{ "type": "genome", "identifier": "GCF_000400485.1", "organism": "Agrococcus pavilionensis RW1", "title": "Agrococcus pavilionensis RW1", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of British Columbia", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000400485.1", "bioproject": "PRJNA224116", "biosample": "SAMN02471611", "wgs_master": "ASHR00000000.1", "refseq_category": "reference genome", "taxid": "1330458", "species_taxid": "1346502", "organism_name": "Agrococcus pavilionensis RW1", "infraspecific_name": "strain=RW1", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/05/20", "asm_name": "k0-k1250", "asm_submitter": "University of British Columbia", "gbrs_paired_asm": "GCA_000400485.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/400/485/GCF_000400485.1_k0-k1250", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2878403", "genome_size_ungapped": "2878403", "gc_percent": "72.500000", "replicon_count": "0", "scaffold_count": "50", "contig_count": "50", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000400485.1-RS_2024_12_09", "annotation_date": "2024-12-09", "total_gene_count": "2869", "protein_coding_gene_count": "2786", "non_coding_gene_count": "53", "pubmed_id": "23814108" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-05-20", "dateModified": "2013-05-20", "datePublished": "2013-05-20", "_annotation": { "sample_count": 1, "sample_organism": [ "Agrococcus pavilionensis RW1" ], "sample_taxid": [ "1330458" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Canada" ], "sample_host_location_id": [], "data_size": "0.744 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)": "2878403", "Number of Sequences": "50", "Longest Sequences (bp)": "308429", "N50 (bp)": "133224", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "72.6", "Number of CDSs": "2781", "Average Protein Length": "316.7", "Coding Ratio (%)": "91.8", "Number of rRNAs": "3", "Number of tRNAs": "51", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Agrococcus pavilionensis", "strain": "strain=RW1", "accession": "GCA_000400485.1", "taxid": 1346502, "species_taxid": 1346502, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 937, "total_fragments": 938, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Agrococcus lahaulensis", "strain": "strain=DSM 17612", "accession": "GCA_000425105.1", "taxid": 341722, "species_taxid": 341722, "relation_to_type": "type", "validated": true, "ani": 94.567, "matched_fragments": 803, "total_fragments": 938, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agrococcus sediminis", "strain": "strain=NS18", "accession": "GCA_007923295.1", "taxid": 2599924, "species_taxid": 2599924, "relation_to_type": "type", "validated": true, "ani": 87.279, "matched_fragments": 715, "total_fragments": 938, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agrococcus carbonis", "strain": "strain=DSM 22965", "accession": "GCA_900104705.1", "taxid": 684552, "species_taxid": 684552, "relation_to_type": "type", "validated": true, "ani": 86.9743, "matched_fragments": 709, "total_fragments": 938, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agrococcus jenensis", "strain": "strain=DSM 9580", "accession": "GCA_003752465.1", "taxid": 46353, "species_taxid": 46353, "relation_to_type": "type", "validated": true, "ani": 86.4798, "matched_fragments": 705, "total_fragments": 938, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agrococcus terreus", "strain": "strain=CGMCC 1.6960", "accession": "GCA_014645235.1", "taxid": 574649, "species_taxid": 574649, "relation_to_type": "type", "validated": true, "ani": 85.6594, "matched_fragments": 689, "total_fragments": 938, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces flavus", "strain": "strain=CPCC 202695", "accession": "GCA_004366335.2", "taxid": 589382, "species_taxid": 589382, "relation_to_type": "type", "validated": true, "ani": 79.0916, "matched_fragments": 438, "total_fragments": 938, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces mariniharenae", "strain": "strain=NEAU-184", "accession": "GCA_008122505.1", "taxid": 2604423, "species_taxid": 2604423, "relation_to_type": "type", "validated": true, "ani": 79.0649, "matched_fragments": 490, "total_fragments": 938, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces agglutinans", "strain": "strain=CFH 90414", "accession": "GCA_009647605.1", "taxid": 2662258, "species_taxid": 2662258, "relation_to_type": "type", "validated": true, "ani": 78.9108, "matched_fragments": 446, "total_fragments": 938, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clavibacter michiganensis subsp. insidiosus", "strain": "strain=ATCC 10253", "accession": "GCA_003076355.1", "taxid": 33014, "species_taxid": 28447, "relation_to_type": "type", "validated": true, "ani": 78.6282, "matched_fragments": 408, "total_fragments": 938, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clavibacter michiganensis", "strain": "strain=LMG7333", "accession": "GCA_021216655.1", "taxid": 28447, "species_taxid": 28447, "relation_to_type": "suspected-type", "validated": true, "ani": 78.5462, "matched_fragments": 403, "total_fragments": 938, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Maribius pelagius", "strain": "strain=DSM 26893", "accession": "GCA_900110115.1", "taxid": 387096, "species_taxid": 387096, "relation_to_type": "type", "validated": true, "ani": 75.1943, "matched_fragments": 57, "total_fragments": 938, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium temperatum", "strain": "strain=SDW018", "accession": "GCA_002284575.1", "taxid": 241416, "species_taxid": 241416, "relation_to_type": "type", "validated": true, "ani": 75.0416, "matched_fragments": 73, "total_fragments": 938, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas ginsenosidivorax", "strain": "strain=KHI67", "accession": "GCA_007995065.1", "taxid": 862135, "species_taxid": 862135, "relation_to_type": "type", "validated": true, "ani": 74.9837, "matched_fragments": 140, "total_fragments": 938, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodobacter viridis", "strain": "strain=JA737", "accession": "GCA_003217355.1", "taxid": 1054202, "species_taxid": 1054202, "relation_to_type": "type", "validated": true, "ani": 74.9197, "matched_fragments": 54, "total_fragments": 938, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000400485.1", "gtdb_species": "s__Agrococcus pavilionensis", "ani": 100.0, "matched_fragments": 937, "total_fragments": 938, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.37", "min_intra_species_ani": "97.37", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_000425105.1", "gtdb_species": "s__Agrococcus lahaulensis", "ani": 94.5913, "matched_fragments": 802, "total_fragments": 938, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus", "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_018308945.1", "gtdb_species": "s__Agrococcus sp018308945", "ani": 94.0475, "matched_fragments": 776, "total_fragments": 938, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus", "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_007923295.1", "gtdb_species": "s__Agrococcus sediminis", "ani": 87.2833, "matched_fragments": 715, "total_fragments": 938, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.99", "min_intra_species_ani": "97.99", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900104705.1", "gtdb_species": "s__Agrococcus carbonis", "ani": 86.9988, "matched_fragments": 707, "total_fragments": 938, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus", "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_003752465.1", "gtdb_species": "s__Agrococcus jenensis", "ani": 86.4795, "matched_fragments": 705, "total_fragments": 938, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus", "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_017168255.1", "gtdb_species": "s__Agrococcus sp017168255", "ani": 85.0719, "matched_fragments": 687, "total_fragments": 938, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus", "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_015655415.1", "gtdb_species": "s__Humibacter sp015655415", "ani": 77.0213, "matched_fragments": 238, "total_fragments": 938, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Humibacter", "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_002929295.1", "gtdb_species": "s__Arthrobacter_D sp002929295", "ani": 76.9303, "matched_fragments": 238, "total_fragments": 938, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D", "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_016190155.1", "gtdb_species": "s__JACPRB01 sp016190155", "ani": 74.606, "matched_fragments": 53, "total_fragments": 938, "gtdb_taxonomy": "d__Bacteria;p__Planctomycetota;c__MHYJ01;o__MHYJ01;f__JACPRB01;g__JACPRB01", "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": -0.296, "cell_length": -0.025, "doubling_h": null, "growth_tmp": 28.222, "optimum_tmp": 26.5, "optimum_ph": 7.4, "genome_size": 2970497.0, "gc_content": 72.304, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.75, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.25, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Agrococcus", "pavilionensis", "RW1" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }