{ "type": "genome", "identifier": "GCF_003182475.1", "organism": "Mangrovibacter plantisponsor", "title": "Mangrovibacter plantisponsor", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003182475.1", "bioproject": "PRJNA224116", "biosample": "SAMN09064728", "wgs_master": "QGTS00000000.1", "refseq_category": "reference genome", "taxid": "451513", "species_taxid": "451513", "organism_name": "Mangrovibacter plantisponsor", "infraspecific_name": "strain=DSM 19579", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/05/31", "asm_name": "ASM318247v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_003182475.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/182/475/GCF_003182475.1_ASM318247v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5352990", "genome_size_ungapped": "5352170", "gc_percent": "50.500000", "replicon_count": "0", "scaffold_count": "56", "contig_count": "56", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003182475.1-RS_2024_05_04", "annotation_date": "2024-05-04", "total_gene_count": "5012", "protein_coding_gene_count": "4795", "non_coding_gene_count": "93", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-05-31", "dateModified": "2018-05-31", "datePublished": "2018-05-31", "_annotation": { "sample_count": 1, "sample_organism": [ "Mangrovibacter plantisponsor" ], "sample_taxid": [ "451513" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "India: Pichavaram, Tamil Nadu" ], "sample_host_location_id": [], "data_size": "1.518 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)": "5352990", "Number of Sequences": "56", "Longest Sequences (bp)": "575719", "N50 (bp)": "356458", "Gap Ratio (%)": "0.015319", "GCcontent (%)": "50.4", "Number of CDSs": "4835", "Average Protein Length": "318.4", "Coding Ratio (%)": "86.3", "Number of rRNAs": "7", "Number of tRNAs": "74", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Mangrovibacter plantisponsor", "strain": "strain=DSM 19579", "accession": "GCA_003182475.1", "taxid": 451513, "species_taxid": 451513, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1750, "total_fragments": 1755, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Mangrovibacter phragmitis", "strain": "strain=MP23", "accession": "GCA_001655675.1", "taxid": 1691903, "species_taxid": 1691903, "relation_to_type": "type", "validated": true, "ani": 92.3946, "matched_fragments": 1437, "total_fragments": 1755, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Franconibacter daqui", "strain": "strain=CGMCC 1.15944", "accession": "GCA_014644275.1", "taxid": 2047724, "species_taxid": 2047724, "relation_to_type": "type", "validated": true, "ani": 79.2203, "matched_fragments": 443, "total_fragments": 1755, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Atlantibacter hermannii", "strain": "strain=NBRC 105704", "accession": "GCA_000248015.2", "taxid": 565, "species_taxid": 565, "relation_to_type": "type", "validated": true, "ani": 79.1335, "matched_fragments": 406, "total_fragments": 1755, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Atlantibacter hermannii", "strain": "strain=FDAARGOS_888", "accession": "GCA_016027855.1", "taxid": 565, "species_taxid": 565, "relation_to_type": "type", "validated": true, "ani": 79.1333, "matched_fragments": 412, "total_fragments": 1755, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shimwellia blattae", "strain": "strain=DSM 4481", "accession": "GCA_000262305.1", "taxid": 563, "species_taxid": 563, "relation_to_type": "type", "validated": true, "ani": 79.093, "matched_fragments": 401, "total_fragments": 1755, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shimwellia blattae", "strain": "strain=NBRC 105725", "accession": "GCA_000327265.1", "taxid": 563, "species_taxid": 563, "relation_to_type": "type", "validated": true, "ani": 79.0684, "matched_fragments": 394, "total_fragments": 1755, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shimwellia pseudoproteus", "strain": "strain=DSM 3038", "accession": "GCA_016415625.1", "taxid": 570012, "species_taxid": 570012, "relation_to_type": "type", "validated": true, "ani": 79.0667, "matched_fragments": 404, "total_fragments": 1755, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leclercia adecarboxylata", "strain": "strain=NBRC 102595", "accession": "GCA_001515505.1", "taxid": 83655, "species_taxid": 83655, "relation_to_type": "suspected-type", "validated": true, "ani": 79.0223, "matched_fragments": 419, "total_fragments": 1755, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leclercia adecarboxylata", "strain": "strain=FDAARGOS_1505", "accession": "GCA_020097395.1", "taxid": 83655, "species_taxid": 83655, "relation_to_type": "suspected-type", "validated": true, "ani": 79.0053, "matched_fragments": 421, "total_fragments": 1755, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leclercia adecarboxylata", "strain": "strain=ATCC 23216", "accession": "GCA_000735515.1", "taxid": 83655, "species_taxid": 83655, "relation_to_type": "suspected-type", "validated": true, "ani": 79.0037, "matched_fragments": 405, "total_fragments": 1755, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Escherichia fergusonii", "strain": "strain=FDAARGOS_1499", "accession": "GCA_020097475.1", "taxid": 564, "species_taxid": 564, "relation_to_type": "type", "validated": true, "ani": 78.9501, "matched_fragments": 435, "total_fragments": 1755, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter ludwigii", "strain": "strain=FDAARGOS 1436", "accession": "GCA_019047005.1", "taxid": 299767, "species_taxid": 299767, "relation_to_type": "type", "validated": true, "ani": 78.9409, "matched_fragments": 460, "total_fragments": 1755, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kosakonia oryzae", "strain": "strain=Ola 51", "accession": "GCA_001658025.2", "taxid": 497725, "species_taxid": 497725, "relation_to_type": "type", "validated": true, "ani": 78.9331, "matched_fragments": 492, "total_fragments": 1755, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter ludwigii", "strain": "strain=EN-119", "accession": "GCA_001750725.1", "taxid": 299767, "species_taxid": 299767, "relation_to_type": "type", "validated": true, "ani": 78.9241, "matched_fragments": 472, "total_fragments": 1755, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter ludwigii", "strain": "strain=EN-119", "accession": "GCA_000818595.1", "taxid": 299767, "species_taxid": 299767, "relation_to_type": "type", "validated": true, "ani": 78.9145, "matched_fragments": 472, "total_fragments": 1755, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kosakonia oryzae", "strain": "strain=CGMCC 1.7012", "accession": "GCA_900112145.1", "taxid": 497725, "species_taxid": 497725, "relation_to_type": "type", "validated": true, "ani": 78.9058, "matched_fragments": 498, "total_fragments": 1755, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lelliottia nimipressuralis", "strain": "strain=CCUG 25894", "accession": "GCA_004115925.1", "taxid": 69220, "species_taxid": 69220, "relation_to_type": "type", "validated": true, "ani": 78.862, "matched_fragments": 422, "total_fragments": 1755, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kosakonia oryzendophytica", "strain": "strain=REICA_082", "accession": "GCA_900094925.1", "taxid": 1005665, "species_taxid": 1005665, "relation_to_type": "type", "validated": true, "ani": 78.8393, "matched_fragments": 465, "total_fragments": 1755, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leclercia pneumoniae", "strain": "strain=49125", "accession": "GCA_017348915.1", "taxid": 2815358, "species_taxid": 2815358, "relation_to_type": "type", "validated": true, "ani": 78.8304, "matched_fragments": 424, "total_fragments": 1755, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kluyvera georgiana", "strain": "strain=ATCC 51603", "accession": "GCA_001654985.1", "taxid": 73098, "species_taxid": 73098, "relation_to_type": "type", "validated": true, "ani": 78.8259, "matched_fragments": 407, "total_fragments": 1755, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leclercia pneumoniae", "strain": "strain=49125", "accession": "GCA_018987305.1", "taxid": 2815358, "species_taxid": 2815358, "relation_to_type": "type", "validated": true, "ani": 78.8259, "matched_fragments": 423, "total_fragments": 1755, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Serratia nevei", "strain": "strain=S15", "accession": "GCA_008364245.1", "taxid": 2703794, "species_taxid": 2703794, "relation_to_type": "type", "validated": true, "ani": 78.3363, "matched_fragments": 225, "total_fragments": 1755, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rahnella bonaserana", "strain": "strain=H11b", "accession": "GCA_019049675.1", "taxid": 2816248, "species_taxid": 2816248, "relation_to_type": "type", "validated": true, "ani": 77.9825, "matched_fragments": 260, "total_fragments": 1755, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Erwinia phyllosphaerae", "strain": "strain=CMYE1", "accession": "GCA_019132875.1", "taxid": 2853256, "species_taxid": 2853256, "relation_to_type": "type", "validated": true, "ani": 77.973, "matched_fragments": 261, "total_fragments": 1755, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003182475.1", "gtdb_species": "s__Mangrovibacter plantisponsor", "ani": 100.0, "matched_fragments": 1750, "total_fragments": 1755, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mangrovibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.41", "min_intra_species_ani": "98.41", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_001655675.1", "gtdb_species": "s__Mangrovibacter phragmitis", "ani": 92.4052, "matched_fragments": 1436, "total_fragments": 1755, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mangrovibacter", "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_001277175.1", "gtdb_species": "s__Cronobacter universalis", "ani": 79.1002, "matched_fragments": 427, "total_fragments": 1755, "gtdb_taxonomy": 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"d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.13", "min_intra_species_ani": "96.37", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.86", "num_clustered_genomes": 16, "status": "-" }, { "accession": "GCA_901472455.1", "gtdb_species": "s__Leclercia adecarboxylata", "ani": 78.9436, "matched_fragments": 410, "total_fragments": 1755, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.53", "min_intra_species_ani": "98.09", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.87", "num_clustered_genomes": 86, "status": "-" }, { "accession": "GCF_000410515.1", "gtdb_species": "s__Kosakonia sp000410515", "ani": 78.9414, "matched_fragments": 473, "total_fragments": 1755, "gtdb_taxonomy": 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"d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Atlantibacter", "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_000280495.2", "gtdb_species": "s__Kosakonia radicincitans", "ani": 78.824, "matched_fragments": 498, "total_fragments": 1755, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia", "ani_circumscription_radius": 95.7299, "mean_intra_species_ani": "99.26", "min_intra_species_ani": "99.13", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.93", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCF_001297775.1", "gtdb_species": "s__Trabulsiella odontotermitis", "ani": 78.8153, "matched_fragments": 431, "total_fragments": 1755, "gtdb_taxonomy": 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