{ "type": "genome", "identifier": "GCF_011927665.1", "organism": "Desulfobaculum xiamenense", "title": "Desulfobaculum xiamenense", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_011927665.1", "bioproject": "PRJNA224116", "biosample": "SAMN13189913", "wgs_master": "JAATJA000000000.1", "refseq_category": "reference genome", "taxid": "995050", "species_taxid": "995050", "organism_name": "Desulfobaculum xiamenense", "infraspecific_name": "strain=DSM 24233", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/04/02", "asm_name": "ASM1192766v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_011927665.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/011/927/665/GCF_011927665.1_ASM1192766v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3643426", "genome_size_ungapped": "3643237", "gc_percent": "63.500000", "replicon_count": "0", "scaffold_count": "8", "contig_count": "8", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_011927665.1-RS_2024_04_29", "annotation_date": "2024-04-29", "total_gene_count": "3228", "protein_coding_gene_count": "3140", "non_coding_gene_count": "77", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-04-02", "dateModified": "2020-04-02", "datePublished": "2020-04-02", "_annotation": { "sample_count": 1, "sample_organism": [ "Desulfobaculum xiamenense" ], "sample_taxid": [ "995050" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.010 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)": "3643426", "Number of Sequences": "8", "Longest Sequences (bp)": "1762566", "N50 (bp)": "1155943", "Gap Ratio (%)": "0.005187", "GCcontent (%)": "63.6", "Number of CDSs": "3198", "Average Protein Length": "337.0", "Coding Ratio (%)": "88.7", "Number of rRNAs": "4", "Number of tRNAs": "72", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Desulfobaculum xiamenense", "strain": "strain=DSM 24233", "accession": "GCA_011927665.1", "taxid": 995050, "species_taxid": 995050, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1211, 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"below_threshold" }, { "organism_name": "Paucidesulfovibrio longus", "strain": "strain=DSM 6739", "accession": "GCA_000420485.1", "taxid": 889, "species_taxid": 889, "relation_to_type": "type", "validated": true, "ani": 77.5589, "matched_fragments": 231, "total_fragments": 1211, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cupidesulfovibrio liaohensis", "strain": "strain=XJ01", "accession": "GCA_011682075.1", "taxid": 2604158, "species_taxid": 2604158, "relation_to_type": "type", "validated": true, "ani": 77.4024, "matched_fragments": 211, "total_fragments": 1211, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudodesulfovibrio tunisiensis", "strain": "strain=RB22", "accession": "GCA_022809775.1", "taxid": 463192, "species_taxid": 463192, "relation_to_type": "type", "validated": true, "ani": 77.3767, "matched_fragments": 198, "total_fragments": 1211, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Fundidesulfovibrio putealis", "strain": "strain=DSM 16056", "accession": "GCA_000429325.1", "taxid": 270496, "species_taxid": 270496, "relation_to_type": "type", "validated": true, "ani": 77.3739, "matched_fragments": 188, "total_fragments": 1211, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cupidesulfovibrio oxamicus", "strain": "strain=NCIMB 9442", "accession": "GCA_015731765.1", "taxid": 32016, "species_taxid": 32016, "relation_to_type": "type", "validated": true, "ani": 77.3378, "matched_fragments": 211, "total_fragments": 1211, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudodesulfovibrio hydrargyri", "strain": "strain=BerOc1", "accession": "GCA_001874525.1", "taxid": 2125990, "species_taxid": 2125990, "relation_to_type": "type", "validated": true, "ani": 77.3356, "matched_fragments": 234, "total_fragments": 1211, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudodesulfovibrio mercurii", "strain": "strain=ND132", "accession": "GCA_000189295.2", "taxid": 641491, "species_taxid": 641491, "relation_to_type": "type", "validated": true, "ani": 77.3327, "matched_fragments": 245, "total_fragments": 1211, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudodesulfovibrio cashew", "strain": "strain=SRB007", "accession": "GCA_009762795.1", "taxid": 2678688, "species_taxid": 2678688, "relation_to_type": "type", "validated": true, "ani": 77.1823, "matched_fragments": 168, "total_fragments": 1211, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cupidesulfovibrio termitidis", "strain": "strain=HI1", "accession": "GCA_000504305.1", "taxid": 42252, "species_taxid": 42252, "relation_to_type": "type", "validated": true, "ani": 76.8935, "matched_fragments": 265, "total_fragments": 1211, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfovibrio carbinoliphilus subsp. oakridgensis", "strain": "strain=FW-101-2B", "accession": "GCA_000177215.2", "taxid": 694327, "species_taxid": 345370, "relation_to_type": "type", "validated": true, "ani": 76.8136, "matched_fragments": 160, "total_fragments": 1211, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfonatronum thiodismutans", "strain": "strain=MLF-1", "accession": "GCA_000717475.2", "taxid": 159290, "species_taxid": 159290, "relation_to_type": "type", "validated": true, "ani": 76.3985, "matched_fragments": 91, "total_fragments": 1211, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_011927665.1", "gtdb_species": "s__Desulfobaculum xiamenense", "ani": 100.0, "matched_fragments": 1211, "total_fragments": 1211, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfobaculum", "ani_circumscription_radius": 95.0, 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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_015709205.1", "gtdb_species": "s__JACCQO01 sp015709205", "ani": 77.5533, "matched_fragments": 288, "total_fragments": 1211, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__JACCQO01", "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_011682075.1", "gtdb_species": "s__Cupidesulfovibrio liaohensis", "ani": 77.4024, "matched_fragments": 211, "total_fragments": 1211, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Cupidesulfovibrio", "ani_circumscription_radius": 95.0, 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