{ "type": "genome", "identifier": "GCF_009733595.1", "organism": "Actinomadura litoris", "title": "Actinomadura litoris", "description": "na", "data type": "Genome sequencing and assembly", "organization": "College of life science", "publication": [ {} ], "properties": { "assembly_accession": "GCF_009733595.1", "bioproject": "PRJNA224116", "biosample": "SAMN13352206", "wgs_master": "WOFH00000000.1", "refseq_category": "reference genome", "taxid": "2678616", "species_taxid": "2678616", "organism_name": "Actinomadura litoris", "infraspecific_name": "strain=NEAU-AAG5", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/12/05", "asm_name": "ASM973359v1", "asm_submitter": "College of life science", "gbrs_paired_asm": "GCA_009733595.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/733/595/GCF_009733595.1_ASM973359v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "9160916", "genome_size_ungapped": "9160856", "gc_percent": "73.000000", "replicon_count": "0", "scaffold_count": "37", "contig_count": "37", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_009733595.1-RS_2024_09_29", "annotation_date": "2024-09-29", "total_gene_count": "8194", "protein_coding_gene_count": "8044", "non_coding_gene_count": "79", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-12-05", "dateModified": "2019-12-05", "datePublished": "2019-12-05", "_annotation": { "sample_count": 1, "sample_organism": [ "Actinomadura litoris" ], "sample_taxid": [ "2678616" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China:Hainan" ], "sample_host_location_id": [], "data_size": "2.428 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 16.67, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "9160916", "Number of Sequences": "37", "Longest Sequences (bp)": "1015624", "N50 (bp)": "632247", "Gap Ratio (%)": "0.000655", "GCcontent (%)": "72.8", "Number of CDSs": "8269", "Average Protein Length": "326.7", "Coding Ratio (%)": "88.5", "Number of rRNAs": "5", "Number of tRNAs": "84", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Actinomadura litoris", "strain": "strain=NEAU-AAG5", "accession": "GCA_009733595.1", "taxid": 2678616, "species_taxid": 2678616, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 3031, "total_fragments": 3033, "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": 86.3328, "matched_fragments": 1959, "total_fragments": 3033, "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": 85.9483, "matched_fragments": 1969, "total_fragments": 3033, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura rubrisoli", "strain": "strain=H3C3", "accession": "GCA_004349215.1", "taxid": 2530368, "species_taxid": 2530368, "relation_to_type": "type", "validated": true, "ani": 85.213, "matched_fragments": 1776, "total_fragments": 3033, "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": 84.6133, "matched_fragments": 1692, "total_fragments": 3033, "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": 83.9294, "matched_fragments": 1742, "total_fragments": 3033, "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": 83.9114, "matched_fragments": 1666, "total_fragments": 3033, "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": 83.8534, "matched_fragments": 1859, "total_fragments": 3033, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura darangshiensis", "strain": "strain=DSM 45941", "accession": "GCA_004349235.1", "taxid": 705336, "species_taxid": 705336, "relation_to_type": "type", "validated": true, "ani": 83.7125, "matched_fragments": 1618, "total_fragments": 3033, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura nitritigenes", "strain": "strain=L46", "accession": "GCA_017573545.1", "taxid": 134602, "species_taxid": 134602, "relation_to_type": "type", "validated": true, "ani": 83.7041, "matched_fragments": 1845, "total_fragments": 3033, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura madurae", "strain": "strain=DSM 43067", "accession": "GCA_900115095.1", "taxid": 1993, "species_taxid": 1993, "relation_to_type": "type", "validated": true, "ani": 83.6539, "matched_fragments": 1753, "total_fragments": 3033, "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": 83.6161, "matched_fragments": 1499, "total_fragments": 3033, "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": 83.1505, "matched_fragments": 1611, "total_fragments": 3033, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura rifamycini", "strain": "strain=DSM 43936", "accession": "GCA_000425065.1", "taxid": 31962, "species_taxid": 31962, "relation_to_type": "type", "validated": true, "ani": 82.7106, "matched_fragments": 1597, "total_fragments": 3033, "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": 81.4335, "matched_fragments": 1505, "total_fragments": 3033, "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": 81.0216, "matched_fragments": 1561, "total_fragments": 3033, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 16.67, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_009733595.1", "gtdb_species": "s__Spirillospora litoris", "ani": 100.0, "matched_fragments": 3031, "total_fragments": 3033, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.22", "min_intra_species_ani": "99.22", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_001552215.1", "gtdb_species": "s__Spirillospora macra", "ani": 85.939, "matched_fragments": 1971, "total_fragments": 3033, "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_004349215.1", "gtdb_species": "s__Spirillospora rubrisoli", "ani": 85.2076, "matched_fragments": 1778, "total_fragments": 3033, "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_900659635.1", "gtdb_species": "s__Spirillospora roseirufa", "ani": 84.644, "matched_fragments": 1685, "total_fragments": 3033, "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_900659615.1", "gtdb_species": "s__Spirillospora fibrosa", "ani": 84.5065, "matched_fragments": 1745, "total_fragments": 3033, "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_013372625.1", "gtdb_species": "s__Spirillospora sp013372625", "ani": 84.0051, "matched_fragments": 1389, "total_fragments": 3033, "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_013211575.1", "gtdb_species": "s__Spirillospora verrucosospora", "ani": 83.9476, "matched_fragments": 1845, "total_fragments": 3033, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.82", "min_intra_species_ani": "95.82", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900188445.1", "gtdb_species": "s__Spirillospora meyerae", "ani": 83.94, "matched_fragments": 1659, "total_fragments": 3033, "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_008923365.1", "gtdb_species": "s__Spirillospora montaniterrae", "ani": 83.9042, "matched_fragments": 1746, "total_fragments": 3033, "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_008327685.1", "gtdb_species": "s__Spirillospora sp008327685", "ani": 83.8631, "matched_fragments": 1737, "total_fragments": 3033, "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_013364275.1", "gtdb_species": "s__Spirillospora sp013364275", "ani": 83.79, "matched_fragments": 1760, "total_fragments": 3033, "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_004349235.1", "gtdb_species": "s__Spirillospora darangshiensis", "ani": 83.743, "matched_fragments": 1613, "total_fragments": 3033, "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_017573545.1", "gtdb_species": "s__Spirillospora nitritigenes", "ani": 83.7006, "matched_fragments": 1846, "total_fragments": 3033, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.12", "min_intra_species_ani": "95.12", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.83", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_006547145.1", "gtdb_species": "s__Spirillospora sp006547145", "ani": 83.6661, "matched_fragments": 1729, "total_fragments": 3033, "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_900115095.1", "gtdb_species": "s__Spirillospora madurae", "ani": 83.6176, "matched_fragments": 1759, "total_fragments": 3033, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.34", "min_intra_species_ani": "99.27", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_005889745.1", "gtdb_species": "s__Spirillospora geliboluensis", "ani": 83.5683, "matched_fragments": 1507, "total_fragments": 3033, "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_004348665.1", "gtdb_species": "s__Spirillospora sp004348665", "ani": 83.391, "matched_fragments": 1286, "total_fragments": 3033, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": 0.301, "cell_length": null, "doubling_h": null, "growth_tmp": 30.967, "optimum_tmp": 32.909, "optimum_ph": 7.142, "genome_size": 8227448.539, "gc_content": 72.459, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 1.0, "sporulation": 0.833, "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": 0.666, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.333, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Actinomadura", "litoris" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }