{ "type": "genome", "identifier": "GCF_014235845.1", "organism": "Pontibrevibacter nitratireducens", "title": "Pontibrevibacter nitratireducens", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Second Institute of Oceanography, Ministry of Natural Resources, P. R. China", "publication": [ {} ], "properties": { "assembly_accession": "GCF_014235845.1", "bioproject": "PRJNA224116", "biosample": "SAMN15594706", "wgs_master": "JACJUQ000000000.1", "refseq_category": "na", "taxid": "2758038", "species_taxid": "2758038", "organism_name": "Pontibrevibacter nitratireducens", "infraspecific_name": "strain=h42", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/08/18", "asm_name": "ASM1423584v1", "asm_submitter": "Second Institute of Oceanography, Ministry of Natural Resources, P. R. China", "gbrs_paired_asm": "GCA_014235845.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/235/845/GCF_014235845.1_ASM1423584v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3545831", "genome_size_ungapped": "3545821", "gc_percent": "62.500000", "replicon_count": "0", "scaffold_count": "43", "contig_count": "43", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_014235845.1-RS_2024_05_26", "annotation_date": "2024-05-26", "total_gene_count": "3477", "protein_coding_gene_count": "3385", "non_coding_gene_count": "47", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-08-18", "dateModified": "2020-08-18", "datePublished": "2020-08-18", "_annotation": { "sample_count": 1, "sample_organism": [ "Pontibrevibacter nitratireducens" ], "sample_taxid": [ "2758038" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Indian Ocean" ], "sample_host_location_id": [], "data_size": "0.994 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)": "3545831", "Number of Sequences": "43", "Longest Sequences (bp)": "526627", "N50 (bp)": "227871", "Gap Ratio (%)": "0.000282", "GCcontent (%)": "62.4", "Number of CDSs": "3422", "Average Protein Length": "314.0", "Coding Ratio (%)": "90.9", "Number of rRNAs": "1", "Number of tRNAs": "42", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Brevirhabdus pacifica", "strain": "strain=22DY15", "accession": "GCA_002094875.1", "taxid": 1267768, "species_taxid": 1267768, "relation_to_type": "type", "validated": true, "ani": 78.833, "matched_fragments": 206, "total_fragments": 1163, "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": 78.6032, "matched_fragments": 431, "total_fragments": 1163, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brevirhabdus pacifica", "strain": "strain=DSM 27767", "accession": "GCA_002797755.1", "taxid": 1267768, "species_taxid": 1267768, "relation_to_type": "type", "validated": true, "ani": 78.4775, "matched_fragments": 221, "total_fragments": 1163, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pontivivens insulae", "strain": "strain=CeCT 8812", "accession": "GCA_900302495.1", "taxid": 1639689, "species_taxid": 1639689, "relation_to_type": "type", "validated": true, "ani": 78.2196, "matched_fragments": 291, "total_fragments": 1163, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pontivivens insulae", "strain": "strain=DSM 103361", "accession": "GCA_003385715.1", "taxid": 1639689, "species_taxid": 1639689, "relation_to_type": "type", "validated": true, "ani": 78.1891, "matched_fragments": 294, "total_fragments": 1163, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseivivax isoporae", "strain": "strain=LMG 25204", "accession": "GCA_000521865.1", "taxid": 591206, "species_taxid": 591206, "relation_to_type": "type", "validated": true, "ani": 77.998, "matched_fragments": 208, "total_fragments": 1163, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseovarius pacificus", "strain": "strain=CGMCC 1.7083", "accession": "GCA_014645335.1", "taxid": 337701, "species_taxid": 337701, "relation_to_type": "type", "validated": true, "ani": 77.7026, "matched_fragments": 227, "total_fragments": 1163, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cribrihabitans marinus", "strain": "strain=CGMCC 1.13219", "accession": "GCA_014640375.1", "taxid": 1227549, "species_taxid": 1227549, "relation_to_type": "type", "validated": true, "ani": 77.6984, "matched_fragments": 233, "total_fragments": 1163, "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": 77.659, "matched_fragments": 257, "total_fragments": 1163, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseivivax marinus", "strain": "strain=DSM 27511", "accession": "GCA_900109705.1", "taxid": 1379903, "species_taxid": 1379903, "relation_to_type": "type", "validated": true, "ani": 77.5423, "matched_fragments": 186, "total_fragments": 1163, "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": 77.5121, "matched_fragments": 278, "total_fragments": 1163, "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": 77.3161, "matched_fragments": 220, "total_fragments": 1163, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodovulum tesquicola", "strain": "strain=A-36s", "accession": "GCA_024128855.1", "taxid": 540254, "species_taxid": 540254, "relation_to_type": "type", "validated": true, "ani": 77.3004, "matched_fragments": 213, "total_fragments": 1163, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nioella sediminis", "strain": "strain=JS7-11", "accession": "GCA_001879695.1", "taxid": 1912092, "species_taxid": 1912092, "relation_to_type": "type", "validated": true, "ani": 77.1513, "matched_fragments": 196, "total_fragments": 1163, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Primorskyibacter sedentarius", "strain": "strain=DSM 104836", "accession": "GCA_004342065.1", "taxid": 745311, "species_taxid": 745311, "relation_to_type": "type", "validated": true, "ani": 77.1306, "matched_fragments": 169, "total_fragments": 1163, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Albimonas pacifica", "strain": "strain=CGMCC 1.11030", "accession": "GCA_900113695.1", "taxid": 1114924, "species_taxid": 1114924, "relation_to_type": "type", "validated": true, "ani": 77.1136, "matched_fragments": 199, "total_fragments": 1163, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudooceanicola endophyticus", "strain": "strain=CBS1P-1", "accession": "GCA_018760365.1", "taxid": 2841273, "species_taxid": 2841273, "relation_to_type": "type", "validated": true, "ani": 77.0801, "matched_fragments": 219, "total_fragments": 1163, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus mutanolyticus", "strain": "strain=RSP-02", "accession": "GCA_003285265.1", "taxid": 1499308, "species_taxid": 1499308, "relation_to_type": "type", "validated": true, "ani": 77.001, "matched_fragments": 172, "total_fragments": 1163, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus xiamenensis", "strain": "strain=12-3", "accession": "GCA_011308835.1", "taxid": 2714901, "species_taxid": 2714901, "relation_to_type": "type", "validated": true, "ani": 76.9916, "matched_fragments": 156, "total_fragments": 1163, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Puniceibacterium sediminis", "strain": "strain=DSM 29052", "accession": "GCA_900188035.1", "taxid": 1608407, "species_taxid": 1608407, "relation_to_type": "type", "validated": true, "ani": 76.943, "matched_fragments": 181, "total_fragments": 1163, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus everestensis", "strain": "strain=S8-55", "accession": "GCA_021491915.1", "taxid": 2903900, "species_taxid": 2903900, "relation_to_type": "type", "validated": true, "ani": 76.9172, "matched_fragments": 145, "total_fragments": 1163, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus aerius", "strain": "strain=KCTC 42845", "accession": "GCA_016757275.1", "taxid": 1915382, "species_taxid": 1915382, "relation_to_type": "type", "validated": true, "ani": 76.9109, "matched_fragments": 172, "total_fragments": 1163, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Albimonas donghaensis", "strain": "strain=DSM 17890", "accession": "GCA_900106695.1", "taxid": 356660, "species_taxid": 356660, "relation_to_type": "type", "validated": true, "ani": 76.9098, "matched_fragments": 236, "total_fragments": 1163, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tabrizicola algicola", "strain": "strain=ETT8", "accession": "GCA_010915705.1", "taxid": 2709381, "species_taxid": 2709381, "relation_to_type": "type", "validated": true, "ani": 76.8948, "matched_fragments": 191, "total_fragments": 1163, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus aerius", "strain": "strain=KCTC 42845", "accession": "GCA_014656455.1", "taxid": 1915382, "species_taxid": 1915382, "relation_to_type": "type", "validated": true, "ani": 76.8868, "matched_fragments": 173, "total_fragments": 1163, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseivivax halodurans", "strain": "strain=JCM 10272", "accession": "GCA_000521785.1", "taxid": 93683, "species_taxid": 93683, "relation_to_type": "type", "validated": true, "ani": 76.8853, "matched_fragments": 174, "total_fragments": 1163, "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": 76.8175, "matched_fragments": 211, "total_fragments": 1163, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amaricoccus macauensis", "strain": "strain=DSM 101730", "accession": "GCA_014201905.1", "taxid": 57001, "species_taxid": 57001, "relation_to_type": "type", "validated": true, "ani": 76.7915, "matched_fragments": 140, "total_fragments": 1163, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_011290545.1", "gtdb_species": "s__Monaibacterium sp011290545", "ani": 96.729, "matched_fragments": 1030, "total_fragments": 1163, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Monaibacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.75", "min_intra_species_ani": "96.75", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_900231835.1", "gtdb_species": "s__Monaibacterium marinum", "ani": 80.2984, "matched_fragments": 587, "total_fragments": 1163, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Monaibacterium", "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_015679265.1", "gtdb_species": "s__MT2928 sp015679265", "ani": 78.5896, "matched_fragments": 432, "total_fragments": 1163, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__MT2928", "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_900302495.1", "gtdb_species": "s__Pontivivens insulae", "ani": 78.2196, "matched_fragments": 291, "total_fragments": 1163, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pontivivens", "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_000521865.1", "gtdb_species": "s__Roseivivax isoporae", "ani": 77.998, "matched_fragments": 208, "total_fragments": 1163, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax", "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_000526275.1", "gtdb_species": "s__Lutimaribacter sp000526275", "ani": 77.5529, "matched_fragments": 220, "total_fragments": 1163, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter", "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_900109705.1", "gtdb_species": "s__Roseivivax marinus", "ani": 77.5423, "matched_fragments": 186, "total_fragments": 1163, 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"d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus", "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_010915705.1", "gtdb_species": "s__ETT8 sp010915705", "ani": 76.9469, "matched_fragments": 187, "total_fragments": 1163, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8", "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_003448965.1", "gtdb_species": "s__Paroceanicella sp003448965", "ani": 76.9424, "matched_fragments": 225, "total_fragments": 1163, "gtdb_taxonomy": 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