{ "type": "genome", "identifier": "GCF_011290485.1", "organism": "Caldichromatium japonicum", "title": "Caldichromatium japonicum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Tokyo Metropolitan University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_011290485.1", "bioproject": "PRJNA224116", "biosample": "SAMN13885595", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "2699430", "species_taxid": "2699430", "organism_name": "Caldichromatium japonicum", "infraspecific_name": "strain=No.7", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/03/14", "asm_name": "ASM1129048v1", "asm_submitter": "Tokyo Metropolitan University", "gbrs_paired_asm": "GCA_011290485.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/011/290/485/GCF_011290485.1_ASM1129048v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2989870", "genome_size_ungapped": "2989870", "gc_percent": "61.000000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_011290485.1-RS_2024_05_05", "annotation_date": "2024-05-05", "total_gene_count": "2957", "protein_coding_gene_count": "2767", "non_coding_gene_count": "63", "pubmed_id": "32931408" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-03-14", "dateModified": "2020-03-14", "datePublished": "2020-03-14", "_annotation": { "sample_count": 1, "sample_organism": [ "Caldichromatium japonicum" ], "sample_taxid": [ "2699430" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Japan" ], "sample_host_location_id": [], "data_size": "0.833 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)": "2989870", "Number of Sequences": "1", "Longest Sequences (bp)": "2989870", "N50 (bp)": "2989870", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "61.2", "Number of CDSs": "2926", "Average Protein Length": "302.8", "Coding Ratio (%)": "88.9", "Number of rRNAs": "6", "Number of tRNAs": "51", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Caldichromatium japonicum", "strain": "strain=No.7", "accession": "GCA_011290485.1", "taxid": 2699430, "species_taxid": 2699430, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 994, 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"below_threshold" }, { "organism_name": "Thiocystis violacea", "strain": "strain=DSM 207", "accession": "GCA_016583575.1", "taxid": 13725, "species_taxid": 13725, "relation_to_type": "type", "validated": true, "ani": 77.4055, "matched_fragments": 260, "total_fragments": 996, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marichromatium gracile", "strain": "strain=DSM 203", "accession": "GCA_004343155.1", "taxid": 1048, "species_taxid": 1048, "relation_to_type": "type", "validated": true, "ani": 77.2154, "matched_fragments": 258, "total_fragments": 996, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marichromatium gracile", "strain": "strain=DSM 203", "accession": "GCA_016583515.1", "taxid": 1048, "species_taxid": 1048, "relation_to_type": "type", "validated": true, "ani": 77.2059, "matched_fragments": 255, "total_fragments": 996, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thiocapsa bogorovii", "strain": 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