{ "type": "genome", "identifier": "GCF_004346265.1", "organism": "Thermomonas haemolytica", "title": "Thermomonas haemolytica", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004346265.1", "bioproject": "PRJNA224116", "biosample": "SAMN10363322", "wgs_master": "SMAP00000000.1", "refseq_category": "reference genome", "taxid": "141949", "species_taxid": "141949", "organism_name": "Thermomonas haemolytica", "infraspecific_name": "strain=DSM 13605", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/03/11", "asm_name": "ASM434626v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_004346265.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/346/265/GCF_004346265.1_ASM434626v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2586957", "genome_size_ungapped": "2586957", "gc_percent": "70.000000", "replicon_count": "0", "scaffold_count": "23", "contig_count": "23", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004346265.1-RS_2024_05_12", "annotation_date": "2024-05-12", "total_gene_count": "2432", "protein_coding_gene_count": "2351", "non_coding_gene_count": "52", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-03-11", "dateModified": "2019-03-11", "datePublished": "2019-03-11", "_annotation": { "sample_count": 1, "sample_organism": [ "Thermomonas haemolytica" ], "sample_taxid": [ "141949" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Finland" ], "sample_host_location_id": [], "data_size": "0.691 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)": "2586957", "Number of Sequences": "23", "Longest Sequences (bp)": "682228", "N50 (bp)": "288138", "Gap Ratio (%)": "0.000425", "GCcontent (%)": "70.0", "Number of CDSs": "2398", "Average Protein Length": "331.7", "Coding Ratio (%)": "92.2", "Number of rRNAs": "1", "Number of tRNAs": "54", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Thermomonas haemolytica", "strain": "strain=DSM 13605", "accession": "GCA_004346265.1", "taxid": 141949, "species_taxid": 141949, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 850, "total_fragments": 851, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Thermomonas haemolytica", "strain": "strain=LMG 19653", "accession": "GCA_006352395.1", "taxid": 141949, "species_taxid": 141949, "relation_to_type": "type", "validated": true, "ani": 99.9389, "matched_fragments": 806, "total_fragments": 851, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Thermomonas fusca", "strain": "strain=DSM 15424", "accession": "GCA_000423885.1", "taxid": 215690, "species_taxid": 215690, "relation_to_type": "type", "validated": true, "ani": 85.62, "matched_fragments": 684, "total_fragments": 851, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thermomonas aquatica", "strain": "strain=SY21", "accession": "GCA_006337105.1", "taxid": 2202149, "species_taxid": 2202149, "relation_to_type": "type", "validated": true, "ani": 84.4076, "matched_fragments": 621, "total_fragments": 851, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thermomonas hydrothermalis", "strain": "strain=DSM 14834", "accession": "GCA_900129205.1", "taxid": 213588, "species_taxid": 213588, "relation_to_type": "type", "validated": true, "ani": 83.4851, "matched_fragments": 586, "total_fragments": 851, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vulcaniibacterium gelatinicum", "strain": "strain=R-5-52-3", "accession": "GCA_008033445.1", "taxid": 2598725, "species_taxid": 2598725, "relation_to_type": "type", "validated": true, "ani": 82.8275, "matched_fragments": 532, "total_fragments": 851, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thermomonas carbonis", "strain": "strain=KCTC 42013", "accession": "GCA_014652775.1", "taxid": 1463158, "species_taxid": 1463158, "relation_to_type": "type", "validated": true, "ani": 82.3827, "matched_fragments": 606, "total_fragments": 851, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Luteimonas lumbrici", "strain": "strain=1.1416", "accession": "GCA_006476065.1", "taxid": 2559601, "species_taxid": 2559601, "relation_to_type": "type", "validated": true, "ani": 82.2427, "matched_fragments": 488, "total_fragments": 851, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Luteimonas arsenica", "strain": "strain=26-35", "accession": "GCA_004352825.1", "taxid": 1586242, "species_taxid": 1586242, "relation_to_type": "type", "validated": true, "ani": 81.6961, "matched_fragments": 524, "total_fragments": 851, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Luteimonas aquatica", "strain": "strain=RIB1-20", "accession": "GCA_022662575.1", "taxid": 450364, "species_taxid": 450364, "relation_to_type": "type", "validated": true, "ani": 81.631, "matched_fragments": 565, "total_fragments": 851, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Luteimonas padinae", "strain": "strain=KCTC 52403", "accession": "GCA_014652935.1", "taxid": 1714359, "species_taxid": 1714359, "relation_to_type": "type", "validated": true, "ani": 81.6167, "matched_fragments": 529, "total_fragments": 851, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Luteimonas colneyensis", "strain": "strain=Sa2BVA3", "accession": "GCA_014836665.1", "taxid": 2762230, "species_taxid": 2762230, "relation_to_type": "type", "validated": true, "ani": 81.4749, "matched_fragments": 521, "total_fragments": 851, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lysobacter chinensis", "strain": "strain=TLK-CK17", "accession": "GCA_021725675.1", "taxid": 2912247, "species_taxid": 2912247, "relation_to_type": "type", "validated": true, "ani": 80.8728, "matched_fragments": 501, "total_fragments": 851, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lysobacter luteus", "strain": "strain=CECT 30171", "accession": "GCA_907164845.1", "taxid": 2822368, "species_taxid": 2822368, "relation_to_type": "type", "validated": true, "ani": 80.8704, "matched_fragments": 482, "total_fragments": 851, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004346265.1", "gtdb_species": "s__Thermomonas haemolytica", "ani": 100.0, "matched_fragments": 850, "total_fragments": 851, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCA_017305095.1", "gtdb_species": "s__Thermomonas sp017305095", "ani": 93.1173, "matched_fragments": 746, "total_fragments": 851, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas", "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_014395425.1", "gtdb_species": "s__Thermomonas brevis", "ani": 86.611, "matched_fragments": 683, "total_fragments": 851, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas", "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_014678725.1", "gtdb_species": "s__Thermomonas sp014678725", "ani": 85.9119, "matched_fragments": 679, "total_fragments": 851, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas", "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_000423885.1", "gtdb_species": "s__Thermomonas fusca", "ani": 85.6407, "matched_fragments": 683, "total_fragments": 851, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.57", "min_intra_species_ani": "96.57", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_006337105.1", "gtdb_species": "s__Thermomonas sp006337105", "ani": 84.4045, "matched_fragments": 621, "total_fragments": 851, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas", "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_017302075.1", "gtdb_species": "s__Thermomonas sp017302075", "ani": 84.2517, "matched_fragments": 522, "total_fragments": 851, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas", "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_017302095.1", "gtdb_species": "s__Thermomonas sp017302095", "ani": 83.8767, "matched_fragments": 402, "total_fragments": 851, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas", "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_004352825.1", "gtdb_species": "s__Luteimonas arsenica", "ani": 81.7043, "matched_fragments": 523, "total_fragments": 851, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas", "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_014652935.1", "gtdb_species": "s__Luteimonas padinae", "ani": 81.6038, "matched_fragments": 530, "total_fragments": 851, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas", "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": -0.155, "cell_length": 0.477, "doubling_h": -0.222, "growth_tmp": 41.1, "optimum_tmp": 37.0, "optimum_ph": null, "genome_size": 2800085.0, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Thermomonas", "haemolytica" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }