{ "type": "genome", "identifier": "GCF_900163565.1", "organism": "Agrococcus casei LMG 22410", "title": "Agrococcus casei LMG 22410", "description": "na", "data type": "Genome sequencing and assembly", "organization": "MICALIS", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900163565.1", "bioproject": "PRJNA224116", "biosample": "SAMEA80359168", "wgs_master": "FUHU00000000.1", "refseq_category": "reference genome", "taxid": "1255656", "species_taxid": "343512", "organism_name": "Agrococcus casei LMG 22410", "infraspecific_name": "strain=LMG 22410", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/02/11", "asm_name": "ASM90016356v1", "asm_submitter": "MICALIS", "gbrs_paired_asm": "GCA_900163565.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/163/565/GCF_900163565.1_ASM90016356v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2787318", "genome_size_ungapped": "2787318", "gc_percent": "65.500000", "replicon_count": "0", "scaffold_count": "48", "contig_count": "48", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900163565.1-RS_2024_12_09", "annotation_date": "2024-12-09", "total_gene_count": "2798", "protein_coding_gene_count": "2716", "non_coding_gene_count": "53", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-02-11", "dateModified": "2017-02-11", "datePublished": "2017-02-11", "_annotation": { "sample_count": 1, "sample_organism": [ "Agrococcus casei LMG 22410" ], "sample_taxid": [ "1255656" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "France" ], "sample_host_location_id": [], "data_size": "0.765 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)": "2787318", "Number of Sequences": "48", "Longest Sequences (bp)": "389534", "N50 (bp)": "135058", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "65.3", "Number of CDSs": "2734", "Average Protein Length": "312.5", "Coding Ratio (%)": "92.0", "Number of rRNAs": "3", "Number of tRNAs": "45", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Agrococcus casei", "strain": "strain=LMG 22410", "accession": "GCA_900163565.1", "taxid": 343512, "species_taxid": 343512, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 907, "total_fragments": 907, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Agrococcus sediminis", "strain": "strain=NS18", "accession": "GCA_007923295.1", "taxid": 2599924, "species_taxid": 2599924, "relation_to_type": "type", "validated": true, "ani": 79.5118, "matched_fragments": 351, "total_fragments": 907, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agrococcus pavilionensis", "strain": "strain=RW1", "accession": "GCA_000400485.1", "taxid": 1346502, "species_taxid": 1346502, "relation_to_type": "type", "validated": true, "ani": 79.2376, "matched_fragments": 354, "total_fragments": 907, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agrococcus lahaulensis", "strain": "strain=DSM 17612", "accession": "GCA_000425105.1", "taxid": 341722, "species_taxid": 341722, "relation_to_type": "type", "validated": true, "ani": 79.208, "matched_fragments": 341, "total_fragments": 907, "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": 79.1623, "matched_fragments": 351, "total_fragments": 907, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agrococcus jejuensis", "strain": "strain=DSM 22002", "accession": "GCA_900099705.1", "taxid": 399736, "species_taxid": 399736, "relation_to_type": "type", "validated": true, "ani": 79.0733, "matched_fragments": 371, "total_fragments": 907, "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": 79.062, "matched_fragments": 348, "total_fragments": 907, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cryobacterium tepidiphilum", "strain": "strain=NEAU-85", "accession": "GCA_003716325.1", "taxid": 2486026, "species_taxid": 2486026, "relation_to_type": "type", "validated": true, "ani": 78.0571, "matched_fragments": 177, "total_fragments": 907, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microcella putealis", "strain": "strain=CV2", "accession": "GCA_004216575.1", "taxid": 337005, "species_taxid": 337005, "relation_to_type": "type", "validated": true, "ani": 78.0469, "matched_fragments": 199, "total_fragments": 907, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium invictum", "strain": "strain=DSM 19600", "accession": "GCA_023155715.1", "taxid": 515415, "species_taxid": 515415, "relation_to_type": "type", "validated": true, "ani": 78.0261, "matched_fragments": 205, "total_fragments": 907, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces cerinus subsp. cerinus", "strain": "strain=DSM 8595", "accession": "GCA_900142065.1", "taxid": 232089, "species_taxid": 33878, "relation_to_type": "type", "validated": true, "ani": 78.0184, "matched_fragments": 277, "total_fragments": 907, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium invictum", "strain": "strain=JCM 17023", "accession": "GCA_015278285.1", "taxid": 515415, "species_taxid": 515415, "relation_to_type": "type", "validated": true, "ani": 78.0175, "matched_fragments": 204, "total_fragments": 907, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces lapidis", "strain": "strain=JCM 14321", "accession": "GCA_009749405.1", "taxid": 279574, "species_taxid": 279574, "relation_to_type": "type", "validated": true, "ani": 77.976, "matched_fragments": 279, "total_fragments": 907, "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": 77.9735, "matched_fragments": 258, "total_fragments": 907, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces hippuratus", "strain": "strain=DSM 8598", "accession": "GCA_013410355.1", "taxid": 286438, "species_taxid": 286438, "relation_to_type": "type", "validated": true, "ani": 77.9603, "matched_fragments": 282, "total_fragments": 907, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces badenianii", "strain": "strain=MF30-A", "accession": "GCA_003070885.1", "taxid": 2080742, "species_taxid": 2080742, "relation_to_type": "type", "validated": true, "ani": 77.9575, "matched_fragments": 246, "total_fragments": 907, "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": 77.8459, "matched_fragments": 272, "total_fragments": 907, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium enclense", "strain": "strain=NIO-1002", "accession": "GCA_001456955.1", "taxid": 993073, "species_taxid": 993073, "relation_to_type": "type", "validated": true, "ani": 77.6987, "matched_fragments": 207, "total_fragments": 907, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900163565.1", "gtdb_species": "s__Agrococcus casei", "ani": 100.0, "matched_fragments": 907, "total_fragments": 907, "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": "conclusive" }, { "accession": "GCF_007923295.1", "gtdb_species": "s__Agrococcus sediminis", "ani": 79.5115, "matched_fragments": 351, "total_fragments": 907, "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": "GCA_900114805.1", "gtdb_species": "s__Agrococcus baldri", "ani": 79.3279, "matched_fragments": 344, "total_fragments": 907, "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_000400485.1", "gtdb_species": "s__Agrococcus pavilionensis", "ani": 79.2502, "matched_fragments": 353, "total_fragments": 907, "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": "-" }, { "accession": "GCF_018308945.1", "gtdb_species": "s__Agrococcus sp018308945", "ani": 79.0882, "matched_fragments": 369, "total_fragments": 907, "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_900099705.1", "gtdb_species": "s__Agrococcus jejuensis", "ani": 79.0732, "matched_fragments": 371, "total_fragments": 907, "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_900117395.1", "gtdb_species": "s__Agrococcus sp900117395", "ani": 79.068, "matched_fragments": 352, "total_fragments": 907, "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_014645235.1", "gtdb_species": "s__Agrococcus terreus", "ani": 79.0486, "matched_fragments": 349, "total_fragments": 907, "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": 79.0411, "matched_fragments": 351, "total_fragments": 907, "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_005484985.1", "gtdb_species": "s__Agrococcus sp005484985", "ani": 78.8992, "matched_fragments": 330, "total_fragments": 907, "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_007679035.1", "gtdb_species": "s__Agrococcus jejuensis_A", "ani": 78.7711, "matched_fragments": 367, "total_fragments": 907, "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_019115685.1", "gtdb_species": "s__Agrococcus pullicola", "ani": 78.5461, "matched_fragments": 255, "total_fragments": 907, "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_013408685.1", "gtdb_species": "s__Schumannella luteola", "ani": 78.1516, "matched_fragments": 256, "total_fragments": 907, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Schumannella", "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_016907835.1", "gtdb_species": "s__Agromyces cerinus_A", "ani": 78.0925, "matched_fragments": 261, "total_fragments": 907, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces", "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_003716325.1", "gtdb_species": "s__Cryobacterium_C tepidiphilum", "ani": 78.0571, "matched_fragments": 177, "total_fragments": 907, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium_C", "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_009749405.1", "gtdb_species": "s__Agromyces lapidis", "ani": 77.9999, "matched_fragments": 277, "total_fragments": 907, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces", "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_006517435.1", "gtdb_species": "s__Schumannella sp006517435", "ani": 77.8983, "matched_fragments": 257, "total_fragments": 907, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Schumannella", "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": -0.456, "cell_length": -0.046, "doubling_h": null, "growth_tmp": 29.0, "optimum_tmp": 25.0, "optimum_ph": 8.0, "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": 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": [ "Agrococcus", "casei", "LMG", "22410" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }