{ "type": "genome", "identifier": "GCF_900176475.1", "organism": "Tropicibacter naphthalenivorans", "title": "Tropicibacter naphthalenivorans", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900176475.1", "bioproject": "PRJNA224116", "biosample": "SAMN04488093", "wgs_master": "FWXX00000000.1", "refseq_category": "na", "taxid": "441103", "species_taxid": "441103", "organism_name": "Tropicibacter naphthalenivorans", "infraspecific_name": "strain=DSM 19561", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/04/08", "asm_name": "IMG-taxon 2622736506 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900176475.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/176/475/GCF_900176475.1_IMG-taxon_2622736506_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": "4449490", "genome_size_ungapped": "4449440", "gc_percent": "63.000000", "replicon_count": "0", "scaffold_count": "32", "contig_count": "32", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2024-01-26", "total_gene_count": "4287", "protein_coding_gene_count": "4166", "non_coding_gene_count": "59", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-04-08", "dateModified": "2017-04-08", "datePublished": "2017-04-08", "_annotation": { "sample_count": 1, "sample_organism": [ "Tropicibacter naphthalenivorans" ], "sample_taxid": [ "441103" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.235 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4449490", "Number of Sequences": "32", "Longest Sequences (bp)": "898086", "N50 (bp)": "370416", "Gap Ratio (%)": "0.001124", "GCcontent (%)": "63.2", "Number of CDSs": "4227", "Average Protein Length": "316.5", "Coding Ratio (%)": "90.2", "Number of rRNAs": "4", "Number of tRNAs": "50", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Mameliella alba", "strain": "strain=CGMCC 1.7290", "accession": "GCA_900101505.1", "taxid": 561184, 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440, "total_fragments": 1469, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Antarcticimicrobium luteum", "strain": "strain=318-1", "accession": "GCA_004358185.1", "taxid": 2547397, "species_taxid": 2547397, "relation_to_type": "type", "validated": true, "ani": 78.2811, "matched_fragments": 496, "total_fragments": 1469, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leisingera daeponensis", "strain": "strain=DSM 23529", "accession": "GCA_000473145.1", "taxid": 405746, "species_taxid": 405746, "relation_to_type": "type", "validated": true, "ani": 78.278, "matched_fragments": 466, "total_fragments": 1469, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leisingera aquaemixtae", "strain": "strain=CECT 8399", "accession": "GCA_001458395.1", "taxid": 1396826, "species_taxid": 1396826, "relation_to_type": "type", "validated": true, "ani": 78.2539, "matched_fragments": 453, "total_fragments": 1469, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pelagimonas phthalicica", "strain": "strain=DSM 26923", "accession": "GCA_004364805.1", "taxid": 1037362, "species_taxid": 1037362, "relation_to_type": "type", "validated": true, "ani": 78.1718, "matched_fragments": 512, "total_fragments": 1469, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudooceanicola nanhaiensis", "strain": "strain=CGMCC 1.6293", "accession": "GCA_014645095.1", "taxid": 375761, "species_taxid": 375761, "relation_to_type": "type", "validated": true, "ani": 78.164, "matched_fragments": 410, "total_fragments": 1469, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudooceanicola nanhaiensis", "strain": "strain=DSM 18065", "accession": "GCA_000688295.1", "taxid": 375761, "species_taxid": 375761, "relation_to_type": "type", "validated": true, "ani": 78.143, "matched_fragments": 409, "total_fragments": 1469, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leisingera caerulea", "strain": "strain=DSM 24564", "accession": "GCA_000473325.1", "taxid": 506591, "species_taxid": 506591, "relation_to_type": "type", "validated": true, "ani": 78.124, "matched_fragments": 451, "total_fragments": 1469, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseovarius nubinhibens", "strain": "strain=ISM", "accession": "GCA_000152625.1", "taxid": 314263, "species_taxid": 314263, "relation_to_type": "type", "validated": true, "ani": 78.0301, "matched_fragments": 406, "total_fragments": 1469, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseivivax marinus", "strain": "strain=DSM 27511", "accession": "GCA_900109705.1", "taxid": 1379903, "species_taxid": 1379903, "relation_to_type": "type", "validated": true, "ani": 78.0017, "matched_fragments": 441, "total_fragments": 1469, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thalassococcus halodurans", "strain": 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"coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Tropicibacter", "naphthalenivorans" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }