{ "type": "genome", "identifier": "GCF_900182605.1", "organism": "Saccharicrinis carchari", "title": "Saccharicrinis carchari", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900182605.1", "bioproject": "PRJNA224116", "biosample": "SAMN06265379", "wgs_master": "FXTB00000000.1", "refseq_category": "reference genome", "taxid": "1168039", "species_taxid": "1168039", "organism_name": "Saccharicrinis carchari", "infraspecific_name": "strain=DSM 27040", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/07/12", "asm_name": "IMG-taxon 2724679709 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900182605.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/182/605/GCF_900182605.1_IMG-taxon_2724679709_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": "4644534", "genome_size_ungapped": "4643731", "gc_percent": "41.000000", "replicon_count": "0", "scaffold_count": "31", "contig_count": "31", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900182605.1-RS_2024_10_23", "annotation_date": "2024-10-23", "total_gene_count": "3557", "protein_coding_gene_count": "3474", "non_coding_gene_count": "58", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-07-12", "dateModified": "2019-07-12", "datePublished": "2019-07-12", "_annotation": { "sample_count": 1, "sample_organism": [ "Saccharicrinis carchari" ], "sample_taxid": [ "1168039" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.317 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)": "4644534", "Number of Sequences": "31", "Longest Sequences (bp)": "1287342", "N50 (bp)": "524340", "Gap Ratio (%)": "0.017289", "GCcontent (%)": "41.1", "Number of CDSs": "3463", "Average Protein Length": "380.1", "Coding Ratio (%)": "85.0", "Number of rRNAs": "3", "Number of tRNAs": "48", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Saccharicrinis carchari", "strain": "strain=DSM 27040", "accession": "GCA_900182605.1", "taxid": 1168039, "species_taxid": 1168039, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1533, "total_fragments": 1536, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Saccharicrinis fermentans", "strain": "strain=DSM 9555", "accession": "GCA_000517085.1", "taxid": 982, "species_taxid": 982, "relation_to_type": "type", "validated": true, "ani": 77.1262, "matched_fragments": 171, "total_fragments": 1536, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Saccharicrinis fermentans", "strain": "strain=JCM 21142", "accession": "GCA_000583675.1", "taxid": 982, "species_taxid": 982, "relation_to_type": "type", "validated": true, "ani": 77.1235, "matched_fragments": 170, "total_fragments": 1536, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Labilibacter marinus", "strain": "strain=Y11", "accession": "GCA_001659685.2", "taxid": 1477105, "species_taxid": 1477105, "relation_to_type": "type", "validated": true, "ani": 76.9688, "matched_fragments": 167, "total_fragments": 1536, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Labilibacter sediminis", "strain": "strain=CG51", "accession": "GCA_005877885.1", "taxid": 2570926, "species_taxid": 2570926, "relation_to_type": "type", "validated": true, "ani": 76.8104, "matched_fragments": 154, "total_fragments": 1536, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Saccharicrinis aurantiacus", "strain": "strain=HQYD1", "accession": "GCA_001660705.2", "taxid": 1849719, "species_taxid": 1849719, "relation_to_type": "type", "validated": true, "ani": 76.604, "matched_fragments": 91, "total_fragments": 1536, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Carboxylicivirga mesophila", "strain": "strain=JCM 18290", "accession": "GCA_018271975.1", "taxid": 1166478, "species_taxid": 1166478, "relation_to_type": "type", "validated": true, "ani": 75.8068, "matched_fragments": 59, "total_fragments": 1536, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900182605.1", "gtdb_species": "s__Saccharicrinis carchari", "ani": 100.0, "matched_fragments": 1534, "total_fragments": 1536, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Saccharicrinis", "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_000517085.1", "gtdb_species": "s__Saccharicrinis fermentans", "ani": 77.1263, "matched_fragments": 172, "total_fragments": 1536, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Saccharicrinis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.97", "min_intra_species_ani": "99.97", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001659685.2", "gtdb_species": "s__Saccharicrinis marinus", "ani": 76.9837, "matched_fragments": 166, "total_fragments": 1536, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Saccharicrinis", "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_005877885.1", "gtdb_species": "s__Saccharicrinis sediminis", "ani": 76.8104, "matched_fragments": 154, "total_fragments": 1536, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Saccharicrinis", "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_001660705.2", "gtdb_species": "s__Saccharicrinis aurantiacus", "ani": 76.5963, "matched_fragments": 90, "total_fragments": 1536, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Saccharicrinis", "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_018271975.1", "gtdb_species": "s__Carboxylicivirga mesophila", "ani": 75.8068, "matched_fragments": 59, "total_fragments": 1536, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Carboxylicivirga", "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": null, "cell_length": null, "doubling_h": null, "growth_tmp": 30.0, "optimum_tmp": 28.0, "optimum_ph": null, "genome_size": 4644534.0, "gc_content": 37.6, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": null, "motility": null, "range_salinity": null, "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": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_genome_taxon": [ "Saccharicrinis", "carchari" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }