{ "type": "genome", "identifier": "GCF_002154335.2", "organism": "Actinomyces ruminis", "title": "Actinomyces ruminis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "MACS Agaharkar Research Institute, Pune", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002154335.2", "bioproject": "PRJNA224116", "biosample": "SAMN06245908", "wgs_master": "MTPX00000000.2", "refseq_category": "reference genome", "taxid": "1937003", "species_taxid": "1937003", "organism_name": "Actinomyces ruminis", "infraspecific_name": "strain=CtC72", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/10/26", "asm_name": "ASM215433v2", "asm_submitter": "MACS Agaharkar Research Institute, Pune", "gbrs_paired_asm": "GCA_002154335.2", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/154/335/GCF_002154335.2_ASM215433v2", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3413161", "genome_size_ungapped": "3413161", "gc_percent": "68.000000", "replicon_count": "0", "scaffold_count": "99", "contig_count": "99", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002154335.2-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "3402", "protein_coding_gene_count": "2806", "non_coding_gene_count": "55", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-10-26", "dateModified": "2017-10-26", "datePublished": "2017-10-26", "_annotation": { "sample_count": 1, "sample_organism": [ "Actinomyces ruminis" ], "sample_taxid": [ "1937003" ], "sample_host_organism": [ "cattle" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "India: Pune" ], "sample_host_location_id": [], "data_size": "0.947 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 97.92, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "3413161", "Number of Sequences": "99", "Longest Sequences (bp)": "225663", "N50 (bp)": "74975", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "68.0", "Number of CDSs": "3639", "Average Protein Length": "264.7", "Coding Ratio (%)": "84.7", "Number of rRNAs": "2", "Number of tRNAs": "51", "Number of CRISPRs": "4" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Actinomyces succiniciruminis", "strain": "strain=AM4", "accession": "GCA_900002405.2", "taxid": 1522002, "species_taxid": 1522002, "relation_to_type": "type", "validated": true, "ani": 89.2342, "matched_fragments": 814, 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"below_threshold" }, { "organism_name": "Actinomyces israelii", "strain": "strain=DSM 43320", "accession": "GCA_000711965.1", "taxid": 1659, "species_taxid": 1659, "relation_to_type": "type", "validated": true, "ani": 81.0886, "matched_fragments": 543, "total_fragments": 1085, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomyces dentalis", "strain": "strain=DSM 19115", "accession": "GCA_000429225.1", "taxid": 272548, "species_taxid": 272548, "relation_to_type": "type", "validated": true, "ani": 81.0275, "matched_fragments": 519, "total_fragments": 1085, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomyces viscosus", "strain": "strain=CCUG 14476", "accession": "GCA_004525795.1", "taxid": 1656, "species_taxid": 1656, "relation_to_type": "type", "validated": true, "ani": 80.7942, "matched_fragments": 452, "total_fragments": 1085, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomyces bowdenii", "strain": "strain=DSM 15435", "accession": "GCA_017592395.1", "taxid": 131109, "species_taxid": 131109, "relation_to_type": "type", "validated": true, "ani": 80.4903, "matched_fragments": 455, "total_fragments": 1085, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomyces radicidentis", "strain": "strain=CCUG 36733", "accession": "GCA_001553565.1", "taxid": 111015, "species_taxid": 111015, "relation_to_type": "type", "validated": true, "ani": 80.3457, "matched_fragments": 479, "total_fragments": 1085, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomyces urogenitalis", "strain": "strain=DSM 15434", "accession": "GCA_000159035.1", "taxid": 103621, "species_taxid": 103621, "relation_to_type": "type", "validated": true, "ani": 80.2934, "matched_fragments": 415, "total_fragments": 1085, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomyces marmotae", "strain": "strain=zg-325", "accession": "GCA_009829655.1", "taxid": 2737173, "species_taxid": 2737173, "relation_to_type": "type", "validated": true, "ani": 80.2803, "matched_fragments": 367, "total_fragments": 1085, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomyces denticolens", "strain": "strain=DSM 20671", "accession": "GCA_002072185.1", "taxid": 52767, "species_taxid": 52767, "relation_to_type": "type", "validated": true, "ani": 80.2395, "matched_fragments": 419, "total_fragments": 1085, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ruania suaedae", "strain": "strain=LR1S40", "accession": "GCA_021049265.1", "taxid": 2897774, "species_taxid": 2897774, "relation_to_type": "type", "validated": true, "ani": 77.0207, "matched_fragments": 174, "total_fragments": 1085, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ruania zhangjianzhongii", "strain": "strain=HY168", "accession": "GCA_008000995.1", "taxid": 2603206, "species_taxid": 2603206, 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"min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "conclusive" }, { "accession": "GCF_900002405.1", "gtdb_species": "s__Actinomyces succiniciruminis", "ani": 89.2342, "matched_fragments": 814, "total_fragments": 1085, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces", "ani_circumscription_radius": 96.3414, "mean_intra_species_ani": "98.30", "min_intra_species_ani": "98.26", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.86", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_900098745.1", "gtdb_species": "s__Actinomyces glycerinitolerans", "ani": 89.1263, "matched_fragments": 906, "total_fragments": 1085, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces", "ani_circumscription_radius": 96.3414, "mean_intra_species_ani": "98.41", "min_intra_species_ani": "98.38", "mean_intra_species_af": "0.91", 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"num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_009930875.1", "gtdb_species": "s__Actinomyces sp009930875", "ani": 86.2646, "matched_fragments": 745, "total_fragments": 1085, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.69", "min_intra_species_ani": "98.69", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_004102025.1", "gtdb_species": "s__Actinomyces qiguomingii", "ani": 84.7187, "matched_fragments": 816, "total_fragments": 1085, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.95", "min_intra_species_ani": "99.95", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.165, "cell_length": 0.258, "doubling_h": null, "growth_tmp": 36.951, "optimum_tmp": 36.833, "optimum_ph": 7.0, "genome_size": 2699137.843, "gc_content": 65.627, "coding_genes": 2308.7, "rRNA16S_genes": 3.0, "tRNA_genes": 49.8, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "facultative_respiration": 0.2, "anaerobic_respiration": 0.428, "aerobic_respiration": 0.371, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.95, "coccus_cell_shape": 0.05, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Actinomyces", "ruminis" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }