{ "type": "genome", "identifier": "GCF_005844085.1", "organism": "Lichenicoccus roseus", "title": "Lichenicoccus roseus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Research Center of Biotechnology RAS", "publication": [ {} ], "properties": { "assembly_accession": "GCF_005844085.1", "bioproject": "PRJNA224116", "biosample": "SAMN11665427", "wgs_master": "VCDI00000000.1", "refseq_category": "reference genome", "taxid": "2683649", "species_taxid": "2683649", "organism_name": "Lichenicoccus roseus", "infraspecific_name": "strain=KEBCLARHB70R", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/05/26", "asm_name": "ASM584408v1", "asm_submitter": "Research Center of Biotechnology RAS", "gbrs_paired_asm": "GCA_005844085.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/005/844/085/GCF_005844085.1_ASM584408v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4788108", "genome_size_ungapped": "4787916", "gc_percent": "68.000000", "replicon_count": "0", "scaffold_count": "26", "contig_count": "26", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_005844085.1-RS_2024_12_16", "annotation_date": "2024-12-16", "total_gene_count": "4454", "protein_coding_gene_count": "4338", "non_coding_gene_count": "53", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-05-26", "dateModified": "2019-05-26", "datePublished": "2019-05-26", "_annotation": { "sample_count": 1, "sample_organism": [ "Lichenicoccus roseus" ], "sample_taxid": [ "2683649" ], "sample_host_organism": [ "Cladonia arbuscula" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Russia: Murmansk region" ], "sample_host_location_id": [], "data_size": "1.302 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)": "4788108", "Number of Sequences": "26", "Longest Sequences (bp)": "1180588", "N50 (bp)": "700473", "Gap Ratio (%)": "0.004010", "GCcontent (%)": "67.8", "Number of CDSs": "4447", "Average Protein Length": "325.1", "Coding Ratio (%)": "90.6", "Number of rRNAs": "3", "Number of tRNAs": "52", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Endobacter medicaginis", "strain": "strain=LMG 26838", "accession": "GCA_013376135.1", "taxid": 1181271, "species_taxid": 1181271, "relation_to_type": "type", "validated": true, "ani": 79.2646, "matched_fragments": 298, "total_fragments": 1586, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Endobacter medicaginis", "strain": "strain=CECT 8088", "accession": "GCA_014192375.1", "taxid": 1181271, "species_taxid": 1181271, "relation_to_type": "type", "validated": true, "ani": 78.9132, "matched_fragments": 454, "total_fragments": 1586, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gluconacetobacter diazotrophicus", "strain": "strain=PAl 5; ATCC 49037", "accession": "GCA_000021325.1", "taxid": 33996, "species_taxid": 33996, "relation_to_type": "type", "validated": true, "ani": 78.1587, "matched_fragments": 348, "total_fragments": 1586, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Acidisphaera rubrifaciens", "strain": "strain=HS-AP3", "accession": "GCA_000964365.1", "taxid": 50715, "species_taxid": 50715, "relation_to_type": "type", "validated": true, "ani": 78.1514, "matched_fragments": 268, "total_fragments": 1586, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gluconacetobacter diazotrophicus", "strain": "strain=PAl 5", "accession": "GCA_000067045.1", "taxid": 33996, "species_taxid": 33996, "relation_to_type": "type", "validated": true, "ani": 78.0981, "matched_fragments": 348, "total_fragments": 1586, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gluconacetobacter diazotrophicus", "strain": "strain=LMG 7603", "accession": "GCA_014174315.1", "taxid": 33996, "species_taxid": 33996, "relation_to_type": "type", "validated": true, "ani": 77.9926, "matched_fragments": 353, "total_fragments": 1586, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gluconacetobacter dulcium", "strain": "strain=LMG 1728", "accession": "GCA_014174165.1", "taxid": 2729096, "species_taxid": 2729096, "relation_to_type": "type", "validated": true, "ani": 77.988, "matched_fragments": 324, "total_fragments": 1586, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Komagataeibacter nataicola", "strain": "strain=LMG 1536", "accession": "GCA_003207795.1", "taxid": 265960, "species_taxid": 265960, "relation_to_type": "type", "validated": true, "ani": 77.7425, "matched_fragments": 196, "total_fragments": 1586, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Komagataeibacter swingsii", "strain": "strain=LMG 22125", "accession": "GCA_003207895.1", "taxid": 215220, "species_taxid": 215220, "relation_to_type": "type", "validated": true, "ani": 77.6348, "matched_fragments": 183, "total_fragments": 1586, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Komagataeibacter xylinus", "strain": "strain=NBRC 15237", "accession": "GCA_001571345.1", "taxid": 28448, "species_taxid": 28448, "relation_to_type": "suspected-type", "validated": true, "ani": 77.5982, "matched_fragments": 207, "total_fragments": 1586, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodovastum atsumiense", "strain": "strain=G2-11", "accession": "GCA_937425535.1", "taxid": 504468, "species_taxid": 504468, "relation_to_type": "type", "validated": true, "ani": 77.5811, "matched_fragments": 485, "total_fragments": 1586, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Komagataeibacter melomenusus", "strain": "strain=AV436", "accession": "GCA_013155395.1", "taxid": 2766578, "species_taxid": 2766578, "relation_to_type": "type", "validated": true, "ani": 77.5802, "matched_fragments": 227, "total_fragments": 1586, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Komagataeibacter xylinus", "strain": "strain=LMG 1515", "accession": "GCA_003207915.1", "taxid": 28448, "species_taxid": 28448, "relation_to_type": "suspected-type", "validated": true, "ani": 77.5681, "matched_fragments": 202, "total_fragments": 1586, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novacetimonas maltaceti", "strain": "strain=LMG 1529", "accession": "GCA_003206475.1", "taxid": 1203393, "species_taxid": 1203393, "relation_to_type": "type", "validated": true, "ani": 77.418, "matched_fragments": 207, "total_fragments": 1586, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novacetimonas maltaceti", "strain": "strain=LMG 1529", "accession": "GCA_002906255.1", "taxid": 1203393, "species_taxid": 1203393, "relation_to_type": "type", "validated": true, "ani": 77.3839, "matched_fragments": 210, "total_fragments": 1586, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodopila globiformis", "strain": "strain=DSM 161", "accession": "GCA_002937115.1", "taxid": 1071, "species_taxid": 1071, "relation_to_type": "type", "validated": true, "ani": 77.2946, "matched_fragments": 412, "total_fragments": 1586, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseomonas rubea", "strain": "strain=MO17", "accession": "GCA_016106015.1", "taxid": 2748666, "species_taxid": 2748666, "relation_to_type": "type", "validated": true, "ani": 77.1649, "matched_fragments": 281, "total_fragments": 1586, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium crusticola", "strain": "strain=KCTC 52305", "accession": "GCA_022179145.1", "taxid": 1697972, "species_taxid": 1697972, "relation_to_type": "type", "validated": true, "ani": 76.2151, "matched_fragments": 323, "total_fragments": 1586, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas corticis", "strain": "strain=36D10-4-7", "accession": "GCA_012035195.1", "taxid": 2722791, "species_taxid": 2722791, "relation_to_type": "type", "validated": true, "ani": 75.9657, "matched_fragments": 198, "total_fragments": 1586, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas citri", "strain": "strain=RRHST34", "accession": "GCA_019429485.1", "taxid": 2862499, "species_taxid": 2862499, "relation_to_type": "type", "validated": true, "ani": 75.9281, "matched_fragments": 220, "total_fragments": 1586, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_005844085.1", "gtdb_species": "s__Lichenicoccus roseus", "ani": 100.0, "matched_fragments": 1586, "total_fragments": 1586, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Lichenicoccus", "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": "GCA_903844135.1", "gtdb_species": "s__Lichenicola sp903844135", "ani": 80.1059, "matched_fragments": 660, "total_fragments": 1586, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Lichenicola", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.79", "min_intra_species_ani": "99.79", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_013201075.1", "gtdb_species": "s__Lichenicola cladoniae", "ani": 79.6708, "matched_fragments": 671, "total_fragments": 1586, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Lichenicola", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014192375.1", "gtdb_species": "s__Endobacter medicaginis", "ani": 78.9287, "matched_fragments": 453, "total_fragments": 1586, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Endobacter", "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": 2, "status": "-" }, { "accession": "GCF_014174275.1", "gtdb_species": "s__Gluconacetobacter takamatsuzukensis", "ani": 78.3012, "matched_fragments": 359, "total_fragments": 1586, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter", "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_014174395.1", "gtdb_species": "s__Gluconacetobacter aggeris", "ani": 78.1585, "matched_fragments": 330, "total_fragments": 1586, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter", "ani_circumscription_radius": 96.2181, "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_000021325.1", "gtdb_species": "s__Gluconacetobacter diazotrophicus", "ani": 78.1484, "matched_fragments": 349, "total_fragments": 1586, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.14", "min_intra_species_ani": "98.86", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.85", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_014174355.1", "gtdb_species": "s__Gluconacetobacter azotocaptans", "ani": 78.1122, "matched_fragments": 339, "total_fragments": 1586, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.32", "min_intra_species_ani": "99.32", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_003133265.1", "gtdb_species": "s__PALSA-911 sp003133265", "ani": 78.0375, "matched_fragments": 275, "total_fragments": 1586, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__PALSA-911", "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_903644035.1", "gtdb_species": "s__CAHJXG01 sp903644035", "ani": 78.034, "matched_fragments": 239, "total_fragments": 1586, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAHJXG01", "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_019240635.1", "gtdb_species": "s__JAFAYA01 sp019240635", "ani": 77.8932, "matched_fragments": 250, "total_fragments": 1586, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFAYA01", "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_017304945.1", "gtdb_species": "s__69-11 sp017304945", "ani": 77.798, "matched_fragments": 406, "total_fragments": 1586, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__69-11", "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_008630155.1", "gtdb_species": "s__Rhodovastum atsumiense", "ani": 77.6134, "matched_fragments": 474, "total_fragments": 1586, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodovastum", "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_003258945.1", "gtdb_species": "s__Paracraurococcus frigidaeris", "ani": 77.3475, "matched_fragments": 448, "total_fragments": 1586, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus", "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_013112485.1", "gtdb_species": "s__Paracraurococcus sp013112485", "ani": 77.2242, "matched_fragments": 436, "total_fragments": 1586, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus", "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_004761865.1", "gtdb_species": "s__Crenalkalicoccus roseus", "ani": 77.1441, "matched_fragments": 382, "total_fragments": 1586, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Crenalkalicoccus", "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_019084075.1", "gtdb_species": "s__G192 sp019084075", "ani": 76.9991, "matched_fragments": 343, "total_fragments": 1586, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__G192", "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": null, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "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": [ "Lichenicoccus", "roseus" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }