{ "type": "genome", "identifier": "GCF_003054195.1", "organism": "Gemmobacter caeni", "title": "Gemmobacter caeni", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003054195.1", "bioproject": "PRJNA224116", "biosample": "SAMN08779094", "wgs_master": "QBKP00000000.1", "refseq_category": "reference genome", "taxid": "589035", "species_taxid": "589035", "organism_name": "Gemmobacter caeni", "infraspecific_name": "strain=DSM 21823", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/04/17", "asm_name": "ASM305419v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_003054195.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/054/195/GCF_003054195.1_ASM305419v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5135347", "genome_size_ungapped": "5134863", "gc_percent": "64.500000", "replicon_count": "0", "scaffold_count": "80", "contig_count": "80", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003054195.1-RS_2024_04_27", "annotation_date": "2024-04-27", "total_gene_count": "5231", "protein_coding_gene_count": "5064", "non_coding_gene_count": "101", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-04-17", "dateModified": "2018-04-17", "datePublished": "2018-04-17", "_annotation": { "sample_count": 1, "sample_organism": [ "Gemmobacter caeni" ], "sample_taxid": [ "589035" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Nantong, Jiangsu province" ], "sample_host_location_id": [], "data_size": "1.415 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)": "5135347", "Number of Sequences": "80", "Longest Sequences (bp)": "571532", "N50 (bp)": "278988", "Gap Ratio (%)": "0.009425", "GCcontent (%)": "64.7", "Number of CDSs": "5103", "Average Protein Length": "303.7", "Coding Ratio (%)": "90.5", "Number of rRNAs": "3", "Number of tRNAs": "95", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Gemmobacter caeni", "strain": "strain=DSM 21823", "accession": "GCA_003054195.1", "taxid": 589035, "species_taxid": 589035, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1665, "total_fragments": 1669, "ani_threshold": 95, "status": "conclusive" }, { "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": 99.9837, "matched_fragments": 1654, "total_fragments": 1669, "ani_threshold": 95, "status": "conclusive" }, { "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": 91.4564, "matched_fragments": 1181, "total_fragments": 1669, "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": 83.1709, "matched_fragments": 853, "total_fragments": 1669, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmobacter fulva", "strain": "strain=con5", "accession": "GCA_018798885.1", "taxid": 2840474, "species_taxid": 2840474, "relation_to_type": "type", "validated": true, "ani": 81.7344, "matched_fragments": 875, "total_fragments": 1669, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmobacter lanyuensis", "strain": "strain=KCTC 23714", "accession": "GCA_014652355.1", "taxid": 1054497, "species_taxid": 1054497, "relation_to_type": "type", "validated": true, "ani": 81.5768, "matched_fragments": 778, "total_fragments": 1669, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmobacter serpentinus", "strain": "strain=HB-1", "accession": "GCA_008973825.1", "taxid": 2652247, "species_taxid": 2652247, "relation_to_type": "type", "validated": true, "ani": 81.0646, "matched_fragments": 765, "total_fragments": 1669, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmobacter aquaticus", "strain": "strain=CGMCC 1.7029", "accession": "GCA_014645295.1", "taxid": 490185, "species_taxid": 490185, "relation_to_type": "type", "validated": true, "ani": 80.4927, "matched_fragments": 648, "total_fragments": 1669, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodobacter amnigenus", "strain": "strain=HSP-20", "accession": "GCA_019130055.1", "taxid": 2852097, "species_taxid": 2852097, "relation_to_type": "type", "validated": true, "ani": 79.711, "matched_fragments": 651, "total_fragments": 1669, "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": 79.6972, "matched_fragments": 654, "total_fragments": 1669, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cereibacter ovatus", "strain": "strain=JA234", "accession": "GCA_900207575.1", "taxid": 439529, "species_taxid": 439529, "relation_to_type": "type", "validated": true, "ani": 79.5945, "matched_fragments": 566, "total_fragments": 1669, "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": 79.1907, "matched_fragments": 579, "total_fragments": 1669, "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": 79.1281, "matched_fragments": 534, "total_fragments": 1669, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tabrizicola alkalilacus", "strain": "strain=DJC", "accession": "GCA_003443995.1", "taxid": 2305252, "species_taxid": 2305252, "relation_to_type": "type", "validated": true, "ani": 79.0199, "matched_fragments": 593, "total_fragments": 1669, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003054195.1", "gtdb_species": "s__Gemmobacter caeni", "ani": 100.0, "matched_fragments": 1665, "total_fragments": 1669, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.77", "min_intra_species_ani": "98.23", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.79", "num_clustered_genomes": 5, "status": "conclusive" }, { "accession": "GCF_003570715.1", "gtdb_species": "s__Gemmobacter lutimaris", "ani": 91.4598, "matched_fragments": 1180, "total_fragments": 1669, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter", "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_008271655.1", "gtdb_species": "s__Gemmobacter caeruleus", "ani": 83.1659, "matched_fragments": 855, "total_fragments": 1669, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter", "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_900110025.1", "gtdb_species": "s__Gemmobacter aquatilis", "ani": 82.1402, "matched_fragments": 839, "total_fragments": 1669, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter", "ani_circumscription_radius": 95.0, 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