{ "type": "genome", "identifier": "GCF_004216855.1", "organism": "Microcella alkaliphila", "title": "Microcella alkaliphila", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004216855.1", "bioproject": "PRJNA224116", "biosample": "SAMN10864719", "wgs_master": "SGXT00000000.1", "refseq_category": "reference genome", "taxid": "279828", "species_taxid": "279828", "organism_name": "Microcella alkaliphila", "infraspecific_name": "strain=AC4r", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/02/20", "asm_name": "ASM421685v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_004216855.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/216/855/GCF_004216855.1_ASM421685v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2687802", "genome_size_ungapped": "2687802", "gc_percent": "68.500000", "replicon_count": "0", "scaffold_count": "20", "contig_count": "20", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004216855.1-RS_2024_04_05", "annotation_date": "2024-04-05", "total_gene_count": "2652", "protein_coding_gene_count": "2573", "non_coding_gene_count": "51", "pubmed_id": "26203337" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-02-20", "dateModified": "2019-02-20", "datePublished": "2019-02-20", "_annotation": { "sample_count": 1, "sample_organism": [ "Microcella alkaliphila" ], "sample_taxid": [ "279828" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "0.732 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)": "2687802", "Number of Sequences": "20", "Longest Sequences (bp)": "545184", "N50 (bp)": "309027", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "68.4", "Number of CDSs": "2625", "Average Protein Length": "315.3", "Coding Ratio (%)": "92.4", "Number of rRNAs": "3", "Number of tRNAs": "50", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Microcella alkaliphila", "strain": "strain=AC4r", "accession": "GCA_004216855.1", "taxid": 279828, "species_taxid": 279828, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 885, "total_fragments": 886, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Microcella putealis", "strain": "strain=DSM 19627", "accession": "GCA_006716545.1", "taxid": 337005, "species_taxid": 337005, "relation_to_type": "type", "validated": true, "ani": 85.5548, "matched_fragments": 651, "total_fragments": 886, "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": 85.497, "matched_fragments": 656, "total_fragments": 886, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chryseoglobus frigidaquae", "strain": "strain=DSM 23889", "accession": "GCA_014200395.1", "taxid": 424758, "species_taxid": 424758, "relation_to_type": "type", "validated": true, "ani": 81.0876, "matched_fragments": 500, "total_fragments": 886, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chryseoglobus frigidaquae", "strain": "strain=DSM 23889", "accession": "GCA_009664385.2", "taxid": 424758, "species_taxid": 424758, "relation_to_type": "type", "validated": true, "ani": 81.0817, "matched_fragments": 494, "total_fragments": 886, "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": 78.6666, "matched_fragments": 336, "total_fragments": 886, "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": 78.6534, "matched_fragments": 345, "total_fragments": 886, "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": 78.6295, "matched_fragments": 366, "total_fragments": 886, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Herbiconiux moechotypicola", "strain": "strain=KCTC 19653", "accession": "GCA_024979255.1", "taxid": 637393, "species_taxid": 637393, "relation_to_type": "type", "validated": true, "ani": 78.3238, "matched_fragments": 309, "total_fragments": 886, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004216855.1", "gtdb_species": "s__Microcella alkaliphila", "ani": 100.0, "matched_fragments": 885, "total_fragments": 886, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microcella", "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_002355395.1", "gtdb_species": "s__Microcella alkaliphila_A", "ani": 93.9547, "matched_fragments": 731, "total_fragments": 886, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microcella", "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_004216575.1", "gtdb_species": "s__Microcella putealis", "ani": 85.5028, "matched_fragments": 656, "total_fragments": 886, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microcella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014595885.1", "gtdb_species": "s__Yonghaparkia alkaliphila_A", "ani": 81.882, "matched_fragments": 524, "total_fragments": 886, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001425665.1", "gtdb_species": "s__Yonghaparkia sp001425665", "ani": 81.4644, "matched_fragments": 521, "total_fragments": 886, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.25", "min_intra_species_ani": "99.25", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_012530535.1", "gtdb_species": "s__Yonghaparkia sp012530535", "ani": 81.4339, "matched_fragments": 526, "total_fragments": 886, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia", "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_002280615.1", "gtdb_species": "s__Chryseoglobus sp002280615", "ani": 81.4145, "matched_fragments": 285, "total_fragments": 886, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus", "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_001464255.1", "gtdb_species": "s__Chryseoglobus sp001464255", "ani": 81.2662, "matched_fragments": 352, "total_fragments": 886, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus", "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_005502445.1", "gtdb_species": "s__Yonghaparkia sp005502445", "ani": 81.2056, "matched_fragments": 452, "total_fragments": 886, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia", "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_014137945.1", "gtdb_species": "s__Yonghaparkia alkaliphila", "ani": 80.8586, "matched_fragments": 493, "total_fragments": 886, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia", "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_009371975.2", "gtdb_species": "s__Marinisubtilis pacificus", "ani": 80.696, "matched_fragments": 477, "total_fragments": 886, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Marinisubtilis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.81", "min_intra_species_ani": "97.81", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.83", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.523, "cell_length": 0.477, "doubling_h": 0.287, "growth_tmp": 36.0, "optimum_tmp": null, "optimum_ph": null, "genome_size": 2702840.0, "gc_content": 68.4, "coding_genes": 2535.0, "rRNA16S_genes": 1.0, "tRNA_genes": 45.0, "gram_stain": 1.0, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_genome_taxon": [ "Microcella", "alkaliphila" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }