 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Aug 22, 2023 |
| Title |
whole exome sequencing of PI542270 |
| Sample type |
SRA |
| |
|
| Source name |
PI542270 leaf
|
| Organism |
Aegilops speltoides |
| Characteristics |
tissue: leaf
cultivar: PI542270
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
genomic DNA
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Library strategy: exome-seq
Raw reads were trimmed with FastQC and Trimmomatic v0.334 with default parameters, and got the clean reads. Then the bwa software was used to map the reads to the IWGSC RefSeq V1.0.
The gatk software was used to call variation, and the variation information was saved as gVCF file.
Genome_build: IWGSC RefSeq v1.0
Supplementary_files_format_and_content: gVCF files were generated using gatk software, represents the variation information.
|
| |
|
| Submission date |
Feb 25, 2022 |
| Last update date |
Aug 22, 2023 |
| Contact name |
Zefu Lu |
| E-mail(s) |
luzefu@live.com
|
| Organization name |
Institute of Crop Sciences
|
| Street address |
No.12 Zhongguancun South St.,Haidian District, Beijing, P.R.China
|
| City |
Beijing |
| State/province |
Haidian |
| ZIP/Postal code |
100081 |
| Country |
China |
| |
|
| Platform ID |
GPL31956 |
| Series (2) |
| GSE197464 |
The genome sequencing of Sitopsis species provide insights into its contribution to the B subgenome in Triticum aestivum [WES] |
| GSE197593 |
The genome sequencing of Sitopsis species provide insights into its contribution to the B subgenome in Triticum aestivum |
|
| Relations |
| BioSample |
SAMN26490925 |
| SRA |
SRX14389662 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5917995_PI542270.cs.bb.dp3mis1.recode.vcf.gz |
1.2 Gb |
(ftp)(http) |
VCF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
