{ "type": "genome", "identifier": "GCF_002797875.1", "organism": "Pseudoscardovia suis", "title": "Pseudoscardovia suis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002797875.1", "bioproject": "PRJNA224116", "biosample": "SAMN07621028", "wgs_master": "PGFC00000000.1", "refseq_category": "reference genome", "taxid": "987063", "species_taxid": "987063", "organism_name": "Pseudoscardovia suis", "infraspecific_name": "strain=DSM 24744", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/11/28", "asm_name": "ASM279787v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_002797875.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/797/875/GCF_002797875.1_ASM279787v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2247459", "genome_size_ungapped": "2247459", "gc_percent": "60.500000", "replicon_count": "0", "scaffold_count": "19", "contig_count": "19", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002797875.1-RS_2024_04_27", "annotation_date": "2024-04-27", "total_gene_count": "1727", "protein_coding_gene_count": "1632", "non_coding_gene_count": "54", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-11-28", "dateModified": "2017-11-28", "datePublished": "2017-11-28", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudoscardovia suis" ], "sample_taxid": [ "987063" ], "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": "0.629 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)": "2247459", "Number of Sequences": "19", "Longest Sequences (bp)": "727315", "N50 (bp)": "431126", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "60.5", "Number of CDSs": "1701", "Average Protein Length": "362.9", "Coding Ratio (%)": "82.4", "Number of rRNAs": "2", "Number of tRNAs": "49", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudoscardovia suis", "strain": "strain=DSM 24744", "accession": "GCA_002797875.1", "taxid": 987063, "species_taxid": 987063, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 740, "total_fragments": 740, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudoscardovia suis", "strain": "strain=DSM 24744", "accession": "GCA_002259715.1", "taxid": 987063, "species_taxid": 987063, "relation_to_type": "type", "validated": true, "ani": 99.9851, "matched_fragments": 735, "total_fragments": 740, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudoscardovia radai", "strain": "strain=DSM 24742", "accession": "GCA_002259605.1", "taxid": 987066, "species_taxid": 987066, "relation_to_type": "type", "validated": true, "ani": 82.377, "matched_fragments": 413, "total_fragments": 740, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium simiiventris", "strain": "strain=81T8", "accession": "GCA_019331715.1", "taxid": 2834434, "species_taxid": 2834434, "relation_to_type": "type", "validated": true, "ani": 79.3404, "matched_fragments": 178, "total_fragments": 740, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium parmae", "strain": "strain=Uis4E", "accession": "GCA_002860365.1", "taxid": 361854, "species_taxid": 361854, "relation_to_type": "type", "validated": true, "ani": 79.3168, "matched_fragments": 199, "total_fragments": 740, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium amazonense", "strain": "strain=MA1", "accession": "GCA_018555435.2", "taxid": 2809027, "species_taxid": 2809027, "relation_to_type": "type", "validated": true, "ani": 79.2682, "matched_fragments": 193, "total_fragments": 740, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium platyrrhinorum", "strain": "strain=SMA15", "accession": "GCA_010667645.1", "taxid": 2661628, "species_taxid": 2661628, "relation_to_type": "type", "validated": true, "ani": 79.1528, "matched_fragments": 200, "total_fragments": 740, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium saimiriisciurei", "strain": "strain=SMA1", "accession": "GCA_010667655.1", "taxid": 2661627, "species_taxid": 2661627, "relation_to_type": "type", "validated": true, "ani": 79.1295, "matched_fragments": 198, "total_fragments": 740, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium stellenboschense", "strain": "strain=DSM 23968", "accession": "GCA_000741785.1", "taxid": 762211, "species_taxid": 762211, "relation_to_type": "type", "validated": true, "ani": 79.0151, "matched_fragments": 211, "total_fragments": 740, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium scardovii", "strain": "strain=DSM 13734", "accession": "GCA_000770985.1", "taxid": 158787, "species_taxid": 158787, "relation_to_type": "type", "validated": true, "ani": 79.0008, "matched_fragments": 197, "total_fragments": 740, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium callimiconis", "strain": "strain=2028B", "accession": "GCA_003952005.1", "taxid": 2306973, "species_taxid": 2306973, "relation_to_type": "type", "validated": true, "ani": 78.9835, "matched_fragments": 185, "total_fragments": 740, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium samirii", "strain": "strain=2033B", "accession": "GCA_003952945.1", "taxid": 2306974, "species_taxid": 2306974, "relation_to_type": "type", "validated": true, "ani": 78.9664, "matched_fragments": 187, "total_fragments": 740, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium simiarum", "strain": "strain=TRI 7", "accession": "GCA_002802905.1", "taxid": 2045441, "species_taxid": 2045441, "relation_to_type": "type", "validated": true, "ani": 78.9574, "matched_fragments": 192, "total_fragments": 740, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium pluvialisilvae", "strain": "strain=82T24", "accession": "GCA_019331695.1", "taxid": 2834436, "species_taxid": 2834436, "relation_to_type": "type", "validated": true, "ani": 78.9544, "matched_fragments": 205, "total_fragments": 740, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium phasiani", "strain": "strain=6T3", "accession": "GCA_019331775.1", "taxid": 2834431, "species_taxid": 2834431, "relation_to_type": "type", "validated": true, "ani": 78.4853, "matched_fragments": 194, "total_fragments": 740, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium colobi", "strain": "strain=LC6", "accession": "GCA_018555455.1", "taxid": 2809026, "species_taxid": 2809026, "relation_to_type": "type", "validated": true, "ani": 78.3838, "matched_fragments": 149, "total_fragments": 740, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium pseudolongum subsp. pseudolongum", "strain": "strain=ATCC 25526", "accession": "GCA_022691205.1", "taxid": 31954, "species_taxid": 1694, "relation_to_type": "type", "validated": true, "ani": 78.2391, "matched_fragments": 156, "total_fragments": 740, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium commune", "strain": "strain=DSM 28792", "accession": "GCA_014191315.1", "taxid": 1505727, "species_taxid": 1505727, "relation_to_type": "type", "validated": true, "ani": 77.0504, "matched_fragments": 68, "total_fragments": 740, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002797875.1", "gtdb_species": "s__Pseudoscardovia suis", "ani": 100.0, "matched_fragments": 740, "total_fragments": 740, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Pseudoscardovia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.86", "min_intra_species_ani": "96.17", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.88", "num_clustered_genomes": 7, "status": "conclusive" }, { "accession": "GCF_002259605.1", "gtdb_species": "s__Pseudoscardovia radai", "ani": 82.4192, "matched_fragments": 410, "total_fragments": 740, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Pseudoscardovia", "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_002353815.1", "gtdb_species": "s__Pseudoscardovia sp002353815", "ani": 81.549, "matched_fragments": 338, "total_fragments": 740, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Pseudoscardovia", "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_002860365.1", "gtdb_species": "s__Bifidobacterium parmae", "ani": 79.2937, "matched_fragments": 200, "total_fragments": 740, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "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_010667645.1", "gtdb_species": "s__Bifidobacterium platyrrhinorum", "ani": 79.1528, "matched_fragments": 200, "total_fragments": 740, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "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_001042635.1", "gtdb_species": "s__Bifidobacterium scardovii", "ani": 79.116, "matched_fragments": 204, "total_fragments": 740, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.51", "min_intra_species_ani": "98.97", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.93", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_002234915.1", "gtdb_species": "s__Galliscardovia vansinderenii", "ani": 79.0517, "matched_fragments": 192, "total_fragments": 740, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia", "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_009299475.1", "gtdb_species": "s__Bifidobacterium avesanii", "ani": 79.0394, "matched_fragments": 191, "total_fragments": 740, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_012932365.1", "gtdb_species": "s__Bifidobacterium sp012932365", "ani": 79.0197, "matched_fragments": 217, "total_fragments": 740, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "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_000741785.1", "gtdb_species": "s__Bifidobacterium stellenboschense", "ani": 78.9962, "matched_fragments": 211, "total_fragments": 740, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "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_003952945.1", "gtdb_species": "s__Bifidobacterium samirii", "ani": 78.9664, "matched_fragments": 187, "total_fragments": 740, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "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_003952005.1", "gtdb_species": "s__Galliscardovia callimiconis", "ani": 78.9472, "matched_fragments": 187, "total_fragments": 740, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.12", "min_intra_species_ani": "98.12", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002802905.1", "gtdb_species": "s__Galliscardovia simiarum", "ani": 78.9151, "matched_fragments": 194, "total_fragments": 740, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.16", "min_intra_species_ani": "98.16", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003129925.1", "gtdb_species": "s__Galliscardovia catulorum", "ani": 78.7914, "matched_fragments": 189, "total_fragments": 740, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia", "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_018555455.1", "gtdb_species": "s__Bifidobacterium sp018555455", "ani": 78.4081, "matched_fragments": 148, "total_fragments": 740, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "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_012932445.1", "gtdb_species": "s__Bifidobacterium sp012932445", "ani": 78.187, "matched_fragments": 108, "total_fragments": 740, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": null, "growth_tmp": 37.0, "optimum_tmp": null, "optimum_ph": null, "genome_size": 2247459.0, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": null, "motility": null, "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": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_genome_taxon": [ "Pseudoscardovia", "suis" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }