{ "type": "genome", "identifier": "GCF_001043895.1", "organism": "Methylobacterium indicum", "title": "Methylobacterium indicum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "CSIR-Institute of Microbial Technology", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001043895.1", "bioproject": "PRJNA224116", "biosample": "SAMN03217758", "wgs_master": "JTHF00000000.1", "refseq_category": "na", "taxid": "1775910", "species_taxid": "1775910", "organism_name": "Methylobacterium indicum", "infraspecific_name": "strain=SE2.11", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2015/06/30", "asm_name": "ASM104389v1", "asm_submitter": "CSIR-Institute of Microbial Technology", "gbrs_paired_asm": "GCA_001043895.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/043/895/GCF_001043895.1_ASM104389v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6921653", "genome_size_ungapped": "6921653", "gc_percent": "70.500000", "replicon_count": "0", "scaffold_count": "506", "contig_count": "506", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001043895.1-RS_2024_04_24", "annotation_date": "2024-04-24", "total_gene_count": "6632", "protein_coding_gene_count": "6328", "non_coding_gene_count": "69", "pubmed_id": "26776106" }, "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 indicum" ], "sample_taxid": [ "1775910" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "India" ], "sample_host_location_id": [], "data_size": "1.876 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)": "6921653", "Number of Sequences": "506", "Longest Sequences (bp)": "92762", "N50 (bp)": "28044", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "70.4", "Number of CDSs": "6101", "Average Protein Length": "301.6", "Coding Ratio (%)": "79.8", "Number of rRNAs": "7", "Number of tRNAs": "69", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Methylobacterium indicum", "strain": "strain=SE2.11", "accession": "GCA_001043895.1", "taxid": 1775910, "species_taxid": 1775910, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2053, "total_fragments": 2072, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Methylobacterium ajmalii", "strain": "strain=IF7SW-B2", "accession": "GCA_016613415.1", "taxid": 2738439, "species_taxid": 2738439, "relation_to_type": "type", "validated": true, "ani": 92.9784, "matched_fragments": 1552, "total_fragments": 2072, "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": 90.1988, "matched_fragments": 1552, "total_fragments": 2072, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium terrae", "strain": "strain=17Sr1-28", "accession": "GCA_003173755.1", "taxid": 2202827, "species_taxid": 2202827, "relation_to_type": "type", "validated": true, "ani": 90.1915, "matched_fragments": 1486, "total_fragments": 2072, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium platani", "strain": "strain=JCM 14648", "accession": "GCA_001043885.1", "taxid": 427683, "species_taxid": 427683, "relation_to_type": "type", "validated": true, "ani": 90.1669, "matched_fragments": 1414, "total_fragments": 2072, "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": 89.7364, "matched_fragments": 1581, "total_fragments": 2072, "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": 89.6785, "matched_fragments": 1525, "total_fragments": 2072, "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": 89.6342, "matched_fragments": 1555, "total_fragments": 2072, "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": 89.5608, "matched_fragments": 1392, "total_fragments": 2072, "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": 89.1077, "matched_fragments": 1511, "total_fragments": 2072, "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": 84.8087, "matched_fragments": 1328, "total_fragments": 2072, "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": 84.564, "matched_fragments": 1269, "total_fragments": 2072, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium isbiliense", "strain": "strain=DSM 17168", "accession": "GCA_022179325.1", "taxid": 315478, "species_taxid": 315478, "relation_to_type": "type", "validated": true, "ani": 83.3274, "matched_fragments": 1176, "total_fragments": 2072, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium haplocladii", "strain": "strain=DSM 24195", "accession": "GCA_022179265.1", "taxid": 1176176, "species_taxid": 1176176, "relation_to_type": "type", "validated": true, "ani": 80.307, "matched_fragments": 712, "total_fragments": 2072, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium haplocladii", "strain": "strain=NBRC 107714", "accession": "GCA_007992175.1", "taxid": 1176176, "species_taxid": 1176176, "relation_to_type": "type", "validated": true, "ani": 80.2273, "matched_fragments": 738, "total_fragments": 2072, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aurantimonas manganoxydans", "strain": "strain=DSM 21871", "accession": "GCA_001463865.1", "taxid": 651183, "species_taxid": 651183, "relation_to_type": "type", "validated": true, "ani": 77.3377, "matched_fragments": 388, "total_fragments": 2072, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aurantimonas manganoxydans", "strain": "strain=SI85-9A1", "accession": "GCA_000153465.1", "taxid": 651183, "species_taxid": 651183, "relation_to_type": "type", "validated": true, "ani": 77.313, "matched_fragments": 386, "total_fragments": 2072, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001043895.1", "gtdb_species": "s__Methylobacterium indicum", "ani": 100.0, "matched_fragments": 2053, "total_fragments": 2072, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.73", "min_intra_species_ani": "98.07", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.87", "num_clustered_genomes": 6, "status": "conclusive" }, { "accession": "GCF_016613415.1", "gtdb_species": "s__Methylobacterium ajmalii", "ani": 93.0139, "matched_fragments": 1549, "total_fragments": 2072, 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