{ "type": "genome", "identifier": "GCF_004369225.1", "organism": "Pelotomaculum propionicicum", "title": "Pelotomaculum propionicicum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "National Institute of Advanced Industrial Science and Technology", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004369225.1", "bioproject": "PRJNA224116", "biosample": "SAMN09009609", "wgs_master": "QFFZ00000000.1", "refseq_category": "reference genome", "taxid": "258475", "species_taxid": "258475", "organism_name": "Pelotomaculum propionicicum", "infraspecific_name": "strain=MGP", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/03/25", "asm_name": "ASM436922v1", "asm_submitter": "National Institute of Advanced Industrial Science and Technology", "gbrs_paired_asm": "GCA_004369225.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/369/225/GCF_004369225.1_ASM436922v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3946752", "genome_size_ungapped": "3946752", "gc_percent": "49.000000", "replicon_count": "0", "scaffold_count": "199", "contig_count": "199", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004369225.1-RS_2024_05_13", "annotation_date": "2024-05-13", "total_gene_count": "3935", "protein_coding_gene_count": "3754", "non_coding_gene_count": "68", "pubmed_id": "30126076" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-03-25", "dateModified": "2019-03-25", "datePublished": "2019-03-25", "_annotation": { "sample_count": 1, "sample_organism": [ "Pelotomaculum propionicicum" ], "sample_taxid": [ "258475" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Japan: Niigata" ], "sample_host_location_id": [], "data_size": "1.130 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "3946752", "Number of Sequences": "199", "Longest Sequences (bp)": "202536", "N50 (bp)": "60997", "Gap Ratio (%)": "0.001292", "GCcontent (%)": "49.2", "Number of CDSs": "3772", "Average Protein Length": "288.2", "Coding Ratio (%)": "82.6", "Number of rRNAs": "5", "Number of tRNAs": "50", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pelotomaculum propionicicum", "strain": "strain=MGP", "accession": "GCA_004369225.1", "taxid": 258475, "species_taxid": 258475, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1234, "total_fragments": 1234, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pelotomaculum terephthalicicum", "strain": "strain=JT", "accession": "GCA_022410535.1", "taxid": 206393, "species_taxid": 206393, "relation_to_type": "type", "validated": true, "ani": 77.8689, "matched_fragments": 115, "total_fragments": 1234, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004369225.1", "gtdb_species": "s__Pelotomaculum_B propionicicum", "ani": 100.0, "matched_fragments": 1234, "total_fragments": 1234, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Pelotomaculaceae;g__Pelotomaculum_B", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.42", "min_intra_species_ani": "99.42", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCA_018435055.1", "gtdb_species": "s__Syntrophopropionicum sp018435055", "ani": 78.9371, "matched_fragments": 272, "total_fragments": 1234, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Pelotomaculaceae;g__Syntrophopropionicum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.89", "min_intra_species_ani": "98.89", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_002365855.1", "gtdb_species": "s__UBA3103 sp002365855", "ani": 78.6628, "matched_fragments": 137, "total_fragments": 1234, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Pelotomaculaceae;g__UBA3103", "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_002402945.1", "gtdb_species": "s__Syntrophopropionicum sp002402945", "ani": 78.2056, "matched_fragments": 163, "total_fragments": 1234, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Pelotomaculaceae;g__Syntrophopropionicum", "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_000010565.1", "gtdb_species": "s__Pelotomaculum thermopropionicum", "ani": 77.641, "matched_fragments": 178, "total_fragments": 1234, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Pelotomaculaceae;g__Pelotomaculum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.96", "min_intra_species_ani": "98.96", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_002067965.1", "gtdb_species": "s__MVRN01 sp002067965", "ani": 77.3911, "matched_fragments": 72, "total_fragments": 1234, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Pelotomaculaceae;g__MVRN01", "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_002365865.1", "gtdb_species": "s__UBA3102 sp002365865", "ani": 76.8883, "matched_fragments": 65, "total_fragments": 1234, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Pelotomaculaceae;g__UBA3102", "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_001512635.1", "gtdb_species": "s__DTU098 sp001512635", "ani": 76.7882, "matched_fragments": 120, "total_fragments": 1234, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Pelotomaculaceae;g__DTU098", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.71", "min_intra_species_ani": "99.66", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_009428905.1", "gtdb_species": "s__Desulfofundulus_A thermobenzoicus", "ani": 76.0274, "matched_fragments": 60, "total_fragments": 1234, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfovirgulaceae;g__Desulfofundulus_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.96", "min_intra_species_ani": "95.37", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.86", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_001655685.1", "gtdb_species": "s__Desulfotomaculum_G copahuensis", "ani": 75.8812, "matched_fragments": 64, "total_fragments": 1234, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfovirgulaceae;g__Desulfotomaculum_G", "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_000214705.1", "gtdb_species": "s__Desulfofundulus kuznetsovii", "ani": 75.7847, "matched_fragments": 54, "total_fragments": 1234, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfovirgulaceae;g__Desulfofundulus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.21", "min_intra_species_ani": "97.21", "mean_intra_species_af": "0.77", "min_intra_species_af": "0.77", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": 0.0, "cell_length": 0.477, "doubling_h": null, "growth_tmp": 37.0, "optimum_tmp": 37.0, "optimum_ph": 6.9, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 1.0, "sporulation": 1.0, "motility": 0.0, "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": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Pelotomaculum", "propionicicum" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }