{ "type": "genome", "identifier": "GCF_000299895.1", "organism": "Idiomarina xiamenensis 10-D-4", "title": "Idiomarina xiamenensis 10-D-4", "description": "na", "data type": "Genome sequencing and assembly", "organization": "The Third Institute of State Oceanic Administration (SOA)", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000299895.1", "bioproject": "PRJNA224116", "biosample": "SAMN02471167", "wgs_master": "AMRG00000000.1", "refseq_category": "reference genome", "taxid": "740709", "species_taxid": "1207041", "organism_name": "Idiomarina xiamenensis 10-D-4", "infraspecific_name": "strain=10-D-4", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2012/09/27", "asm_name": "ASM29989v1", "asm_submitter": "The Third Institute of State Oceanic Administration (SOA)", "gbrs_paired_asm": "GCA_000299895.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/299/895/GCF_000299895.1_ASM29989v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2899282", "genome_size_ungapped": "2899282", "gc_percent": "49.500000", "replicon_count": "0", "scaffold_count": "77", "contig_count": "77", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000299895.1-RS_2024_03_20", "annotation_date": "2024-03-20", "total_gene_count": "2726", "protein_coding_gene_count": "2630", "non_coding_gene_count": "50", "pubmed_id": "23209204" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2012-09-27", "dateModified": "2012-09-27", "datePublished": "2012-09-27", "_annotation": { "sample_count": 1, "sample_organism": [ "Idiomarina xiamenensis 10-D-4" ], "sample_taxid": [ "740709" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China" ], "sample_host_location_id": [], "data_size": "0.828 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)": "2899282", "Number of Sequences": "77", "Longest Sequences (bp)": "284251", "N50 (bp)": "149450", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "49.5", "Number of CDSs": "2649", "Average Protein Length": "328.0", "Coding Ratio (%)": "89.9", "Number of rRNAs": "3", "Number of tRNAs": "43", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Idiomarina xiamenensis", "strain": "strain=10-D-4", "accession": "GCA_000299895.1", "taxid": 1207041, "species_taxid": 1207041, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 934, "total_fragments": 937, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Idiomarina baltica", "strain": "strain=OS145", "accession": "GCA_000152885.1", "taxid": 190892, "species_taxid": 190892, "relation_to_type": "type", "validated": true, "ani": 79.0876, "matched_fragments": 83, "total_fragments": 937, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudidiomarina tainanensis", "strain": "strain=PIN1", "accession": "GCA_004214835.1", "taxid": 502365, "species_taxid": 502365, "relation_to_type": "type", "validated": true, "ani": 78.4143, "matched_fragments": 91, "total_fragments": 937, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudidiomarina maritima", "strain": "strain=CGMCC 1.7285", "accession": "GCA_900115255.1", "taxid": 519453, "species_taxid": 519453, "relation_to_type": "type", "validated": true, "ani": 78.3543, "matched_fragments": 91, "total_fragments": 937, "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": 78.2693, "matched_fragments": 62, "total_fragments": 937, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudidiomarina donghaiensis", "strain": "strain=908033", "accession": "GCA_003987405.1", "taxid": 519452, "species_taxid": 519452, "relation_to_type": "type", "validated": true, "ani": 78.1553, "matched_fragments": 89, "total_fragments": 937, "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": 78.1261, "matched_fragments": 85, "total_fragments": 937, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Idiomarina fontislapidosi", "strain": "strain=CECT 5859", "accession": "GCA_003226255.1", "taxid": 263723, "species_taxid": 263723, "relation_to_type": "type", "validated": true, "ani": 78.019, "matched_fragments": 82, "total_fragments": 937, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Idiomarina aquatica", "strain": "strain=SN-14", "accession": "GCA_003987185.1", "taxid": 1327752, "species_taxid": 1327752, "relation_to_type": "type", "validated": true, "ani": 77.9936, "matched_fragments": 108, "total_fragments": 937, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudidiomarina donghaiensis", "strain": "strain=CGMCC 1.7284", "accession": "GCA_900116895.1", "taxid": 519452, "species_taxid": 519452, "relation_to_type": "type", "validated": true, "ani": 77.9354, "matched_fragments": 88, "total_fragments": 937, "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": 77.8581, "matched_fragments": 67, "total_fragments": 937, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudidiomarina planktonica", "strain": "strain=CGMCC 1.12458", "accession": "GCA_900177775.1", "taxid": 1323738, "species_taxid": 1323738, "relation_to_type": "type", "validated": true, "ani": 77.4975, "matched_fragments": 101, "total_fragments": 937, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudidiomarina planktonica", "strain": "strain=TS-T11", "accession": "GCA_003987425.1", "taxid": 1323738, "species_taxid": 1323738, "relation_to_type": "type", "validated": true, "ani": 77.4786, "matched_fragments": 99, "total_fragments": 937, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aliidiomarina maris", "strain": "strain=CF12-14", "accession": "GCA_003987335.1", "taxid": 531312, "species_taxid": 531312, "relation_to_type": "type", "validated": true, "ani": 77.3804, "matched_fragments": 71, "total_fragments": 937, "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": 76.7824, "matched_fragments": 52, "total_fragments": 937, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000299895.1", "gtdb_species": "s__Idiomarina xiamenensis", "ani": 100.0, "matched_fragments": 934, "total_fragments": 937, "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": "conclusive" }, { "accession": "GCF_000152885.1", "gtdb_species": "s__Idiomarina baltica", "ani": 79.0876, "matched_fragments": 83, "total_fragments": 937, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.48", "min_intra_species_ani": "98.19", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.79", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_001870515.1", "gtdb_species": "s__Idiomarina sp001870515", "ani": 78.443, "matched_fragments": 89, "total_fragments": 937, "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_004214835.1", "gtdb_species": "s__Pseudidiomarina tainanensis", "ani": 78.4318, "matched_fragments": 90, "total_fragments": 937, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.72", "min_intra_species_ani": "97.72", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900104245.1", "gtdb_species": "s__Pseudidiomarina indica", "ani": 78.3906, "matched_fragments": 54, "total_fragments": 937, "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": "-" }, { "accession": "GCF_003226255.1", "gtdb_species": "s__Idiomarina fontislapidosi", "ani": 78.019, "matched_fragments": 82, "total_fragments": 937, "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_900116895.1", "gtdb_species": "s__Pseudidiomarina donghaiensis", "ani": 78.0005, "matched_fragments": 87, "total_fragments": 937, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_004362895.1", "gtdb_species": "s__Idiomarina sp002729675", "ani": 77.9656, "matched_fragments": 99, "total_fragments": 937, "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_003987355.1", "gtdb_species": "s__Pseudidiomarina aestuarii", "ani": 77.8581, "matched_fragments": 67, "total_fragments": 937, "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": "-" }, { "accession": "GCF_001418345.1", "gtdb_species": "s__Pseudidiomarina woesei", "ani": 77.8333, "matched_fragments": 93, "total_fragments": 937, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina", "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": "GCA_002685255.1", "gtdb_species": "s__Idiomarina sp002685255", "ani": 77.6902, "matched_fragments": 75, "total_fragments": 937, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.23", "min_intra_species_ani": "98.54", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.91", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_002279005.1", "gtdb_species": "s__Pseudidiomarina sp002279005", "ani": 77.6016, "matched_fragments": 70, "total_fragments": 937, "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": "-" }, { "accession": "GCF_900177775.1", "gtdb_species": "s__Pseudidiomarina planktonica", "ani": 77.4975, "matched_fragments": 101, "total_fragments": 937, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina", "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_003987335.1", "gtdb_species": "s__Aliidiomarina maris", "ani": 77.3804, "matched_fragments": 71, "total_fragments": 937, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.15", "min_intra_species_ani": "98.30", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.95", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_009734345.1", "gtdb_species": "s__Pseudidiomarina andamanensis", "ani": 77.3542, "matched_fragments": 93, "total_fragments": 937, "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": "-" }, { "accession": "GCF_007096385.1", "gtdb_species": "s__Aliidiomarina sp007096385", "ani": 76.7895, "matched_fragments": 53, "total_fragments": 937, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina", "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_015354615.1", "gtdb_species": "s__Aliidiomarina sp015354615", "ani": 76.757, "matched_fragments": 62, "total_fragments": 937, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina", "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": 29.875, "optimum_tmp": 32.333, "optimum_ph": 7.729, "genome_size": 2574576.461, "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": 0.052, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.947, "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", "xiamenensis", "10-D-4" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }