{ "type": "genome", "identifier": "GCF_009711185.1", "organism": "Paracoccus limosus", "title": "Paracoccus limosus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Chinese center for disease control and prevention", "publication": [ {} ], "properties": { "assembly_accession": "GCF_009711185.1", "bioproject": "PRJNA224116", "biosample": "SAMN13324932", "wgs_master": "WMIF00000000.1", "refseq_category": "reference genome", "taxid": "913252", "species_taxid": "913252", "organism_name": "Paracoccus limosus", "infraspecific_name": "strain=JCM 17370", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/11/26", "asm_name": "ASM971118v1", "asm_submitter": "Chinese center for disease control and prevention", "gbrs_paired_asm": "GCA_009711185.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/711/185/GCF_009711185.1_ASM971118v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3906278", "genome_size_ungapped": "3906268", "gc_percent": "66.000000", "replicon_count": "0", "scaffold_count": "72", "contig_count": "72", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_009711185.1-RS_2024_05_05", "annotation_date": "2024-05-05", "total_gene_count": "3847", "protein_coding_gene_count": "3744", "non_coding_gene_count": "52", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-11-26", "dateModified": "2019-11-26", "datePublished": "2019-11-26", "_annotation": { "sample_count": 1, "sample_organism": [ "Paracoccus limosus" ], "sample_taxid": [ "913252" ], "sample_host_organism": [ "not collected" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "not collected" ], "sample_host_location_id": [], "data_size": "1.066 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)": "3906278", "Number of Sequences": "72", "Longest Sequences (bp)": "324677", "N50 (bp)": "120657", "Gap Ratio (%)": "0.000256", "GCcontent (%)": "66.1", "Number of CDSs": "3763", "Average Protein Length": "314.0", "Coding Ratio (%)": "90.7", "Number of rRNAs": "3", "Number of tRNAs": "49", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Paracoccus limosus", "strain": "strain=JCM 17370", "accession": "GCA_009711185.1", "taxid": 913252, "species_taxid": 913252, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1261, "total_fragments": 1264, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Paracoccus yeei", "strain": "strain=G1212", "accession": "GCA_002196965.1", "taxid": 147645, "species_taxid": 147645, "relation_to_type": "type", "validated": true, "ani": 84.8023, "matched_fragments": 850, "total_fragments": 1264, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus yeei", "strain": "strain=ATCC BAA-599", "accession": "GCA_000622145.1", "taxid": 147645, "species_taxid": 147645, "relation_to_type": "type", "validated": true, "ani": 84.7833, "matched_fragments": 878, "total_fragments": 1264, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus binzhouensis", "strain": "strain=wg1", "accession": "GCA_016446475.1", "taxid": 2796149, "species_taxid": 2796149, "relation_to_type": "type", "validated": true, "ani": 84.5467, "matched_fragments": 809, "total_fragments": 1264, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus aminovorans", "strain": "strain=DSM 8537", "accession": "GCA_900113565.1", "taxid": 34004, "species_taxid": 34004, "relation_to_type": "type", "validated": true, "ani": 84.504, "matched_fragments": 819, "total_fragments": 1264, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus aminovorans", "strain": "", "accession": "GCA_900005615.1", "taxid": 34004, "species_taxid": 34004, "relation_to_type": "type", "validated": true, "ani": 84.4377, "matched_fragments": 832, "total_fragments": 1264, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus lutimaris", "strain": "strain=CECT 8525", "accession": "GCA_003337565.1", "taxid": 1490030, "species_taxid": 1490030, "relation_to_type": "type", "validated": true, "ani": 84.2696, "matched_fragments": 800, "total_fragments": 1264, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus mutanolyticus", "strain": "strain=RSP-02", "accession": "GCA_003285265.1", "taxid": 1499308, "species_taxid": 1499308, "relation_to_type": "type", "validated": true, "ani": 84.2651, "matched_fragments": 775, "total_fragments": 1264, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus pantotrophus", "strain": "strain=DSM 2944", "accession": "GCA_003633525.1", "taxid": 82367, "species_taxid": 82367, "relation_to_type": "type", "validated": true, "ani": 84.1709, "matched_fragments": 823, "total_fragments": 1264, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus pantotrophus", "strain": "strain=DSM 2944", "accession": "GCA_008824185.1", "taxid": 82367, "species_taxid": 82367, "relation_to_type": "type", "validated": true, "ani": 84.1459, "matched_fragments": 827, "total_fragments": 1264, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus litorisediminis", "strain": "strain=NBRC 112902", "accession": "GCA_009711205.1", "taxid": 2006130, "species_taxid": 2006130, "relation_to_type": "type", "validated": true, "ani": 83.2195, "matched_fragments": 791, "total_fragments": 1264, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus laeviglucosivorans", "strain": "strain=DSM 100094", "accession": "GCA_900182695.1", "taxid": 1197861, "species_taxid": 1197861, "relation_to_type": "type", "validated": true, "ani": 82.9612, "matched_fragments": 785, "total_fragments": 1264, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus nototheniae", "strain": "strain=I-41R45", "accession": "GCA_004335005.1", "taxid": 2489002, "species_taxid": 2489002, "relation_to_type": "type", "validated": true, "ani": 79.9258, "matched_fragments": 611, "total_fragments": 1264, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus salsus", "strain": "strain=EGI L200073", "accession": "GCA_021556615.1", "taxid": 2911061, "species_taxid": 2911061, "relation_to_type": "type", "validated": true, "ani": 79.9061, "matched_fragments": 487, "total_fragments": 1264, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus everestensis", "strain": "strain=S8-55", "accession": "GCA_021491915.1", "taxid": 2903900, "species_taxid": 2903900, "relation_to_type": "type", "validated": true, "ani": 79.6973, "matched_fragments": 528, "total_fragments": 1264, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus tegillarcae", "strain": "strain=BM15", "accession": "GCA_002847305.1", "taxid": 1529068, "species_taxid": 1529068, "relation_to_type": "type", "validated": true, "ani": 79.1183, "matched_fragments": 536, "total_fragments": 1264, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_009711185.1", "gtdb_species": "s__Paracoccus limosus", "ani": 100.0, "matched_fragments": 1261, "total_fragments": 1264, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus", "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": "conclusive" }, { "accession": "GCF_001546115.1", "gtdb_species": "s__Paracoccus aminovorans_B", "ani": 85.064, "matched_fragments": 884, "total_fragments": 1264, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.35", "min_intra_species_ani": "95.35", "mean_intra_species_af": "0.81", "min_intra_species_af": "0.81", "num_clustered_genomes": 2, "status": "-" }, { "accession": 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