{ "type": "genome", "identifier": "GCF_000428825.1", "organism": "Desulfomicrobium escambiense DSM 10707", "title": "Desulfomicrobium escambiense DSM 10707", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000428825.1", "bioproject": "PRJNA224116", "biosample": "SAMN02440873", "wgs_master": "AUAR00000000.1", "refseq_category": "reference genome", "taxid": "1121411", "species_taxid": "29503", "organism_name": "Desulfomicrobium escambiense DSM 10707", "infraspecific_name": "strain=DSM 10707", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/09/05", "asm_name": "ASM42882v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_000428825.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/428/825/GCF_000428825.1_ASM42882v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3782107", "genome_size_ungapped": "3779471", "gc_percent": "63.500000", "replicon_count": "0", "scaffold_count": "38", "contig_count": "41", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000428825.1-RS_2024_05_02", "annotation_date": "2024-05-02", "total_gene_count": "3449", "protein_coding_gene_count": "3347", "non_coding_gene_count": "72", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-09-05", "dateModified": "2013-09-05", "datePublished": "2013-09-05", "_annotation": { "sample_count": 1, "sample_organism": [ "Desulfomicrobium escambiense DSM 10707" ], "sample_taxid": [ "1121411" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA" ], "sample_host_location_id": [], "data_size": "1.051 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 98.06, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "3782107", "Number of Sequences": "38", "Longest Sequences (bp)": "419795", "N50 (bp)": "212955", "Gap Ratio (%)": "0.069697", "GCcontent (%)": "63.7", "Number of CDSs": "3381", "Average Protein Length": "335.9", "Coding Ratio (%)": "90.1", "Number of rRNAs": "2", "Number of tRNAs": "70", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Desulfomicrobium escambiense", "strain": "strain=DSM 10707", "accession": "GCA_000428825.1", "taxid": 29503, "species_taxid": 29503, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1236, "total_fragments": 1239, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Desulfomicrobium baculatum", "strain": "strain=DSM 4028", "accession": "GCA_000023225.1", "taxid": 899, "species_taxid": 899, "relation_to_type": "type", "validated": true, "ani": 82.5269, "matched_fragments": 783, "total_fragments": 1239, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfomicrobium apsheronum", "strain": "strain=DSM 5918", "accession": "GCA_900114115.1", "taxid": 52560, "species_taxid": 52560, "relation_to_type": "type", "validated": true, "ani": 82.2809, "matched_fragments": 800, "total_fragments": 1239, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfohalovibrio alkalitolerans", "strain": "strain=DSM 16529", "accession": "GCA_000422245.1", "taxid": 293256, "species_taxid": 293256, "relation_to_type": "type", "validated": true, "ani": 79.0819, "matched_fragments": 244, "total_fragments": 1239, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfomicrobium orale", "strain": "strain=DSM 12838", "accession": "GCA_001553625.1", "taxid": 132132, "species_taxid": 132132, "relation_to_type": "type", "validated": true, "ani": 79.0817, "matched_fragments": 383, "total_fragments": 1239, "ani_threshold": 95, "status": "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": 78.9558, "matched_fragments": 291, "total_fragments": 1239, "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": 77.9245, "matched_fragments": 310, "total_fragments": 1239, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudodesulfovibrio indicus", "strain": "strain=J2", "accession": "GCA_001563225.1", "taxid": 1716143, "species_taxid": 1716143, "relation_to_type": "type", "validated": true, "ani": 77.8032, "matched_fragments": 280, "total_fragments": 1239, "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": 77.5802, "matched_fragments": 213, "total_fragments": 1239, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfovibrio piger", "strain": "strain=ATCC 29098", "accession": "GCA_000156375.1", "taxid": 901, "species_taxid": 901, "relation_to_type": "suspected-type", "validated": true, "ani": 77.2764, "matched_fragments": 154, "total_fragments": 1239, "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": 77.1663, "matched_fragments": 200, "total_fragments": 1239, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Megalodesulfovibrio gigas", "strain": "strain=DSM 1382", "accession": "GCA_000429285.1", "taxid": 879, "species_taxid": 879, "relation_to_type": "type", "validated": true, "ani": 77.0002, "matched_fragments": 188, "total_fragments": 1239, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfovibrio porci", "strain": "strain=PG-178-WT-4", "accession": "GCA_009696265.1", "taxid": 2605782, "species_taxid": 2605782, "relation_to_type": "type", "validated": true, "ani": 76.4923, "matched_fragments": 126, "total_fragments": 1239, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": 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92.3109, "matched_fragments": 559, "total_fragments": 1239, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfomicrobiaceae;g__Desulfomicrobium", "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_014873765.1", "gtdb_species": "s__Desulfomicrobium macestii", "ani": 82.7466, "matched_fragments": 822, "total_fragments": 1239, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfomicrobiaceae;g__Desulfomicrobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.27", "min_intra_species_ani": "98.27", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.85", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000023225.1", "gtdb_species": "s__Desulfomicrobium baculatum", "ani": 82.5331, "matched_fragments": 784, "total_fragments": 1239, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfomicrobiaceae;g__Desulfomicrobium", "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_018902545.1", "gtdb_species": "s__Desulfomicrobium sp018902545", "ani": 82.3387, "matched_fragments": 744, "total_fragments": 1239, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfomicrobiaceae;g__Desulfomicrobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.98", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.97", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_900114115.1", "gtdb_species": "s__Desulfomicrobium apsheronum", 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75.6696, "matched_fragments": 70, "total_fragments": 1239, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas", "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_007049795.1", "gtdb_species": "s__Pseudomonas_E mendocina_D", "ani": 75.3886, "matched_fragments": 52, "total_fragments": 1239, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.17", "min_intra_species_ani": "96.47", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.84", "num_clustered_genomes": 6, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.302, "cell_length": 0.23, "doubling_h": 0.703, 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