| データタイトル | 分類 | 菌株番号 | 基準株 | データID |
|---|
解析情報 ゲノム
| データID |
ANGE0000000004105
|
|---|---|
| データタイトル |
ゲノム（TPA_asm: Pseudomonas putida strain NBRC 14671, whole genome shotgun sequencing project）
|
| 生物種名 |
Pseudomonas putida
|
| アクセッション番号またはID |
DAOKCV000000000
|
| コメント |
TPA_asm: Pseudomonas putida strain NBRC 14671, whole genome shotgun sequencing project.
|
| ゲノム配列のバージョン |
DAOKCV000000000.1
|
| 登録日または更新日 |
2023-04-14
|
| 配列取得用URL | |
| 配列ファイルダウンロード | |
| 配列長（bp）または配列数（rc） |
79
|
| 形態 |
linear
|
| BioProject | |
| BioSample | |
| 配列の種類 |
genomic DNA
|
| strain |
NBRC 14671
|
| 分離源 |
|
| plasmid |
|
| 備考 |
|
| 菌株へのコメント |
The Pseudomonas putida whole genome shotgun (WGS) project has the project accession DAOKCV000000000. This version of the project (01) has the accession number DAOKCV010000000, and consists of sequences DAOKCV010000001-DAOKCV010000079.; The annotation was added by the assembly submitters using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about stand-alone PGAP can be found here: https://github.com/ncbi/pgap/; This draft WGS assembly was generated by running SKESA to generate a de-novo assembly. The de-novo assembly was then concatenated with contigs generated using a guided assembler using antimicrobial resistance genes as baits to comprehensively catalog the set of resistance genes in the isolate. Note, some parts of the contigs derived from the guided assembler may overlap de-novo contigs, and other guided assembler contigs. De-novo contigs can be differentiated from guided assembler contigs by their names , which include either 'denovo' or 'guided'.; ##Genome-Assembly-Data-START## ; Assembly Date :: 22-FEB-2023 ; Assembly Method :: SKESA v. 2.2 ; Assembly Name :: PDT001638960.1 ; Long Assembly Name :: NCBI Pathogen Detection Assembly PDT001638960.1 ; Genome Coverage :: 292x ; Sequencing Technology :: ILLUMINA ; ##Genome-Assembly-Data-END##; ##Genome-Annotation-Data-START## ; Annotation Date :: 02/23/2023 01:44:07 ; Annotation Method :: Best-placed reference protein set; GeneMarkS-2+ ; Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline (PGAP) ; Annotation Provider :: NCBI ; Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region ; Annotation Software revision :: 2021-01-11.build5132 ; Genes (total) :: 5,366 ; CDSs (total) :: 5,303 ; Genes (coding) :: 5,247 ; CDSs (with protein) :: 5,247 ; Genes (RNA) :: 63 ; rRNAs :: 1, 3 (16S, 23S) ; partial rRNAs :: 1, 3 (16S, 23S) ; tRNAs :: 55 ; ncRNAs :: 4 ; Pseudo Genes (total) :: 56 ; CDSs (without protein) :: 56 ; Pseudo Genes (ambiguous residues) :: 0 of 56 ; Pseudo Genes (frameshifted) :: 14 of 56 ; Pseudo Genes (incomplete) :: 38 of 56 ; Pseudo Genes (internal stop) :: 11 of 56 ; Pseudo Genes (multiple problems) :: 6 of 56 ; ##Genome-Annotation-Data-END##
|
| 参照 |
1
|
| タイトル |
SKESA: strategic k-mer extension for scrupulous assemblies
|
| 雑誌名/登録機関名 |
Genome Biol 19 (1), 153 (2018)
|
| 出版年月 |
|
| 巻・号・ページ |
|
| 著者 |
Souvorov,A. Agarwala,R. Lipman,D.J.
|
| PubMed | |
| 参照 |
2
|
| タイトル |
Direct Submission
|
| 雑誌名/登録機関名 |
Submitted (22-FEB-2023) National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg 45, Center Drive, Bethesda, MD, USA
|
| 出版年月 |
|
| 巻・号・ページ |
|
| 著者 |
|
| PubMed |
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| 関連情報 |
このデータにリンクしている情報 |
