{ "type": "genome", "identifier": "GCF_004361835.1", "organism": "Stakelama pacifica", "title": "Stakelama pacifica", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004361835.1", "bioproject": "PRJNA224116", "biosample": "SAMN10866376", "wgs_master": "SNWD00000000.1", "refseq_category": "reference genome", "taxid": "517720", "species_taxid": "517720", "organism_name": "Stakelama pacifica", "infraspecific_name": "strain=DSM 25059", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/03/22", "asm_name": "ASM436183v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_004361835.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/361/835/GCF_004361835.1_ASM436183v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3981765", "genome_size_ungapped": "3981765", "gc_percent": "63.000000", "replicon_count": "0", "scaffold_count": "31", "contig_count": "31", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004361835.1-RS_2024_04_27", "annotation_date": "2024-04-27", "total_gene_count": "3849", "protein_coding_gene_count": "3752", "non_coding_gene_count": "52", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-03-22", "dateModified": "2019-03-22", "datePublished": "2019-03-22", "_annotation": { "sample_count": 1, "sample_organism": [ "Stakelama pacifica" ], "sample_taxid": [ "517720" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.102 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)": "3981765", "Number of Sequences": "31", "Longest Sequences (bp)": "722469", "N50 (bp)": "203394", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "62.9", "Number of CDSs": "3787", "Average Protein Length": "316.2", "Coding Ratio (%)": "90.2", "Number of rRNAs": "3", "Number of tRNAs": "50", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Stakelama pacifica", "strain": "strain=DSM 25059", "accession": "GCA_004361835.1", "taxid": 517720, "species_taxid": 517720, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1310, "total_fragments": 1311, "ani_threshold": 95, 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"GCA_001721295.1", "taxid": 1888892, "species_taxid": 1888892, "relation_to_type": "type", "validated": true, "ani": 78.3805, "matched_fragments": 403, "total_fragments": 1311, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas pseudosanguinis", "strain": "strain=DSM 19512", "accession": "GCA_017052355.1", "taxid": 413712, "species_taxid": 413712, "relation_to_type": "type", "validated": true, "ani": 78.3735, "matched_fragments": 453, "total_fragments": 1311, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas paucimobilis", "strain": "strain=FDAARGOS_908", "accession": "GCA_016027095.1", "taxid": 13689, "species_taxid": 13689, "relation_to_type": "type", "validated": true, "ani": 78.3591, "matched_fragments": 448, "total_fragments": 1311, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas pseudosanguinis", "strain": "strain=DSM 19512", "accession": "GCA_014196255.1", "taxid": 413712, 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381, "total_fragments": 1311, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas desiccabilis", "strain": "strain=DSM 16792", "accession": "GCA_014196135.1", "taxid": 429134, "species_taxid": 429134, "relation_to_type": "type", "validated": true, "ani": 77.937, "matched_fragments": 384, "total_fragments": 1311, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas hylomeconis", "strain": "strain=CCTCC AB 2013304", "accession": "GCA_025370105.1", "taxid": 1395958, "species_taxid": 1395958, "relation_to_type": "type", "validated": true, "ani": 77.7813, "matched_fragments": 415, "total_fragments": 1311, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas yunnanensis", "strain": "strain=YIM 3", "accession": "GCA_019898765.1", "taxid": 310400, "species_taxid": 310400, "relation_to_type": "type", "validated": true, "ani": 77.3824, "matched_fragments": 334, "total_fragments": 1311, 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78.4992, "matched_fragments": 424, "total_fragments": 1311, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "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": "-" }, { "accession": "GCA_003240755.1", "gtdb_species": "s__Sphingomonas hengshuiensis_A", "ani": 78.4816, "matched_fragments": 423, "total_fragments": 1311, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "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": "-" }, { "accession": "GCF_001721295.1", "gtdb_species": "s__Sphingomonas turrisvirgatae", "ani": 78.3764, 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