{ "type": "genome", "identifier": "GCF_001312005.1", "organism": "Methylomonas koyamae JCM 16701", "title": "Methylomonas koyamae JCM 16701", "description": "na", "data type": "Genome sequencing and assembly", "organization": "The University of Tokyo", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001312005.1", "bioproject": "PRJNA224116", "biosample": "SAMD00000536", "wgs_master": "BBCK00000000.1", "refseq_category": "na", "taxid": "1294261", "species_taxid": "702114", "organism_name": "Methylomonas koyamae JCM 16701", "infraspecific_name": "strain=JCM 16701", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2015/10/02", "asm_name": "ASM131200v1", "asm_submitter": "The University of Tokyo", "gbrs_paired_asm": "GCA_001312005.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/312/005/GCF_001312005.1_ASM131200v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4954151", "genome_size_ungapped": "4954151", "gc_percent": "56.000000", "replicon_count": "0", "scaffold_count": "382", "contig_count": "382", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001312005.1-RS_2024_09_02", "annotation_date": "2024-09-02", "total_gene_count": "5811", "protein_coding_gene_count": "4897", "non_coding_gene_count": "50", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2015-10-02", "dateModified": "2015-10-02", "datePublished": "2015-10-02", "_annotation": { "sample_count": 1, "sample_organism": [ "Methylomonas koyamae JCM 16701" ], "sample_taxid": [ "1294261" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "NA" ], "sample_host_location_id": [], "data_size": "1.399 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 90.25, "contamination": 1.04, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4954151", "Number of Sequences": "382", "Longest Sequences (bp)": "167909", "N50 (bp)": "31116", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "56.1", "Number of CDSs": "5698", "Average Protein Length": "232.5", "Coding Ratio (%)": "80.2", "Number of rRNAs": "3", "Number of tRNAs": "48", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Methylomonas koyamae", "strain": "strain=JCM 16701", "accession": "GCA_001312005.1", "taxid": 702114, "species_taxid": 702114, "relation_to_type": "suspected-type", "validated": true, "ani": 100.0, "matched_fragments": 1450, "total_fragments": 1465, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Methylomonas koyamae", "strain": "strain=Fw12E-Y", "accession": "GCA_019669905.1", "taxid": 702114, "species_taxid": 702114, "relation_to_type": "suspected-type", "validated": true, "ani": 99.92, "matched_fragments": 1463, "total_fragments": 1465, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Methylomonas denitrificans", "strain": "strain=FJG1", "accession": "GCA_000785705.2", "taxid": 1538553, "species_taxid": 1538553, "relation_to_type": "type", "validated": true, "ani": 80.0001, "matched_fragments": 694, "total_fragments": 1465, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylomonas albis", "strain": "strain=EbA", "accession": "GCA_014850955.1", "taxid": 1854563, "species_taxid": 1854563, "relation_to_type": "type", "validated": true, "ani": 79.4726, "matched_fragments": 592, "total_fragments": 1465, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylomonas rhizoryzae", "strain": "strain=GJ1", "accession": "GCA_008632455.1", "taxid": 2608981, "species_taxid": 2608981, "relation_to_type": "type", "validated": true, "ani": 79.2205, "matched_fragments": 375, "total_fragments": 1465, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylomarinum vadi", "strain": "strain=IT-4", "accession": "GCA_000733935.1", "taxid": 438855, "species_taxid": 438855, "relation_to_type": "type", "validated": true, "ani": 77.0887, "matched_fragments": 212, "total_fragments": 1465, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylomicrobium lacus", "strain": "strain=LW14", "accession": "GCA_000527095.1", "taxid": 136992, "species_taxid": 136992, "relation_to_type": "type", "validated": true, "ani": 77.0107, "matched_fragments": 223, "total_fragments": 1465, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylotuvimicrobium alcaliphilum", "strain": "strain=20Z", "accession": "GCA_000968535.1", "taxid": 271065, "species_taxid": 271065, "relation_to_type": "type", "validated": true, "ani": 76.6003, "matched_fragments": 113, "total_fragments": 1465, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylococcus geothermalis", "strain": "strain=IM1", "accession": "GCA_012769535.1", "taxid": 2681310, "species_taxid": 2681310, "relation_to_type": "type", "validated": true, "ani": 76.4664, "matched_fragments": 111, "total_fragments": 1465, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacter tundripaludum", "strain": "strain=SV96", "accession": "GCA_000190755.3", "taxid": 173365, "species_taxid": 173365, "relation_to_type": "type", "validated": true, "ani": 76.3342, "matched_fragments": 144, "total_fragments": 1465, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudoxanthomonas helianthi", "strain": "strain=110414", "accession": "GCA_017939625.1", "taxid": 1453541, "species_taxid": 1453541, "relation_to_type": "type", "validated": true, "ani": 76.0464, "matched_fragments": 63, "total_fragments": 1465, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas capeferrum", "strain": "strain=WCS358", "accession": "GCA_022548835.1", "taxid": 1495066, "species_taxid": 1495066, "relation_to_type": "type", "validated": true, "ani": 75.5307, "matched_fragments": 60, "total_fragments": 1465, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Serratia bockelmannii", "strain": "strain=S3", "accession": "GCA_008011855.1", "taxid": 2703793, "species_taxid": 2703793, "relation_to_type": "type", "validated": true, "ani": 75.4375, "matched_fragments": 56, "total_fragments": 1465, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 90.25, "contamination": 1.04, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_001312005.1", 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