{ "type": "genome", "identifier": "GCF_002871005.1", "organism": "Acidimangrovimonas sediminis", "title": "Acidimangrovimonas sediminis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Xiamen University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002871005.1", "bioproject": "PRJNA224116", "biosample": "SAMN08048889", "wgs_master": "PHSN00000000.1", "refseq_category": "reference genome", "taxid": "2056283", "species_taxid": "2056283", "organism_name": "Acidimangrovimonas sediminis", "infraspecific_name": "strain=MS2-2", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/01/10", "asm_name": "ASM287100v1", "asm_submitter": "Xiamen University", "gbrs_paired_asm": "GCA_002871005.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/871/005/GCF_002871005.1_ASM287100v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5284268", "genome_size_ungapped": "5284268", "gc_percent": "68.000000", "replicon_count": "0", "scaffold_count": "111", "contig_count": "111", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002871005.1-RS_2024_12_13", "annotation_date": "2024-12-13", "total_gene_count": "4971", "protein_coding_gene_count": "4863", "non_coding_gene_count": "51", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-01-10", "dateModified": "2018-01-10", "datePublished": "2018-01-10", "_annotation": { "sample_count": 1, "sample_organism": [ "Acidimangrovimonas sediminis" ], "sample_taxid": [ "2056283" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Jiulong River, Fujian" ], "sample_host_location_id": [], "data_size": "1.444 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)": "5284268", "Number of Sequences": "111", "Longest Sequences (bp)": "478643", "N50 (bp)": "240909", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "67.8", "Number of CDSs": "4914", "Average Protein Length": "317.5", "Coding Ratio (%)": "88.6", "Number of rRNAs": "1", "Number of tRNAs": "46", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Allgaiera indica", "strain": "strain=CGMCC 1.10859", "accession": "GCA_014653075.1", "taxid": 765699, "species_taxid": 765699, "relation_to_type": "type", "validated": true, "ani": 81.8359, "matched_fragments": 831, "total_fragments": 1721, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Allgaiera indica", "strain": "strain=DSM 24802", "accession": "GCA_900106675.1", "taxid": 765699, "species_taxid": 765699, "relation_to_type": "type", "validated": true, "ani": 81.8097, "matched_fragments": 837, "total_fragments": 1721, "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": 79.462, "matched_fragments": 614, "total_fragments": 1721, "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": 79.3979, "matched_fragments": 652, "total_fragments": 1721, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sinirhodobacter hankyongi", "strain": "strain=BO-81", "accession": "GCA_003664585.1", "taxid": 2294033, "species_taxid": 2294033, "relation_to_type": "type", "validated": true, "ani": 79.3569, "matched_fragments": 588, "total_fragments": 1721, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sinirhodobacter ferrireducens", "strain": "strain=CCTCC AB2012026", "accession": "GCA_004022265.1", "taxid": 1215032, "species_taxid": 1215032, "relation_to_type": "type", "validated": true, "ani": 79.2247, "matched_fragments": 588, "total_fragments": 1721, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sinirhodobacter huangdaonensis", "strain": "strain=CGMCC 1.12963", "accession": "GCA_004022465.1", "taxid": 2501515, "species_taxid": 2501515, "relation_to_type": "type", "validated": true, "ani": 79.2094, "matched_fragments": 600, "total_fragments": 1721, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudooceanicola nanhaiensis", "strain": "strain=DSM 18065", "accession": "GCA_000688295.1", "taxid": 375761, "species_taxid": 375761, "relation_to_type": "type", "validated": true, "ani": 78.7909, "matched_fragments": 584, "total_fragments": 1721, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudooceanicola nanhaiensis", "strain": "strain=CGMCC 1.6293", "accession": "GCA_014645095.1", "taxid": 375761, "species_taxid": 375761, "relation_to_type": "type", "validated": true, "ani": 78.7736, "matched_fragments": 586, "total_fragments": 1721, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodovulum robiginosum", "strain": "strain=DSM 12329", "accession": "GCA_003944755.1", "taxid": 68292, "species_taxid": 68292, "relation_to_type": "type", "validated": true, "ani": 78.6965, "matched_fragments": 527, "total_fragments": 1721, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thioclava electrotropha", "strain": "strain=Elox9", "accession": "GCA_002085925.2", "taxid": 1549850, "species_taxid": 1549850, "relation_to_type": "type", "validated": true, "ani": 78.5952, "matched_fragments": 514, "total_fragments": 1721, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thioclava sediminum", "strain": "strain=TAW-CT134", "accession": "GCA_002020355.1", "taxid": 1915319, "species_taxid": 1915319, "relation_to_type": "type", "validated": true, "ani": 78.5474, "matched_fragments": 505, "total_fragments": 1721, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thioclava nitratireducens", "strain": "strain=25B10_4", "accession": "GCA_001940525.2", "taxid": 1915078, "species_taxid": 1915078, "relation_to_type": "type", "validated": true, "ani": 78.5141, "matched_fragments": 503, "total_fragments": 1721, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodovulum tesquicola", "strain": "strain=A-36s", "accession": "GCA_024128855.1", "taxid": 540254, "species_taxid": 540254, "relation_to_type": "type", "validated": true, "ani": 78.4764, "matched_fragments": 495, "total_fragments": 1721, "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": 78.4425, "matched_fragments": 469, "total_fragments": 1721, "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": 78.4339, "matched_fragments": 471, "total_fragments": 1721, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pararhodobacter aggregans", "strain": "strain=D1-19", "accession": "GCA_003075525.1", "taxid": 404875, "species_taxid": 404875, "relation_to_type": "type", "validated": true, "ani": 78.4314, "matched_fragments": 557, "total_fragments": 1721, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus aeridis", "strain": "strain=JC501", "accession": "GCA_004923205.2", "taxid": 1966466, "species_taxid": 1966466, "relation_to_type": "type", "validated": true, "ani": 78.4252, "matched_fragments": 426, "total_fragments": 1721, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pararhodobacter aggregans", "strain": "strain=DSM 18938", "accession": "GCA_003054005.1", "taxid": 404875, "species_taxid": 404875, "relation_to_type": "type", "validated": true, "ani": 78.4126, "matched_fragments": 554, "total_fragments": 1721, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Yangia pacifica", "strain": "strain=DSM 26894", "accession": "GCA_900116195.1", "taxid": 311180, "species_taxid": 311180, "relation_to_type": "suspected-type", "validated": true, "ani": 78.3817, "matched_fragments": 628, "total_fragments": 1721, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseibacterium elongatum", "strain": "strain=DFL-43", "accession": "GCA_000590925.1", "taxid": 159346, "species_taxid": 159346, "relation_to_type": "type", "validated": true, "ani": 78.0521, "matched_fragments": 397, "total_fragments": 1721, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Salipiger pallidus", "strain": "strain=CGMCC 1.15762", "accession": "GCA_014643635.1", "taxid": 1775170, "species_taxid": 1775170, "relation_to_type": "type", "validated": true, "ani": 77.8329, "matched_fragments": 428, "total_fragments": 1721, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Palleronia sediminis", "strain": "strain=SS33", "accession": "GCA_004358695.1", "taxid": 2547833, "species_taxid": 2547833, "relation_to_type": "type", "validated": true, "ani": 77.6694, "matched_fragments": 407, "total_fragments": 1721, "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": 77.6623, "matched_fragments": 451, "total_fragments": 1721, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Haematobacter massiliensis", "strain": "strain=CCUG 47968", "accession": "GCA_000740795.1", "taxid": 195105, "species_taxid": 195105, "relation_to_type": "type", "validated": true, "ani": 77.5681, "matched_fragments": 300, "total_fragments": 1721, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhabdonatronobacter sediminivivens", "strain": "strain=IM2376", "accession": "GCA_013415485.1", "taxid": 2743469, "species_taxid": 2743469, "relation_to_type": "type", "validated": true, "ani": 77.3704, "matched_fragments": 364, "total_fragments": 1721, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002871005.1", "gtdb_species": "s__Acidimangrovimonas sediminis", "ani": 100.0, "matched_fragments": 1718, "total_fragments": 1721, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Acidimangrovimonas", "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": "GCF_900106675.1", "gtdb_species": "s__Acidimangrovimonas indica", "ani": 81.7774, "matched_fragments": 841, "total_fragments": 1721, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Acidimangrovimonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", 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"mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCA_016124615.1", "gtdb_species": "s__Solirhodobacter sp016124615", "ani": 79.3355, "matched_fragments": 633, "total_fragments": 1721, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Solirhodobacter", "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_004342445.1", "gtdb_species": "s__Rhodovulum euryhalinum", "ani": 78.946, "matched_fragments": 514, "total_fragments": 1721, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum", "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_000688295.1", "gtdb_species": "s__Pseudooceanicola nanhaiensis", "ani": 78.8076, "matched_fragments": 583, "total_fragments": 1721, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_004799285.1", "gtdb_species": "s__Gemmobacter_D aestuarii", "ani": 78.6983, "matched_fragments": 531, "total_fragments": 1721, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", 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"-" }, { "accession": "GCF_001940525.2", "gtdb_species": "s__Thioclava nitratireducens", "ani": 78.5198, "matched_fragments": 501, "total_fragments": 1721, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.60", "min_intra_species_ani": "98.50", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.89", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_004923205.2", "gtdb_species": "s__Paracoccus aeridis", "ani": 78.4503, "matched_fragments": 422, "total_fragments": 1721, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus", "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": 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