{ "type": "genome", "identifier": "GCF_002207865.1", "organism": "Colwellia marinimaniae", "title": "Colwellia marinimaniae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "National Institute of Technology, Wakayama College", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002207865.1", "bioproject": "PRJNA224116", "biosample": "SAMD00081185", "wgs_master": "BDQM00000000.1", "refseq_category": "reference genome", "taxid": "1513592", "species_taxid": "1513592", "organism_name": "Colwellia marinimaniae", "infraspecific_name": "strain=MTCD1", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/06/12", "asm_name": "ASM220786v1", "asm_submitter": "National Institute of Technology, Wakayama College", "gbrs_paired_asm": "GCA_002207865.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/207/865/GCF_002207865.1_ASM220786v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4387599", "genome_size_ungapped": "4387599", "gc_percent": "39.500000", "replicon_count": "0", "scaffold_count": "588", "contig_count": "588", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002207865.1-RS_2024_08_03", "annotation_date": "2024-08-03", "total_gene_count": "4108", "protein_coding_gene_count": "3839", "non_coding_gene_count": "86", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-06-12", "dateModified": "2017-06-12", "datePublished": "2017-06-12", "_annotation": { "sample_count": 1, "sample_organism": [ "Colwellia marinimaniae" ], "sample_taxid": [ "1513592" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA" ], "sample_host_location_id": [], "data_size": "1.245 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 6.25, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4387599", "Number of Sequences": "588", "Longest Sequences (bp)": "382887", "N50 (bp)": "116758", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "39.6", "Number of CDSs": "3636", "Average Protein Length": "324.8", "Coding Ratio (%)": "80.7", "Number of rRNAs": "7", "Number of tRNAs": "61", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Colwellia marinimaniae", "strain": "strain=MTCD1", "accession": "GCA_002207865.1", "taxid": 1513592, "species_taxid": 1513592, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1364, "total_fragments": 1367, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Colwellia piezophila", "strain": "strain=ATCC BAA-637", "accession": "GCA_000378625.1", "taxid": 211668, "species_taxid": 211668, "relation_to_type": "type", "validated": true, "ani": 82.8288, "matched_fragments": 942, "total_fragments": 1367, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Colwellia demingiae", "strain": "strain=ACAM 459", "accession": "GCA_007954275.1", "taxid": 89401, "species_taxid": 89401, "relation_to_type": "type", "validated": true, "ani": 81.0515, "matched_fragments": 820, "total_fragments": 1367, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Colwellia ponticola", "strain": "strain=OISW-25", "accession": "GCA_005885605.1", "taxid": 2304625, "species_taxid": 2304625, "relation_to_type": "type", "validated": true, "ani": 79.5225, 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95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 6.25, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002207865.1", "gtdb_species": "s__Colwellia marinimaniae", "ani": 100.0, "matched_fragments": 1364, "total_fragments": 1367, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.40", "min_intra_species_ani": "98.81", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.94", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_001440345.1", "gtdb_species": "s__Colwellia sp001440345", "ani": 94.5245, "matched_fragments": 1126, "total_fragments": 1367, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia", "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_013214175.1", "gtdb_species": "s__Colwellia sp013214175", "ani": 85.1298, "matched_fragments": 1060, "total_fragments": 1367, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.17", "min_intra_species_ani": "95.17", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000378625.1", "gtdb_species": "s__Colwellia piezophila", "ani": 82.8492, "matched_fragments": 940, "total_fragments": 1367, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", 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"min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_002836255.1", "gtdb_species": "s__Colwellia sp002836255", "ani": 81.0117, "matched_fragments": 859, "total_fragments": 1367, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia", "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_000012325.1", "gtdb_species": "s__Colwellia psychrerythraea_A", "ani": 80.8864, "matched_fragments": 809, "total_fragments": 1367, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.43", "min_intra_species_ani": "98.43", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_013215465.1", "gtdb_species": "s__Colwellia sp013215465", "ani": 79.3772, "matched_fragments": 421, "total_fragments": 1367, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.15", "min_intra_species_ani": "96.15", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.84", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_002733765.1", "gtdb_species": "s__Colwellia sp002733765", "ani": 78.9856, "matched_fragments": 349, "total_fragments": 1367, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.46", "min_intra_species_ani": "99.46", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.305, "cell_length": 0.2, "doubling_h": 0.613, "growth_tmp": 15.878, "optimum_tmp": 17.5, "optimum_ph": 7.5, "genome_size": 4965719.023, "gc_content": 38.45, "coding_genes": 4581.333, "rRNA16S_genes": 9.0, "tRNA_genes": 88.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": null, "facultative_respiration": 0.666, "anaerobic_respiration": 0.111, "aerobic_respiration": 0.222, "mesophilic_range_tmp": 0.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 1.0, "bacillus_cell_shape": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Colwellia", "marinimaniae" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }