{ "type": "genome", "identifier": "GCF_001043975.1", "organism": "Methylobacterium variabile", "title": "Methylobacterium variabile", "description": "na", "data type": "Genome sequencing and assembly", "organization": "CSIR-Institute of Microbial Technology", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001043975.1", "bioproject": "PRJNA224116", "biosample": "SAMN03406604", "wgs_master": "LABY00000000.1", "refseq_category": "reference genome", "taxid": "298794", "species_taxid": "298794", "organism_name": "Methylobacterium variabile", "infraspecific_name": "strain=DSM 16961", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2015/06/30", "asm_name": "ASM104397v1", "asm_submitter": "CSIR-Institute of Microbial Technology", "gbrs_paired_asm": "GCA_001043975.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/043/975/GCF_001043975.1_ASM104397v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "7433592", "genome_size_ungapped": "7433592", "gc_percent": "70.500000", "replicon_count": "0", "scaffold_count": "562", "contig_count": "562", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001043975.1-RS_2024_04_29", "annotation_date": "2024-04-29", "total_gene_count": "7248", "protein_coding_gene_count": "6863", "non_coding_gene_count": "65", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2015-06-30", "dateModified": "2015-06-30", "datePublished": "2015-06-30", "_annotation": { "sample_count": 1, "sample_organism": [ "Methylobacterium variabile" ], "sample_taxid": [ "298794" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Spain:Seville" ], "sample_host_location_id": [], "data_size": "2.017 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.83, "contamination": 1.04, "strain_heterogeneity": 100.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "7433592", "Number of Sequences": "562", "Longest Sequences (bp)": "104997", "N50 (bp)": "32726", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "70.7", "Number of CDSs": "6725", "Average Protein Length": "296.1", "Coding Ratio (%)": "80.4", "Number of rRNAs": "4", "Number of tRNAs": "70", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Methylobacterium variabile", "strain": "strain=DSM 16961", "accession": "GCA_001043975.1", "taxid": 298794, "species_taxid": 298794, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2213, "total_fragments": 2234, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Methylobacterium terrae", "strain": "strain=17Sr1-28", "accession": "GCA_003173755.1", "taxid": 2202827, "species_taxid": 2202827, "relation_to_type": "type", "validated": true, "ani": 90.0693, "matched_fragments": 1488, "total_fragments": 2234, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium nonmethylotrophicum", "strain": "strain=6HR-1", "accession": "GCA_004745635.1", "taxid": 1141884, "species_taxid": 1141884, "relation_to_type": "type", "validated": true, "ani": 89.9838, "matched_fragments": 1645, "total_fragments": 2234, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium frigidaeris", "strain": "strain=JCM 32048", "accession": "GCA_022179185.1", "taxid": 2038277, "species_taxid": 2038277, "relation_to_type": "type", "validated": true, "ani": 89.7898, "matched_fragments": 1637, "total_fragments": 2234, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium platani", "strain": "strain=PMB02", "accession": "GCA_001653715.1", "taxid": 427683, "species_taxid": 427683, "relation_to_type": "type", "validated": true, "ani": 89.5767, "matched_fragments": 1499, "total_fragments": 2234, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium tarhaniae", "strain": "strain=DSM 25844", "accession": "GCA_001043955.1", "taxid": 1187852, "species_taxid": 1187852, "relation_to_type": "type", "validated": true, "ani": 89.5655, "matched_fragments": 1392, "total_fragments": 2234, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium frigidaeris", "strain": "strain=IER25-16", "accession": "GCA_002759055.1", "taxid": 2038277, "species_taxid": 2038277, "relation_to_type": "type", "validated": true, "ani": 89.365, "matched_fragments": 1030, "total_fragments": 2234, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium currus", "strain": "strain=PR1016A", "accession": "GCA_003058325.1", "taxid": 2051553, "species_taxid": 2051553, "relation_to_type": "type", "validated": true, "ani": 89.3369, "matched_fragments": 1618, "total_fragments": 2234, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium terricola", "strain": "strain=17Sr1-39", "accession": "GCA_006151805.1", "taxid": 2583531, "species_taxid": 2583531, "relation_to_type": "type", "validated": true, "ani": 89.1721, "matched_fragments": 1595, "total_fragments": 2234, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium crusticola", "strain": "strain=KCTC 52305", "accession": "GCA_022179145.1", "taxid": 1697972, "species_taxid": 1697972, "relation_to_type": "type", "validated": true, "ani": 85.4466, "matched_fragments": 1399, "total_fragments": 2234, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium oryzihabitans", "strain": "strain=TER-1", "accession": "GCA_004004555.2", "taxid": 2499852, "species_taxid": 2499852, "relation_to_type": "type", "validated": true, "ani": 84.7423, "matched_fragments": 1296, "total_fragments": 2234, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 1.04, "strain_heterogeneity": 100.0 }, "gtdb_result": [ { "accession": "GCF_001043975.1", "gtdb_species": "s__Methylobacterium variabile", "ani": 100.0, "matched_fragments": 2213, "total_fragments": 2234, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium", "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": 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"s__Methylobacterium sp006151805", "ani": 89.2286, "matched_fragments": 1589, "total_fragments": 2234, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium", "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": 0.096, "cell_length": 0.602, "doubling_h": 0.623, "growth_tmp": 28.0, "optimum_tmp": 28.0, "optimum_ph": 6.0, "genome_size": 7432100.0, "gc_content": 68.2, "coding_genes": 6044.758, "rRNA16S_genes": 6.142, "tRNA_genes": 64.375, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 0.333, "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": [ "Methylobacterium", "variabile" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }