{ "type": "genome", "identifier": "GCF_000381065.1", "organism": "Propionispira raffinosivorans DSM 20765", "title": "Propionispira raffinosivorans DSM 20765", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000381065.1", "bioproject": "PRJNA224116", "biosample": "SAMN02441335", "wgs_master": "ARLE00000000.1", "refseq_category": "reference genome", "taxid": "1123511", "species_taxid": "86959", "organism_name": "Propionispira raffinosivorans DSM 20765", "infraspecific_name": "strain=DSM 20765", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/04/24", "asm_name": "ASM38106v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_000381065.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/381/065/GCF_000381065.1_ASM38106v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4134382", "genome_size_ungapped": "4131539", "gc_percent": "38.000000", "replicon_count": "0", "scaffold_count": "60", "contig_count": "66", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000381065.1-RS_2024_12_09", "annotation_date": "2024-12-09", "total_gene_count": "3996", "protein_coding_gene_count": "3870", "non_coding_gene_count": "84", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-04-24", "dateModified": "2013-04-24", "datePublished": "2013-04-24", "_annotation": { "sample_count": 1, "sample_organism": [ "Propionispira raffinosivorans DSM 20765" ], "sample_taxid": [ "1123511" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Missing" ], "sample_host_location_id": [], "data_size": "1.170 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)": "4134382", "Number of Sequences": "60", "Longest Sequences (bp)": "349422", "N50 (bp)": "119111", "Gap Ratio (%)": "0.068765", "GCcontent (%)": "38.1", "Number of CDSs": "3851", "Average Protein Length": "307.1", "Coding Ratio (%)": "85.8", "Number of rRNAs": "6", "Number of tRNAs": "66", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Propionispira raffinosivorans", "strain": "strain=DSM 20765", "accession": "GCA_000381065.1", "taxid": 86959, "species_taxid": 86959, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1342, "total_fragments": 1348, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Propionispira arboris", "strain": "strain=DSM 2179", "accession": "GCA_900109225.1", "taxid": 84035, "species_taxid": 84035, "relation_to_type": "type", "validated": true, "ani": 96.356, "matched_fragments": 1151, "total_fragments": 1348, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Pelosinus propionicus", "strain": "strain=DSM 13327", "accession": "GCA_900114615.1", "taxid": 380084, "species_taxid": 380084, "relation_to_type": "type", "validated": true, "ani": 76.6772, "matched_fragments": 62, "total_fragments": 1348, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pectinatus brassicae", "strain": "strain=DSM 24661", "accession": "GCA_014201835.1", "taxid": 862415, "species_taxid": 862415, "relation_to_type": "type", "validated": true, "ani": 76.5886, "matched_fragments": 69, "total_fragments": 1348, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pectinatus brassicae", "strain": "strain=MB591", "accession": "GCA_015732205.1", "taxid": 862415, "species_taxid": 862415, "relation_to_type": "type", "validated": true, "ani": 76.5485, "matched_fragments": 75, "total_fragments": 1348, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000381065.1", "gtdb_species": "s__Propionispira raffinosivorans", "ani": 100.0, "matched_fragments": 1344, "total_fragments": 1348, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Propionispira", "ani_circumscription_radius": 96.4486, "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": "GCF_900109225.1", "gtdb_species": "s__Propionispira arboris", "ani": 96.3746, "matched_fragments": 1149, "total_fragments": 1348, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Propionispira", "ani_circumscription_radius": 96.4486, "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_902363205.1", "gtdb_species": "s__CABIZH01 sp902363205", "ani": 77.2572, "matched_fragments": 104, "total_fragments": 1348, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Massilibacillaceae;g__CABIZH01", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.61", "min_intra_species_ani": "97.54", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.81", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_000725345.1", "gtdb_species": "s__Pelosinus sp000725345", "ani": 76.8456, "matched_fragments": 85, "total_fragments": 1348, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Propionisporales;f__Propionisporaceae;g__Pelosinus", "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_900114615.1", "gtdb_species": "s__Pelosinus propionicus", "ani": 76.7185, "matched_fragments": 62, "total_fragments": 1348, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Propionisporales;f__Propionisporaceae;g__Pelosinus", "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_014201835.1", "gtdb_species": "s__Pectinatus brassicae", "ani": 76.5886, "matched_fragments": 69, "total_fragments": 1348, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Pectinatus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.155, "cell_length": 0.477, "doubling_h": null, "growth_tmp": 29.0, "optimum_tmp": 30.0, "optimum_ph": null, "genome_size": 4136083.0, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 1.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": 0.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 1.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Propionispira", "raffinosivorans", "DSM", "20765" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }