{ "type": "genome", "identifier": "GCF_004349215.1", "organism": "Actinomadura rubrisoli", "title": "Actinomadura rubrisoli", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Ondokuz Mayis University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004349215.1", "bioproject": "PRJNA224116", "biosample": "SAMN11032564", "wgs_master": "SMKU00000000.1", "refseq_category": "reference genome", "taxid": "2530368", "species_taxid": "2530368", "organism_name": "Actinomadura rubrisoli", "infraspecific_name": "strain=H3C3", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/03/13", "asm_name": "ASM434921v1", "asm_submitter": "Ondokuz Mayis University", "gbrs_paired_asm": "GCA_004349215.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/349/215/GCF_004349215.1_ASM434921v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "10227186", "genome_size_ungapped": "10227186", "gc_percent": "71.500000", "replicon_count": "0", "scaffold_count": "805", "contig_count": "805", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004349215.1-RS_2024_04_19", "annotation_date": "2024-04-19", "total_gene_count": "9664", "protein_coding_gene_count": "9305", "non_coding_gene_count": "89", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-03-13", "dateModified": "2019-03-13", "datePublished": "2019-03-13", "_annotation": { "sample_count": 1, "sample_organism": [ "Actinomadura rubrisoli" ], "sample_taxid": [ "2530368" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Turkey: Malatya" ], "sample_host_location_id": [], "data_size": "2.780 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 8.33, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "10227186", "Number of Sequences": "805", "Longest Sequences (bp)": "131904", "N50 (bp)": "24093", "Gap Ratio (%)": "0.000010", "GCcontent (%)": "71.6", "Number of CDSs": "9005", "Average Protein Length": "306.4", "Coding Ratio (%)": "80.9", "Number of rRNAs": "5", "Number of tRNAs": "105", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Actinomadura rubrisoli", "strain": "strain=H3C3", "accession": "GCA_004349215.1", "taxid": 2530368, "species_taxid": 2530368, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2992, "total_fragments": 3022, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Actinomadura graeca", "strain": "strain=32-07", "accession": "GCA_019175365.1", "taxid": 2750812, "species_taxid": 2750812, "relation_to_type": "type", "validated": true, "ani": 85.6405, "matched_fragments": 1814, "total_fragments": 3022, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura macra", "strain": "strain=NBRC 14102", "accession": "GCA_001552215.1", "taxid": 46164, "species_taxid": 46164, "relation_to_type": "type", "validated": true, "ani": 85.5873, "matched_fragments": 1833, "total_fragments": 3022, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura litoris", "strain": "strain=NEAU-AAG5", "accession": "GCA_009733595.1", "taxid": 2678616, "species_taxid": 2678616, "relation_to_type": "type", "validated": true, "ani": 85.1591, "matched_fragments": 1800, "total_fragments": 3022, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura roseirufa", "strain": "", "accession": "GCA_900659635.1", "taxid": 2094049, "species_taxid": 2094049, "relation_to_type": "type", "validated": true, "ani": 85.1076, "matched_fragments": 1570, "total_fragments": 3022, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura bangladeshensis", "strain": "strain=DSM 45347", "accession": "GCA_004348335.1", "taxid": 453573, "species_taxid": 453573, "relation_to_type": "type", "validated": true, "ani": 84.2994, "matched_fragments": 1430, "total_fragments": 3022, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura violacea", "strain": "strain=LCR2-06", "accession": "GCA_017573465.1", "taxid": 2819934, "species_taxid": 2819934, "relation_to_type": "type", "validated": true, "ani": 84.2967, "matched_fragments": 1743, "total_fragments": 3022, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura latina", "strain": "strain=ATCC BAA-277", "accession": "GCA_012396395.1", "taxid": 163603, "species_taxid": 163603, "relation_to_type": "type", "validated": true, "ani": 84.2731, "matched_fragments": 1492, "total_fragments": 3022, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura latina", "strain": "strain=NBRC 106108", "accession": "GCA_001552195.1", "taxid": 163603, "species_taxid": 163603, "relation_to_type": "type", "validated": true, "ani": 84.2364, "matched_fragments": 1532, "total_fragments": 3022, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura montaniterrae", "strain": "strain=CYP1-1B", "accession": "GCA_008923365.1", "taxid": 1803903, "species_taxid": 1803903, "relation_to_type": "type", "validated": true, "ani": 84.1998, "matched_fragments": 1650, "total_fragments": 3022, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura meyerae", "strain": "strain=DSM 44715", "accession": "GCA_900188445.1", "taxid": 240840, "species_taxid": 240840, "relation_to_type": "type", "validated": true, "ani": 84.1076, "matched_fragments": 1549, "total_fragments": 3022, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura geliboluensis", "strain": "strain=A8036", "accession": "GCA_005889745.1", "taxid": 882440, "species_taxid": 882440, "relation_to_type": "type", "validated": true, "ani": 84.0101, "matched_fragments": 1419, "total_fragments": 3022, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura spongiicola", "strain": "strain=LHW52907", "accession": "GCA_003432485.1", "taxid": 2303421, "species_taxid": 2303421, "relation_to_type": "type", "validated": true, "ani": 83.2602, "matched_fragments": 1491, "total_fragments": 3022, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura cremea", "strain": "strain=JCM 3308", "accession": "GCA_014648495.1", "taxid": 1991, "species_taxid": 1991, "relation_to_type": "type", "validated": true, "ani": 82.8124, "matched_fragments": 1510, "total_fragments": 3022, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura parmotrematis", "strain": "strain=PM05-2", "accession": "GCA_019458805.1", "taxid": 2864039, "species_taxid": 2864039, "relation_to_type": "type", "validated": true, "ani": 81.313, "matched_fragments": 1403, "total_fragments": 3022, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura rupiterrae", "strain": "strain=DSM 45251", "accession": "GCA_024172125.1", "taxid": 559627, "species_taxid": 559627, "relation_to_type": "type", "validated": true, "ani": 81.0656, "matched_fragments": 1443, "total_fragments": 3022, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 8.33, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004349215.1", "gtdb_species": "s__Spirillospora rubrisoli", "ani": 100.0, "matched_fragments": 2992, "total_fragments": 3022, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora", "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_900659615.1", "gtdb_species": "s__Spirillospora fibrosa", "ani": 85.8421, "matched_fragments": 1727, "total_fragments": 3022, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora", "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_001552215.1", "gtdb_species": "s__Spirillospora macra", "ani": 85.5456, "matched_fragments": 1840, 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