{ "type": "genome", "identifier": "GCF_900109555.1", "organism": "Pacificibacter marinus", "title": "Pacificibacter marinus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900109555.1", "bioproject": "PRJNA224116", "biosample": "SAMN04488032", "wgs_master": "FNZV00000000.1", "refseq_category": "na", "taxid": "658057", "species_taxid": "658057", "organism_name": "Pacificibacter marinus", "infraspecific_name": "strain=DSM 25228", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/10/31", "asm_name": "IMG-taxon 2622736522 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900109555.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/109/555/GCF_900109555.1_IMG-taxon_2622736522_annotated_assembly", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3870734", "genome_size_ungapped": "3869979", "gc_percent": "52.000000", "replicon_count": "0", "scaffold_count": "43", "contig_count": "43", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900109555.1-RS_2024_04_24", "annotation_date": "2024-04-24", "total_gene_count": "3764", "protein_coding_gene_count": "3656", "non_coding_gene_count": "50", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-10-31", "dateModified": "2016-10-31", "datePublished": "2016-10-31", "_annotation": { "sample_count": 1, "sample_organism": [ "Pacificibacter marinus" ], "sample_taxid": [ "658057" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.100 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)": "3870734", "Number of Sequences": "43", "Longest Sequences (bp)": "674142", "N50 (bp)": "217138", "Gap Ratio (%)": "0.019505", "GCcontent (%)": "52.0", "Number of CDSs": "3729", "Average Protein Length": "303.7", "Coding Ratio (%)": "87.8", "Number of rRNAs": "4", "Number of tRNAs": "43", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pacificibacter marinus", "strain": "strain=DSM 25228", "accession": "GCA_900109555.1", "taxid": 658057, 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"validated": true, "ani": 77.641, "matched_fragments": 218, "total_fragments": 1265, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Celeribacter baekdonensis", "strain": "strain=DSM 27375", "accession": "GCA_900102315.1", "taxid": 875171, "species_taxid": 875171, "relation_to_type": "type", "validated": true, "ani": 77.5819, "matched_fragments": 263, "total_fragments": 1265, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cochlodiniinecator piscidefendens", "strain": "strain=M26A2M", "accession": "GCA_011326755.1", "taxid": 2715756, "species_taxid": 2715756, "relation_to_type": "type", "validated": true, "ani": 77.3473, "matched_fragments": 81, "total_fragments": 1265, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Celeribacter litoreus", "strain": "strain=ASW11-22", "accession": "GCA_020165855.1", "taxid": 2876714, "species_taxid": 2876714, "relation_to_type": "type", "validated": true, "ani": 77.2185, "matched_fragments": 140, "total_fragments": 1265, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Celeribacter halophilus", "strain": "strain=ZXM137", "accession": "GCA_001550085.1", "taxid": 576117, "species_taxid": 576117, "relation_to_type": "type", "validated": true, "ani": 77.1238, "matched_fragments": 170, "total_fragments": 1265, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Celeribacter halophilus", "strain": "strain=DSM 26270", "accession": "GCA_003254175.1", "taxid": 576117, "species_taxid": 576117, "relation_to_type": "type", "validated": true, "ani": 77.1028, "matched_fragments": 166, "total_fragments": 1265, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Celeribacter halophilus", "strain": "strain=CGMCC 1.8891", "accession": "GCA_900114135.1", "taxid": 576117, "species_taxid": 576117, "relation_to_type": "type", "validated": true, "ani": 77.0731, "matched_fragments": 169, "total_fragments": 1265, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shimia haliotis", "strain": "strain=DSM 28453", "accession": "GCA_900114415.1", "taxid": 1280847, "species_taxid": 1280847, "relation_to_type": "type", "validated": true, "ani": 76.7967, "matched_fragments": 76, "total_fragments": 1265, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Octadecabacter antarcticus", "strain": "strain=307", "accession": "GCA_000155675.2", "taxid": 1217908, "species_taxid": 1217908, "relation_to_type": "type", "validated": true, "ani": 76.7924, "matched_fragments": 101, "total_fragments": 1265, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pelagivirga sediminicola", "strain": "strain=BH-SD19", "accession": "GCA_003072125.1", "taxid": 2170575, "species_taxid": 2170575, "relation_to_type": "type", "validated": true, "ani": 76.5597, "matched_fragments": 52, "total_fragments": 1265, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thalassorhabdomicrobium marinisediminis", "strain": "strain=BH-SD16", "accession": "GCA_003072065.1", "taxid": 2170577, "species_taxid": 2170577, "relation_to_type": "type", "validated": true, "ani": 76.4934, "matched_fragments": 58, "total_fragments": 1265, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nioella nitratireducens", "strain": "strain=SSW136", "accession": "GCA_001879715.1", "taxid": 1287720, "species_taxid": 1287720, "relation_to_type": "type", "validated": true, "ani": 76.3649, "matched_fragments": 55, "total_fragments": 1265, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aliiroseovarius halocynthiae", "strain": "strain=MA1-10", "accession": "GCA_007004645.1", "taxid": 985055, "species_taxid": 985055, "relation_to_type": "type", "validated": true, "ani": 76.1947, "matched_fragments": 82, "total_fragments": 1265, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ruegeria faecimaris", "strain": "strain=DSM 28009", "accession": "GCA_900182615.1", "taxid": 686389, "species_taxid": 686389, "relation_to_type": "type", "validated": true, "ani": 76.051, "matched_fragments": 62, "total_fragments": 1265, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900109555.1", "gtdb_species": "s__Pacificibacter marinus", "ani": 100.0, "matched_fragments": 1262, "total_fragments": 1265, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pacificibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_018860665.1", "gtdb_species": "s__Pacificibacter marinus_A", "ani": 81.1341, 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"d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella", "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.125, "cell_length": 0.602, "doubling_h": null, "growth_tmp": 30.0, "optimum_tmp": 30.0, "optimum_ph": 7.5, "genome_size": 3870734.0, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": null, "motility": 0.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": 0.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 1.0, "vibrio_cell_shape": 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