{ "type": "genome", "identifier": "GCF_021568905.1", "organism": "Zavarzinia marina", "title": "Zavarzinia marina", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Third Institute of Oceanography, Ministry of Natural Resources, P.R.China", "publication": [ {} ], "properties": { "assembly_accession": "GCF_021568905.1", "bioproject": "PRJNA224116", "biosample": "SAMN25062265", "wgs_master": "JAKGSB000000000.1", "refseq_category": "reference genome", "taxid": "2911065", "species_taxid": "2911065", "organism_name": "Zavarzinia marina", "infraspecific_name": "strain=Adcm-6A", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/01/24", "asm_name": "ASM2156890v1", "asm_submitter": "Third Institute of Oceanography, Ministry of Natural Resources, P.R.China", "gbrs_paired_asm": "GCA_021568905.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/021/568/905/GCF_021568905.1_ASM2156890v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3954847", "genome_size_ungapped": "3954847", "gc_percent": "67.500000", "replicon_count": "0", "scaffold_count": "17", "contig_count": "17", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_021568905.1-RS_2024_12_11", "annotation_date": "2024-12-11", "total_gene_count": "3811", "protein_coding_gene_count": "3738", "non_coding_gene_count": "55", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-01-24", "dateModified": "2022-01-24", "datePublished": "2022-01-24", "_annotation": { "sample_count": 1, "sample_organism": [ "Zavarzinia marina" ], "sample_taxid": [ "2911065" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Pacific Ocean: Western Pacific Ocean" ], "sample_host_location_id": [], "data_size": "1.069 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)": "3954847", "Number of Sequences": "17", "Longest Sequences (bp)": "1217711", "N50 (bp)": "490215", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "67.7", "Number of CDSs": "3796", "Average Protein Length": "319.5", "Coding Ratio (%)": "92.0", "Number of rRNAs": "3", "Number of tRNAs": "56", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Zavarzinia compransoris", "strain": "strain=DSM 1231", "accession": "GCA_004362995.1", "taxid": 1264899, "species_taxid": 1264899, "relation_to_type": "type", "validated": true, "ani": 83.7401, "matched_fragments": 918, "total_fragments": 1311, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Zavarzinia compransoris", "strain": "strain=DSM 1231", "accession": "GCA_003173055.1", "taxid": 1264899, "species_taxid": 1264899, "relation_to_type": "type", "validated": true, "ani": 83.6765, "matched_fragments": 928, "total_fragments": 1311, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Zavarzinia aquatilis", "strain": "strain=HR-AS", "accession": "GCA_003173035.1", "taxid": 2211142, "species_taxid": 2211142, "relation_to_type": "type", "validated": true, "ani": 83.0967, "matched_fragments": 917, "total_fragments": 1311, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pelagibius marinus", "strain": "strain=NBU2595", "accession": "GCA_014925385.1", "taxid": 2762760, "species_taxid": 2762760, "relation_to_type": "type", "validated": true, "ani": 77.0901, "matched_fragments": 295, "total_fragments": 1311, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobrevis pamukkalensis", "strain": "strain=PK2", "accession": "GCA_001720135.1", "taxid": 1439726, "species_taxid": 1439726, "relation_to_type": "type", "validated": true, "ani": 77.0296, "matched_fragments": 292, "total_fragments": 1311, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Azospirillum oryzae", "strain": "strain=COC8", "accession": "GCA_008364795.1", "taxid": 286727, "species_taxid": 286727, "relation_to_type": "type", "validated": true, "ani": 76.9833, "matched_fragments": 378, "total_fragments": 1311, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nisaea sediminum", "strain": "strain=NBU1469", "accession": "GCA_014904705.1", "taxid": 2775867, "species_taxid": 2775867, "relation_to_type": "type", "validated": true, "ani": 76.9794, "matched_fragments": 210, "total_fragments": 1311, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Azospirillum thermophilum", "strain": "strain=CFH 70021", "accession": "GCA_003130795.1", "taxid": 2202148, "species_taxid": 2202148, "relation_to_type": "type", "validated": true, "ani": 76.8755, "matched_fragments": 398, "total_fragments": 1311, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Skermanella rosea", "strain": "strain=KEMB 2255-458", "accession": "GCA_016806835.2", "taxid": 1817965, "species_taxid": 1817965, "relation_to_type": "type", "validated": true, "ani": 76.8342, "matched_fragments": 344, "total_fragments": 1311, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Minwuia thermotolerans", "strain": "strain=SY3-15", "accession": "GCA_002924445.1", "taxid": 2056226, "species_taxid": 2056226, "relation_to_type": "type", "validated": true, "ani": 76.8316, "matched_fragments": 275, "total_fragments": 1311, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Jiella sonneratiae", "strain": "strain=MQZ13P-4", "accession": "GCA_017353515.1", "taxid": 2816856, "species_taxid": 2816856, "relation_to_type": "type", "validated": true, "ani": 76.7314, "matched_fragments": 265, "total_fragments": 1311, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudaminobacter soli", "strain": "strain=19-2017", "accession": "GCA_018310375.1", "taxid": 2831468, "species_taxid": 2831468, "relation_to_type": "type", "validated": true, "ani": 76.5511, "matched_fragments": 179, "total_fragments": 1311, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudaminobacter soli", "strain": "strain=HC19", "accession": "GCA_014595955.1", "taxid": 2831468, "species_taxid": 2831468, "relation_to_type": "type", "validated": true, "ani": 76.5511, "matched_fragments": 179, "total_fragments": 1311, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lutibaculum baratangense", "strain": "strain=AMV1", "accession": "GCA_000496075.1", "taxid": 1358440, "species_taxid": 1358440, "relation_to_type": "type", "validated": true, "ani": 76.5392, "matched_fragments": 197, "total_fragments": 1311, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodoplanes elegans", "strain": "strain=DSM 11907", "accession": "GCA_003258805.1", "taxid": 29408, "species_taxid": 29408, "relation_to_type": "type", "validated": true, "ani": 76.4519, "matched_fragments": 259, "total_fragments": 1311, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rubellimicrobium roseum", "strain": "strain=YIM 48858", "accession": "GCA_006152145.1", "taxid": 687525, "species_taxid": 687525, "relation_to_type": "type", "validated": true, "ani": 76.4054, "matched_fragments": 159, "total_fragments": 1311, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodovastum atsumiense", "strain": "strain=G2-11", "accession": "GCA_937425535.1", "taxid": 504468, "species_taxid": 504468, "relation_to_type": "type", "validated": true, "ani": 76.3423, "matched_fragments": 287, "total_fragments": 1311, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium platani", "strain": "strain=JCM 14648", "accession": "GCA_001043885.1", "taxid": 427683, "species_taxid": 427683, "relation_to_type": "type", "validated": true, "ani": 76.338, "matched_fragments": 310, "total_fragments": 1311, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium platani", "strain": "strain=PMB02", "accession": "GCA_001653715.1", "taxid": 427683, "species_taxid": 427683, "relation_to_type": "type", "validated": true, "ani": 76.336, "matched_fragments": 326, "total_fragments": 1311, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseomonas alkaliterrae", "strain": "strain=DSM 25895", "accession": "GCA_014199195.1", "taxid": 1452450, "species_taxid": 1452450, "relation_to_type": "type", "validated": true, "ani": 76.1644, "matched_fragments": 267, "total_fragments": 1311, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003173055.1", "gtdb_species": "s__Zavarzinia compransoris", "ani": 83.7018, "matched_fragments": 927, "total_fragments": 1311, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Zavarziniales;f__Zavarziniaceae;g__Zavarzinia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003173035.1", "gtdb_species": "s__Zavarzinia aquatilis", "ani": 83.1, "matched_fragments": 917, "total_fragments": 1311, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Zavarziniales;f__Zavarziniaceae;g__Zavarzinia", "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_003590945.1", "gtdb_species": "s__Zavarzinia sp003590945", "ani": 81.0081, "matched_fragments": 844, "total_fragments": 1311, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Zavarziniales;f__Zavarziniaceae;g__Zavarzinia", "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_014197805.1", "gtdb_species": "s__Rhodospirillum_A centenum", "ani": 77.159, "matched_fragments": 261, "total_fragments": 1311, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Rhodospirillum_A", "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": "GCA_003576705.1", "gtdb_species": "s__SYSU-D60015 sp003576705", "ani": 76.9789, "matched_fragments": 359, "total_fragments": 1311, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__SYSU-D60015", "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_003116035.1", "gtdb_species": "s__Azospirillum sp003116035", "ani": 76.9447, "matched_fragments": 394, "total_fragments": 1311, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum", "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_900102465.1", "gtdb_species": "s__Thalassobaculum litoreum", "ani": 76.9263, "matched_fragments": 278, "total_fragments": 1311, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.83", "min_intra_species_ani": "98.83", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003130795.1", "gtdb_species": "s__Azospirillum thermophilum", "ani": 76.8826, "matched_fragments": 396, "total_fragments": 1311, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum", "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_002924445.1", "gtdb_species": "s__Minwuia thermotolerans", "ani": 76.8067, "matched_fragments": 277, "total_fragments": 1311, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Minwuiales;f__Minwuiaceae;g__Minwuia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.67", "min_intra_species_ani": "95.35", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.86", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_003336875.1", "gtdb_species": "s__Oleisolibacter albus", "ani": 76.7698, "matched_fragments": 268, "total_fragments": 1311, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Oleisolibacter", "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_900177295.1", "gtdb_species": "s__Tistlia consotensis", "ani": 76.6484, "matched_fragments": 383, "total_fragments": 1311, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000496075.1", "gtdb_species": "s__Lutibaculum baratangense", "ani": 76.5479, "matched_fragments": 196, "total_fragments": 1311, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Tepidamorphaceae;g__Lutibaculum", "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_018131225.1", "gtdb_species": "s__U87765 sp018131225", "ani": 76.5479, "matched_fragments": 272, "total_fragments": 1311, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__U87765", "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": 5, "status": "-" }, { "accession": "GCF_016653355.1", "gtdb_species": "s__Rhodoplanes elegans", "ani": 76.4448, "matched_fragments": 301, "total_fragments": 1311, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.89", "min_intra_species_ani": "99.89", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001653715.1", "gtdb_species": "s__Methylobacterium platani", "ani": 76.3499, "matched_fragments": 325, "total_fragments": 1311, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.94", "min_intra_species_ani": "99.94", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_009377375.1", "gtdb_species": "s__WHUE01 sp009377375", "ani": 76.3017, "matched_fragments": 232, "total_fragments": 1311, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__WHUE01", "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_010032545.1", "gtdb_species": "s__Reyranella sp010032545", "ani": 76.2643, "matched_fragments": 182, "total_fragments": 1311, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella", "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_016869145.1", "gtdb_species": "s__VGEU01 sp016869145", "ani": 76.2323, "matched_fragments": 211, "total_fragments": 1311, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__VGEU01;g__VGEU01", "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": null, "cell_length": null, "doubling_h": 1.255, "growth_tmp": 30.0, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "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": [ "Zavarzinia", "marina" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }