{ "type": "genome", "identifier": "GCF_900291955.1", "organism": "Pseudoruminococcus massiliensis", "title": "Pseudoruminococcus massiliensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "URMITE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900291955.1", "bioproject": "PRJNA224116", "biosample": "SAMEA104651786", "wgs_master": "OLMR00000000.1", "refseq_category": "reference genome", "taxid": "2086583", "species_taxid": "2086583", "organism_name": "Pseudoruminococcus massiliensis", "infraspecific_name": "strain=Marseille-P3876", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/03/17", "asm_name": "PRJEB24956", "asm_submitter": "URMITE", "gbrs_paired_asm": "GCA_900291955.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/291/955/GCF_900291955.1_PRJEB24956", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2428410", "genome_size_ungapped": "2428410", "gc_percent": "37.500000", "replicon_count": "0", "scaffold_count": "19", "contig_count": "19", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900291955.1-RS_2024_12_11", "annotation_date": "2024-12-11", "total_gene_count": "2282", "protein_coding_gene_count": "2196", "non_coding_gene_count": "56", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-03-17", "dateModified": "2018-03-17", "datePublished": "2018-03-17", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudoruminococcus massiliensis" ], "sample_taxid": [ "2086583" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "0.676 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)": "2428410", "Number of Sequences": "19", "Longest Sequences (bp)": "628657", "N50 (bp)": "329808", "Gap Ratio (%)": "0.000288", "GCcontent (%)": "37.6", "Number of CDSs": "2220", "Average Protein Length": "313.0", "Coding Ratio (%)": "85.8", "Number of rRNAs": "4", "Number of tRNAs": "46", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudoruminococcus massiliensis", "strain": "strain=Marseille-P3876", "accession": "GCA_900291955.1", "taxid": 2086583, "species_taxid": 2086583, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 796, "total_fragments": 798, "ani_threshold": 95, "status": "conclusive" } ], "cc_result": { "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900291955.1", "gtdb_species": "s__Pseudoruminococcus_A massiliensis", "ani": 100.0, "matched_fragments": 796, "total_fragments": 798, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Pseudoruminococcus_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.32", "min_intra_species_ani": "98.05", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.77", "num_clustered_genomes": 12, "status": "conclusive" }, { "accession": "GCA_902765855.1", "gtdb_species": "s__Pseudoruminococcus_A sp902765855", "ani": 91.1814, "matched_fragments": 588, "total_fragments": 798, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Pseudoruminococcus_A", "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_002834235.1", "gtdb_species": "s__Ruminococcus_E bromii_B", "ani": 79.2057, "matched_fragments": 102, "total_fragments": 798, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.64", "min_intra_species_ani": "96.93", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.80", "num_clustered_genomes": 74, "status": "-" }, { "accession": "GCF_002160515.1", "gtdb_species": "s__Limousia pullorum", "ani": 78.2041, "matched_fragments": 82, "total_fragments": 798, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Limousia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.77", "min_intra_species_ani": "97.06", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.87", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_004560275.1", "gtdb_species": "s__Ruminococcus_E sp004560275", "ani": 77.4665, "matched_fragments": 56, "total_fragments": 798, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E", "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_002493635.1", "gtdb_species": "s__Ruminococcus_E sp002493635", "ani": 77.444, "matched_fragments": 66, "total_fragments": 798, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.92", "min_intra_species_ani": "97.46", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.85", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_902801245.1", "gtdb_species": "s__RUG592 sp902801245", "ani": 76.2474, "matched_fragments": 56, "total_fragments": 798, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__RUG592", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.19", "min_intra_species_ani": "99.19", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_017475765.1", "gtdb_species": "s__UBA1213 sp017475765", "ani": 76.0554, "matched_fragments": 57, "total_fragments": 798, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213", "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_900317395.1", "gtdb_species": "s__UBA1213 sp900317395", "ani": 76.0198, "matched_fragments": 51, "total_fragments": 798, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.75", "min_intra_species_ani": "99.75", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": null, "growth_tmp": null, "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": null, "anaerobic_respiration": null, "aerobic_respiration": null, "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": [ "Pseudoruminococcus", "massiliensis" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }