{ "type": "genome", "identifier": "GCF_021764745.1", "organism": "Joostella atrarenae", "title": "Joostella atrarenae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "FACULTY OF SCIENCE, UNIVERSITI TEKNOLOGI MALAYSIA", "publication": [ {} ], "properties": { "assembly_accession": "GCF_021764745.1", "bioproject": "PRJNA224116", "biosample": "SAMN17525809", "wgs_master": "JAETXX000000000.1", "refseq_category": "reference genome", "taxid": "679257", "species_taxid": "679257", "organism_name": "Joostella atrarenae", "infraspecific_name": "strain=M1-2", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/02/01", "asm_name": "ASM2176474v1", "asm_submitter": "FACULTY OF SCIENCE, UNIVERSITI TEKNOLOGI MALAYSIA", "gbrs_paired_asm": "GCA_021764745.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/021/764/745/GCF_021764745.1_ASM2176474v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3990592", "genome_size_ungapped": "3990592", "gc_percent": "33.000000", "replicon_count": "0", "scaffold_count": "71", "contig_count": "71", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_021764745.1-RS_2024_10_25", "annotation_date": "2024-10-25", "total_gene_count": "3433", "protein_coding_gene_count": "3360", "non_coding_gene_count": "47", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-02-01", "dateModified": "2022-02-01", "datePublished": "2022-02-01", "_annotation": { "sample_count": 1, "sample_organism": [ "Joostella atrarenae" ], "sample_taxid": [ "679257" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea: Jeju Island" ], "sample_host_location_id": [], "data_size": "1.113 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)": "3990592", "Number of Sequences": "71", "Longest Sequences (bp)": "1073049", "N50 (bp)": "267267", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "33.2", "Number of CDSs": "3342", "Average Protein Length": "351.0", "Coding Ratio (%)": "88.2", "Number of rRNAs": "2", "Number of tRNAs": "40", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Joostella atrarenae", "strain": "strain=M1-2", "accession": "GCA_021764745.1", "taxid": 679257, "species_taxid": 679257, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1301, "total_fragments": 1306, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Joostella marina", "strain": "strain=DSM 19592", "accession": "GCA_000260115.1", "taxid": 453852, "species_taxid": 453852, "relation_to_type": "type", "validated": true, "ani": 80.8276, "matched_fragments": 746, "total_fragments": 1306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Galbibacter marinus", "strain": "strain=ck-I2-15", "accession": "GCA_000300875.1", "taxid": 555500, "species_taxid": 555500, "relation_to_type": "type", "validated": true, "ani": 77.5169, "matched_fragments": 192, "total_fragments": 1306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Robertkochia solimangrovi", "strain": "strain=CL23", "accession": "GCA_007279655.1", "taxid": 2213046, "species_taxid": 2213046, "relation_to_type": "type", "validated": true, "ani": 77.202, "matched_fragments": 117, "total_fragments": 1306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Oceanihabitans sediminis", "strain": "strain=S9-10", "accession": "GCA_003337215.1", "taxid": 1812012, "species_taxid": 1812012, "relation_to_type": "type", "validated": true, "ani": 76.8635, "matched_fragments": 139, "total_fragments": 1306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hyunsoonleella ulvae", "strain": "strain=HU1-3", "accession": "GCA_016827605.1", "taxid": 2799948, "species_taxid": 2799948, "relation_to_type": "type", "validated": true, "ani": 76.8604, "matched_fragments": 99, "total_fragments": 1306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Abyssalbus ytuae", "strain": "strain=MT3330", "accession": "GCA_022807975.1", "taxid": 2926907, "species_taxid": 2926907, "relation_to_type": "type", "validated": true, "ani": 76.7791, "matched_fragments": 106, "total_fragments": 1306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cellulophaga omnivescoria", "strain": "strain=W5C", "accession": "GCA_001999725.1", "taxid": 1888890, "species_taxid": 1888890, "relation_to_type": "type", "validated": true, "ani": 76.7472, "matched_fragments": 168, "total_fragments": 1306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Algibacter pacificus", "strain": "strain=H164", "accession": "GCA_008033385.1", "taxid": 2599389, "species_taxid": 2599389, "relation_to_type": "type", "validated": true, "ani": 76.708, "matched_fragments": 122, "total_fragments": 1306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kordia aestuariivivens", "strain": "strain=YSTF-M3", "accession": "GCA_014397005.1", "taxid": 2759037, "species_taxid": 2759037, "relation_to_type": "type", "validated": true, "ani": 76.5633, "matched_fragments": 123, "total_fragments": 1306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Winogradskyella wichelsiae", "strain": "strain=Z738", "accession": "GCA_013403925.1", "taxid": 2697007, "species_taxid": 2697007, "relation_to_type": "type", "validated": true, "ani": 76.5622, "matched_fragments": 141, "total_fragments": 1306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pustulibacterium marinum", "strain": "strain=CGMCC 1.12333", "accession": "GCA_900116665.1", "taxid": 1224947, "species_taxid": 1224947, "relation_to_type": "type", "validated": true, "ani": 76.5538, "matched_fragments": 133, "total_fragments": 1306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Psychroserpens jangbogonensis", "strain": "strain=PAMC 27130", "accession": "GCA_000797465.1", "taxid": 1484460, "species_taxid": 1484460, "relation_to_type": "type", "validated": true, "ani": 76.55, "matched_fragments": 129, "total_fragments": 1306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aestuariivivens marinum", "strain": "strain=MT3-5-12", "accession": "GCA_022662175.1", "taxid": 2913555, "species_taxid": 2913555, "relation_to_type": "type", "validated": true, "ani": 76.5048, "matched_fragments": 85, "total_fragments": 1306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Winogradskyella litoriviva", "strain": "strain=KMM6491", "accession": "GCA_013249065.1", "taxid": 1220182, "species_taxid": 1220182, "relation_to_type": "type", "validated": true, "ani": 76.5036, "matched_fragments": 135, "total_fragments": 1306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lacinutrix himadriensis", "strain": "strain=E4-9a", "accession": "GCA_001418105.1", "taxid": 641549, "species_taxid": 641549, "relation_to_type": "type", "validated": true, "ani": 76.4881, "matched_fragments": 153, "total_fragments": 1306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Seonamhaeicola algicola", "strain": "strain=Gy8", "accession": "GCA_007997385.1", "taxid": 1719036, "species_taxid": 1719036, "relation_to_type": "type", "validated": true, "ani": 76.4318, "matched_fragments": 108, "total_fragments": 1306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Maribacter vaceletii", "strain": "strain=DSM 25230", "accession": "GCA_003634105.1", "taxid": 1206816, "species_taxid": 1206816, "relation_to_type": "type", "validated": true, "ani": 76.4274, "matched_fragments": 183, "total_fragments": 1306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Formosa sediminum", "strain": "strain=PS13", "accession": "GCA_007197735.1", "taxid": 2594004, "species_taxid": 2594004, "relation_to_type": "type", "validated": true, "ani": 76.3684, "matched_fragments": 146, "total_fragments": 1306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavivirga algicola", "strain": "strain=Y03", "accession": "GCA_012910715.1", "taxid": 2729136, "species_taxid": 2729136, "relation_to_type": "type", "validated": true, "ani": 76.3505, "matched_fragments": 120, "total_fragments": 1306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cellulophaga baltica", "strain": "strain=DSM 24729", "accession": "GCA_900102165.1", "taxid": 76594, "species_taxid": 76594, "relation_to_type": "type", "validated": true, "ani": 76.3433, "matched_fragments": 149, "total_fragments": 1306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lacinutrix mariniflava", "strain": "strain=AKS432", "accession": "GCA_001418015.1", "taxid": 342955, "species_taxid": 342955, "relation_to_type": "type", "validated": true, "ani": 76.2572, "matched_fragments": 145, "total_fragments": 1306, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000260115.1", "gtdb_species": "s__Joostella marina", "ani": 80.8224, "matched_fragments": 747, "total_fragments": 1306, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Joostella", "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_013391805.1", "gtdb_species": "s__Galbibacter_A sp013391805", "ani": 78.9985, "matched_fragments": 410, "total_fragments": 1306, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Galbibacter_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_016734785.1", "gtdb_species": "s__Galbibacter_A mesophilus", "ani": 78.6329, "matched_fragments": 413, "total_fragments": 1306, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Galbibacter_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_000300875.1", "gtdb_species": "s__Galbibacter_B marinus", "ani": 77.5169, "matched_fragments": 192, "total_fragments": 1306, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Galbibacter_B", "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_007279655.1", "gtdb_species": "s__Robertkochia solimangrovi", "ani": 77.202, "matched_fragments": 117, "total_fragments": 1306, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robertkochia", "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_003337215.1", "gtdb_species": "s__Oceanihabitans sediminis", "ani": 76.8635, "matched_fragments": 139, "total_fragments": 1306, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_009797025.1", "gtdb_species": "s__Cellulophaga sp009797025", "ani": 76.8454, "matched_fragments": 149, "total_fragments": 1306, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga", "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_003386165.1", "gtdb_species": "s__Winogradskyella eximia", "ani": 76.6035, "matched_fragments": 140, "total_fragments": 1306, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella", "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_016864015.1", "gtdb_species": "s__Oceanihabitans sp016864015", "ani": 76.5928, "matched_fragments": 145, "total_fragments": 1306, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans", "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_003663945.1", "gtdb_species": "s__Lacinutrix venerupis", "ani": 76.5541, "matched_fragments": 151, "total_fragments": 1306, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.08", "min_intra_species_ani": "98.08", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000797465.1", "gtdb_species": "s__Psychroserpens jangbogonensis", "ani": 76.55, "matched_fragments": 129, "total_fragments": 1306, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens", "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_013403925.1", "gtdb_species": "s__Winogradskyella wichelsiae", "ani": 76.5482, "matched_fragments": 142, "total_fragments": 1306, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella", "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_018860825.1", "gtdb_species": "s__Oceanihabitans sp018860825", "ani": 76.5412, "matched_fragments": 167, "total_fragments": 1306, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans", "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_018067265.1", "gtdb_species": "s__Oceanihabitans sp018067265", "ani": 76.4768, "matched_fragments": 112, "total_fragments": 1306, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans", "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_014202195.1", "gtdb_species": "s__Oceanihabitans iliipiscarium", "ani": 76.4727, "matched_fragments": 125, "total_fragments": 1306, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans", "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_007997385.1", "gtdb_species": "s__Seonamhaeicola algicola", "ani": 76.4318, "matched_fragments": 108, "total_fragments": 1306, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola", "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_003634105.1", "gtdb_species": "s__Maribacter_B vaceletii", "ani": 76.4274, "matched_fragments": 183, "total_fragments": 1306, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_B", "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_900102165.1", "gtdb_species": "s__Cellulophaga baltica", "ani": 76.3575, "matched_fragments": 150, "total_fragments": 1306, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.62", "min_intra_species_ani": "97.40", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.89", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_001418015.1", "gtdb_species": "s__Lacinutrix mariniflava", "ani": 76.2572, "matched_fragments": 145, "total_fragments": 1306, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix", "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": -0.603, "cell_length": 0.176, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": 30.0, "optimum_ph": 6.45, "genome_size": 4508243.0, "gc_content": null, "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": [ "Joostella", "atrarenae" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }