{ "type": "genome", "identifier": "GCF_019623905.1", "organism": "Neotabrizicola shimadae", "title": "Neotabrizicola shimadae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Tokyo Metropolitan University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_019623905.1", "bioproject": "PRJNA224116", "biosample": "SAMN17704904", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "2807096", "species_taxid": "2807096", "organism_name": "Neotabrizicola shimadae", "infraspecific_name": "strain=N10", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/08/16", "asm_name": "ASM1962390v1", "asm_submitter": "Tokyo Metropolitan University", "gbrs_paired_asm": "GCA_019623905.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/019/623/905/GCF_019623905.1_ASM1962390v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4392453", "genome_size_ungapped": "4392453", "gc_percent": "66.500000", "replicon_count": "5", "scaffold_count": "5", "contig_count": "5", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_019623905.1-RS_2024_09_20", "annotation_date": "2024-09-20", "total_gene_count": "4251", "protein_coding_gene_count": "4175", "non_coding_gene_count": "57", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-08-16", "dateModified": "2021-08-16", "datePublished": "2021-08-16", "_annotation": { "sample_count": 1, "sample_organism": [ "Neotabrizicola shimadae" ], "sample_taxid": [ "2807096" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Japan: Nakabusa Hotspring Nagano" ], "sample_host_location_id": [], "data_size": "1.201 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)": "4392453", "Number of Sequences": "5", "Longest Sequences (bp)": "4154010", "N50 (bp)": "4154010", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "66.6", "Number of CDSs": "4242", "Average Protein Length": "316.3", "Coding Ratio (%)": "91.6", "Number of rRNAs": "6", "Number of tRNAs": "52", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Rhodobacter amnigenus", "strain": "strain=HSP-20", "accession": "GCA_019130055.1", "taxid": 2852097, "species_taxid": 2852097, "relation_to_type": "type", "validated": true, "ani": 80.077, "matched_fragments": 644, "total_fragments": 1461, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodobacter amnigenus", "strain": "strain=HSP-20", "accession": "GCA_009908265.2", "taxid": 2852097, "species_taxid": 2852097, "relation_to_type": "type", "validated": true, "ani": 80.0719, "matched_fragments": 645, "total_fragments": 1461, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodobacter flagellatus", "strain": "strain=SYSU G03088", "accession": "GCA_008271465.1", "taxid": 2593021, "species_taxid": 2593021, "relation_to_type": "type", "validated": true, "ani": 80.002, "matched_fragments": 659, "total_fragments": 1461, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodobacter thermarum", "strain": "strain=YIM 73036", "accession": "GCA_003574395.1", "taxid": 2670345, "species_taxid": 2670345, "relation_to_type": "type", "validated": true, "ani": 79.8291, "matched_fragments": 642, "total_fragments": 1461, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodobacter ruber", "strain": "strain=CCP-1", "accession": "GCA_009908315.1", "taxid": 1985673, "species_taxid": 1985673, "relation_to_type": "type", "validated": true, "ani": 79.692, "matched_fragments": 631, "total_fragments": 1461, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodobacter calidifons", "strain": "strain=M37P", "accession": "GCA_011174775.1", "taxid": 2715277, "species_taxid": 2715277, "relation_to_type": "type", "validated": true, "ani": 79.6881, "matched_fragments": 669, "total_fragments": 1461, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cereibacter changlensis", "strain": "strain=JA139", "accession": "GCA_003034985.1", "taxid": 402884, "species_taxid": 402884, "relation_to_type": "type", "validated": true, "ani": 79.5709, "matched_fragments": 604, "total_fragments": 1461, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cereibacter changlensis", "strain": "strain=DSM 18774", "accession": "GCA_003254335.1", "taxid": 402884, "species_taxid": 402884, "relation_to_type": "type", "validated": true, "ani": 79.4771, "matched_fragments": 632, "total_fragments": 1461, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmobacter caeruleus", "strain": "strain=N8", "accession": "GCA_008271655.1", "taxid": 2595004, "species_taxid": 2595004, "relation_to_type": "type", "validated": true, "ani": 79.4458, "matched_fragments": 600, "total_fragments": 1461, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmobacter straminiformis", "strain": "strain=CAM-8", "accession": "GCA_014243445.1", "taxid": 2045119, "species_taxid": 2045119, "relation_to_type": "type", "validated": true, "ani": 79.2087, "matched_fragments": 607, "total_fragments": 1461, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cereibacter sediminicola", "strain": "strain=JA983", "accession": "GCA_007668225.1", "taxid": 2584941, "species_taxid": 2584941, "relation_to_type": "type", "validated": true, "ani": 79.1206, "matched_fragments": 518, "total_fragments": 1461, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmobacter aquatilis", "strain": "strain=DSM 3857", "accession": "GCA_900110025.1", "taxid": 933059, "species_taxid": 933059, "relation_to_type": "type", "validated": true, "ani": 79.1174, "matched_fragments": 597, "total_fragments": 1461, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmobacter caeni", "strain": "strain=DSM 21823", "accession": "GCA_003054195.1", "taxid": 589035, "species_taxid": 589035, "relation_to_type": "type", "validated": true, "ani": 79.1133, "matched_fragments": 568, "total_fragments": 1461, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmobacter caeni", "strain": "strain=CGMCC 1.7745", "accession": "GCA_007830625.1", "taxid": 589035, "species_taxid": 589035, "relation_to_type": "type", "validated": true, "ani": 79.0482, "matched_fragments": 578, "total_fragments": 1461, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmobacter lutimaris", "strain": "strain=YJ-T1-11", "accession": "GCA_003570715.1", "taxid": 2306023, "species_taxid": 2306023, "relation_to_type": "type", "validated": true, "ani": 79.0339, "matched_fragments": 600, "total_fragments": 1461, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tabrizicola algicola", "strain": "strain=ETT8", "accession": "GCA_010915705.1", "taxid": 2709381, "species_taxid": 2709381, "relation_to_type": "type", "validated": true, "ani": 79.0322, "matched_fragments": 556, "total_fragments": 1461, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmobacter aquarius", "strain": "strain=HYN0069", "accession": "GCA_003060865.1", "taxid": 2169400, "species_taxid": 2169400, "relation_to_type": "type", "validated": true, "ani": 78.9666, "matched_fragments": 544, "total_fragments": 1461, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cereibacter sphaeroides", "strain": "strain=2.4.1", "accession": "GCA_000273405.1", "taxid": 1063, "species_taxid": 1063, "relation_to_type": "type", "validated": true, "ani": 78.9564, "matched_fragments": 531, "total_fragments": 1461, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Frigidibacter albus", "strain": "strain=CGMCC 1.13995", "accession": "GCA_014640395.1", "taxid": 1465486, "species_taxid": 1465486, "relation_to_type": "type", "validated": true, "ani": 78.7141, "matched_fragments": 548, "total_fragments": 1461, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Frigidibacter albus", "strain": "strain=SP32", "accession": "GCA_009881095.1", "taxid": 1465486, "species_taxid": 1465486, "relation_to_type": "type", "validated": true, "ani": 78.6385, "matched_fragments": 555, 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"below_threshold" }, { "organism_name": "Paracoccus aerius", "strain": "strain=KCTC 42845", "accession": "GCA_016757275.1", "taxid": 1915382, "species_taxid": 1915382, "relation_to_type": "type", "validated": true, "ani": 78.375, "matched_fragments": 377, "total_fragments": 1461, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_013693875.1", "gtdb_species": "s__SSD5 sp013693875", "ani": 86.5387, "matched_fragments": 1040, "total_fragments": 1461, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SSD5", "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_011043545.1", "gtdb_species": "s__JAAKGP01 sp011043545", "ani": 80.5881, "matched_fragments": 701, "total_fragments": 1461, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAAKGP01", "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": "GCA_014859945.1", "gtdb_species": "s__UBA1943 sp014859945", "ani": 80.2108, "matched_fragments": 576, "total_fragments": 1461, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA1943", "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": "GCA_009908265.2", "gtdb_species": "s__Gemmobacter_B sp009908265", "ani": 80.0792, "matched_fragments": 643, 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