "Thalassospira alkalitolerans", "infraspecific_name": "strain=JCM 18968", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/04/28", "asm_name": "ASM211574v1", "asm_submitter": "The Third Institute of State Oceanic Administration (SOA)", "gbrs_paired_asm": "GCA_002115745.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/115/745/GCF_002115745.1_ASM211574v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4788947", "genome_size_ungapped": "4788947", "gc_percent": "53.000000", "replicon_count": "0", "scaffold_count": "72", "contig_count": "72", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002115745.1-RS_2024_05_03", "annotation_date": "2024-05-03", "total_gene_count": "4358", "protein_coding_gene_count": "4276", "non_coding_gene_count": "63", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-04-28", "dateModified": "2017-04-28", "datePublished": "2017-04-28", "_annotation": { "sample_count": 1, "sample_organism": [ "Thalassospira alkalitolerans" ], "sample_taxid": [ "1293890" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Japan" ], "sample_host_location_id": [], "data_size": "1.349 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)": "4788947", "Number of Sequences": "72", "Longest Sequences (bp)": "656187", "N50 (bp)": "299695", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "53.1", "Number of CDSs": "4329", "Average Protein Length": "322.8", "Coding Ratio (%)": "87.5", "Number of rRNAs": "1", "Number of tRNAs": "53", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Thalassospira alkalitolerans", "strain": "strain=JCM 18968", "accession": "GCA_002115745.1", "taxid": 1293890, "species_taxid": 1293890, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1560, "total_fragments": 1566, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Thalassospira xiamenensis", "strain": "strain=DSM 17429", "accession": "GCA_900156715.1", "taxid": 220697, "species_taxid": 220697, "relation_to_type": "suspected-type", "validated": true, "ani": 83.3881, "matched_fragments": 1131, "total_fragments": 1566, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thalassospira xiamenensis", "strain": "strain=M-5", "accession": "GCA_000300235.2", "taxid": 220697, "species_taxid": 220697, "relation_to_type": "suspected-type", "validated": true, "ani": 83.3024, "matched_fragments": 1149, "total_fragments": 1566, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thalassospira permensis", "strain": "strain=NBRC 106175", "accession": "GCA_000714555.1", "taxid": 680197, "species_taxid": 680197, "relation_to_type": "type", "validated": true, "ani": 83.2973, "matched_fragments": 1123, "total_fragments": 1566, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thalassospira xianhensis", "strain": "strain=MCCC 1A02616", "accession": "GCA_003326475.1", "taxid": 478503, "species_taxid": 478503, "relation_to_type": "type", "validated": true, "ani": 83.2292, "matched_fragments": 1090, "total_fragments": 1566, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thalassospira tepidiphila", "strain": "strain=DSM 18888", "accession": "GCA_011927685.1", "taxid": 393657, "species_taxid": 393657, "relation_to_type": "type", "validated": true, "ani": 80.4179, "matched_fragments": 831, "total_fragments": 1566, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thalassospira profundimaris", "strain": "strain=WP0211", "accession": "GCA_000300275.1", "taxid": 502049, "species_taxid": 502049, "relation_to_type": "suspected-type", "validated": true, "ani": 80.2888, "matched_fragments": 831, "total_fragments": 1566, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thalassospira tepidiphila", "strain": "strain=MCCC 1A03514", "accession": "GCA_001662875.1", "taxid": 393657, "species_taxid": 393657, "relation_to_type": "type", "validated": true, "ani": 80.2811, "matched_fragments": 842, "total_fragments": 1566, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002115745.1", "gtdb_species": "s__Thalassospira alkalitolerans", "ani": 100.0, "matched_fragments": 1560, "total_fragments": 1566, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira", "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_000300235.2", "gtdb_species": "s__Thalassospira xiamenensis", "ani": 83.3024, "matched_fragments": 1149, "total_fragments": 1566, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.55", "min_intra_species_ani": "97.14", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.82", "num_clustered_genomes": 23, "status": "-" }, { "accession": "GCF_002115785.1", "gtdb_species": "s__Thalassospira sp002115785", "ani": 83.2711, "matched_fragments": 1109, "total_fragments": 1566, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira", "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_001613805.1", "gtdb_species": "s__Thalassospira lucentensis_A", "ani": 83.2454, "matched_fragments": 1139, "total_fragments": 1566, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.23", "min_intra_species_ani": "97.17", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.86", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_003326475.1", "gtdb_species": "s__Thalassospira xianhensis", "ani": 83.2335, "matched_fragments": 1089, "total_fragments": 1566, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira", "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_000300275.1", "gtdb_species": "s__Thalassospira profundimaris", "ani": 80.2889, "matched_fragments": 831, "total_fragments": 1566, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira", "ani_circumscription_radius": 95.4963, "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_001662875.1", "gtdb_species": "s__Thalassospira tepidiphila", "ani": 80.288, "matched_fragments": 841, "total_fragments": 1566, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira", "ani_circumscription_radius": 95.4963, "mean_intra_species_ani": "96.58", "min_intra_species_ani": "95.57", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.88", "num_clustered_genomes": 15, "status": "-" }, { "accession": "GCF_017922435.1", "gtdb_species": "s__Thalassospira sp017922435", "ani": 80.2788, "matched_fragments": 842, "total_fragments": 1566, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira", "ani_circumscription_radius": 95.2246, "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_001613795.1", "gtdb_species": "s__Thalassospira sp001613795", "ani": 79.8989, "matched_fragments": 794, "total_fragments": 1566, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.77", "min_intra_species_ani": "97.25", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.91", "num_clustered_genomes": 10, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.275, "cell_length": 0.288, "doubling_h": null, "growth_tmp": 24.6, "optimum_tmp": 29.25, "optimum_ph": 7.1, "genome_size": 4666349.975, "gc_content": 54.269, "coding_genes": 4288.166, "rRNA16S_genes": 4.0, "tRNA_genes": 63.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.5, "range_salinity": 1.0, "facultative_respiration": 0.166, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.833, "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": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 1.0 }, "_genome_taxon": [ "Thalassospira", "alkalitolerans" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }