{ "type": "genome", "identifier": "GCF_003387225.1", "organism": "Methylovirgula ligni", "title": "Methylovirgula ligni", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003387225.1", "bioproject": "PRJNA224116", "biosample": "SAMN09064159", "wgs_master": "QUMO00000000.1", "refseq_category": "na", "taxid": "569860", "species_taxid": "569860", "organism_name": "Methylovirgula ligni", "infraspecific_name": "strain=BW863", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/08/14", "asm_name": "ASM338722v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_003387225.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/387/225/GCF_003387225.1_ASM338722v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3292724", "genome_size_ungapped": "3292527", "gc_percent": "62.500000", "replicon_count": "0", "scaffold_count": "8", "contig_count": "8", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003387225.1-RS_2024_05_01", "annotation_date": "2024-05-01", "total_gene_count": "3242", "protein_coding_gene_count": "3170", "non_coding_gene_count": "52", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-08-14", "dateModified": "2018-08-14", "datePublished": "2018-08-14", "_annotation": { "sample_count": 1, "sample_organism": [ "Methylovirgula ligni" ], "sample_taxid": [ "569860" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Netherlands:The Netherlands, Veluwe" ], "sample_host_location_id": [], "data_size": "0.914 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)": "3292724", "Number of Sequences": "8", "Longest Sequences (bp)": "937703", "N50 (bp)": "931588", "Gap Ratio (%)": "0.005983", "GCcontent (%)": "62.3", "Number of CDSs": "3189", "Average Protein Length": "304.7", "Coding Ratio (%)": "88.5", "Number of rRNAs": "3", "Number of tRNAs": "53", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Methylovirgula ligni", "strain": "strain=BW863", "accession": "GCA_003387225.1", "taxid": 569860, "species_taxid": 569860, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1091, 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"organism_name": "Methylosinus trichosporium", "strain": "strain=OB3b", "accession": "GCA_000178815.2", "taxid": 426, "species_taxid": 426, "relation_to_type": "type", "validated": true, "ani": 78.0017, "matched_fragments": 323, "total_fragments": 1093, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylosinus trichosporium", "strain": "strain=OB3b", "accession": "GCA_002752655.1", "taxid": 426, "species_taxid": 426, "relation_to_type": "type", "validated": true, "ani": 77.9818, "matched_fragments": 324, "total_fragments": 1093, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Candidatus Rhodoblastus alkanivorans", "strain": "", "accession": "GCA_022760755.1", "taxid": 2954117, "species_taxid": 2954117, "relation_to_type": "type", "validated": true, "ani": 77.9366, "matched_fragments": 256, "total_fragments": 1093, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylocystis parvus", "strain": "strain=OBBP", "accession": "GCA_000283235.1", "taxid": 134, "species_taxid": 134, "relation_to_type": "type", "validated": true, "ani": 77.8932, "matched_fragments": 223, "total_fragments": 1093, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylosinus sporium", "strain": "strain=DSM 17706", "accession": "GCA_003113265.1", "taxid": 428, "species_taxid": 428, "relation_to_type": "type", "validated": true, "ani": 77.8084, "matched_fragments": 291, "total_fragments": 1093, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylocapsa aurea", "strain": "strain=KYG", "accession": "GCA_000746085.1", "taxid": 663610, "species_taxid": 663610, "relation_to_type": "type", "validated": true, "ani": 77.8055, "matched_fragments": 263, "total_fragments": 1093, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Beijerinckia indica subsp. indica", "strain": "strain=ATCC 9039", "accession": "GCA_000019845.1", "taxid": 31994, "species_taxid": 533, "relation_to_type": "type", "validated": true, "ani": 77.7693, "matched_fragments": 197, "total_fragments": 1093, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylocystis silviterrae", "strain": "strain=FS", "accession": "GCA_013350005.1", "taxid": 2743612, "species_taxid": 2743612, "relation_to_type": "type", "validated": true, "ani": 77.6878, "matched_fragments": 225, "total_fragments": 1093, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Beijerinckia mobilis", "strain": "strain=UQM 1969", "accession": "GCA_000745425.1", "taxid": 231434, "species_taxid": 231434, "relation_to_type": "type", "validated": true, "ani": 77.6792, "matched_fragments": 197, "total_fragments": 1093, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bosea caraganae", "strain": "strain=RCAM 04680", "accession": "GCA_003351345.1", "taxid": 2763117, "species_taxid": 2763117, "relation_to_type": "type", "validated": true, "ani": 77.2007, "matched_fragments": 257, "total_fragments": 1093, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Saliniramus fredricksonii", "strain": "strain=HL-109", "accession": "GCA_900094735.1", "taxid": 1653334, "species_taxid": 1653334, "relation_to_type": "type", "validated": true, "ani": 77.1591, "matched_fragments": 159, "total_fragments": 1093, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium cajani", "strain": "strain=1010", "accession": "GCA_009759665.1", "taxid": 1928661, "species_taxid": 1928661, "relation_to_type": "type", "validated": true, "ani": 77.1573, "matched_fragments": 212, "total_fragments": 1093, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthobacter tagetidis", "strain": "strain=DSM 11105", "accession": "GCA_014206845.1", "taxid": 60216, "species_taxid": 60216, "relation_to_type": "type", "validated": true, "ani": 77.0611, "matched_fragments": 194, "total_fragments": 1093, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthobacter tagetidis", "strain": "strain=ATCC 700314", "accession": "GCA_003667445.1", "taxid": 60216, "species_taxid": 60216, "relation_to_type": "type", "validated": true, "ani": 77.0406, "matched_fragments": 189, "total_fragments": 1093, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium sediminis", "strain": "strain=S2-20-1", "accession": "GCA_018736085.1", "taxid": 2840469, "species_taxid": 2840469, "relation_to_type": "type", "validated": true, "ani": 77.0376, "matched_fragments": 206, "total_fragments": 1093, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004135935.1", "gtdb_species": "s__Methylovirgula ligni", "ani": 99.9994, "matched_fragments": 1092, "total_fragments": 1093, "gtdb_taxonomy": 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