{ "type": "genome", "identifier": "GCF_003346775.1", "organism": "Malaciobacter mytili LMG 24559", "title": "Malaciobacter mytili LMG 24559", "description": "na", "data type": "Genome sequencing and assembly", "organization": "USDA, ARS, WRRC", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003346775.1", "bioproject": "PRJNA224116", "biosample": "SAMN03737955", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "1032238", "species_taxid": "603050", "organism_name": "Malaciobacter mytili LMG 24559", "infraspecific_name": "strain=LMG 24559", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/07/31", "asm_name": "ASM334677v1", "asm_submitter": "USDA, ARS, WRRC", "gbrs_paired_asm": "GCA_003346775.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/346/775/GCF_003346775.1_ASM334677v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3037595", "genome_size_ungapped": "3037595", "gc_percent": "26.500000", "replicon_count": "2", "scaffold_count": "2", "contig_count": "2", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003346775.1-RS_2024_12_09", "annotation_date": "2024-12-09", "total_gene_count": "3014", "protein_coding_gene_count": "2926", "non_coding_gene_count": "84", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-07-31", "dateModified": "2018-07-31", "datePublished": "2018-07-31", "_annotation": { "sample_count": 1, "sample_organism": [ "Malaciobacter mytili LMG 24559" ], "sample_taxid": [ "1032238" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Spain: Tarragona, Catalonia" ], "sample_host_location_id": [], "data_size": "0.800 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)": "3037595", "Number of Sequences": "2", "Longest Sequences (bp)": "2867150", "N50 (bp)": "2867150", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "26.5", "Number of CDSs": "2938", "Average Protein Length": "319.6", "Coding Ratio (%)": "92.7", "Number of rRNAs": "12", "Number of tRNAs": "63", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Malaciobacter mytili", "strain": "strain=LMG 24559", "accession": "GCA_003346775.1", "taxid": 603050, "species_taxid": 603050, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1005, "total_fragments": 1011, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Malaciobacter mytili", "strain": "strain=CECT 7386", "accession": "GCA_004116555.1", "taxid": 603050, "species_taxid": 603050, "relation_to_type": "type", "validated": true, "ani": 99.927, "matched_fragments": 935, "total_fragments": 1011, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Malaciobacter halophilus", "strain": "strain=DSM 18005", "accession": "GCA_002837275.1", "taxid": 197482, "species_taxid": 197482, "relation_to_type": "type", "validated": true, "ani": 82.4053, "matched_fragments": 628, "total_fragments": 1011, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Malaciobacter canalis", "strain": "strain=LMG 29148", "accession": "GCA_008000835.1", "taxid": 1912871, "species_taxid": 1912871, "relation_to_type": "type", "validated": true, "ani": 82.3459, "matched_fragments": 653, "total_fragments": 1011, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Malaciobacter canalis", "strain": "strain=F138-33", "accession": "GCA_002723485.1", "taxid": 1912871, "species_taxid": 1912871, "relation_to_type": "type", "validated": true, "ani": 82.288, "matched_fragments": 635, "total_fragments": 1011, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Malaciobacter marinus", "strain": "strain=JCM 15502", "accession": "GCA_003544855.1", "taxid": 505249, "species_taxid": 505249, "relation_to_type": "type", "validated": true, "ani": 82.2566, "matched_fragments": 659, "total_fragments": 1011, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Malaciobacter molluscorum", "strain": "strain=CECT 7696", "accession": "GCA_003544935.1", "taxid": 1032072, "species_taxid": 1032072, "relation_to_type": "type", "validated": true, "ani": 81.8212, "matched_fragments": 606, "total_fragments": 1011, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Malaciobacter molluscorum", "strain": "strain=F98-3", "accession": "GCA_002701265.1", "taxid": 1032072, "species_taxid": 1032072, "relation_to_type": "type", "validated": true, "ani": 81.6842, "matched_fragments": 586, "total_fragments": 1011, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Arcobacter ellisii", "strain": "strain=LMG 26155", "accession": "GCA_003544915.1", "taxid": 913109, "species_taxid": 913109, "relation_to_type": "type", "validated": true, "ani": 80.0481, "matched_fragments": 474, "total_fragments": 1011, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003346775.1", "gtdb_species": "s__Malaciobacter mytili", "ani": 100.0, "matched_fragments": 1005, "total_fragments": 1011, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.45", "min_intra_species_ani": "98.91", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_002837275.1", "gtdb_species": "s__Malaciobacter halophilus", "ani": 82.4307, "matched_fragments": 626, "total_fragments": 1011, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003544855.1", "gtdb_species": "s__Malaciobacter marinus", "ani": 82.2559, "matched_fragments": 661, "total_fragments": 1011, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.03", "min_intra_species_ani": "95.41", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.86", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCA_004116725.1", "gtdb_species": "s__Malaciobacter sp004116725", "ani": 81.987, "matched_fragments": 597, "total_fragments": 1011, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter", "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_003544935.1", "gtdb_species": "s__Malaciobacter molluscorum", "ani": 81.8275, "matched_fragments": 606, "total_fragments": 1011, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.44", "min_intra_species_ani": "98.88", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.91", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_004116495.1", "gtdb_species": "s__Malaciobacter sp004116495", "ani": 81.7522, "matched_fragments": 556, "total_fragments": 1011, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter", "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_003544915.1", "gtdb_species": "s__Aliarcobacter ellisii", "ani": 80.0016, "matched_fragments": 473, "total_fragments": 1011, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.73", "min_intra_species_ani": "97.46", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.84", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_004214815.1", "gtdb_species": "s__Aliarcobacter thereius", "ani": 78.8211, "matched_fragments": 319, "total_fragments": 1011, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.14", "min_intra_species_ani": "98.62", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.89", "num_clustered_genomes": 8, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": null, "growth_tmp": null, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_genome_taxon": [ "Malaciobacter", "mytili", "LMG", "24559" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }