{ "type": "genome", "identifier": "GCF_031432295.1", "organism": "Agromyces indicus", "title": "Agromyces indicus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Hohai University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_031432295.1", "bioproject": "PRJNA224116", "biosample": "SAMN37297852", "wgs_master": "JAVKGS000000000.1", "refseq_category": "reference genome", "taxid": "758919", "species_taxid": "758919", "organism_name": "Agromyces indicus", "infraspecific_name": "strain=CCTCC AB 2011122", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2023/09/12", "asm_name": "ASM3143229v1", "asm_submitter": "Hohai University", "gbrs_paired_asm": "GCA_031432295.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/031/432/295/GCF_031432295.1_ASM3143229v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3382068", "genome_size_ungapped": "3381768", "gc_percent": "72.000000", "replicon_count": "0", "scaffold_count": "9", "contig_count": "9", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_031432295.1-RS_2024_09_16", "annotation_date": "2024-09-16", "total_gene_count": "3270", "protein_coding_gene_count": "3202", "non_coding_gene_count": "54", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2023-09-12", "dateModified": "2023-09-12", "datePublished": "2023-09-12", "_annotation": { "sample_count": 1, "sample_organism": [ "Agromyces indicus" ], "sample_taxid": [ "758919" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "India: Goa" ], "sample_host_location_id": [], "data_size": "0.888 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)": "3382068", "Number of Sequences": "9", "Longest Sequences (bp)": "1297593", "N50 (bp)": "730399", "Gap Ratio (%)": "0.008870", "GCcontent (%)": "72.0", "Number of CDSs": "3235", "Average Protein Length": "320.8", "Coding Ratio (%)": "92.1", "Number of rRNAs": "2", "Number of tRNAs": "54", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Agromyces aurantiacus", "strain": "strain=DSM 14598", "accession": "GCA_016907355.1", "taxid": 165814, "species_taxid": 165814, "relation_to_type": "type", "validated": true, "ani": 85.5254, "matched_fragments": 890, "total_fragments": 1124, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces binzhouensis", "strain": "strain=CGMCC 4.7180", "accession": "GCA_004135055.1", "taxid": 1817495, "species_taxid": 1817495, "relation_to_type": "type", "validated": true, "ani": 85.2196, "matched_fragments": 590, "total_fragments": 1124, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces bracchium", "strain": "strain=JCM 11433", "accession": "GCA_009709675.1", "taxid": 88376, "species_taxid": 88376, "relation_to_type": "type", "validated": true, "ani": 85.1973, "matched_fragments": 864, "total_fragments": 1124, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces luteolus", "strain": "strain=JCM 11431", "accession": "GCA_009729855.1", "taxid": 88373, "species_taxid": 88373, "relation_to_type": "type", "validated": true, "ani": 85.1357, "matched_fragments": 852, "total_fragments": 1124, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces flavus", "strain": "strain=CCM 7623", "accession": "GCA_014635805.1", "taxid": 589382, "species_taxid": 589382, "relation_to_type": "type", "validated": true, "ani": 85.0531, "matched_fragments": 855, "total_fragments": 1124, "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": 85.0459, "matched_fragments": 864, "total_fragments": 1124, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces flavus", "strain": "strain=CPCC 202695", "accession": "GCA_900104685.1", "taxid": 589382, "species_taxid": 589382, "relation_to_type": "type", "validated": true, "ani": 85.019, "matched_fragments": 862, "total_fragments": 1124, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces kandeliae", "strain": "strain=Q22", "accession": "GCA_009674665.1", "taxid": 2666141, "species_taxid": 2666141, "relation_to_type": "type", "validated": true, "ani": 84.8291, "matched_fragments": 817, "total_fragments": 1124, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces marinus", "strain": "strain=DSM 26151", "accession": "GCA_021442325.1", "taxid": 1389020, "species_taxid": 1389020, "relation_to_type": "type", "validated": true, "ani": 84.0728, "matched_fragments": 759, "total_fragments": 1124, "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": 83.2956, "matched_fragments": 786, "total_fragments": 1124, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces ramosus", "strain": "strain=DSM 43045", "accession": "GCA_004216665.1", "taxid": 33879, "species_taxid": 33879, "relation_to_type": "type", "validated": true, "ani": 82.856, "matched_fragments": 733, "total_fragments": 1124, "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": 82.3975, "matched_fragments": 715, "total_fragments": 1124, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces cavernae", "strain": "strain=SYSU K20354", "accession": "GCA_021044935.1", "taxid": 2898659, "species_taxid": 2898659, "relation_to_type": "type", "validated": true, "ani": 82.1643, "matched_fragments": 715, "total_fragments": 1124, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001620055.1", "gtdb_species": "s__Agromyces sp001620055", "ani": 97.148, "matched_fragments": 998, "total_fragments": 1124, "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": "conclusive" }, { "accession": "GCF_016907355.1", "gtdb_species": "s__Agromyces aurantiacus", "ani": 85.5786, "matched_fragments": 886, "total_fragments": 1124, "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_004135055.1", "gtdb_species": "s__Agromyces binzhouensis", "ani": 85.2746, "matched_fragments": 587, "total_fragments": 1124, "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_009729855.1", "gtdb_species": "s__Agromyces luteolus", "ani": 85.1516, "matched_fragments": 849, "total_fragments": 1124, "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_009709675.1", "gtdb_species": "s__Agromyces bracchium", "ani": 85.1513, "matched_fragments": 867, "total_fragments": 1124, "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_900104685.1", "gtdb_species": "s__Agromyces flavus", "ani": 84.9949, "matched_fragments": 864, "total_fragments": 1124, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_009674665.1", "gtdb_species": "s__Agromyces kandeliae", "ani": 84.8171, "matched_fragments": 818, "total_fragments": 1124, "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_008122505.1", "gtdb_species": "s__Agromyces sp008122505", "ani": 83.2807, "matched_fragments": 787, "total_fragments": 1124, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.501, "cell_length": 0.065, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": 27.525, "optimum_ph": 7.25, "genome_size": 3317480.857, "gc_content": 69.898, "coding_genes": 3766.5, "rRNA16S_genes": 3.0, "tRNA_genes": 51.0, "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": [ "Agromyces", "indicus" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }