{ "type": "genome", "identifier": "GCF_006385685.1", "organism": "Amaricoccus solimangrovi", "title": "Amaricoccus solimangrovi", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Chinese Academy of Tropical Agricultural Sciences", "publication": [ {} ], "properties": { "assembly_accession": "GCF_006385685.1", "bioproject": "PRJNA224116", "biosample": "SAMN12071578", "wgs_master": "VFRP00000000.1", "refseq_category": "reference genome", "taxid": "2589815", "species_taxid": "2589815", "organism_name": "Amaricoccus solimangrovi", "infraspecific_name": "strain=HB172011", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/06/23", "asm_name": "ASM638568v1", "asm_submitter": "Chinese Academy of Tropical Agricultural Sciences", "gbrs_paired_asm": "GCA_006385685.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/006/385/685/GCF_006385685.1_ASM638568v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4869094", "genome_size_ungapped": "4869094", "gc_percent": "69.500000", "replicon_count": "0", "scaffold_count": "136", "contig_count": "136", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_006385685.1-RS_2024_08_01", "annotation_date": "2024-08-01", "total_gene_count": "4702", "protein_coding_gene_count": "4531", "non_coding_gene_count": "63", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-06-23", "dateModified": "2019-06-23", "datePublished": "2019-06-23", "_annotation": { "sample_count": 1, "sample_organism": [ "Amaricoccus solimangrovi" ], "sample_taxid": [ "2589815" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Wenchang" ], "sample_host_location_id": [], "data_size": "1.310 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)": "4869094", "Number of Sequences": "136", "Longest Sequences (bp)": "532329", "N50 (bp)": "133182", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "69.6", "Number of CDSs": "4657", "Average Protein Length": "311.0", "Coding Ratio (%)": "89.2", "Number of rRNAs": "6", "Number of tRNAs": "58", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Amaricoccus solimangrovi", "strain": "strain=HB172011", "accession": "GCA_006385685.1", "taxid": 2589815, "species_taxid": 2589815, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1555, "total_fragments": 1561, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Amaricoccus macauensis", "strain": "strain=DSM 101730", "accession": "GCA_014201905.1", "taxid": 57001, "species_taxid": 57001, "relation_to_type": "type", "validated": true, "ani": 79.6537, "matched_fragments": 684, "total_fragments": 1561, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cereibacter johrii", "strain": "strain=JA192", "accession": "GCA_001720585.1", "taxid": 445629, "species_taxid": 445629, "relation_to_type": "type", "validated": true, "ani": 78.6062, "matched_fragments": 473, "total_fragments": 1561, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cereibacter johrii", "strain": "strain=JA192", "accession": "GCA_003046325.1", "taxid": 445629, "species_taxid": 445629, "relation_to_type": "type", "validated": true, "ani": 78.457, "matched_fragments": 504, "total_fragments": 1561, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cereibacter sphaeroides", "strain": "strain=2.4.1", "accession": "GCA_000273405.1", "taxid": 1063, "species_taxid": 1063, "relation_to_type": "type", "validated": true, "ani": 78.4093, "matched_fragments": 521, "total_fragments": 1561, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sinirhodobacter hankyongi", "strain": "strain=BO-81", "accession": "GCA_003664585.1", "taxid": 2294033, "species_taxid": 2294033, "relation_to_type": "type", "validated": true, "ani": 78.3159, "matched_fragments": 474, "total_fragments": 1561, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halovulum marinum", "strain": "strain=2CG4", "accession": "GCA_009697225.1", "taxid": 2662447, "species_taxid": 2662447, "relation_to_type": "type", "validated": true, "ani": 78.2936, "matched_fragments": 534, "total_fragments": 1561, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halovulum dunhuangense", "strain": "strain=YYQ-30", "accession": "GCA_013093415.1", "taxid": 1505036, "species_taxid": 1505036, "relation_to_type": "type", "validated": true, "ani": 78.1975, "matched_fragments": 427, "total_fragments": 1561, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pontivivens ytuae", "strain": "strain=MT2928", "accession": "GCA_015679265.1", "taxid": 2789856, "species_taxid": 2789856, "relation_to_type": "type", "validated": true, "ani": 78.0247, "matched_fragments": 425, "total_fragments": 1561, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Oceanomicrobium pacificus", "strain": "strain=KN286", "accession": "GCA_009833495.1", "taxid": 2692916, "species_taxid": 2692916, "relation_to_type": "type", "validated": true, "ani": 77.9533, "matched_fragments": 324, "total_fragments": 1561, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Meinhardsimonia xiamenensis", "strain": "strain=DSM 24422", "accession": "GCA_003001835.1", "taxid": 990712, "species_taxid": 990712, "relation_to_type": "type", "validated": true, "ani": 77.9278, "matched_fragments": 342, "total_fragments": 1561, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Meinhardsimonia xiamenensis", "strain": "strain=CGMCC 1.10789", "accession": "GCA_900102905.1", "taxid": 990712, "species_taxid": 990712, "relation_to_type": "type", "validated": true, "ani": 77.9253, "matched_fragments": 337, "total_fragments": 1561, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paroceanicella profunda", "strain": "strain=D4M1", "accession": "GCA_005887635.2", "taxid": 2579971, "species_taxid": 2579971, "relation_to_type": "type", "validated": true, "ani": 77.7904, "matched_fragments": 513, "total_fragments": 1561, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mangrovicoccus ximenensis", "strain": "strain=T1lg56", "accession": "GCA_003056725.1", "taxid": 1911570, "species_taxid": 1911570, "relation_to_type": "type", "validated": true, "ani": 77.7422, "matched_fragments": 531, "total_fragments": 1561, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Salipiger bermudensis", "strain": "strain=HTCC2601", "accession": "GCA_000153725.1", "taxid": 344736, "species_taxid": 344736, "relation_to_type": "type", "validated": true, "ani": 77.6758, "matched_fragments": 491, "total_fragments": 1561, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mangrovicoccus algicola", "strain": "strain=HB182678", "accession": "GCA_014903745.1", "taxid": 2771008, "species_taxid": 2771008, "relation_to_type": "type", "validated": true, "ani": 77.4643, "matched_fragments": 447, "total_fragments": 1561, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ruegeria marina", "strain": "strain=CGMCC 1.9108", "accession": "GCA_900101475.1", "taxid": 639004, "species_taxid": 639004, "relation_to_type": "type", "validated": true, "ani": 77.4033, "matched_fragments": 250, "total_fragments": 1561, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Oceanicella actignis", "strain": "strain=DSM 22673", "accession": "GCA_008124525.1", "taxid": 1189325, "species_taxid": 1189325, "relation_to_type": "type", "validated": true, "ani": 77.4023, "matched_fragments": 447, "total_fragments": 1561, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseovarius indicus", "strain": "strain=DSM 26383", "accession": "GCA_008728195.1", "taxid": 540747, "species_taxid": 540747, "relation_to_type": "type", "validated": true, "ani": 77.1537, "matched_fragments": 351, "total_fragments": 1561, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_006385685.1", "gtdb_species": "s__Amaricoccus solimangrovi", "ani": 100.0, "matched_fragments": 1555, "total_fragments": 1561, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus", "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_003241785.1", "gtdb_species": "s__Amaricoccus sp003241785", "ani": 85.6631, "matched_fragments": 967, "total_fragments": 1561, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus", "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_017993425.1", "gtdb_species": "s__Amaricoccus sp017993425", "ani": 80.0479, "matched_fragments": 731, "total_fragments": 1561, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus", "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_014201905.1", "gtdb_species": "s__Amaricoccus macauensis", "ani": 79.6529, "matched_fragments": 685, "total_fragments": 1561, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus", "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_017995835.1", "gtdb_species": "s__Amaricoccus sp017995835", "ani": 79.6346, "matched_fragments": 566, "total_fragments": 1561, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus", "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_003258405.1", "gtdb_species": "s__Amaricoccus sp003258405", "ani": 79.3212, "matched_fragments": 586, "total_fragments": 1561, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus", "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_013093415.1", "gtdb_species": "s__Halovulum dunhuangense", "ani": 78.2148, "matched_fragments": 425, "total_fragments": 1561, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halovulum", "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_000153305.1", "gtdb_species": "s__Oceanicola granulosus", "ani": 77.7932, "matched_fragments": 506, "total_fragments": 1561, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola", "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_003056725.1", "gtdb_species": "s__Mangrovicoccus ximenensis", "ani": 77.7355, "matched_fragments": 533, "total_fragments": 1561, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus", "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_007131685.1", "gtdb_species": "s__Rhodobaculum sp007131685", "ani": 77.0434, "matched_fragments": 292, "total_fragments": 1561, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.44", "min_intra_species_ani": "99.41", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_018241455.1", "gtdb_species": "s__FEN-1191 sp018241455", "ani": 74.9412, "matched_fragments": 89, "total_fragments": 1561, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__FEN-1191", "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_903828805.1", "gtdb_species": "s__Sandaracinus sp903828805", "ani": 74.8445, "matched_fragments": 168, "total_fragments": 1561, "gtdb_taxonomy": "d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Sandaracinaceae;g__Sandaracinus", "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": 0.171, "cell_length": null, "doubling_h": null, "growth_tmp": 25.0, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": null, "motility": null, "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": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_genome_taxon": [ "Amaricoccus", "solimangrovi" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }