{ "type": "genome", "identifier": "GCF_001294685.1", "organism": "Idiomarina abyssalis", "title": "Idiomarina abyssalis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of New Hampshire at Manchester", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001294685.1", "bioproject": "PRJNA224116", "biosample": "SAMN03801268", "wgs_master": "LGOW00000000.1", "refseq_category": "na", "taxid": "86102", "species_taxid": "86102", "organism_name": "Idiomarina abyssalis", "infraspecific_name": "strain=KMM 227", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2015/09/18", "asm_name": "IdioAbyss1", "asm_submitter": "University of New Hampshire at Manchester", "gbrs_paired_asm": "GCA_001294685.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/294/685/GCF_001294685.1_IdioAbyss1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2684812", "genome_size_ungapped": "2684812", "gc_percent": "47.000000", "replicon_count": "0", "scaffold_count": "68", "contig_count": "68", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001294685.1-RS_2024_08_05", "annotation_date": "2024-08-05", "total_gene_count": "2627", "protein_coding_gene_count": "2547", "non_coding_gene_count": "62", "pubmed_id": "26514763" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2015-09-18", "dateModified": "2015-09-18", "datePublished": "2015-09-18", "_annotation": { "sample_count": 1, "sample_organism": [ "Idiomarina abyssalis" ], "sample_taxid": [ "86102" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Pacific Ocean: North-Western" ], "sample_host_location_id": [], "data_size": "0.769 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)": "2684812", "Number of Sequences": "68", "Longest Sequences (bp)": "983913", "N50 (bp)": "170438", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "47.2", "Number of CDSs": "2525", "Average Protein Length": "328.6", "Coding Ratio (%)": "92.7", "Number of rRNAs": "4", "Number of tRNAs": "53", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Idiomarina abyssalis", "strain": "strain=KMM 227", "accession": "GCA_001294685.1", "taxid": 86102, "species_taxid": 86102, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 876, "total_fragments": 877, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Idiomarina abyssalis", "strain": "strain=KMM 227", "accession": "GCA_900116625.1", "taxid": 86102, "species_taxid": 86102, "relation_to_type": "type", "validated": true, "ani": 99.982, "matched_fragments": 875, "total_fragments": 877, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Idiomarina ramblicola", "strain": "strain=R22", "accession": "GCA_003987255.1", "taxid": 263724, "species_taxid": 263724, "relation_to_type": "type", "validated": true, "ani": 85.9543, "matched_fragments": 682, "total_fragments": 877, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Idiomarina loihiensis", "strain": "strain=L2TR", "accession": "GCA_000008465.1", "taxid": 135577, "species_taxid": 135577, "relation_to_type": "type", "validated": true, "ani": 85.0842, "matched_fragments": 641, "total_fragments": 877, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Idiomarina zobellii", "strain": "strain=KMM 231", "accession": "GCA_001294745.1", "taxid": 86103, "species_taxid": 86103, "relation_to_type": "type", "validated": true, "ani": 82.2073, "matched_fragments": 400, "total_fragments": 877, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Idiomarina piscisalsi", "strain": "strain=TPS4-2", "accession": "GCA_003987095.1", "taxid": 1096243, "species_taxid": 1096243, "relation_to_type": "type", "validated": true, "ani": 81.3078, "matched_fragments": 409, "total_fragments": 877, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Idiomarina fontislapidosi", "strain": "strain=F23", "accession": "GCA_003987025.1", "taxid": 263723, "species_taxid": 263723, "relation_to_type": "type", "validated": true, "ani": 78.507, "matched_fragments": 128, "total_fragments": 877, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudidiomarina aestuarii", "strain": "strain=KYW314", "accession": "GCA_003987355.1", "taxid": 624146, "species_taxid": 624146, "relation_to_type": "suspected-type", "validated": true, "ani": 77.2927, "matched_fragments": 73, "total_fragments": 877, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aliidiomarina halalkaliphila", "strain": "strain=IM 1326", "accession": "GCA_007096385.1", "taxid": 2593535, "species_taxid": 2593535, "relation_to_type": "type", "validated": true, "ani": 76.9405, "matched_fragments": 53, "total_fragments": 877, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900116625.1", "gtdb_species": "s__Idiomarina abyssalis", "ani": 99.982, "matched_fragments": 875, "total_fragments": 877, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.70", "min_intra_species_ani": "97.34", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.79", "num_clustered_genomes": 25, "status": "conclusive" }, { "accession": "GCF_003987255.1", "gtdb_species": "s__Idiomarina ramblicola", "ani": 85.9543, "matched_fragments": 682, "total_fragments": 877, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina", "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_000008465.1", "gtdb_species": "s__Idiomarina loihiensis", "ani": 85.0842, "matched_fragments": 641, "total_fragments": 877, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.95", "min_intra_species_ani": "95.80", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.86", "num_clustered_genomes": 17, "status": "-" }, { "accession": "GCF_900100855.1", "gtdb_species": "s__Idiomarina zobellii", "ani": 82.3396, "matched_fragments": 395, "total_fragments": 877, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.93", "min_intra_species_ani": "96.27", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.85", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_002808045.1", "gtdb_species": "s__Idiomarina sp002808045", "ani": 81.2887, "matched_fragments": 421, "total_fragments": 877, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.72", "min_intra_species_ani": "96.72", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003987095.1", "gtdb_species": "s__Idiomarina piscisalsi", "ani": 81.2849, "matched_fragments": 411, "total_fragments": 877, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina", "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_002211765.1", "gtdb_species": "s__Idiomarina piscisalsi_A", "ani": 80.832, "matched_fragments": 384, "total_fragments": 877, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.69", "min_intra_species_ani": "97.69", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_004362895.1", "gtdb_species": "s__Idiomarina sp002729675", "ani": 80.4824, "matched_fragments": 219, "total_fragments": 877, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.61", "min_intra_species_ani": "97.37", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.80", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_003226255.1", "gtdb_species": "s__Idiomarina fontislapidosi", "ani": 78.4357, "matched_fragments": 126, "total_fragments": 877, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina", "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_003987355.1", "gtdb_species": "s__Pseudidiomarina aestuarii", "ani": 77.2931, "matched_fragments": 73, "total_fragments": 877, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina", "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": -0.266, "cell_length": 0.272, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": 32.333, "optimum_ph": 7.729, "genome_size": 2675401.0, "gc_content": 47.82, "coding_genes": 2491.7, "rRNA16S_genes": 4.0, "tRNA_genes": 56.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.642, "range_salinity": 1.0, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.933, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.066, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Idiomarina", "abyssalis" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }