{ "type": "genome", "identifier": "GCF_022601735.1", "organism": "Atopomonas sediminilitoris", "title": "Atopomonas sediminilitoris", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Zhejiang University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_022601735.1", "bioproject": "PRJNA224116", "biosample": "SAMN26186988", "wgs_master": "JAKUMM000000000.1", "refseq_category": "reference genome", "taxid": "2919919", "species_taxid": "2919919", "organism_name": "Atopomonas sediminilitoris", "infraspecific_name": "strain=A3.4", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/03/16", "asm_name": "ASM2260173v1", "asm_submitter": "Zhejiang University", "gbrs_paired_asm": "GCA_022601735.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/022/601/735/GCF_022601735.1_ASM2260173v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3554601", "genome_size_ungapped": "3554301", "gc_percent": "57.500000", "replicon_count": "0", "scaffold_count": "22", "contig_count": "22", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_022601735.1-RS_2024_08_20", "annotation_date": "2024-08-20", "total_gene_count": "3369", "protein_coding_gene_count": "3282", "non_coding_gene_count": "60", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-03-16", "dateModified": "2022-03-16", "datePublished": "2022-03-16", "_annotation": { "sample_count": 1, "sample_organism": [ "Atopomonas sediminilitoris" ], "sample_taxid": [ "2919919" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China" ], "sample_host_location_id": [], "data_size": "1.000 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)": "3554601", "Number of Sequences": "22", "Longest Sequences (bp)": "509189", "N50 (bp)": "384567", "Gap Ratio (%)": "0.008440", "GCcontent (%)": "57.7", "Number of CDSs": "3303", "Average Protein Length": "325.3", "Coding Ratio (%)": "90.7", "Number of rRNAs": "4", "Number of tRNAs": "53", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Atopomonas hussainii", "strain": "strain=JCM 19513", "accession": "GCA_900109735.1", "taxid": 1429083, "species_taxid": 1429083, "relation_to_type": "type", "validated": true, "ani": 82.2456, "matched_fragments": 847, "total_fragments": 1175, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas chengduensis", "strain": "strain=MBR", "accession": "GCA_017905455.1", "taxid": 489632, "species_taxid": 489632, "relation_to_type": "type", "validated": true, "ani": 78.5266, "matched_fragments": 310, "total_fragments": 1175, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas chengduensis", "strain": "strain=DSM 26382", "accession": "GCA_012986985.1", "taxid": 489632, "species_taxid": 489632, "relation_to_type": "type", "validated": true, "ani": 78.4341, "matched_fragments": 313, "total_fragments": 1175, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas chengduensis", "strain": "strain=DSM 26382", "accession": "GCA_900102635.1", "taxid": 489632, "species_taxid": 489632, "relation_to_type": "type", "validated": true, "ani": 78.3961, "matched_fragments": 320, "total_fragments": 1175, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas guguanensis", "strain": "strain=JCM 18416", "accession": "GCA_900104265.1", "taxid": 1198456, "species_taxid": 1198456, "relation_to_type": "type", "validated": true, "ani": 78.3019, "matched_fragments": 322, "total_fragments": 1175, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas fluvialis", "strain": "strain=CCM 8778", "accession": "GCA_014635625.1", "taxid": 1793966, "species_taxid": 1793966, "relation_to_type": "suspected-type", "validated": true, "ani": 78.2931, "matched_fragments": 275, "total_fragments": 1175, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stutzerimonas chloritidismutans", "strain": "strain=AW-1", "accession": "GCA_000495915.1", "taxid": 203192, "species_taxid": 203192, "relation_to_type": "type", "validated": true, "ani": 78.2775, "matched_fragments": 221, "total_fragments": 1175, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas oleovorans subsp. oleovorans", "strain": "strain=NBRC 13583", "accession": "GCA_002091815.1", "taxid": 1218129, "species_taxid": 301, "relation_to_type": "type", "validated": true, "ani": 78.2771, "matched_fragments": 313, "total_fragments": 1175, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas alcaligenes", "strain": "strain=NCTC10367", "accession": "GCA_900455475.1", "taxid": 43263, "species_taxid": 43263, "relation_to_type": "type", "validated": true, "ani": 78.1704, "matched_fragments": 352, "total_fragments": 1175, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas aromaticivorans", "strain": "strain=MAP12", "accession": "GCA_019097855.1", "taxid": 2849492, "species_taxid": 2849492, "relation_to_type": "type", "validated": true, "ani": 78.1647, "matched_fragments": 241, "total_fragments": 1175, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas otitidis", "strain": "strain=DSM 17224", "accession": "GCA_900111835.1", "taxid": 319939, "species_taxid": 319939, "relation_to_type": "suspected-type", "validated": true, "ani": 78.148, "matched_fragments": 285, "total_fragments": 1175, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas toyotomiensis", "strain": "strain=DSM 26169", "accession": "GCA_002741095.1", "taxid": 554344, "species_taxid": 554344, "relation_to_type": "type", "validated": true, "ani": 78.1314, "matched_fragments": 318, "total_fragments": 1175, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas insulae", "strain": "strain=UL073", "accession": "GCA_016901015.1", "taxid": 2809017, "species_taxid": 2809017, "relation_to_type": "type", "validated": true, "ani": 78.0983, "matched_fragments": 291, "total_fragments": 1175, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stutzerimonas kunmingensis", "strain": "strain=DSM 25974", "accession": "GCA_024397575.1", "taxid": 1211807, "species_taxid": 1211807, "relation_to_type": "type", "validated": true, "ani": 78.075, "matched_fragments": 218, "total_fragments": 1175, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas toyotomiensis", "strain": "strain=JCM 15604", "accession": "GCA_900115695.1", "taxid": 554344, "species_taxid": 554344, "relation_to_type": "type", "validated": true, "ani": 78.0721, "matched_fragments": 322, "total_fragments": 1175, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas alcaligenes", "strain": "strain=NBRC 14159", "accession": "GCA_000467105.1", "taxid": 43263, "species_taxid": 43263, "relation_to_type": "type", "validated": true, "ani": 78.0634, "matched_fragments": 352, "total_fragments": 1175, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas hydrolytica", "strain": "strain=DSWY01", "accession": "GCA_021495345.2", "taxid": 2493633, "species_taxid": 2493633, "relation_to_type": "type", "validated": true, "ani": 78.0595, "matched_fragments": 353, "total_fragments": 1175, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stutzerimonas kunmingensis", "strain": "strain=DSM 25974", "accession": "GCA_900114065.1", "taxid": 1211807, "species_taxid": 1211807, "relation_to_type": "type", "validated": true, "ani": 78.0193, "matched_fragments": 223, "total_fragments": 1175, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas tohonis", "strain": "strain=TUM18999", "accession": "GCA_012767755.2", "taxid": 2725477, "species_taxid": 2725477, "relation_to_type": "type", "validated": true, "ani": 77.9798, "matched_fragments": 307, "total_fragments": 1175, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas citronellolis", "strain": "strain=NBRC 103043", "accession": "GCA_002091555.1", "taxid": 53408, "species_taxid": 53408, "relation_to_type": "type", "validated": true, "ani": 77.978, "matched_fragments": 278, "total_fragments": 1175, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas jinjuensis", "strain": "strain=NBRC 103047", "accession": "GCA_002091655.1", "taxid": 198616, "species_taxid": 198616, "relation_to_type": "type", "validated": true, "ani": 77.9418, "matched_fragments": 269, "total_fragments": 1175, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas jinjuensis", "strain": "strain=JCM 21621", "accession": "GCA_900103845.1", "taxid": 198616, "species_taxid": 198616, "relation_to_type": "type", "validated": true, "ani": 77.884, "matched_fragments": 268, "total_fragments": 1175, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas benzenivorans", "strain": "strain=DSM 8628", "accession": "GCA_900100495.1", "taxid": 556533, "species_taxid": 556533, "relation_to_type": "type", "validated": true, "ani": 77.8671, "matched_fragments": 317, "total_fragments": 1175, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas linyingensis", "strain": "strain=LMG 25967", "accession": "GCA_900109175.1", "taxid": 915471, "species_taxid": 915471, "relation_to_type": "type", "validated": true, "ani": 77.7412, "matched_fragments": 265, "total_fragments": 1175, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas muyukensis", "strain": "strain=COW39", "accession": "GCA_019139535.1", "taxid": 2842357, "species_taxid": 2842357, "relation_to_type": "type", "validated": true, "ani": 77.7291, "matched_fragments": 228, "total_fragments": 1175, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas asgharzadehiana", "strain": "strain=SWRI132", "accession": "GCA_019139815.1", "taxid": 2842349, "species_taxid": 2842349, "relation_to_type": "type", "validated": true, "ani": 77.6293, "matched_fragments": 216, "total_fragments": 1175, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Azotobacter beijerinckii", "strain": "strain=DSM 378", "accession": "GCA_900110885.1", "taxid": 170623, "species_taxid": 170623, "relation_to_type": "type", "validated": true, "ani": 77.5457, "matched_fragments": 206, "total_fragments": 1175, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas japonica", "strain": "strain=DSM 22348", "accession": "GCA_900188455.1", "taxid": 256466, "species_taxid": 256466, "relation_to_type": "type", "validated": true, "ani": 77.3844, "matched_fragments": 235, "total_fragments": 1175, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas batumici", "strain": "strain=UCM B-321", "accession": "GCA_000820515.1", "taxid": 226910, "species_taxid": 226910, "relation_to_type": "type", "validated": true, "ani": 77.3293, "matched_fragments": 242, "total_fragments": 1175, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900109735.1", "gtdb_species": "s__Pseudomonas_L hussainii", "ani": 82.2594, "matched_fragments": 846, "total_fragments": 1175, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_L", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.93", "min_intra_species_ani": "95.93", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_008041835.1", "gtdb_species": "s__Pseudomonas_E sp002282595", "ani": 78.5392, "matched_fragments": 306, "total_fragments": 1175, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.53", "min_intra_species_ani": "95.53", "mean_intra_species_af": "0.75", "min_intra_species_af": "0.75", 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1, "status": "-" }, { "accession": "GCF_014490745.1", "gtdb_species": "s__Pseudomonas_E alcaligenes_C", "ani": 78.2009, "matched_fragments": 321, "total_fragments": 1175, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "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_900111835.1", "gtdb_species": "s__Pseudomonas_F otitidis", "ani": 78.143, "matched_fragments": 284, "total_fragments": 1175, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.35", "min_intra_species_ani": "95.43", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.84", "num_clustered_genomes": 21, "status": "-" }, { 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